Starting phenix.real_space_refine on Sat Feb 24 04:05:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ew0_3965/02_2024/6ew0_3965.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ew0_3965/02_2024/6ew0_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ew0_3965/02_2024/6ew0_3965.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ew0_3965/02_2024/6ew0_3965.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ew0_3965/02_2024/6ew0_3965.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ew0_3965/02_2024/6ew0_3965.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 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 Residue "E ARG 64": "NH1" <-> "NH2" Residue "E ARG 390": "NH1" <-> "NH2" Residue "J ARG 64": "NH1" <-> "NH2" Residue "J ARG 390": "NH1" <-> "NH2" Residue "C ARG 64": "NH1" <-> "NH2" Residue "C ARG 390": "NH1" <-> "NH2" Residue "L ARG 64": "NH1" <-> "NH2" Residue "L ARG 390": "NH1" <-> "NH2" Residue "A ARG 64": "NH1" <-> "NH2" Residue "A ARG 390": "NH1" <-> "NH2" Residue "K ARG 64": "NH1" <-> "NH2" Residue "K ARG 390": "NH1" <-> "NH2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 41238 Number of models: 1 Model: "" Number of chains: 24 Chain: "E" Number of atoms: 3382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3382 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "J" Number of atoms: 3382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3382 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 3382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3382 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 3382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3382 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 3382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3382 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 3382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3382 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "I" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 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: "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: 21.80, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 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: 15.52 Conformation dependent library (CDL) restraints added in 7.1 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: 4.43 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: 15.88 Time building geometry restraints manager: 16.73 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: 82.58 - 92.88: 30 92.88 - 103.18: 434 103.18 - 113.48: 23915 113.48 - 123.78: 31854 123.78 - 134.08: 1181 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: 25048 34.18 - 68.35: 246 68.35 - 102.53: 120 102.53 - 136.70: 63 136.70 - 170.88: 17 Dihedral angle restraints: 25494 sinusoidal: 10566 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 25491 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 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: 0.100 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: 0.040 Extract box with map and model: 3.580 Check model and map are aligned: 0.620 Set scattering table: 0.390 Process input model: 104.500 Find NCS groups from input model: 3.390 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 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= 0.388 Angle : 0.934 19.905 57414 Z= 0.447 Chirality : 0.054 0.325 6282 Planarity : 0.007 0.059 7452 Dihedral : 15.271 170.877 15918 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.027 0.003 TRP I 101 HIS 0.014 0.002 HIS A 8 PHE 0.015 0.002 PHE C 202 TYR 0.023 0.002 TYR H 208 ARG 0.011 0.001 ARG L 390 *********************** 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 fitting. rotamer outliers: 0 poor density : 1472 time to evaluate : 4.673 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: 0.8148 (mp0) REVERT: E 31 GLN cc_start: 0.8728 (mm-40) cc_final: 0.8474 (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: 0.8960 (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: 0.7906 (m) REVERT: E 145 THR cc_start: 0.9291 (m) cc_final: 0.8944 (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: 0.8771 (p) REVERT: E 205 ASP cc_start: 0.8565 (t0) cc_final: 0.8134 (t0) REVERT: E 210 TYR cc_start: 0.8934 (m-80) cc_final: 0.8637 (m-10) REVERT: E 221 ARG cc_start: 0.8905 (mtt90) cc_final: 0.8397 (mtt-85) REVERT: E 254 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7879 (mt-10) REVERT: E 313 MET cc_start: 0.8643 (mtm) cc_final: 0.7542 (mtm) REVERT: E 341 ILE cc_start: 0.9229 (mp) cc_final: 0.9015 (mp) REVERT: E 351 PHE cc_start: 0.9119 (m-80) cc_final: 0.8600 (m-10) 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: 0.7902 (tt0) REVERT: E 431 ASP cc_start: 0.8565 (m-30) cc_final: 0.8125 (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: 0.8209 (p) REVERT: F 136 THR cc_start: 0.9297 (m) cc_final: 0.8665 (p) REVERT: F 166 THR cc_start: 0.9238 (p) cc_final: 0.8974 (p) REVERT: F 174 LYS cc_start: 0.9384 (mtpt) cc_final: 0.9154 (mtpp) REVERT: F 181 GLU cc_start: 0.8410 (pt0) cc_final: 0.8190 (pt0) REVERT: F 233 MET cc_start: 0.8939 (mtp) cc_final: 0.8518 (mtp) REVERT: F 288 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7210 (tm-30) REVERT: F 355 ASP cc_start: 0.8219 (m-30) cc_final: 0.7757 (m-30) REVERT: F 377 LEU cc_start: 0.9438 (tp) cc_final: 0.9195 (tt) REVERT: F 379 LYS cc_start: 0.9284 (mtpt) cc_final: 0.8508 (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: 0.9137 (mtmm) REVERT: F 412 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7865 (tp30) REVERT: J 2 ARG cc_start: 0.7676 (mtm180) cc_final: 0.7079 (mmt90) REVERT: J 3 GLU cc_start: 0.8462 (mp0) cc_final: 0.8251 (mp0) REVERT: J 21 TRP cc_start: 0.9162 (m100) cc_final: 0.8741 (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: 0.8443 (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: 0.8765 (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: 0.7575 (mt-10) REVERT: J 203 MET cc_start: 0.8799 (mmp) cc_final: 0.8435 (mmm) REVERT: J 221 ARG cc_start: 0.8971 (mtt90) cc_final: 0.8727 (mtm-85) 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: 0.8150 (mtm) REVERT: J 357 TYR cc_start: 0.7918 (m-80) cc_final: 0.7573 (m-80) REVERT: J 398 MET cc_start: 0.9102 (mtp) cc_final: 0.8701 (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: 0.8047 (mt0) REVERT: C 121 ARG cc_start: 0.8548 (mmm160) cc_final: 0.8058 (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: 0.9024 (mmm) REVERT: C 155 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8646 (mt-10) REVERT: C 170 SER cc_start: 0.8988 (m) cc_final: 0.8765 (t) REVERT: C 207 GLU cc_start: 0.8029 (tt0) cc_final: 0.7581 (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: 0.8674 (t0) REVERT: C 248 LEU cc_start: 0.9068 (tp) cc_final: 0.8851 (tt) REVERT: C 254 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8289 (mt-10) REVERT: C 351 PHE cc_start: 0.9005 (m-80) cc_final: 0.8643 (m-10) REVERT: C 376 CYS cc_start: 0.9089 (t) cc_final: 0.8813 (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: 0.8713 (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: 0.6945 (mmt90) REVERT: L 31 GLN cc_start: 0.8630 (mm-40) cc_final: 0.8124 (mt0) REVERT: L 145 THR cc_start: 0.9383 (m) cc_final: 0.9023 (p) REVERT: L 170 SER cc_start: 0.9160 (m) cc_final: 0.8885 (t) REVERT: L 207 GLU cc_start: 0.8106 (tt0) cc_final: 0.7804 (tm-30) REVERT: L 254 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8175 (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: 0.9057 (p) REVERT: L 326 LYS cc_start: 0.9103 (tmtm) cc_final: 0.8859 (mttp) 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: 0.8695 (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: 0.8305 (mp0) REVERT: A 35 GLN cc_start: 0.8421 (mm-40) cc_final: 0.8101 (mp10) REVERT: A 36 MET cc_start: 0.8772 (ptm) cc_final: 0.8555 (ptm) REVERT: A 50 ASN cc_start: 0.9138 (t0) cc_final: 0.8625 (t0) 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: 0.8765 (ttm110) REVERT: A 145 THR cc_start: 0.9401 (m) cc_final: 0.8896 (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: 0.8838 (mmm) REVERT: A 205 ASP cc_start: 0.8549 (t0) cc_final: 0.8285 (t0) REVERT: A 207 GLU cc_start: 0.7994 (tt0) cc_final: 0.7781 (tm-30) REVERT: A 279 GLU cc_start: 0.8826 (pt0) cc_final: 0.8478 (pm20) REVERT: A 351 PHE cc_start: 0.9045 (m-80) cc_final: 0.8747 (m-80) REVERT: A 415 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8439 (tm-30) REVERT: A 417 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8256 (tm-30) REVERT: A 431 ASP cc_start: 0.8696 (m-30) cc_final: 0.8338 (m-30) REVERT: K 2 ARG cc_start: 0.7879 (mtm180) cc_final: 0.6900 (mmt90) REVERT: K 3 GLU cc_start: 0.8625 (mp0) cc_final: 0.8079 (mp0) REVERT: K 23 LEU cc_start: 0.9634 (tp) cc_final: 0.9313 (tp) REVERT: K 36 MET cc_start: 0.8763 (ptm) cc_final: 0.8559 (ttp) REVERT: K 50 ASN cc_start: 0.9121 (t0) cc_final: 0.8598 (t0) REVERT: K 113 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8434 (mp0) REVERT: K 129 CYS cc_start: 0.8057 (m) cc_final: 0.7736 (m) REVERT: K 145 THR cc_start: 0.9466 (m) cc_final: 0.9217 (p) REVERT: K 155 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8632 (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: 0.8175 (mt-10) REVERT: K 203 MET cc_start: 0.9156 (mmp) cc_final: 0.8711 (mmm) REVERT: K 205 ASP cc_start: 0.8660 (t0) cc_final: 0.8394 (t70) REVERT: K 313 MET cc_start: 0.9054 (mtm) cc_final: 0.8413 (mtm) REVERT: K 326 LYS cc_start: 0.9293 (tmtm) cc_final: 0.8810 (mtmt) REVERT: K 397 LEU cc_start: 0.9147 (mt) cc_final: 0.8946 (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: 0.8281 (m-30) REVERT: K 434 GLU cc_start: 0.8585 (tt0) cc_final: 0.8173 (mm-30) REVERT: G 6 HIS cc_start: 0.9133 (t70) cc_final: 0.8932 (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: 0.9048 (p) REVERT: G 218 THR cc_start: 0.8406 (p) cc_final: 0.8153 (p) REVERT: G 288 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7384 (tm-30) REVERT: G 289 LEU cc_start: 0.8811 (mp) cc_final: 0.8125 (mt) REVERT: G 313 VAL cc_start: 0.9590 (t) cc_final: 0.9236 (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: 0.8521 (ptp) REVERT: G 377 LEU cc_start: 0.9422 (tp) cc_final: 0.9031 (tt) REVERT: G 379 LYS cc_start: 0.9365 (mtpt) cc_final: 0.8538 (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: 0.7844 (t) REVERT: D 136 THR cc_start: 0.9371 (m) cc_final: 0.8760 (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: 0.6563 (tm-30) REVERT: D 329 GLN cc_start: 0.8789 (mm-40) cc_final: 0.7929 (mt0) REVERT: D 340 TYR cc_start: 0.8077 (m-80) cc_final: 0.7643 (m-80) REVERT: D 364 SER cc_start: 0.9335 (t) cc_final: 0.9058 (m) REVERT: D 374 ILE cc_start: 0.9200 (pp) cc_final: 0.8937 (mp) REVERT: D 377 LEU cc_start: 0.9367 (tp) cc_final: 0.9075 (tt) REVERT: I 129 CYS cc_start: 0.8676 (t) cc_final: 0.8047 (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: 0.8312 (mtmm) REVERT: I 329 GLN cc_start: 0.8742 (mm-40) cc_final: 0.7838 (mt0) REVERT: I 340 TYR cc_start: 0.8027 (m-80) cc_final: 0.7545 (m-80) REVERT: I 364 SER cc_start: 0.9275 (t) cc_final: 0.9051 (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: 0.9099 (tt) REVERT: I 380 ARG cc_start: 0.8492 (ttp-110) cc_final: 0.8126 (ttm170) REVERT: I 397 TRP cc_start: 0.9152 (m100) cc_final: 0.8637 (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: 0.7135 (mp0) REVERT: B 108 GLU cc_start: 0.8648 (mp0) cc_final: 0.8409 (mp0) REVERT: B 129 CYS cc_start: 0.8278 (t) cc_final: 0.7943 (p) REVERT: B 136 THR cc_start: 0.9523 (m) cc_final: 0.8897 (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: 0.8972 (t) REVERT: B 190 HIS cc_start: 0.8949 (t-90) cc_final: 0.8665 (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: 0.6738 (tm-30) REVERT: B 313 VAL cc_start: 0.9415 (t) cc_final: 0.8834 (m) REVERT: B 329 GLN cc_start: 0.8946 (mm-40) cc_final: 0.8226 (mt0) REVERT: B 340 TYR cc_start: 0.7832 (m-80) cc_final: 0.7593 (m-80) REVERT: B 363 MET cc_start: 0.9058 (ptp) cc_final: 0.8764 (ptp) REVERT: H 6 HIS cc_start: 0.9223 (t70) cc_final: 0.9001 (t-170) REVERT: H 7 ILE cc_start: 0.9125 (mt) cc_final: 0.8878 (mt) REVERT: H 129 CYS cc_start: 0.8552 (t) cc_final: 0.8040 (p) REVERT: H 136 THR cc_start: 0.9529 (m) cc_final: 0.8878 (p) REVERT: H 166 THR cc_start: 0.9326 (p) cc_final: 0.9112 (p) REVERT: H 180 VAL cc_start: 0.9516 (m) cc_final: 0.9036 (p) REVERT: H 198 GLU cc_start: 0.8766 (pt0) cc_final: 0.8354 (pm20) REVERT: H 245 GLN cc_start: 0.8805 (mt0) cc_final: 0.8560 (mt0) REVERT: H 288 GLU cc_start: 0.7537 (tm-30) cc_final: 0.6590 (tm-30) REVERT: H 329 GLN cc_start: 0.8859 (mm-40) cc_final: 0.8032 (mt0) REVERT: H 363 MET cc_start: 0.8908 (ptp) cc_final: 0.8437 (ptp) outliers start: 0 outliers final: 0 residues processed: 1472 average time/residue: 0.5479 time to fit residues: 1291.8785 Evaluate side-chains 778 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 778 time to evaluate : 4.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 430 optimal weight: 0.9980 chunk 386 optimal weight: 10.0000 chunk 214 optimal weight: 20.0000 chunk 132 optimal weight: 20.0000 chunk 260 optimal weight: 2.9990 chunk 206 optimal weight: 20.0000 chunk 399 optimal weight: 9.9990 chunk 154 optimal weight: 9.9990 chunk 243 optimal weight: 9.9990 chunk 297 optimal weight: 0.9980 chunk 463 optimal weight: 7.9990 overall best weight: 4.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 226 ASN F 291 GLN F 307 HIS F 329 GLN F 396 HIS J 28 HIS J 88 HIS J 107 HIS J 192 HIS ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 283 HIS J 301 GLN C 28 HIS C 85 GLN C 88 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 197 HIS L 206 ASN A 28 HIS A 88 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 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 ASN G 307 HIS G 329 GLN G 396 HIS ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 ASN D 307 HIS D 396 HIS ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 226 ASN I 307 HIS I 329 GLN 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 ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 226 ASN H 307 HIS H 329 GLN H 332 ASN H 396 HIS ** H 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 42204 Z= 0.231 Angle : 0.661 10.766 57414 Z= 0.329 Chirality : 0.048 0.488 6282 Planarity : 0.005 0.046 7452 Dihedral : 13.863 179.759 6402 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.03 % Allowed : 10.18 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.10), residues: 5130 helix: -1.58 (0.09), residues: 2244 sheet: -0.20 (0.18), residues: 822 loop : -2.15 (0.12), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 21 HIS 0.006 0.001 HIS F 307 PHE 0.016 0.001 PHE L 351 TYR 0.020 0.001 TYR D 208 ARG 0.009 0.001 ARG F 282 *********************** 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 943 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 854 time to evaluate : 4.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 50 ASN cc_start: 0.9286 (t0) cc_final: 0.8729 (t0) REVERT: E 84 ARG cc_start: 0.8756 (ttp-110) cc_final: 0.8516 (mtm110) REVERT: E 120 ASP cc_start: 0.9081 (t70) cc_final: 0.8878 (t0) REVERT: E 124 LYS cc_start: 0.9162 (mttm) cc_final: 0.8948 (mmtm) REVERT: E 221 ARG cc_start: 0.8855 (mtt90) cc_final: 0.8552 (mtm-85) REVERT: E 254 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7570 (mt-10) REVERT: E 351 PHE cc_start: 0.9191 (m-80) cc_final: 0.8594 (m-10) REVERT: E 377 MET cc_start: 0.8997 (tmm) cc_final: 0.8773 (tmm) REVERT: E 392 ASP cc_start: 0.8949 (m-30) cc_final: 0.8737 (t0) REVERT: E 419 SER cc_start: 0.8046 (t) cc_final: 0.7282 (m) REVERT: E 431 ASP cc_start: 0.8675 (m-30) cc_final: 0.8456 (m-30) REVERT: E 434 GLU cc_start: 0.8522 (tt0) cc_final: 0.8242 (mm-30) REVERT: F 121 ARG cc_start: 0.8636 (ttm110) cc_final: 0.8386 (ptp-110) REVERT: F 166 THR cc_start: 0.9404 (p) cc_final: 0.8996 (t) REVERT: F 181 GLU cc_start: 0.8323 (pt0) cc_final: 0.7992 (pt0) REVERT: F 203 ASP cc_start: 0.8060 (t0) cc_final: 0.7769 (t70) REVERT: F 291 GLN cc_start: 0.8754 (pt0) cc_final: 0.8250 (pt0) REVERT: F 293 MET cc_start: 0.8891 (mtm) cc_final: 0.8579 (mtt) REVERT: F 421 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8292 (mt-10) REVERT: J 2 ARG cc_start: 0.7595 (mtm180) cc_final: 0.6753 (mmt90) REVERT: J 23 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9096 (tt) REVERT: J 31 GLN cc_start: 0.7912 (mm-40) cc_final: 0.7683 (mt0) REVERT: J 50 ASN cc_start: 0.9097 (t0) cc_final: 0.8511 (t0) REVERT: J 163 LYS cc_start: 0.8968 (mtpp) cc_final: 0.8752 (mmtt) REVERT: J 168 GLU cc_start: 0.6971 (mt-10) cc_final: 0.6715 (mt-10) REVERT: J 207 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7877 (tm-30) REVERT: J 301 GLN cc_start: 0.8424 (mt0) cc_final: 0.8105 (mm110) REVERT: J 302 MET cc_start: 0.8951 (mpp) cc_final: 0.7526 (mpp) REVERT: J 313 MET cc_start: 0.8747 (mtm) cc_final: 0.6994 (mtm) REVERT: J 319 TYR cc_start: 0.9495 (m-10) cc_final: 0.9222 (m-10) REVERT: J 357 TYR cc_start: 0.7944 (m-80) cc_final: 0.7554 (m-80) REVERT: J 380 ASN cc_start: 0.8901 (t0) cc_final: 0.8120 (t0) REVERT: J 420 GLU cc_start: 0.8526 (tt0) cc_final: 0.8312 (tt0) REVERT: J 433 GLU cc_start: 0.9121 (mp0) cc_final: 0.8802 (mp0) REVERT: C 31 GLN cc_start: 0.8509 (mm-40) cc_final: 0.8010 (mt0) REVERT: C 50 ASN cc_start: 0.9317 (t0) cc_final: 0.8814 (t0) REVERT: C 147 SER cc_start: 0.9117 (p) cc_final: 0.8875 (t) REVERT: C 154 MET cc_start: 0.9383 (mmm) cc_final: 0.8950 (mmm) REVERT: C 155 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8767 (mt-10) REVERT: C 170 SER cc_start: 0.9045 (m) cc_final: 0.8787 (t) REVERT: C 207 GLU cc_start: 0.7825 (tt0) cc_final: 0.7618 (tm-30) REVERT: C 218 ASP cc_start: 0.8921 (m-30) cc_final: 0.8710 (t0) REVERT: C 254 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8241 (mt-10) REVERT: C 302 MET cc_start: 0.8614 (mpp) cc_final: 0.8381 (mpp) REVERT: C 313 MET cc_start: 0.8703 (mtm) cc_final: 0.8489 (mtm) REVERT: C 351 PHE cc_start: 0.9059 (m-80) cc_final: 0.8766 (m-10) REVERT: C 392 ASP cc_start: 0.9121 (m-30) cc_final: 0.8905 (m-30) REVERT: C 425 MET cc_start: 0.9151 (tpp) cc_final: 0.8928 (tpp) REVERT: C 431 ASP cc_start: 0.9035 (m-30) cc_final: 0.8804 (m-30) REVERT: L 2 ARG cc_start: 0.7864 (mtm180) cc_final: 0.7045 (mpt180) REVERT: L 31 GLN cc_start: 0.8528 (mm-40) cc_final: 0.7962 (mt0) REVERT: L 35 GLN cc_start: 0.8164 (mm-40) cc_final: 0.7917 (mp10) REVERT: L 50 ASN cc_start: 0.9256 (t0) cc_final: 0.8752 (t0) REVERT: L 136 LEU cc_start: 0.9057 (mt) cc_final: 0.8847 (mt) REVERT: L 147 SER cc_start: 0.9121 (p) cc_final: 0.8815 (t) REVERT: L 170 SER cc_start: 0.9114 (m) cc_final: 0.8794 (t) REVERT: L 205 ASP cc_start: 0.8582 (t0) cc_final: 0.8351 (t0) REVERT: L 279 GLU cc_start: 0.8654 (pt0) cc_final: 0.8012 (pm20) REVERT: L 301 GLN cc_start: 0.7923 (mm-40) cc_final: 0.7493 (mm110) REVERT: L 392 ASP cc_start: 0.9056 (m-30) cc_final: 0.8819 (m-30) REVERT: L 431 ASP cc_start: 0.9032 (m-30) cc_final: 0.8755 (m-30) REVERT: A 2 ARG cc_start: 0.7930 (mtm180) cc_final: 0.7571 (ptp90) REVERT: A 35 GLN cc_start: 0.8262 (mm-40) cc_final: 0.8060 (mp10) REVERT: A 50 ASN cc_start: 0.9227 (t0) cc_final: 0.8665 (t0) REVERT: A 77 GLU cc_start: 0.8975 (mm-30) cc_final: 0.8657 (tp30) REVERT: A 170 SER cc_start: 0.9386 (m) cc_final: 0.8795 (p) REVERT: A 203 MET cc_start: 0.9110 (mmp) cc_final: 0.8790 (mmm) REVERT: A 227 LEU cc_start: 0.9300 (mp) cc_final: 0.8995 (mp) REVERT: A 279 GLU cc_start: 0.8806 (pt0) cc_final: 0.8477 (pm20) REVERT: A 313 MET cc_start: 0.8756 (mtm) cc_final: 0.7570 (mtm) REVERT: A 319 TYR cc_start: 0.9521 (m-80) cc_final: 0.9083 (m-80) REVERT: A 351 PHE cc_start: 0.9122 (m-80) cc_final: 0.8750 (m-80) REVERT: A 417 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7778 (tm-30) REVERT: A 431 ASP cc_start: 0.8883 (m-30) cc_final: 0.8440 (m-30) REVERT: K 2 ARG cc_start: 0.7974 (mtm180) cc_final: 0.6871 (mmt90) REVERT: K 23 LEU cc_start: 0.9626 (tp) cc_final: 0.9347 (tp) REVERT: K 36 MET cc_start: 0.8807 (ptm) cc_final: 0.8512 (ttp) REVERT: K 50 ASN cc_start: 0.9180 (t0) cc_final: 0.8641 (t0) REVERT: K 155 GLU cc_start: 0.9033 (mt-10) cc_final: 0.8744 (mt-10) REVERT: K 170 SER cc_start: 0.9435 (m) cc_final: 0.9131 (t) REVERT: K 183 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7912 (mt-10) REVERT: K 203 MET cc_start: 0.9124 (mmp) cc_final: 0.8762 (mmm) REVERT: K 301 GLN cc_start: 0.8093 (mm-40) cc_final: 0.7754 (mm-40) REVERT: K 313 MET cc_start: 0.9121 (mtm) cc_final: 0.7926 (mtm) REVERT: K 377 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8654 (tmm) REVERT: K 397 LEU cc_start: 0.9146 (mt) cc_final: 0.8941 (mt) REVERT: K 417 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7767 (tm-30) REVERT: K 431 ASP cc_start: 0.8899 (m-30) cc_final: 0.8484 (m-30) REVERT: K 434 GLU cc_start: 0.8461 (tt0) cc_final: 0.8199 (mm-30) REVERT: G 6 HIS cc_start: 0.9156 (t70) cc_final: 0.8937 (t-170) REVERT: G 121 ARG cc_start: 0.8791 (ttm110) cc_final: 0.8570 (ptp-110) REVERT: G 166 THR cc_start: 0.9462 (p) cc_final: 0.8982 (t) REVERT: G 288 GLU cc_start: 0.7804 (tm-30) cc_final: 0.7441 (tm-30) REVERT: G 313 VAL cc_start: 0.9652 (t) cc_final: 0.9364 (p) REVERT: G 323 MET cc_start: 0.8270 (mmm) cc_final: 0.8003 (mmm) REVERT: G 363 MET cc_start: 0.8781 (ptp) cc_final: 0.8306 (ptp) REVERT: G 379 LYS cc_start: 0.9188 (mtpt) cc_final: 0.8811 (ptpt) REVERT: G 397 TRP cc_start: 0.9105 (m100) cc_final: 0.8721 (m-10) REVERT: D 129 CYS cc_start: 0.8921 (t) cc_final: 0.8651 (t) REVERT: D 136 THR cc_start: 0.9268 (m) cc_final: 0.8559 (p) REVERT: D 263 LEU cc_start: 0.9148 (mp) cc_final: 0.8876 (mt) REVERT: D 280 GLN cc_start: 0.8997 (pt0) cc_final: 0.8602 (pm20) REVERT: D 340 TYR cc_start: 0.8074 (m-80) cc_final: 0.7719 (m-80) REVERT: D 379 LYS cc_start: 0.9227 (mtpt) cc_final: 0.8971 (ptpp) REVERT: D 401 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8020 (mp0) REVERT: I 22 GLU cc_start: 0.8724 (tt0) cc_final: 0.8253 (tm-30) REVERT: I 129 CYS cc_start: 0.8893 (t) cc_final: 0.8646 (t) REVERT: I 135 LEU cc_start: 0.9400 (tt) cc_final: 0.9192 (tp) REVERT: I 136 THR cc_start: 0.9219 (m) cc_final: 0.8495 (p) REVERT: I 205 GLU cc_start: 0.8382 (tt0) cc_final: 0.8104 (tm-30) REVERT: I 263 LEU cc_start: 0.9204 (mp) cc_final: 0.8936 (mt) REVERT: I 297 LYS cc_start: 0.8873 (ptpt) cc_final: 0.8594 (mtmm) REVERT: I 340 TYR cc_start: 0.8000 (m-80) cc_final: 0.7600 (m-80) REVERT: I 397 TRP cc_start: 0.9132 (m100) cc_final: 0.8126 (m-10) REVERT: I 401 GLU cc_start: 0.8411 (mm-30) cc_final: 0.7949 (mp0) REVERT: I 410 GLU cc_start: 0.8181 (pt0) cc_final: 0.7764 (pt0) REVERT: B 129 CYS cc_start: 0.8436 (t) cc_final: 0.8014 (p) REVERT: B 136 THR cc_start: 0.9379 (m) cc_final: 0.8611 (p) REVERT: B 180 VAL cc_start: 0.9425 (m) cc_final: 0.8919 (t) REVERT: B 340 TYR cc_start: 0.7900 (m-80) cc_final: 0.7579 (m-80) REVERT: B 363 MET cc_start: 0.8870 (ptp) cc_final: 0.8623 (ptp) REVERT: B 401 GLU cc_start: 0.8674 (mp0) cc_final: 0.8464 (mp0) REVERT: H 117 LEU cc_start: 0.9653 (OUTLIER) cc_final: 0.9409 (mp) REVERT: H 121 ARG cc_start: 0.8735 (ttm110) cc_final: 0.8529 (ptp-110) REVERT: H 129 CYS cc_start: 0.8392 (t) cc_final: 0.8115 (p) REVERT: H 136 THR cc_start: 0.9253 (m) cc_final: 0.8574 (p) REVERT: H 363 MET cc_start: 0.8492 (ptp) cc_final: 0.8261 (ptp) outliers start: 89 outliers final: 44 residues processed: 917 average time/residue: 0.5810 time to fit residues: 887.8826 Evaluate side-chains 740 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 693 time to evaluate : 4.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 284 GLU Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 321 MET 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 367 ASP Chi-restraints excluded: chain J residue 428 LEU Chi-restraints excluded: chain C residue 26 LEU 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 158 SER Chi-restraints excluded: chain A residue 248 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 377 MET 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 323 MET Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 395 LEU Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain H residue 117 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 257 optimal weight: 20.0000 chunk 143 optimal weight: 0.6980 chunk 385 optimal weight: 9.9990 chunk 315 optimal weight: 20.0000 chunk 127 optimal weight: 0.9990 chunk 463 optimal weight: 8.9990 chunk 501 optimal weight: 20.0000 chunk 413 optimal weight: 4.9990 chunk 460 optimal weight: 7.9990 chunk 158 optimal weight: 20.0000 chunk 372 optimal weight: 0.9980 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 88 HIS ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 301 GLN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 GLN ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 107 HIS A 91 GLN ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 206 ASN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 ASN ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN B 332 ASN ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 ASN H 332 ASN ** H 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 42204 Z= 0.178 Angle : 0.571 8.110 57414 Z= 0.281 Chirality : 0.046 0.488 6282 Planarity : 0.004 0.040 7452 Dihedral : 12.258 177.182 6402 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.16 % Allowed : 12.16 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.11), residues: 5130 helix: -0.40 (0.11), residues: 2244 sheet: 0.03 (0.18), residues: 822 loop : -1.86 (0.12), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 346 HIS 0.006 0.001 HIS B 6 PHE 0.010 0.001 PHE L 351 TYR 0.014 0.001 TYR E 24 ARG 0.007 0.000 ARG A 214 *********************** 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 864 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 769 time to evaluate : 4.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 127 ASP cc_start: 0.8398 (m-30) cc_final: 0.8159 (m-30) REVERT: E 245 ASP cc_start: 0.7995 (p0) cc_final: 0.7670 (p0) REVERT: E 254 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7610 (mt-10) REVERT: E 259 LEU cc_start: 0.9442 (mt) cc_final: 0.9159 (mt) REVERT: E 351 PHE cc_start: 0.9115 (m-80) cc_final: 0.8826 (m-10) REVERT: E 357 TYR cc_start: 0.8091 (m-80) cc_final: 0.7129 (m-80) REVERT: E 377 MET cc_start: 0.8972 (tmm) cc_final: 0.8687 (tmm) REVERT: E 424 ASP cc_start: 0.8897 (t70) cc_final: 0.8516 (t0) REVERT: E 431 ASP cc_start: 0.8644 (m-30) cc_final: 0.8419 (m-30) REVERT: E 434 GLU cc_start: 0.8614 (tt0) cc_final: 0.8307 (mm-30) REVERT: F 14 ASN cc_start: 0.9216 (m-40) cc_final: 0.8950 (m-40) REVERT: F 166 THR cc_start: 0.9410 (p) cc_final: 0.9206 (p) REVERT: F 181 GLU cc_start: 0.8349 (pt0) cc_final: 0.8003 (pt0) REVERT: F 203 ASP cc_start: 0.8111 (t70) cc_final: 0.7865 (t70) REVERT: F 291 GLN cc_start: 0.8391 (pt0) cc_final: 0.8008 (pt0) REVERT: F 421 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8240 (mt-10) REVERT: J 2 ARG cc_start: 0.7660 (mtm180) cc_final: 0.6766 (mmt90) REVERT: J 31 GLN cc_start: 0.8016 (mm-40) cc_final: 0.7775 (mt0) REVERT: J 50 ASN cc_start: 0.9150 (t0) cc_final: 0.8585 (t0) REVERT: J 168 GLU cc_start: 0.7042 (mt-10) cc_final: 0.6776 (mt-10) REVERT: J 193 THR cc_start: 0.8623 (m) cc_final: 0.8229 (p) REVERT: J 203 MET cc_start: 0.8607 (mmm) cc_final: 0.8348 (mmm) REVERT: J 207 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7921 (tm-30) REVERT: J 301 GLN cc_start: 0.8479 (mt0) cc_final: 0.8130 (mm110) REVERT: J 302 MET cc_start: 0.9072 (mpp) cc_final: 0.7454 (mpp) REVERT: J 313 MET cc_start: 0.8853 (mtm) cc_final: 0.6976 (mtm) REVERT: J 357 TYR cc_start: 0.8116 (m-80) cc_final: 0.7717 (m-80) REVERT: J 380 ASN cc_start: 0.8908 (t0) cc_final: 0.8141 (t0) REVERT: J 420 GLU cc_start: 0.8512 (tt0) cc_final: 0.8270 (tt0) REVERT: J 428 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.7784 (tp) REVERT: C 31 GLN cc_start: 0.8496 (mm-40) cc_final: 0.8046 (mt0) REVERT: C 154 MET cc_start: 0.9392 (mmm) cc_final: 0.8918 (mmm) REVERT: C 155 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8758 (mt-10) REVERT: C 170 SER cc_start: 0.9114 (m) cc_final: 0.8831 (t) REVERT: C 218 ASP cc_start: 0.8922 (m-30) cc_final: 0.8665 (t0) REVERT: C 254 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8215 (mt-10) REVERT: C 297 GLU cc_start: 0.9032 (mm-30) cc_final: 0.8687 (mm-30) REVERT: C 302 MET cc_start: 0.8750 (mpp) cc_final: 0.8099 (mpp) REVERT: C 313 MET cc_start: 0.8735 (mtm) cc_final: 0.8327 (mtm) REVERT: C 351 PHE cc_start: 0.9137 (m-80) cc_final: 0.8852 (m-10) REVERT: C 392 ASP cc_start: 0.9098 (m-30) cc_final: 0.8894 (m-30) REVERT: L 2 ARG cc_start: 0.7938 (mtm180) cc_final: 0.6767 (mpt180) REVERT: L 31 GLN cc_start: 0.8509 (mm-40) cc_final: 0.8085 (mt0) REVERT: L 35 GLN cc_start: 0.8078 (mm-40) cc_final: 0.7728 (mp10) REVERT: L 170 SER cc_start: 0.9213 (m) cc_final: 0.8942 (t) REVERT: L 279 GLU cc_start: 0.8676 (pt0) cc_final: 0.8005 (pm20) REVERT: L 301 GLN cc_start: 0.7903 (mm-40) cc_final: 0.7450 (mm110) REVERT: L 302 MET cc_start: 0.8595 (mpp) cc_final: 0.8349 (mpp) REVERT: L 322 ASP cc_start: 0.8442 (t0) cc_final: 0.8236 (t0) REVERT: L 392 ASP cc_start: 0.9014 (m-30) cc_final: 0.8788 (m-30) REVERT: L 419 SER cc_start: 0.8999 (OUTLIER) cc_final: 0.8686 (p) REVERT: L 431 ASP cc_start: 0.9004 (m-30) cc_final: 0.8762 (m-30) REVERT: A 2 ARG cc_start: 0.8005 (mtm180) cc_final: 0.7502 (ptp90) REVERT: A 50 ASN cc_start: 0.9215 (t0) cc_final: 0.8675 (t0) REVERT: A 54 SER cc_start: 0.8841 (p) cc_final: 0.8618 (p) REVERT: A 77 GLU cc_start: 0.8994 (mm-30) cc_final: 0.8712 (tp30) REVERT: A 170 SER cc_start: 0.9394 (m) cc_final: 0.9012 (t) REVERT: A 227 LEU cc_start: 0.9271 (mp) cc_final: 0.9062 (mp) REVERT: A 279 GLU cc_start: 0.8818 (pt0) cc_final: 0.8473 (pm20) REVERT: A 319 TYR cc_start: 0.9472 (m-80) cc_final: 0.9179 (m-80) REVERT: A 351 PHE cc_start: 0.9052 (m-80) cc_final: 0.8710 (m-80) REVERT: A 377 MET cc_start: 0.9016 (tmm) cc_final: 0.8253 (tmm) REVERT: A 417 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7682 (tm-30) REVERT: A 431 ASP cc_start: 0.8922 (m-30) cc_final: 0.8479 (m-30) REVERT: K 2 ARG cc_start: 0.8066 (mtm180) cc_final: 0.6883 (mmt90) REVERT: K 23 LEU cc_start: 0.9621 (tp) cc_final: 0.9418 (tp) REVERT: K 36 MET cc_start: 0.8771 (ptm) cc_final: 0.8505 (ttp) REVERT: K 50 ASN cc_start: 0.9202 (t0) cc_final: 0.8674 (t0) REVERT: K 155 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8824 (mt-10) REVERT: K 183 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7628 (mt-10) REVERT: K 203 MET cc_start: 0.9099 (mmp) cc_final: 0.8753 (mmm) REVERT: K 301 GLN cc_start: 0.8208 (mm-40) cc_final: 0.7825 (mm-40) REVERT: K 313 MET cc_start: 0.9084 (mtm) cc_final: 0.8001 (mtm) REVERT: K 397 LEU cc_start: 0.9176 (mt) cc_final: 0.8882 (mt) REVERT: K 417 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7600 (tm-30) REVERT: K 431 ASP cc_start: 0.8857 (m-30) cc_final: 0.8551 (m-30) REVERT: K 434 GLU cc_start: 0.8358 (tt0) cc_final: 0.8096 (mm-30) REVERT: G 14 ASN cc_start: 0.9238 (m-40) cc_final: 0.8943 (m-40) REVERT: G 136 THR cc_start: 0.9242 (m) cc_final: 0.8521 (p) REVERT: G 166 THR cc_start: 0.9515 (p) cc_final: 0.9003 (t) REVERT: G 205 GLU cc_start: 0.8397 (tm-30) cc_final: 0.8126 (tm-30) REVERT: G 257 MET cc_start: 0.8844 (mmm) cc_final: 0.8392 (mmm) REVERT: G 288 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7527 (tm-30) REVERT: G 323 MET cc_start: 0.7989 (mmm) cc_final: 0.7717 (mmm) REVERT: G 363 MET cc_start: 0.8752 (ptp) cc_final: 0.8317 (ptp) REVERT: G 379 LYS cc_start: 0.9203 (mtpt) cc_final: 0.8900 (mmmt) REVERT: D 129 CYS cc_start: 0.8943 (t) cc_final: 0.8643 (t) REVERT: D 136 THR cc_start: 0.9264 (m) cc_final: 0.8531 (p) REVERT: D 181 GLU cc_start: 0.9001 (pp20) cc_final: 0.8684 (pt0) REVERT: D 263 LEU cc_start: 0.9142 (mp) cc_final: 0.8865 (mt) REVERT: D 280 GLN cc_start: 0.9099 (OUTLIER) cc_final: 0.8670 (pm20) REVERT: D 340 TYR cc_start: 0.8084 (m-80) cc_final: 0.7739 (m-80) REVERT: D 379 LYS cc_start: 0.9228 (mtpt) cc_final: 0.8987 (ptpp) REVERT: D 401 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8063 (mp0) REVERT: I 73 MET cc_start: 0.9043 (mmt) cc_final: 0.8732 (mmm) REVERT: I 129 CYS cc_start: 0.8908 (t) cc_final: 0.8610 (t) REVERT: I 136 THR cc_start: 0.9239 (m) cc_final: 0.8578 (p) REVERT: I 181 GLU cc_start: 0.9056 (pp20) cc_final: 0.8670 (pt0) REVERT: I 205 GLU cc_start: 0.8478 (tt0) cc_final: 0.8180 (tm-30) REVERT: I 225 LEU cc_start: 0.9638 (mt) cc_final: 0.9414 (mt) REVERT: I 263 LEU cc_start: 0.9180 (mp) cc_final: 0.8923 (mt) REVERT: I 297 LYS cc_start: 0.8834 (ptpt) cc_final: 0.8600 (mtmm) REVERT: I 325 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8321 (mp0) REVERT: I 340 TYR cc_start: 0.8039 (m-80) cc_final: 0.7671 (m-80) REVERT: I 379 LYS cc_start: 0.9211 (mtpt) cc_final: 0.8981 (ptpp) REVERT: I 397 TRP cc_start: 0.9205 (m100) cc_final: 0.8138 (m-10) REVERT: I 401 GLU cc_start: 0.8451 (mm-30) cc_final: 0.7969 (mp0) REVERT: I 410 GLU cc_start: 0.8079 (pt0) cc_final: 0.7799 (pt0) REVERT: B 57 ASN cc_start: 0.8207 (t0) cc_final: 0.7983 (t0) REVERT: B 74 ASP cc_start: 0.8714 (m-30) cc_final: 0.8508 (m-30) REVERT: B 129 CYS cc_start: 0.8468 (t) cc_final: 0.8066 (t) REVERT: B 136 THR cc_start: 0.9351 (m) cc_final: 0.8602 (p) REVERT: B 180 VAL cc_start: 0.9384 (m) cc_final: 0.9009 (t) REVERT: B 192 LEU cc_start: 0.9251 (mt) cc_final: 0.9028 (mt) REVERT: B 340 TYR cc_start: 0.7929 (m-80) cc_final: 0.7582 (m-80) REVERT: B 363 MET cc_start: 0.8798 (ptp) cc_final: 0.8369 (ptp) REVERT: B 401 GLU cc_start: 0.8705 (mp0) cc_final: 0.8459 (mp0) REVERT: H 103 LYS cc_start: 0.8991 (mttt) cc_final: 0.8699 (mmtp) REVERT: H 136 THR cc_start: 0.9336 (m) cc_final: 0.8677 (p) REVERT: H 180 VAL cc_start: 0.9366 (m) cc_final: 0.8706 (t) REVERT: H 347 ASN cc_start: 0.9149 (p0) cc_final: 0.8946 (p0) REVERT: H 363 MET cc_start: 0.8462 (ptp) cc_final: 0.8209 (ptp) REVERT: H 376 GLU cc_start: 0.8484 (pt0) cc_final: 0.8267 (pt0) REVERT: H 379 LYS cc_start: 0.9314 (mtpt) cc_final: 0.9078 (ptpt) outliers start: 95 outliers final: 67 residues processed: 841 average time/residue: 0.5148 time to fit residues: 721.1868 Evaluate side-chains 731 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 661 time to evaluate : 4.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 284 GLU Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 423 GLU Chi-restraints excluded: chain F residue 304 ASP 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 150 THR Chi-restraints excluded: chain J residue 204 VAL Chi-restraints excluded: chain J residue 232 SER 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 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 259 LEU Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain L residue 26 LEU 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 L residue 349 THR 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 250 VAL 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 122 ILE Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 335 ILE 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 232 THR Chi-restraints excluded: chain G residue 333 VAL Chi-restraints excluded: chain D residue 280 GLN Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain I residue 41 ASP 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 313 VAL 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 253 LEU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 293 MET Chi-restraints excluded: chain B residue 406 MET 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 458 optimal weight: 1.9990 chunk 348 optimal weight: 30.0000 chunk 240 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 221 optimal weight: 5.9990 chunk 311 optimal weight: 20.0000 chunk 465 optimal weight: 20.0000 chunk 492 optimal weight: 10.0000 chunk 243 optimal weight: 8.9990 chunk 441 optimal weight: 8.9990 chunk 132 optimal weight: 20.0000 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 334 GLN J 85 GLN J 133 GLN ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 91 GLN A 186 ASN A 393 HIS K 11 GLN K 15 GLN K 91 GLN ** K 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 283 HIS G 291 GLN G 334 GLN ** G 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 334 GLN B 99 ASN B 332 ASN H 99 ASN H 332 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 42204 Z= 0.200 Angle : 0.562 8.705 57414 Z= 0.278 Chirality : 0.045 0.328 6282 Planarity : 0.004 0.040 7452 Dihedral : 11.894 178.654 6402 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.78 % Allowed : 12.66 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.12), residues: 5130 helix: 0.19 (0.11), residues: 2238 sheet: 0.10 (0.18), residues: 822 loop : -1.69 (0.13), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 21 HIS 0.004 0.001 HIS A 61 PHE 0.016 0.001 PHE F 167 TYR 0.012 0.001 TYR D 183 ARG 0.009 0.000 ARG I 320 *********************** 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 823 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 701 time to evaluate : 5.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 127 ASP cc_start: 0.8375 (m-30) cc_final: 0.8171 (m-30) REVERT: E 245 ASP cc_start: 0.8066 (p0) cc_final: 0.7635 (p0) REVERT: E 254 GLU cc_start: 0.8359 (mt-10) cc_final: 0.7804 (mt-10) REVERT: E 313 MET cc_start: 0.8406 (mtm) cc_final: 0.7547 (mtm) REVERT: E 351 PHE cc_start: 0.9180 (m-80) cc_final: 0.8963 (m-10) REVERT: E 357 TYR cc_start: 0.8169 (m-80) cc_final: 0.7170 (m-80) REVERT: E 424 ASP cc_start: 0.8907 (t70) cc_final: 0.8519 (t0) REVERT: E 431 ASP cc_start: 0.8612 (m-30) cc_final: 0.8404 (m-30) REVERT: F 14 ASN cc_start: 0.9183 (m-40) cc_final: 0.8905 (m-40) REVERT: F 136 THR cc_start: 0.9198 (m) cc_final: 0.8492 (p) REVERT: F 181 GLU cc_start: 0.8389 (pt0) cc_final: 0.8154 (pt0) REVERT: F 291 GLN cc_start: 0.8396 (pt0) cc_final: 0.8008 (pt0) REVERT: F 376 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7654 (tm-30) REVERT: F 421 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8136 (mt-10) REVERT: J 2 ARG cc_start: 0.7896 (mtm180) cc_final: 0.6780 (mmt90) REVERT: J 31 GLN cc_start: 0.8216 (mm-40) cc_final: 0.7995 (mt0) REVERT: J 50 ASN cc_start: 0.9216 (t0) cc_final: 0.8651 (t0) REVERT: J 193 THR cc_start: 0.9044 (m) cc_final: 0.8646 (p) REVERT: J 207 GLU cc_start: 0.8283 (tm-30) cc_final: 0.7906 (tm-30) REVERT: J 210 TYR cc_start: 0.8486 (m-10) cc_final: 0.8219 (m-10) REVERT: J 302 MET cc_start: 0.9186 (mpp) cc_final: 0.7439 (mpp) REVERT: J 313 MET cc_start: 0.8779 (mtm) cc_final: 0.6765 (mtm) REVERT: J 319 TYR cc_start: 0.9441 (m-10) cc_final: 0.9060 (m-10) REVERT: J 357 TYR cc_start: 0.8251 (m-80) cc_final: 0.7835 (m-80) REVERT: J 380 ASN cc_start: 0.8965 (t0) cc_final: 0.8170 (t0) REVERT: J 428 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.7900 (tp) REVERT: J 433 GLU cc_start: 0.9110 (mp0) cc_final: 0.8730 (mp0) REVERT: C 31 GLN cc_start: 0.8542 (mm-40) cc_final: 0.8189 (mt0) REVERT: C 170 SER cc_start: 0.9170 (m) cc_final: 0.8873 (t) REVERT: C 183 GLU cc_start: 0.7362 (mt-10) cc_final: 0.7136 (mt-10) REVERT: C 187 SER cc_start: 0.9405 (m) cc_final: 0.9154 (p) REVERT: C 218 ASP cc_start: 0.8937 (m-30) cc_final: 0.8666 (t0) REVERT: C 254 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8126 (mt-10) REVERT: C 297 GLU cc_start: 0.9093 (mm-30) cc_final: 0.8671 (mm-30) REVERT: C 302 MET cc_start: 0.8804 (mpp) cc_final: 0.8167 (mpp) REVERT: C 345 ASP cc_start: 0.8371 (OUTLIER) cc_final: 0.8092 (p0) REVERT: C 351 PHE cc_start: 0.9149 (m-80) cc_final: 0.8876 (m-10) REVERT: L 2 ARG cc_start: 0.8026 (mtm180) cc_final: 0.7076 (mpt180) REVERT: L 31 GLN cc_start: 0.8434 (mm-40) cc_final: 0.8089 (mt0) REVERT: L 35 GLN cc_start: 0.8153 (mm-40) cc_final: 0.7823 (mp10) REVERT: L 170 SER cc_start: 0.9286 (m) cc_final: 0.9036 (t) REVERT: L 279 GLU cc_start: 0.8700 (pt0) cc_final: 0.7997 (pm20) REVERT: L 301 GLN cc_start: 0.8175 (mm-40) cc_final: 0.7835 (mm110) REVERT: L 392 ASP cc_start: 0.9002 (m-30) cc_final: 0.8799 (m-30) REVERT: L 413 MET cc_start: 0.9035 (ttp) cc_final: 0.8757 (ttp) REVERT: A 2 ARG cc_start: 0.8022 (mtm180) cc_final: 0.7574 (ptp90) REVERT: A 77 GLU cc_start: 0.9001 (mm-30) cc_final: 0.8733 (tp30) REVERT: A 155 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8621 (mt-10) REVERT: A 170 SER cc_start: 0.9476 (m) cc_final: 0.9185 (t) REVERT: A 279 GLU cc_start: 0.8827 (pt0) cc_final: 0.8483 (pm20) REVERT: A 301 GLN cc_start: 0.8091 (mm-40) cc_final: 0.7622 (mm-40) REVERT: A 313 MET cc_start: 0.8732 (mtm) cc_final: 0.7462 (mtm) REVERT: A 319 TYR cc_start: 0.9490 (m-80) cc_final: 0.9179 (m-80) REVERT: A 377 MET cc_start: 0.9011 (tmm) cc_final: 0.8184 (tmm) REVERT: A 417 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7767 (tm-30) REVERT: A 431 ASP cc_start: 0.8773 (m-30) cc_final: 0.8407 (m-30) REVERT: K 2 ARG cc_start: 0.8154 (mtm180) cc_final: 0.6950 (mmt90) REVERT: K 36 MET cc_start: 0.8770 (ptm) cc_final: 0.8567 (ttp) REVERT: K 50 ASN cc_start: 0.9236 (t0) cc_final: 0.8769 (t0) REVERT: K 203 MET cc_start: 0.9124 (mmp) cc_final: 0.8764 (mmm) REVERT: K 301 GLN cc_start: 0.8262 (mm-40) cc_final: 0.7954 (mm-40) REVERT: K 397 LEU cc_start: 0.9183 (mt) cc_final: 0.8895 (mt) REVERT: K 417 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7766 (tm-30) REVERT: K 431 ASP cc_start: 0.8847 (m-30) cc_final: 0.8562 (m-30) REVERT: K 434 GLU cc_start: 0.8390 (tt0) cc_final: 0.8094 (mm-30) REVERT: G 14 ASN cc_start: 0.9239 (m-40) cc_final: 0.8903 (m-40) REVERT: G 136 THR cc_start: 0.9237 (m) cc_final: 0.8505 (p) REVERT: G 166 THR cc_start: 0.9501 (p) cc_final: 0.9097 (t) REVERT: G 181 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8202 (pp20) REVERT: G 205 GLU cc_start: 0.8401 (tm-30) cc_final: 0.8143 (tm-30) REVERT: G 255 VAL cc_start: 0.9185 (OUTLIER) cc_final: 0.8943 (p) REVERT: G 323 MET cc_start: 0.8073 (mmm) cc_final: 0.7750 (mmm) REVERT: G 363 MET cc_start: 0.8779 (ptp) cc_final: 0.8364 (ptp) REVERT: G 379 LYS cc_start: 0.9275 (mtpt) cc_final: 0.9030 (mtpp) REVERT: D 129 CYS cc_start: 0.9060 (t) cc_final: 0.8737 (t) REVERT: D 136 THR cc_start: 0.9257 (m) cc_final: 0.8552 (p) REVERT: D 181 GLU cc_start: 0.9012 (pp20) cc_final: 0.8638 (pt0) REVERT: D 257 MET cc_start: 0.8512 (mmm) cc_final: 0.8179 (mmm) REVERT: D 263 LEU cc_start: 0.9170 (mp) cc_final: 0.8871 (mt) REVERT: D 280 GLN cc_start: 0.9144 (OUTLIER) cc_final: 0.8686 (pm20) REVERT: D 340 TYR cc_start: 0.8109 (m-80) cc_final: 0.7772 (m-80) REVERT: D 379 LYS cc_start: 0.9252 (mtpt) cc_final: 0.9045 (mttm) REVERT: D 401 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8115 (mp0) REVERT: I 57 ASN cc_start: 0.8199 (t0) cc_final: 0.7940 (t0) REVERT: I 73 MET cc_start: 0.9161 (mmt) cc_final: 0.8753 (mmm) REVERT: I 129 CYS cc_start: 0.8971 (t) cc_final: 0.8580 (t) REVERT: I 130 LEU cc_start: 0.9223 (tp) cc_final: 0.8824 (tt) REVERT: I 136 THR cc_start: 0.9226 (m) cc_final: 0.8618 (p) REVERT: I 181 GLU cc_start: 0.9012 (pp20) cc_final: 0.8658 (pt0) REVERT: I 192 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.8907 (tt) REVERT: I 257 MET cc_start: 0.8799 (mmm) cc_final: 0.8543 (mmm) REVERT: I 263 LEU cc_start: 0.9209 (mp) cc_final: 0.8942 (mt) REVERT: I 325 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8240 (mp0) REVERT: I 340 TYR cc_start: 0.8106 (m-80) cc_final: 0.7765 (m-80) REVERT: I 397 TRP cc_start: 0.9288 (m100) cc_final: 0.8104 (m-10) REVERT: I 401 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8110 (mp0) REVERT: I 410 GLU cc_start: 0.8214 (pt0) cc_final: 0.7868 (pt0) REVERT: B 57 ASN cc_start: 0.8249 (t0) cc_final: 0.7886 (t0) REVERT: B 129 CYS cc_start: 0.8442 (t) cc_final: 0.8009 (t) REVERT: B 136 THR cc_start: 0.9362 (m) cc_final: 0.8611 (p) REVERT: B 340 TYR cc_start: 0.8001 (m-80) cc_final: 0.7609 (m-80) REVERT: B 347 ASN cc_start: 0.9122 (p0) cc_final: 0.8695 (p0) REVERT: B 363 MET cc_start: 0.8660 (ptp) cc_final: 0.8382 (ptp) REVERT: B 401 GLU cc_start: 0.8727 (mp0) cc_final: 0.8492 (mp0) REVERT: H 22 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7268 (tm-30) REVERT: H 57 ASN cc_start: 0.8077 (t0) cc_final: 0.7670 (t0) REVERT: H 103 LYS cc_start: 0.9066 (mttt) cc_final: 0.8734 (mmtp) REVERT: H 129 CYS cc_start: 0.8297 (t) cc_final: 0.7837 (t) REVERT: H 136 THR cc_start: 0.9348 (m) cc_final: 0.8689 (p) REVERT: H 180 VAL cc_start: 0.9189 (m) cc_final: 0.8936 (t) REVERT: H 327 ASP cc_start: 0.8055 (t0) cc_final: 0.7847 (t70) REVERT: H 363 MET cc_start: 0.8538 (ptp) cc_final: 0.8259 (ptp) REVERT: H 379 LYS cc_start: 0.9298 (mtpt) cc_final: 0.9035 (mtpp) outliers start: 122 outliers final: 88 residues processed: 792 average time/residue: 0.5042 time to fit residues: 668.0958 Evaluate side-chains 741 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 647 time to evaluate : 4.625 ------------------------------------------------------------------------------- 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 187 SER Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 232 SER 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 428 LEU Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 304 ASP Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain F residue 407 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 150 THR 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 428 LEU Chi-restraints excluded: chain C residue 130 THR 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 9 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 232 SER 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 119 LEU Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 232 SER 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 G residue 49 VAL Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain G residue 230 SER Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G 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 351 THR Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 177 ASP Chi-restraints excluded: chain I residue 192 LEU 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 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 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 300 MET Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 406 MET 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 300 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 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 410 optimal weight: 7.9990 chunk 279 optimal weight: 7.9990 chunk 7 optimal weight: 20.0000 chunk 367 optimal weight: 6.9990 chunk 203 optimal weight: 5.9990 chunk 420 optimal weight: 7.9990 chunk 340 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 251 optimal weight: 7.9990 chunk 442 optimal weight: 8.9990 chunk 124 optimal weight: 0.0980 overall best weight: 5.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 301 GLN ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 190 HIS F 334 GLN ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 GLN ** 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 91 GLN K 186 ASN ** K 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 HIS G 291 GLN ** G 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN I 190 HIS ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 42204 Z= 0.244 Angle : 0.573 7.719 57414 Z= 0.285 Chirality : 0.045 0.263 6282 Planarity : 0.004 0.043 7452 Dihedral : 11.699 176.113 6402 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.01 % Allowed : 13.41 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.12), residues: 5130 helix: 0.52 (0.11), residues: 2238 sheet: 0.17 (0.18), residues: 840 loop : -1.61 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 21 HIS 0.009 0.001 HIS J 197 PHE 0.012 0.001 PHE F 167 TYR 0.013 0.001 TYR J 210 ARG 0.010 0.000 ARG D 320 *********************** 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 790 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 658 time to evaluate : 4.561 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 127 ASP cc_start: 0.8291 (m-30) cc_final: 0.7988 (m-30) REVERT: E 254 GLU cc_start: 0.8277 (mt-10) cc_final: 0.7766 (mt-10) REVERT: E 313 MET cc_start: 0.8460 (mtm) cc_final: 0.7382 (mtm) REVERT: E 339 ARG cc_start: 0.7454 (mmp-170) cc_final: 0.6865 (mmt180) REVERT: E 351 PHE cc_start: 0.9177 (m-80) cc_final: 0.8936 (m-10) REVERT: E 357 TYR cc_start: 0.8280 (m-80) cc_final: 0.7899 (m-80) REVERT: E 424 ASP cc_start: 0.8872 (t70) cc_final: 0.8489 (t0) REVERT: E 431 ASP cc_start: 0.8679 (m-30) cc_final: 0.8463 (m-30) REVERT: F 14 ASN cc_start: 0.9175 (m-40) cc_final: 0.8895 (m-40) REVERT: F 22 GLU cc_start: 0.8712 (tt0) cc_final: 0.8187 (tm-30) REVERT: F 136 THR cc_start: 0.9190 (m) cc_final: 0.8493 (p) REVERT: F 267 MET cc_start: 0.8626 (mtm) cc_final: 0.8417 (mtm) REVERT: F 291 GLN cc_start: 0.8382 (pt0) cc_final: 0.7983 (pt0) REVERT: F 327 ASP cc_start: 0.7291 (p0) cc_final: 0.7074 (p0) REVERT: J 2 ARG cc_start: 0.8150 (mtm180) cc_final: 0.6828 (mmt90) REVERT: J 31 GLN cc_start: 0.8299 (mm-40) cc_final: 0.8031 (mt0) REVERT: J 302 MET cc_start: 0.9219 (mpp) cc_final: 0.7835 (mpp) REVERT: J 313 MET cc_start: 0.8788 (mtm) cc_final: 0.6796 (mtm) REVERT: J 357 TYR cc_start: 0.8278 (m-80) cc_final: 0.7870 (m-80) REVERT: J 380 ASN cc_start: 0.8957 (t0) cc_final: 0.8140 (t0) REVERT: J 428 LEU cc_start: 0.9074 (tt) cc_final: 0.8027 (tp) REVERT: J 433 GLU cc_start: 0.9101 (mp0) cc_final: 0.8728 (mp0) REVERT: C 31 GLN cc_start: 0.8582 (mm-40) cc_final: 0.8228 (mt0) REVERT: C 170 SER cc_start: 0.9286 (m) cc_final: 0.9013 (t) REVERT: C 187 SER cc_start: 0.9419 (m) cc_final: 0.9177 (p) REVERT: C 218 ASP cc_start: 0.8950 (m-30) cc_final: 0.8739 (t0) REVERT: C 254 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8150 (mt-10) REVERT: C 297 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8667 (mm-30) REVERT: C 345 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.8235 (p0) REVERT: L 2 ARG cc_start: 0.8161 (mtm180) cc_final: 0.7098 (mpt180) REVERT: L 31 GLN cc_start: 0.8448 (mm-40) cc_final: 0.8127 (mt0) REVERT: L 35 GLN cc_start: 0.8170 (mm-40) cc_final: 0.7829 (mp10) REVERT: L 36 MET cc_start: 0.8711 (ptm) cc_final: 0.8479 (ttp) REVERT: L 170 SER cc_start: 0.9338 (m) cc_final: 0.9118 (t) REVERT: L 279 GLU cc_start: 0.8723 (pt0) cc_final: 0.7997 (pm20) REVERT: L 302 MET cc_start: 0.8471 (mpp) cc_final: 0.7796 (mpp) REVERT: L 392 ASP cc_start: 0.8990 (m-30) cc_final: 0.8715 (m-30) REVERT: L 431 ASP cc_start: 0.9051 (m-30) cc_final: 0.8700 (m-30) REVERT: A 2 ARG cc_start: 0.8161 (mtm180) cc_final: 0.7650 (ptp90) REVERT: A 170 SER cc_start: 0.9504 (m) cc_final: 0.9184 (t) REVERT: A 254 GLU cc_start: 0.8308 (mt-10) cc_final: 0.8013 (mt-10) REVERT: A 279 GLU cc_start: 0.8890 (pt0) cc_final: 0.8557 (pm20) REVERT: A 301 GLN cc_start: 0.8023 (mm-40) cc_final: 0.7524 (mm-40) REVERT: A 313 MET cc_start: 0.8773 (mtm) cc_final: 0.7731 (mtm) REVERT: A 319 TYR cc_start: 0.9449 (m-80) cc_final: 0.9018 (m-80) REVERT: A 377 MET cc_start: 0.9019 (tmm) cc_final: 0.8717 (tmm) REVERT: A 417 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7847 (tm-30) REVERT: A 431 ASP cc_start: 0.8804 (m-30) cc_final: 0.8547 (m-30) REVERT: K 2 ARG cc_start: 0.8275 (mtm180) cc_final: 0.6960 (mmt90) REVERT: K 36 MET cc_start: 0.8781 (ptm) cc_final: 0.8548 (ttp) REVERT: K 50 ASN cc_start: 0.9290 (t0) cc_final: 0.8917 (t0) REVERT: K 203 MET cc_start: 0.9124 (mmp) cc_final: 0.8669 (mmm) REVERT: K 301 GLN cc_start: 0.8215 (mm-40) cc_final: 0.7846 (mm-40) REVERT: K 302 MET cc_start: 0.8886 (mpp) cc_final: 0.8215 (mtm) REVERT: K 313 MET cc_start: 0.8897 (mtm) cc_final: 0.8507 (mtm) REVERT: K 397 LEU cc_start: 0.9125 (mt) cc_final: 0.8846 (mt) REVERT: K 417 GLU cc_start: 0.8256 (tm-30) cc_final: 0.7809 (tm-30) REVERT: K 431 ASP cc_start: 0.8912 (m-30) cc_final: 0.8622 (m-30) REVERT: K 434 GLU cc_start: 0.8405 (tt0) cc_final: 0.8142 (mm-30) REVERT: G 14 ASN cc_start: 0.9216 (m-40) cc_final: 0.8913 (m-40) REVERT: G 136 THR cc_start: 0.9238 (m) cc_final: 0.8497 (p) REVERT: G 166 THR cc_start: 0.9528 (p) cc_final: 0.9124 (t) REVERT: G 181 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8190 (pp20) REVERT: G 205 GLU cc_start: 0.8382 (tm-30) cc_final: 0.8085 (tm-30) REVERT: G 257 MET cc_start: 0.8592 (mmm) cc_final: 0.7875 (mmm) REVERT: G 323 MET cc_start: 0.8116 (mmm) cc_final: 0.7792 (mmm) REVERT: G 327 ASP cc_start: 0.8505 (t70) cc_final: 0.8274 (t0) REVERT: G 363 MET cc_start: 0.8844 (ptp) cc_final: 0.8374 (ptp) REVERT: G 379 LYS cc_start: 0.9281 (mtpt) cc_final: 0.9058 (mtpp) REVERT: D 129 CYS cc_start: 0.9054 (t) cc_final: 0.8731 (t) REVERT: D 130 LEU cc_start: 0.9170 (tp) cc_final: 0.8756 (tt) REVERT: D 136 THR cc_start: 0.9268 (m) cc_final: 0.8608 (p) REVERT: D 181 GLU cc_start: 0.9013 (pp20) cc_final: 0.8769 (pt0) REVERT: D 263 LEU cc_start: 0.9179 (mp) cc_final: 0.8899 (mt) REVERT: D 280 GLN cc_start: 0.9234 (OUTLIER) cc_final: 0.8725 (pm20) REVERT: D 325 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7356 (mp0) REVERT: D 340 TYR cc_start: 0.8191 (m-80) cc_final: 0.7871 (m-80) REVERT: I 57 ASN cc_start: 0.8266 (t0) cc_final: 0.7950 (t0) REVERT: I 129 CYS cc_start: 0.8980 (t) cc_final: 0.8599 (t) REVERT: I 130 LEU cc_start: 0.9245 (tp) cc_final: 0.8833 (tt) REVERT: I 136 THR cc_start: 0.9237 (m) cc_final: 0.8645 (p) REVERT: I 181 GLU cc_start: 0.9032 (pp20) cc_final: 0.8729 (pt0) REVERT: I 192 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.8975 (tt) REVERT: I 263 LEU cc_start: 0.9251 (mp) cc_final: 0.8976 (mt) REVERT: I 340 TYR cc_start: 0.8186 (m-80) cc_final: 0.7816 (m-80) REVERT: I 397 TRP cc_start: 0.9289 (m100) cc_final: 0.8393 (m-10) REVERT: I 410 GLU cc_start: 0.8221 (pt0) cc_final: 0.7914 (pt0) REVERT: B 57 ASN cc_start: 0.8201 (t0) cc_final: 0.7752 (t0) REVERT: B 129 CYS cc_start: 0.8388 (t) cc_final: 0.7946 (t) REVERT: B 197 ASP cc_start: 0.8493 (m-30) cc_final: 0.8128 (m-30) REVERT: B 347 ASN cc_start: 0.9167 (p0) cc_final: 0.8581 (p0) REVERT: B 363 MET cc_start: 0.8711 (ptp) cc_final: 0.8422 (ptp) REVERT: B 379 LYS cc_start: 0.9303 (mtpt) cc_final: 0.9040 (mtpp) REVERT: B 401 GLU cc_start: 0.8726 (mp0) cc_final: 0.8494 (mp0) REVERT: H 22 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7495 (tm-30) REVERT: H 57 ASN cc_start: 0.8072 (t0) cc_final: 0.7571 (t0) REVERT: H 129 CYS cc_start: 0.8279 (t) cc_final: 0.7792 (t) REVERT: H 197 ASP cc_start: 0.8492 (m-30) cc_final: 0.8181 (m-30) REVERT: H 363 MET cc_start: 0.8677 (ptp) cc_final: 0.8381 (ptp) REVERT: H 379 LYS cc_start: 0.9307 (mtpt) cc_final: 0.9056 (mtpp) outliers start: 132 outliers final: 104 residues processed: 756 average time/residue: 0.5057 time to fit residues: 638.2751 Evaluate side-chains 728 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 618 time to evaluate : 4.479 ------------------------------------------------------------------------------- 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 187 SER Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 232 SER 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 203 ASP Chi-restraints excluded: chain F residue 304 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 150 THR Chi-restraints excluded: chain J residue 204 VAL Chi-restraints excluded: chain J residue 232 SER 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 C residue 26 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 98 ASP 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 232 SER 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 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 232 SER 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 130 THR Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 250 VAL 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 130 THR Chi-restraints excluded: chain K residue 187 SER Chi-restraints excluded: chain K residue 232 SER 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 49 VAL Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain G residue 218 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 27 GLU Chi-restraints excluded: chain D residue 177 ASP 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 325 GLU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 407 GLU Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 180 VAL Chi-restraints excluded: chain I residue 192 LEU 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 293 MET Chi-restraints excluded: chain I residue 313 VAL Chi-restraints excluded: chain I residue 351 THR Chi-restraints excluded: chain I residue 419 VAL 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 300 MET Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain H residue 22 GLU Chi-restraints excluded: chain H residue 166 THR Chi-restraints excluded: chain H residue 177 ASP 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 300 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 Chi-restraints excluded: chain H residue 419 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 165 optimal weight: 6.9990 chunk 443 optimal weight: 0.9980 chunk 97 optimal weight: 20.0000 chunk 289 optimal weight: 5.9990 chunk 121 optimal weight: 20.0000 chunk 493 optimal weight: 7.9990 chunk 409 optimal weight: 20.0000 chunk 228 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 163 optimal weight: 7.9990 chunk 259 optimal weight: 9.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 334 GLN ** F 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 ASN L 301 GLN A 197 HIS K 11 GLN K 15 GLN ** K 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 291 GLN ** G 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 42204 Z= 0.241 Angle : 0.570 8.022 57414 Z= 0.282 Chirality : 0.045 0.245 6282 Planarity : 0.004 0.047 7452 Dihedral : 11.519 173.913 6402 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.19 % Allowed : 13.57 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.12), residues: 5130 helix: 0.71 (0.11), residues: 2244 sheet: 0.19 (0.18), residues: 840 loop : -1.52 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 21 HIS 0.004 0.001 HIS E 192 PHE 0.031 0.001 PHE F 167 TYR 0.016 0.001 TYR J 210 ARG 0.008 0.000 ARG F 282 *********************** 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 795 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 655 time to evaluate : 4.639 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 127 ASP cc_start: 0.8349 (m-30) cc_final: 0.8002 (m-30) REVERT: E 313 MET cc_start: 0.8509 (mtm) cc_final: 0.7343 (mtm) REVERT: E 339 ARG cc_start: 0.7591 (mmp-170) cc_final: 0.7039 (mmt180) REVERT: E 351 PHE cc_start: 0.9196 (m-80) cc_final: 0.8927 (m-10) REVERT: E 357 TYR cc_start: 0.8301 (m-80) cc_final: 0.7856 (m-80) REVERT: E 424 ASP cc_start: 0.8892 (t70) cc_final: 0.8476 (t0) REVERT: E 431 ASP cc_start: 0.8535 (m-30) cc_final: 0.8328 (m-30) REVERT: F 14 ASN cc_start: 0.9158 (m-40) cc_final: 0.8822 (m110) REVERT: F 22 GLU cc_start: 0.8720 (tt0) cc_final: 0.8182 (tm-30) REVERT: F 136 THR cc_start: 0.9161 (m) cc_final: 0.8460 (p) REVERT: F 291 GLN cc_start: 0.8417 (pt0) cc_final: 0.8033 (pt0) REVERT: F 313 VAL cc_start: 0.9462 (t) cc_final: 0.9230 (p) REVERT: J 2 ARG cc_start: 0.8200 (mtm180) cc_final: 0.7130 (mmt90) REVERT: J 31 GLN cc_start: 0.8423 (mm-40) cc_final: 0.8147 (mt0) REVERT: J 207 GLU cc_start: 0.8303 (tm-30) cc_final: 0.7945 (tm-30) REVERT: J 302 MET cc_start: 0.9209 (mpp) cc_final: 0.7916 (mpp) REVERT: J 313 MET cc_start: 0.8898 (mtm) cc_final: 0.6838 (mtm) REVERT: J 357 TYR cc_start: 0.8305 (m-80) cc_final: 0.7892 (m-80) REVERT: J 380 ASN cc_start: 0.8986 (t0) cc_final: 0.8192 (t0) REVERT: J 428 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8941 (tp) REVERT: J 433 GLU cc_start: 0.9017 (mp0) cc_final: 0.8643 (mp0) REVERT: C 31 GLN cc_start: 0.8597 (mm-40) cc_final: 0.8146 (mt0) REVERT: C 170 SER cc_start: 0.9308 (m) cc_final: 0.9038 (t) REVERT: C 187 SER cc_start: 0.9364 (m) cc_final: 0.9076 (p) REVERT: C 218 ASP cc_start: 0.8952 (m-30) cc_final: 0.8727 (t0) REVERT: C 297 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8590 (mm-30) REVERT: C 345 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8261 (p0) REVERT: C 351 PHE cc_start: 0.8940 (m-10) cc_final: 0.8672 (m-10) REVERT: L 2 ARG cc_start: 0.8253 (mtm180) cc_final: 0.6800 (mpt180) REVERT: L 31 GLN cc_start: 0.8502 (mm-40) cc_final: 0.8161 (mt0) REVERT: L 36 MET cc_start: 0.8724 (ptm) cc_final: 0.8493 (ttp) REVERT: L 170 SER cc_start: 0.9361 (m) cc_final: 0.9081 (t) REVERT: L 279 GLU cc_start: 0.8737 (pt0) cc_final: 0.7991 (pm20) REVERT: L 302 MET cc_start: 0.8599 (mpp) cc_final: 0.7851 (mpp) REVERT: L 313 MET cc_start: 0.8928 (mtm) cc_final: 0.8635 (mtm) REVERT: L 322 ASP cc_start: 0.8532 (t0) cc_final: 0.8272 (t0) REVERT: L 392 ASP cc_start: 0.9011 (m-30) cc_final: 0.8703 (m-30) REVERT: A 2 ARG cc_start: 0.8242 (mtm180) cc_final: 0.7685 (ptp90) REVERT: A 170 SER cc_start: 0.9522 (m) cc_final: 0.9167 (t) REVERT: A 254 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8033 (mt-10) REVERT: A 279 GLU cc_start: 0.8902 (pt0) cc_final: 0.8563 (pm20) REVERT: A 301 GLN cc_start: 0.7730 (mm-40) cc_final: 0.7180 (mm-40) REVERT: A 302 MET cc_start: 0.9078 (mpp) cc_final: 0.8850 (mpp) REVERT: A 319 TYR cc_start: 0.9455 (m-80) cc_final: 0.9052 (m-80) REVERT: A 322 ASP cc_start: 0.8331 (t0) cc_final: 0.8122 (t0) REVERT: A 377 MET cc_start: 0.9056 (tmm) cc_final: 0.8728 (tmm) REVERT: A 417 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7826 (tm-30) REVERT: A 431 ASP cc_start: 0.8803 (m-30) cc_final: 0.8554 (m-30) REVERT: K 2 ARG cc_start: 0.8355 (mtm180) cc_final: 0.6944 (mmt90) REVERT: K 33 ASP cc_start: 0.9028 (m-30) cc_final: 0.8575 (t0) REVERT: K 203 MET cc_start: 0.9150 (mmp) cc_final: 0.8669 (mmm) REVERT: K 205 ASP cc_start: 0.8514 (t0) cc_final: 0.8205 (t0) REVERT: K 301 GLN cc_start: 0.8233 (mm-40) cc_final: 0.7899 (mm-40) REVERT: K 313 MET cc_start: 0.8789 (mtm) cc_final: 0.8395 (mtm) REVERT: K 397 LEU cc_start: 0.9135 (mt) cc_final: 0.8837 (mt) REVERT: K 417 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7817 (tm-30) REVERT: K 431 ASP cc_start: 0.8825 (m-30) cc_final: 0.8607 (m-30) REVERT: K 434 GLU cc_start: 0.8356 (tt0) cc_final: 0.8085 (mm-30) REVERT: G 14 ASN cc_start: 0.9182 (m-40) cc_final: 0.8889 (m-40) REVERT: G 136 THR cc_start: 0.9225 (m) cc_final: 0.8457 (p) REVERT: G 166 THR cc_start: 0.9535 (p) cc_final: 0.9273 (p) REVERT: G 181 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8219 (pp20) REVERT: G 205 GLU cc_start: 0.8576 (tm-30) cc_final: 0.8212 (tm-30) REVERT: G 257 MET cc_start: 0.8355 (mmm) cc_final: 0.7780 (mmm) REVERT: G 323 MET cc_start: 0.8135 (mmm) cc_final: 0.7843 (mmm) REVERT: G 363 MET cc_start: 0.8854 (ptp) cc_final: 0.8402 (ptp) REVERT: G 379 LYS cc_start: 0.9214 (mtpt) cc_final: 0.8902 (mtpp) REVERT: D 73 MET cc_start: 0.9193 (mmt) cc_final: 0.8772 (mmm) REVERT: D 129 CYS cc_start: 0.9029 (t) cc_final: 0.8724 (t) REVERT: D 130 LEU cc_start: 0.9198 (tp) cc_final: 0.8809 (tt) REVERT: D 136 THR cc_start: 0.9306 (m) cc_final: 0.8701 (p) REVERT: D 181 GLU cc_start: 0.9013 (pp20) cc_final: 0.8729 (pt0) REVERT: D 263 LEU cc_start: 0.9221 (mp) cc_final: 0.8934 (mt) REVERT: D 280 GLN cc_start: 0.9272 (OUTLIER) cc_final: 0.8798 (pm20) REVERT: D 325 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7301 (mp0) REVERT: D 340 TYR cc_start: 0.8246 (m-80) cc_final: 0.7905 (m-80) REVERT: I 57 ASN cc_start: 0.8284 (t0) cc_final: 0.7917 (t0) REVERT: I 129 CYS cc_start: 0.8976 (t) cc_final: 0.8591 (t) REVERT: I 130 LEU cc_start: 0.9261 (tp) cc_final: 0.8860 (tt) REVERT: I 136 THR cc_start: 0.9270 (m) cc_final: 0.8652 (p) REVERT: I 181 GLU cc_start: 0.9095 (pp20) cc_final: 0.8668 (pt0) REVERT: I 192 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9118 (tt) REVERT: I 263 LEU cc_start: 0.9275 (mp) cc_final: 0.9009 (mt) REVERT: I 340 TYR cc_start: 0.8209 (m-80) cc_final: 0.7833 (m-80) REVERT: I 410 GLU cc_start: 0.8204 (pt0) cc_final: 0.7936 (pt0) REVERT: B 57 ASN cc_start: 0.8200 (t0) cc_final: 0.7712 (t0) REVERT: B 129 CYS cc_start: 0.8410 (t) cc_final: 0.7955 (t) REVERT: B 156 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7884 (tpt-90) REVERT: B 197 ASP cc_start: 0.8542 (m-30) cc_final: 0.8249 (m-30) REVERT: B 347 ASN cc_start: 0.9133 (p0) cc_final: 0.8591 (p0) REVERT: B 363 MET cc_start: 0.8747 (ptp) cc_final: 0.8461 (ptp) REVERT: B 376 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8382 (pp20) REVERT: B 379 LYS cc_start: 0.9309 (mtpt) cc_final: 0.9039 (mtpp) REVERT: B 401 GLU cc_start: 0.8714 (mp0) cc_final: 0.8487 (mp0) REVERT: H 22 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7393 (tm-30) REVERT: H 57 ASN cc_start: 0.8104 (t0) cc_final: 0.7570 (t0) REVERT: H 129 CYS cc_start: 0.8306 (t) cc_final: 0.7806 (t) REVERT: H 197 ASP cc_start: 0.8521 (m-30) cc_final: 0.8184 (m-30) REVERT: H 363 MET cc_start: 0.8737 (ptp) cc_final: 0.8441 (ptp) REVERT: H 379 LYS cc_start: 0.9302 (mtpt) cc_final: 0.9051 (mtpp) outliers start: 140 outliers final: 117 residues processed: 760 average time/residue: 0.4955 time to fit residues: 631.0528 Evaluate side-chains 741 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 615 time to evaluate : 4.544 ------------------------------------------------------------------------------- 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 232 SER 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 41 ASP Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 304 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 68 VAL Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 204 VAL Chi-restraints excluded: chain J residue 232 SER 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 428 LEU 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 98 ASP 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 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 98 ASP Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 232 SER 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 4 CYS 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 232 SER 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 363 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 119 LEU Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 232 SER Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 335 ILE Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 181 GLU Chi-restraints excluded: chain G residue 218 THR Chi-restraints excluded: chain G residue 232 THR Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 293 MET Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 165 ASN Chi-restraints excluded: chain D residue 177 ASP 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 407 GLU Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 180 VAL Chi-restraints excluded: chain I residue 192 LEU 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 156 ARG 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 376 GLU Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain B residue 419 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 475 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 chunk 281 optimal weight: 8.9990 chunk 360 optimal weight: 7.9990 chunk 279 optimal weight: 10.0000 chunk 415 optimal weight: 7.9990 chunk 275 optimal weight: 10.0000 chunk 491 optimal weight: 0.0020 chunk 307 optimal weight: 20.0000 chunk 299 optimal weight: 1.9990 chunk 226 optimal weight: 20.0000 overall best weight: 5.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 11 GLN ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 334 GLN ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 11 GLN K 15 GLN ** K 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 291 GLN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 GLN B 334 GLN ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 329 GLN ** H 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.4449 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= 0.222 Angle : 0.569 9.243 57414 Z= 0.279 Chirality : 0.045 0.232 6282 Planarity : 0.003 0.047 7452 Dihedral : 11.296 178.440 6402 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.30 % Allowed : 14.18 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.12), residues: 5130 helix: 0.87 (0.11), residues: 2232 sheet: 0.22 (0.18), residues: 834 loop : -1.48 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 21 HIS 0.004 0.001 HIS C 197 PHE 0.037 0.001 PHE F 167 TYR 0.012 0.001 TYR F 425 ARG 0.007 0.000 ARG D 320 *********************** 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 779 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 634 time to evaluate : 5.054 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 4 CYS cc_start: 0.9048 (t) cc_final: 0.8359 (t) REVERT: E 127 ASP cc_start: 0.8348 (m-30) cc_final: 0.8007 (m-30) REVERT: E 254 GLU cc_start: 0.8328 (mt-10) cc_final: 0.7752 (mt-10) REVERT: E 313 MET cc_start: 0.8519 (mtm) cc_final: 0.7342 (mtm) REVERT: E 351 PHE cc_start: 0.9189 (m-80) cc_final: 0.8975 (m-10) REVERT: E 357 TYR cc_start: 0.8304 (m-80) cc_final: 0.7832 (m-80) REVERT: E 424 ASP cc_start: 0.8921 (t70) cc_final: 0.8494 (t0) REVERT: E 431 ASP cc_start: 0.8533 (m-30) cc_final: 0.8326 (m-30) REVERT: F 6 HIS cc_start: 0.9193 (t70) cc_final: 0.8745 (t-170) REVERT: F 14 ASN cc_start: 0.9194 (m-40) cc_final: 0.8829 (m110) REVERT: F 22 GLU cc_start: 0.8710 (tt0) cc_final: 0.8153 (tm-30) REVERT: F 136 THR cc_start: 0.9175 (m) cc_final: 0.8503 (p) REVERT: F 163 ILE cc_start: 0.9402 (mm) cc_final: 0.9142 (tt) REVERT: F 291 GLN cc_start: 0.8409 (pt0) cc_final: 0.8019 (pt0) REVERT: J 2 ARG cc_start: 0.8272 (mtm180) cc_final: 0.7141 (mmt90) REVERT: J 31 GLN cc_start: 0.8480 (mm-40) cc_final: 0.8193 (mt0) REVERT: J 207 GLU cc_start: 0.8324 (tm-30) cc_final: 0.7968 (tm-30) REVERT: J 302 MET cc_start: 0.9162 (mpp) cc_final: 0.7963 (mpp) REVERT: J 313 MET cc_start: 0.8932 (mtm) cc_final: 0.6913 (mtm) REVERT: J 357 TYR cc_start: 0.8307 (m-80) cc_final: 0.7892 (m-80) REVERT: J 380 ASN cc_start: 0.9009 (t0) cc_final: 0.8230 (t0) REVERT: J 433 GLU cc_start: 0.8987 (mp0) cc_final: 0.8616 (mp0) REVERT: C 31 GLN cc_start: 0.8521 (mm-40) cc_final: 0.8159 (mt0) REVERT: C 36 MET cc_start: 0.8771 (ptm) cc_final: 0.8513 (ttp) REVERT: C 170 SER cc_start: 0.9359 (m) cc_final: 0.9095 (t) REVERT: C 187 SER cc_start: 0.9358 (m) cc_final: 0.9078 (p) REVERT: C 218 ASP cc_start: 0.8958 (m-30) cc_final: 0.8725 (t0) REVERT: C 254 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8209 (mt-10) REVERT: C 297 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8536 (mm-30) REVERT: C 345 ASP cc_start: 0.8537 (OUTLIER) cc_final: 0.8253 (p0) REVERT: C 351 PHE cc_start: 0.9008 (m-10) cc_final: 0.8611 (m-10) REVERT: L 2 ARG cc_start: 0.8293 (mtm180) cc_final: 0.6774 (mpt180) REVERT: L 31 GLN cc_start: 0.8515 (mm-40) cc_final: 0.8184 (mt0) REVERT: L 36 MET cc_start: 0.8730 (ptm) cc_final: 0.8504 (ttp) REVERT: L 170 SER cc_start: 0.9338 (m) cc_final: 0.9102 (t) REVERT: L 279 GLU cc_start: 0.8733 (pt0) cc_final: 0.7982 (pm20) REVERT: L 302 MET cc_start: 0.8717 (mpp) cc_final: 0.8030 (mpp) REVERT: L 322 ASP cc_start: 0.8554 (t0) cc_final: 0.8288 (t0) REVERT: L 380 ASN cc_start: 0.9409 (t0) cc_final: 0.9010 (t0) REVERT: L 392 ASP cc_start: 0.8999 (m-30) cc_final: 0.8699 (m-30) REVERT: A 2 ARG cc_start: 0.8313 (mtm180) cc_final: 0.7725 (ptp90) REVERT: A 170 SER cc_start: 0.9541 (m) cc_final: 0.9201 (t) REVERT: A 279 GLU cc_start: 0.8907 (pt0) cc_final: 0.8570 (pm20) REVERT: A 284 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8523 (pt0) REVERT: A 301 GLN cc_start: 0.7794 (mm-40) cc_final: 0.7216 (mm-40) REVERT: A 313 MET cc_start: 0.8841 (mtm) cc_final: 0.7743 (mtm) REVERT: A 319 TYR cc_start: 0.9454 (m-80) cc_final: 0.9049 (m-80) REVERT: A 377 MET cc_start: 0.9042 (tmm) cc_final: 0.8708 (tmm) REVERT: A 417 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7798 (tm-30) REVERT: A 431 ASP cc_start: 0.8825 (m-30) cc_final: 0.8561 (m-30) REVERT: K 2 ARG cc_start: 0.8073 (mtm180) cc_final: 0.6737 (mmt90) REVERT: K 33 ASP cc_start: 0.9028 (m-30) cc_final: 0.8596 (t0) REVERT: K 203 MET cc_start: 0.9159 (mmp) cc_final: 0.8649 (mmm) REVERT: K 301 GLN cc_start: 0.8276 (mm-40) cc_final: 0.7927 (mm-40) REVERT: K 304 LYS cc_start: 0.8444 (tppt) cc_final: 0.8115 (tppt) REVERT: K 313 MET cc_start: 0.8794 (mtm) cc_final: 0.7552 (mtm) REVERT: K 397 LEU cc_start: 0.9108 (mt) cc_final: 0.8792 (mt) REVERT: K 417 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7779 (tm-30) REVERT: K 431 ASP cc_start: 0.8832 (m-30) cc_final: 0.8623 (m-30) REVERT: K 434 GLU cc_start: 0.8380 (tt0) cc_final: 0.8120 (mm-30) REVERT: G 14 ASN cc_start: 0.9187 (m-40) cc_final: 0.8839 (m110) REVERT: G 22 GLU cc_start: 0.8823 (tt0) cc_final: 0.8305 (tm-30) REVERT: G 136 THR cc_start: 0.9227 (m) cc_final: 0.8499 (p) REVERT: G 166 THR cc_start: 0.9539 (p) cc_final: 0.9241 (p) REVERT: G 205 GLU cc_start: 0.8579 (tm-30) cc_final: 0.8240 (tm-30) REVERT: G 257 MET cc_start: 0.8281 (mmm) cc_final: 0.7697 (mmm) REVERT: G 323 MET cc_start: 0.8086 (mmm) cc_final: 0.7761 (mmm) REVERT: G 363 MET cc_start: 0.8864 (ptp) cc_final: 0.8426 (ptp) REVERT: G 379 LYS cc_start: 0.9221 (mtpt) cc_final: 0.8895 (mtpp) REVERT: D 129 CYS cc_start: 0.9031 (t) cc_final: 0.8711 (t) REVERT: D 130 LEU cc_start: 0.9202 (tp) cc_final: 0.8822 (tt) REVERT: D 136 THR cc_start: 0.9329 (m) cc_final: 0.8716 (p) REVERT: D 181 GLU cc_start: 0.9005 (pp20) cc_final: 0.8670 (pt0) REVERT: D 263 LEU cc_start: 0.9217 (mp) cc_final: 0.8945 (mt) REVERT: D 280 GLN cc_start: 0.9306 (OUTLIER) cc_final: 0.8924 (pm20) REVERT: D 325 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7270 (mp0) REVERT: D 340 TYR cc_start: 0.8221 (m-80) cc_final: 0.7864 (m-80) REVERT: I 57 ASN cc_start: 0.8261 (t0) cc_final: 0.7858 (t0) REVERT: I 129 CYS cc_start: 0.8975 (t) cc_final: 0.8589 (t) REVERT: I 130 LEU cc_start: 0.9252 (tp) cc_final: 0.8878 (tt) REVERT: I 136 THR cc_start: 0.9271 (m) cc_final: 0.8650 (p) REVERT: I 181 GLU cc_start: 0.9104 (pp20) cc_final: 0.8665 (pt0) REVERT: I 192 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9130 (tt) REVERT: I 263 LEU cc_start: 0.9265 (mp) cc_final: 0.9010 (mt) REVERT: I 340 TYR cc_start: 0.8205 (m-80) cc_final: 0.7832 (m-80) REVERT: I 410 GLU cc_start: 0.8194 (pt0) cc_final: 0.7920 (pt0) REVERT: B 57 ASN cc_start: 0.8139 (t0) cc_final: 0.7646 (t0) REVERT: B 129 CYS cc_start: 0.8329 (t) cc_final: 0.7833 (t) REVERT: B 156 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.8033 (tpt-90) REVERT: B 197 ASP cc_start: 0.8532 (m-30) cc_final: 0.8245 (m-30) REVERT: B 363 MET cc_start: 0.8754 (ptp) cc_final: 0.8437 (ptp) REVERT: B 376 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8397 (pp20) REVERT: B 379 LYS cc_start: 0.9329 (mtpt) cc_final: 0.9034 (mtpp) REVERT: B 401 GLU cc_start: 0.8695 (mp0) cc_final: 0.8381 (mp0) REVERT: H 22 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7393 (tm-30) REVERT: H 57 ASN cc_start: 0.8104 (t0) cc_final: 0.7543 (t0) REVERT: H 103 LYS cc_start: 0.9133 (mttt) cc_final: 0.8930 (mmtp) REVERT: H 129 CYS cc_start: 0.8305 (t) cc_final: 0.7793 (t) REVERT: H 156 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7920 (tpt-90) REVERT: H 166 THR cc_start: 0.9017 (OUTLIER) cc_final: 0.8738 (t) REVERT: H 197 ASP cc_start: 0.8535 (m-30) cc_final: 0.8245 (m-30) REVERT: H 363 MET cc_start: 0.8739 (ptp) cc_final: 0.8441 (ptp) REVERT: H 379 LYS cc_start: 0.9308 (mtpt) cc_final: 0.9081 (mtpp) outliers start: 145 outliers final: 119 residues processed: 739 average time/residue: 0.5124 time to fit residues: 632.8517 Evaluate side-chains 739 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 610 time to evaluate : 4.570 ------------------------------------------------------------------------------- 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 232 SER 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 41 ASP Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 304 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 68 VAL Chi-restraints excluded: chain J residue 112 LYS Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 204 VAL Chi-restraints excluded: chain J residue 232 SER 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 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 98 ASP 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 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 98 ASP Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 232 SER 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 68 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 232 SER 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 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 130 THR Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 335 ILE Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 218 THR 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 293 MET Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 165 ASN 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 293 MET Chi-restraints excluded: chain D residue 295 ASP 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 D residue 419 VAL Chi-restraints excluded: chain I residue 41 ASP Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain I residue 177 ASP Chi-restraints excluded: chain I residue 180 VAL Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 209 ASP Chi-restraints excluded: chain I residue 234 SER 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 156 ARG 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 376 GLU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain H residue 22 GLU Chi-restraints excluded: chain H residue 156 ARG Chi-restraints excluded: chain H residue 164 MET 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 380 ARG 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 304 optimal weight: 3.9990 chunk 196 optimal weight: 9.9990 chunk 293 optimal weight: 8.9990 chunk 148 optimal weight: 10.0000 chunk 96 optimal weight: 5.9990 chunk 95 optimal weight: 7.9990 chunk 312 optimal weight: 5.9990 chunk 334 optimal weight: 9.9990 chunk 243 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 386 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 301 GLN ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 GLN ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 11 GLN K 15 GLN K 197 HIS ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 291 GLN ** G 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN B 204 ASN B 334 GLN ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 332 ASN H 416 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 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 0.039 42204 Z= 0.211 Angle : 0.572 11.075 57414 Z= 0.279 Chirality : 0.045 0.230 6282 Planarity : 0.003 0.046 7452 Dihedral : 11.043 179.314 6402 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.28 % Allowed : 14.66 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.12), residues: 5130 helix: 0.88 (0.11), residues: 2274 sheet: 0.25 (0.18), residues: 834 loop : -1.39 (0.13), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 21 HIS 0.004 0.001 HIS C 197 PHE 0.013 0.001 PHE C 351 TYR 0.013 0.001 TYR J 210 ARG 0.007 0.000 ARG I 320 *********************** 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 777 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 633 time to evaluate : 4.593 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 4 CYS cc_start: 0.9023 (t) cc_final: 0.8321 (t) REVERT: E 127 ASP cc_start: 0.8381 (m-30) cc_final: 0.8052 (m-30) REVERT: E 254 GLU cc_start: 0.8312 (mt-10) cc_final: 0.7739 (mt-10) REVERT: E 313 MET cc_start: 0.8510 (mtm) cc_final: 0.7987 (mtm) REVERT: E 319 TYR cc_start: 0.9557 (m-80) cc_final: 0.9169 (m-10) REVERT: E 357 TYR cc_start: 0.8334 (m-80) cc_final: 0.7867 (m-80) REVERT: E 424 ASP cc_start: 0.8974 (t70) cc_final: 0.8589 (t0) REVERT: E 431 ASP cc_start: 0.8574 (m-30) cc_final: 0.8356 (m-30) REVERT: F 14 ASN cc_start: 0.9167 (m-40) cc_final: 0.8697 (m110) REVERT: F 22 GLU cc_start: 0.8707 (tt0) cc_final: 0.8149 (tm-30) REVERT: F 136 THR cc_start: 0.9149 (m) cc_final: 0.8557 (p) REVERT: F 163 ILE cc_start: 0.9411 (mm) cc_final: 0.9180 (tt) REVERT: F 291 GLN cc_start: 0.8399 (pt0) cc_final: 0.8028 (pt0) REVERT: J 2 ARG cc_start: 0.8274 (mtm180) cc_final: 0.7181 (mmt90) REVERT: J 4 CYS cc_start: 0.9090 (t) cc_final: 0.8399 (t) REVERT: J 31 GLN cc_start: 0.8657 (mm-40) cc_final: 0.8344 (mt0) REVERT: J 207 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8159 (tm-30) REVERT: J 302 MET cc_start: 0.9127 (mpp) cc_final: 0.7876 (mpp) REVERT: J 313 MET cc_start: 0.8904 (mtm) cc_final: 0.6879 (mtm) REVERT: J 357 TYR cc_start: 0.8319 (m-80) cc_final: 0.7907 (m-80) REVERT: J 380 ASN cc_start: 0.9017 (t0) cc_final: 0.8232 (t0) REVERT: J 433 GLU cc_start: 0.8956 (mp0) cc_final: 0.8583 (mp0) REVERT: C 31 GLN cc_start: 0.8550 (mm-40) cc_final: 0.8180 (mt0) REVERT: C 36 MET cc_start: 0.8717 (ptm) cc_final: 0.8458 (ttp) REVERT: C 170 SER cc_start: 0.9364 (m) cc_final: 0.9090 (t) REVERT: C 187 SER cc_start: 0.9356 (m) cc_final: 0.9073 (p) REVERT: C 218 ASP cc_start: 0.9010 (m-30) cc_final: 0.8792 (t0) REVERT: C 254 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8197 (mt-10) REVERT: C 297 GLU cc_start: 0.9027 (mm-30) cc_final: 0.8768 (tm-30) REVERT: C 345 ASP cc_start: 0.8541 (OUTLIER) cc_final: 0.8261 (p0) REVERT: C 357 TYR cc_start: 0.8493 (m-80) cc_final: 0.8067 (m-80) REVERT: L 2 ARG cc_start: 0.8316 (mtm180) cc_final: 0.7006 (mpt180) REVERT: L 31 GLN cc_start: 0.8541 (mm-40) cc_final: 0.8198 (mt0) REVERT: L 36 MET cc_start: 0.8689 (ptm) cc_final: 0.8449 (ttp) REVERT: L 170 SER cc_start: 0.9356 (m) cc_final: 0.9109 (t) REVERT: L 187 SER cc_start: 0.9348 (m) cc_final: 0.8965 (p) REVERT: L 218 ASP cc_start: 0.9120 (t0) cc_final: 0.8761 (t0) REVERT: L 279 GLU cc_start: 0.8715 (pt0) cc_final: 0.7938 (pm20) REVERT: L 302 MET cc_start: 0.8759 (mpp) cc_final: 0.8092 (mpp) REVERT: L 322 ASP cc_start: 0.8541 (t0) cc_final: 0.8276 (t0) REVERT: L 380 ASN cc_start: 0.9409 (t0) cc_final: 0.9034 (t0) REVERT: L 392 ASP cc_start: 0.8997 (m-30) cc_final: 0.8706 (m-30) REVERT: A 2 ARG cc_start: 0.8157 (mtm180) cc_final: 0.7764 (ptp90) REVERT: A 33 ASP cc_start: 0.8912 (m-30) cc_final: 0.8580 (t0) REVERT: A 170 SER cc_start: 0.9560 (m) cc_final: 0.9196 (t) REVERT: A 205 ASP cc_start: 0.8470 (t0) cc_final: 0.8222 (t0) REVERT: A 254 GLU cc_start: 0.8353 (mt-10) cc_final: 0.8047 (mt-10) REVERT: A 279 GLU cc_start: 0.8906 (pt0) cc_final: 0.8567 (pm20) REVERT: A 284 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8516 (pt0) REVERT: A 313 MET cc_start: 0.8820 (mtm) cc_final: 0.7698 (mtm) REVERT: A 319 TYR cc_start: 0.9456 (m-80) cc_final: 0.9044 (m-80) REVERT: A 377 MET cc_start: 0.9035 (tmm) cc_final: 0.8678 (tmm) REVERT: A 417 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7781 (tm-30) REVERT: A 431 ASP cc_start: 0.8776 (m-30) cc_final: 0.8488 (m-30) REVERT: K 2 ARG cc_start: 0.8111 (mtm180) cc_final: 0.6722 (mmt90) REVERT: K 33 ASP cc_start: 0.9017 (m-30) cc_final: 0.8627 (t0) REVERT: K 203 MET cc_start: 0.9163 (mmp) cc_final: 0.8649 (mmm) REVERT: K 301 GLN cc_start: 0.8381 (mm-40) cc_final: 0.8026 (mm-40) REVERT: K 304 LYS cc_start: 0.8446 (tppt) cc_final: 0.8109 (tppt) REVERT: K 313 MET cc_start: 0.8786 (mtm) cc_final: 0.7523 (mtm) REVERT: K 397 LEU cc_start: 0.9120 (mt) cc_final: 0.8798 (mt) REVERT: K 417 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7751 (tm-30) REVERT: K 431 ASP cc_start: 0.8829 (m-30) cc_final: 0.8597 (m-30) REVERT: K 434 GLU cc_start: 0.8371 (tt0) cc_final: 0.8125 (mm-30) REVERT: G 14 ASN cc_start: 0.9158 (m-40) cc_final: 0.8784 (m110) REVERT: G 136 THR cc_start: 0.9215 (m) cc_final: 0.8475 (p) REVERT: G 166 THR cc_start: 0.9524 (p) cc_final: 0.9262 (p) REVERT: G 181 GLU cc_start: 0.8742 (pp20) cc_final: 0.8532 (pt0) REVERT: G 205 GLU cc_start: 0.8553 (tm-30) cc_final: 0.8260 (tm-30) REVERT: G 257 MET cc_start: 0.8261 (mmm) cc_final: 0.7770 (mmm) REVERT: G 323 MET cc_start: 0.8042 (mmm) cc_final: 0.7695 (mmm) REVERT: G 363 MET cc_start: 0.8826 (ptp) cc_final: 0.8375 (ptp) REVERT: G 379 LYS cc_start: 0.9223 (mtpt) cc_final: 0.8901 (mtpp) REVERT: D 129 CYS cc_start: 0.9033 (t) cc_final: 0.8218 (p) REVERT: D 130 LEU cc_start: 0.9186 (tp) cc_final: 0.8778 (tt) REVERT: D 136 THR cc_start: 0.9328 (m) cc_final: 0.8726 (p) REVERT: D 181 GLU cc_start: 0.9015 (pp20) cc_final: 0.8675 (pt0) REVERT: D 263 LEU cc_start: 0.9227 (mp) cc_final: 0.8979 (mt) REVERT: D 280 GLN cc_start: 0.9348 (OUTLIER) cc_final: 0.8930 (pm20) REVERT: D 325 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7242 (mp0) REVERT: D 340 TYR cc_start: 0.8227 (m-80) cc_final: 0.7831 (m-80) REVERT: I 57 ASN cc_start: 0.8320 (t0) cc_final: 0.7880 (t0) REVERT: I 129 CYS cc_start: 0.9000 (t) cc_final: 0.8616 (t) REVERT: I 130 LEU cc_start: 0.9251 (tp) cc_final: 0.8871 (tt) REVERT: I 136 THR cc_start: 0.9259 (m) cc_final: 0.8638 (p) REVERT: I 181 GLU cc_start: 0.9107 (pp20) cc_final: 0.8709 (pt0) REVERT: I 192 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9118 (tt) REVERT: I 263 LEU cc_start: 0.9265 (mp) cc_final: 0.9001 (mt) REVERT: I 340 TYR cc_start: 0.8225 (m-80) cc_final: 0.7860 (m-80) REVERT: I 380 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8287 (ptt180) REVERT: I 407 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8275 (mm-30) REVERT: I 410 GLU cc_start: 0.8168 (pt0) cc_final: 0.7622 (pt0) REVERT: B 57 ASN cc_start: 0.8127 (t0) cc_final: 0.7622 (t0) REVERT: B 156 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.8089 (tpt-90) REVERT: B 197 ASP cc_start: 0.8555 (m-30) cc_final: 0.8188 (m-30) REVERT: B 363 MET cc_start: 0.8745 (ptp) cc_final: 0.8425 (ptp) REVERT: B 376 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8384 (pp20) REVERT: B 379 LYS cc_start: 0.9274 (mtpt) cc_final: 0.9015 (mtpp) REVERT: B 401 GLU cc_start: 0.8676 (mp0) cc_final: 0.8388 (mp0) REVERT: H 22 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7395 (tm-30) REVERT: H 57 ASN cc_start: 0.8060 (t0) cc_final: 0.7503 (t0) REVERT: H 129 CYS cc_start: 0.8334 (t) cc_final: 0.7823 (t) REVERT: H 156 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7924 (tpt-90) REVERT: H 197 ASP cc_start: 0.8560 (m-30) cc_final: 0.8182 (m-30) REVERT: H 363 MET cc_start: 0.8751 (ptp) cc_final: 0.8454 (ptp) REVERT: H 379 LYS cc_start: 0.9288 (mtpt) cc_final: 0.9026 (mtpp) outliers start: 144 outliers final: 119 residues processed: 740 average time/residue: 0.5076 time to fit residues: 625.7982 Evaluate side-chains 735 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 606 time to evaluate : 4.658 ------------------------------------------------------------------------------- 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 232 SER 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 41 ASP Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 304 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 68 VAL Chi-restraints excluded: chain J residue 112 LYS Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 204 VAL Chi-restraints excluded: chain J residue 232 SER 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 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 98 ASP 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 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 98 ASP Chi-restraints excluded: chain L residue 119 LEU Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 232 SER 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 4 CYS Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 232 SER 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 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 130 THR Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 335 ILE Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain G residue 49 VAL 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 293 MET Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 165 ASN 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 293 MET Chi-restraints excluded: chain D residue 295 ASP 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 41 ASP Chi-restraints excluded: chain I residue 177 ASP Chi-restraints excluded: chain I residue 180 VAL Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 209 ASP Chi-restraints excluded: chain I residue 234 SER 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 380 ARG Chi-restraints excluded: chain I residue 419 VAL Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 156 ARG 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 376 GLU Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain H residue 22 GLU Chi-restraints excluded: chain H residue 156 ARG Chi-restraints excluded: chain H residue 164 MET 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 380 ARG 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 447 optimal weight: 10.0000 chunk 470 optimal weight: 9.9990 chunk 429 optimal weight: 8.9990 chunk 458 optimal weight: 0.7980 chunk 275 optimal weight: 8.9990 chunk 199 optimal weight: 1.9990 chunk 359 optimal weight: 9.9990 chunk 140 optimal weight: 8.9990 chunk 413 optimal weight: 7.9990 chunk 433 optimal weight: 20.0000 chunk 456 optimal weight: 0.6980 overall best weight: 4.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 301 GLN ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 292 GLN ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 HIS L 11 GLN ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 139 HIS ** K 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 ASN G 291 GLN ** G 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 332 ASN H 334 GLN ** H 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.4651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 42204 Z= 0.192 Angle : 0.572 10.056 57414 Z= 0.277 Chirality : 0.044 0.223 6282 Planarity : 0.003 0.044 7452 Dihedral : 10.826 173.314 6402 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.03 % Allowed : 15.10 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.12), residues: 5130 helix: 0.95 (0.11), residues: 2280 sheet: 0.29 (0.18), residues: 822 loop : -1.39 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP I 344 HIS 0.006 0.001 HIS F 137 PHE 0.011 0.001 PHE C 351 TYR 0.015 0.001 TYR F 200 ARG 0.008 0.000 ARG J 84 *********************** 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 768 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 635 time to evaluate : 4.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 4 CYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8284 (t) REVERT: E 127 ASP cc_start: 0.8374 (m-30) cc_final: 0.8049 (m-30) REVERT: E 313 MET cc_start: 0.8524 (mtm) cc_final: 0.8020 (mtm) REVERT: E 319 TYR cc_start: 0.9554 (m-80) cc_final: 0.9166 (m-10) REVERT: E 357 TYR cc_start: 0.8324 (m-80) cc_final: 0.7878 (m-80) REVERT: E 424 ASP cc_start: 0.8970 (t70) cc_final: 0.8581 (t0) REVERT: E 431 ASP cc_start: 0.8567 (m-30) cc_final: 0.8344 (m-30) REVERT: F 6 HIS cc_start: 0.9236 (t70) cc_final: 0.8978 (t-170) REVERT: F 22 GLU cc_start: 0.8694 (tt0) cc_final: 0.8126 (tm-30) REVERT: F 136 THR cc_start: 0.9166 (m) cc_final: 0.8563 (p) REVERT: F 291 GLN cc_start: 0.8400 (pt0) cc_final: 0.8024 (pt0) REVERT: J 2 ARG cc_start: 0.8308 (mtm180) cc_final: 0.7187 (mmt90) REVERT: J 4 CYS cc_start: 0.9018 (t) cc_final: 0.8179 (t) REVERT: J 31 GLN cc_start: 0.8658 (mm-40) cc_final: 0.8384 (mt0) REVERT: J 207 GLU cc_start: 0.8447 (tm-30) cc_final: 0.8147 (tm-30) REVERT: J 284 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7790 (pm20) REVERT: J 302 MET cc_start: 0.9150 (mpp) cc_final: 0.7980 (mpp) REVERT: J 313 MET cc_start: 0.8869 (mtm) cc_final: 0.7120 (mtm) REVERT: J 357 TYR cc_start: 0.8315 (m-80) cc_final: 0.7912 (m-80) REVERT: J 380 ASN cc_start: 0.9025 (t0) cc_final: 0.8243 (t0) REVERT: C 31 GLN cc_start: 0.8548 (mm-40) cc_final: 0.8194 (mt0) REVERT: C 36 MET cc_start: 0.8666 (ptm) cc_final: 0.8395 (ttp) REVERT: C 170 SER cc_start: 0.9358 (m) cc_final: 0.9093 (t) REVERT: C 187 SER cc_start: 0.9351 (m) cc_final: 0.9073 (p) REVERT: C 218 ASP cc_start: 0.9008 (m-30) cc_final: 0.8790 (t0) REVERT: C 254 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8176 (mt-10) REVERT: C 345 ASP cc_start: 0.8581 (OUTLIER) cc_final: 0.8288 (p0) REVERT: C 357 TYR cc_start: 0.8524 (m-80) cc_final: 0.8051 (m-80) REVERT: L 2 ARG cc_start: 0.8334 (mtm180) cc_final: 0.7006 (mpt180) REVERT: L 31 GLN cc_start: 0.8543 (mm-40) cc_final: 0.8202 (mt0) REVERT: L 36 MET cc_start: 0.8677 (ptm) cc_final: 0.8366 (ttp) REVERT: L 170 SER cc_start: 0.9360 (m) cc_final: 0.9130 (t) REVERT: L 218 ASP cc_start: 0.9116 (t0) cc_final: 0.8775 (t0) REVERT: L 302 MET cc_start: 0.8772 (mpp) cc_final: 0.8026 (mpp) REVERT: L 380 ASN cc_start: 0.9393 (t0) cc_final: 0.9042 (t0) REVERT: L 392 ASP cc_start: 0.8998 (m-30) cc_final: 0.8709 (m-30) REVERT: A 2 ARG cc_start: 0.8024 (mtm180) cc_final: 0.7742 (ptp90) REVERT: A 33 ASP cc_start: 0.8920 (m-30) cc_final: 0.8593 (t0) REVERT: A 170 SER cc_start: 0.9569 (m) cc_final: 0.9227 (t) REVERT: A 254 GLU cc_start: 0.8340 (mt-10) cc_final: 0.8037 (mt-10) REVERT: A 279 GLU cc_start: 0.8904 (pt0) cc_final: 0.8566 (pm20) REVERT: A 284 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8511 (pt0) REVERT: A 301 GLN cc_start: 0.7319 (mm-40) cc_final: 0.7024 (mm110) REVERT: A 302 MET cc_start: 0.9110 (mpp) cc_final: 0.8857 (mpp) REVERT: A 313 MET cc_start: 0.8805 (mtm) cc_final: 0.7670 (mtm) REVERT: A 319 TYR cc_start: 0.9453 (m-80) cc_final: 0.9045 (m-80) REVERT: A 377 MET cc_start: 0.9066 (tmm) cc_final: 0.8709 (tmm) REVERT: A 417 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7748 (tm-30) REVERT: A 431 ASP cc_start: 0.8775 (m-30) cc_final: 0.8482 (m-30) REVERT: K 2 ARG cc_start: 0.8098 (mtm180) cc_final: 0.6682 (mmt90) REVERT: K 33 ASP cc_start: 0.9019 (m-30) cc_final: 0.8633 (t0) REVERT: K 203 MET cc_start: 0.9162 (mmp) cc_final: 0.8609 (mmm) REVERT: K 301 GLN cc_start: 0.8316 (mm-40) cc_final: 0.7949 (mm-40) REVERT: K 304 LYS cc_start: 0.8451 (tppt) cc_final: 0.8103 (tppt) REVERT: K 313 MET cc_start: 0.8770 (mtm) cc_final: 0.7503 (mtm) REVERT: K 397 LEU cc_start: 0.9121 (mt) cc_final: 0.8797 (mt) REVERT: K 417 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7739 (tm-30) REVERT: K 431 ASP cc_start: 0.8835 (m-30) cc_final: 0.8603 (m-30) REVERT: K 434 GLU cc_start: 0.8386 (tt0) cc_final: 0.8115 (mm-30) REVERT: G 14 ASN cc_start: 0.9210 (m-40) cc_final: 0.8845 (m110) REVERT: G 136 THR cc_start: 0.9190 (m) cc_final: 0.8484 (p) REVERT: G 166 THR cc_start: 0.9521 (p) cc_final: 0.9264 (p) REVERT: G 205 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8278 (tm-30) REVERT: G 257 MET cc_start: 0.8232 (mmm) cc_final: 0.7757 (mmm) REVERT: G 323 MET cc_start: 0.8030 (mmm) cc_final: 0.7680 (mmm) REVERT: G 379 LYS cc_start: 0.9223 (mtpt) cc_final: 0.8900 (mtpp) REVERT: D 73 MET cc_start: 0.8998 (mmt) cc_final: 0.8486 (mpp) REVERT: D 129 CYS cc_start: 0.9020 (t) cc_final: 0.8208 (p) REVERT: D 130 LEU cc_start: 0.9178 (tp) cc_final: 0.8769 (tt) REVERT: D 136 THR cc_start: 0.9323 (m) cc_final: 0.8709 (p) REVERT: D 181 GLU cc_start: 0.8998 (pp20) cc_final: 0.8702 (pt0) REVERT: D 263 LEU cc_start: 0.9223 (mp) cc_final: 0.8966 (mt) REVERT: D 280 GLN cc_start: 0.9361 (OUTLIER) cc_final: 0.8929 (pm20) REVERT: D 325 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7226 (mp0) REVERT: D 340 TYR cc_start: 0.8231 (m-80) cc_final: 0.7839 (m-80) REVERT: I 57 ASN cc_start: 0.8316 (t0) cc_final: 0.7858 (t0) REVERT: I 129 CYS cc_start: 0.8991 (t) cc_final: 0.8606 (t) REVERT: I 130 LEU cc_start: 0.9245 (tp) cc_final: 0.8868 (tt) REVERT: I 136 THR cc_start: 0.9242 (m) cc_final: 0.8636 (p) REVERT: I 181 GLU cc_start: 0.9120 (pp20) cc_final: 0.8704 (pt0) REVERT: I 192 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9113 (tt) REVERT: I 263 LEU cc_start: 0.9241 (mp) cc_final: 0.8971 (mt) REVERT: I 340 TYR cc_start: 0.8243 (m-80) cc_final: 0.7882 (m-80) REVERT: I 407 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8316 (mm-30) REVERT: I 410 GLU cc_start: 0.8135 (pt0) cc_final: 0.7591 (pt0) REVERT: B 57 ASN cc_start: 0.8137 (t0) cc_final: 0.7580 (t0) REVERT: B 156 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7922 (tpt-90) REVERT: B 197 ASP cc_start: 0.8569 (m-30) cc_final: 0.8183 (m-30) REVERT: B 363 MET cc_start: 0.8731 (ptp) cc_final: 0.8416 (ptp) REVERT: B 376 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8370 (pp20) REVERT: B 379 LYS cc_start: 0.9269 (mtpt) cc_final: 0.9037 (mtpp) REVERT: B 401 GLU cc_start: 0.8695 (mp0) cc_final: 0.8474 (mp0) REVERT: H 22 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7382 (tm-30) REVERT: H 57 ASN cc_start: 0.8057 (t0) cc_final: 0.7498 (t0) REVERT: H 156 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7915 (tpt-90) REVERT: H 166 THR cc_start: 0.8963 (OUTLIER) cc_final: 0.8690 (t) REVERT: H 197 ASP cc_start: 0.8548 (m-30) cc_final: 0.8175 (m-30) REVERT: H 363 MET cc_start: 0.8756 (ptp) cc_final: 0.8455 (ptp) REVERT: H 379 LYS cc_start: 0.9283 (mtpt) cc_final: 0.9021 (mtpp) outliers start: 133 outliers final: 109 residues processed: 731 average time/residue: 0.4956 time to fit residues: 608.9292 Evaluate side-chains 733 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 612 time to evaluate : 4.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 4 CYS Chi-restraints excluded: chain E residue 26 LEU 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 F residue 41 ASP Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 304 ASP Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain F residue 363 MET 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 68 VAL Chi-restraints excluded: chain J residue 112 LYS Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 204 VAL Chi-restraints excluded: chain J residue 232 SER 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 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 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 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 98 ASP 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 77 GLU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 232 SER 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 363 VAL Chi-restraints excluded: chain A residue 367 ASP 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 130 THR Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 335 ILE Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain G residue 49 VAL 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 293 MET Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 165 ASN 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 293 MET Chi-restraints excluded: chain D residue 295 ASP 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 407 GLU Chi-restraints excluded: chain D residue 415 MET Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain I residue 180 VAL Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 209 ASP Chi-restraints excluded: chain I residue 234 SER 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 380 ARG Chi-restraints excluded: chain B residue 156 ARG 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 376 GLU 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 164 MET 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 380 ARG 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 300 optimal weight: 20.0000 chunk 484 optimal weight: 6.9990 chunk 295 optimal weight: 20.0000 chunk 229 optimal weight: 20.0000 chunk 336 optimal weight: 10.0000 chunk 508 optimal weight: 0.6980 chunk 467 optimal weight: 5.9990 chunk 404 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 312 optimal weight: 5.9990 chunk 248 optimal weight: 6.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 301 GLN ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 291 GLN ** G 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 332 ASN H 334 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.4730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 42204 Z= 0.218 Angle : 0.591 10.386 57414 Z= 0.285 Chirality : 0.045 0.224 6282 Planarity : 0.003 0.041 7452 Dihedral : 10.649 173.935 6402 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.01 % Allowed : 15.46 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.12), residues: 5130 helix: 0.97 (0.11), residues: 2292 sheet: 0.28 (0.19), residues: 828 loop : -1.34 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP I 344 HIS 0.008 0.001 HIS H 137 PHE 0.012 0.001 PHE C 351 TYR 0.015 0.001 TYR F 200 ARG 0.009 0.000 ARG I 320 ********************** 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 754 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 622 time to evaluate : 4.519 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 4 CYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8276 (t) REVERT: E 127 ASP cc_start: 0.8375 (m-30) cc_final: 0.8057 (m-30) REVERT: E 254 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7756 (mt-10) REVERT: E 313 MET cc_start: 0.8586 (mtm) cc_final: 0.8077 (mtm) REVERT: E 319 TYR cc_start: 0.9547 (m-80) cc_final: 0.9158 (m-10) REVERT: E 339 ARG cc_start: 0.7595 (mmp-170) cc_final: 0.6825 (mmp-170) REVERT: E 357 TYR cc_start: 0.8345 (m-80) cc_final: 0.7898 (m-80) REVERT: E 424 ASP cc_start: 0.8967 (t70) cc_final: 0.8547 (t0) REVERT: E 431 ASP cc_start: 0.8575 (m-30) cc_final: 0.8364 (m-30) REVERT: F 6 HIS cc_start: 0.9232 (t70) cc_final: 0.8935 (t-170) REVERT: F 14 ASN cc_start: 0.8900 (m-40) cc_final: 0.8568 (m110) REVERT: F 22 GLU cc_start: 0.8725 (tt0) cc_final: 0.8167 (tm-30) REVERT: F 73 MET cc_start: 0.8855 (mmt) cc_final: 0.8547 (mpp) REVERT: F 291 GLN cc_start: 0.8399 (pt0) cc_final: 0.8033 (pt0) REVERT: J 2 ARG cc_start: 0.8285 (mtm180) cc_final: 0.7152 (mmt90) REVERT: J 4 CYS cc_start: 0.8952 (t) cc_final: 0.8115 (t) REVERT: J 31 GLN cc_start: 0.8628 (mm-40) cc_final: 0.8249 (mt0) REVERT: J 207 GLU cc_start: 0.8449 (tm-30) cc_final: 0.8154 (tm-30) REVERT: J 302 MET cc_start: 0.9153 (mpp) cc_final: 0.7980 (mpp) REVERT: J 313 MET cc_start: 0.8853 (mtm) cc_final: 0.8385 (mtm) REVERT: J 357 TYR cc_start: 0.8332 (m-80) cc_final: 0.7931 (m-80) REVERT: J 380 ASN cc_start: 0.9033 (t0) cc_final: 0.8648 (t0) REVERT: C 31 GLN cc_start: 0.8586 (mm-40) cc_final: 0.8210 (mt0) REVERT: C 36 MET cc_start: 0.8716 (ptm) cc_final: 0.8448 (ttp) REVERT: C 170 SER cc_start: 0.9359 (m) cc_final: 0.9094 (t) REVERT: C 187 SER cc_start: 0.9345 (m) cc_final: 0.9068 (p) REVERT: C 218 ASP cc_start: 0.9006 (m-30) cc_final: 0.8787 (t0) REVERT: C 254 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8179 (mt-10) REVERT: C 345 ASP cc_start: 0.8595 (OUTLIER) cc_final: 0.8294 (p0) REVERT: C 357 TYR cc_start: 0.8543 (m-80) cc_final: 0.8112 (m-80) REVERT: L 2 ARG cc_start: 0.8362 (mtm180) cc_final: 0.7008 (mpt180) REVERT: L 31 GLN cc_start: 0.8573 (mm-40) cc_final: 0.8200 (mt0) REVERT: L 35 GLN cc_start: 0.8123 (mm-40) cc_final: 0.7848 (mp10) REVERT: L 36 MET cc_start: 0.8684 (ptm) cc_final: 0.8369 (ttp) REVERT: L 170 SER cc_start: 0.9329 (m) cc_final: 0.9085 (t) REVERT: L 187 SER cc_start: 0.9417 (m) cc_final: 0.9118 (p) REVERT: L 218 ASP cc_start: 0.9161 (t0) cc_final: 0.8827 (t0) REVERT: L 302 MET cc_start: 0.8864 (mpp) cc_final: 0.8162 (mpp) REVERT: L 322 ASP cc_start: 0.8551 (t0) cc_final: 0.8284 (t0) REVERT: L 380 ASN cc_start: 0.9394 (t0) cc_final: 0.9041 (t0) REVERT: L 392 ASP cc_start: 0.9000 (m-30) cc_final: 0.8721 (m-30) REVERT: A 2 ARG cc_start: 0.8067 (mtm180) cc_final: 0.7735 (ptp90) REVERT: A 33 ASP cc_start: 0.8958 (m-30) cc_final: 0.8663 (t0) REVERT: A 170 SER cc_start: 0.9577 (m) cc_final: 0.9209 (t) REVERT: A 254 GLU cc_start: 0.8338 (mt-10) cc_final: 0.8035 (mt-10) REVERT: A 279 GLU cc_start: 0.8909 (pt0) cc_final: 0.8567 (pm20) REVERT: A 284 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8560 (pt0) REVERT: A 301 GLN cc_start: 0.7355 (mm-40) cc_final: 0.6986 (mm110) REVERT: A 302 MET cc_start: 0.9133 (mpp) cc_final: 0.8845 (mpp) REVERT: A 313 MET cc_start: 0.8809 (mtm) cc_final: 0.7680 (mtm) REVERT: A 319 TYR cc_start: 0.9464 (m-80) cc_final: 0.9062 (m-80) REVERT: A 377 MET cc_start: 0.9070 (tmm) cc_final: 0.8712 (tmm) REVERT: A 417 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7757 (tm-30) REVERT: A 431 ASP cc_start: 0.8774 (m-30) cc_final: 0.8453 (m-30) REVERT: K 2 ARG cc_start: 0.8059 (mtm180) cc_final: 0.6686 (mmt90) REVERT: K 33 ASP cc_start: 0.9040 (m-30) cc_final: 0.8660 (t0) REVERT: K 203 MET cc_start: 0.9171 (mmp) cc_final: 0.8628 (mmm) REVERT: K 301 GLN cc_start: 0.8455 (mm-40) cc_final: 0.8104 (mm-40) REVERT: K 313 MET cc_start: 0.8776 (mtm) cc_final: 0.7543 (mtm) REVERT: K 397 LEU cc_start: 0.9126 (mt) cc_final: 0.8797 (mt) REVERT: K 417 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7747 (tm-30) REVERT: K 431 ASP cc_start: 0.8842 (m-30) cc_final: 0.8614 (m-30) REVERT: K 434 GLU cc_start: 0.8392 (tt0) cc_final: 0.8125 (mm-30) REVERT: G 136 THR cc_start: 0.9181 (m) cc_final: 0.8486 (p) REVERT: G 166 THR cc_start: 0.9526 (p) cc_final: 0.9261 (p) REVERT: G 205 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8282 (tm-30) REVERT: G 257 MET cc_start: 0.8198 (mmm) cc_final: 0.7750 (mmm) REVERT: G 323 MET cc_start: 0.8058 (mmm) cc_final: 0.7711 (mmm) REVERT: G 379 LYS cc_start: 0.9226 (mtpt) cc_final: 0.8903 (mtpp) REVERT: D 129 CYS cc_start: 0.9020 (t) cc_final: 0.8207 (p) REVERT: D 130 LEU cc_start: 0.9185 (tp) cc_final: 0.8782 (tt) REVERT: D 136 THR cc_start: 0.9316 (m) cc_final: 0.8698 (p) REVERT: D 181 GLU cc_start: 0.9020 (pp20) cc_final: 0.8713 (pt0) REVERT: D 257 MET cc_start: 0.8973 (mmm) cc_final: 0.8751 (mmp) REVERT: D 263 LEU cc_start: 0.9246 (mp) cc_final: 0.8985 (mt) REVERT: D 280 GLN cc_start: 0.9397 (OUTLIER) cc_final: 0.8985 (pm20) REVERT: D 325 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7208 (mp0) REVERT: D 340 TYR cc_start: 0.8255 (m-80) cc_final: 0.7861 (m-80) REVERT: I 57 ASN cc_start: 0.8338 (t0) cc_final: 0.7865 (t0) REVERT: I 129 CYS cc_start: 0.8995 (t) cc_final: 0.8606 (t) REVERT: I 130 LEU cc_start: 0.9254 (tp) cc_final: 0.8879 (tt) REVERT: I 136 THR cc_start: 0.9237 (m) cc_final: 0.8640 (p) REVERT: I 181 GLU cc_start: 0.9141 (pp20) cc_final: 0.8693 (pt0) REVERT: I 192 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9127 (tt) REVERT: I 257 MET cc_start: 0.9085 (mmm) cc_final: 0.8878 (mmp) REVERT: I 263 LEU cc_start: 0.9268 (mp) cc_final: 0.8995 (mt) REVERT: I 340 TYR cc_start: 0.8255 (m-80) cc_final: 0.7893 (m-80) REVERT: I 380 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.8282 (ptt180) REVERT: I 407 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8326 (mm-30) REVERT: I 410 GLU cc_start: 0.8120 (pt0) cc_final: 0.7614 (pt0) REVERT: B 57 ASN cc_start: 0.8139 (t0) cc_final: 0.7583 (t0) REVERT: B 156 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.8078 (tpt-90) REVERT: B 164 MET cc_start: 0.8046 (ttp) cc_final: 0.7495 (ptp) REVERT: B 197 ASP cc_start: 0.8586 (m-30) cc_final: 0.8209 (m-30) REVERT: B 363 MET cc_start: 0.8762 (ptp) cc_final: 0.8440 (ptp) REVERT: B 379 LYS cc_start: 0.9269 (mtpt) cc_final: 0.9018 (mtpp) REVERT: B 401 GLU cc_start: 0.8679 (mp0) cc_final: 0.8383 (mp0) REVERT: H 22 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7410 (tm-30) REVERT: H 57 ASN cc_start: 0.8084 (t0) cc_final: 0.7514 (t0) REVERT: H 156 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7973 (tpt-90) REVERT: H 197 ASP cc_start: 0.8580 (m-30) cc_final: 0.8208 (m-30) REVERT: H 363 MET cc_start: 0.8784 (ptp) cc_final: 0.8481 (ptp) REVERT: H 379 LYS cc_start: 0.9285 (mtpt) cc_final: 0.9022 (mtpp) REVERT: H 410 GLU cc_start: 0.8586 (pt0) cc_final: 0.8215 (pt0) outliers start: 132 outliers final: 114 residues processed: 718 average time/residue: 0.5034 time to fit residues: 608.9208 Evaluate side-chains 733 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 609 time to evaluate : 4.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 4 CYS 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 232 SER 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 F residue 41 ASP Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 304 ASP Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain F residue 363 MET 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 68 VAL Chi-restraints excluded: chain J residue 112 LYS Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 204 VAL Chi-restraints excluded: chain J residue 232 SER 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 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 98 ASP 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 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 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 98 ASP 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 4 CYS Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 232 SER 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 363 VAL 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 130 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 G residue 49 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 293 MET Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 165 ASN 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 293 MET Chi-restraints excluded: chain D residue 295 ASP 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 407 GLU Chi-restraints excluded: chain D residue 415 MET Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain I residue 180 VAL Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 209 ASP Chi-restraints excluded: chain I residue 234 SER 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 380 ARG Chi-restraints excluded: chain B residue 156 ARG 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 376 GLU Chi-restraints excluded: chain B residue 407 GLU Chi-restraints excluded: chain B residue 419 VAL 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 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 380 ARG 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 321 optimal weight: 20.0000 chunk 430 optimal weight: 0.4980 chunk 123 optimal weight: 7.9990 chunk 373 optimal weight: 0.7980 chunk 59 optimal weight: 7.9990 chunk 112 optimal weight: 20.0000 chunk 405 optimal weight: 8.9990 chunk 169 optimal weight: 20.0000 chunk 416 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 74 optimal weight: 10.0000 overall best weight: 4.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 ASN J 11 GLN ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.080322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.069380 restraints weight = 98753.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.072062 restraints weight = 47323.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.073894 restraints weight = 27859.749| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.4811 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= 0.190 Angle : 0.580 11.988 57414 Z= 0.279 Chirality : 0.044 0.218 6282 Planarity : 0.003 0.040 7452 Dihedral : 10.392 175.356 6402 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.91 % Allowed : 15.78 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.12), residues: 5130 helix: 1.05 (0.11), residues: 2292 sheet: 0.32 (0.19), residues: 828 loop : -1.27 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP I 344 HIS 0.007 0.001 HIS H 137 PHE 0.030 0.001 PHE F 167 TYR 0.014 0.001 TYR J 210 ARG 0.008 0.000 ARG D 320 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10700.53 seconds wall clock time: 193 minutes 53.56 seconds (11633.56 seconds total)