Starting phenix.real_space_refine on Sun Mar 24 10:04:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6evx_3962/03_2024/6evx_3962.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6evx_3962/03_2024/6evx_3962.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6evx_3962/03_2024/6evx_3962.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6evx_3962/03_2024/6evx_3962.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6evx_3962/03_2024/6evx_3962.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6evx_3962/03_2024/6evx_3962.pdb" } resolution = 4.2 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= 0.010 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 6 5.21 5 S 276 5.16 5 C 25674 2.51 5 N 6978 2.21 5 O 7926 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 64": "NH1" <-> "NH2" Residue "A ARG 390": "NH1" <-> "NH2" Residue "E PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 64": "NH1" <-> "NH2" Residue "E ARG 390": "NH1" <-> "NH2" Residue "J PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 64": "NH1" <-> "NH2" Residue "J ARG 390": "NH1" <-> "NH2" Residue "C PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 64": "NH1" <-> "NH2" Residue "C ARG 390": "NH1" <-> "NH2" Residue "L PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 64": "NH1" <-> "NH2" Residue "L ARG 390": "NH1" <-> "NH2" Residue "K PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 64": "NH1" <-> "NH2" Residue "K ARG 390": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 40896 Number of models: 1 Model: "" Number of chains: 24 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: "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: "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: 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: "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: "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: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {' MG': 1, 'GTP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'GDP': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'GDP': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'GDP': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {' MG': 1, 'GTP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {' MG': 1, 'GTP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: "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} Time building chain proxies: 20.54, per 1000 atoms: 0.50 Number of scatterers: 40896 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 36 15.00 Mg 6 11.99 O 7926 8.00 N 6978 7.00 C 25674 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 15.26 Conformation dependent library (CDL) restraints added in 6.6 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: 204 helices and 42 sheets defined 46.9% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.21 Creating SS restraints... Processing helix chain 'F' and resid 10 through 27 removed outlier: 3.668A pdb=" N GLN F 15 " --> pdb=" O GLN F 11 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLY F 17 " --> pdb=" O GLY F 13 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU F 22 " --> pdb=" O ALA F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 45 removed outlier: 3.573A pdb=" N GLN F 43 " --> pdb=" O SER F 40 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU F 44 " --> pdb=" O ASP F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 49 removed outlier: 3.655A 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 55 through 57 No H-bonds generated for 'chain 'F' and resid 55 through 57' Processing helix chain 'F' and resid 72 through 78 removed outlier: 3.760A pdb=" N ARG F 77 " --> pdb=" O MET F 73 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER F 78 " --> pdb=" O ASP F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 113 removed outlier: 3.528A pdb=" N VAL F 113 " --> pdb=" O GLY F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 127 removed outlier: 3.837A pdb=" N ASP F 118 " --> pdb=" O ASP F 114 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N VAL F 119 " --> pdb=" O SER F 115 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER F 126 " --> pdb=" O LYS F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 159 removed outlier: 4.199A pdb=" N GLY F 148 " --> pdb=" O GLY F 144 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR F 149 " --> pdb=" O SER F 145 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS F 154 " --> pdb=" O LEU F 150 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU F 157 " --> pdb=" O SER F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 196 removed outlier: 3.637A pdb=" N SER F 188 " --> pdb=" O ASN F 184 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLN F 191 " --> pdb=" O LEU F 187 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL F 193 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLU F 194 " --> pdb=" O HIS F 190 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN F 195 " --> pdb=" O GLN F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 214 removed outlier: 3.631A pdb=" N ASP F 209 " --> pdb=" O GLU F 205 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS F 211 " --> pdb=" O LEU F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 237 removed outlier: 4.643A pdb=" N HIS F 227 " --> pdb=" O GLY F 223 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU F 228 " --> pdb=" O ASP F 224 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL F 229 " --> pdb=" O LEU F 225 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR F 237 " --> pdb=" O MET F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 256 Processing helix chain 'F' and resid 285 through 294 removed outlier: 3.654A pdb=" N GLN F 291 " --> pdb=" O PRO F 287 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN F 292 " --> pdb=" O GLU F 288 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET F 293 " --> pdb=" O LEU F 289 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE F 294 " --> pdb=" O THR F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 337 removed outlier: 4.321A pdb=" N GLN F 329 " --> pdb=" O GLU F 325 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN F 334 " --> pdb=" O MET F 330 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN F 337 " --> pdb=" O VAL F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 390 removed outlier: 3.808A pdb=" N ILE F 381 " --> pdb=" O LEU F 377 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG F 390 " --> pdb=" O THR F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 401 removed outlier: 4.434A pdb=" N TYR F 398 " --> pdb=" O PHE F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 427 removed outlier: 3.873A pdb=" N PHE F 408 " --> pdb=" O ASP F 404 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET F 415 " --> pdb=" O ALA F 411 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU F 421 " --> pdb=" O ASP F 417 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASP F 427 " --> pdb=" O GLN F 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 28 removed outlier: 3.559A pdb=" N ILE A 16 " --> pdb=" O ALA A 12 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N HIS A 28 " --> pdb=" O TYR A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 80 removed outlier: 3.693A pdb=" N GLU A 77 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 Processing helix chain 'A' and resid 114 through 128 removed outlier: 3.895A pdb=" N LEU A 119 " --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASP A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 161 removed outlier: 4.523A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU A 155 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 195 removed outlier: 4.326A pdb=" N ILE A 188 " --> pdb=" O PRO A 184 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR A 190 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 216 removed outlier: 3.511A pdb=" N ARG A 214 " --> pdb=" O TYR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 239 removed outlier: 3.556A pdb=" N ARG A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU A 230 " --> pdb=" O ASN A 226 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN A 233 " --> pdb=" O ARG A 229 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 244 removed outlier: 3.750A pdb=" N ARG A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 259 removed outlier: 3.662A pdb=" N PHE A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLN A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 297 removed outlier: 3.559A pdb=" N ALA A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N CYS A 295 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 301 removed outlier: 3.893A pdb=" N GLN A 301 " --> pdb=" O PRO A 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 298 through 301' Processing helix chain 'A' and resid 306 through 310 removed outlier: 3.552A pdb=" N HIS A 309 " --> pdb=" O ASP A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 337 removed outlier: 3.526A pdb=" N ALA A 333 " --> pdb=" O ASN A 329 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE A 335 " --> pdb=" O ALA A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 401 removed outlier: 3.820A pdb=" N LEU A 397 " --> pdb=" O HIS A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 416 through 437 removed outlier: 3.518A pdb=" N GLU A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 27 removed outlier: 3.667A pdb=" N GLN G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLY G 17 " --> pdb=" O GLY G 13 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU G 22 " --> pdb=" O ALA G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 45 removed outlier: 3.572A pdb=" N GLN G 43 " --> pdb=" O SER G 40 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU G 44 " --> pdb=" O ASP G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 49 removed outlier: 3.655A 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 55 through 57 No H-bonds generated for 'chain 'G' and resid 55 through 57' Processing helix chain 'G' and resid 72 through 78 removed outlier: 3.759A pdb=" N ARG G 77 " --> pdb=" O MET G 73 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER G 78 " --> pdb=" O ASP G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 113 removed outlier: 3.528A pdb=" N VAL G 113 " --> pdb=" O GLY G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 127 removed outlier: 3.838A pdb=" N ASP G 118 " --> pdb=" O ASP G 114 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N VAL G 119 " --> pdb=" O SER G 115 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER G 126 " --> pdb=" O LYS G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 159 removed outlier: 4.199A pdb=" N GLY G 148 " --> pdb=" O GLY G 144 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR G 149 " --> pdb=" O SER G 145 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS G 154 " --> pdb=" O LEU G 150 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU G 157 " --> pdb=" O SER G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 196 removed outlier: 3.637A pdb=" N SER G 188 " --> pdb=" O ASN G 184 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLN G 191 " --> pdb=" O LEU G 187 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL G 193 " --> pdb=" O VAL G 189 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU G 194 " --> pdb=" O HIS G 190 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN G 195 " --> pdb=" O GLN G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 214 removed outlier: 3.630A pdb=" N ASP G 209 " --> pdb=" O GLU G 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS G 211 " --> pdb=" O LEU G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 237 removed outlier: 4.643A pdb=" N HIS G 227 " --> pdb=" O GLY G 223 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU G 228 " --> pdb=" O ASP G 224 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL G 229 " --> pdb=" O LEU G 225 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR G 237 " --> pdb=" O MET G 233 " (cutoff:3.500A) Processing helix chain 'G' and resid 251 through 256 Processing helix chain 'G' and resid 285 through 294 removed outlier: 3.655A pdb=" N GLN G 291 " --> pdb=" O PRO G 287 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN G 292 " --> pdb=" O GLU G 288 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET G 293 " --> pdb=" O LEU G 289 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE G 294 " --> pdb=" O THR G 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 323 through 337 removed outlier: 4.321A pdb=" N GLN G 329 " --> pdb=" O GLU G 325 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN G 334 " --> pdb=" O MET G 330 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN G 337 " --> pdb=" O VAL G 333 " (cutoff:3.500A) Processing helix chain 'G' and resid 374 through 390 removed outlier: 3.808A pdb=" N ILE G 381 " --> pdb=" O LEU G 377 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG G 390 " --> pdb=" O THR G 386 " (cutoff:3.500A) Processing helix chain 'G' and resid 394 through 401 removed outlier: 4.435A pdb=" N TYR G 398 " --> pdb=" O PHE G 394 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 427 removed outlier: 3.873A pdb=" N PHE G 408 " --> pdb=" O ASP G 404 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET G 415 " --> pdb=" O ALA G 411 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU G 421 " --> pdb=" O ASP G 417 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASP G 427 " --> pdb=" O GLN G 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 27 removed outlier: 3.667A pdb=" N GLN D 15 " --> pdb=" O GLN D 11 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLY D 17 " --> pdb=" O GLY D 13 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU D 22 " --> pdb=" O ALA D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 45 removed outlier: 3.573A pdb=" N GLN D 43 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU D 44 " --> pdb=" O ASP D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 49 removed outlier: 3.655A 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 55 through 57 No H-bonds generated for 'chain 'D' and resid 55 through 57' Processing helix chain 'D' and resid 72 through 78 removed outlier: 3.759A pdb=" N ARG D 77 " --> pdb=" O MET D 73 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER D 78 " --> pdb=" O ASP D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 113 removed outlier: 3.528A pdb=" N VAL D 113 " --> pdb=" O GLY D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 127 removed outlier: 3.837A pdb=" N ASP D 118 " --> pdb=" O ASP D 114 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL D 119 " --> pdb=" O SER D 115 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER D 126 " --> pdb=" O LYS D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 159 removed outlier: 4.199A pdb=" N GLY D 148 " --> pdb=" O GLY D 144 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS D 154 " --> pdb=" O LEU D 150 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU D 157 " --> pdb=" O SER D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 196 removed outlier: 3.636A pdb=" N SER D 188 " --> pdb=" O ASN D 184 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLN D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL D 193 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLU D 194 " --> pdb=" O HIS D 190 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN D 195 " --> pdb=" O GLN D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 214 removed outlier: 3.630A pdb=" N ASP D 209 " --> pdb=" O GLU D 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS D 211 " --> pdb=" O LEU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 237 removed outlier: 4.643A pdb=" N HIS D 227 " --> pdb=" O GLY D 223 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU D 228 " --> pdb=" O ASP D 224 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL D 229 " --> pdb=" O LEU D 225 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR D 237 " --> pdb=" O MET D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 256 Processing helix chain 'D' and resid 285 through 294 removed outlier: 3.655A pdb=" N GLN D 291 " --> pdb=" O PRO D 287 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN D 292 " --> pdb=" O GLU D 288 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET D 293 " --> pdb=" O LEU D 289 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE D 294 " --> pdb=" O THR D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 337 removed outlier: 4.321A pdb=" N GLN D 329 " --> pdb=" O GLU D 325 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN D 334 " --> pdb=" O MET D 330 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN D 337 " --> pdb=" O VAL D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 390 removed outlier: 3.807A pdb=" N ILE D 381 " --> pdb=" O LEU D 377 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG D 390 " --> pdb=" O THR D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 401 removed outlier: 4.434A pdb=" N TYR D 398 " --> pdb=" O PHE D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 427 removed outlier: 3.873A pdb=" N PHE D 408 " --> pdb=" O ASP D 404 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET D 415 " --> pdb=" O ALA D 411 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU D 421 " --> pdb=" O ASP D 417 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASP D 427 " --> pdb=" O GLN D 423 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 27 removed outlier: 3.667A pdb=" N GLN I 15 " --> pdb=" O GLN I 11 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLY I 17 " --> pdb=" O GLY I 13 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU I 22 " --> pdb=" O ALA I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 45 removed outlier: 3.573A pdb=" N GLN I 43 " --> pdb=" O SER I 40 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU I 44 " --> pdb=" O ASP I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 49 removed outlier: 3.656A 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 55 through 57 No H-bonds generated for 'chain 'I' and resid 55 through 57' Processing helix chain 'I' and resid 72 through 78 removed outlier: 3.760A pdb=" N ARG I 77 " --> pdb=" O MET I 73 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER I 78 " --> pdb=" O ASP I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 113 removed outlier: 3.528A pdb=" N VAL I 113 " --> pdb=" O GLY I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 113 through 127 removed outlier: 3.837A pdb=" N ASP I 118 " --> pdb=" O ASP I 114 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL I 119 " --> pdb=" O SER I 115 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER I 126 " --> pdb=" O LYS I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 159 removed outlier: 4.200A pdb=" N GLY I 148 " --> pdb=" O GLY I 144 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR I 149 " --> pdb=" O SER I 145 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS I 154 " --> pdb=" O LEU I 150 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU I 157 " --> pdb=" O SER I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 180 through 196 removed outlier: 3.636A pdb=" N SER I 188 " --> pdb=" O ASN I 184 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLN I 191 " --> pdb=" O LEU I 187 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL I 193 " --> pdb=" O VAL I 189 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU I 194 " --> pdb=" O HIS I 190 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN I 195 " --> pdb=" O GLN I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 204 through 214 removed outlier: 3.631A pdb=" N ASP I 209 " --> pdb=" O GLU I 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS I 211 " --> pdb=" O LEU I 207 " (cutoff:3.500A) Processing helix chain 'I' and resid 221 through 237 removed outlier: 4.643A pdb=" N HIS I 227 " --> pdb=" O GLY I 223 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU I 228 " --> pdb=" O ASP I 224 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL I 229 " --> pdb=" O LEU I 225 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR I 237 " --> pdb=" O MET I 233 " (cutoff:3.500A) Processing helix chain 'I' and resid 251 through 256 Processing helix chain 'I' and resid 285 through 294 removed outlier: 3.655A pdb=" N GLN I 291 " --> pdb=" O PRO I 287 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN I 292 " --> pdb=" O GLU I 288 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET I 293 " --> pdb=" O LEU I 289 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE I 294 " --> pdb=" O THR I 290 " (cutoff:3.500A) Processing helix chain 'I' and resid 323 through 337 removed outlier: 4.321A pdb=" N GLN I 329 " --> pdb=" O GLU I 325 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN I 334 " --> pdb=" O MET I 330 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN I 337 " --> pdb=" O VAL I 333 " (cutoff:3.500A) Processing helix chain 'I' and resid 374 through 390 removed outlier: 3.807A pdb=" N ILE I 381 " --> pdb=" O LEU I 377 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG I 390 " --> pdb=" O THR I 386 " (cutoff:3.500A) Processing helix chain 'I' and resid 394 through 401 removed outlier: 4.433A pdb=" N TYR I 398 " --> pdb=" O PHE I 394 " (cutoff:3.500A) Processing helix chain 'I' and resid 404 through 427 removed outlier: 3.873A pdb=" N PHE I 408 " --> pdb=" O ASP I 404 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET I 415 " --> pdb=" O ALA I 411 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU I 421 " --> pdb=" O ASP I 417 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASP I 427 " --> pdb=" O GLN I 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 27 removed outlier: 3.667A pdb=" N GLN B 15 " --> pdb=" O GLN B 11 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLY B 17 " --> pdb=" O GLY B 13 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 removed outlier: 3.572A pdb=" N GLN B 43 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B 44 " --> pdb=" O ASP B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 49 removed outlier: 3.655A 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 55 through 57 No H-bonds generated for 'chain 'B' and resid 55 through 57' Processing helix chain 'B' and resid 72 through 78 removed outlier: 3.760A pdb=" N ARG B 77 " --> pdb=" O MET B 73 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER B 78 " --> pdb=" O ASP B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 113 removed outlier: 3.528A pdb=" N VAL B 113 " --> pdb=" O GLY B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 127 removed outlier: 3.837A pdb=" N ASP B 118 " --> pdb=" O ASP B 114 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N VAL B 119 " --> pdb=" O SER B 115 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 removed outlier: 4.199A pdb=" N GLY B 148 " --> pdb=" O GLY B 144 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS B 154 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 196 removed outlier: 3.636A pdb=" N SER B 188 " --> pdb=" O ASN B 184 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL B 193 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN B 195 " --> pdb=" O GLN B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 removed outlier: 3.629A pdb=" N ASP B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS B 211 " --> pdb=" O LEU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 237 removed outlier: 4.643A pdb=" N HIS B 227 " --> pdb=" O GLY B 223 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 256 Processing helix chain 'B' and resid 285 through 294 removed outlier: 3.654A pdb=" N GLN B 291 " --> pdb=" O PRO B 287 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN B 292 " --> pdb=" O GLU B 288 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET B 293 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE B 294 " --> pdb=" O THR B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 337 removed outlier: 4.320A pdb=" N GLN B 329 " --> pdb=" O GLU B 325 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN B 334 " --> pdb=" O MET B 330 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN B 337 " --> pdb=" O VAL B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 390 removed outlier: 3.808A pdb=" N ILE B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG B 390 " --> pdb=" O THR B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 401 removed outlier: 4.433A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 427 removed outlier: 3.873A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET B 415 " --> pdb=" O ALA B 411 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU B 421 " --> pdb=" O ASP B 417 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASP B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 27 removed outlier: 3.667A pdb=" N GLN H 15 " --> pdb=" O GLN H 11 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLY H 17 " --> pdb=" O GLY H 13 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 45 removed outlier: 3.574A pdb=" N GLN H 43 " --> pdb=" O SER H 40 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU H 44 " --> pdb=" O ASP H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 49 removed outlier: 3.654A 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 55 through 57 No H-bonds generated for 'chain 'H' and resid 55 through 57' Processing helix chain 'H' and resid 72 through 78 removed outlier: 3.759A pdb=" N ARG H 77 " --> pdb=" O MET H 73 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER H 78 " --> pdb=" O ASP H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 113 removed outlier: 3.528A pdb=" N VAL H 113 " --> pdb=" O GLY H 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 127 removed outlier: 3.837A pdb=" N ASP H 118 " --> pdb=" O ASP H 114 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL H 119 " --> pdb=" O SER H 115 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER H 126 " --> pdb=" O LYS H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 159 removed outlier: 4.199A pdb=" N GLY H 148 " --> pdb=" O GLY H 144 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR H 149 " --> pdb=" O SER H 145 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS H 154 " --> pdb=" O LEU H 150 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU H 157 " --> pdb=" O SER H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 180 through 196 removed outlier: 3.636A pdb=" N SER H 188 " --> pdb=" O ASN H 184 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLN H 191 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL H 193 " --> pdb=" O VAL H 189 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU H 194 " --> pdb=" O HIS H 190 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN H 195 " --> pdb=" O GLN H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 214 removed outlier: 3.630A pdb=" N ASP H 209 " --> pdb=" O GLU H 205 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS H 211 " --> pdb=" O LEU H 207 " (cutoff:3.500A) Processing helix chain 'H' and resid 221 through 237 removed outlier: 4.643A pdb=" N HIS H 227 " --> pdb=" O GLY H 223 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU H 228 " --> pdb=" O ASP H 224 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL H 229 " --> pdb=" O LEU H 225 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR H 237 " --> pdb=" O MET H 233 " (cutoff:3.500A) Processing helix chain 'H' and resid 251 through 256 Processing helix chain 'H' and resid 285 through 294 removed outlier: 3.655A pdb=" N GLN H 291 " --> pdb=" O PRO H 287 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN H 292 " --> pdb=" O GLU H 288 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET H 293 " --> pdb=" O LEU H 289 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE H 294 " --> pdb=" O THR H 290 " (cutoff:3.500A) Processing helix chain 'H' and resid 323 through 337 removed outlier: 4.321A pdb=" N GLN H 329 " --> pdb=" O GLU H 325 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN H 334 " --> pdb=" O MET H 330 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN H 337 " --> pdb=" O VAL H 333 " (cutoff:3.500A) Processing helix chain 'H' and resid 374 through 390 removed outlier: 3.807A pdb=" N ILE H 381 " --> pdb=" O LEU H 377 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG H 390 " --> pdb=" O THR H 386 " (cutoff:3.500A) Processing helix chain 'H' and resid 394 through 401 removed outlier: 4.434A pdb=" N TYR H 398 " --> pdb=" O PHE H 394 " (cutoff:3.500A) Processing helix chain 'H' and resid 404 through 427 removed outlier: 3.873A pdb=" N PHE H 408 " --> pdb=" O ASP H 404 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET H 415 " --> pdb=" O ALA H 411 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU H 421 " --> pdb=" O ASP H 417 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASP H 427 " --> pdb=" O GLN H 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 28 removed outlier: 3.559A pdb=" N ILE E 16 " --> pdb=" O ALA E 12 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA E 19 " --> pdb=" O GLN E 15 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU E 23 " --> pdb=" O ALA E 19 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N HIS E 28 " --> pdb=" O TYR E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 80 removed outlier: 3.693A pdb=" N GLU E 77 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 108 Processing helix chain 'E' and resid 114 through 128 removed outlier: 3.895A pdb=" N LEU E 119 " --> pdb=" O ILE E 115 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASP E 120 " --> pdb=" O ASP E 116 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG E 121 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN E 128 " --> pdb=" O LYS E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 161 removed outlier: 4.523A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU E 155 " --> pdb=" O SER E 151 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG E 156 " --> pdb=" O LEU E 152 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER E 158 " --> pdb=" O MET E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 195 removed outlier: 4.327A pdb=" N ILE E 188 " --> pdb=" O PRO E 184 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR E 190 " --> pdb=" O ASN E 186 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR E 193 " --> pdb=" O LEU E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 216 removed outlier: 3.511A pdb=" N ARG E 214 " --> pdb=" O TYR E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 239 removed outlier: 3.556A pdb=" N ARG E 229 " --> pdb=" O THR E 225 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU E 230 " --> pdb=" O ASN E 226 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE E 231 " --> pdb=" O LEU E 227 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN E 233 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE E 234 " --> pdb=" O LEU E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 244 removed outlier: 3.751A pdb=" N ARG E 243 " --> pdb=" O THR E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 259 removed outlier: 3.662A pdb=" N PHE E 255 " --> pdb=" O ASP E 251 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLN E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR E 257 " --> pdb=" O THR E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 297 removed outlier: 3.559A pdb=" N ALA E 294 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N CYS E 295 " --> pdb=" O ILE E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 301 removed outlier: 3.893A pdb=" N GLN E 301 " --> pdb=" O PRO E 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 298 through 301' Processing helix chain 'E' and resid 306 through 310 removed outlier: 3.553A pdb=" N HIS E 309 " --> pdb=" O ASP E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 337 removed outlier: 3.526A pdb=" N ALA E 333 " --> pdb=" O ASN E 329 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR E 334 " --> pdb=" O ALA E 330 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE E 335 " --> pdb=" O ALA E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 401 removed outlier: 3.820A pdb=" N LEU E 397 " --> pdb=" O HIS E 393 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 Processing helix chain 'E' and resid 416 through 437 removed outlier: 3.518A pdb=" N GLU E 423 " --> pdb=" O SER E 419 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR E 432 " --> pdb=" O LEU E 428 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLU E 433 " --> pdb=" O GLU E 429 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 28 removed outlier: 3.559A pdb=" N ILE J 16 " --> pdb=" O ALA J 12 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA J 19 " --> pdb=" O GLN J 15 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU J 23 " --> pdb=" O ALA J 19 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N HIS J 28 " --> pdb=" O TYR J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 72 through 80 removed outlier: 3.693A pdb=" N GLU J 77 " --> pdb=" O THR J 73 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL J 78 " --> pdb=" O VAL J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 108 Processing helix chain 'J' and resid 114 through 128 removed outlier: 3.895A pdb=" N LEU J 119 " --> pdb=" O ILE J 115 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASP J 120 " --> pdb=" O ASP J 116 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG J 121 " --> pdb=" O LEU J 117 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN J 128 " --> pdb=" O LYS J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 144 through 161 removed outlier: 4.523A pdb=" N THR J 150 " --> pdb=" O GLY J 146 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU J 155 " --> pdb=" O SER J 151 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG J 156 " --> pdb=" O LEU J 152 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER J 158 " --> pdb=" O MET J 154 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 195 removed outlier: 4.327A pdb=" N ILE J 188 " --> pdb=" O PRO J 184 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR J 190 " --> pdb=" O ASN J 186 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR J 193 " --> pdb=" O LEU J 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 216 removed outlier: 3.511A pdb=" N ARG J 214 " --> pdb=" O TYR J 210 " (cutoff:3.500A) Processing helix chain 'J' and resid 223 through 239 removed outlier: 3.555A pdb=" N ARG J 229 " --> pdb=" O THR J 225 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU J 230 " --> pdb=" O ASN J 226 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE J 231 " --> pdb=" O LEU J 227 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN J 233 " --> pdb=" O ARG J 229 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE J 234 " --> pdb=" O LEU J 230 " (cutoff:3.500A) Processing helix chain 'J' and resid 239 through 244 removed outlier: 3.750A pdb=" N ARG J 243 " --> pdb=" O THR J 239 " (cutoff:3.500A) Processing helix chain 'J' and resid 251 through 259 removed outlier: 3.662A pdb=" N PHE J 255 " --> pdb=" O ASP J 251 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLN J 256 " --> pdb=" O LEU J 252 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR J 257 " --> pdb=" O THR J 253 " (cutoff:3.500A) Processing helix chain 'J' and resid 289 through 297 removed outlier: 3.558A pdb=" N ALA J 294 " --> pdb=" O GLU J 290 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N CYS J 295 " --> pdb=" O ILE J 291 " (cutoff:3.500A) Processing helix chain 'J' and resid 298 through 301 removed outlier: 3.894A pdb=" N GLN J 301 " --> pdb=" O PRO J 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 298 through 301' Processing helix chain 'J' and resid 306 through 310 removed outlier: 3.552A pdb=" N HIS J 309 " --> pdb=" O ASP J 306 " (cutoff:3.500A) Processing helix chain 'J' and resid 324 through 337 removed outlier: 3.526A pdb=" N ALA J 333 " --> pdb=" O ASN J 329 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR J 334 " --> pdb=" O ALA J 330 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE J 335 " --> pdb=" O ALA J 331 " (cutoff:3.500A) Processing helix chain 'J' and resid 384 through 401 removed outlier: 3.820A pdb=" N LEU J 397 " --> pdb=" O HIS J 393 " (cutoff:3.500A) Processing helix chain 'J' and resid 405 through 410 Processing helix chain 'J' and resid 416 through 437 removed outlier: 3.519A pdb=" N GLU J 423 " --> pdb=" O SER J 419 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR J 432 " --> pdb=" O LEU J 428 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU J 433 " --> pdb=" O GLU J 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 28 removed outlier: 3.560A pdb=" N ILE C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA C 19 " --> pdb=" O GLN C 15 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU C 23 " --> pdb=" O ALA C 19 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N HIS C 28 " --> pdb=" O TYR C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 80 removed outlier: 3.693A pdb=" N GLU C 77 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 108 Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.895A pdb=" N LEU C 119 " --> pdb=" O ILE C 115 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ASP C 120 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG C 121 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 161 removed outlier: 4.523A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) removed outlier: 3.774A 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: 3.750A pdb=" N SER C 158 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 195 removed outlier: 4.327A pdb=" N ILE C 188 " --> pdb=" O PRO C 184 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR C 190 " --> pdb=" O ASN C 186 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR C 193 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 216 removed outlier: 3.511A pdb=" N ARG C 214 " --> pdb=" O TYR C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 239 removed outlier: 3.556A pdb=" N ARG C 229 " --> pdb=" O THR C 225 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU C 230 " --> pdb=" O ASN C 226 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE C 231 " --> pdb=" O LEU C 227 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN C 233 " --> pdb=" O ARG C 229 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE C 234 " --> pdb=" O LEU C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 244 removed outlier: 3.750A pdb=" N ARG C 243 " --> pdb=" O THR C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 259 removed outlier: 3.662A pdb=" N PHE C 255 " --> pdb=" O ASP C 251 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLN C 256 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR C 257 " --> pdb=" O THR C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 297 removed outlier: 3.558A pdb=" N ALA C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N CYS C 295 " --> pdb=" O ILE C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 301 removed outlier: 3.893A pdb=" N GLN C 301 " --> pdb=" O PRO C 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 298 through 301' Processing helix chain 'C' and resid 306 through 310 removed outlier: 3.552A pdb=" N HIS C 309 " --> pdb=" O ASP C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 337 removed outlier: 3.526A pdb=" N ALA C 333 " --> pdb=" O ASN C 329 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR C 334 " --> pdb=" O ALA C 330 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE C 335 " --> pdb=" O ALA C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 401 removed outlier: 3.819A pdb=" N LEU C 397 " --> pdb=" O HIS C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'C' and resid 416 through 437 removed outlier: 3.517A pdb=" N GLU C 423 " --> pdb=" O SER C 419 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR C 432 " --> pdb=" O LEU C 428 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLU C 433 " --> pdb=" O GLU C 429 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 28 removed outlier: 3.560A pdb=" N ILE L 16 " --> pdb=" O ALA L 12 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA L 19 " --> pdb=" O GLN L 15 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU L 23 " --> pdb=" O ALA L 19 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N HIS L 28 " --> pdb=" O TYR L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 80 removed outlier: 3.693A pdb=" N GLU L 77 " --> pdb=" O THR L 73 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL L 78 " --> pdb=" O VAL L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 108 Processing helix chain 'L' and resid 114 through 128 removed outlier: 3.895A pdb=" N LEU L 119 " --> pdb=" O ILE L 115 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASP L 120 " --> pdb=" O ASP L 116 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG L 121 " --> pdb=" O LEU L 117 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN L 128 " --> pdb=" O LYS L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 144 through 161 removed outlier: 4.523A pdb=" N THR L 150 " --> pdb=" O GLY L 146 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU L 155 " --> pdb=" O SER L 151 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG L 156 " --> pdb=" O LEU L 152 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER L 158 " --> pdb=" O MET L 154 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 195 removed outlier: 4.326A pdb=" N ILE L 188 " --> pdb=" O PRO L 184 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR L 190 " --> pdb=" O ASN L 186 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR L 193 " --> pdb=" O LEU L 189 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 216 removed outlier: 3.512A pdb=" N ARG L 214 " --> pdb=" O TYR L 210 " (cutoff:3.500A) Processing helix chain 'L' and resid 223 through 239 removed outlier: 3.556A pdb=" N ARG L 229 " --> pdb=" O THR L 225 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU L 230 " --> pdb=" O ASN L 226 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE L 231 " --> pdb=" O LEU L 227 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN L 233 " --> pdb=" O ARG L 229 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE L 234 " --> pdb=" O LEU L 230 " (cutoff:3.500A) Processing helix chain 'L' and resid 239 through 244 removed outlier: 3.751A pdb=" N ARG L 243 " --> pdb=" O THR L 239 " (cutoff:3.500A) Processing helix chain 'L' and resid 251 through 259 removed outlier: 3.662A pdb=" N PHE L 255 " --> pdb=" O ASP L 251 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLN L 256 " --> pdb=" O LEU L 252 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR L 257 " --> pdb=" O THR L 253 " (cutoff:3.500A) Processing helix chain 'L' and resid 289 through 297 removed outlier: 3.558A pdb=" N ALA L 294 " --> pdb=" O GLU L 290 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N CYS L 295 " --> pdb=" O ILE L 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 301 removed outlier: 3.893A pdb=" N GLN L 301 " --> pdb=" O PRO L 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 298 through 301' Processing helix chain 'L' and resid 306 through 310 removed outlier: 3.552A pdb=" N HIS L 309 " --> pdb=" O ASP L 306 " (cutoff:3.500A) Processing helix chain 'L' and resid 324 through 337 removed outlier: 3.526A pdb=" N ALA L 333 " --> pdb=" O ASN L 329 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR L 334 " --> pdb=" O ALA L 330 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE L 335 " --> pdb=" O ALA L 331 " (cutoff:3.500A) Processing helix chain 'L' and resid 384 through 401 removed outlier: 3.820A pdb=" N LEU L 397 " --> pdb=" O HIS L 393 " (cutoff:3.500A) Processing helix chain 'L' and resid 405 through 410 Processing helix chain 'L' and resid 416 through 437 removed outlier: 3.518A pdb=" N GLU L 423 " --> pdb=" O SER L 419 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR L 432 " --> pdb=" O LEU L 428 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU L 433 " --> pdb=" O GLU L 429 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 28 removed outlier: 3.559A pdb=" N ILE K 16 " --> pdb=" O ALA K 12 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA K 19 " --> pdb=" O GLN K 15 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU K 23 " --> pdb=" O ALA K 19 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N HIS K 28 " --> pdb=" O TYR K 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 80 removed outlier: 3.692A pdb=" N GLU K 77 " --> pdb=" O THR K 73 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL K 78 " --> pdb=" O VAL K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 103 through 108 Processing helix chain 'K' and resid 114 through 128 removed outlier: 3.895A pdb=" N LEU K 119 " --> pdb=" O ILE K 115 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASP K 120 " --> pdb=" O ASP K 116 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG K 121 " --> pdb=" O LEU K 117 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN K 128 " --> pdb=" O LYS K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 144 through 161 removed outlier: 4.523A pdb=" N THR K 150 " --> pdb=" O GLY K 146 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU K 155 " --> pdb=" O SER K 151 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG K 156 " --> pdb=" O LEU K 152 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER K 158 " --> pdb=" O MET K 154 " (cutoff:3.500A) Processing helix chain 'K' and resid 182 through 195 removed outlier: 4.326A pdb=" N ILE K 188 " --> pdb=" O PRO K 184 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR K 190 " --> pdb=" O ASN K 186 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR K 193 " --> pdb=" O LEU K 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 216 removed outlier: 3.511A pdb=" N ARG K 214 " --> pdb=" O TYR K 210 " (cutoff:3.500A) Processing helix chain 'K' and resid 223 through 239 removed outlier: 3.555A pdb=" N ARG K 229 " --> pdb=" O THR K 225 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU K 230 " --> pdb=" O ASN K 226 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE K 231 " --> pdb=" O LEU K 227 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN K 233 " --> pdb=" O ARG K 229 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE K 234 " --> pdb=" O LEU K 230 " (cutoff:3.500A) Processing helix chain 'K' and resid 239 through 244 removed outlier: 3.751A pdb=" N ARG K 243 " --> pdb=" O THR K 239 " (cutoff:3.500A) Processing helix chain 'K' and resid 251 through 259 removed outlier: 3.663A pdb=" N PHE K 255 " --> pdb=" O ASP K 251 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLN K 256 " --> pdb=" O LEU K 252 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR K 257 " --> pdb=" O THR K 253 " (cutoff:3.500A) Processing helix chain 'K' and resid 289 through 297 removed outlier: 3.559A pdb=" N ALA K 294 " --> pdb=" O GLU K 290 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N CYS K 295 " --> pdb=" O ILE K 291 " (cutoff:3.500A) Processing helix chain 'K' and resid 298 through 301 removed outlier: 3.893A pdb=" N GLN K 301 " --> pdb=" O PRO K 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 298 through 301' Processing helix chain 'K' and resid 306 through 310 removed outlier: 3.553A pdb=" N HIS K 309 " --> pdb=" O ASP K 306 " (cutoff:3.500A) Processing helix chain 'K' and resid 324 through 337 removed outlier: 3.527A pdb=" N ALA K 333 " --> pdb=" O ASN K 329 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR K 334 " --> pdb=" O ALA K 330 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE K 335 " --> pdb=" O ALA K 331 " (cutoff:3.500A) Processing helix chain 'K' and resid 384 through 401 removed outlier: 3.820A pdb=" N LEU K 397 " --> pdb=" O HIS K 393 " (cutoff:3.500A) Processing helix chain 'K' and resid 405 through 410 Processing helix chain 'K' and resid 416 through 437 removed outlier: 3.519A pdb=" N GLU K 423 " --> pdb=" O SER K 419 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR K 432 " --> pdb=" O LEU K 428 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU K 433 " --> pdb=" O GLU K 429 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 90 through 92 removed outlier: 8.013A pdb=" N VAL F 91 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N LEU F 65 " --> pdb=" O VAL F 91 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N ILE F 64 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N HIS F 6 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N VAL F 66 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N GLN F 8 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N GLU F 3 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N PHE F 133 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL F 5 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LEU F 135 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE F 7 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N GLN F 131 " --> pdb=" O ILE F 163 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N ASN F 165 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N PHE F 133 " --> pdb=" O ASN F 165 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N PHE F 167 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LEU F 135 " --> pdb=" O PHE F 167 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR F 166 " --> pdb=" O GLU F 198 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR F 199 " --> pdb=" O PHE F 266 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N PHE F 265 " --> pdb=" O SER F 371 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N SER F 371 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA F 271 " --> pdb=" O ALA F 365 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N SER F 364 " --> pdb=" O PHE F 317 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N PHE F 317 " --> pdb=" O SER F 364 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR F 366 " --> pdb=" O ALA F 315 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ALA F 315 " --> pdb=" O THR F 366 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE F 368 " --> pdb=" O VAL F 313 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N VAL F 313 " --> pdb=" O ILE F 368 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ASN F 370 " --> pdb=" O LEU F 311 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 51 through 53 Processing sheet with id=AA3, first strand: chain 'F' and resid 169 through 170 Processing sheet with id=AA4, first strand: chain 'A' and resid 92 through 93 removed outlier: 8.071A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.916A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLU A 3 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLY A 134 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE A 5 " --> pdb=" O GLY A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA6, first strand: chain 'A' and resid 168 through 172 removed outlier: 6.040A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 269 through 273 removed outlier: 4.031A pdb=" N ALA A 314 " --> pdb=" O ASN A 380 " (cutoff:3.500A) removed outlier: 9.528A pdb=" N LYS A 352 " --> pdb=" O MET A 313 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N CYS A 315 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N GLY A 354 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU A 317 " --> pdb=" O GLY A 354 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ASN A 356 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N TYR A 319 " --> pdb=" O ASN A 356 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 90 through 92 removed outlier: 8.012A pdb=" N VAL G 91 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LEU G 65 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N ILE G 64 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N HIS G 6 " --> pdb=" O ILE G 64 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N VAL G 66 " --> pdb=" O HIS G 6 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLN G 8 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N GLU G 3 " --> pdb=" O GLN G 131 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N PHE G 133 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL G 5 " --> pdb=" O PHE G 133 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LEU G 135 " --> pdb=" O VAL G 5 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE G 7 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N GLN G 131 " --> pdb=" O ILE G 163 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N ASN G 165 " --> pdb=" O GLN G 131 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N PHE G 133 " --> pdb=" O ASN G 165 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N PHE G 167 " --> pdb=" O PHE G 133 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU G 135 " --> pdb=" O PHE G 167 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR G 166 " --> pdb=" O GLU G 198 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR G 199 " --> pdb=" O PHE G 266 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N PHE G 265 " --> pdb=" O SER G 371 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N SER G 371 " --> pdb=" O PHE G 265 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA G 271 " --> pdb=" O ALA G 365 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N SER G 364 " --> pdb=" O PHE G 317 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N PHE G 317 " --> pdb=" O SER G 364 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N THR G 366 " --> pdb=" O ALA G 315 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ALA G 315 " --> pdb=" O THR G 366 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE G 368 " --> pdb=" O VAL G 313 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N VAL G 313 " --> pdb=" O ILE G 368 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ASN G 370 " --> pdb=" O LEU G 311 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 51 through 53 Processing sheet with id=AB1, first strand: chain 'G' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'D' and resid 90 through 92 removed outlier: 8.013A pdb=" N VAL D 91 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LEU D 65 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N ILE D 64 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N HIS D 6 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N VAL D 66 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N GLN D 8 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N GLU D 3 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N PHE D 133 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL D 5 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N LEU D 135 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE D 7 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N GLN D 131 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N ASN D 165 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N PHE D 133 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N PHE D 167 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU D 135 " --> pdb=" O PHE D 167 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR D 166 " --> pdb=" O GLU D 198 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR D 199 " --> pdb=" O PHE D 266 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N PHE D 265 " --> pdb=" O SER D 371 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N SER D 371 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA D 271 " --> pdb=" O ALA D 365 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N SER D 364 " --> pdb=" O PHE D 317 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N PHE D 317 " --> pdb=" O SER D 364 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR D 366 " --> pdb=" O ALA D 315 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ALA D 315 " --> pdb=" O THR D 366 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE D 368 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N VAL D 313 " --> pdb=" O ILE D 368 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ASN D 370 " --> pdb=" O LEU D 311 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 51 through 53 Processing sheet with id=AB4, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AB5, first strand: chain 'I' and resid 90 through 92 removed outlier: 8.013A pdb=" N VAL I 91 " --> pdb=" O ALA I 63 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N LEU I 65 " --> pdb=" O VAL I 91 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N ILE I 64 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N HIS I 6 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N VAL I 66 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLN I 8 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N GLU I 3 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N PHE I 133 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL I 5 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LEU I 135 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE I 7 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N GLN I 131 " --> pdb=" O ILE I 163 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N ASN I 165 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N PHE I 133 " --> pdb=" O ASN I 165 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N PHE I 167 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU I 135 " --> pdb=" O PHE I 167 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR I 166 " --> pdb=" O GLU I 198 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N THR I 199 " --> pdb=" O PHE I 266 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N PHE I 265 " --> pdb=" O SER I 371 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N SER I 371 " --> pdb=" O PHE I 265 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA I 271 " --> pdb=" O ALA I 365 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N SER I 364 " --> pdb=" O PHE I 317 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N PHE I 317 " --> pdb=" O SER I 364 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N THR I 366 " --> pdb=" O ALA I 315 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ALA I 315 " --> pdb=" O THR I 366 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE I 368 " --> pdb=" O VAL I 313 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N VAL I 313 " --> pdb=" O ILE I 368 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ASN I 370 " --> pdb=" O LEU I 311 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 51 through 53 Processing sheet with id=AB7, first strand: chain 'I' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.013A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N GLN B 131 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N ASN B 165 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N PHE B 133 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR B 166 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA B 271 " --> pdb=" O ALA B 365 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N SER B 364 " --> pdb=" O PHE B 317 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N PHE B 317 " --> pdb=" O SER B 364 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N THR B 366 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ALA B 315 " --> pdb=" O THR B 366 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE B 368 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N VAL B 313 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ASN B 370 " --> pdb=" O LEU B 311 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AC1, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AC2, first strand: chain 'H' and resid 90 through 92 removed outlier: 8.012A pdb=" N VAL H 91 " --> pdb=" O ALA H 63 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LEU H 65 " --> pdb=" O VAL H 91 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N ILE H 64 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N HIS H 6 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N VAL H 66 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N GLN H 8 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N GLU H 3 " --> pdb=" O GLN H 131 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N PHE H 133 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL H 5 " --> pdb=" O PHE H 133 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N LEU H 135 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE H 7 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N GLN H 131 " --> pdb=" O ILE H 163 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N ASN H 165 " --> pdb=" O GLN H 131 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N PHE H 133 " --> pdb=" O ASN H 165 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N PHE H 167 " --> pdb=" O PHE H 133 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LEU H 135 " --> pdb=" O PHE H 167 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR H 166 " --> pdb=" O GLU H 198 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR H 199 " --> pdb=" O PHE H 266 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N PHE H 265 " --> pdb=" O SER H 371 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N SER H 371 " --> pdb=" O PHE H 265 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA H 271 " --> pdb=" O ALA H 365 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N SER H 364 " --> pdb=" O PHE H 317 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N PHE H 317 " --> pdb=" O SER H 364 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR H 366 " --> pdb=" O ALA H 315 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ALA H 315 " --> pdb=" O THR H 366 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE H 368 " --> pdb=" O VAL H 313 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N VAL H 313 " --> pdb=" O ILE H 368 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ASN H 370 " --> pdb=" O LEU H 311 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 51 through 53 Processing sheet with id=AC4, first strand: chain 'H' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'E' and resid 92 through 93 removed outlier: 8.071A pdb=" N ILE E 93 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N PHE E 67 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 8.915A pdb=" N VAL E 66 " --> pdb=" O CYS E 4 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N SER E 6 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N VAL E 68 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N HIS E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLU E 3 " --> pdb=" O LEU E 132 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY E 134 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE E 5 " --> pdb=" O GLY E 134 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC7, first strand: chain 'E' and resid 168 through 172 removed outlier: 6.040A pdb=" N GLU E 168 " --> pdb=" O PHE E 202 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N VAL E 204 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N SER E 170 " --> pdb=" O VAL E 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'E' and resid 269 through 273 removed outlier: 4.031A pdb=" N ALA E 314 " --> pdb=" O ASN E 380 " (cutoff:3.500A) removed outlier: 9.528A pdb=" N LYS E 352 " --> pdb=" O MET E 313 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N CYS E 315 " --> pdb=" O LYS E 352 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N GLY E 354 " --> pdb=" O CYS E 315 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU E 317 " --> pdb=" O GLY E 354 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ASN E 356 " --> pdb=" O LEU E 317 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N TYR E 319 " --> pdb=" O ASN E 356 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 92 through 93 removed outlier: 8.071A pdb=" N ILE J 93 " --> pdb=" O ALA J 65 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N PHE J 67 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 8.916A pdb=" N VAL J 66 " --> pdb=" O CYS J 4 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER J 6 " --> pdb=" O VAL J 66 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N VAL J 68 " --> pdb=" O SER J 6 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N HIS J 8 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLU J 3 " --> pdb=" O LEU J 132 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLY J 134 " --> pdb=" O GLU J 3 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE J 5 " --> pdb=" O GLY J 134 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 53 through 55 Processing sheet with id=AD2, first strand: chain 'J' and resid 168 through 172 removed outlier: 6.041A pdb=" N GLU J 168 " --> pdb=" O PHE J 202 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL J 204 " --> pdb=" O GLU J 168 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N SER J 170 " --> pdb=" O VAL J 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'J' and resid 269 through 273 removed outlier: 4.031A pdb=" N ALA J 314 " --> pdb=" O ASN J 380 " (cutoff:3.500A) removed outlier: 9.528A pdb=" N LYS J 352 " --> pdb=" O MET J 313 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N CYS J 315 " --> pdb=" O LYS J 352 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N GLY J 354 " --> pdb=" O CYS J 315 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU J 317 " --> pdb=" O GLY J 354 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ASN J 356 " --> pdb=" O LEU J 317 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N TYR J 319 " --> pdb=" O ASN J 356 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 92 through 93 removed outlier: 8.071A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 8.915A pdb=" N VAL C 66 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLU C 3 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY C 134 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE C 5 " --> pdb=" O GLY C 134 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AD6, first strand: chain 'C' and resid 168 through 172 removed outlier: 6.041A pdb=" N GLU C 168 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL C 204 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N SER C 170 " --> pdb=" O VAL C 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'C' and resid 269 through 273 removed outlier: 4.030A pdb=" N ALA C 314 " --> pdb=" O ASN C 380 " (cutoff:3.500A) removed outlier: 9.528A pdb=" N LYS C 352 " --> pdb=" O MET C 313 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N CYS C 315 " --> pdb=" O LYS C 352 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N GLY C 354 " --> pdb=" O CYS C 315 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU C 317 " --> pdb=" O GLY C 354 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ASN C 356 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N TYR C 319 " --> pdb=" O ASN C 356 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 92 through 93 removed outlier: 8.070A pdb=" N ILE L 93 " --> pdb=" O ALA L 65 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N PHE L 67 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 8.916A pdb=" N VAL L 66 " --> pdb=" O CYS L 4 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N SER L 6 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N VAL L 68 " --> pdb=" O SER L 6 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N HIS L 8 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLU L 3 " --> pdb=" O LEU L 132 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY L 134 " --> pdb=" O GLU L 3 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE L 5 " --> pdb=" O GLY L 134 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 53 through 55 Processing sheet with id=AE1, first strand: chain 'L' and resid 168 through 172 removed outlier: 6.040A pdb=" N GLU L 168 " --> pdb=" O PHE L 202 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL L 204 " --> pdb=" O GLU L 168 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N SER L 170 " --> pdb=" O VAL L 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'L' and resid 269 through 273 removed outlier: 4.032A pdb=" N ALA L 314 " --> pdb=" O ASN L 380 " (cutoff:3.500A) removed outlier: 9.528A pdb=" N LYS L 352 " --> pdb=" O MET L 313 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N CYS L 315 " --> pdb=" O LYS L 352 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N GLY L 354 " --> pdb=" O CYS L 315 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU L 317 " --> pdb=" O GLY L 354 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ASN L 356 " --> pdb=" O LEU L 317 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N TYR L 319 " --> pdb=" O ASN L 356 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 92 through 93 removed outlier: 8.070A pdb=" N ILE K 93 " --> pdb=" O ALA K 65 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N PHE K 67 " --> pdb=" O ILE K 93 " (cutoff:3.500A) removed outlier: 8.916A pdb=" N VAL K 66 " --> pdb=" O CYS K 4 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N SER K 6 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N VAL K 68 " --> pdb=" O SER K 6 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N HIS K 8 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLU K 3 " --> pdb=" O LEU K 132 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY K 134 " --> pdb=" O GLU K 3 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE K 5 " --> pdb=" O GLY K 134 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 53 through 55 Processing sheet with id=AE5, first strand: chain 'K' and resid 168 through 172 removed outlier: 6.041A pdb=" N GLU K 168 " --> pdb=" O PHE K 202 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL K 204 " --> pdb=" O GLU K 168 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N SER K 170 " --> pdb=" O VAL K 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'K' and resid 269 through 273 removed outlier: 4.031A pdb=" N ALA K 314 " --> pdb=" O ASN K 380 " (cutoff:3.500A) removed outlier: 9.528A pdb=" N LYS K 352 " --> pdb=" O MET K 313 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N CYS K 315 " --> pdb=" O LYS K 352 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N GLY K 354 " --> pdb=" O CYS K 315 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU K 317 " --> pdb=" O GLY K 354 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N ASN K 356 " --> pdb=" O LEU K 317 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N TYR K 319 " --> pdb=" O ASN K 356 " (cutoff:3.500A) 1368 hydrogen bonds defined for protein. 4032 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: 15.93 Time building geometry restraints manager: 16.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 13569 1.34 - 1.46: 8550 1.46 - 1.57: 19222 1.57 - 1.69: 47 1.69 - 1.81: 432 Bond restraints: 41820 Sorted by residual: bond pdb=" C5 GDP D 501 " pdb=" C4 GDP D 501 " ideal model delta sigma weight residual 1.490 1.375 0.115 2.00e-02 2.50e+03 3.33e+01 bond pdb=" C5 GDP G 502 " pdb=" C4 GDP G 502 " ideal model delta sigma weight residual 1.490 1.375 0.115 2.00e-02 2.50e+03 3.32e+01 bond pdb=" C5 GDP F 501 " pdb=" C4 GDP F 501 " ideal model delta sigma weight residual 1.490 1.375 0.115 2.00e-02 2.50e+03 3.30e+01 bond pdb=" C5 GDP H 502 " pdb=" C4 GDP H 502 " ideal model delta sigma weight residual 1.490 1.375 0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" C5 GDP B 501 " pdb=" C4 GDP B 501 " ideal model delta sigma weight residual 1.490 1.376 0.114 2.00e-02 2.50e+03 3.27e+01 ... (remaining 41815 not shown) Histogram of bond angle deviations from ideal: 99.69 - 106.55: 1407 106.55 - 113.41: 22386 113.41 - 120.26: 16048 120.26 - 127.12: 16496 127.12 - 133.98: 483 Bond angle restraints: 56820 Sorted by residual: angle pdb=" C THR D 285 " pdb=" N VAL D 286 " pdb=" CA VAL D 286 " ideal model delta sigma weight residual 120.24 123.44 -3.20 6.30e-01 2.52e+00 2.58e+01 angle pdb=" C THR F 285 " pdb=" N VAL F 286 " pdb=" CA VAL F 286 " ideal model delta sigma weight residual 120.24 123.37 -3.13 6.30e-01 2.52e+00 2.47e+01 angle pdb=" C THR G 285 " pdb=" N VAL G 286 " pdb=" CA VAL G 286 " ideal model delta sigma weight residual 120.24 123.37 -3.13 6.30e-01 2.52e+00 2.47e+01 angle pdb=" C THR I 285 " pdb=" N VAL I 286 " pdb=" CA VAL I 286 " ideal model delta sigma weight residual 120.24 123.36 -3.12 6.30e-01 2.52e+00 2.45e+01 angle pdb=" C THR B 285 " pdb=" N VAL B 286 " pdb=" CA VAL B 286 " ideal model delta sigma weight residual 120.24 123.34 -3.10 6.30e-01 2.52e+00 2.42e+01 ... (remaining 56815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.81: 24616 33.81 - 67.63: 180 67.63 - 101.44: 28 101.44 - 135.25: 9 135.25 - 169.06: 19 Dihedral angle restraints: 24852 sinusoidal: 9924 harmonic: 14928 Sorted by residual: dihedral pdb=" C5' GTP J 501 " pdb=" O5' GTP J 501 " pdb=" PA GTP J 501 " pdb=" O3A GTP J 501 " ideal model delta sinusoidal sigma weight residual 69.27 -121.67 -169.06 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C5' GTP E 502 " pdb=" O5' GTP E 502 " pdb=" PA GTP E 502 " pdb=" O3A GTP E 502 " ideal model delta sinusoidal sigma weight residual 69.27 -121.71 -169.02 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C5' GTP L 501 " pdb=" O5' GTP L 501 " pdb=" PA GTP L 501 " pdb=" O3A GTP L 501 " ideal model delta sinusoidal sigma weight residual 69.27 -121.71 -169.02 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 24849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 4083 0.045 - 0.091: 1658 0.091 - 0.136: 403 0.136 - 0.182: 46 0.182 - 0.227: 26 Chirality restraints: 6216 Sorted by residual: chirality pdb=" C2' GTP C 502 " pdb=" C1' GTP C 502 " pdb=" C3' GTP C 502 " pdb=" O2' GTP C 502 " both_signs ideal model delta sigma weight residual False -2.47 -2.70 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" C2' GTP J 501 " pdb=" C1' GTP J 501 " pdb=" C3' GTP J 501 " pdb=" O2' GTP J 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.70 0.22 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" C2' GTP K 501 " pdb=" C1' GTP K 501 " pdb=" C3' GTP K 501 " pdb=" O2' GTP K 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.70 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 6213 not shown) Planarity restraints: 7398 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' GDP F 501 " 0.056 2.00e-02 2.50e+03 2.37e-02 1.69e+01 pdb=" N9 GDP F 501 " -0.010 2.00e-02 2.50e+03 pdb=" C8 GDP F 501 " -0.008 2.00e-02 2.50e+03 pdb=" N7 GDP F 501 " -0.012 2.00e-02 2.50e+03 pdb=" C5 GDP F 501 " -0.019 2.00e-02 2.50e+03 pdb=" C6 GDP F 501 " 0.011 2.00e-02 2.50e+03 pdb=" O6 GDP F 501 " 0.022 2.00e-02 2.50e+03 pdb=" N1 GDP F 501 " 0.023 2.00e-02 2.50e+03 pdb=" C2 GDP F 501 " -0.002 2.00e-02 2.50e+03 pdb=" N2 GDP F 501 " -0.001 2.00e-02 2.50e+03 pdb=" N3 GDP F 501 " -0.030 2.00e-02 2.50e+03 pdb=" C4 GDP F 501 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GDP H 502 " 0.045 2.00e-02 2.50e+03 2.12e-02 1.34e+01 pdb=" N9 GDP H 502 " -0.007 2.00e-02 2.50e+03 pdb=" C8 GDP H 502 " 0.003 2.00e-02 2.50e+03 pdb=" N7 GDP H 502 " -0.006 2.00e-02 2.50e+03 pdb=" C5 GDP H 502 " -0.021 2.00e-02 2.50e+03 pdb=" C6 GDP H 502 " 0.002 2.00e-02 2.50e+03 pdb=" O6 GDP H 502 " 0.025 2.00e-02 2.50e+03 pdb=" N1 GDP H 502 " 0.011 2.00e-02 2.50e+03 pdb=" C2 GDP H 502 " -0.005 2.00e-02 2.50e+03 pdb=" N2 GDP H 502 " 0.014 2.00e-02 2.50e+03 pdb=" N3 GDP H 502 " -0.030 2.00e-02 2.50e+03 pdb=" C4 GDP H 502 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GDP I 502 " -0.043 2.00e-02 2.50e+03 1.94e-02 1.13e+01 pdb=" N9 GDP I 502 " 0.005 2.00e-02 2.50e+03 pdb=" C8 GDP I 502 " 0.003 2.00e-02 2.50e+03 pdb=" N7 GDP I 502 " 0.013 2.00e-02 2.50e+03 pdb=" C5 GDP I 502 " 0.020 2.00e-02 2.50e+03 pdb=" C6 GDP I 502 " -0.000 2.00e-02 2.50e+03 pdb=" O6 GDP I 502 " -0.033 2.00e-02 2.50e+03 pdb=" N1 GDP I 502 " -0.005 2.00e-02 2.50e+03 pdb=" C2 GDP I 502 " 0.005 2.00e-02 2.50e+03 pdb=" N2 GDP I 502 " -0.006 2.00e-02 2.50e+03 pdb=" N3 GDP I 502 " 0.020 2.00e-02 2.50e+03 pdb=" C4 GDP I 502 " 0.022 2.00e-02 2.50e+03 ... (remaining 7395 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.32: 18 2.32 - 2.96: 17665 2.96 - 3.61: 57708 3.61 - 4.25: 93896 4.25 - 4.90: 154518 Nonbonded interactions: 323805 Sorted by model distance: nonbonded pdb=" O1G GTP A 501 " pdb="MG MG A 502 " model vdw 1.671 2.170 nonbonded pdb=" O1G GTP C 502 " pdb="MG MG C 503 " model vdw 1.671 2.170 nonbonded pdb=" O1G GTP L 501 " pdb="MG MG L 502 " model vdw 1.671 2.170 nonbonded pdb=" O1G GTP J 501 " pdb="MG MG J 502 " model vdw 1.671 2.170 nonbonded pdb=" O1G GTP E 502 " pdb="MG MG E 503 " model vdw 1.672 2.170 ... (remaining 323800 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' and resid 1 through 441) selection = (chain 'C' and resid 1 through 441) selection = (chain 'E' and resid 1 through 441) selection = (chain 'J' and resid 1 through 441) selection = (chain 'K' and resid 1 through 441) selection = (chain 'L' and resid 1 through 441) } ncs_group { reference = (chain 'B' and resid 1 through 429) selection = (chain 'D' and resid 1 through 429) selection = (chain 'F' and resid 1 through 429) selection = (chain 'G' and resid 1 through 429) selection = (chain 'H' and resid 1 through 429) selection = (chain 'I' and resid 1 through 429) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 2.930 Check model and map are aligned: 0.580 Set scattering table: 0.340 Process input model: 101.750 Find NCS groups from input model: 4.000 Set up NCS constraints: 0.260 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 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 : 0.005 0.115 41820 Z= 0.322 Angle : 0.789 12.270 56820 Z= 0.400 Chirality : 0.051 0.227 6216 Planarity : 0.006 0.062 7398 Dihedral : 11.490 169.063 15276 Min Nonbonded Distance : 1.671 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.77 (0.08), residues: 5130 helix: -4.02 (0.05), residues: 2088 sheet: -1.33 (0.18), residues: 780 loop : -2.85 (0.10), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 101 HIS 0.006 0.001 HIS A 8 PHE 0.012 0.002 PHE B 92 TYR 0.018 0.002 TYR K 224 ARG 0.005 0.001 ARG F 318 *********************** 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 1778 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1778 time to evaluate : 4.637 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: 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: F 21 TRP cc_start: 0.8964 (m100) cc_final: 0.8652 (m100) REVERT: F 59 TYR cc_start: 0.8924 (m-80) cc_final: 0.8624 (m-80) REVERT: F 65 LEU cc_start: 0.8665 (mp) cc_final: 0.8439 (mp) REVERT: F 95 SER cc_start: 0.9065 (m) cc_final: 0.8749 (t) REVERT: F 125 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7942 (mt-10) REVERT: F 162 ARG cc_start: 0.8354 (mmt-90) cc_final: 0.8039 (mmp80) REVERT: F 164 MET cc_start: 0.9118 (tpt) cc_final: 0.8632 (mmm) REVERT: F 205 GLU cc_start: 0.8900 (tp30) cc_final: 0.8640 (mm-30) REVERT: F 233 MET cc_start: 0.8730 (mtp) cc_final: 0.8469 (mtm) REVERT: F 264 HIS cc_start: 0.8044 (p-80) cc_final: 0.7224 (p-80) REVERT: F 288 GLU cc_start: 0.6311 (tm-30) cc_final: 0.5845 (tm-30) REVERT: F 300 MET cc_start: 0.7739 (mtt) cc_final: 0.7122 (mtm) REVERT: F 303 CYS cc_start: 0.7382 (p) cc_final: 0.6663 (p) REVERT: F 322 SER cc_start: 0.8668 (m) cc_final: 0.8387 (t) REVERT: F 334 GLN cc_start: 0.8849 (tt0) cc_final: 0.8627 (tm-30) REVERT: F 340 TYR cc_start: 0.7798 (m-80) cc_final: 0.7563 (m-10) REVERT: F 367 PHE cc_start: 0.8636 (t80) cc_final: 0.8029 (t80) REVERT: A 2 ARG cc_start: 0.8070 (mpp-170) cc_final: 0.7507 (ptp90) REVERT: A 24 TYR cc_start: 0.8677 (m-80) cc_final: 0.8298 (m-80) REVERT: A 31 GLN cc_start: 0.8516 (mm-40) cc_final: 0.8245 (mm-40) REVERT: A 33 ASP cc_start: 0.8444 (m-30) cc_final: 0.7512 (p0) REVERT: A 50 ASN cc_start: 0.8405 (t0) cc_final: 0.7758 (t0) REVERT: A 56 THR cc_start: 0.7959 (p) cc_final: 0.7649 (t) REVERT: A 85 GLN cc_start: 0.8672 (mm-40) cc_final: 0.8392 (mm110) REVERT: A 90 GLU cc_start: 0.7788 (mm-30) cc_final: 0.6878 (tp30) REVERT: A 93 ILE cc_start: 0.8904 (mt) cc_final: 0.8702 (mm) REVERT: A 97 GLU cc_start: 0.7684 (mt-10) cc_final: 0.6826 (tt0) REVERT: A 120 ASP cc_start: 0.8041 (t70) cc_final: 0.7617 (t0) REVERT: A 151 SER cc_start: 0.8970 (m) cc_final: 0.8451 (p) REVERT: A 154 MET cc_start: 0.9037 (mmm) cc_final: 0.8598 (mmm) REVERT: A 172 TYR cc_start: 0.8099 (t80) cc_final: 0.7894 (t80) REVERT: A 188 ILE cc_start: 0.8710 (mm) cc_final: 0.8415 (mt) REVERT: A 210 TYR cc_start: 0.8929 (m-80) cc_final: 0.8585 (m-10) REVERT: A 233 GLN cc_start: 0.8821 (mm-40) cc_final: 0.8293 (mm-40) REVERT: A 252 LEU cc_start: 0.8962 (mp) cc_final: 0.8696 (mt) REVERT: A 258 ASN cc_start: 0.8902 (m110) cc_final: 0.8673 (t0) REVERT: A 295 CYS cc_start: 0.8463 (m) cc_final: 0.8120 (m) REVERT: A 368 LEU cc_start: 0.9035 (mp) cc_final: 0.8659 (pp) REVERT: A 378 LEU cc_start: 0.8085 (mt) cc_final: 0.7581 (mm) REVERT: A 388 TRP cc_start: 0.8860 (m100) cc_final: 0.8639 (m100) REVERT: A 435 VAL cc_start: 0.8255 (t) cc_final: 0.8003 (t) REVERT: G 4 ILE cc_start: 0.9553 (mt) cc_final: 0.9344 (mm) REVERT: G 26 ASP cc_start: 0.9016 (m-30) cc_final: 0.8743 (t70) REVERT: G 101 TRP cc_start: 0.9198 (t60) cc_final: 0.8726 (t60) REVERT: G 147 MET cc_start: 0.8954 (tpt) cc_final: 0.8661 (tpp) REVERT: G 184 ASN cc_start: 0.8456 (m-40) cc_final: 0.7860 (t0) REVERT: G 245 GLN cc_start: 0.8275 (mt0) cc_final: 0.8006 (mm110) REVERT: G 264 HIS cc_start: 0.7639 (p-80) cc_final: 0.7225 (p-80) REVERT: G 300 MET cc_start: 0.7873 (mtt) cc_final: 0.6928 (mtm) REVERT: G 324 LYS cc_start: 0.8455 (tttm) cc_final: 0.8100 (ttmm) REVERT: G 388 MET cc_start: 0.8316 (mtp) cc_final: 0.7828 (mmp) REVERT: D 6 HIS cc_start: 0.8231 (t70) cc_final: 0.7882 (t70) REVERT: D 14 ASN cc_start: 0.7792 (m-40) cc_final: 0.7345 (m-40) REVERT: D 26 ASP cc_start: 0.9189 (m-30) cc_final: 0.8763 (t0) REVERT: D 65 LEU cc_start: 0.8835 (mp) cc_final: 0.8487 (mp) REVERT: D 73 MET cc_start: 0.7065 (mmt) cc_final: 0.6757 (mmm) REVERT: D 101 TRP cc_start: 0.9042 (t60) cc_final: 0.8712 (t60) REVERT: D 164 MET cc_start: 0.9148 (tpt) cc_final: 0.8129 (tpp) REVERT: D 207 LEU cc_start: 0.8846 (mp) cc_final: 0.8104 (tp) REVERT: D 210 ILE cc_start: 0.8635 (mt) cc_final: 0.8356 (mt) REVERT: D 222 TYR cc_start: 0.8122 (m-80) cc_final: 0.7752 (m-80) REVERT: D 264 HIS cc_start: 0.7555 (p-80) cc_final: 0.6870 (p-80) REVERT: D 300 MET cc_start: 0.7514 (mtt) cc_final: 0.6700 (mmm) REVERT: D 310 TYR cc_start: 0.8792 (m-80) cc_final: 0.8502 (m-10) REVERT: D 324 LYS cc_start: 0.8456 (tttm) cc_final: 0.7900 (ttmm) REVERT: I 4 ILE cc_start: 0.9642 (mt) cc_final: 0.9342 (mm) REVERT: I 14 ASN cc_start: 0.8492 (m-40) cc_final: 0.8037 (m-40) REVERT: I 26 ASP cc_start: 0.8853 (m-30) cc_final: 0.8519 (t70) REVERT: I 65 LEU cc_start: 0.9292 (mp) cc_final: 0.8873 (mp) REVERT: I 264 HIS cc_start: 0.7550 (p-80) cc_final: 0.7128 (p-80) REVERT: I 297 LYS cc_start: 0.9164 (ptpt) cc_final: 0.8818 (ptpp) REVERT: I 310 TYR cc_start: 0.8306 (m-80) cc_final: 0.8008 (m-10) REVERT: I 324 LYS cc_start: 0.8181 (tttm) cc_final: 0.7642 (ttmm) REVERT: I 388 MET cc_start: 0.8375 (mtp) cc_final: 0.7696 (mmt) REVERT: I 406 MET cc_start: 0.7921 (tpp) cc_final: 0.7659 (mmp) REVERT: I 409 THR cc_start: 0.9250 (m) cc_final: 0.8820 (p) REVERT: B 6 HIS cc_start: 0.8358 (t70) cc_final: 0.8144 (t-170) REVERT: B 14 ASN cc_start: 0.7769 (m-40) cc_final: 0.7462 (m-40) REVERT: B 59 TYR cc_start: 0.8925 (m-80) cc_final: 0.8652 (m-80) REVERT: B 65 LEU cc_start: 0.8890 (mp) cc_final: 0.8527 (mp) REVERT: B 101 TRP cc_start: 0.8823 (t60) cc_final: 0.8276 (t60) REVERT: B 137 HIS cc_start: 0.8869 (p90) cc_final: 0.8629 (p90) REVERT: B 139 LEU cc_start: 0.8871 (mt) cc_final: 0.8511 (mp) REVERT: B 164 MET cc_start: 0.9134 (tpt) cc_final: 0.8877 (tpp) REVERT: B 187 LEU cc_start: 0.9302 (mt) cc_final: 0.8877 (tp) REVERT: B 201 CYS cc_start: 0.8830 (m) cc_final: 0.8569 (t) REVERT: B 245 GLN cc_start: 0.8481 (mt0) cc_final: 0.8187 (mm-40) REVERT: B 264 HIS cc_start: 0.7847 (p-80) cc_final: 0.6687 (p-80) REVERT: B 279 GLN cc_start: 0.8586 (pt0) cc_final: 0.8340 (pm20) REVERT: B 300 MET cc_start: 0.7678 (mtt) cc_final: 0.7394 (mtt) REVERT: B 303 CYS cc_start: 0.7230 (p) cc_final: 0.6773 (p) REVERT: B 324 LYS cc_start: 0.8174 (tttm) cc_final: 0.7874 (ttmm) REVERT: B 334 GLN cc_start: 0.8823 (tt0) cc_final: 0.8617 (mt0) REVERT: B 367 PHE cc_start: 0.8467 (t80) cc_final: 0.8223 (t80) REVERT: H 4 ILE cc_start: 0.9614 (mt) cc_final: 0.9309 (mm) REVERT: H 14 ASN cc_start: 0.8165 (m-40) cc_final: 0.7580 (m-40) REVERT: H 26 ASP cc_start: 0.9151 (m-30) cc_final: 0.8725 (t70) REVERT: H 37 HIS cc_start: 0.8689 (m90) cc_final: 0.8049 (m-70) REVERT: H 112 LEU cc_start: 0.9300 (tp) cc_final: 0.9094 (tt) REVERT: H 147 MET cc_start: 0.9021 (tpt) cc_final: 0.8757 (tpt) REVERT: H 184 ASN cc_start: 0.8376 (m-40) cc_final: 0.8149 (t0) REVERT: H 245 GLN cc_start: 0.8171 (mt0) cc_final: 0.7805 (mm-40) REVERT: H 279 GLN cc_start: 0.8792 (pt0) cc_final: 0.8532 (pm20) REVERT: H 300 MET cc_start: 0.7675 (mtt) cc_final: 0.7475 (mtt) REVERT: H 303 CYS cc_start: 0.7351 (p) cc_final: 0.6838 (p) REVERT: H 363 MET cc_start: 0.7991 (ptp) cc_final: 0.7764 (ptt) REVERT: H 388 MET cc_start: 0.8587 (mtp) cc_final: 0.7955 (mmp) REVERT: H 406 MET cc_start: 0.7813 (tpp) cc_final: 0.7569 (mmm) REVERT: E 32 PRO cc_start: 0.9416 (Cg_exo) cc_final: 0.9059 (Cg_endo) REVERT: E 33 ASP cc_start: 0.8635 (m-30) cc_final: 0.7830 (p0) REVERT: E 90 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8185 (tt0) REVERT: E 112 LYS cc_start: 0.8595 (mmtt) cc_final: 0.8240 (ttpt) REVERT: E 121 ARG cc_start: 0.7626 (mmm160) cc_final: 0.7335 (mmp-170) REVERT: E 151 SER cc_start: 0.9065 (m) cc_final: 0.8817 (p) REVERT: E 170 SER cc_start: 0.9209 (m) cc_final: 0.8822 (p) REVERT: E 233 GLN cc_start: 0.8937 (mm-40) cc_final: 0.8394 (mm-40) REVERT: E 254 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7832 (mt-10) REVERT: E 258 ASN cc_start: 0.8817 (m110) cc_final: 0.8584 (t0) REVERT: E 295 CYS cc_start: 0.8391 (m) cc_final: 0.7647 (m) REVERT: E 308 ARG cc_start: 0.8837 (mtm180) cc_final: 0.8586 (ptp90) REVERT: E 368 LEU cc_start: 0.8891 (mp) cc_final: 0.8660 (pp) REVERT: E 388 TRP cc_start: 0.8726 (m100) cc_final: 0.8506 (m100) REVERT: E 398 MET cc_start: 0.7643 (mtp) cc_final: 0.7381 (mmm) REVERT: E 407 TRP cc_start: 0.8945 (m100) cc_final: 0.8435 (m100) REVERT: J 21 TRP cc_start: 0.8592 (m100) cc_final: 0.7355 (m100) REVERT: J 33 ASP cc_start: 0.8571 (m-30) cc_final: 0.7872 (p0) REVERT: J 50 ASN cc_start: 0.8270 (t0) cc_final: 0.7806 (t0) REVERT: J 69 ASP cc_start: 0.7840 (t0) cc_final: 0.7600 (t0) REVERT: J 75 ILE cc_start: 0.9483 (mm) cc_final: 0.9261 (tt) REVERT: J 85 GLN cc_start: 0.8787 (mm-40) cc_final: 0.8538 (mm110) REVERT: J 90 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7277 (tp30) REVERT: J 91 GLN cc_start: 0.8537 (mt0) cc_final: 0.7952 (mm110) REVERT: J 151 SER cc_start: 0.9330 (m) cc_final: 0.8848 (p) REVERT: J 205 ASP cc_start: 0.7807 (t0) cc_final: 0.7399 (m-30) REVERT: J 271 THR cc_start: 0.8898 (m) cc_final: 0.8591 (p) REVERT: J 291 ILE cc_start: 0.9010 (pt) cc_final: 0.8323 (pt) REVERT: J 295 CYS cc_start: 0.8609 (m) cc_final: 0.8320 (m) REVERT: J 368 LEU cc_start: 0.9258 (mp) cc_final: 0.8967 (pp) REVERT: C 31 GLN cc_start: 0.8852 (mm-40) cc_final: 0.8149 (mp10) REVERT: C 33 ASP cc_start: 0.8517 (m-30) cc_final: 0.7989 (p0) REVERT: C 50 ASN cc_start: 0.7831 (t0) cc_final: 0.7498 (t0) REVERT: C 85 GLN cc_start: 0.8972 (mm-40) cc_final: 0.8629 (mm-40) REVERT: C 86 LEU cc_start: 0.8701 (tp) cc_final: 0.8422 (tt) REVERT: C 109 THR cc_start: 0.8436 (m) cc_final: 0.8062 (p) REVERT: C 169 PHE cc_start: 0.8175 (m-10) cc_final: 0.7845 (m-10) REVERT: C 214 ARG cc_start: 0.8338 (ttp80) cc_final: 0.7833 (ttp80) REVERT: C 232 SER cc_start: 0.8947 (p) cc_final: 0.8501 (m) REVERT: C 258 ASN cc_start: 0.8476 (m110) cc_final: 0.8069 (m-40) REVERT: C 271 THR cc_start: 0.9104 (m) cc_final: 0.8776 (p) REVERT: C 285 GLN cc_start: 0.8296 (pt0) cc_final: 0.7322 (mm-40) REVERT: C 295 CYS cc_start: 0.8512 (m) cc_final: 0.8265 (m) REVERT: C 356 ASN cc_start: 0.8650 (t0) cc_final: 0.8402 (m110) REVERT: C 368 LEU cc_start: 0.8971 (mp) cc_final: 0.8665 (pp) REVERT: C 378 LEU cc_start: 0.7914 (mt) cc_final: 0.7661 (mm) REVERT: C 388 TRP cc_start: 0.8815 (m100) cc_final: 0.8422 (m100) REVERT: L 31 GLN cc_start: 0.8800 (mm-40) cc_final: 0.7807 (mt0) REVERT: L 33 ASP cc_start: 0.8630 (m-30) cc_final: 0.7939 (p0) REVERT: L 50 ASN cc_start: 0.8063 (t0) cc_final: 0.7696 (t0) REVERT: L 90 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7419 (tp30) REVERT: L 115 ILE cc_start: 0.8476 (tp) cc_final: 0.8225 (tp) REVERT: L 119 LEU cc_start: 0.8853 (mt) cc_final: 0.8555 (pp) REVERT: L 120 ASP cc_start: 0.8091 (t70) cc_final: 0.7860 (t0) REVERT: L 123 ARG cc_start: 0.7743 (ttp-110) cc_final: 0.7538 (ttm110) REVERT: L 132 LEU cc_start: 0.9054 (tp) cc_final: 0.8721 (tt) REVERT: L 138 PHE cc_start: 0.8780 (m-10) cc_final: 0.8578 (m-10) REVERT: L 151 SER cc_start: 0.8773 (m) cc_final: 0.8533 (p) REVERT: L 154 MET cc_start: 0.8903 (mmm) cc_final: 0.8457 (mmt) REVERT: L 196 GLU cc_start: 0.8300 (mm-30) cc_final: 0.8033 (tm-30) REVERT: L 199 ASP cc_start: 0.7542 (m-30) cc_final: 0.7274 (t0) REVERT: L 214 ARG cc_start: 0.8414 (ttp80) cc_final: 0.7666 (ttp80) REVERT: L 233 GLN cc_start: 0.9101 (mm-40) cc_final: 0.8372 (mm-40) REVERT: L 271 THR cc_start: 0.9012 (m) cc_final: 0.8664 (p) REVERT: L 285 GLN cc_start: 0.8181 (pt0) cc_final: 0.7129 (mm-40) REVERT: L 290 GLU cc_start: 0.7642 (tt0) cc_final: 0.7398 (tt0) REVERT: L 326 LYS cc_start: 0.7559 (tmtm) cc_final: 0.7062 (mmtt) REVERT: L 329 ASN cc_start: 0.8421 (t0) cc_final: 0.8066 (m110) REVERT: L 368 LEU cc_start: 0.9277 (mp) cc_final: 0.8883 (pp) REVERT: L 378 LEU cc_start: 0.7977 (mt) cc_final: 0.7626 (mm) REVERT: L 402 ARG cc_start: 0.8543 (mmt-90) cc_final: 0.8331 (mmm160) REVERT: L 407 TRP cc_start: 0.8964 (m100) cc_final: 0.8685 (m100) REVERT: K 33 ASP cc_start: 0.8338 (m-30) cc_final: 0.7700 (p0) REVERT: K 90 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7438 (tp30) REVERT: K 132 LEU cc_start: 0.9101 (tp) cc_final: 0.8729 (tp) REVERT: K 154 MET cc_start: 0.9074 (mmm) cc_final: 0.8717 (mmm) REVERT: K 202 PHE cc_start: 0.8178 (m-80) cc_final: 0.7782 (m-10) REVERT: K 233 GLN cc_start: 0.9002 (mm-40) cc_final: 0.8446 (mm-40) REVERT: K 249 ASN cc_start: 0.7766 (m-40) cc_final: 0.7526 (p0) REVERT: K 271 THR cc_start: 0.9023 (m) cc_final: 0.8783 (p) REVERT: K 295 CYS cc_start: 0.8990 (m) cc_final: 0.8593 (m) REVERT: K 302 MET cc_start: 0.7592 (mtt) cc_final: 0.6779 (mmm) REVERT: K 308 ARG cc_start: 0.8502 (mtm180) cc_final: 0.7963 (ptp-110) REVERT: K 368 LEU cc_start: 0.9363 (mp) cc_final: 0.8977 (pp) REVERT: K 378 LEU cc_start: 0.8053 (mt) cc_final: 0.7806 (mm) REVERT: K 388 TRP cc_start: 0.8801 (m100) cc_final: 0.8571 (m100) REVERT: K 407 TRP cc_start: 0.9063 (m100) cc_final: 0.8690 (m100) outliers start: 0 outliers final: 0 residues processed: 1778 average time/residue: 0.5214 time to fit residues: 1496.0131 Evaluate side-chains 1003 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1003 time to evaluate : 5.059 ------------------------------------------------------------------------------- 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: 5.9990 chunk 386 optimal weight: 20.0000 chunk 214 optimal weight: 0.0980 chunk 132 optimal weight: 7.9990 chunk 260 optimal weight: 9.9990 chunk 206 optimal weight: 20.0000 chunk 399 optimal weight: 7.9990 chunk 154 optimal weight: 0.0470 chunk 243 optimal weight: 5.9990 chunk 297 optimal weight: 9.9990 chunk 463 optimal weight: 7.9990 overall best weight: 4.0284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 11 GLN F 14 ASN F 37 HIS ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 ASN F 226 ASN F 307 HIS ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 18 ASN A 28 HIS A 88 HIS A 107 HIS A 192 HIS A 206 ASN A 301 GLN G 37 HIS ** G 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 226 ASN G 247 ASN G 307 HIS G 423 GLN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 HIS D 190 HIS D 247 ASN ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 HIS D 396 HIS I 37 HIS ** I 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 264 HIS I 291 GLN I 307 HIS B 11 GLN B 105 HIS B 134 GLN B 190 HIS B 280 GLN B 307 HIS ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 HIS H 204 ASN H 226 ASN H 247 ASN H 280 GLN H 307 HIS H 334 GLN ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 ASN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 HIS E 107 HIS E 186 ASN E 192 HIS ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 ASN E 283 HIS ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 18 ASN ** J 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 88 HIS J 107 HIS J 192 HIS J 206 ASN J 258 ASN J 309 HIS ** C 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN C 28 HIS C 88 HIS ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 HIS ** L 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 HIS L 107 HIS ** L 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 206 ASN L 258 ASN ** K 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 28 HIS K 88 HIS ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 206 ASN K 258 ASN K 283 HIS Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 41820 Z= 0.214 Angle : 0.588 8.827 56820 Z= 0.306 Chirality : 0.045 0.191 6216 Planarity : 0.005 0.044 7398 Dihedral : 11.959 179.223 5760 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.23 % Allowed : 2.37 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.22 (0.10), residues: 5130 helix: -2.24 (0.08), residues: 2232 sheet: -0.91 (0.18), residues: 756 loop : -2.34 (0.12), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 344 HIS 0.005 0.001 HIS A 192 PHE 0.015 0.001 PHE G 270 TYR 0.032 0.001 TYR J 185 ARG 0.006 0.001 ARG C 221 *********************** 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 1282 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1272 time to evaluate : 4.375 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: 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: F 26 ASP cc_start: 0.8944 (m-30) cc_final: 0.8715 (t70) REVERT: F 95 SER cc_start: 0.8946 (m) cc_final: 0.8574 (t) REVERT: F 101 TRP cc_start: 0.9229 (t60) cc_final: 0.8798 (t60) REVERT: F 163 ILE cc_start: 0.8983 (pt) cc_final: 0.8641 (pt) REVERT: F 187 LEU cc_start: 0.9548 (mp) cc_final: 0.9273 (mp) REVERT: F 205 GLU cc_start: 0.8932 (tp30) cc_final: 0.8704 (tp30) REVERT: F 264 HIS cc_start: 0.7912 (p-80) cc_final: 0.7012 (p-80) REVERT: F 268 PRO cc_start: 0.9557 (Cg_endo) cc_final: 0.9237 (Cg_exo) REVERT: F 324 LYS cc_start: 0.8262 (tttm) cc_final: 0.7941 (ttmm) REVERT: F 329 GLN cc_start: 0.8541 (mm-40) cc_final: 0.8193 (mt0) REVERT: F 330 MET cc_start: 0.8836 (tpp) cc_final: 0.8574 (tpt) REVERT: F 334 GLN cc_start: 0.8926 (tt0) cc_final: 0.8717 (tm-30) REVERT: F 340 TYR cc_start: 0.7791 (m-80) cc_final: 0.7539 (m-10) REVERT: F 367 PHE cc_start: 0.8628 (t80) cc_final: 0.8092 (t80) REVERT: F 406 MET cc_start: 0.6660 (tpt) cc_final: 0.6308 (mmm) REVERT: A 33 ASP cc_start: 0.8423 (m-30) cc_final: 0.7860 (p0) REVERT: A 69 ASP cc_start: 0.8003 (t0) cc_final: 0.7665 (t0) REVERT: A 90 GLU cc_start: 0.7861 (mm-30) cc_final: 0.6969 (tp30) REVERT: A 120 ASP cc_start: 0.8115 (t70) cc_final: 0.7717 (t0) REVERT: A 154 MET cc_start: 0.9108 (mmm) cc_final: 0.8631 (mmm) REVERT: A 157 LEU cc_start: 0.8815 (mt) cc_final: 0.8595 (mp) REVERT: A 188 ILE cc_start: 0.8377 (mm) cc_final: 0.8108 (mt) REVERT: A 254 GLU cc_start: 0.8491 (mt-10) cc_final: 0.7960 (mt-10) REVERT: A 291 ILE cc_start: 0.8397 (pt) cc_final: 0.8189 (pt) REVERT: A 368 LEU cc_start: 0.8980 (mp) cc_final: 0.8609 (pp) REVERT: A 377 MET cc_start: 0.8077 (tmm) cc_final: 0.7744 (tmm) REVERT: A 423 GLU cc_start: 0.8360 (tp30) cc_final: 0.8137 (tp30) REVERT: G 4 ILE cc_start: 0.9613 (mt) cc_final: 0.9355 (mm) REVERT: G 12 CYS cc_start: 0.6738 (t) cc_final: 0.6504 (t) REVERT: G 14 ASN cc_start: 0.8044 (m-40) cc_final: 0.7837 (m-40) REVERT: G 37 HIS cc_start: 0.8914 (m-70) cc_final: 0.8403 (m-70) REVERT: G 67 ASP cc_start: 0.8952 (t0) cc_final: 0.8396 (t70) REVERT: G 101 TRP cc_start: 0.9318 (t60) cc_final: 0.8837 (t60) REVERT: G 147 MET cc_start: 0.8933 (tpt) cc_final: 0.8642 (tpp) REVERT: G 213 ARG cc_start: 0.7350 (ptp-110) cc_final: 0.7143 (ptp90) REVERT: G 264 HIS cc_start: 0.7589 (p-80) cc_final: 0.7173 (p-80) REVERT: G 268 PRO cc_start: 0.9477 (Cg_endo) cc_final: 0.9269 (Cg_exo) REVERT: G 280 GLN cc_start: 0.7800 (mm-40) cc_final: 0.7258 (mm-40) REVERT: G 299 MET cc_start: 0.8815 (mmm) cc_final: 0.8543 (mmm) REVERT: G 300 MET cc_start: 0.7941 (mtt) cc_final: 0.7565 (mtm) REVERT: G 303 CYS cc_start: 0.7990 (p) cc_final: 0.7718 (p) REVERT: G 306 ARG cc_start: 0.8403 (mtt90) cc_final: 0.8173 (mpt180) REVERT: G 324 LYS cc_start: 0.8484 (tttm) cc_final: 0.8126 (ttmm) REVERT: G 388 MET cc_start: 0.8231 (mtp) cc_final: 0.7951 (mmp) REVERT: G 406 MET cc_start: 0.6772 (mmm) cc_final: 0.5982 (tpp) REVERT: D 14 ASN cc_start: 0.8252 (m-40) cc_final: 0.7665 (m-40) REVERT: D 65 LEU cc_start: 0.8880 (mp) cc_final: 0.8673 (mp) REVERT: D 101 TRP cc_start: 0.9170 (t60) cc_final: 0.8966 (t60) REVERT: D 133 PHE cc_start: 0.7968 (m-10) cc_final: 0.7705 (m-10) REVERT: D 187 LEU cc_start: 0.9500 (mp) cc_final: 0.8941 (tp) REVERT: D 222 TYR cc_start: 0.8102 (m-80) cc_final: 0.7364 (m-80) REVERT: D 264 HIS cc_start: 0.8024 (p-80) cc_final: 0.7120 (p-80) REVERT: D 297 LYS cc_start: 0.9419 (ptpp) cc_final: 0.9118 (ptmt) REVERT: D 310 TYR cc_start: 0.8833 (m-80) cc_final: 0.8494 (m-10) REVERT: D 321 MET cc_start: 0.7829 (pmm) cc_final: 0.7178 (pmm) REVERT: D 324 LYS cc_start: 0.8148 (tttm) cc_final: 0.7914 (ttmm) REVERT: D 367 PHE cc_start: 0.8543 (t80) cc_final: 0.8280 (t80) REVERT: D 403 MET cc_start: 0.7281 (ttp) cc_final: 0.5707 (ttp) REVERT: I 4 ILE cc_start: 0.9687 (mt) cc_final: 0.9391 (mm) REVERT: I 6 HIS cc_start: 0.7892 (t70) cc_final: 0.7616 (t-170) REVERT: I 65 LEU cc_start: 0.9326 (mp) cc_final: 0.9062 (mp) REVERT: I 101 TRP cc_start: 0.8971 (t60) cc_final: 0.8581 (t60) REVERT: I 264 HIS cc_start: 0.7427 (p90) cc_final: 0.7047 (p-80) REVERT: I 297 LYS cc_start: 0.9281 (ptpt) cc_final: 0.9027 (ptpp) REVERT: I 310 TYR cc_start: 0.8594 (m-80) cc_final: 0.8257 (m-10) REVERT: I 324 LYS cc_start: 0.8008 (tttm) cc_final: 0.7763 (ttmm) REVERT: I 388 MET cc_start: 0.8606 (mtp) cc_final: 0.8218 (mmt) REVERT: I 406 MET cc_start: 0.7489 (tpp) cc_final: 0.7284 (mmp) REVERT: I 409 THR cc_start: 0.9323 (m) cc_final: 0.8985 (p) REVERT: I 426 GLN cc_start: 0.7879 (tp40) cc_final: 0.7403 (tp40) REVERT: I 427 ASP cc_start: 0.7989 (m-30) cc_final: 0.7473 (m-30) REVERT: B 6 HIS cc_start: 0.8260 (t70) cc_final: 0.8010 (t70) REVERT: B 26 ASP cc_start: 0.9125 (m-30) cc_final: 0.8780 (t70) REVERT: B 101 TRP cc_start: 0.8765 (t60) cc_final: 0.8168 (t60) REVERT: B 139 LEU cc_start: 0.9020 (mt) cc_final: 0.8810 (mt) REVERT: B 187 LEU cc_start: 0.9575 (mt) cc_final: 0.9373 (mm) REVERT: B 198 GLU cc_start: 0.8640 (pm20) cc_final: 0.8134 (pm20) REVERT: B 256 ASN cc_start: 0.8234 (m-40) cc_final: 0.7536 (t0) REVERT: B 264 HIS cc_start: 0.8004 (p-80) cc_final: 0.7132 (p-80) REVERT: B 324 LYS cc_start: 0.8327 (tttm) cc_final: 0.8039 (ttmm) REVERT: B 334 GLN cc_start: 0.8914 (tt0) cc_final: 0.8519 (tm-30) REVERT: B 397 TRP cc_start: 0.8052 (m100) cc_final: 0.7840 (m-10) REVERT: H 4 ILE cc_start: 0.9591 (mt) cc_final: 0.9314 (mm) REVERT: H 37 HIS cc_start: 0.8852 (m-70) cc_final: 0.8463 (m-70) REVERT: H 112 LEU cc_start: 0.9504 (tp) cc_final: 0.9292 (tt) REVERT: H 203 ASP cc_start: 0.8281 (t0) cc_final: 0.8047 (t70) REVERT: H 204 ASN cc_start: 0.8743 (m110) cc_final: 0.8455 (t0) REVERT: H 245 GLN cc_start: 0.8166 (mt0) cc_final: 0.7771 (mm-40) REVERT: H 297 LYS cc_start: 0.9396 (ptpp) cc_final: 0.8911 (mtmm) REVERT: H 349 VAL cc_start: 0.9589 (t) cc_final: 0.9263 (t) REVERT: H 367 PHE cc_start: 0.8510 (t80) cc_final: 0.8229 (t80) REVERT: H 388 MET cc_start: 0.8370 (mtp) cc_final: 0.8029 (mmt) REVERT: E 27 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7793 (mm-30) REVERT: E 32 PRO cc_start: 0.9335 (Cg_exo) cc_final: 0.8971 (Cg_endo) REVERT: E 33 ASP cc_start: 0.8606 (m-30) cc_final: 0.8063 (p0) REVERT: E 85 GLN cc_start: 0.8354 (mm-40) cc_final: 0.7848 (mm-40) REVERT: E 90 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8252 (mt-10) REVERT: E 112 LYS cc_start: 0.8513 (mmtt) cc_final: 0.8279 (ttpt) REVERT: E 157 LEU cc_start: 0.8608 (mt) cc_final: 0.8381 (mt) REVERT: E 168 GLU cc_start: 0.7202 (mt-10) cc_final: 0.6929 (tt0) REVERT: E 170 SER cc_start: 0.9044 (m) cc_final: 0.8202 (p) REVERT: E 210 TYR cc_start: 0.8764 (m-80) cc_final: 0.8523 (m-10) REVERT: E 213 CYS cc_start: 0.8687 (m) cc_final: 0.8217 (p) REVERT: E 230 LEU cc_start: 0.9216 (mp) cc_final: 0.8954 (tt) REVERT: E 258 ASN cc_start: 0.8849 (m-40) cc_final: 0.8507 (m-40) REVERT: E 308 ARG cc_start: 0.8741 (mtm180) cc_final: 0.8467 (ptp90) REVERT: E 377 MET cc_start: 0.8228 (tmm) cc_final: 0.7755 (tmm) REVERT: E 407 TRP cc_start: 0.8960 (m100) cc_final: 0.8438 (m100) REVERT: E 413 MET cc_start: 0.8690 (tpp) cc_final: 0.7614 (tpp) REVERT: J 30 ILE cc_start: 0.9463 (mm) cc_final: 0.8960 (mm) REVERT: J 31 GLN cc_start: 0.8657 (mm-40) cc_final: 0.7241 (mt0) REVERT: J 33 ASP cc_start: 0.8515 (m-30) cc_final: 0.7847 (p0) REVERT: J 36 MET cc_start: 0.8268 (ppp) cc_final: 0.8015 (ppp) REVERT: J 69 ASP cc_start: 0.8041 (t0) cc_final: 0.7767 (t0) REVERT: J 90 GLU cc_start: 0.8518 (mm-30) cc_final: 0.7079 (tp30) REVERT: J 91 GLN cc_start: 0.8410 (mt0) cc_final: 0.7967 (mm110) REVERT: J 151 SER cc_start: 0.9407 (m) cc_final: 0.9021 (p) REVERT: J 172 TYR cc_start: 0.8253 (t80) cc_final: 0.7894 (t80) REVERT: J 221 ARG cc_start: 0.8861 (mtt90) cc_final: 0.8639 (mmm-85) REVERT: J 271 THR cc_start: 0.9313 (m) cc_final: 0.9060 (p) REVERT: J 295 CYS cc_start: 0.8252 (m) cc_final: 0.8040 (m) REVERT: J 315 CYS cc_start: 0.7945 (m) cc_final: 0.7726 (m) REVERT: J 368 LEU cc_start: 0.9220 (mp) cc_final: 0.8949 (pp) REVERT: J 407 TRP cc_start: 0.8980 (m100) cc_final: 0.8385 (m100) REVERT: J 413 MET cc_start: 0.8534 (tpp) cc_final: 0.6991 (tpp) REVERT: C 27 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7998 (mm-30) REVERT: C 33 ASP cc_start: 0.8761 (m-30) cc_final: 0.8178 (p0) REVERT: C 86 LEU cc_start: 0.8599 (tp) cc_final: 0.8255 (tt) REVERT: C 90 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7705 (tp30) REVERT: C 109 THR cc_start: 0.8785 (m) cc_final: 0.8396 (p) REVERT: C 154 MET cc_start: 0.9027 (mmm) cc_final: 0.8601 (mmt) REVERT: C 169 PHE cc_start: 0.8287 (m-10) cc_final: 0.7829 (m-10) REVERT: C 188 ILE cc_start: 0.8489 (mm) cc_final: 0.8163 (mt) REVERT: C 203 MET cc_start: 0.8320 (mmm) cc_final: 0.8113 (mmm) REVERT: C 210 TYR cc_start: 0.8562 (m-80) cc_final: 0.8270 (m-10) REVERT: C 214 ARG cc_start: 0.8576 (ttp80) cc_final: 0.8255 (ttp-110) REVERT: C 233 GLN cc_start: 0.8738 (mm-40) cc_final: 0.8342 (mm-40) REVERT: C 258 ASN cc_start: 0.8401 (m110) cc_final: 0.8147 (m-40) REVERT: C 271 THR cc_start: 0.9344 (m) cc_final: 0.9104 (p) REVERT: C 285 GLN cc_start: 0.8303 (pt0) cc_final: 0.7326 (mm110) REVERT: C 290 GLU cc_start: 0.7199 (tt0) cc_final: 0.6977 (tt0) REVERT: C 352 LYS cc_start: 0.8631 (tptp) cc_final: 0.8261 (tppt) REVERT: C 358 GLN cc_start: 0.8666 (tt0) cc_final: 0.8068 (tt0) REVERT: C 368 LEU cc_start: 0.8968 (mp) cc_final: 0.8617 (pp) REVERT: C 413 MET cc_start: 0.8508 (tpp) cc_final: 0.8174 (tpp) REVERT: L 33 ASP cc_start: 0.8674 (m-30) cc_final: 0.7981 (p0) REVERT: L 49 PHE cc_start: 0.7752 (p90) cc_final: 0.7261 (p90) REVERT: L 90 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7411 (tp30) REVERT: L 115 ILE cc_start: 0.8398 (tp) cc_final: 0.8146 (tp) REVERT: L 123 ARG cc_start: 0.8084 (ttp-110) cc_final: 0.7711 (ttm110) REVERT: L 154 MET cc_start: 0.8917 (mmm) cc_final: 0.8509 (mmt) REVERT: L 169 PHE cc_start: 0.7778 (m-10) cc_final: 0.7373 (m-10) REVERT: L 196 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7982 (tm-30) REVERT: L 213 CYS cc_start: 0.8619 (m) cc_final: 0.8254 (p) REVERT: L 230 LEU cc_start: 0.9091 (mp) cc_final: 0.8553 (tt) REVERT: L 271 THR cc_start: 0.9287 (m) cc_final: 0.9047 (p) REVERT: L 285 GLN cc_start: 0.8223 (pt0) cc_final: 0.7480 (mm-40) REVERT: L 290 GLU cc_start: 0.7233 (tt0) cc_final: 0.7000 (tt0) REVERT: L 356 ASN cc_start: 0.8532 (t0) cc_final: 0.8198 (m-40) REVERT: L 368 LEU cc_start: 0.9205 (mp) cc_final: 0.8842 (pp) REVERT: L 398 MET cc_start: 0.8077 (mtt) cc_final: 0.7485 (mtp) REVERT: L 407 TRP cc_start: 0.8996 (m100) cc_final: 0.8684 (m100) REVERT: L 420 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7978 (mm-30) REVERT: K 33 ASP cc_start: 0.8421 (m-30) cc_final: 0.7801 (p0) REVERT: K 69 ASP cc_start: 0.7928 (t0) cc_final: 0.7679 (t0) REVERT: K 90 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7688 (tp30) REVERT: K 154 MET cc_start: 0.9086 (mmm) cc_final: 0.8648 (mmm) REVERT: K 168 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7597 (tt0) REVERT: K 186 ASN cc_start: 0.8177 (m-40) cc_final: 0.7833 (m-40) REVERT: K 188 ILE cc_start: 0.8452 (mm) cc_final: 0.8176 (mt) REVERT: K 202 PHE cc_start: 0.8026 (m-80) cc_final: 0.7693 (m-10) REVERT: K 213 CYS cc_start: 0.8626 (m) cc_final: 0.8206 (p) REVERT: K 230 LEU cc_start: 0.9117 (mp) cc_final: 0.8691 (tt) REVERT: K 251 ASP cc_start: 0.8576 (t70) cc_final: 0.8371 (t70) REVERT: K 338 LYS cc_start: 0.9001 (mtpt) cc_final: 0.8676 (mtpp) REVERT: K 368 LEU cc_start: 0.9310 (mp) cc_final: 0.8960 (pp) REVERT: K 398 MET cc_start: 0.7891 (mtm) cc_final: 0.7158 (ttp) REVERT: K 413 MET cc_start: 0.8662 (tpp) cc_final: 0.8045 (tpp) outliers start: 10 outliers final: 2 residues processed: 1280 average time/residue: 0.5505 time to fit residues: 1166.1920 Evaluate side-chains 905 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 903 time to evaluate : 5.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 385 optimal weight: 20.0000 chunk 315 optimal weight: 10.0000 chunk 127 optimal weight: 20.0000 chunk 463 optimal weight: 2.9990 chunk 501 optimal weight: 7.9990 chunk 413 optimal weight: 8.9990 chunk 460 optimal weight: 8.9990 chunk 158 optimal weight: 20.0000 chunk 372 optimal weight: 5.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN A 258 ASN A 283 HIS A 356 ASN G 280 GLN D 11 GLN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 ASN ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 423 GLN I 292 GLN I 414 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 396 HIS ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 HIS ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 266 HIS ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 88 HIS J 186 ASN ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 293 ASN J 301 GLN J 356 ASN C 18 ASN ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 HIS C 356 ASN ** L 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 256 GLN ** L 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 266 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 41820 Z= 0.306 Angle : 0.616 8.879 56820 Z= 0.319 Chirality : 0.046 0.194 6216 Planarity : 0.005 0.053 7398 Dihedral : 11.669 179.967 5760 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.09 % Allowed : 3.73 % Favored : 96.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.31 (0.11), residues: 5130 helix: -1.17 (0.10), residues: 2196 sheet: -1.01 (0.18), residues: 768 loop : -2.01 (0.13), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 344 HIS 0.006 0.001 HIS F 105 PHE 0.018 0.002 PHE G 408 TYR 0.018 0.002 TYR I 222 ARG 0.005 0.001 ARG E 221 *********************** 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 1092 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1088 time to evaluate : 4.608 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 26 ASP cc_start: 0.9106 (m-30) cc_final: 0.8904 (t70) REVERT: F 86 ARG cc_start: 0.7947 (mtp180) cc_final: 0.7634 (tpp80) REVERT: F 205 GLU cc_start: 0.8874 (tp30) cc_final: 0.8527 (mm-30) REVERT: F 264 HIS cc_start: 0.7958 (p-80) cc_final: 0.7154 (p-80) REVERT: F 297 LYS cc_start: 0.9572 (ptpt) cc_final: 0.9243 (mtmt) REVERT: F 323 MET cc_start: 0.8777 (mmm) cc_final: 0.8560 (mmm) REVERT: F 324 LYS cc_start: 0.8571 (tttm) cc_final: 0.8252 (ttmm) REVERT: F 334 GLN cc_start: 0.9058 (tt0) cc_final: 0.8823 (tm-30) REVERT: F 340 TYR cc_start: 0.7976 (m-80) cc_final: 0.7650 (m-10) REVERT: F 350 LYS cc_start: 0.9111 (tptp) cc_final: 0.8615 (tppt) REVERT: F 367 PHE cc_start: 0.8588 (t80) cc_final: 0.8150 (t80) REVERT: A 69 ASP cc_start: 0.7919 (t0) cc_final: 0.7561 (t0) REVERT: A 120 ASP cc_start: 0.8173 (t70) cc_final: 0.7847 (t0) REVERT: A 154 MET cc_start: 0.9215 (mmm) cc_final: 0.8693 (mmm) REVERT: A 168 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7362 (tt0) REVERT: A 230 LEU cc_start: 0.9255 (mm) cc_final: 0.8964 (tt) REVERT: A 254 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8086 (mt-10) REVERT: A 368 LEU cc_start: 0.8990 (mp) cc_final: 0.8733 (pp) REVERT: A 407 TRP cc_start: 0.9131 (m100) cc_final: 0.8928 (m100) REVERT: A 415 GLU cc_start: 0.7735 (tp30) cc_final: 0.7279 (tp30) REVERT: G 4 ILE cc_start: 0.9653 (mt) cc_final: 0.9299 (mm) REVERT: G 67 ASP cc_start: 0.8803 (t0) cc_final: 0.8346 (t70) REVERT: G 147 MET cc_start: 0.9003 (tpt) cc_final: 0.8676 (tpp) REVERT: G 216 LYS cc_start: 0.9027 (mptt) cc_final: 0.8770 (mmtm) REVERT: G 264 HIS cc_start: 0.7608 (p-80) cc_final: 0.6608 (p-80) REVERT: G 268 PRO cc_start: 0.9553 (Cg_endo) cc_final: 0.9314 (Cg_exo) REVERT: G 282 ARG cc_start: 0.7568 (tpp80) cc_final: 0.7349 (tpp80) REVERT: G 300 MET cc_start: 0.8195 (mtt) cc_final: 0.7834 (mtm) REVERT: G 306 ARG cc_start: 0.8486 (mtt90) cc_final: 0.8173 (mmt180) REVERT: G 323 MET cc_start: 0.8664 (mmm) cc_final: 0.8365 (mmm) REVERT: G 324 LYS cc_start: 0.8751 (tttm) cc_final: 0.8484 (ttmm) REVERT: G 350 LYS cc_start: 0.9255 (tptp) cc_final: 0.8731 (tppt) REVERT: G 357 PRO cc_start: 0.8515 (Cg_endo) cc_final: 0.8228 (Cg_exo) REVERT: D 14 ASN cc_start: 0.8420 (m-40) cc_final: 0.7900 (m-40) REVERT: D 203 ASP cc_start: 0.8620 (t0) cc_final: 0.8359 (t0) REVERT: D 222 TYR cc_start: 0.8234 (m-80) cc_final: 0.7345 (m-80) REVERT: D 264 HIS cc_start: 0.8078 (p-80) cc_final: 0.7350 (p-80) REVERT: D 293 MET cc_start: 0.8638 (mtm) cc_final: 0.8238 (mtm) REVERT: D 297 LYS cc_start: 0.9437 (ptpp) cc_final: 0.9237 (mtpt) REVERT: D 321 MET cc_start: 0.8222 (pmm) cc_final: 0.7772 (pmm) REVERT: D 324 LYS cc_start: 0.8335 (tttm) cc_final: 0.8024 (ttmt) REVERT: D 336 LYS cc_start: 0.7898 (ptpt) cc_final: 0.7560 (ptpp) REVERT: D 348 ASN cc_start: 0.8657 (p0) cc_final: 0.8376 (p0) REVERT: I 4 ILE cc_start: 0.9668 (mt) cc_final: 0.9387 (mm) REVERT: I 6 HIS cc_start: 0.7983 (t70) cc_final: 0.7662 (t-170) REVERT: I 67 ASP cc_start: 0.8319 (t0) cc_final: 0.7776 (t70) REVERT: I 133 PHE cc_start: 0.8186 (m-10) cc_final: 0.7922 (m-80) REVERT: I 147 MET cc_start: 0.9120 (tpp) cc_final: 0.8871 (mmp) REVERT: I 264 HIS cc_start: 0.7853 (p90) cc_final: 0.7216 (p-80) REVERT: I 297 LYS cc_start: 0.9305 (ptpt) cc_final: 0.9055 (ptpp) REVERT: I 323 MET cc_start: 0.8566 (mmt) cc_final: 0.8252 (mmt) REVERT: I 324 LYS cc_start: 0.8221 (tttm) cc_final: 0.7909 (tttp) REVERT: I 355 ASP cc_start: 0.8766 (m-30) cc_final: 0.8504 (m-30) REVERT: I 388 MET cc_start: 0.8585 (mtp) cc_final: 0.8211 (mmt) REVERT: B 6 HIS cc_start: 0.8252 (t70) cc_final: 0.7934 (t70) REVERT: B 21 TRP cc_start: 0.8816 (m100) cc_final: 0.8459 (m100) REVERT: B 26 ASP cc_start: 0.9186 (m-30) cc_final: 0.8788 (t70) REVERT: B 101 TRP cc_start: 0.9047 (t60) cc_final: 0.8809 (t60) REVERT: B 164 MET cc_start: 0.8481 (mmm) cc_final: 0.8111 (tpp) REVERT: B 187 LEU cc_start: 0.9651 (mt) cc_final: 0.9430 (mm) REVERT: B 203 ASP cc_start: 0.8538 (t0) cc_final: 0.8219 (t0) REVERT: B 256 ASN cc_start: 0.8398 (m-40) cc_final: 0.7945 (m-40) REVERT: B 264 HIS cc_start: 0.8132 (p-80) cc_final: 0.7295 (p90) REVERT: B 324 LYS cc_start: 0.8479 (tttm) cc_final: 0.8263 (ttmt) REVERT: B 334 GLN cc_start: 0.8960 (tt0) cc_final: 0.8602 (tm-30) REVERT: H 4 ILE cc_start: 0.9619 (mt) cc_final: 0.9371 (mm) REVERT: H 178 THR cc_start: 0.8414 (m) cc_final: 0.7939 (p) REVERT: H 204 ASN cc_start: 0.8746 (m110) cc_final: 0.8509 (t0) REVERT: H 245 GLN cc_start: 0.8094 (mt0) cc_final: 0.7773 (tt0) REVERT: H 264 HIS cc_start: 0.7384 (p-80) cc_final: 0.6560 (p-80) REVERT: H 297 LYS cc_start: 0.9370 (ptpp) cc_final: 0.8842 (mtmm) REVERT: H 321 MET cc_start: 0.8630 (ptp) cc_final: 0.7742 (pmm) REVERT: H 350 LYS cc_start: 0.9177 (tppt) cc_final: 0.8876 (tppt) REVERT: H 356 ILE cc_start: 0.9204 (mm) cc_final: 0.8336 (tt) REVERT: H 367 PHE cc_start: 0.8634 (t80) cc_final: 0.8331 (t80) REVERT: H 388 MET cc_start: 0.8566 (mtp) cc_final: 0.8236 (mmt) REVERT: H 412 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8473 (tm-30) REVERT: E 27 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7856 (mm-30) REVERT: E 49 PHE cc_start: 0.8001 (p90) cc_final: 0.7615 (p90) REVERT: E 90 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8364 (tt0) REVERT: E 96 LYS cc_start: 0.8310 (mmmm) cc_final: 0.8068 (mmmt) REVERT: E 157 LEU cc_start: 0.8702 (mt) cc_final: 0.8470 (mt) REVERT: E 218 ASP cc_start: 0.7831 (m-30) cc_final: 0.7288 (t0) REVERT: E 254 GLU cc_start: 0.8408 (mt-10) cc_final: 0.7507 (mt-10) REVERT: E 308 ARG cc_start: 0.8838 (mtm180) cc_final: 0.8601 (ptp90) REVERT: E 315 CYS cc_start: 0.7973 (m) cc_final: 0.7748 (m) REVERT: E 407 TRP cc_start: 0.8958 (m100) cc_final: 0.8478 (m100) REVERT: E 413 MET cc_start: 0.8678 (tpp) cc_final: 0.8272 (tpp) REVERT: J 24 TYR cc_start: 0.8292 (m-80) cc_final: 0.7635 (m-80) REVERT: J 33 ASP cc_start: 0.8768 (m-30) cc_final: 0.8050 (p0) REVERT: J 90 GLU cc_start: 0.8516 (mm-30) cc_final: 0.7360 (tp30) REVERT: J 91 GLN cc_start: 0.8578 (mt0) cc_final: 0.8049 (mm110) REVERT: J 151 SER cc_start: 0.9470 (m) cc_final: 0.9189 (p) REVERT: J 168 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7258 (tt0) REVERT: J 172 TYR cc_start: 0.8324 (t80) cc_final: 0.7937 (t80) REVERT: J 230 LEU cc_start: 0.9384 (mp) cc_final: 0.8916 (tt) REVERT: J 271 THR cc_start: 0.9337 (m) cc_final: 0.9089 (p) REVERT: J 285 GLN cc_start: 0.8376 (pm20) cc_final: 0.8163 (pm20) REVERT: J 315 CYS cc_start: 0.7899 (m) cc_final: 0.7696 (m) REVERT: J 352 LYS cc_start: 0.8934 (tptt) cc_final: 0.8163 (tppt) REVERT: J 368 LEU cc_start: 0.9180 (mp) cc_final: 0.8859 (pp) REVERT: J 413 MET cc_start: 0.8587 (tpp) cc_final: 0.8020 (tpp) REVERT: C 33 ASP cc_start: 0.8757 (m-30) cc_final: 0.8109 (p0) REVERT: C 96 LYS cc_start: 0.8125 (mmtp) cc_final: 0.7384 (mmmm) REVERT: C 154 MET cc_start: 0.9148 (mmm) cc_final: 0.8800 (mmt) REVERT: C 168 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7223 (tt0) REVERT: C 169 PHE cc_start: 0.8190 (m-10) cc_final: 0.7895 (m-10) REVERT: C 203 MET cc_start: 0.8297 (mmm) cc_final: 0.8006 (mmm) REVERT: C 214 ARG cc_start: 0.8732 (ttp80) cc_final: 0.8206 (ttp80) REVERT: C 230 LEU cc_start: 0.9156 (mp) cc_final: 0.8813 (tt) REVERT: C 233 GLN cc_start: 0.8995 (mm-40) cc_final: 0.8459 (mm-40) REVERT: C 285 GLN cc_start: 0.8047 (pt0) cc_final: 0.7034 (mm-40) REVERT: C 290 GLU cc_start: 0.7234 (tt0) cc_final: 0.7021 (tt0) REVERT: C 352 LYS cc_start: 0.8821 (tptp) cc_final: 0.8602 (tppt) REVERT: C 368 LEU cc_start: 0.9062 (mp) cc_final: 0.8701 (pp) REVERT: C 398 MET cc_start: 0.8136 (mtt) cc_final: 0.7308 (ttm) REVERT: C 402 ARG cc_start: 0.8464 (mmm-85) cc_final: 0.8071 (mmm160) REVERT: C 413 MET cc_start: 0.8614 (tpp) cc_final: 0.8348 (tpp) REVERT: L 33 ASP cc_start: 0.8603 (m-30) cc_final: 0.7820 (p0) REVERT: L 36 MET cc_start: 0.8056 (ppp) cc_final: 0.7774 (ppp) REVERT: L 49 PHE cc_start: 0.7749 (p90) cc_final: 0.7320 (p90) REVERT: L 90 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7483 (tp30) REVERT: L 123 ARG cc_start: 0.8075 (ttp-110) cc_final: 0.7832 (ttm110) REVERT: L 154 MET cc_start: 0.9132 (mmm) cc_final: 0.8880 (mmt) REVERT: L 168 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7462 (tt0) REVERT: L 169 PHE cc_start: 0.7889 (m-10) cc_final: 0.7563 (m-10) REVERT: L 213 CYS cc_start: 0.8775 (m) cc_final: 0.8358 (p) REVERT: L 230 LEU cc_start: 0.9132 (mp) cc_final: 0.8512 (tt) REVERT: L 285 GLN cc_start: 0.8308 (pt0) cc_final: 0.7439 (mp10) REVERT: L 291 ILE cc_start: 0.8794 (pt) cc_final: 0.8544 (pt) REVERT: L 315 CYS cc_start: 0.7890 (m) cc_final: 0.7579 (m) REVERT: L 338 LYS cc_start: 0.8999 (mtpt) cc_final: 0.8764 (mtpp) REVERT: L 368 LEU cc_start: 0.9218 (mp) cc_final: 0.8848 (pp) REVERT: L 398 MET cc_start: 0.8096 (mtt) cc_final: 0.7506 (ttp) REVERT: L 407 TRP cc_start: 0.9015 (m100) cc_final: 0.8708 (m100) REVERT: K 31 GLN cc_start: 0.8699 (OUTLIER) cc_final: 0.8226 (mt0) REVERT: K 69 ASP cc_start: 0.7804 (t0) cc_final: 0.7512 (t0) REVERT: K 90 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7436 (tp30) REVERT: K 120 ASP cc_start: 0.8469 (t0) cc_final: 0.8210 (t0) REVERT: K 154 MET cc_start: 0.9196 (mmm) cc_final: 0.8805 (mmm) REVERT: K 168 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7780 (tt0) REVERT: K 200 CYS cc_start: 0.7495 (t) cc_final: 0.7173 (t) REVERT: K 202 PHE cc_start: 0.8226 (m-80) cc_final: 0.7911 (m-10) REVERT: K 213 CYS cc_start: 0.8715 (m) cc_final: 0.8212 (p) REVERT: K 230 LEU cc_start: 0.9068 (mp) cc_final: 0.8662 (tt) REVERT: K 302 MET cc_start: 0.8643 (mmm) cc_final: 0.8121 (mmm) REVERT: K 313 MET cc_start: 0.7184 (mtp) cc_final: 0.6864 (mtt) REVERT: K 338 LYS cc_start: 0.8997 (mtpt) cc_final: 0.8682 (mtpp) REVERT: K 368 LEU cc_start: 0.9363 (mp) cc_final: 0.8974 (pp) REVERT: K 380 ASN cc_start: 0.8960 (t0) cc_final: 0.8675 (t0) REVERT: K 398 MET cc_start: 0.7826 (mtm) cc_final: 0.7226 (ttp) REVERT: K 420 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8190 (mm-30) outliers start: 4 outliers final: 1 residues processed: 1092 average time/residue: 0.4895 time to fit residues: 886.4234 Evaluate side-chains 800 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 798 time to evaluate : 4.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 458 optimal weight: 20.0000 chunk 348 optimal weight: 7.9990 chunk 240 optimal weight: 7.9990 chunk 51 optimal weight: 20.0000 chunk 221 optimal weight: 20.0000 chunk 311 optimal weight: 7.9990 chunk 465 optimal weight: 6.9990 chunk 492 optimal weight: 4.9990 chunk 243 optimal weight: 9.9990 chunk 441 optimal weight: 0.9980 chunk 132 optimal weight: 7.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 423 GLN ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 ASN A 266 HIS A 293 ASN A 300 ASN A 301 GLN A 309 HIS ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 HIS ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 ASN ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 247 ASN I 423 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 ASN ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 ASN ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 356 ASN C 18 ASN ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 18 ASN ** L 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 266 HIS ** K 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 309 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.4763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 41820 Z= 0.255 Angle : 0.580 9.138 56820 Z= 0.298 Chirality : 0.046 0.187 6216 Planarity : 0.004 0.084 7398 Dihedral : 11.333 179.937 5760 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.07 % Allowed : 2.12 % Favored : 97.81 % 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: -1.71 (0.11), residues: 5130 helix: -0.51 (0.11), residues: 2142 sheet: -0.95 (0.19), residues: 756 loop : -1.75 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 21 HIS 0.005 0.001 HIS D 6 PHE 0.017 0.001 PHE D 367 TYR 0.019 0.002 TYR F 222 ARG 0.006 0.001 ARG B 282 *********************** 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 1067 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1064 time to evaluate : 4.773 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: F 26 ASP cc_start: 0.9176 (m-30) cc_final: 0.8892 (t70) REVERT: F 205 GLU cc_start: 0.8878 (tp30) cc_final: 0.8596 (mm-30) REVERT: F 321 MET cc_start: 0.8516 (ptp) cc_final: 0.8171 (pmm) REVERT: F 323 MET cc_start: 0.8796 (mmm) cc_final: 0.8519 (mmm) REVERT: F 324 LYS cc_start: 0.8486 (tttm) cc_final: 0.8263 (ttmm) REVERT: F 334 GLN cc_start: 0.8947 (tt0) cc_final: 0.8661 (tm-30) REVERT: F 340 TYR cc_start: 0.7933 (m-80) cc_final: 0.7649 (m-10) REVERT: F 350 LYS cc_start: 0.9068 (tptp) cc_final: 0.8604 (tppt) REVERT: F 367 PHE cc_start: 0.8624 (t80) cc_final: 0.8261 (t80) REVERT: A 69 ASP cc_start: 0.7888 (t0) cc_final: 0.7464 (t0) REVERT: A 90 GLU cc_start: 0.8425 (mm-30) cc_final: 0.7518 (tp30) REVERT: A 120 ASP cc_start: 0.8376 (t70) cc_final: 0.7990 (t0) REVERT: A 154 MET cc_start: 0.9198 (mmm) cc_final: 0.8671 (mmm) REVERT: A 168 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7461 (tt0) REVERT: A 203 MET cc_start: 0.8612 (mmm) cc_final: 0.8370 (mmm) REVERT: A 230 LEU cc_start: 0.9294 (mm) cc_final: 0.8992 (tt) REVERT: A 233 GLN cc_start: 0.8878 (mm-40) cc_final: 0.8300 (mm-40) REVERT: A 254 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7752 (tm-30) REVERT: A 258 ASN cc_start: 0.8172 (t0) cc_final: 0.7150 (t160) REVERT: A 291 ILE cc_start: 0.8619 (pt) cc_final: 0.8354 (pt) REVERT: A 368 LEU cc_start: 0.9034 (mp) cc_final: 0.8744 (pp) REVERT: A 398 MET cc_start: 0.7895 (mtp) cc_final: 0.7364 (ttp) REVERT: A 399 TYR cc_start: 0.7251 (t80) cc_final: 0.6965 (t80) REVERT: A 407 TRP cc_start: 0.9146 (m100) cc_final: 0.8901 (m100) REVERT: A 413 MET cc_start: 0.7840 (tpt) cc_final: 0.6232 (tpp) REVERT: G 4 ILE cc_start: 0.9626 (mt) cc_final: 0.9302 (mm) REVERT: G 67 ASP cc_start: 0.8662 (t0) cc_final: 0.8211 (t70) REVERT: G 147 MET cc_start: 0.9028 (tpt) cc_final: 0.8741 (tpp) REVERT: G 203 ASP cc_start: 0.8376 (t70) cc_final: 0.8165 (t0) REVERT: G 264 HIS cc_start: 0.7392 (p-80) cc_final: 0.6402 (p-80) REVERT: G 268 PRO cc_start: 0.9560 (Cg_endo) cc_final: 0.9275 (Cg_exo) REVERT: G 300 MET cc_start: 0.8197 (mtt) cc_final: 0.7831 (mtm) REVERT: G 323 MET cc_start: 0.8660 (mmm) cc_final: 0.8326 (mmm) REVERT: G 406 MET cc_start: 0.6994 (mmm) cc_final: 0.6442 (tpp) REVERT: D 3 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7785 (mt-10) REVERT: D 222 TYR cc_start: 0.8249 (m-80) cc_final: 0.7629 (m-80) REVERT: D 264 HIS cc_start: 0.7909 (p-80) cc_final: 0.7275 (p-80) REVERT: D 321 MET cc_start: 0.8335 (pmm) cc_final: 0.7809 (pmm) REVERT: D 324 LYS cc_start: 0.8321 (tttm) cc_final: 0.8118 (ttmm) REVERT: D 336 LYS cc_start: 0.7920 (ptpt) cc_final: 0.7623 (ptpp) REVERT: D 348 ASN cc_start: 0.8607 (p0) cc_final: 0.8284 (p0) REVERT: D 354 CYS cc_start: 0.8262 (t) cc_final: 0.7979 (t) REVERT: D 409 THR cc_start: 0.9158 (m) cc_final: 0.8727 (p) REVERT: I 4 ILE cc_start: 0.9646 (mt) cc_final: 0.9348 (mm) REVERT: I 6 HIS cc_start: 0.7896 (t70) cc_final: 0.7565 (t70) REVERT: I 133 PHE cc_start: 0.8075 (m-10) cc_final: 0.7769 (m-80) REVERT: I 147 MET cc_start: 0.9072 (tpp) cc_final: 0.8800 (mmp) REVERT: I 178 THR cc_start: 0.8559 (m) cc_final: 0.8316 (m) REVERT: I 264 HIS cc_start: 0.7878 (p90) cc_final: 0.7159 (p-80) REVERT: I 324 LYS cc_start: 0.8215 (tttm) cc_final: 0.7962 (ttmm) REVERT: I 355 ASP cc_start: 0.8829 (m-30) cc_final: 0.8454 (m-30) REVERT: I 388 MET cc_start: 0.8609 (mtp) cc_final: 0.8255 (mmt) REVERT: B 26 ASP cc_start: 0.9208 (m-30) cc_final: 0.8806 (t70) REVERT: B 101 TRP cc_start: 0.9163 (t60) cc_final: 0.8959 (t60) REVERT: B 198 GLU cc_start: 0.8802 (pm20) cc_final: 0.8200 (pm20) REVERT: B 256 ASN cc_start: 0.8490 (m-40) cc_final: 0.8247 (m-40) REVERT: B 264 HIS cc_start: 0.7957 (p-80) cc_final: 0.7321 (p90) REVERT: B 297 LYS cc_start: 0.9229 (ptmt) cc_final: 0.8700 (ttmm) REVERT: B 324 LYS cc_start: 0.8580 (tttm) cc_final: 0.8316 (ttmt) REVERT: B 334 GLN cc_start: 0.8977 (tt0) cc_final: 0.8555 (tm-30) REVERT: B 347 ASN cc_start: 0.5776 (m-40) cc_final: 0.5563 (m-40) REVERT: H 57 ASN cc_start: 0.9191 (m110) cc_final: 0.8822 (m110) REVERT: H 196 THR cc_start: 0.8331 (p) cc_final: 0.8095 (p) REVERT: H 245 GLN cc_start: 0.8031 (mt0) cc_final: 0.7688 (mm-40) REVERT: H 264 HIS cc_start: 0.7280 (p-80) cc_final: 0.6847 (p90) REVERT: H 297 LYS cc_start: 0.9386 (ptpp) cc_final: 0.8879 (mtmm) REVERT: H 321 MET cc_start: 0.8637 (ptp) cc_final: 0.7894 (pmm) REVERT: H 356 ILE cc_start: 0.9232 (mm) cc_final: 0.8711 (tt) REVERT: H 367 PHE cc_start: 0.8641 (t80) cc_final: 0.8399 (t80) REVERT: H 388 MET cc_start: 0.8450 (mtp) cc_final: 0.7982 (mmp) REVERT: H 412 GLU cc_start: 0.8701 (tm-30) cc_final: 0.8438 (tm-30) REVERT: E 27 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7994 (mm-30) REVERT: E 49 PHE cc_start: 0.7953 (p90) cc_final: 0.7623 (p90) REVERT: E 96 LYS cc_start: 0.8247 (mmmm) cc_final: 0.7915 (mmmm) REVERT: E 205 ASP cc_start: 0.8152 (t0) cc_final: 0.7801 (t0) REVERT: E 218 ASP cc_start: 0.7911 (m-30) cc_final: 0.7437 (t0) REVERT: E 230 LEU cc_start: 0.9218 (mm) cc_final: 0.8785 (tt) REVERT: E 233 GLN cc_start: 0.9080 (mm-40) cc_final: 0.8407 (mm-40) REVERT: E 251 ASP cc_start: 0.8343 (t0) cc_final: 0.8083 (t0) REVERT: E 254 GLU cc_start: 0.8509 (mt-10) cc_final: 0.7355 (mt-10) REVERT: E 258 ASN cc_start: 0.8862 (m-40) cc_final: 0.8395 (m110) REVERT: E 308 ARG cc_start: 0.8827 (mtm180) cc_final: 0.8468 (ptp90) REVERT: E 352 LYS cc_start: 0.8835 (tptp) cc_final: 0.8054 (tppt) REVERT: E 407 TRP cc_start: 0.8946 (m100) cc_final: 0.8348 (m100) REVERT: J 24 TYR cc_start: 0.8278 (m-80) cc_final: 0.7675 (m-80) REVERT: J 31 GLN cc_start: 0.8872 (mm-40) cc_final: 0.7798 (mt0) REVERT: J 90 GLU cc_start: 0.8408 (mm-30) cc_final: 0.7486 (tp30) REVERT: J 91 GLN cc_start: 0.8470 (mt0) cc_final: 0.8083 (mm110) REVERT: J 151 SER cc_start: 0.9452 (m) cc_final: 0.9164 (p) REVERT: J 172 TYR cc_start: 0.8330 (t80) cc_final: 0.7988 (t80) REVERT: J 192 HIS cc_start: 0.8129 (t-90) cc_final: 0.7245 (t70) REVERT: J 233 GLN cc_start: 0.8954 (mm-40) cc_final: 0.8319 (mm-40) REVERT: J 305 CYS cc_start: 0.8631 (m) cc_final: 0.8198 (m) REVERT: J 352 LYS cc_start: 0.8954 (tptt) cc_final: 0.8188 (tppt) REVERT: J 368 LEU cc_start: 0.9159 (mp) cc_final: 0.8842 (pp) REVERT: J 423 GLU cc_start: 0.8055 (pp20) cc_final: 0.7783 (pp20) REVERT: C 96 LYS cc_start: 0.8168 (mmtp) cc_final: 0.7421 (mmmm) REVERT: C 154 MET cc_start: 0.9221 (mmm) cc_final: 0.8985 (mmt) REVERT: C 168 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7244 (tt0) REVERT: C 169 PHE cc_start: 0.8053 (m-10) cc_final: 0.7732 (m-10) REVERT: C 203 MET cc_start: 0.8484 (mmm) cc_final: 0.8196 (mmm) REVERT: C 214 ARG cc_start: 0.8756 (ttp80) cc_final: 0.8227 (ttp80) REVERT: C 221 ARG cc_start: 0.8917 (mtt-85) cc_final: 0.8704 (mtt-85) REVERT: C 230 LEU cc_start: 0.9104 (mp) cc_final: 0.8740 (tt) REVERT: C 233 GLN cc_start: 0.9005 (mm-40) cc_final: 0.8528 (mm-40) REVERT: C 241 SER cc_start: 0.8311 (p) cc_final: 0.7393 (t) REVERT: C 285 GLN cc_start: 0.8133 (pt0) cc_final: 0.7141 (mm-40) REVERT: C 290 GLU cc_start: 0.7039 (tt0) cc_final: 0.6822 (tt0) REVERT: C 291 ILE cc_start: 0.8766 (pt) cc_final: 0.8410 (pt) REVERT: C 352 LYS cc_start: 0.8757 (tptp) cc_final: 0.8308 (tppt) REVERT: C 368 LEU cc_start: 0.9004 (mp) cc_final: 0.8635 (pp) REVERT: C 398 MET cc_start: 0.8259 (mtt) cc_final: 0.7504 (ttm) REVERT: L 31 GLN cc_start: 0.8822 (mm-40) cc_final: 0.8173 (mt0) REVERT: L 123 ARG cc_start: 0.8139 (ttp-110) cc_final: 0.7833 (ttm110) REVERT: L 154 MET cc_start: 0.9130 (mmm) cc_final: 0.8822 (mmt) REVERT: L 169 PHE cc_start: 0.7876 (m-10) cc_final: 0.7541 (m-10) REVERT: L 203 MET cc_start: 0.8881 (mmm) cc_final: 0.8653 (mmm) REVERT: L 213 CYS cc_start: 0.8802 (m) cc_final: 0.8350 (p) REVERT: L 233 GLN cc_start: 0.9081 (mm-40) cc_final: 0.8390 (mm-40) REVERT: L 285 GLN cc_start: 0.8276 (pt0) cc_final: 0.7439 (mp10) REVERT: L 291 ILE cc_start: 0.8842 (pt) cc_final: 0.8638 (pt) REVERT: L 315 CYS cc_start: 0.7805 (m) cc_final: 0.7496 (m) REVERT: L 368 LEU cc_start: 0.9170 (mp) cc_final: 0.8710 (pp) REVERT: L 372 GLN cc_start: 0.8419 (tp-100) cc_final: 0.8020 (tt0) REVERT: L 398 MET cc_start: 0.8222 (mtt) cc_final: 0.7709 (ttp) REVERT: K 3 GLU cc_start: 0.6931 (mp0) cc_final: 0.6558 (pm20) REVERT: K 31 GLN cc_start: 0.8734 (mm110) cc_final: 0.8446 (mt0) REVERT: K 69 ASP cc_start: 0.7845 (t0) cc_final: 0.7541 (t0) REVERT: K 90 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7502 (tp30) REVERT: K 96 LYS cc_start: 0.8603 (tptm) cc_final: 0.8373 (tptm) REVERT: K 120 ASP cc_start: 0.8393 (t0) cc_final: 0.8181 (t0) REVERT: K 154 MET cc_start: 0.9208 (mmm) cc_final: 0.8887 (mmm) REVERT: K 168 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7464 (tt0) REVERT: K 202 PHE cc_start: 0.8312 (m-80) cc_final: 0.7948 (m-10) REVERT: K 213 CYS cc_start: 0.8638 (m) cc_final: 0.8146 (p) REVERT: K 230 LEU cc_start: 0.9104 (mp) cc_final: 0.8735 (tt) REVERT: K 233 GLN cc_start: 0.9031 (mm-40) cc_final: 0.8389 (mm-40) REVERT: K 301 GLN cc_start: 0.9321 (mm-40) cc_final: 0.8694 (mm-40) REVERT: K 338 LYS cc_start: 0.8986 (mtpt) cc_final: 0.8664 (mtpp) REVERT: K 368 LEU cc_start: 0.9377 (mp) cc_final: 0.8957 (pp) outliers start: 3 outliers final: 0 residues processed: 1067 average time/residue: 0.5043 time to fit residues: 890.5389 Evaluate side-chains 787 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 787 time to evaluate : 4.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 410 optimal weight: 6.9990 chunk 279 optimal weight: 6.9990 chunk 7 optimal weight: 0.1980 chunk 367 optimal weight: 5.9990 chunk 203 optimal weight: 9.9990 chunk 420 optimal weight: 8.9990 chunk 340 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 251 optimal weight: 20.0000 chunk 442 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 overall best weight: 5.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 HIS I 247 ASN I 414 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN B 247 ASN ** B 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 GLN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 423 GLN ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 HIS ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 186 ASN ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 356 ASN C 18 ASN ** C 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 85 GLN ** L 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.5070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 41820 Z= 0.256 Angle : 0.580 8.358 56820 Z= 0.295 Chirality : 0.045 0.211 6216 Planarity : 0.004 0.082 7398 Dihedral : 11.174 178.548 5760 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.07 % Allowed : 1.98 % Favored : 97.95 % 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: -1.44 (0.12), residues: 5130 helix: -0.18 (0.11), residues: 2142 sheet: -0.98 (0.19), residues: 762 loop : -1.65 (0.13), residues: 2226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 21 HIS 0.010 0.001 HIS J 192 PHE 0.017 0.001 PHE G 408 TYR 0.035 0.001 TYR K 185 ARG 0.010 0.001 ARG F 213 *********************** 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 1028 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1025 time to evaluate : 4.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: F 25 SER cc_start: 0.9176 (t) cc_final: 0.8553 (p) REVERT: F 26 ASP cc_start: 0.9210 (m-30) cc_final: 0.8945 (t70) REVERT: F 164 MET cc_start: 0.8293 (tpp) cc_final: 0.8023 (mmm) REVERT: F 205 GLU cc_start: 0.8872 (tp30) cc_final: 0.8628 (tp30) REVERT: F 213 ARG cc_start: 0.7750 (ttp-110) cc_final: 0.7271 (ttm110) REVERT: F 264 HIS cc_start: 0.7660 (p-80) cc_final: 0.7082 (p-80) REVERT: F 297 LYS cc_start: 0.9538 (mtpt) cc_final: 0.9218 (ttmm) REVERT: F 321 MET cc_start: 0.8547 (ptp) cc_final: 0.8215 (pmm) REVERT: F 323 MET cc_start: 0.8858 (mmm) cc_final: 0.8529 (mmm) REVERT: F 334 GLN cc_start: 0.8962 (tt0) cc_final: 0.8668 (tm-30) REVERT: F 340 TYR cc_start: 0.7909 (m-80) cc_final: 0.7666 (m-10) REVERT: F 350 LYS cc_start: 0.9041 (tptp) cc_final: 0.8627 (tppt) REVERT: A 24 TYR cc_start: 0.8332 (m-80) cc_final: 0.8092 (m-80) REVERT: A 69 ASP cc_start: 0.7951 (t0) cc_final: 0.7451 (t0) REVERT: A 90 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7622 (tp30) REVERT: A 120 ASP cc_start: 0.8392 (t70) cc_final: 0.7944 (t0) REVERT: A 154 MET cc_start: 0.9179 (mmm) cc_final: 0.8720 (mmm) REVERT: A 203 MET cc_start: 0.8665 (mmm) cc_final: 0.8395 (mmm) REVERT: A 233 GLN cc_start: 0.8872 (mm-40) cc_final: 0.8297 (mm-40) REVERT: A 254 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7815 (tm-30) REVERT: A 301 GLN cc_start: 0.9269 (mm-40) cc_final: 0.8634 (mm110) REVERT: A 302 MET cc_start: 0.8130 (mtt) cc_final: 0.7905 (mtt) REVERT: A 368 LEU cc_start: 0.9058 (mp) cc_final: 0.8723 (pp) REVERT: A 398 MET cc_start: 0.7952 (mtp) cc_final: 0.7390 (ttp) REVERT: A 407 TRP cc_start: 0.9103 (m100) cc_final: 0.8838 (m100) REVERT: A 425 MET cc_start: 0.8007 (tpp) cc_final: 0.7693 (tpp) REVERT: G 4 ILE cc_start: 0.9608 (mt) cc_final: 0.9301 (mm) REVERT: G 25 SER cc_start: 0.8531 (t) cc_final: 0.8040 (p) REVERT: G 67 ASP cc_start: 0.8819 (t0) cc_final: 0.8327 (t70) REVERT: G 147 MET cc_start: 0.9049 (tpt) cc_final: 0.8787 (tpp) REVERT: G 216 LYS cc_start: 0.9008 (mptt) cc_final: 0.8687 (mmtm) REVERT: G 264 HIS cc_start: 0.7373 (p-80) cc_final: 0.6440 (p-80) REVERT: G 268 PRO cc_start: 0.9530 (Cg_endo) cc_final: 0.9322 (Cg_exo) REVERT: G 300 MET cc_start: 0.8233 (mtt) cc_final: 0.7833 (mtm) REVERT: G 321 MET cc_start: 0.8239 (pmm) cc_final: 0.7836 (pmm) REVERT: G 323 MET cc_start: 0.8699 (mmm) cc_final: 0.8347 (mmm) REVERT: D 3 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7897 (mt-10) REVERT: D 222 TYR cc_start: 0.8194 (m-80) cc_final: 0.7712 (m-80) REVERT: D 264 HIS cc_start: 0.7873 (p-80) cc_final: 0.7215 (p-80) REVERT: D 321 MET cc_start: 0.8385 (pmm) cc_final: 0.7806 (pmm) REVERT: D 324 LYS cc_start: 0.8431 (tttm) cc_final: 0.8151 (ttmm) REVERT: D 336 LYS cc_start: 0.7931 (ptpt) cc_final: 0.7685 (ptpp) REVERT: D 354 CYS cc_start: 0.8230 (t) cc_final: 0.7952 (t) REVERT: D 403 MET cc_start: 0.8273 (ptm) cc_final: 0.6936 (ptp) REVERT: D 409 THR cc_start: 0.9179 (m) cc_final: 0.8766 (p) REVERT: I 4 ILE cc_start: 0.9657 (mt) cc_final: 0.9359 (mm) REVERT: I 6 HIS cc_start: 0.7843 (t70) cc_final: 0.7498 (t70) REVERT: I 67 ASP cc_start: 0.8609 (t0) cc_final: 0.8172 (t70) REVERT: I 133 PHE cc_start: 0.8073 (m-10) cc_final: 0.7836 (m-80) REVERT: I 147 MET cc_start: 0.9066 (tpp) cc_final: 0.8845 (mmp) REVERT: I 247 ASN cc_start: 0.9125 (OUTLIER) cc_final: 0.8629 (m110) REVERT: I 264 HIS cc_start: 0.7888 (p90) cc_final: 0.7097 (p-80) REVERT: I 293 MET cc_start: 0.8507 (ptp) cc_final: 0.7736 (mtm) REVERT: I 297 LYS cc_start: 0.9431 (ptpt) cc_final: 0.9189 (mtmt) REVERT: I 355 ASP cc_start: 0.8720 (m-30) cc_final: 0.8341 (m-30) REVERT: I 388 MET cc_start: 0.8568 (mtp) cc_final: 0.8312 (mmt) REVERT: I 426 GLN cc_start: 0.8200 (tp40) cc_final: 0.7974 (tp40) REVERT: I 427 ASP cc_start: 0.8223 (m-30) cc_final: 0.7905 (m-30) REVERT: B 26 ASP cc_start: 0.9235 (m-30) cc_final: 0.8863 (t70) REVERT: B 203 ASP cc_start: 0.8627 (t0) cc_final: 0.8310 (t0) REVERT: B 264 HIS cc_start: 0.7836 (p-80) cc_final: 0.7354 (p90) REVERT: B 334 GLN cc_start: 0.9012 (tt0) cc_final: 0.8612 (tm-30) REVERT: B 340 TYR cc_start: 0.8064 (m-80) cc_final: 0.7863 (m-10) REVERT: B 406 MET cc_start: 0.7215 (mmp) cc_final: 0.6812 (tpp) REVERT: H 37 HIS cc_start: 0.8804 (m-70) cc_final: 0.8229 (m-70) REVERT: H 57 ASN cc_start: 0.9116 (m110) cc_final: 0.8770 (m110) REVERT: H 108 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7484 (mm-30) REVERT: H 196 THR cc_start: 0.8396 (p) cc_final: 0.8111 (p) REVERT: H 203 ASP cc_start: 0.8412 (t0) cc_final: 0.8134 (t0) REVERT: H 245 GLN cc_start: 0.8037 (mt0) cc_final: 0.7698 (mm-40) REVERT: H 264 HIS cc_start: 0.7332 (p-80) cc_final: 0.6902 (p90) REVERT: H 297 LYS cc_start: 0.9375 (ptpp) cc_final: 0.8840 (mtmm) REVERT: H 324 LYS cc_start: 0.8840 (tttm) cc_final: 0.8611 (ttmt) REVERT: H 329 GLN cc_start: 0.9037 (mm-40) cc_final: 0.8698 (mm-40) REVERT: H 356 ILE cc_start: 0.9262 (mm) cc_final: 0.8721 (tt) REVERT: H 359 ARG cc_start: 0.8250 (tpp80) cc_final: 0.7700 (mtt180) REVERT: H 367 PHE cc_start: 0.8551 (t80) cc_final: 0.8263 (t80) REVERT: H 412 GLU cc_start: 0.8708 (tm-30) cc_final: 0.8466 (tm-30) REVERT: E 49 PHE cc_start: 0.7975 (p90) cc_final: 0.7670 (p90) REVERT: E 96 LYS cc_start: 0.8281 (mmmm) cc_final: 0.7880 (mmmm) REVERT: E 205 ASP cc_start: 0.8242 (t0) cc_final: 0.7899 (t0) REVERT: E 218 ASP cc_start: 0.7970 (m-30) cc_final: 0.7512 (t0) REVERT: E 254 GLU cc_start: 0.8544 (mt-10) cc_final: 0.7148 (mt-10) REVERT: E 308 ARG cc_start: 0.8908 (mtm180) cc_final: 0.8561 (ptp90) REVERT: E 352 LYS cc_start: 0.8873 (tptp) cc_final: 0.8408 (tptt) REVERT: E 407 TRP cc_start: 0.8777 (m100) cc_final: 0.8187 (m100) REVERT: J 24 TYR cc_start: 0.8261 (m-80) cc_final: 0.7719 (m-80) REVERT: J 90 GLU cc_start: 0.8442 (mm-30) cc_final: 0.7498 (tp30) REVERT: J 91 GLN cc_start: 0.8630 (mt0) cc_final: 0.8357 (mm110) REVERT: J 151 SER cc_start: 0.9377 (m) cc_final: 0.9155 (p) REVERT: J 172 TYR cc_start: 0.8476 (t80) cc_final: 0.8143 (t80) REVERT: J 213 CYS cc_start: 0.8807 (m) cc_final: 0.8508 (p) REVERT: J 315 CYS cc_start: 0.8056 (m) cc_final: 0.7667 (m) REVERT: J 352 LYS cc_start: 0.8914 (tptt) cc_final: 0.8183 (tppt) REVERT: J 368 LEU cc_start: 0.9181 (mp) cc_final: 0.8837 (pp) REVERT: C 96 LYS cc_start: 0.8079 (mmtp) cc_final: 0.7400 (mmmm) REVERT: C 154 MET cc_start: 0.9269 (mmm) cc_final: 0.9041 (mmt) REVERT: C 168 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7371 (tt0) REVERT: C 169 PHE cc_start: 0.8007 (m-10) cc_final: 0.7754 (m-10) REVERT: C 203 MET cc_start: 0.8450 (mmm) cc_final: 0.8138 (mmm) REVERT: C 214 ARG cc_start: 0.8763 (ttp80) cc_final: 0.8205 (ttp80) REVERT: C 230 LEU cc_start: 0.9137 (mp) cc_final: 0.8719 (tt) REVERT: C 233 GLN cc_start: 0.8981 (mm-40) cc_final: 0.8494 (mm-40) REVERT: C 241 SER cc_start: 0.8303 (p) cc_final: 0.7459 (t) REVERT: C 285 GLN cc_start: 0.8200 (pt0) cc_final: 0.7164 (mm-40) REVERT: C 291 ILE cc_start: 0.8772 (pt) cc_final: 0.8460 (pt) REVERT: C 368 LEU cc_start: 0.8990 (mp) cc_final: 0.8642 (pp) REVERT: C 398 MET cc_start: 0.8282 (mtt) cc_final: 0.7520 (ttm) REVERT: C 402 ARG cc_start: 0.8427 (mmm-85) cc_final: 0.8056 (mmm160) REVERT: L 31 GLN cc_start: 0.8847 (mm-40) cc_final: 0.8309 (mt0) REVERT: L 123 ARG cc_start: 0.8168 (ttp-110) cc_final: 0.7889 (ttm110) REVERT: L 154 MET cc_start: 0.9114 (mmm) cc_final: 0.8830 (mmt) REVERT: L 170 SER cc_start: 0.8831 (m) cc_final: 0.8280 (t) REVERT: L 213 CYS cc_start: 0.8829 (m) cc_final: 0.8375 (p) REVERT: L 233 GLN cc_start: 0.9054 (mm-40) cc_final: 0.8435 (mm-40) REVERT: L 285 GLN cc_start: 0.8234 (pt0) cc_final: 0.7347 (mp10) REVERT: L 315 CYS cc_start: 0.7814 (m) cc_final: 0.7496 (m) REVERT: L 368 LEU cc_start: 0.9167 (mp) cc_final: 0.8698 (pp) REVERT: L 372 GLN cc_start: 0.8458 (tp-100) cc_final: 0.8028 (tt0) REVERT: K 31 GLN cc_start: 0.8893 (mm110) cc_final: 0.8571 (mt0) REVERT: K 36 MET cc_start: 0.8353 (ppp) cc_final: 0.8141 (ppp) REVERT: K 69 ASP cc_start: 0.7903 (t0) cc_final: 0.7553 (t0) REVERT: K 90 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7479 (tp30) REVERT: K 120 ASP cc_start: 0.8520 (t0) cc_final: 0.8151 (t0) REVERT: K 154 MET cc_start: 0.9220 (mmm) cc_final: 0.8989 (mmm) REVERT: K 168 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7350 (tt0) REVERT: K 202 PHE cc_start: 0.8279 (m-80) cc_final: 0.8017 (m-10) REVERT: K 230 LEU cc_start: 0.9149 (mp) cc_final: 0.8783 (tt) REVERT: K 233 GLN cc_start: 0.9028 (mm-40) cc_final: 0.8408 (mm-40) REVERT: K 338 LYS cc_start: 0.8958 (mtpt) cc_final: 0.8739 (mtpp) REVERT: K 368 LEU cc_start: 0.9374 (mp) cc_final: 0.8948 (pp) outliers start: 3 outliers final: 0 residues processed: 1028 average time/residue: 0.5024 time to fit residues: 864.6756 Evaluate side-chains 766 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 765 time to evaluate : 4.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 165 optimal weight: 2.9990 chunk 443 optimal weight: 20.0000 chunk 97 optimal weight: 0.6980 chunk 289 optimal weight: 4.9990 chunk 121 optimal weight: 20.0000 chunk 493 optimal weight: 6.9990 chunk 409 optimal weight: 5.9990 chunk 228 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 163 optimal weight: 10.0000 chunk 259 optimal weight: 8.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 ASN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 ASN ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN B 191 GLN B 247 ASN B 256 ASN B 329 GLN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 247 ASN ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 ASN E 192 HIS ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 ASN ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 186 ASN ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 356 ASN C 18 ASN ** L 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 18 ASN L 28 HIS ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.5292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 41820 Z= 0.181 Angle : 0.543 9.455 56820 Z= 0.273 Chirality : 0.044 0.227 6216 Planarity : 0.004 0.077 7398 Dihedral : 10.896 176.666 5760 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.09 % Allowed : 1.43 % Favored : 98.47 % 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: -1.25 (0.12), residues: 5130 helix: -0.04 (0.11), residues: 2202 sheet: -0.77 (0.19), residues: 756 loop : -1.60 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 21 HIS 0.006 0.001 HIS J 192 PHE 0.016 0.001 PHE D 367 TYR 0.022 0.001 TYR K 185 ARG 0.007 0.000 ARG E 123 *********************** 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 1060 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1056 time to evaluate : 5.143 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 25 SER cc_start: 0.9125 (t) cc_final: 0.8572 (p) REVERT: F 26 ASP cc_start: 0.9132 (m-30) cc_final: 0.8857 (t70) REVERT: F 67 ASP cc_start: 0.8446 (t0) cc_final: 0.8221 (t70) REVERT: F 203 ASP cc_start: 0.8108 (t0) cc_final: 0.7823 (t70) REVERT: F 205 GLU cc_start: 0.8869 (tp30) cc_final: 0.8652 (tp30) REVERT: F 264 HIS cc_start: 0.7530 (p-80) cc_final: 0.6950 (p-80) REVERT: F 323 MET cc_start: 0.8864 (mmm) cc_final: 0.8590 (mmm) REVERT: F 334 GLN cc_start: 0.8951 (tt0) cc_final: 0.8609 (tm-30) REVERT: F 340 TYR cc_start: 0.7956 (m-80) cc_final: 0.7109 (m-80) REVERT: F 350 LYS cc_start: 0.9017 (tptp) cc_final: 0.8547 (tppt) REVERT: A 3 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7332 (mm-30) REVERT: A 24 TYR cc_start: 0.8339 (m-80) cc_final: 0.8073 (m-80) REVERT: A 69 ASP cc_start: 0.7751 (t0) cc_final: 0.7313 (t0) REVERT: A 90 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7539 (tp30) REVERT: A 120 ASP cc_start: 0.8346 (t70) cc_final: 0.7894 (t0) REVERT: A 154 MET cc_start: 0.9184 (mmm) cc_final: 0.8720 (mmm) REVERT: A 168 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7527 (tt0) REVERT: A 203 MET cc_start: 0.8677 (mmm) cc_final: 0.8429 (mmm) REVERT: A 233 GLN cc_start: 0.8866 (mm-40) cc_final: 0.8287 (mm-40) REVERT: A 291 ILE cc_start: 0.8683 (pt) cc_final: 0.8408 (pt) REVERT: A 368 LEU cc_start: 0.9106 (mp) cc_final: 0.8801 (pp) REVERT: A 398 MET cc_start: 0.7918 (mtp) cc_final: 0.7413 (ttp) REVERT: A 407 TRP cc_start: 0.9035 (m100) cc_final: 0.8729 (m100) REVERT: G 4 ILE cc_start: 0.9623 (mt) cc_final: 0.9302 (mm) REVERT: G 25 SER cc_start: 0.8453 (t) cc_final: 0.7974 (p) REVERT: G 67 ASP cc_start: 0.8814 (t0) cc_final: 0.8321 (t70) REVERT: G 147 MET cc_start: 0.8995 (tpt) cc_final: 0.8748 (tpp) REVERT: G 203 ASP cc_start: 0.8632 (t70) cc_final: 0.8189 (t70) REVERT: G 264 HIS cc_start: 0.7183 (p-80) cc_final: 0.6226 (p-80) REVERT: G 268 PRO cc_start: 0.9531 (Cg_endo) cc_final: 0.9299 (Cg_exo) REVERT: G 300 MET cc_start: 0.8213 (mtt) cc_final: 0.7967 (mtm) REVERT: G 321 MET cc_start: 0.8215 (pmm) cc_final: 0.7502 (pmm) REVERT: G 323 MET cc_start: 0.8633 (mmm) cc_final: 0.8244 (mmm) REVERT: G 350 LYS cc_start: 0.9163 (tptp) cc_final: 0.8655 (tppt) REVERT: G 406 MET cc_start: 0.7109 (mmp) cc_final: 0.6227 (tpp) REVERT: D 3 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7838 (mt-10) REVERT: D 222 TYR cc_start: 0.8205 (m-80) cc_final: 0.7617 (m-80) REVERT: D 257 MET cc_start: 0.7407 (mmm) cc_final: 0.7075 (mmm) REVERT: D 264 HIS cc_start: 0.7838 (p-80) cc_final: 0.7174 (p-80) REVERT: D 324 LYS cc_start: 0.8423 (tttm) cc_final: 0.8165 (ttmm) REVERT: D 348 ASN cc_start: 0.8458 (p0) cc_final: 0.8143 (p0) REVERT: D 403 MET cc_start: 0.8179 (ptm) cc_final: 0.6235 (ptp) REVERT: D 409 THR cc_start: 0.9227 (m) cc_final: 0.8864 (p) REVERT: I 4 ILE cc_start: 0.9638 (mt) cc_final: 0.9369 (mm) REVERT: I 257 MET cc_start: 0.7564 (mmm) cc_final: 0.6604 (mmt) REVERT: I 264 HIS cc_start: 0.7697 (p90) cc_final: 0.6952 (p-80) REVERT: I 293 MET cc_start: 0.8685 (ptp) cc_final: 0.7968 (mtm) REVERT: I 313 VAL cc_start: 0.8995 (t) cc_final: 0.8767 (t) REVERT: I 348 ASN cc_start: 0.8479 (p0) cc_final: 0.8266 (p0) REVERT: I 355 ASP cc_start: 0.8714 (m-30) cc_final: 0.8294 (m-30) REVERT: I 388 MET cc_start: 0.8531 (mtp) cc_final: 0.8319 (mmt) REVERT: B 26 ASP cc_start: 0.9208 (m-30) cc_final: 0.8843 (t70) REVERT: B 37 HIS cc_start: 0.8921 (m90) cc_final: 0.8689 (m-70) REVERT: B 101 TRP cc_start: 0.9142 (t60) cc_final: 0.8558 (t60) REVERT: B 198 GLU cc_start: 0.8740 (pm20) cc_final: 0.8113 (pm20) REVERT: B 203 ASP cc_start: 0.8575 (t0) cc_final: 0.8232 (t0) REVERT: B 264 HIS cc_start: 0.7630 (p-80) cc_final: 0.7232 (p90) REVERT: B 334 GLN cc_start: 0.9005 (tt0) cc_final: 0.8564 (tm-30) REVERT: B 406 MET cc_start: 0.7240 (mmp) cc_final: 0.6934 (tpp) REVERT: H 57 ASN cc_start: 0.9134 (m110) cc_final: 0.8782 (m110) REVERT: H 67 ASP cc_start: 0.8905 (t0) cc_final: 0.8309 (t70) REVERT: H 108 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7841 (mm-30) REVERT: H 178 THR cc_start: 0.8475 (m) cc_final: 0.8024 (p) REVERT: H 196 THR cc_start: 0.8355 (p) cc_final: 0.8055 (p) REVERT: H 203 ASP cc_start: 0.8407 (t0) cc_final: 0.7854 (t0) REVERT: H 245 GLN cc_start: 0.8120 (mt0) cc_final: 0.7847 (mm-40) REVERT: H 264 HIS cc_start: 0.7152 (p-80) cc_final: 0.6837 (p90) REVERT: H 321 MET cc_start: 0.8612 (ptp) cc_final: 0.7735 (pmm) REVERT: H 412 GLU cc_start: 0.8875 (tm-30) cc_final: 0.8557 (tm-30) REVERT: E 33 ASP cc_start: 0.8888 (m-30) cc_final: 0.8013 (p0) REVERT: E 49 PHE cc_start: 0.7953 (p90) cc_final: 0.7634 (p90) REVERT: E 96 LYS cc_start: 0.8280 (mmmm) cc_final: 0.7911 (mmmm) REVERT: E 168 GLU cc_start: 0.7563 (mt-10) cc_final: 0.6887 (tt0) REVERT: E 218 ASP cc_start: 0.7956 (m-30) cc_final: 0.7393 (t0) REVERT: E 308 ARG cc_start: 0.8855 (mtm180) cc_final: 0.8531 (ptp90) REVERT: E 352 LYS cc_start: 0.8773 (tptp) cc_final: 0.8380 (tptp) REVERT: E 407 TRP cc_start: 0.8687 (m100) cc_final: 0.8032 (m100) REVERT: J 24 TYR cc_start: 0.8208 (m-80) cc_final: 0.7884 (m-80) REVERT: J 31 GLN cc_start: 0.8593 (mm-40) cc_final: 0.7476 (mt0) REVERT: J 90 GLU cc_start: 0.8483 (mm-30) cc_final: 0.7427 (tp30) REVERT: J 91 GLN cc_start: 0.8599 (mt0) cc_final: 0.8266 (mm110) REVERT: J 172 TYR cc_start: 0.8458 (t80) cc_final: 0.8117 (t80) REVERT: J 186 ASN cc_start: 0.7635 (OUTLIER) cc_final: 0.7361 (m-40) REVERT: J 205 ASP cc_start: 0.8083 (t70) cc_final: 0.7357 (m-30) REVERT: J 213 CYS cc_start: 0.8794 (m) cc_final: 0.8544 (p) REVERT: J 352 LYS cc_start: 0.8912 (tptt) cc_final: 0.8215 (tppt) REVERT: J 368 LEU cc_start: 0.9173 (mp) cc_final: 0.8810 (pp) REVERT: C 36 MET cc_start: 0.8213 (ppp) cc_final: 0.7973 (ppp) REVERT: C 120 ASP cc_start: 0.8491 (t70) cc_final: 0.8098 (t0) REVERT: C 154 MET cc_start: 0.9171 (mmm) cc_final: 0.8723 (mmt) REVERT: C 168 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7392 (tt0) REVERT: C 169 PHE cc_start: 0.7985 (m-10) cc_final: 0.7760 (m-10) REVERT: C 203 MET cc_start: 0.8416 (mmm) cc_final: 0.8094 (mmm) REVERT: C 214 ARG cc_start: 0.8658 (ttp80) cc_final: 0.8058 (ttp80) REVERT: C 233 GLN cc_start: 0.9000 (mm-40) cc_final: 0.8540 (mm-40) REVERT: C 241 SER cc_start: 0.7996 (p) cc_final: 0.7098 (t) REVERT: C 285 GLN cc_start: 0.8186 (pt0) cc_final: 0.7130 (mm-40) REVERT: C 368 LEU cc_start: 0.8909 (mp) cc_final: 0.8569 (pp) REVERT: C 398 MET cc_start: 0.8143 (ttm) cc_final: 0.7778 (ttm) REVERT: C 428 LEU cc_start: 0.8657 (tt) cc_final: 0.8111 (mm) REVERT: L 24 TYR cc_start: 0.8379 (m-80) cc_final: 0.8057 (m-80) REVERT: L 27 GLU cc_start: 0.8384 (mm-30) cc_final: 0.8001 (mm-30) REVERT: L 31 GLN cc_start: 0.8807 (mm-40) cc_final: 0.8349 (mt0) REVERT: L 123 ARG cc_start: 0.8164 (ttp-110) cc_final: 0.7870 (ttm110) REVERT: L 154 MET cc_start: 0.9111 (mmm) cc_final: 0.8880 (mmt) REVERT: L 194 THR cc_start: 0.8895 (p) cc_final: 0.8551 (p) REVERT: L 213 CYS cc_start: 0.8748 (m) cc_final: 0.8337 (p) REVERT: L 285 GLN cc_start: 0.8380 (pt0) cc_final: 0.7381 (mp10) REVERT: L 368 LEU cc_start: 0.9140 (mp) cc_final: 0.8756 (pp) REVERT: L 372 GLN cc_start: 0.8410 (tp-100) cc_final: 0.8049 (tt0) REVERT: K 3 GLU cc_start: 0.6592 (mp0) cc_final: 0.6352 (pm20) REVERT: K 31 GLN cc_start: 0.8779 (mm110) cc_final: 0.8164 (mt0) REVERT: K 69 ASP cc_start: 0.7884 (t0) cc_final: 0.7496 (t0) REVERT: K 90 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7278 (tp30) REVERT: K 91 GLN cc_start: 0.8848 (mt0) cc_final: 0.8642 (mm110) REVERT: K 93 ILE cc_start: 0.8734 (mm) cc_final: 0.8488 (mm) REVERT: K 120 ASP cc_start: 0.8447 (t0) cc_final: 0.8105 (t0) REVERT: K 154 MET cc_start: 0.9229 (mmm) cc_final: 0.8958 (mmm) REVERT: K 168 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7375 (tt0) REVERT: K 202 PHE cc_start: 0.8362 (m-80) cc_final: 0.7935 (m-10) REVERT: K 230 LEU cc_start: 0.9151 (mp) cc_final: 0.8796 (tt) REVERT: K 233 GLN cc_start: 0.8986 (mm-40) cc_final: 0.8353 (mm-40) REVERT: K 291 ILE cc_start: 0.8813 (pt) cc_final: 0.8609 (pt) REVERT: K 338 LYS cc_start: 0.8954 (mtpt) cc_final: 0.8733 (mtpp) REVERT: K 368 LEU cc_start: 0.9220 (mp) cc_final: 0.8897 (pp) outliers start: 4 outliers final: 1 residues processed: 1059 average time/residue: 0.4877 time to fit residues: 866.7630 Evaluate side-chains 787 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 785 time to evaluate : 4.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 475 optimal weight: 5.9990 chunk 55 optimal weight: 30.0000 chunk 281 optimal weight: 6.9990 chunk 360 optimal weight: 5.9990 chunk 279 optimal weight: 8.9990 chunk 415 optimal weight: 9.9990 chunk 275 optimal weight: 5.9990 chunk 491 optimal weight: 1.9990 chunk 307 optimal weight: 10.0000 chunk 299 optimal weight: 20.0000 chunk 226 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 247 ASN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 226 ASN I 247 ASN ** I 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 ASN B 256 ASN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 HIS ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 ASN ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 356 ASN C 18 ASN C 192 HIS ** L 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 192 HIS ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.5503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 41820 Z= 0.244 Angle : 0.574 8.534 56820 Z= 0.291 Chirality : 0.045 0.218 6216 Planarity : 0.004 0.075 7398 Dihedral : 10.809 177.750 5760 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.02 % Allowed : 1.32 % Favored : 98.66 % 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: -1.16 (0.12), residues: 5130 helix: 0.06 (0.11), residues: 2196 sheet: -0.94 (0.19), residues: 786 loop : -1.50 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 21 HIS 0.008 0.001 HIS J 192 PHE 0.021 0.001 PHE B 167 TYR 0.019 0.001 TYR K 185 ARG 0.007 0.001 ARG B 282 *********************** 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 1019 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1018 time to evaluate : 5.111 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 25 SER cc_start: 0.9161 (t) cc_final: 0.8551 (p) REVERT: F 26 ASP cc_start: 0.9157 (m-30) cc_final: 0.8887 (t70) REVERT: F 264 HIS cc_start: 0.7619 (p-80) cc_final: 0.7058 (p-80) REVERT: F 297 LYS cc_start: 0.9352 (mtpp) cc_final: 0.8992 (ttmm) REVERT: F 323 MET cc_start: 0.8865 (mmm) cc_final: 0.8579 (mmm) REVERT: F 334 GLN cc_start: 0.8987 (tt0) cc_final: 0.8617 (tm-30) REVERT: F 340 TYR cc_start: 0.8196 (m-80) cc_final: 0.7935 (m-10) REVERT: F 350 LYS cc_start: 0.9061 (tptp) cc_final: 0.8596 (tppt) REVERT: F 363 MET cc_start: 0.8672 (pmm) cc_final: 0.8174 (pmm) REVERT: A 3 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7229 (mm-30) REVERT: A 24 TYR cc_start: 0.8385 (m-80) cc_final: 0.8093 (m-80) REVERT: A 36 MET cc_start: 0.8289 (ppp) cc_final: 0.8079 (ppp) REVERT: A 69 ASP cc_start: 0.7829 (t0) cc_final: 0.7401 (t0) REVERT: A 90 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7495 (tp30) REVERT: A 154 MET cc_start: 0.9262 (mmm) cc_final: 0.8794 (mmm) REVERT: A 168 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7518 (tt0) REVERT: A 203 MET cc_start: 0.8753 (mmm) cc_final: 0.8546 (mmm) REVERT: A 233 GLN cc_start: 0.8877 (mm-40) cc_final: 0.8249 (mm-40) REVERT: A 276 ILE cc_start: 0.8944 (pt) cc_final: 0.8707 (mt) REVERT: A 291 ILE cc_start: 0.8671 (pt) cc_final: 0.8467 (pt) REVERT: A 368 LEU cc_start: 0.9068 (mp) cc_final: 0.8734 (pp) REVERT: A 398 MET cc_start: 0.7947 (mtp) cc_final: 0.7406 (ttp) REVERT: G 4 ILE cc_start: 0.9610 (mt) cc_final: 0.9316 (mm) REVERT: G 21 TRP cc_start: 0.9051 (m100) cc_final: 0.8406 (m100) REVERT: G 25 SER cc_start: 0.8662 (t) cc_final: 0.8285 (p) REVERT: G 67 ASP cc_start: 0.8811 (t0) cc_final: 0.8317 (t70) REVERT: G 147 MET cc_start: 0.9026 (tpt) cc_final: 0.8727 (tpp) REVERT: G 203 ASP cc_start: 0.8722 (t70) cc_final: 0.8400 (t70) REVERT: G 264 HIS cc_start: 0.7312 (p-80) cc_final: 0.6519 (p-80) REVERT: G 268 PRO cc_start: 0.9537 (Cg_endo) cc_final: 0.9285 (Cg_exo) REVERT: G 300 MET cc_start: 0.8256 (mtt) cc_final: 0.7942 (mtm) REVERT: G 321 MET cc_start: 0.8130 (pmm) cc_final: 0.7755 (pmm) REVERT: G 323 MET cc_start: 0.8565 (mmm) cc_final: 0.8156 (mmm) REVERT: G 406 MET cc_start: 0.7081 (mmp) cc_final: 0.6865 (tpp) REVERT: D 203 ASP cc_start: 0.8381 (t0) cc_final: 0.8125 (t0) REVERT: D 222 TYR cc_start: 0.8225 (m-80) cc_final: 0.7913 (m-80) REVERT: D 264 HIS cc_start: 0.7894 (p-80) cc_final: 0.7253 (p-80) REVERT: D 324 LYS cc_start: 0.8435 (tttm) cc_final: 0.8195 (ttmm) REVERT: D 348 ASN cc_start: 0.8673 (p0) cc_final: 0.8321 (p0) REVERT: D 367 PHE cc_start: 0.8600 (t80) cc_final: 0.8299 (t80) REVERT: D 403 MET cc_start: 0.8170 (ptm) cc_final: 0.6624 (ptp) REVERT: D 409 THR cc_start: 0.9284 (m) cc_final: 0.8805 (p) REVERT: D 426 GLN cc_start: 0.8412 (tp40) cc_final: 0.8013 (tp40) REVERT: I 4 ILE cc_start: 0.9664 (mt) cc_final: 0.9321 (mm) REVERT: I 6 HIS cc_start: 0.7850 (t70) cc_final: 0.7504 (t70) REVERT: I 264 HIS cc_start: 0.7784 (p90) cc_final: 0.7033 (p-80) REVERT: I 297 LYS cc_start: 0.9469 (mtmt) cc_final: 0.9210 (mtmt) REVERT: I 324 LYS cc_start: 0.8411 (tttm) cc_final: 0.8175 (ttmm) REVERT: I 348 ASN cc_start: 0.8630 (p0) cc_final: 0.8361 (p0) REVERT: I 355 ASP cc_start: 0.8736 (m-30) cc_final: 0.8302 (m-30) REVERT: I 388 MET cc_start: 0.8633 (mtp) cc_final: 0.8315 (mmt) REVERT: I 403 MET cc_start: 0.8307 (mmp) cc_final: 0.8088 (mmm) REVERT: B 26 ASP cc_start: 0.9242 (m-30) cc_final: 0.8840 (t70) REVERT: B 37 HIS cc_start: 0.8941 (m90) cc_final: 0.8723 (m-70) REVERT: B 198 GLU cc_start: 0.8696 (pm20) cc_final: 0.8071 (pm20) REVERT: B 203 ASP cc_start: 0.8605 (t0) cc_final: 0.8129 (t0) REVERT: B 264 HIS cc_start: 0.7729 (p-80) cc_final: 0.7307 (p90) REVERT: B 267 MET cc_start: 0.8620 (mtm) cc_final: 0.8358 (mtt) REVERT: B 334 GLN cc_start: 0.9034 (tt0) cc_final: 0.8579 (tm-30) REVERT: B 403 MET cc_start: 0.8485 (mmm) cc_final: 0.7662 (mmp) REVERT: B 406 MET cc_start: 0.7318 (mmp) cc_final: 0.7065 (tpp) REVERT: H 37 HIS cc_start: 0.8752 (m-70) cc_final: 0.8244 (m-70) REVERT: H 57 ASN cc_start: 0.9128 (m110) cc_final: 0.8779 (m110) REVERT: H 196 THR cc_start: 0.8435 (p) cc_final: 0.8154 (p) REVERT: H 203 ASP cc_start: 0.8367 (t0) cc_final: 0.7798 (t0) REVERT: H 264 HIS cc_start: 0.7224 (p-80) cc_final: 0.6963 (p90) REVERT: H 297 LYS cc_start: 0.9226 (mtmm) cc_final: 0.8966 (mmtt) REVERT: H 321 MET cc_start: 0.8641 (ptp) cc_final: 0.7871 (pmm) REVERT: H 330 MET cc_start: 0.8896 (mmm) cc_final: 0.8516 (mmm) REVERT: H 403 MET cc_start: 0.8052 (mmp) cc_final: 0.7831 (mmp) REVERT: H 412 GLU cc_start: 0.8750 (tm-30) cc_final: 0.8508 (tm-30) REVERT: E 49 PHE cc_start: 0.8003 (p90) cc_final: 0.7683 (p90) REVERT: E 205 ASP cc_start: 0.8097 (t0) cc_final: 0.7692 (t0) REVERT: E 218 ASP cc_start: 0.7883 (m-30) cc_final: 0.7430 (t0) REVERT: E 221 ARG cc_start: 0.8982 (mtt90) cc_final: 0.8765 (mmm-85) REVERT: E 258 ASN cc_start: 0.7426 (t0) cc_final: 0.7225 (t160) REVERT: E 308 ARG cc_start: 0.8859 (mtm180) cc_final: 0.8400 (ptp90) REVERT: E 352 LYS cc_start: 0.8338 (tptp) cc_final: 0.7613 (tppt) REVERT: E 407 TRP cc_start: 0.8602 (m100) cc_final: 0.7982 (m100) REVERT: J 24 TYR cc_start: 0.8358 (m-80) cc_final: 0.7934 (m-80) REVERT: J 31 GLN cc_start: 0.8768 (mm-40) cc_final: 0.7653 (mt0) REVERT: J 90 GLU cc_start: 0.8532 (mm-30) cc_final: 0.7464 (tp30) REVERT: J 91 GLN cc_start: 0.8696 (mt0) cc_final: 0.8352 (mm110) REVERT: J 172 TYR cc_start: 0.8468 (t80) cc_final: 0.8135 (t80) REVERT: J 213 CYS cc_start: 0.8869 (m) cc_final: 0.8619 (p) REVERT: J 352 LYS cc_start: 0.8925 (tptt) cc_final: 0.8223 (tppt) REVERT: J 368 LEU cc_start: 0.9127 (mp) cc_final: 0.8796 (pp) REVERT: J 398 MET cc_start: 0.8012 (ttm) cc_final: 0.7609 (ttm) REVERT: J 417 GLU cc_start: 0.8230 (pt0) cc_final: 0.7955 (pt0) REVERT: C 115 ILE cc_start: 0.9100 (tp) cc_final: 0.8873 (tp) REVERT: C 120 ASP cc_start: 0.8500 (t70) cc_final: 0.8109 (t0) REVERT: C 123 ARG cc_start: 0.8422 (mmm-85) cc_final: 0.8104 (mmm-85) REVERT: C 154 MET cc_start: 0.9245 (mmm) cc_final: 0.8845 (mmt) REVERT: C 168 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7489 (tt0) REVERT: C 169 PHE cc_start: 0.7948 (m-10) cc_final: 0.7743 (m-10) REVERT: C 203 MET cc_start: 0.8420 (mmm) cc_final: 0.8115 (mmm) REVERT: C 214 ARG cc_start: 0.8668 (ttp80) cc_final: 0.8059 (ttp80) REVERT: C 221 ARG cc_start: 0.8906 (mtt-85) cc_final: 0.8615 (mtt-85) REVERT: C 233 GLN cc_start: 0.9026 (mm-40) cc_final: 0.8564 (mm-40) REVERT: C 241 SER cc_start: 0.8259 (p) cc_final: 0.7437 (t) REVERT: C 285 GLN cc_start: 0.8241 (pt0) cc_final: 0.7207 (mm-40) REVERT: C 291 ILE cc_start: 0.8783 (pt) cc_final: 0.8452 (pt) REVERT: C 368 LEU cc_start: 0.8932 (mp) cc_final: 0.8565 (pp) REVERT: C 398 MET cc_start: 0.8221 (ttm) cc_final: 0.7701 (ttm) REVERT: C 402 ARG cc_start: 0.8422 (mmm-85) cc_final: 0.8056 (mmm160) REVERT: L 24 TYR cc_start: 0.8462 (m-80) cc_final: 0.8202 (m-80) REVERT: L 31 GLN cc_start: 0.8810 (mm-40) cc_final: 0.8306 (mt0) REVERT: L 123 ARG cc_start: 0.8224 (ttp-110) cc_final: 0.7966 (ttm110) REVERT: L 154 MET cc_start: 0.9205 (mmm) cc_final: 0.8923 (mmt) REVERT: L 157 LEU cc_start: 0.9176 (mt) cc_final: 0.8976 (mt) REVERT: L 179 THR cc_start: 0.7943 (p) cc_final: 0.7570 (p) REVERT: L 198 SER cc_start: 0.9179 (m) cc_final: 0.8928 (m) REVERT: L 213 CYS cc_start: 0.8738 (m) cc_final: 0.8326 (p) REVERT: L 233 GLN cc_start: 0.9032 (mm-40) cc_final: 0.8577 (mm-40) REVERT: L 285 GLN cc_start: 0.8387 (pt0) cc_final: 0.7387 (mp10) REVERT: L 368 LEU cc_start: 0.9093 (mp) cc_final: 0.8640 (pp) REVERT: L 372 GLN cc_start: 0.8501 (tp-100) cc_final: 0.8046 (tt0) REVERT: K 31 GLN cc_start: 0.8858 (mm110) cc_final: 0.8211 (mt0) REVERT: K 69 ASP cc_start: 0.7984 (t0) cc_final: 0.7569 (t0) REVERT: K 90 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7308 (tp30) REVERT: K 93 ILE cc_start: 0.8761 (mm) cc_final: 0.8525 (mm) REVERT: K 120 ASP cc_start: 0.8457 (t0) cc_final: 0.8113 (t0) REVERT: K 154 MET cc_start: 0.9237 (mmm) cc_final: 0.8929 (mmm) REVERT: K 168 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7420 (tt0) REVERT: K 202 PHE cc_start: 0.8404 (m-80) cc_final: 0.7977 (m-10) REVERT: K 230 LEU cc_start: 0.9195 (mp) cc_final: 0.8845 (tt) REVERT: K 233 GLN cc_start: 0.9013 (mm-40) cc_final: 0.8427 (mm-40) REVERT: K 338 LYS cc_start: 0.8941 (mtpt) cc_final: 0.8741 (mtpp) REVERT: K 368 LEU cc_start: 0.9234 (mp) cc_final: 0.8882 (pp) outliers start: 1 outliers final: 0 residues processed: 1019 average time/residue: 0.4824 time to fit residues: 824.8102 Evaluate side-chains 751 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 751 time to evaluate : 4.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 304 optimal weight: 10.0000 chunk 196 optimal weight: 7.9990 chunk 293 optimal weight: 20.0000 chunk 148 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 95 optimal weight: 8.9990 chunk 312 optimal weight: 5.9990 chunk 334 optimal weight: 9.9990 chunk 243 optimal weight: 20.0000 chunk 45 optimal weight: 0.9980 chunk 386 optimal weight: 5.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN B 247 ASN B 256 ASN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 247 ASN ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 HIS E 192 HIS ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 ASN ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 28 HIS J 186 ASN ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 356 ASN C 18 ASN C 192 HIS ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 18 ASN ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.5665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 41820 Z= 0.217 Angle : 0.569 8.552 56820 Z= 0.286 Chirality : 0.045 0.206 6216 Planarity : 0.004 0.075 7398 Dihedral : 10.650 179.954 5760 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.05 % Allowed : 0.75 % Favored : 99.20 % 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: -1.08 (0.12), residues: 5130 helix: 0.09 (0.11), residues: 2238 sheet: -0.93 (0.18), residues: 786 loop : -1.42 (0.14), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 21 HIS 0.007 0.001 HIS J 192 PHE 0.017 0.001 PHE G 408 TYR 0.019 0.001 TYR K 185 ARG 0.007 0.001 ARG B 282 *********************** 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 997 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 995 time to evaluate : 4.661 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 25 SER cc_start: 0.9151 (t) cc_final: 0.8539 (p) REVERT: F 26 ASP cc_start: 0.9133 (m-30) cc_final: 0.8884 (t70) REVERT: F 297 LYS cc_start: 0.9404 (mtpp) cc_final: 0.9196 (ttmt) REVERT: F 321 MET cc_start: 0.8588 (ptp) cc_final: 0.8213 (pmm) REVERT: F 323 MET cc_start: 0.8869 (mmm) cc_final: 0.8545 (mmm) REVERT: F 334 GLN cc_start: 0.8985 (tt0) cc_final: 0.8601 (tm-30) REVERT: F 340 TYR cc_start: 0.8242 (m-80) cc_final: 0.8032 (m-10) REVERT: F 362 LYS cc_start: 0.8494 (tttm) cc_final: 0.8248 (ttpp) REVERT: F 363 MET cc_start: 0.8556 (pmm) cc_final: 0.8114 (pmm) REVERT: A 3 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7307 (mm-30) REVERT: A 24 TYR cc_start: 0.8379 (m-80) cc_final: 0.8080 (m-80) REVERT: A 69 ASP cc_start: 0.8015 (t0) cc_final: 0.7801 (t0) REVERT: A 90 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7461 (tp30) REVERT: A 120 ASP cc_start: 0.8462 (t70) cc_final: 0.8037 (t0) REVERT: A 154 MET cc_start: 0.9247 (mmm) cc_final: 0.8753 (mmm) REVERT: A 168 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7629 (tt0) REVERT: A 202 PHE cc_start: 0.8501 (m-80) cc_final: 0.8052 (m-10) REVERT: A 203 MET cc_start: 0.8799 (mmm) cc_final: 0.8553 (mmm) REVERT: A 233 GLN cc_start: 0.8890 (mm-40) cc_final: 0.8255 (mm-40) REVERT: A 276 ILE cc_start: 0.8915 (pt) cc_final: 0.8676 (mt) REVERT: A 291 ILE cc_start: 0.8667 (pt) cc_final: 0.8444 (pt) REVERT: A 368 LEU cc_start: 0.9171 (mp) cc_final: 0.8819 (pp) REVERT: A 398 MET cc_start: 0.7957 (mtp) cc_final: 0.7428 (ttp) REVERT: A 428 LEU cc_start: 0.8755 (tt) cc_final: 0.8546 (tt) REVERT: G 4 ILE cc_start: 0.9609 (mt) cc_final: 0.9305 (mm) REVERT: G 21 TRP cc_start: 0.8984 (m100) cc_final: 0.8365 (m100) REVERT: G 25 SER cc_start: 0.8652 (t) cc_final: 0.8281 (p) REVERT: G 67 ASP cc_start: 0.8413 (t0) cc_final: 0.8185 (t70) REVERT: G 147 MET cc_start: 0.8998 (tpt) cc_final: 0.8714 (tpp) REVERT: G 203 ASP cc_start: 0.8713 (t70) cc_final: 0.8290 (t0) REVERT: G 264 HIS cc_start: 0.7177 (p-80) cc_final: 0.6422 (p-80) REVERT: G 268 PRO cc_start: 0.9529 (Cg_endo) cc_final: 0.9251 (Cg_exo) REVERT: G 300 MET cc_start: 0.8259 (mtt) cc_final: 0.7946 (mtm) REVERT: G 321 MET cc_start: 0.8178 (pmm) cc_final: 0.7492 (pmm) REVERT: G 323 MET cc_start: 0.8553 (mmm) cc_final: 0.8128 (mmm) REVERT: G 406 MET cc_start: 0.7064 (mmp) cc_final: 0.6849 (tpp) REVERT: D 203 ASP cc_start: 0.8541 (t0) cc_final: 0.8286 (t0) REVERT: D 222 TYR cc_start: 0.8247 (m-80) cc_final: 0.7895 (m-80) REVERT: D 257 MET cc_start: 0.7509 (mmm) cc_final: 0.7252 (mmm) REVERT: D 264 HIS cc_start: 0.7841 (p-80) cc_final: 0.7211 (p-80) REVERT: D 324 LYS cc_start: 0.8413 (tttm) cc_final: 0.8210 (ttmm) REVERT: D 385 PHE cc_start: 0.9191 (t80) cc_final: 0.8946 (t80) REVERT: D 403 MET cc_start: 0.8437 (ptm) cc_final: 0.6823 (ttp) REVERT: D 409 THR cc_start: 0.9193 (m) cc_final: 0.8805 (p) REVERT: D 426 GLN cc_start: 0.8484 (tp40) cc_final: 0.8034 (tp40) REVERT: I 4 ILE cc_start: 0.9620 (mt) cc_final: 0.9341 (mm) REVERT: I 6 HIS cc_start: 0.7747 (t70) cc_final: 0.7241 (t70) REVERT: I 147 MET cc_start: 0.9063 (mmt) cc_final: 0.8766 (mmp) REVERT: I 257 MET cc_start: 0.7601 (mmm) cc_final: 0.6674 (mmt) REVERT: I 264 HIS cc_start: 0.7688 (p90) cc_final: 0.6995 (p-80) REVERT: I 293 MET cc_start: 0.8505 (ptm) cc_final: 0.6932 (ttm) REVERT: I 313 VAL cc_start: 0.8927 (t) cc_final: 0.8727 (t) REVERT: I 324 LYS cc_start: 0.8430 (tttm) cc_final: 0.8161 (ttmm) REVERT: I 348 ASN cc_start: 0.8595 (p0) cc_final: 0.8333 (p0) REVERT: I 355 ASP cc_start: 0.8772 (m-30) cc_final: 0.8272 (m-30) REVERT: I 388 MET cc_start: 0.8622 (mtp) cc_final: 0.8311 (mmt) REVERT: I 403 MET cc_start: 0.8503 (mmp) cc_final: 0.8271 (mmm) REVERT: B 26 ASP cc_start: 0.9232 (m-30) cc_final: 0.8863 (t70) REVERT: B 37 HIS cc_start: 0.8926 (m90) cc_final: 0.8704 (m-70) REVERT: B 101 TRP cc_start: 0.9142 (t60) cc_final: 0.8542 (t60) REVERT: B 198 GLU cc_start: 0.8707 (pm20) cc_final: 0.8036 (pm20) REVERT: B 203 ASP cc_start: 0.8554 (t0) cc_final: 0.8042 (t0) REVERT: B 264 HIS cc_start: 0.7634 (p-80) cc_final: 0.7275 (p90) REVERT: B 267 MET cc_start: 0.8593 (mtm) cc_final: 0.8358 (mtt) REVERT: B 297 LYS cc_start: 0.9389 (mtpp) cc_final: 0.9047 (ttmm) REVERT: B 334 GLN cc_start: 0.9034 (tt0) cc_final: 0.8564 (tm-30) REVERT: B 407 GLU cc_start: 0.7525 (tt0) cc_final: 0.7307 (tt0) REVERT: H 37 HIS cc_start: 0.8729 (m-70) cc_final: 0.8217 (m-70) REVERT: H 57 ASN cc_start: 0.9117 (m110) cc_final: 0.8781 (m110) REVERT: H 67 ASP cc_start: 0.8893 (t0) cc_final: 0.8616 (t70) REVERT: H 196 THR cc_start: 0.8410 (p) cc_final: 0.8133 (p) REVERT: H 203 ASP cc_start: 0.8332 (t0) cc_final: 0.7779 (t0) REVERT: H 264 HIS cc_start: 0.7101 (p-80) cc_final: 0.6880 (p90) REVERT: H 297 LYS cc_start: 0.9270 (mtmm) cc_final: 0.9003 (mmtt) REVERT: H 321 MET cc_start: 0.8576 (ptp) cc_final: 0.7988 (pmm) REVERT: H 330 MET cc_start: 0.8894 (mmm) cc_final: 0.8471 (mmm) REVERT: H 390 ARG cc_start: 0.8827 (ptp90) cc_final: 0.8541 (ptp90) REVERT: H 403 MET cc_start: 0.7670 (mmp) cc_final: 0.7391 (mmp) REVERT: H 407 GLU cc_start: 0.7765 (tt0) cc_final: 0.7276 (tt0) REVERT: H 408 PHE cc_start: 0.8149 (m-10) cc_final: 0.7921 (m-10) REVERT: H 412 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8552 (tm-30) REVERT: E 49 PHE cc_start: 0.8017 (p90) cc_final: 0.7691 (p90) REVERT: E 194 THR cc_start: 0.8763 (p) cc_final: 0.8549 (p) REVERT: E 205 ASP cc_start: 0.8110 (t0) cc_final: 0.7718 (t0) REVERT: E 213 CYS cc_start: 0.8725 (m) cc_final: 0.8421 (p) REVERT: E 218 ASP cc_start: 0.7866 (m-30) cc_final: 0.7419 (t0) REVERT: E 221 ARG cc_start: 0.9220 (mtt90) cc_final: 0.8951 (mmm-85) REVERT: E 252 LEU cc_start: 0.8983 (mp) cc_final: 0.8703 (mt) REVERT: E 308 ARG cc_start: 0.8830 (mtm180) cc_final: 0.8502 (ptp90) REVERT: E 398 MET cc_start: 0.8210 (ttm) cc_final: 0.7890 (ttm) REVERT: J 24 TYR cc_start: 0.8307 (m-80) cc_final: 0.7987 (m-80) REVERT: J 31 GLN cc_start: 0.8652 (mm-40) cc_final: 0.7551 (mt0) REVERT: J 90 GLU cc_start: 0.8518 (mm-30) cc_final: 0.7460 (tp30) REVERT: J 91 GLN cc_start: 0.8690 (mt0) cc_final: 0.8188 (mm110) REVERT: J 172 TYR cc_start: 0.8454 (t80) cc_final: 0.8140 (t80) REVERT: J 213 CYS cc_start: 0.8755 (m) cc_final: 0.8489 (p) REVERT: J 352 LYS cc_start: 0.8711 (tptt) cc_final: 0.8088 (tppt) REVERT: J 368 LEU cc_start: 0.9127 (mp) cc_final: 0.8792 (pp) REVERT: C 31 GLN cc_start: 0.8799 (mm-40) cc_final: 0.8010 (mt0) REVERT: C 96 LYS cc_start: 0.8223 (mmtp) cc_final: 0.7930 (mmmm) REVERT: C 115 ILE cc_start: 0.9078 (tp) cc_final: 0.8664 (tp) REVERT: C 120 ASP cc_start: 0.8528 (t70) cc_final: 0.8280 (t0) REVERT: C 123 ARG cc_start: 0.8573 (mmm-85) cc_final: 0.8201 (mmm-85) REVERT: C 154 MET cc_start: 0.9241 (mmm) cc_final: 0.8889 (mmt) REVERT: C 168 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7538 (tt0) REVERT: C 169 PHE cc_start: 0.7944 (m-10) cc_final: 0.7714 (m-10) REVERT: C 203 MET cc_start: 0.8451 (mmm) cc_final: 0.8101 (mmm) REVERT: C 214 ARG cc_start: 0.8662 (ttp80) cc_final: 0.8002 (ttp80) REVERT: C 221 ARG cc_start: 0.8899 (mtt-85) cc_final: 0.8638 (mtt-85) REVERT: C 241 SER cc_start: 0.8219 (p) cc_final: 0.7375 (t) REVERT: C 285 GLN cc_start: 0.8226 (pt0) cc_final: 0.7190 (mm-40) REVERT: C 291 ILE cc_start: 0.8761 (pt) cc_final: 0.8469 (pt) REVERT: C 368 LEU cc_start: 0.8902 (mp) cc_final: 0.8581 (pp) REVERT: C 398 MET cc_start: 0.8172 (ttm) cc_final: 0.7639 (ttm) REVERT: C 428 LEU cc_start: 0.8632 (tt) cc_final: 0.8071 (mm) REVERT: L 24 TYR cc_start: 0.8462 (m-80) cc_final: 0.8242 (m-80) REVERT: L 31 GLN cc_start: 0.8773 (mm-40) cc_final: 0.8339 (mt0) REVERT: L 36 MET cc_start: 0.8235 (ppp) cc_final: 0.7938 (ppp) REVERT: L 83 TYR cc_start: 0.8428 (m-10) cc_final: 0.8131 (m-10) REVERT: L 123 ARG cc_start: 0.8262 (ttp-110) cc_final: 0.8031 (ttm110) REVERT: L 154 MET cc_start: 0.9240 (mmm) cc_final: 0.9014 (mmt) REVERT: L 198 SER cc_start: 0.9163 (m) cc_final: 0.8945 (m) REVERT: L 213 CYS cc_start: 0.8602 (m) cc_final: 0.8177 (p) REVERT: L 285 GLN cc_start: 0.8370 (pt0) cc_final: 0.7376 (mp10) REVERT: L 368 LEU cc_start: 0.9115 (mp) cc_final: 0.8755 (pp) REVERT: L 372 GLN cc_start: 0.8438 (tp-100) cc_final: 0.7994 (tt0) REVERT: K 3 GLU cc_start: 0.7265 (mm-30) cc_final: 0.7060 (mm-30) REVERT: K 31 GLN cc_start: 0.8833 (mm110) cc_final: 0.8190 (mt0) REVERT: K 69 ASP cc_start: 0.7941 (t0) cc_final: 0.7578 (t0) REVERT: K 90 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7471 (tp30) REVERT: K 93 ILE cc_start: 0.8644 (mm) cc_final: 0.8399 (mm) REVERT: K 120 ASP cc_start: 0.8457 (t0) cc_final: 0.8232 (t0) REVERT: K 154 MET cc_start: 0.9252 (mmm) cc_final: 0.8964 (mmm) REVERT: K 168 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7685 (tt0) REVERT: K 202 PHE cc_start: 0.8358 (m-80) cc_final: 0.7950 (m-10) REVERT: K 230 LEU cc_start: 0.9098 (mp) cc_final: 0.8768 (tt) REVERT: K 233 GLN cc_start: 0.8949 (mm-40) cc_final: 0.8414 (mm-40) REVERT: K 291 ILE cc_start: 0.8864 (pt) cc_final: 0.8659 (pt) REVERT: K 338 LYS cc_start: 0.8917 (mtpt) cc_final: 0.8628 (mtpp) REVERT: K 368 LEU cc_start: 0.9209 (mp) cc_final: 0.8893 (pp) outliers start: 2 outliers final: 1 residues processed: 997 average time/residue: 0.4839 time to fit residues: 811.4658 Evaluate side-chains 759 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 758 time to evaluate : 4.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 447 optimal weight: 1.9990 chunk 470 optimal weight: 10.0000 chunk 429 optimal weight: 6.9990 chunk 458 optimal weight: 8.9990 chunk 275 optimal weight: 3.9990 chunk 199 optimal weight: 10.0000 chunk 359 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 chunk 413 optimal weight: 20.0000 chunk 433 optimal weight: 7.9990 chunk 456 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 247 ASN ** I 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 ASN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 HIS ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 ASN ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 356 ASN C 18 ASN C 192 HIS ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.5786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 41820 Z= 0.242 Angle : 0.582 9.486 56820 Z= 0.293 Chirality : 0.045 0.197 6216 Planarity : 0.004 0.075 7398 Dihedral : 10.551 177.539 5760 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.02 % Allowed : 0.52 % Favored : 99.45 % 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: -1.09 (0.12), residues: 5130 helix: 0.08 (0.11), residues: 2256 sheet: -0.98 (0.18), residues: 786 loop : -1.41 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP K 21 HIS 0.007 0.001 HIS J 192 PHE 0.017 0.001 PHE G 408 TYR 0.024 0.001 TYR B 222 ARG 0.007 0.001 ARG B 282 *********************** 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 984 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 983 time to evaluate : 4.706 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 25 SER cc_start: 0.9153 (t) cc_final: 0.8543 (p) REVERT: F 26 ASP cc_start: 0.9119 (m-30) cc_final: 0.8809 (t70) REVERT: F 264 HIS cc_start: 0.7441 (p-80) cc_final: 0.6951 (p-80) REVERT: F 297 LYS cc_start: 0.9394 (mtpp) cc_final: 0.9191 (ttmt) REVERT: F 323 MET cc_start: 0.8879 (mmm) cc_final: 0.8566 (mmm) REVERT: F 334 GLN cc_start: 0.9014 (tt0) cc_final: 0.8608 (tm-30) REVERT: F 340 TYR cc_start: 0.8297 (m-80) cc_final: 0.8056 (m-10) REVERT: F 362 LYS cc_start: 0.8506 (tttm) cc_final: 0.8237 (ttpp) REVERT: F 363 MET cc_start: 0.8593 (pmm) cc_final: 0.8060 (pmm) REVERT: A 3 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7210 (mm-30) REVERT: A 24 TYR cc_start: 0.8418 (m-80) cc_final: 0.8051 (m-80) REVERT: A 69 ASP cc_start: 0.7822 (t0) cc_final: 0.7348 (t0) REVERT: A 90 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7478 (tp30) REVERT: A 120 ASP cc_start: 0.8460 (t70) cc_final: 0.8164 (t0) REVERT: A 154 MET cc_start: 0.9270 (mmm) cc_final: 0.8774 (mmm) REVERT: A 203 MET cc_start: 0.8790 (mmm) cc_final: 0.8575 (mmm) REVERT: A 233 GLN cc_start: 0.8912 (mm-40) cc_final: 0.8271 (mm-40) REVERT: A 368 LEU cc_start: 0.9176 (mp) cc_final: 0.8798 (pp) REVERT: A 398 MET cc_start: 0.7951 (mtp) cc_final: 0.7415 (ttp) REVERT: A 428 LEU cc_start: 0.8280 (tt) cc_final: 0.7667 (mm) REVERT: G 4 ILE cc_start: 0.9610 (mt) cc_final: 0.9300 (mm) REVERT: G 25 SER cc_start: 0.8696 (t) cc_final: 0.8305 (p) REVERT: G 67 ASP cc_start: 0.8609 (t0) cc_final: 0.8085 (t70) REVERT: G 147 MET cc_start: 0.8988 (tpt) cc_final: 0.8673 (tpp) REVERT: G 203 ASP cc_start: 0.8668 (t70) cc_final: 0.8329 (t70) REVERT: G 264 HIS cc_start: 0.7170 (p-80) cc_final: 0.6489 (p-80) REVERT: G 268 PRO cc_start: 0.9513 (Cg_endo) cc_final: 0.9253 (Cg_exo) REVERT: G 300 MET cc_start: 0.8268 (mtt) cc_final: 0.7962 (mtm) REVERT: G 321 MET cc_start: 0.8199 (pmm) cc_final: 0.7840 (pmm) REVERT: G 323 MET cc_start: 0.8575 (mmm) cc_final: 0.8138 (mmm) REVERT: G 406 MET cc_start: 0.7135 (mmp) cc_final: 0.6888 (tpp) REVERT: D 203 ASP cc_start: 0.8437 (t0) cc_final: 0.8190 (t0) REVERT: D 257 MET cc_start: 0.7432 (mmm) cc_final: 0.7207 (mmm) REVERT: D 264 HIS cc_start: 0.7783 (p-80) cc_final: 0.7142 (p-80) REVERT: D 267 MET cc_start: 0.8825 (mtp) cc_final: 0.8610 (mtt) REVERT: D 324 LYS cc_start: 0.8459 (tttm) cc_final: 0.8246 (ttmm) REVERT: D 403 MET cc_start: 0.8105 (ptm) cc_final: 0.6399 (ptp) REVERT: D 409 THR cc_start: 0.9230 (m) cc_final: 0.8832 (p) REVERT: D 426 GLN cc_start: 0.8490 (tp40) cc_final: 0.8030 (tp40) REVERT: I 4 ILE cc_start: 0.9622 (mt) cc_final: 0.9282 (mm) REVERT: I 6 HIS cc_start: 0.7522 (t70) cc_final: 0.7219 (t70) REVERT: I 147 MET cc_start: 0.8997 (mmt) cc_final: 0.8713 (mmp) REVERT: I 257 MET cc_start: 0.7443 (mmm) cc_final: 0.6601 (mmt) REVERT: I 264 HIS cc_start: 0.7713 (p90) cc_final: 0.7021 (p-80) REVERT: I 293 MET cc_start: 0.8681 (ptm) cc_final: 0.6829 (ttm) REVERT: I 297 LYS cc_start: 0.9451 (mtpp) cc_final: 0.9119 (mmtt) REVERT: I 324 LYS cc_start: 0.8346 (tttm) cc_final: 0.8072 (ttmm) REVERT: I 348 ASN cc_start: 0.8660 (p0) cc_final: 0.8379 (p0) REVERT: I 355 ASP cc_start: 0.8771 (m-30) cc_final: 0.8306 (m-30) REVERT: I 388 MET cc_start: 0.8643 (mtp) cc_final: 0.8309 (mmt) REVERT: I 403 MET cc_start: 0.8509 (mmp) cc_final: 0.8300 (mmm) REVERT: B 26 ASP cc_start: 0.9251 (m-30) cc_final: 0.8850 (t70) REVERT: B 37 HIS cc_start: 0.8929 (m90) cc_final: 0.8715 (m-70) REVERT: B 101 TRP cc_start: 0.9189 (t60) cc_final: 0.8566 (t60) REVERT: B 198 GLU cc_start: 0.8781 (pm20) cc_final: 0.8187 (pm20) REVERT: B 203 ASP cc_start: 0.8415 (t0) cc_final: 0.8205 (t0) REVERT: B 267 MET cc_start: 0.8736 (mtm) cc_final: 0.8464 (mtt) REVERT: B 297 LYS cc_start: 0.9382 (mtpp) cc_final: 0.9026 (ttmm) REVERT: B 321 MET cc_start: 0.8196 (pmm) cc_final: 0.6996 (pmm) REVERT: B 334 GLN cc_start: 0.9047 (tt0) cc_final: 0.8583 (tm-30) REVERT: B 388 MET cc_start: 0.8390 (mtp) cc_final: 0.8177 (mtp) REVERT: H 37 HIS cc_start: 0.8772 (m-70) cc_final: 0.8265 (m-70) REVERT: H 57 ASN cc_start: 0.9141 (m110) cc_final: 0.8785 (m110) REVERT: H 196 THR cc_start: 0.8448 (p) cc_final: 0.8171 (p) REVERT: H 203 ASP cc_start: 0.8353 (t0) cc_final: 0.7770 (t0) REVERT: H 297 LYS cc_start: 0.9308 (mtmm) cc_final: 0.9052 (mmtt) REVERT: H 330 MET cc_start: 0.8903 (mmm) cc_final: 0.8505 (mmm) REVERT: H 390 ARG cc_start: 0.8832 (ptp90) cc_final: 0.8314 (ptp90) REVERT: H 403 MET cc_start: 0.7866 (mmp) cc_final: 0.7460 (mmp) REVERT: H 407 GLU cc_start: 0.7709 (tt0) cc_final: 0.7207 (tt0) REVERT: H 412 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8498 (tm-30) REVERT: E 49 PHE cc_start: 0.8092 (p90) cc_final: 0.7741 (p90) REVERT: E 205 ASP cc_start: 0.8091 (t0) cc_final: 0.7756 (t0) REVERT: E 213 CYS cc_start: 0.8749 (m) cc_final: 0.8436 (p) REVERT: E 218 ASP cc_start: 0.7859 (m-30) cc_final: 0.7438 (t0) REVERT: E 258 ASN cc_start: 0.7562 (t160) cc_final: 0.7165 (t160) REVERT: E 308 ARG cc_start: 0.8755 (mtm180) cc_final: 0.8457 (ptp90) REVERT: E 398 MET cc_start: 0.8354 (ttm) cc_final: 0.7939 (ttm) REVERT: J 24 TYR cc_start: 0.8326 (m-80) cc_final: 0.7852 (m-80) REVERT: J 31 GLN cc_start: 0.8691 (mm-40) cc_final: 0.7598 (mt0) REVERT: J 69 ASP cc_start: 0.7450 (t70) cc_final: 0.7054 (t70) REVERT: J 90 GLU cc_start: 0.8546 (mm-30) cc_final: 0.7474 (tp30) REVERT: J 91 GLN cc_start: 0.8626 (mt0) cc_final: 0.8279 (mm110) REVERT: J 172 TYR cc_start: 0.8462 (t80) cc_final: 0.8143 (t80) REVERT: J 213 CYS cc_start: 0.8864 (m) cc_final: 0.8638 (p) REVERT: J 352 LYS cc_start: 0.8711 (tptt) cc_final: 0.8084 (tppt) REVERT: J 368 LEU cc_start: 0.9115 (mp) cc_final: 0.8797 (pp) REVERT: C 96 LYS cc_start: 0.8259 (mmtp) cc_final: 0.7961 (mmmm) REVERT: C 110 ILE cc_start: 0.9563 (mm) cc_final: 0.9363 (mp) REVERT: C 115 ILE cc_start: 0.8961 (tp) cc_final: 0.8655 (tp) REVERT: C 120 ASP cc_start: 0.8649 (t70) cc_final: 0.8358 (t0) REVERT: C 154 MET cc_start: 0.9309 (mmm) cc_final: 0.8990 (mmt) REVERT: C 168 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7569 (tt0) REVERT: C 203 MET cc_start: 0.8535 (mmm) cc_final: 0.8169 (mmm) REVERT: C 214 ARG cc_start: 0.8650 (ttp80) cc_final: 0.7985 (ttp80) REVERT: C 221 ARG cc_start: 0.8890 (mtt-85) cc_final: 0.8608 (mtt-85) REVERT: C 241 SER cc_start: 0.8230 (p) cc_final: 0.7371 (t) REVERT: C 285 GLN cc_start: 0.8299 (pt0) cc_final: 0.7241 (mm-40) REVERT: C 291 ILE cc_start: 0.8775 (pt) cc_final: 0.8468 (pt) REVERT: C 368 LEU cc_start: 0.8929 (mp) cc_final: 0.8577 (pp) REVERT: C 398 MET cc_start: 0.8172 (ttm) cc_final: 0.7607 (ttm) REVERT: C 428 LEU cc_start: 0.8636 (tt) cc_final: 0.8065 (mm) REVERT: L 24 TYR cc_start: 0.8470 (m-80) cc_final: 0.8180 (m-80) REVERT: L 27 GLU cc_start: 0.8375 (mm-30) cc_final: 0.8156 (mm-30) REVERT: L 31 GLN cc_start: 0.8794 (mm-40) cc_final: 0.8383 (mt0) REVERT: L 36 MET cc_start: 0.7911 (ppp) cc_final: 0.7609 (ppp) REVERT: L 123 ARG cc_start: 0.8287 (ttp-110) cc_final: 0.8055 (ttm110) REVERT: L 154 MET cc_start: 0.9243 (mmm) cc_final: 0.9024 (mmt) REVERT: L 198 SER cc_start: 0.9188 (m) cc_final: 0.8980 (m) REVERT: L 213 CYS cc_start: 0.8664 (m) cc_final: 0.8249 (p) REVERT: L 285 GLN cc_start: 0.8390 (pt0) cc_final: 0.7376 (mp10) REVERT: L 368 LEU cc_start: 0.9130 (mp) cc_final: 0.8754 (pp) REVERT: L 372 GLN cc_start: 0.8488 (tp-100) cc_final: 0.8026 (tt0) REVERT: K 31 GLN cc_start: 0.8811 (mm110) cc_final: 0.8102 (mt0) REVERT: K 36 MET cc_start: 0.8266 (ppp) cc_final: 0.8032 (ppp) REVERT: K 69 ASP cc_start: 0.7936 (t0) cc_final: 0.7556 (t0) REVERT: K 90 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7531 (tp30) REVERT: K 93 ILE cc_start: 0.8746 (mm) cc_final: 0.8508 (mm) REVERT: K 120 ASP cc_start: 0.8406 (t0) cc_final: 0.8107 (t0) REVERT: K 154 MET cc_start: 0.9268 (mmm) cc_final: 0.8974 (mmm) REVERT: K 168 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7409 (tt0) REVERT: K 202 PHE cc_start: 0.8397 (m-80) cc_final: 0.8063 (m-10) REVERT: K 230 LEU cc_start: 0.9196 (mp) cc_final: 0.8814 (tt) REVERT: K 233 GLN cc_start: 0.8922 (mm-40) cc_final: 0.8362 (mm-40) REVERT: K 291 ILE cc_start: 0.8871 (pt) cc_final: 0.8665 (pt) REVERT: K 338 LYS cc_start: 0.8952 (mtpt) cc_final: 0.8625 (mtpp) REVERT: K 368 LEU cc_start: 0.9210 (mp) cc_final: 0.8893 (pp) outliers start: 1 outliers final: 0 residues processed: 984 average time/residue: 0.4931 time to fit residues: 819.1381 Evaluate side-chains 731 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 731 time to evaluate : 4.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 300 optimal weight: 10.0000 chunk 484 optimal weight: 4.9990 chunk 295 optimal weight: 6.9990 chunk 229 optimal weight: 0.0980 chunk 336 optimal weight: 7.9990 chunk 508 optimal weight: 3.9990 chunk 467 optimal weight: 3.9990 chunk 404 optimal weight: 9.9990 chunk 42 optimal weight: 8.9990 chunk 312 optimal weight: 5.9990 chunk 248 optimal weight: 8.9990 overall best weight: 3.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 204 ASN ** I 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN B 247 ASN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 HIS ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 186 ASN ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 356 ASN C 18 ASN C 192 HIS ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 18 ASN L 192 HIS ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.5904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 41820 Z= 0.197 Angle : 0.572 10.265 56820 Z= 0.285 Chirality : 0.045 0.202 6216 Planarity : 0.004 0.076 7398 Dihedral : 10.345 173.199 5760 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.02 % Allowed : 0.27 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.92 (0.12), residues: 5130 helix: 0.23 (0.11), residues: 2250 sheet: -1.05 (0.17), residues: 882 loop : -1.24 (0.14), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 21 HIS 0.006 0.001 HIS J 192 PHE 0.016 0.001 PHE G 408 TYR 0.020 0.001 TYR B 222 ARG 0.007 0.001 ARG B 282 ********************** 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 991 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 990 time to evaluate : 4.909 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 25 SER cc_start: 0.9128 (t) cc_final: 0.8554 (p) REVERT: F 26 ASP cc_start: 0.9123 (m-30) cc_final: 0.8827 (t70) REVERT: F 108 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7779 (mm-30) REVERT: F 323 MET cc_start: 0.8808 (mmm) cc_final: 0.8518 (mmm) REVERT: F 334 GLN cc_start: 0.9020 (tt0) cc_final: 0.8578 (tm-30) REVERT: F 340 TYR cc_start: 0.8251 (m-80) cc_final: 0.8010 (m-10) REVERT: F 362 LYS cc_start: 0.8533 (tttm) cc_final: 0.8222 (ttpp) REVERT: F 363 MET cc_start: 0.8552 (pmm) cc_final: 0.7948 (pmm) REVERT: A 3 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7224 (mm-30) REVERT: A 24 TYR cc_start: 0.8407 (m-80) cc_final: 0.8060 (m-80) REVERT: A 69 ASP cc_start: 0.7962 (t0) cc_final: 0.7746 (t0) REVERT: A 90 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7401 (tp30) REVERT: A 120 ASP cc_start: 0.8421 (t70) cc_final: 0.8150 (t0) REVERT: A 154 MET cc_start: 0.9270 (mmm) cc_final: 0.8765 (mmm) REVERT: A 202 PHE cc_start: 0.8553 (m-80) cc_final: 0.8101 (m-80) REVERT: A 203 MET cc_start: 0.8793 (mmm) cc_final: 0.8430 (mmm) REVERT: A 218 ASP cc_start: 0.8192 (m-30) cc_final: 0.7327 (t0) REVERT: A 233 GLN cc_start: 0.8907 (mm-40) cc_final: 0.8256 (mm-40) REVERT: A 291 ILE cc_start: 0.8715 (pt) cc_final: 0.8497 (pt) REVERT: A 368 LEU cc_start: 0.9200 (mp) cc_final: 0.8826 (pp) REVERT: A 398 MET cc_start: 0.7943 (mtp) cc_final: 0.7434 (ttp) REVERT: A 428 LEU cc_start: 0.8372 (tt) cc_final: 0.8151 (mm) REVERT: G 4 ILE cc_start: 0.9613 (mt) cc_final: 0.9314 (mm) REVERT: G 21 TRP cc_start: 0.8812 (m100) cc_final: 0.8345 (m100) REVERT: G 25 SER cc_start: 0.8657 (t) cc_final: 0.8287 (p) REVERT: G 67 ASP cc_start: 0.8995 (t0) cc_final: 0.8499 (t70) REVERT: G 147 MET cc_start: 0.8972 (tpt) cc_final: 0.8701 (tpp) REVERT: G 203 ASP cc_start: 0.8675 (t70) cc_final: 0.8271 (t0) REVERT: G 264 HIS cc_start: 0.7137 (p-80) cc_final: 0.6483 (p-80) REVERT: G 268 PRO cc_start: 0.9498 (Cg_endo) cc_final: 0.9236 (Cg_exo) REVERT: G 297 LYS cc_start: 0.9445 (ptpt) cc_final: 0.9186 (mtmt) REVERT: G 300 MET cc_start: 0.8140 (mtt) cc_final: 0.7896 (mtm) REVERT: G 321 MET cc_start: 0.8235 (pmm) cc_final: 0.7875 (pmm) REVERT: G 323 MET cc_start: 0.8532 (mmm) cc_final: 0.8075 (mmm) REVERT: G 406 MET cc_start: 0.7074 (mmp) cc_final: 0.6849 (tpp) REVERT: D 222 TYR cc_start: 0.8180 (m-80) cc_final: 0.7684 (m-80) REVERT: D 264 HIS cc_start: 0.7733 (p-80) cc_final: 0.7144 (p-80) REVERT: D 403 MET cc_start: 0.8188 (ptm) cc_final: 0.6578 (ptp) REVERT: D 426 GLN cc_start: 0.8461 (tp40) cc_final: 0.8035 (tp40) REVERT: I 4 ILE cc_start: 0.9561 (mt) cc_final: 0.9313 (mm) REVERT: I 6 HIS cc_start: 0.7471 (t70) cc_final: 0.7267 (t70) REVERT: I 101 TRP cc_start: 0.8992 (t60) cc_final: 0.8595 (t60) REVERT: I 147 MET cc_start: 0.8928 (mmt) cc_final: 0.8700 (mmp) REVERT: I 250 LEU cc_start: 0.9059 (tp) cc_final: 0.8724 (tp) REVERT: I 257 MET cc_start: 0.7622 (mmm) cc_final: 0.6890 (mmt) REVERT: I 264 HIS cc_start: 0.7596 (p90) cc_final: 0.6922 (p-80) REVERT: I 293 MET cc_start: 0.8315 (ptm) cc_final: 0.7129 (ptm) REVERT: I 297 LYS cc_start: 0.9429 (mtpp) cc_final: 0.9115 (mmtt) REVERT: I 324 LYS cc_start: 0.8296 (tttm) cc_final: 0.8048 (ttmm) REVERT: I 330 MET cc_start: 0.8652 (mmt) cc_final: 0.8423 (mmm) REVERT: I 348 ASN cc_start: 0.8531 (p0) cc_final: 0.8279 (p0) REVERT: I 355 ASP cc_start: 0.8765 (m-30) cc_final: 0.8332 (m-30) REVERT: I 367 PHE cc_start: 0.8441 (t80) cc_final: 0.7884 (t80) REVERT: I 388 MET cc_start: 0.8630 (mtp) cc_final: 0.8304 (mmt) REVERT: I 427 ASP cc_start: 0.7937 (m-30) cc_final: 0.7702 (t0) REVERT: B 26 ASP cc_start: 0.9202 (m-30) cc_final: 0.8838 (t70) REVERT: B 37 HIS cc_start: 0.8900 (m90) cc_final: 0.8676 (m-70) REVERT: B 101 TRP cc_start: 0.9176 (t60) cc_final: 0.8590 (t60) REVERT: B 198 GLU cc_start: 0.8841 (pm20) cc_final: 0.8266 (pm20) REVERT: B 203 ASP cc_start: 0.8533 (t0) cc_final: 0.7948 (t0) REVERT: B 264 HIS cc_start: 0.7848 (p90) cc_final: 0.7358 (p-80) REVERT: B 267 MET cc_start: 0.8721 (mtm) cc_final: 0.8484 (mtt) REVERT: B 297 LYS cc_start: 0.9424 (mtpp) cc_final: 0.9054 (ttmm) REVERT: B 321 MET cc_start: 0.8338 (pmm) cc_final: 0.7400 (pmm) REVERT: B 334 GLN cc_start: 0.9058 (tt0) cc_final: 0.8536 (tm-30) REVERT: B 407 GLU cc_start: 0.7668 (tt0) cc_final: 0.7228 (tt0) REVERT: H 37 HIS cc_start: 0.8705 (m-70) cc_final: 0.8180 (m-70) REVERT: H 57 ASN cc_start: 0.9122 (m110) cc_final: 0.8792 (m110) REVERT: H 196 THR cc_start: 0.8350 (p) cc_final: 0.8128 (p) REVERT: H 203 ASP cc_start: 0.8323 (t0) cc_final: 0.7739 (t0) REVERT: H 264 HIS cc_start: 0.7837 (p90) cc_final: 0.7054 (p90) REVERT: H 297 LYS cc_start: 0.9314 (mtmm) cc_final: 0.9105 (mmtt) REVERT: H 321 MET cc_start: 0.8583 (ptp) cc_final: 0.7960 (pmm) REVERT: H 330 MET cc_start: 0.8830 (mmm) cc_final: 0.8400 (mmm) REVERT: H 359 ARG cc_start: 0.8232 (tpp80) cc_final: 0.7764 (ttt180) REVERT: H 403 MET cc_start: 0.7903 (mmp) cc_final: 0.7590 (mmp) REVERT: H 407 GLU cc_start: 0.7769 (tt0) cc_final: 0.7319 (tt0) REVERT: H 412 GLU cc_start: 0.8705 (tm-30) cc_final: 0.8487 (tm-30) REVERT: H 425 TYR cc_start: 0.9044 (m-80) cc_final: 0.8696 (m-10) REVERT: E 49 PHE cc_start: 0.8057 (p90) cc_final: 0.7702 (p90) REVERT: E 168 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7021 (tt0) REVERT: E 205 ASP cc_start: 0.8094 (t0) cc_final: 0.7726 (t0) REVERT: E 213 CYS cc_start: 0.8653 (m) cc_final: 0.8430 (p) REVERT: E 218 ASP cc_start: 0.7872 (m-30) cc_final: 0.7436 (t0) REVERT: E 252 LEU cc_start: 0.8970 (mp) cc_final: 0.8654 (mt) REVERT: E 308 ARG cc_start: 0.8742 (mtm180) cc_final: 0.8472 (ptp90) REVERT: E 398 MET cc_start: 0.8329 (ttm) cc_final: 0.7926 (ttm) REVERT: J 24 TYR cc_start: 0.8301 (m-80) cc_final: 0.7894 (m-80) REVERT: J 31 GLN cc_start: 0.8691 (mm-40) cc_final: 0.7685 (mt0) REVERT: J 69 ASP cc_start: 0.7391 (t70) cc_final: 0.7018 (t70) REVERT: J 90 GLU cc_start: 0.8517 (mm-30) cc_final: 0.7462 (tp30) REVERT: J 91 GLN cc_start: 0.8566 (mt0) cc_final: 0.8263 (mm110) REVERT: J 96 LYS cc_start: 0.8622 (mmmt) cc_final: 0.8357 (mmmt) REVERT: J 154 MET cc_start: 0.9009 (mmm) cc_final: 0.8609 (mmm) REVERT: J 172 TYR cc_start: 0.8456 (t80) cc_final: 0.8134 (t80) REVERT: J 213 CYS cc_start: 0.8731 (m) cc_final: 0.8466 (p) REVERT: J 352 LYS cc_start: 0.8731 (tptt) cc_final: 0.8079 (tppt) REVERT: J 368 LEU cc_start: 0.9156 (mp) cc_final: 0.8899 (pp) REVERT: J 398 MET cc_start: 0.8119 (ttm) cc_final: 0.7798 (ttm) REVERT: C 31 GLN cc_start: 0.8757 (mm-40) cc_final: 0.7992 (mt0) REVERT: C 96 LYS cc_start: 0.8254 (mmtp) cc_final: 0.7951 (mmmm) REVERT: C 110 ILE cc_start: 0.9564 (mm) cc_final: 0.9362 (mp) REVERT: C 115 ILE cc_start: 0.8874 (tp) cc_final: 0.8673 (tp) REVERT: C 120 ASP cc_start: 0.8632 (t70) cc_final: 0.8239 (t0) REVERT: C 154 MET cc_start: 0.9213 (mmm) cc_final: 0.8864 (mmt) REVERT: C 168 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7499 (tt0) REVERT: C 203 MET cc_start: 0.8522 (mmm) cc_final: 0.8159 (mmm) REVERT: C 214 ARG cc_start: 0.8652 (ttp80) cc_final: 0.7861 (ttp80) REVERT: C 221 ARG cc_start: 0.8900 (mtt-85) cc_final: 0.8606 (mtt-85) REVERT: C 233 GLN cc_start: 0.8936 (mm-40) cc_final: 0.8510 (mm-40) REVERT: C 241 SER cc_start: 0.8194 (p) cc_final: 0.7322 (t) REVERT: C 285 GLN cc_start: 0.8287 (pt0) cc_final: 0.7236 (mm-40) REVERT: C 291 ILE cc_start: 0.8745 (pt) cc_final: 0.8410 (pt) REVERT: C 368 LEU cc_start: 0.8917 (mp) cc_final: 0.8597 (pp) REVERT: C 398 MET cc_start: 0.8217 (ttm) cc_final: 0.7648 (ttm) REVERT: C 428 LEU cc_start: 0.8604 (tt) cc_final: 0.8029 (mm) REVERT: L 24 TYR cc_start: 0.8399 (m-80) cc_final: 0.8127 (m-80) REVERT: L 27 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8144 (mm-30) REVERT: L 31 GLN cc_start: 0.8798 (mm-40) cc_final: 0.8433 (mt0) REVERT: L 36 MET cc_start: 0.8002 (ppp) cc_final: 0.7697 (ppp) REVERT: L 123 ARG cc_start: 0.8302 (ttp-110) cc_final: 0.8038 (ttm110) REVERT: L 194 THR cc_start: 0.8831 (p) cc_final: 0.8623 (p) REVERT: L 198 SER cc_start: 0.9124 (m) cc_final: 0.8859 (m) REVERT: L 213 CYS cc_start: 0.8620 (m) cc_final: 0.8248 (p) REVERT: L 285 GLN cc_start: 0.8371 (pt0) cc_final: 0.7419 (mp10) REVERT: L 291 ILE cc_start: 0.8970 (pt) cc_final: 0.8423 (pt) REVERT: L 368 LEU cc_start: 0.9038 (mp) cc_final: 0.8718 (pp) REVERT: L 372 GLN cc_start: 0.8367 (tp-100) cc_final: 0.8056 (tt0) REVERT: L 407 TRP cc_start: 0.8990 (m100) cc_final: 0.8537 (m100) REVERT: K 31 GLN cc_start: 0.8754 (mm110) cc_final: 0.8005 (mt0) REVERT: K 36 MET cc_start: 0.8316 (ppp) cc_final: 0.8078 (ppp) REVERT: K 69 ASP cc_start: 0.7862 (t0) cc_final: 0.7475 (t0) REVERT: K 90 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7518 (tp30) REVERT: K 93 ILE cc_start: 0.8724 (mm) cc_final: 0.8470 (mm) REVERT: K 96 LYS cc_start: 0.8703 (tptm) cc_final: 0.8464 (tptm) REVERT: K 120 ASP cc_start: 0.8355 (t0) cc_final: 0.8067 (t0) REVERT: K 154 MET cc_start: 0.9269 (mmm) cc_final: 0.8925 (mmm) REVERT: K 168 GLU cc_start: 0.7702 (mt-10) cc_final: 0.6956 (tt0) REVERT: K 192 HIS cc_start: 0.7703 (t70) cc_final: 0.7335 (t70) REVERT: K 202 PHE cc_start: 0.8418 (m-80) cc_final: 0.8079 (m-10) REVERT: K 230 LEU cc_start: 0.9189 (mp) cc_final: 0.8823 (tt) REVERT: K 233 GLN cc_start: 0.8950 (mm-40) cc_final: 0.8421 (mm-40) REVERT: K 291 ILE cc_start: 0.8843 (pt) cc_final: 0.8631 (pt) REVERT: K 338 LYS cc_start: 0.8931 (mtpt) cc_final: 0.8618 (mtpp) REVERT: K 368 LEU cc_start: 0.9228 (mp) cc_final: 0.8929 (pp) outliers start: 1 outliers final: 0 residues processed: 991 average time/residue: 0.4801 time to fit residues: 799.6443 Evaluate side-chains 759 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 759 time to evaluate : 4.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 321 optimal weight: 5.9990 chunk 430 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 chunk 373 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 112 optimal weight: 20.0000 chunk 405 optimal weight: 0.0040 chunk 169 optimal weight: 30.0000 chunk 416 optimal weight: 0.0060 chunk 51 optimal weight: 20.0000 chunk 74 optimal weight: 5.9990 overall best weight: 3.2014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 165 ASN ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 ASN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 HIS ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 356 ASN C 18 ASN C 192 HIS ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.106468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.095701 restraints weight = 95461.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.098659 restraints weight = 48205.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.100634 restraints weight = 28277.147| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.6002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 41820 Z= 0.182 Angle : 0.563 10.524 56820 Z= 0.280 Chirality : 0.044 0.201 6216 Planarity : 0.004 0.076 7398 Dihedral : 10.212 169.499 5760 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.05 % Allowed : 0.20 % Favored : 99.75 % 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: -0.77 (0.12), residues: 5130 helix: 0.36 (0.11), residues: 2226 sheet: -0.97 (0.17), residues: 882 loop : -1.16 (0.14), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 344 HIS 0.004 0.001 HIS J 192 PHE 0.020 0.001 PHE B 260 TYR 0.025 0.001 TYR I 208 ARG 0.007 0.000 ARG B 282 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12910.30 seconds wall clock time: 230 minutes 55.68 seconds (13855.68 seconds total)