Starting phenix.real_space_refine on Sun Mar 24 10:00:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6evy_3963/03_2024/6evy_3963_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6evy_3963/03_2024/6evy_3963.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6evy_3963/03_2024/6evy_3963.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6evy_3963/03_2024/6evy_3963.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6evy_3963/03_2024/6evy_3963_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6evy_3963/03_2024/6evy_3963_updated.pdb" } resolution = 4.4 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= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 6 5.21 5 S 282 5.16 5 C 25674 2.51 5 N 6978 2.21 5 O 7914 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ARG 64": "NH1" <-> "NH2" Residue "E ARG 390": "NH1" <-> "NH2" Residue "J ARG 64": "NH1" <-> "NH2" Residue "J ARG 390": "NH1" <-> "NH2" Residue "C ARG 64": "NH1" <-> "NH2" Residue "C ARG 390": "NH1" <-> "NH2" Residue "L ARG 64": "NH1" <-> "NH2" Residue "L ARG 390": "NH1" <-> "NH2" Residue "A ARG 64": "NH1" <-> "NH2" Residue "A ARG 390": "NH1" <-> "NH2" Residue "K ARG 64": "NH1" <-> "NH2" Residue "K ARG 390": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 40890 Number of models: 1 Model: "" Number of chains: 24 Chain: "E" Number of atoms: 3382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3382 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "J" Number of atoms: 3382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3382 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 3382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3382 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 3382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3382 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 3382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3382 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 3382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3382 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "I" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "H" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GSP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GSP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GSP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GSP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GSP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GSP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 20.55, per 1000 atoms: 0.50 Number of scatterers: 40890 At special positions: 0 Unit cell: (119.54, 173.75, 212.67, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 282 16.00 P 36 15.00 Mg 6 11.99 O 7914 8.00 N 6978 7.00 C 25674 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 15.17 Conformation dependent library (CDL) restraints added in 7.0 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... running ksdssp... Secondary structure from input PDB file: 186 helices and 30 sheets defined 43.6% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.50 Creating SS restraints... Processing helix chain 'E' and resid 10 through 26 removed outlier: 3.893A pdb=" N ILE E 16 " --> pdb=" O ALA E 12 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA E 19 " --> pdb=" O GLN E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 80 removed outlier: 3.551A pdb=" N ARG E 79 " --> pdb=" O ASP E 76 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR E 80 " --> pdb=" O GLU E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 107 Processing helix chain 'E' and resid 111 through 128 removed outlier: 5.999A pdb=" N ASP E 116 " --> pdb=" O LYS E 112 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LEU E 117 " --> pdb=" O GLU E 113 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP E 127 " --> pdb=" O ARG E 123 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN E 128 " --> pdb=" O LYS E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 160 removed outlier: 4.514A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU E 155 " --> pdb=" O SER E 151 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG E 156 " --> pdb=" O LEU E 152 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER E 158 " --> pdb=" O MET E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 197 removed outlier: 3.618A pdb=" N ASN E 186 " --> pdb=" O GLU E 183 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N SER E 187 " --> pdb=" O PRO E 184 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE E 188 " --> pdb=" O TYR E 185 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR E 190 " --> pdb=" O SER E 187 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR E 193 " --> pdb=" O THR E 190 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LEU E 195 " --> pdb=" O HIS E 192 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU E 196 " --> pdb=" O THR E 193 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS E 197 " --> pdb=" O THR E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 215 Processing helix chain 'E' and resid 224 through 243 removed outlier: 3.752A pdb=" N LEU E 230 " --> pdb=" O ASN E 226 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE E 234 " --> pdb=" O LEU E 230 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N SER E 241 " --> pdb=" O SER E 237 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N LEU E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 258 Processing helix chain 'E' and resid 288 through 295 removed outlier: 3.699A pdb=" N ASN E 293 " --> pdb=" O ALA E 289 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA E 294 " --> pdb=" O GLU E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 300 No H-bonds generated for 'chain 'E' and resid 298 through 300' Processing helix chain 'E' and resid 325 through 337 removed outlier: 3.768A pdb=" N ASN E 329 " --> pdb=" O PRO E 325 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA E 333 " --> pdb=" O ASN E 329 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR E 334 " --> pdb=" O ALA E 330 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR E 337 " --> pdb=" O ALA E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 400 removed outlier: 3.506A pdb=" N ALA E 389 " --> pdb=" O GLU E 386 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG E 390 " --> pdb=" O ALA E 387 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP E 392 " --> pdb=" O ALA E 389 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU E 397 " --> pdb=" O LYS E 394 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET E 398 " --> pdb=" O PHE E 395 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR E 399 " --> pdb=" O ASP E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 411 removed outlier: 3.771A pdb=" N GLY E 410 " --> pdb=" O HIS E 406 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLU E 411 " --> pdb=" O TRP E 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 406 through 411' Processing helix chain 'E' and resid 415 through 436 removed outlier: 3.533A pdb=" N PHE E 418 " --> pdb=" O GLU E 415 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU E 420 " --> pdb=" O GLU E 417 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG E 422 " --> pdb=" O SER E 419 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP E 424 " --> pdb=" O ALA E 421 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS E 430 " --> pdb=" O ALA E 427 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR E 432 " --> pdb=" O GLU E 429 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU E 434 " --> pdb=" O ASP E 431 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY E 436 " --> pdb=" O GLU E 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 28 removed outlier: 3.594A pdb=" N ILE F 16 " --> pdb=" O CYS F 12 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY F 17 " --> pdb=" O GLY F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 49 No H-bonds generated for 'chain 'F' and resid 47 through 49' Processing helix chain 'F' and resid 70 through 78 Processing helix chain 'F' and resid 87 through 89 No H-bonds generated for 'chain 'F' and resid 87 through 89' Processing helix chain 'F' and resid 101 through 105 Processing helix chain 'F' and resid 109 through 125 removed outlier: 4.457A pdb=" N ASP F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N SER F 115 " --> pdb=" O GLU F 111 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP F 118 " --> pdb=" O ASP F 114 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL F 119 " --> pdb=" O SER F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 158 removed outlier: 3.604A pdb=" N LEU F 151 " --> pdb=" O MET F 147 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE F 152 " --> pdb=" O GLY F 148 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU F 157 " --> pdb=" O SER F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 195 Proline residue: F 182 - end of helix removed outlier: 3.525A pdb=" N ALA F 185 " --> pdb=" O PRO F 182 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR F 186 " --> pdb=" O TYR F 183 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU F 187 " --> pdb=" O ASN F 184 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL F 189 " --> pdb=" O THR F 186 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N HIS F 190 " --> pdb=" O LEU F 187 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL F 193 " --> pdb=" O HIS F 190 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASN F 195 " --> pdb=" O LEU F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 213 Processing helix chain 'F' and resid 222 through 239 removed outlier: 3.506A pdb=" N HIS F 227 " --> pdb=" O GLY F 223 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU F 228 " --> pdb=" O ASP F 224 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL F 229 " --> pdb=" O LEU F 225 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR F 237 " --> pdb=" O MET F 233 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N CYS F 239 " --> pdb=" O GLY F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 257 removed outlier: 3.579A pdb=" N MET F 257 " --> pdb=" O LEU F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 293 removed outlier: 3.583A pdb=" N THR F 290 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN F 292 " --> pdb=" O GLU F 288 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET F 293 " --> pdb=" O LEU F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 335 removed outlier: 3.858A pdb=" N GLN F 329 " --> pdb=" O GLU F 325 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN F 334 " --> pdb=" O MET F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 391 removed outlier: 3.800A pdb=" N PHE F 378 " --> pdb=" O GLN F 375 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS F 379 " --> pdb=" O GLU F 376 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU F 383 " --> pdb=" O ARG F 380 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR F 386 " --> pdb=" O GLU F 383 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA F 387 " --> pdb=" O GLN F 384 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG F 390 " --> pdb=" O ALA F 387 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG F 391 " --> pdb=" O MET F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 401 removed outlier: 3.880A pdb=" N GLU F 401 " --> pdb=" O TRP F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 426 removed outlier: 3.647A pdb=" N ASN F 414 " --> pdb=" O GLU F 410 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 26 removed outlier: 3.893A pdb=" N ILE J 16 " --> pdb=" O ALA J 12 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA J 19 " --> pdb=" O GLN J 15 " (cutoff:3.500A) Processing helix chain 'J' and resid 74 through 80 removed outlier: 3.551A pdb=" N ARG J 79 " --> pdb=" O ASP J 76 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR J 80 " --> pdb=" O GLU J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 107 Processing helix chain 'J' and resid 111 through 128 removed outlier: 5.998A pdb=" N ASP J 116 " --> pdb=" O LYS J 112 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N LEU J 117 " --> pdb=" O GLU J 113 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP J 127 " --> pdb=" O ARG J 123 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN J 128 " --> pdb=" O LYS J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 144 through 160 removed outlier: 4.513A pdb=" N THR J 150 " --> pdb=" O GLY J 146 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU J 155 " --> pdb=" O SER J 151 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG J 156 " --> pdb=" O LEU J 152 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER J 158 " --> pdb=" O MET J 154 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 197 removed outlier: 3.617A pdb=" N ASN J 186 " --> pdb=" O GLU J 183 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N SER J 187 " --> pdb=" O PRO J 184 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE J 188 " --> pdb=" O TYR J 185 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR J 190 " --> pdb=" O SER J 187 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR J 193 " --> pdb=" O THR J 190 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LEU J 195 " --> pdb=" O HIS J 192 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU J 196 " --> pdb=" O THR J 193 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS J 197 " --> pdb=" O THR J 194 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 215 Processing helix chain 'J' and resid 224 through 243 removed outlier: 3.751A pdb=" N LEU J 230 " --> pdb=" O ASN J 226 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE J 234 " --> pdb=" O LEU J 230 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N SER J 241 " --> pdb=" O SER J 237 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N LEU J 242 " --> pdb=" O ILE J 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 254 through 258 Processing helix chain 'J' and resid 288 through 295 removed outlier: 3.700A pdb=" N ASN J 293 " --> pdb=" O ALA J 289 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA J 294 " --> pdb=" O GLU J 290 " (cutoff:3.500A) Processing helix chain 'J' and resid 298 through 300 No H-bonds generated for 'chain 'J' and resid 298 through 300' Processing helix chain 'J' and resid 325 through 337 removed outlier: 3.768A pdb=" N ASN J 329 " --> pdb=" O PRO J 325 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA J 333 " --> pdb=" O ASN J 329 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR J 334 " --> pdb=" O ALA J 330 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N THR J 337 " --> pdb=" O ALA J 333 " (cutoff:3.500A) Processing helix chain 'J' and resid 383 through 400 removed outlier: 3.505A pdb=" N ALA J 389 " --> pdb=" O GLU J 386 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG J 390 " --> pdb=" O ALA J 387 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP J 392 " --> pdb=" O ALA J 389 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU J 397 " --> pdb=" O LYS J 394 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET J 398 " --> pdb=" O PHE J 395 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR J 399 " --> pdb=" O ASP J 396 " (cutoff:3.500A) Processing helix chain 'J' and resid 406 through 411 removed outlier: 3.771A pdb=" N GLY J 410 " --> pdb=" O HIS J 406 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N GLU J 411 " --> pdb=" O TRP J 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 406 through 411' Processing helix chain 'J' and resid 415 through 436 removed outlier: 3.532A pdb=" N PHE J 418 " --> pdb=" O GLU J 415 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU J 420 " --> pdb=" O GLU J 417 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG J 422 " --> pdb=" O SER J 419 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP J 424 " --> pdb=" O ALA J 421 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS J 430 " --> pdb=" O ALA J 427 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR J 432 " --> pdb=" O GLU J 429 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU J 434 " --> pdb=" O ASP J 431 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY J 436 " --> pdb=" O GLU J 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 26 removed outlier: 3.893A pdb=" N ILE C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA C 19 " --> pdb=" O GLN C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 80 removed outlier: 3.550A pdb=" N ARG C 79 " --> pdb=" O ASP C 76 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR C 80 " --> pdb=" O GLU C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 107 Processing helix chain 'C' and resid 111 through 128 removed outlier: 5.998A pdb=" N ASP C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N LEU C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP C 127 " --> pdb=" O ARG C 123 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 160 removed outlier: 4.513A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU C 155 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER C 158 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.618A pdb=" N ASN C 186 " --> pdb=" O GLU C 183 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N SER C 187 " --> pdb=" O PRO C 184 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE C 188 " --> pdb=" O TYR C 185 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR C 190 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR C 193 " --> pdb=" O THR C 190 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LEU C 195 " --> pdb=" O HIS C 192 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU C 196 " --> pdb=" O THR C 193 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS C 197 " --> pdb=" O THR C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 215 Processing helix chain 'C' and resid 224 through 243 removed outlier: 3.751A pdb=" N LEU C 230 " --> pdb=" O ASN C 226 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE C 234 " --> pdb=" O LEU C 230 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N LEU C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 258 Processing helix chain 'C' and resid 288 through 295 removed outlier: 3.699A pdb=" N ASN C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 300 No H-bonds generated for 'chain 'C' and resid 298 through 300' Processing helix chain 'C' and resid 325 through 337 removed outlier: 3.769A pdb=" N ASN C 329 " --> pdb=" O PRO C 325 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA C 333 " --> pdb=" O ASN C 329 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR C 334 " --> pdb=" O ALA C 330 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR C 337 " --> pdb=" O ALA C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 400 removed outlier: 3.506A pdb=" N ALA C 389 " --> pdb=" O GLU C 386 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG C 390 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP C 392 " --> pdb=" O ALA C 389 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU C 397 " --> pdb=" O LYS C 394 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET C 398 " --> pdb=" O PHE C 395 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR C 399 " --> pdb=" O ASP C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 411 removed outlier: 3.772A pdb=" N GLY C 410 " --> pdb=" O HIS C 406 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLU C 411 " --> pdb=" O TRP C 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 406 through 411' Processing helix chain 'C' and resid 415 through 436 removed outlier: 3.531A pdb=" N PHE C 418 " --> pdb=" O GLU C 415 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU C 420 " --> pdb=" O GLU C 417 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG C 422 " --> pdb=" O SER C 419 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP C 424 " --> pdb=" O ALA C 421 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS C 430 " --> pdb=" O ALA C 427 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR C 432 " --> pdb=" O GLU C 429 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU C 434 " --> pdb=" O ASP C 431 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY C 436 " --> pdb=" O GLU C 433 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 26 removed outlier: 3.893A pdb=" N ILE L 16 " --> pdb=" O ALA L 12 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA L 19 " --> pdb=" O GLN L 15 " (cutoff:3.500A) Processing helix chain 'L' and resid 74 through 80 removed outlier: 3.551A pdb=" N ARG L 79 " --> pdb=" O ASP L 76 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR L 80 " --> pdb=" O GLU L 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 107 Processing helix chain 'L' and resid 111 through 128 removed outlier: 5.999A pdb=" N ASP L 116 " --> pdb=" O LYS L 112 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LEU L 117 " --> pdb=" O GLU L 113 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP L 127 " --> pdb=" O ARG L 123 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN L 128 " --> pdb=" O LYS L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 144 through 160 removed outlier: 4.513A pdb=" N THR L 150 " --> pdb=" O GLY L 146 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU L 155 " --> pdb=" O SER L 151 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG L 156 " --> pdb=" O LEU L 152 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER L 158 " --> pdb=" O MET L 154 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 197 removed outlier: 3.618A pdb=" N ASN L 186 " --> pdb=" O GLU L 183 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N SER L 187 " --> pdb=" O PRO L 184 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE L 188 " --> pdb=" O TYR L 185 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR L 190 " --> pdb=" O SER L 187 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR L 193 " --> pdb=" O THR L 190 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LEU L 195 " --> pdb=" O HIS L 192 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU L 196 " --> pdb=" O THR L 193 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS L 197 " --> pdb=" O THR L 194 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 215 Processing helix chain 'L' and resid 224 through 243 removed outlier: 3.751A pdb=" N LEU L 230 " --> pdb=" O ASN L 226 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE L 234 " --> pdb=" O LEU L 230 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N SER L 241 " --> pdb=" O SER L 237 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N LEU L 242 " --> pdb=" O ILE L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 254 through 258 Processing helix chain 'L' and resid 288 through 295 removed outlier: 3.700A pdb=" N ASN L 293 " --> pdb=" O ALA L 289 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA L 294 " --> pdb=" O GLU L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 300 No H-bonds generated for 'chain 'L' and resid 298 through 300' Processing helix chain 'L' and resid 325 through 337 removed outlier: 3.768A pdb=" N ASN L 329 " --> pdb=" O PRO L 325 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA L 333 " --> pdb=" O ASN L 329 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR L 334 " --> pdb=" O ALA L 330 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR L 337 " --> pdb=" O ALA L 333 " (cutoff:3.500A) Processing helix chain 'L' and resid 383 through 400 removed outlier: 3.506A pdb=" N ALA L 389 " --> pdb=" O GLU L 386 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG L 390 " --> pdb=" O ALA L 387 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP L 392 " --> pdb=" O ALA L 389 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU L 397 " --> pdb=" O LYS L 394 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET L 398 " --> pdb=" O PHE L 395 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR L 399 " --> pdb=" O ASP L 396 " (cutoff:3.500A) Processing helix chain 'L' and resid 406 through 411 removed outlier: 3.771A pdb=" N GLY L 410 " --> pdb=" O HIS L 406 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLU L 411 " --> pdb=" O TRP L 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 406 through 411' Processing helix chain 'L' and resid 415 through 436 removed outlier: 3.532A pdb=" N PHE L 418 " --> pdb=" O GLU L 415 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU L 420 " --> pdb=" O GLU L 417 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG L 422 " --> pdb=" O SER L 419 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP L 424 " --> pdb=" O ALA L 421 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS L 430 " --> pdb=" O ALA L 427 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR L 432 " --> pdb=" O GLU L 429 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU L 434 " --> pdb=" O ASP L 431 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY L 436 " --> pdb=" O GLU L 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 26 removed outlier: 3.893A pdb=" N ILE A 16 " --> pdb=" O ALA A 12 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 80 removed outlier: 3.551A pdb=" N ARG A 79 " --> pdb=" O ASP A 76 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR A 80 " --> pdb=" O GLU A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 111 through 128 removed outlier: 5.999A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP A 127 " --> pdb=" O ARG A 123 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 160 removed outlier: 4.513A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU A 155 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.619A pdb=" N ASN A 186 " --> pdb=" O GLU A 183 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N SER A 187 " --> pdb=" O PRO A 184 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE A 188 " --> pdb=" O TYR A 185 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR A 190 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR A 193 " --> pdb=" O THR A 190 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LEU A 195 " --> pdb=" O HIS A 192 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU A 196 " --> pdb=" O THR A 193 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS A 197 " --> pdb=" O THR A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 215 Processing helix chain 'A' and resid 224 through 243 removed outlier: 3.752A pdb=" N LEU A 230 " --> pdb=" O ASN A 226 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 258 Processing helix chain 'A' and resid 288 through 295 removed outlier: 3.698A pdb=" N ASN A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 325 through 337 removed outlier: 3.767A pdb=" N ASN A 329 " --> pdb=" O PRO A 325 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A 333 " --> pdb=" O ASN A 329 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 400 removed outlier: 3.504A pdb=" N ALA A 389 " --> pdb=" O GLU A 386 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG A 390 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP A 392 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 397 " --> pdb=" O LYS A 394 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET A 398 " --> pdb=" O PHE A 395 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR A 399 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 411 removed outlier: 3.771A pdb=" N GLY A 410 " --> pdb=" O HIS A 406 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N GLU A 411 " --> pdb=" O TRP A 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 406 through 411' Processing helix chain 'A' and resid 415 through 436 removed outlier: 3.531A pdb=" N PHE A 418 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU A 420 " --> pdb=" O GLU A 417 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG A 422 " --> pdb=" O SER A 419 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP A 424 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS A 430 " --> pdb=" O ALA A 427 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR A 432 " --> pdb=" O GLU A 429 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU A 434 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY A 436 " --> pdb=" O GLU A 433 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 26 removed outlier: 3.893A pdb=" N ILE K 16 " --> pdb=" O ALA K 12 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA K 19 " --> pdb=" O GLN K 15 " (cutoff:3.500A) Processing helix chain 'K' and resid 74 through 80 removed outlier: 3.550A pdb=" N ARG K 79 " --> pdb=" O ASP K 76 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR K 80 " --> pdb=" O GLU K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 103 through 107 Processing helix chain 'K' and resid 111 through 128 removed outlier: 5.998A pdb=" N ASP K 116 " --> pdb=" O LYS K 112 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LEU K 117 " --> pdb=" O GLU K 113 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP K 127 " --> pdb=" O ARG K 123 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN K 128 " --> pdb=" O LYS K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 144 through 160 removed outlier: 4.513A pdb=" N THR K 150 " --> pdb=" O GLY K 146 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU K 155 " --> pdb=" O SER K 151 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG K 156 " --> pdb=" O LEU K 152 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER K 158 " --> pdb=" O MET K 154 " (cutoff:3.500A) Processing helix chain 'K' and resid 182 through 197 removed outlier: 3.618A pdb=" N ASN K 186 " --> pdb=" O GLU K 183 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N SER K 187 " --> pdb=" O PRO K 184 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE K 188 " --> pdb=" O TYR K 185 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR K 190 " --> pdb=" O SER K 187 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR K 193 " --> pdb=" O THR K 190 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LEU K 195 " --> pdb=" O HIS K 192 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU K 196 " --> pdb=" O THR K 193 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS K 197 " --> pdb=" O THR K 194 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 215 Processing helix chain 'K' and resid 224 through 243 removed outlier: 3.751A pdb=" N LEU K 230 " --> pdb=" O ASN K 226 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE K 234 " --> pdb=" O LEU K 230 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N SER K 241 " --> pdb=" O SER K 237 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N LEU K 242 " --> pdb=" O ILE K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 254 through 258 Processing helix chain 'K' and resid 288 through 295 removed outlier: 3.698A pdb=" N ASN K 293 " --> pdb=" O ALA K 289 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA K 294 " --> pdb=" O GLU K 290 " (cutoff:3.500A) Processing helix chain 'K' and resid 298 through 300 No H-bonds generated for 'chain 'K' and resid 298 through 300' Processing helix chain 'K' and resid 325 through 337 removed outlier: 3.768A pdb=" N ASN K 329 " --> pdb=" O PRO K 325 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA K 333 " --> pdb=" O ASN K 329 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR K 334 " --> pdb=" O ALA K 330 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR K 337 " --> pdb=" O ALA K 333 " (cutoff:3.500A) Processing helix chain 'K' and resid 383 through 400 removed outlier: 3.505A pdb=" N ALA K 389 " --> pdb=" O GLU K 386 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP K 392 " --> pdb=" O ALA K 389 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU K 397 " --> pdb=" O LYS K 394 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET K 398 " --> pdb=" O PHE K 395 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR K 399 " --> pdb=" O ASP K 396 " (cutoff:3.500A) Processing helix chain 'K' and resid 406 through 411 removed outlier: 3.772A pdb=" N GLY K 410 " --> pdb=" O HIS K 406 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLU K 411 " --> pdb=" O TRP K 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 406 through 411' Processing helix chain 'K' and resid 415 through 436 removed outlier: 3.532A pdb=" N PHE K 418 " --> pdb=" O GLU K 415 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU K 420 " --> pdb=" O GLU K 417 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG K 422 " --> pdb=" O SER K 419 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP K 424 " --> pdb=" O ALA K 421 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS K 430 " --> pdb=" O ALA K 427 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR K 432 " --> pdb=" O GLU K 429 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU K 434 " --> pdb=" O ASP K 431 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY K 436 " --> pdb=" O GLU K 433 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 28 removed outlier: 3.594A pdb=" N ILE G 16 " --> pdb=" O CYS G 12 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY G 17 " --> pdb=" O GLY G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 49 No H-bonds generated for 'chain 'G' and resid 47 through 49' Processing helix chain 'G' and resid 70 through 78 Processing helix chain 'G' and resid 87 through 89 No H-bonds generated for 'chain 'G' and resid 87 through 89' Processing helix chain 'G' and resid 101 through 105 Processing helix chain 'G' and resid 109 through 125 removed outlier: 4.457A pdb=" N ASP G 114 " --> pdb=" O ALA G 110 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N SER G 115 " --> pdb=" O GLU G 111 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP G 118 " --> pdb=" O ASP G 114 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL G 119 " --> pdb=" O SER G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 158 removed outlier: 3.604A pdb=" N LEU G 151 " --> pdb=" O MET G 147 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE G 152 " --> pdb=" O GLY G 148 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU G 157 " --> pdb=" O SER G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 195 Proline residue: G 182 - end of helix removed outlier: 3.524A pdb=" N ALA G 185 " --> pdb=" O PRO G 182 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR G 186 " --> pdb=" O TYR G 183 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU G 187 " --> pdb=" O ASN G 184 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL G 189 " --> pdb=" O THR G 186 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N HIS G 190 " --> pdb=" O LEU G 187 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL G 193 " --> pdb=" O HIS G 190 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASN G 195 " --> pdb=" O LEU G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 213 Processing helix chain 'G' and resid 222 through 239 removed outlier: 3.506A pdb=" N HIS G 227 " --> pdb=" O GLY G 223 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU G 228 " --> pdb=" O ASP G 224 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL G 229 " --> pdb=" O LEU G 225 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR G 237 " --> pdb=" O MET G 233 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N CYS G 239 " --> pdb=" O GLY G 235 " (cutoff:3.500A) Processing helix chain 'G' and resid 250 through 257 removed outlier: 3.579A pdb=" N MET G 257 " --> pdb=" O LEU G 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 293 removed outlier: 3.583A pdb=" N THR G 290 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN G 292 " --> pdb=" O GLU G 288 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET G 293 " --> pdb=" O LEU G 289 " (cutoff:3.500A) Processing helix chain 'G' and resid 323 through 335 removed outlier: 3.858A pdb=" N GLN G 329 " --> pdb=" O GLU G 325 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN G 334 " --> pdb=" O MET G 330 " (cutoff:3.500A) Processing helix chain 'G' and resid 373 through 391 removed outlier: 3.799A pdb=" N PHE G 378 " --> pdb=" O GLN G 375 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS G 379 " --> pdb=" O GLU G 376 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU G 383 " --> pdb=" O ARG G 380 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR G 386 " --> pdb=" O GLU G 383 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA G 387 " --> pdb=" O GLN G 384 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG G 390 " --> pdb=" O ALA G 387 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG G 391 " --> pdb=" O MET G 388 " (cutoff:3.500A) Processing helix chain 'G' and resid 395 through 401 removed outlier: 3.880A pdb=" N GLU G 401 " --> pdb=" O TRP G 397 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 426 removed outlier: 3.647A pdb=" N ASN G 414 " --> pdb=" O GLU G 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 28 removed outlier: 3.595A pdb=" N ILE D 16 " --> pdb=" O CYS D 12 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY D 17 " --> pdb=" O GLY D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 70 through 78 Processing helix chain 'D' and resid 87 through 89 No H-bonds generated for 'chain 'D' and resid 87 through 89' Processing helix chain 'D' and resid 101 through 105 Processing helix chain 'D' and resid 109 through 125 removed outlier: 4.457A pdb=" N ASP D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N SER D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP D 118 " --> pdb=" O ASP D 114 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL D 119 " --> pdb=" O SER D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 158 removed outlier: 3.604A pdb=" N LEU D 151 " --> pdb=" O MET D 147 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE D 152 " --> pdb=" O GLY D 148 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU D 157 " --> pdb=" O SER D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 195 Proline residue: D 182 - end of helix removed outlier: 3.525A pdb=" N ALA D 185 " --> pdb=" O PRO D 182 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR D 186 " --> pdb=" O TYR D 183 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU D 187 " --> pdb=" O ASN D 184 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL D 189 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N HIS D 190 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL D 193 " --> pdb=" O HIS D 190 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASN D 195 " --> pdb=" O LEU D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 213 Processing helix chain 'D' and resid 222 through 239 removed outlier: 3.506A pdb=" N HIS D 227 " --> pdb=" O GLY D 223 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU D 228 " --> pdb=" O ASP D 224 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL D 229 " --> pdb=" O LEU D 225 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR D 237 " --> pdb=" O MET D 233 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N CYS D 239 " --> pdb=" O GLY D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 257 removed outlier: 3.579A pdb=" N MET D 257 " --> pdb=" O LEU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 293 removed outlier: 3.583A pdb=" N THR D 290 " --> pdb=" O VAL D 286 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN D 292 " --> pdb=" O GLU D 288 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET D 293 " --> pdb=" O LEU D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 335 removed outlier: 3.858A pdb=" N GLN D 329 " --> pdb=" O GLU D 325 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN D 334 " --> pdb=" O MET D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 391 removed outlier: 3.799A pdb=" N PHE D 378 " --> pdb=" O GLN D 375 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS D 379 " --> pdb=" O GLU D 376 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU D 383 " --> pdb=" O ARG D 380 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR D 386 " --> pdb=" O GLU D 383 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA D 387 " --> pdb=" O GLN D 384 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ARG D 390 " --> pdb=" O ALA D 387 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG D 391 " --> pdb=" O MET D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 401 removed outlier: 3.880A pdb=" N GLU D 401 " --> pdb=" O TRP D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 426 removed outlier: 3.647A pdb=" N ASN D 414 " --> pdb=" O GLU D 410 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 28 removed outlier: 3.594A pdb=" N ILE I 16 " --> pdb=" O CYS I 12 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY I 17 " --> pdb=" O GLY I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 49 No H-bonds generated for 'chain 'I' and resid 47 through 49' Processing helix chain 'I' and resid 70 through 78 Processing helix chain 'I' and resid 87 through 89 No H-bonds generated for 'chain 'I' and resid 87 through 89' Processing helix chain 'I' and resid 101 through 105 Processing helix chain 'I' and resid 109 through 125 removed outlier: 4.456A pdb=" N ASP I 114 " --> pdb=" O ALA I 110 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N SER I 115 " --> pdb=" O GLU I 111 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP I 118 " --> pdb=" O ASP I 114 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL I 119 " --> pdb=" O SER I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 146 through 158 removed outlier: 3.604A pdb=" N LEU I 151 " --> pdb=" O MET I 147 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE I 152 " --> pdb=" O GLY I 148 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU I 157 " --> pdb=" O SER I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 179 through 195 Proline residue: I 182 - end of helix removed outlier: 3.525A pdb=" N ALA I 185 " --> pdb=" O PRO I 182 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR I 186 " --> pdb=" O TYR I 183 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU I 187 " --> pdb=" O ASN I 184 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL I 189 " --> pdb=" O THR I 186 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N HIS I 190 " --> pdb=" O LEU I 187 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL I 193 " --> pdb=" O HIS I 190 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASN I 195 " --> pdb=" O LEU I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 204 through 213 Processing helix chain 'I' and resid 222 through 239 removed outlier: 3.506A pdb=" N HIS I 227 " --> pdb=" O GLY I 223 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU I 228 " --> pdb=" O ASP I 224 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL I 229 " --> pdb=" O LEU I 225 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR I 237 " --> pdb=" O MET I 233 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N CYS I 239 " --> pdb=" O GLY I 235 " (cutoff:3.500A) Processing helix chain 'I' and resid 250 through 257 removed outlier: 3.579A pdb=" N MET I 257 " --> pdb=" O LEU I 253 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 293 removed outlier: 3.583A pdb=" N THR I 290 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN I 292 " --> pdb=" O GLU I 288 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET I 293 " --> pdb=" O LEU I 289 " (cutoff:3.500A) Processing helix chain 'I' and resid 323 through 335 removed outlier: 3.858A pdb=" N GLN I 329 " --> pdb=" O GLU I 325 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN I 334 " --> pdb=" O MET I 330 " (cutoff:3.500A) Processing helix chain 'I' and resid 373 through 391 removed outlier: 3.799A pdb=" N PHE I 378 " --> pdb=" O GLN I 375 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS I 379 " --> pdb=" O GLU I 376 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU I 383 " --> pdb=" O ARG I 380 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR I 386 " --> pdb=" O GLU I 383 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA I 387 " --> pdb=" O GLN I 384 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG I 390 " --> pdb=" O ALA I 387 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG I 391 " --> pdb=" O MET I 388 " (cutoff:3.500A) Processing helix chain 'I' and resid 395 through 401 removed outlier: 3.881A pdb=" N GLU I 401 " --> pdb=" O TRP I 397 " (cutoff:3.500A) Processing helix chain 'I' and resid 405 through 426 removed outlier: 3.647A pdb=" N ASN I 414 " --> pdb=" O GLU I 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 28 removed outlier: 3.594A pdb=" N ILE B 16 " --> pdb=" O CYS B 12 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY B 17 " --> pdb=" O GLY B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 70 through 78 Processing helix chain 'B' and resid 87 through 89 No H-bonds generated for 'chain 'B' and resid 87 through 89' Processing helix chain 'B' and resid 101 through 105 Processing helix chain 'B' and resid 109 through 125 removed outlier: 4.456A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP B 118 " --> pdb=" O ASP B 114 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL B 119 " --> pdb=" O SER B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 158 removed outlier: 3.604A pdb=" N LEU B 151 " --> pdb=" O MET B 147 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B 152 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU B 157 " --> pdb=" O SER B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 195 Proline residue: B 182 - end of helix removed outlier: 3.525A pdb=" N ALA B 185 " --> pdb=" O PRO B 182 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR B 186 " --> pdb=" O TYR B 183 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU B 187 " --> pdb=" O ASN B 184 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL B 189 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N HIS B 190 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL B 193 " --> pdb=" O HIS B 190 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASN B 195 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 213 Processing helix chain 'B' and resid 222 through 239 removed outlier: 3.506A pdb=" N HIS B 227 " --> pdb=" O GLY B 223 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N CYS B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 257 removed outlier: 3.580A pdb=" N MET B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 293 removed outlier: 3.583A pdb=" N THR B 290 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN B 292 " --> pdb=" O GLU B 288 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET B 293 " --> pdb=" O LEU B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 335 removed outlier: 3.858A pdb=" N GLN B 329 " --> pdb=" O GLU B 325 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN B 334 " --> pdb=" O MET B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 391 removed outlier: 3.799A pdb=" N PHE B 378 " --> pdb=" O GLN B 375 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS B 379 " --> pdb=" O GLU B 376 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU B 383 " --> pdb=" O ARG B 380 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR B 386 " --> pdb=" O GLU B 383 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA B 387 " --> pdb=" O GLN B 384 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG B 390 " --> pdb=" O ALA B 387 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG B 391 " --> pdb=" O MET B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 401 removed outlier: 3.880A pdb=" N GLU B 401 " --> pdb=" O TRP B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 426 removed outlier: 3.647A pdb=" N ASN B 414 " --> pdb=" O GLU B 410 " (cutoff:3.500A) Processing helix chain 'H' and resid 11 through 28 removed outlier: 3.594A pdb=" N ILE H 16 " --> pdb=" O CYS H 12 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY H 17 " --> pdb=" O GLY H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 49 No H-bonds generated for 'chain 'H' and resid 47 through 49' Processing helix chain 'H' and resid 70 through 78 Processing helix chain 'H' and resid 87 through 89 No H-bonds generated for 'chain 'H' and resid 87 through 89' Processing helix chain 'H' and resid 101 through 105 Processing helix chain 'H' and resid 109 through 125 removed outlier: 4.457A pdb=" N ASP H 114 " --> pdb=" O ALA H 110 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N SER H 115 " --> pdb=" O GLU H 111 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP H 118 " --> pdb=" O ASP H 114 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL H 119 " --> pdb=" O SER H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 146 through 158 removed outlier: 3.604A pdb=" N LEU H 151 " --> pdb=" O MET H 147 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE H 152 " --> pdb=" O GLY H 148 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU H 157 " --> pdb=" O SER H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 195 Proline residue: H 182 - end of helix removed outlier: 3.525A pdb=" N ALA H 185 " --> pdb=" O PRO H 182 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR H 186 " --> pdb=" O TYR H 183 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU H 187 " --> pdb=" O ASN H 184 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL H 189 " --> pdb=" O THR H 186 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N HIS H 190 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL H 193 " --> pdb=" O HIS H 190 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASN H 195 " --> pdb=" O LEU H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 213 Processing helix chain 'H' and resid 222 through 239 removed outlier: 3.507A pdb=" N HIS H 227 " --> pdb=" O GLY H 223 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU H 228 " --> pdb=" O ASP H 224 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL H 229 " --> pdb=" O LEU H 225 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR H 237 " --> pdb=" O MET H 233 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N CYS H 239 " --> pdb=" O GLY H 235 " (cutoff:3.500A) Processing helix chain 'H' and resid 250 through 257 removed outlier: 3.579A pdb=" N MET H 257 " --> pdb=" O LEU H 253 " (cutoff:3.500A) Processing helix chain 'H' and resid 286 through 293 removed outlier: 3.583A pdb=" N THR H 290 " --> pdb=" O VAL H 286 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN H 292 " --> pdb=" O GLU H 288 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET H 293 " --> pdb=" O LEU H 289 " (cutoff:3.500A) Processing helix chain 'H' and resid 323 through 335 removed outlier: 3.857A pdb=" N GLN H 329 " --> pdb=" O GLU H 325 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN H 334 " --> pdb=" O MET H 330 " (cutoff:3.500A) Processing helix chain 'H' and resid 373 through 391 removed outlier: 3.799A pdb=" N PHE H 378 " --> pdb=" O GLN H 375 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS H 379 " --> pdb=" O GLU H 376 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU H 383 " --> pdb=" O ARG H 380 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR H 386 " --> pdb=" O GLU H 383 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA H 387 " --> pdb=" O GLN H 384 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG H 390 " --> pdb=" O ALA H 387 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG H 391 " --> pdb=" O MET H 388 " (cutoff:3.500A) Processing helix chain 'H' and resid 395 through 401 removed outlier: 3.881A pdb=" N GLU H 401 " --> pdb=" O TRP H 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 405 through 426 removed outlier: 3.647A pdb=" N ASN H 414 " --> pdb=" O GLU H 410 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'E' and resid 65 through 68 removed outlier: 6.396A pdb=" N SER E 6 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N VAL E 68 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N HIS E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE E 5 " --> pdb=" O GLY E 134 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N SER E 165 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N VAL E 137 " --> pdb=" O SER E 165 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU E 167 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N CYS E 200 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N SER E 170 " --> pdb=" O CYS E 200 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N PHE E 202 " --> pdb=" O SER E 170 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA E 270 " --> pdb=" O MET E 203 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N PHE E 267 " --> pdb=" O THR E 381 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N THR E 381 " --> pdb=" O PHE E 267 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'E' and resid 53 through 55 removed outlier: 3.735A pdb=" N VAL E 62 " --> pdb=" O SER E 54 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'F' and resid 90 through 92 removed outlier: 7.855A pdb=" N VAL F 91 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LEU F 65 " --> pdb=" O VAL F 91 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N ILE F 64 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N HIS F 6 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N VAL F 66 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLN F 8 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N VAL F 5 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N PHE F 133 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILE F 7 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LEU F 135 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ALA F 9 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE F 163 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N LEU F 135 " --> pdb=" O ILE F 163 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASN F 165 " --> pdb=" O LEU F 135 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'F' and resid 51 through 54 removed outlier: 3.809A pdb=" N LYS F 58 " --> pdb=" O ALA F 54 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'F' and resid 266 through 271 removed outlier: 3.962A pdb=" N ALA F 271 " --> pdb=" O ALA F 365 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'J' and resid 65 through 68 removed outlier: 6.396A pdb=" N SER J 6 " --> pdb=" O VAL J 66 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N VAL J 68 " --> pdb=" O SER J 6 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N HIS J 8 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE J 5 " --> pdb=" O GLY J 134 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N SER J 165 " --> pdb=" O PHE J 135 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N VAL J 137 " --> pdb=" O SER J 165 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU J 167 " --> pdb=" O VAL J 137 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N CYS J 200 " --> pdb=" O GLU J 168 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N SER J 170 " --> pdb=" O CYS J 200 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N PHE J 202 " --> pdb=" O SER J 170 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA J 270 " --> pdb=" O MET J 203 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N PHE J 267 " --> pdb=" O THR J 381 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N THR J 381 " --> pdb=" O PHE J 267 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'J' and resid 53 through 55 removed outlier: 3.735A pdb=" N VAL J 62 " --> pdb=" O SER J 54 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 65 through 68 removed outlier: 6.397A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE C 5 " --> pdb=" O GLY C 134 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N SER C 165 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N VAL C 137 " --> pdb=" O SER C 165 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU C 167 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N CYS C 200 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N SER C 170 " --> pdb=" O CYS C 200 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N PHE C 202 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA C 270 " --> pdb=" O MET C 203 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N PHE C 267 " --> pdb=" O THR C 381 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N THR C 381 " --> pdb=" O PHE C 267 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 53 through 55 removed outlier: 3.734A pdb=" N VAL C 62 " --> pdb=" O SER C 54 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'L' and resid 65 through 68 removed outlier: 6.396A pdb=" N SER L 6 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N VAL L 68 " --> pdb=" O SER L 6 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N HIS L 8 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE L 5 " --> pdb=" O GLY L 134 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N SER L 165 " --> pdb=" O PHE L 135 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N VAL L 137 " --> pdb=" O SER L 165 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU L 167 " --> pdb=" O VAL L 137 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N CYS L 200 " --> pdb=" O GLU L 168 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N SER L 170 " --> pdb=" O CYS L 200 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N PHE L 202 " --> pdb=" O SER L 170 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA L 270 " --> pdb=" O MET L 203 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N PHE L 267 " --> pdb=" O THR L 381 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N THR L 381 " --> pdb=" O PHE L 267 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'L' and resid 53 through 55 removed outlier: 3.735A pdb=" N VAL L 62 " --> pdb=" O SER L 54 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 65 through 68 removed outlier: 6.396A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE A 5 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N SER A 165 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N VAL A 137 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU A 167 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N CYS A 200 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N SER A 170 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N PHE A 202 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA A 270 " --> pdb=" O MET A 203 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N PHE A 267 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N THR A 381 " --> pdb=" O PHE A 267 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 53 through 55 removed outlier: 3.736A pdb=" N VAL A 62 " --> pdb=" O SER A 54 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'K' and resid 65 through 68 removed outlier: 6.396A pdb=" N SER K 6 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N VAL K 68 " --> pdb=" O SER K 6 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N HIS K 8 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE K 5 " --> pdb=" O GLY K 134 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N SER K 165 " --> pdb=" O PHE K 135 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N VAL K 137 " --> pdb=" O SER K 165 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU K 167 " --> pdb=" O VAL K 137 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N CYS K 200 " --> pdb=" O GLU K 168 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N SER K 170 " --> pdb=" O CYS K 200 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N PHE K 202 " --> pdb=" O SER K 170 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA K 270 " --> pdb=" O MET K 203 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N PHE K 267 " --> pdb=" O THR K 381 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N THR K 381 " --> pdb=" O PHE K 267 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'K' and resid 53 through 55 removed outlier: 3.735A pdb=" N VAL K 62 " --> pdb=" O SER K 54 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 90 through 92 removed outlier: 7.856A pdb=" N VAL G 91 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LEU G 65 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N ILE G 64 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N HIS G 6 " --> pdb=" O ILE G 64 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL G 66 " --> pdb=" O HIS G 6 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLN G 8 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N VAL G 5 " --> pdb=" O GLN G 131 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N PHE G 133 " --> pdb=" O VAL G 5 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ILE G 7 " --> pdb=" O PHE G 133 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LEU G 135 " --> pdb=" O ILE G 7 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ALA G 9 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE G 163 " --> pdb=" O PHE G 133 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N LEU G 135 " --> pdb=" O ILE G 163 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASN G 165 " --> pdb=" O LEU G 135 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 51 through 54 removed outlier: 3.810A pdb=" N LYS G 58 " --> pdb=" O ALA G 54 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'G' and resid 266 through 271 removed outlier: 3.962A pdb=" N ALA G 271 " --> pdb=" O ALA G 365 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 90 through 92 removed outlier: 7.855A pdb=" N VAL D 91 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LEU D 65 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N ILE D 64 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N HIS D 6 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N VAL D 66 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLN D 8 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N VAL D 5 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N PHE D 133 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILE D 7 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU D 135 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ALA D 9 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE D 163 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N LEU D 135 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASN D 165 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 51 through 54 removed outlier: 3.809A pdb=" N LYS D 58 " --> pdb=" O ALA D 54 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 266 through 271 removed outlier: 3.962A pdb=" N ALA D 271 " --> pdb=" O ALA D 365 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'I' and resid 90 through 92 removed outlier: 7.856A pdb=" N VAL I 91 " --> pdb=" O ALA I 63 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LEU I 65 " --> pdb=" O VAL I 91 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N ILE I 64 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N HIS I 6 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N VAL I 66 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLN I 8 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N VAL I 5 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N PHE I 133 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ILE I 7 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LEU I 135 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ALA I 9 " --> pdb=" O LEU I 135 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE I 163 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N LEU I 135 " --> pdb=" O ILE I 163 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASN I 165 " --> pdb=" O LEU I 135 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'I' and resid 51 through 54 removed outlier: 3.809A pdb=" N LYS I 58 " --> pdb=" O ALA I 54 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'I' and resid 266 through 271 removed outlier: 3.962A pdb=" N ALA I 271 " --> pdb=" O ALA I 365 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 90 through 92 removed outlier: 7.855A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N VAL B 5 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N PHE B 133 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILE B 7 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LEU B 135 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ALA B 9 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE B 163 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N LEU B 135 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASN B 165 " --> pdb=" O LEU B 135 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 51 through 54 removed outlier: 3.810A pdb=" N LYS B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'B' and resid 266 through 271 removed outlier: 3.962A pdb=" N ALA B 271 " --> pdb=" O ALA B 365 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'H' and resid 90 through 92 removed outlier: 7.856A pdb=" N VAL H 91 " --> pdb=" O ALA H 63 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LEU H 65 " --> pdb=" O VAL H 91 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N ILE H 64 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N HIS H 6 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N VAL H 66 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLN H 8 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N VAL H 5 " --> pdb=" O GLN H 131 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N PHE H 133 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ILE H 7 " --> pdb=" O PHE H 133 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LEU H 135 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ALA H 9 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE H 163 " --> pdb=" O PHE H 133 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N LEU H 135 " --> pdb=" O ILE H 163 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASN H 165 " --> pdb=" O LEU H 135 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'H' and resid 51 through 54 removed outlier: 3.809A pdb=" N LYS H 58 " --> pdb=" O ALA H 54 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'H' and resid 266 through 271 removed outlier: 3.962A pdb=" N ALA H 271 " --> pdb=" O ALA H 365 " (cutoff:3.500A) 1309 hydrogen bonds defined for protein. 3186 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: 12.29 Time building geometry restraints manager: 16.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 13782 1.36 - 1.49: 10952 1.49 - 1.63: 16648 1.63 - 1.76: 0 1.76 - 1.90: 438 Bond restraints: 41820 Sorted by residual: bond pdb=" PG GSP G 501 " pdb=" S1G GSP G 501 " ideal model delta sigma weight residual 1.700 1.900 -0.200 2.00e-02 2.50e+03 1.00e+02 bond pdb=" PG GSP F 501 " pdb=" S1G GSP F 501 " ideal model delta sigma weight residual 1.700 1.899 -0.199 2.00e-02 2.50e+03 9.93e+01 bond pdb=" PG GSP H 501 " pdb=" S1G GSP H 501 " ideal model delta sigma weight residual 1.700 1.899 -0.199 2.00e-02 2.50e+03 9.92e+01 bond pdb=" PG GSP I 501 " pdb=" S1G GSP I 501 " ideal model delta sigma weight residual 1.700 1.899 -0.199 2.00e-02 2.50e+03 9.89e+01 bond pdb=" PG GSP B 501 " pdb=" S1G GSP B 501 " ideal model delta sigma weight residual 1.700 1.899 -0.199 2.00e-02 2.50e+03 9.89e+01 ... (remaining 41815 not shown) Histogram of bond angle deviations from ideal: 95.43 - 103.15: 476 103.15 - 110.87: 14605 110.87 - 118.59: 18062 118.59 - 126.31: 23045 126.31 - 134.03: 638 Bond angle restraints: 56826 Sorted by residual: angle pdb=" O2G GSP D 501 " pdb=" PG GSP D 501 " pdb=" O3G GSP D 501 " ideal model delta sigma weight residual 109.50 95.43 14.07 3.00e+00 1.11e-01 2.20e+01 angle pdb=" O2G GSP B 501 " pdb=" PG GSP B 501 " pdb=" O3G GSP B 501 " ideal model delta sigma weight residual 109.50 95.53 13.97 3.00e+00 1.11e-01 2.17e+01 angle pdb=" O2G GSP H 501 " pdb=" PG GSP H 501 " pdb=" O3G GSP H 501 " ideal model delta sigma weight residual 109.50 95.58 13.92 3.00e+00 1.11e-01 2.15e+01 angle pdb=" O2G GSP I 501 " pdb=" PG GSP I 501 " pdb=" O3G GSP I 501 " ideal model delta sigma weight residual 109.50 95.61 13.89 3.00e+00 1.11e-01 2.15e+01 angle pdb=" O2G GSP F 501 " pdb=" PG GSP F 501 " pdb=" O3G GSP F 501 " ideal model delta sigma weight residual 109.50 95.63 13.87 3.00e+00 1.11e-01 2.14e+01 ... (remaining 56821 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.39: 24623 32.39 - 64.78: 184 64.78 - 97.18: 31 97.18 - 129.57: 15 129.57 - 161.96: 17 Dihedral angle restraints: 24870 sinusoidal: 9942 harmonic: 14928 Sorted by residual: dihedral pdb=" C5' GTP E 501 " pdb=" O5' GTP E 501 " pdb=" PA GTP E 501 " pdb=" O3A GTP E 501 " ideal model delta sinusoidal sigma weight residual 69.27 -128.77 -161.96 1 2.00e+01 2.50e-03 4.68e+01 dihedral pdb=" C5' GTP C 501 " pdb=" O5' GTP C 501 " pdb=" PA GTP C 501 " pdb=" O3A GTP C 501 " ideal model delta sinusoidal sigma weight residual 69.27 -130.88 -159.85 1 2.00e+01 2.50e-03 4.65e+01 dihedral pdb=" C4' GTP K 501 " pdb=" C5' GTP K 501 " pdb=" O5' GTP K 501 " pdb=" PA GTP K 501 " ideal model delta sinusoidal sigma weight residual 260.87 104.42 156.45 1 2.00e+01 2.50e-03 4.60e+01 ... (remaining 24867 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 4516 0.051 - 0.103: 1374 0.103 - 0.154: 267 0.154 - 0.206: 47 0.206 - 0.257: 12 Chirality restraints: 6216 Sorted by residual: chirality pdb=" C2' GSP H 501 " pdb=" C1' GSP H 501 " pdb=" C3' GSP H 501 " pdb=" O2' GSP H 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.73 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" C2' GSP B 501 " pdb=" C1' GSP B 501 " pdb=" C3' GSP B 501 " pdb=" O2' GSP B 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.72 0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" C2' GSP D 501 " pdb=" C1' GSP D 501 " pdb=" C3' GSP D 501 " pdb=" O2' GSP D 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.71 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 6213 not shown) Planarity restraints: 7398 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' GTP A 501 " 0.080 2.00e-02 2.50e+03 3.18e-02 3.04e+01 pdb=" C2 GTP A 501 " -0.009 2.00e-02 2.50e+03 pdb=" C4 GTP A 501 " -0.029 2.00e-02 2.50e+03 pdb=" C5 GTP A 501 " -0.016 2.00e-02 2.50e+03 pdb=" C6 GTP A 501 " 0.015 2.00e-02 2.50e+03 pdb=" C8 GTP A 501 " -0.023 2.00e-02 2.50e+03 pdb=" N1 GTP A 501 " 0.019 2.00e-02 2.50e+03 pdb=" N2 GTP A 501 " -0.002 2.00e-02 2.50e+03 pdb=" N3 GTP A 501 " -0.036 2.00e-02 2.50e+03 pdb=" N7 GTP A 501 " -0.019 2.00e-02 2.50e+03 pdb=" N9 GTP A 501 " -0.017 2.00e-02 2.50e+03 pdb=" O6 GTP A 501 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GSP I 501 " -0.063 2.00e-02 2.50e+03 2.60e-02 2.03e+01 pdb=" C2 GSP I 501 " 0.007 2.00e-02 2.50e+03 pdb=" C4 GSP I 501 " 0.022 2.00e-02 2.50e+03 pdb=" C5 GSP I 501 " 0.017 2.00e-02 2.50e+03 pdb=" C6 GSP I 501 " -0.008 2.00e-02 2.50e+03 pdb=" C8 GSP I 501 " 0.016 2.00e-02 2.50e+03 pdb=" N1 GSP I 501 " -0.013 2.00e-02 2.50e+03 pdb=" N2 GSP I 501 " 0.003 2.00e-02 2.50e+03 pdb=" N3 GSP I 501 " 0.027 2.00e-02 2.50e+03 pdb=" N7 GSP I 501 " 0.022 2.00e-02 2.50e+03 pdb=" N9 GSP I 501 " 0.008 2.00e-02 2.50e+03 pdb=" O6 GSP I 501 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GTP L 501 " -0.059 2.00e-02 2.50e+03 2.43e-02 1.78e+01 pdb=" C2 GTP L 501 " 0.002 2.00e-02 2.50e+03 pdb=" C4 GTP L 501 " 0.019 2.00e-02 2.50e+03 pdb=" C5 GTP L 501 " 0.008 2.00e-02 2.50e+03 pdb=" C6 GTP L 501 " -0.020 2.00e-02 2.50e+03 pdb=" C8 GTP L 501 " 0.023 2.00e-02 2.50e+03 pdb=" N1 GTP L 501 " -0.026 2.00e-02 2.50e+03 pdb=" N2 GTP L 501 " 0.016 2.00e-02 2.50e+03 pdb=" N3 GTP L 501 " 0.025 2.00e-02 2.50e+03 pdb=" N7 GTP L 501 " 0.016 2.00e-02 2.50e+03 pdb=" N9 GTP L 501 " 0.013 2.00e-02 2.50e+03 pdb=" O6 GTP L 501 " -0.016 2.00e-02 2.50e+03 ... (remaining 7395 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 382 2.62 - 3.19: 34745 3.19 - 3.76: 61557 3.76 - 4.33: 86867 4.33 - 4.90: 140853 Nonbonded interactions: 324404 Sorted by model distance: nonbonded pdb=" O3G GTP L 501 " pdb="MG MG L 502 " model vdw 2.046 2.170 nonbonded pdb=" O1G GTP A 501 " pdb="MG MG A 502 " model vdw 2.054 2.170 nonbonded pdb=" O2G GTP J 501 " pdb="MG MG J 502 " model vdw 2.057 2.170 nonbonded pdb=" O2B GTP J 501 " pdb="MG MG J 502 " model vdw 2.061 2.170 nonbonded pdb=" O2B GTP L 501 " pdb="MG MG L 502 " model vdw 2.069 2.170 ... (remaining 324399 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 2.940 Check model and map are aligned: 0.550 Set scattering table: 0.330 Process input model: 97.420 Find NCS groups from input model: 2.910 Set up NCS constraints: 0.330 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: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.200 41820 Z= 0.392 Angle : 0.907 14.069 56826 Z= 0.482 Chirality : 0.051 0.257 6216 Planarity : 0.007 0.064 7398 Dihedral : 11.403 161.960 15294 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.55 (0.08), residues: 5130 helix: -3.93 (0.05), residues: 2064 sheet: -1.47 (0.17), residues: 804 loop : -2.55 (0.10), residues: 2262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP G 101 HIS 0.010 0.002 HIS C 8 PHE 0.015 0.002 PHE A 49 TYR 0.022 0.002 TYR K 224 ARG 0.009 0.001 ARG E 390 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1848 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1848 time to evaluate : 4.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 2 ARG cc_start: 0.8487 (mtm180) cc_final: 0.8162 (ptt-90) REVERT: E 18 ASN cc_start: 0.9299 (m-40) cc_final: 0.9043 (t0) REVERT: E 21 TRP cc_start: 0.9606 (m100) cc_final: 0.9129 (m100) REVERT: E 85 GLN cc_start: 0.8526 (mm-40) cc_final: 0.8005 (tp-100) REVERT: E 88 HIS cc_start: 0.7454 (t-170) cc_final: 0.6597 (m-70) REVERT: E 121 ARG cc_start: 0.8045 (mmm160) cc_final: 0.7665 (tpt170) REVERT: E 127 ASP cc_start: 0.9015 (m-30) cc_final: 0.8644 (m-30) REVERT: E 129 CYS cc_start: 0.7683 (m) cc_final: 0.7159 (p) REVERT: E 160 ASP cc_start: 0.8915 (t70) cc_final: 0.8153 (t0) REVERT: E 163 LYS cc_start: 0.8683 (mtpp) cc_final: 0.8139 (mmtt) REVERT: E 202 PHE cc_start: 0.8759 (m-80) cc_final: 0.8338 (m-10) REVERT: E 217 LEU cc_start: 0.9055 (mt) cc_final: 0.8705 (mt) REVERT: E 305 CYS cc_start: 0.8649 (m) cc_final: 0.8401 (m) REVERT: E 345 ASP cc_start: 0.8228 (t70) cc_final: 0.7857 (t0) REVERT: E 355 ILE cc_start: 0.9062 (mp) cc_final: 0.8345 (mt) REVERT: E 368 LEU cc_start: 0.9329 (mp) cc_final: 0.9095 (mp) REVERT: E 376 CYS cc_start: 0.8981 (t) cc_final: 0.8073 (t) REVERT: E 425 MET cc_start: 0.9366 (tpp) cc_final: 0.9115 (tpp) REVERT: E 431 ASP cc_start: 0.8664 (m-30) cc_final: 0.8332 (t0) REVERT: F 14 ASN cc_start: 0.9228 (m-40) cc_final: 0.8870 (m-40) REVERT: F 21 TRP cc_start: 0.9348 (m100) cc_final: 0.8958 (m100) REVERT: F 51 TYR cc_start: 0.8966 (m-80) cc_final: 0.8630 (m-80) REVERT: F 86 ARG cc_start: 0.7045 (mtp180) cc_final: 0.5221 (mmm160) REVERT: F 91 VAL cc_start: 0.9521 (t) cc_final: 0.9290 (p) REVERT: F 100 ASN cc_start: 0.8856 (t0) cc_final: 0.8612 (t0) REVERT: F 107 THR cc_start: 0.9136 (m) cc_final: 0.8720 (m) REVERT: F 152 ILE cc_start: 0.9397 (mt) cc_final: 0.9009 (mm) REVERT: F 163 ILE cc_start: 0.8981 (pp) cc_final: 0.8743 (mt) REVERT: F 164 MET cc_start: 0.8464 (tpt) cc_final: 0.8163 (tpt) REVERT: F 239 CYS cc_start: 0.8506 (m) cc_final: 0.8250 (t) REVERT: F 265 PHE cc_start: 0.9243 (m-80) cc_final: 0.8670 (m-10) REVERT: F 276 ARG cc_start: 0.8609 (mmm-85) cc_final: 0.8298 (mmp80) REVERT: F 297 LYS cc_start: 0.8743 (ptpt) cc_final: 0.7669 (mppt) REVERT: F 300 MET cc_start: 0.8517 (mtt) cc_final: 0.8275 (mtm) REVERT: F 340 TYR cc_start: 0.8674 (m-80) cc_final: 0.8459 (m-80) REVERT: F 355 ASP cc_start: 0.8276 (m-30) cc_final: 0.7573 (m-30) REVERT: F 367 PHE cc_start: 0.9149 (t80) cc_final: 0.8889 (t80) REVERT: F 377 LEU cc_start: 0.8114 (tp) cc_final: 0.7881 (tp) REVERT: F 406 MET cc_start: 0.8695 (tpp) cc_final: 0.8100 (mpp) REVERT: F 427 ASP cc_start: 0.7995 (m-30) cc_final: 0.7433 (t70) REVERT: J 2 ARG cc_start: 0.8502 (mtm180) cc_final: 0.8204 (ptt-90) REVERT: J 18 ASN cc_start: 0.9310 (m-40) cc_final: 0.9023 (t0) REVERT: J 21 TRP cc_start: 0.9621 (m100) cc_final: 0.9144 (m100) REVERT: J 85 GLN cc_start: 0.8634 (mm-40) cc_final: 0.8075 (tp40) REVERT: J 88 HIS cc_start: 0.7785 (t-170) cc_final: 0.6732 (m-70) REVERT: J 121 ARG cc_start: 0.7978 (mmm160) cc_final: 0.7651 (tpt170) REVERT: J 127 ASP cc_start: 0.8950 (m-30) cc_final: 0.8569 (m-30) REVERT: J 129 CYS cc_start: 0.7818 (m) cc_final: 0.7549 (p) REVERT: J 160 ASP cc_start: 0.8986 (t70) cc_final: 0.7471 (t70) REVERT: J 163 LYS cc_start: 0.8712 (mtpp) cc_final: 0.8175 (mptt) REVERT: J 202 PHE cc_start: 0.8757 (m-80) cc_final: 0.8420 (m-10) REVERT: J 210 TYR cc_start: 0.8782 (m-80) cc_final: 0.8390 (m-80) REVERT: J 217 LEU cc_start: 0.9064 (mt) cc_final: 0.8650 (mt) REVERT: J 221 ARG cc_start: 0.8657 (mtt90) cc_final: 0.8383 (mmt90) REVERT: J 234 ILE cc_start: 0.8941 (mt) cc_final: 0.8578 (mm) REVERT: J 235 VAL cc_start: 0.8850 (t) cc_final: 0.8556 (t) REVERT: J 256 GLN cc_start: 0.8906 (pt0) cc_final: 0.8659 (tm-30) REVERT: J 271 THR cc_start: 0.9053 (m) cc_final: 0.8772 (p) REVERT: J 297 GLU cc_start: 0.9013 (tt0) cc_final: 0.8785 (tm-30) REVERT: J 304 LYS cc_start: 0.9204 (tppt) cc_final: 0.8954 (mmmt) REVERT: J 305 CYS cc_start: 0.8425 (m) cc_final: 0.7933 (m) REVERT: J 332 ILE cc_start: 0.9592 (mt) cc_final: 0.9326 (pt) REVERT: J 343 PHE cc_start: 0.8649 (m-80) cc_final: 0.8399 (m-10) REVERT: J 345 ASP cc_start: 0.8505 (t70) cc_final: 0.7973 (t0) REVERT: J 355 ILE cc_start: 0.9171 (mp) cc_final: 0.8556 (mm) REVERT: J 357 TYR cc_start: 0.7328 (m-80) cc_final: 0.7082 (m-10) REVERT: J 367 ASP cc_start: 0.8879 (p0) cc_final: 0.8663 (p0) REVERT: J 380 ASN cc_start: 0.9109 (t0) cc_final: 0.8572 (t0) REVERT: J 425 MET cc_start: 0.9436 (tpp) cc_final: 0.9173 (tpp) REVERT: C 2 ARG cc_start: 0.8535 (mtm180) cc_final: 0.8127 (ptt-90) REVERT: C 18 ASN cc_start: 0.9134 (m-40) cc_final: 0.8931 (t0) REVERT: C 25 CYS cc_start: 0.8655 (m) cc_final: 0.8124 (m) REVERT: C 85 GLN cc_start: 0.8808 (mm-40) cc_final: 0.7827 (mm-40) REVERT: C 91 GLN cc_start: 0.8460 (mt0) cc_final: 0.8254 (mt0) REVERT: C 157 LEU cc_start: 0.9627 (mt) cc_final: 0.9295 (mt) REVERT: C 160 ASP cc_start: 0.8975 (t70) cc_final: 0.8083 (t70) REVERT: C 163 LYS cc_start: 0.8476 (mtpp) cc_final: 0.8156 (mptt) REVERT: C 205 ASP cc_start: 0.8651 (t0) cc_final: 0.8349 (t70) REVERT: C 210 TYR cc_start: 0.8274 (m-80) cc_final: 0.7844 (m-80) REVERT: C 220 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7541 (tp30) REVERT: C 256 GLN cc_start: 0.8813 (pt0) cc_final: 0.8559 (pt0) REVERT: C 266 HIS cc_start: 0.9128 (p-80) cc_final: 0.8870 (p90) REVERT: C 305 CYS cc_start: 0.8685 (m) cc_final: 0.8423 (m) REVERT: C 357 TYR cc_start: 0.7193 (m-80) cc_final: 0.6384 (m-80) REVERT: C 376 CYS cc_start: 0.9076 (t) cc_final: 0.8318 (t) REVERT: C 380 ASN cc_start: 0.8698 (t0) cc_final: 0.7757 (t0) REVERT: C 401 LYS cc_start: 0.9243 (mmtt) cc_final: 0.9025 (mmmm) REVERT: C 425 MET cc_start: 0.9174 (tpp) cc_final: 0.8946 (tpp) REVERT: L 2 ARG cc_start: 0.8402 (mtm180) cc_final: 0.8032 (ptt-90) REVERT: L 18 ASN cc_start: 0.9162 (m-40) cc_final: 0.8886 (t0) REVERT: L 25 CYS cc_start: 0.8621 (m) cc_final: 0.8072 (m) REVERT: L 85 GLN cc_start: 0.8822 (mm-40) cc_final: 0.7861 (mm-40) REVERT: L 91 GLN cc_start: 0.8485 (mt0) cc_final: 0.8160 (mt0) REVERT: L 121 ARG cc_start: 0.8338 (mmm160) cc_final: 0.7895 (mmm160) REVERT: L 145 THR cc_start: 0.8837 (m) cc_final: 0.8438 (m) REVERT: L 160 ASP cc_start: 0.8879 (t70) cc_final: 0.8306 (t0) REVERT: L 163 LYS cc_start: 0.8537 (mtpp) cc_final: 0.8184 (mptt) REVERT: L 183 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8583 (pt0) REVERT: L 209 ILE cc_start: 0.9420 (mt) cc_final: 0.9131 (mm) REVERT: L 210 TYR cc_start: 0.8511 (m-80) cc_final: 0.8053 (m-80) REVERT: L 230 LEU cc_start: 0.9051 (mp) cc_final: 0.8768 (tt) REVERT: L 253 THR cc_start: 0.8892 (m) cc_final: 0.8666 (t) REVERT: L 256 GLN cc_start: 0.8591 (pt0) cc_final: 0.7786 (tm-30) REVERT: L 266 HIS cc_start: 0.9095 (p-80) cc_final: 0.8533 (p90) REVERT: L 302 MET cc_start: 0.8961 (mtt) cc_final: 0.8181 (mtt) REVERT: L 308 ARG cc_start: 0.9030 (mtm180) cc_final: 0.8804 (mtm-85) REVERT: L 345 ASP cc_start: 0.8575 (t70) cc_final: 0.8369 (t0) REVERT: L 355 ILE cc_start: 0.9078 (mp) cc_final: 0.8723 (mp) REVERT: L 357 TYR cc_start: 0.7181 (m-80) cc_final: 0.6573 (m-80) REVERT: L 376 CYS cc_start: 0.9196 (t) cc_final: 0.8289 (t) REVERT: L 378 LEU cc_start: 0.8693 (mt) cc_final: 0.8458 (mp) REVERT: L 380 ASN cc_start: 0.9006 (t0) cc_final: 0.7887 (t0) REVERT: L 430 LYS cc_start: 0.8603 (ptmm) cc_final: 0.8260 (mmmt) REVERT: A 2 ARG cc_start: 0.8699 (mtm180) cc_final: 0.8488 (mtm180) REVERT: A 21 TRP cc_start: 0.9489 (m100) cc_final: 0.8954 (m100) REVERT: A 85 GLN cc_start: 0.8631 (mm-40) cc_final: 0.8023 (mm-40) REVERT: A 129 CYS cc_start: 0.8049 (m) cc_final: 0.7568 (p) REVERT: A 160 ASP cc_start: 0.8894 (t70) cc_final: 0.8272 (t70) REVERT: A 163 LYS cc_start: 0.8829 (mtpp) cc_final: 0.8201 (mptt) REVERT: A 177 VAL cc_start: 0.8854 (t) cc_final: 0.8347 (p) REVERT: A 202 PHE cc_start: 0.8695 (m-80) cc_final: 0.8245 (m-10) REVERT: A 205 ASP cc_start: 0.8660 (t0) cc_final: 0.8365 (t70) REVERT: A 210 TYR cc_start: 0.8863 (m-80) cc_final: 0.8235 (m-80) REVERT: A 211 ASP cc_start: 0.8682 (t0) cc_final: 0.8237 (t70) REVERT: A 217 LEU cc_start: 0.9091 (mt) cc_final: 0.8878 (mt) REVERT: A 345 ASP cc_start: 0.8252 (t70) cc_final: 0.7830 (t0) REVERT: A 376 CYS cc_start: 0.8880 (t) cc_final: 0.8441 (t) REVERT: A 402 ARG cc_start: 0.7964 (mmt-90) cc_final: 0.7754 (mmt180) REVERT: A 415 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7591 (tm-30) REVERT: A 425 MET cc_start: 0.9334 (tpp) cc_final: 0.8973 (tpt) REVERT: K 2 ARG cc_start: 0.8737 (mtm180) cc_final: 0.8002 (ptt-90) REVERT: K 18 ASN cc_start: 0.9141 (m-40) cc_final: 0.8816 (t0) REVERT: K 21 TRP cc_start: 0.9547 (m100) cc_final: 0.9026 (m100) REVERT: K 85 GLN cc_start: 0.8678 (mm-40) cc_final: 0.7785 (tp-100) REVERT: K 125 LEU cc_start: 0.9341 (mt) cc_final: 0.9112 (mt) REVERT: K 129 CYS cc_start: 0.7951 (m) cc_final: 0.7642 (p) REVERT: K 152 LEU cc_start: 0.9328 (tp) cc_final: 0.8973 (tp) REVERT: K 157 LEU cc_start: 0.9397 (mt) cc_final: 0.9110 (mt) REVERT: K 160 ASP cc_start: 0.8863 (t70) cc_final: 0.8211 (t0) REVERT: K 163 LYS cc_start: 0.8735 (mtpp) cc_final: 0.8356 (mptt) REVERT: K 172 TYR cc_start: 0.8570 (t80) cc_final: 0.8324 (t80) REVERT: K 177 VAL cc_start: 0.8647 (t) cc_final: 0.8226 (p) REVERT: K 202 PHE cc_start: 0.8663 (m-80) cc_final: 0.8056 (m-10) REVERT: K 205 ASP cc_start: 0.8356 (t0) cc_final: 0.8060 (t70) REVERT: K 210 TYR cc_start: 0.8957 (m-80) cc_final: 0.8389 (m-80) REVERT: K 227 LEU cc_start: 0.9403 (mp) cc_final: 0.9181 (mp) REVERT: K 256 GLN cc_start: 0.8760 (pt0) cc_final: 0.8076 (tm-30) REVERT: K 345 ASP cc_start: 0.8412 (t70) cc_final: 0.8137 (t0) REVERT: K 355 ILE cc_start: 0.8930 (mp) cc_final: 0.8590 (mp) REVERT: K 357 TYR cc_start: 0.6723 (m-80) cc_final: 0.6356 (m-80) REVERT: K 376 CYS cc_start: 0.9117 (t) cc_final: 0.8758 (t) REVERT: K 380 ASN cc_start: 0.9055 (t0) cc_final: 0.7888 (t0) REVERT: K 425 MET cc_start: 0.9374 (tpp) cc_final: 0.8948 (tpt) REVERT: K 430 LYS cc_start: 0.8713 (ptmm) cc_final: 0.8433 (tmtt) REVERT: G 14 ASN cc_start: 0.9194 (m-40) cc_final: 0.8670 (m-40) REVERT: G 21 TRP cc_start: 0.9363 (m100) cc_final: 0.8633 (m100) REVERT: G 51 TYR cc_start: 0.8850 (m-80) cc_final: 0.8648 (m-80) REVERT: G 81 PHE cc_start: 0.7427 (m-80) cc_final: 0.7162 (m-80) REVERT: G 86 ARG cc_start: 0.7118 (mtp180) cc_final: 0.5335 (mmm160) REVERT: G 91 VAL cc_start: 0.9515 (t) cc_final: 0.9222 (p) REVERT: G 115 SER cc_start: 0.9596 (m) cc_final: 0.9317 (p) REVERT: G 152 ILE cc_start: 0.9331 (mt) cc_final: 0.9073 (mm) REVERT: G 195 ASN cc_start: 0.8177 (m-40) cc_final: 0.7707 (m-40) REVERT: G 257 MET cc_start: 0.8865 (mmp) cc_final: 0.8615 (mmp) REVERT: G 265 PHE cc_start: 0.9302 (m-80) cc_final: 0.9090 (m-10) REVERT: G 297 LYS cc_start: 0.8655 (ptpt) cc_final: 0.7555 (mppt) REVERT: G 300 MET cc_start: 0.8547 (mtt) cc_final: 0.8296 (mtm) REVERT: G 306 ARG cc_start: 0.8844 (mtt90) cc_final: 0.8631 (mtt180) REVERT: G 312 THR cc_start: 0.9078 (p) cc_final: 0.8754 (p) REVERT: G 322 SER cc_start: 0.9043 (m) cc_final: 0.8713 (m) REVERT: G 355 ASP cc_start: 0.8222 (m-30) cc_final: 0.7744 (m-30) REVERT: G 367 PHE cc_start: 0.9144 (t80) cc_final: 0.8865 (t80) REVERT: G 377 LEU cc_start: 0.8064 (tp) cc_final: 0.7768 (tp) REVERT: G 406 MET cc_start: 0.8623 (tpp) cc_final: 0.8178 (mpp) REVERT: G 423 GLN cc_start: 0.9015 (tp-100) cc_final: 0.8734 (tp40) REVERT: G 427 ASP cc_start: 0.8030 (m-30) cc_final: 0.7525 (t70) REVERT: D 6 HIS cc_start: 0.9229 (t70) cc_final: 0.9011 (t-90) REVERT: D 14 ASN cc_start: 0.9242 (m-40) cc_final: 0.8759 (m-40) REVERT: D 64 ILE cc_start: 0.9289 (mt) cc_final: 0.9059 (mt) REVERT: D 100 ASN cc_start: 0.8959 (t0) cc_final: 0.8676 (t0) REVERT: D 103 LYS cc_start: 0.9448 (mttt) cc_final: 0.9023 (mttt) REVERT: D 107 THR cc_start: 0.9086 (m) cc_final: 0.8654 (m) REVERT: D 130 LEU cc_start: 0.9047 (tp) cc_final: 0.8632 (tt) REVERT: D 152 ILE cc_start: 0.9434 (mt) cc_final: 0.9223 (mm) REVERT: D 163 ILE cc_start: 0.9135 (pp) cc_final: 0.8681 (mt) REVERT: D 164 MET cc_start: 0.8770 (tpt) cc_final: 0.8460 (tpt) REVERT: D 195 ASN cc_start: 0.8178 (m-40) cc_final: 0.7393 (m-40) REVERT: D 199 THR cc_start: 0.8739 (m) cc_final: 0.8165 (p) REVERT: D 205 GLU cc_start: 0.8379 (tp30) cc_final: 0.8072 (tp30) REVERT: D 207 LEU cc_start: 0.9492 (mp) cc_final: 0.9002 (tp) REVERT: D 239 CYS cc_start: 0.8223 (m) cc_final: 0.7802 (t) REVERT: D 247 ASN cc_start: 0.8530 (m-40) cc_final: 0.7910 (m-40) REVERT: D 276 ARG cc_start: 0.8568 (mmm-85) cc_final: 0.7970 (mmp80) REVERT: D 293 MET cc_start: 0.7893 (mtm) cc_final: 0.7637 (mtt) REVERT: D 306 ARG cc_start: 0.8845 (mtt90) cc_final: 0.8349 (ttm110) REVERT: D 312 THR cc_start: 0.9156 (p) cc_final: 0.8821 (t) REVERT: D 313 VAL cc_start: 0.9197 (t) cc_final: 0.8650 (m) REVERT: D 323 MET cc_start: 0.8578 (mmm) cc_final: 0.7897 (mmm) REVERT: D 324 LYS cc_start: 0.9201 (tttm) cc_final: 0.8555 (tttp) REVERT: D 327 ASP cc_start: 0.8887 (m-30) cc_final: 0.8466 (p0) REVERT: D 349 VAL cc_start: 0.9418 (t) cc_final: 0.9161 (t) REVERT: D 377 LEU cc_start: 0.8415 (tp) cc_final: 0.7968 (tp) REVERT: D 379 LYS cc_start: 0.9133 (mtpt) cc_final: 0.8694 (ttmm) REVERT: D 397 TRP cc_start: 0.8535 (m100) cc_final: 0.8257 (m100) REVERT: D 406 MET cc_start: 0.8363 (tpp) cc_final: 0.7986 (mpp) REVERT: D 427 ASP cc_start: 0.7805 (m-30) cc_final: 0.7312 (t70) REVERT: I 14 ASN cc_start: 0.9191 (m-40) cc_final: 0.8614 (m-40) REVERT: I 52 ASN cc_start: 0.9142 (m-40) cc_final: 0.8843 (m-40) REVERT: I 73 MET cc_start: 0.8812 (mmt) cc_final: 0.8573 (mmm) REVERT: I 74 ASP cc_start: 0.8541 (t70) cc_final: 0.8274 (t70) REVERT: I 103 LYS cc_start: 0.9363 (mttt) cc_final: 0.9011 (mttt) REVERT: I 107 THR cc_start: 0.9046 (m) cc_final: 0.8749 (m) REVERT: I 130 LEU cc_start: 0.9222 (tp) cc_final: 0.8885 (tt) REVERT: I 143 THR cc_start: 0.9327 (m) cc_final: 0.9053 (p) REVERT: I 163 ILE cc_start: 0.9078 (pp) cc_final: 0.8836 (mt) REVERT: I 170 VAL cc_start: 0.9145 (t) cc_final: 0.8865 (m) REVERT: I 187 LEU cc_start: 0.9336 (mt) cc_final: 0.9115 (mp) REVERT: I 195 ASN cc_start: 0.8383 (m-40) cc_final: 0.7793 (m-40) REVERT: I 199 THR cc_start: 0.8736 (m) cc_final: 0.8240 (p) REVERT: I 205 GLU cc_start: 0.8363 (tp30) cc_final: 0.7572 (tp30) REVERT: I 207 LEU cc_start: 0.9403 (mp) cc_final: 0.8851 (tp) REVERT: I 247 ASN cc_start: 0.8787 (m-40) cc_final: 0.7892 (m-40) REVERT: I 276 ARG cc_start: 0.8429 (mmm-85) cc_final: 0.7889 (mmp80) REVERT: I 300 MET cc_start: 0.8215 (mtt) cc_final: 0.7932 (mtm) REVERT: I 312 THR cc_start: 0.9187 (p) cc_final: 0.8861 (t) REVERT: I 313 VAL cc_start: 0.9220 (t) cc_final: 0.8804 (m) REVERT: I 323 MET cc_start: 0.8427 (mmm) cc_final: 0.7724 (mmm) REVERT: I 324 LYS cc_start: 0.9146 (tttm) cc_final: 0.8528 (tttp) REVERT: I 327 ASP cc_start: 0.8741 (m-30) cc_final: 0.8412 (p0) REVERT: I 349 VAL cc_start: 0.9433 (t) cc_final: 0.9148 (t) REVERT: I 363 MET cc_start: 0.8862 (ptp) cc_final: 0.8638 (pmm) REVERT: I 377 LEU cc_start: 0.8256 (tp) cc_final: 0.7913 (tp) REVERT: I 379 LYS cc_start: 0.9160 (mtpt) cc_final: 0.8891 (ttmm) REVERT: I 397 TRP cc_start: 0.8473 (m100) cc_final: 0.7970 (m-10) REVERT: I 406 MET cc_start: 0.8541 (tpp) cc_final: 0.8143 (mpp) REVERT: I 415 MET cc_start: 0.9166 (ttm) cc_final: 0.8740 (ttp) REVERT: I 427 ASP cc_start: 0.7654 (m-30) cc_final: 0.7418 (t70) REVERT: B 14 ASN cc_start: 0.9127 (m-40) cc_final: 0.8790 (m-40) REVERT: B 37 HIS cc_start: 0.7636 (m90) cc_final: 0.7265 (m90) REVERT: B 65 LEU cc_start: 0.9014 (mp) cc_final: 0.8691 (mp) REVERT: B 91 VAL cc_start: 0.9675 (t) cc_final: 0.9472 (p) REVERT: B 107 THR cc_start: 0.9175 (m) cc_final: 0.8673 (m) REVERT: B 130 LEU cc_start: 0.8814 (tp) cc_final: 0.8478 (tt) REVERT: B 152 ILE cc_start: 0.9348 (mt) cc_final: 0.9145 (mm) REVERT: B 203 ASP cc_start: 0.8036 (m-30) cc_final: 0.7831 (t0) REVERT: B 257 MET cc_start: 0.8842 (mmp) cc_final: 0.8215 (mmm) REVERT: B 297 LYS cc_start: 0.8836 (ptpt) cc_final: 0.7381 (mppt) REVERT: B 306 ARG cc_start: 0.8796 (mtt90) cc_final: 0.8305 (mpp80) REVERT: B 312 THR cc_start: 0.8927 (p) cc_final: 0.8475 (t) REVERT: B 313 VAL cc_start: 0.9110 (t) cc_final: 0.8789 (m) REVERT: B 343 GLU cc_start: 0.8420 (tp30) cc_final: 0.8170 (tp30) REVERT: B 397 TRP cc_start: 0.8745 (m100) cc_final: 0.8511 (m100) REVERT: B 406 MET cc_start: 0.8557 (tpp) cc_final: 0.8154 (tpp) REVERT: B 427 ASP cc_start: 0.8134 (m-30) cc_final: 0.7589 (t70) REVERT: H 4 ILE cc_start: 0.9581 (mt) cc_final: 0.9378 (mm) REVERT: H 14 ASN cc_start: 0.9150 (m-40) cc_final: 0.8616 (m-40) REVERT: H 21 TRP cc_start: 0.9418 (m100) cc_final: 0.9179 (m100) REVERT: H 91 VAL cc_start: 0.9706 (t) cc_final: 0.9464 (p) REVERT: H 107 THR cc_start: 0.9209 (m) cc_final: 0.8733 (m) REVERT: H 115 SER cc_start: 0.9674 (m) cc_final: 0.9430 (p) REVERT: H 130 LEU cc_start: 0.9071 (tp) cc_final: 0.8683 (tt) REVERT: H 152 ILE cc_start: 0.9355 (mt) cc_final: 0.9094 (mm) REVERT: H 155 ILE cc_start: 0.9566 (mt) cc_final: 0.9030 (mt) REVERT: H 178 THR cc_start: 0.8693 (m) cc_final: 0.8408 (m) REVERT: H 257 MET cc_start: 0.8889 (mmp) cc_final: 0.8313 (mmm) REVERT: H 297 LYS cc_start: 0.8687 (ptpt) cc_final: 0.7381 (mppt) REVERT: H 306 ARG cc_start: 0.8820 (mtt90) cc_final: 0.8353 (mpp80) REVERT: H 312 THR cc_start: 0.8898 (p) cc_final: 0.8483 (t) REVERT: H 313 VAL cc_start: 0.9238 (t) cc_final: 0.8948 (m) REVERT: H 349 VAL cc_start: 0.9413 (t) cc_final: 0.9194 (t) REVERT: H 379 LYS cc_start: 0.8949 (mtpt) cc_final: 0.8629 (ttmm) REVERT: H 392 LYS cc_start: 0.9003 (mtmt) cc_final: 0.8787 (mtmm) REVERT: H 397 TRP cc_start: 0.8688 (m100) cc_final: 0.8240 (m-10) REVERT: H 406 MET cc_start: 0.8570 (tpp) cc_final: 0.8033 (tpp) REVERT: H 427 ASP cc_start: 0.8078 (m-30) cc_final: 0.7610 (t70) outliers start: 0 outliers final: 0 residues processed: 1848 average time/residue: 0.5308 time to fit residues: 1582.5552 Evaluate side-chains 1114 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1114 time to evaluate : 4.536 ------------------------------------------------------------------------------- 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: 4.9990 chunk 386 optimal weight: 9.9990 chunk 214 optimal weight: 20.0000 chunk 132 optimal weight: 9.9990 chunk 260 optimal weight: 30.0000 chunk 206 optimal weight: 30.0000 chunk 399 optimal weight: 5.9990 chunk 154 optimal weight: 5.9990 chunk 243 optimal weight: 10.0000 chunk 297 optimal weight: 20.0000 chunk 463 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 15 GLN E 18 ASN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 HIS ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 356 ASN F 131 GLN F 190 HIS F 226 ASN ** F 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 HIS F 396 HIS J 15 GLN J 18 ASN ** J 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 107 HIS ** J 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 356 ASN C 15 GLN C 18 ASN ** C 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 HIS C 107 HIS ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 ASN L 15 GLN L 18 ASN ** L 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 107 HIS ** L 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 ASN L 197 HIS L 356 ASN A 15 GLN ** A 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 ASN A 356 ASN K 15 GLN K 18 ASN ** K 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 ASN ** K 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 356 ASN G 190 HIS G 226 ASN ** G 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 396 HIS D 131 GLN D 190 HIS D 226 ASN D 247 ASN ** D 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 HIS ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN I 131 GLN I 190 HIS I 226 ASN ** I 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 396 HIS B 190 HIS B 226 ASN ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 HIS H 190 HIS H 226 ASN ** H 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 347 ASN H 396 HIS Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 41820 Z= 0.312 Angle : 0.631 11.986 56826 Z= 0.327 Chirality : 0.044 0.158 6216 Planarity : 0.005 0.048 7398 Dihedral : 11.484 166.587 5778 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.02 % Allowed : 2.14 % Favored : 97.84 % 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: -2.81 (0.10), residues: 5130 helix: -2.00 (0.09), residues: 2256 sheet: -0.62 (0.18), residues: 732 loop : -2.00 (0.11), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 21 HIS 0.006 0.001 HIS L 283 PHE 0.020 0.002 PHE F 341 TYR 0.024 0.002 TYR E 224 ARG 0.009 0.001 ARG J 121 *********************** 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 1280 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1279 time to evaluate : 4.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 2 ARG cc_start: 0.8745 (mtm180) cc_final: 0.8191 (ptt-90) REVERT: E 3 GLU cc_start: 0.8416 (mp0) cc_final: 0.8165 (mp0) REVERT: E 21 TRP cc_start: 0.9502 (m100) cc_final: 0.9010 (m100) REVERT: E 36 MET cc_start: 0.8884 (ptm) cc_final: 0.8570 (ptm) REVERT: E 85 GLN cc_start: 0.8563 (mm-40) cc_final: 0.8147 (tp40) REVERT: E 121 ARG cc_start: 0.7600 (mmm160) cc_final: 0.7314 (tpt170) REVERT: E 125 LEU cc_start: 0.9430 (mt) cc_final: 0.9155 (tt) REVERT: E 127 ASP cc_start: 0.9110 (m-30) cc_final: 0.8776 (m-30) REVERT: E 129 CYS cc_start: 0.8014 (m) cc_final: 0.7508 (p) REVERT: E 132 LEU cc_start: 0.8054 (tt) cc_final: 0.7850 (tt) REVERT: E 163 LYS cc_start: 0.8603 (mtpp) cc_final: 0.8076 (mmtt) REVERT: E 202 PHE cc_start: 0.9213 (m-80) cc_final: 0.8486 (m-10) REVERT: E 203 MET cc_start: 0.9245 (mmp) cc_final: 0.8881 (mmp) REVERT: E 266 HIS cc_start: 0.8978 (p90) cc_final: 0.8668 (p90) REVERT: E 302 MET cc_start: 0.8938 (mtp) cc_final: 0.8553 (mtp) REVERT: E 313 MET cc_start: 0.7548 (ptp) cc_final: 0.7257 (ptp) REVERT: E 355 ILE cc_start: 0.8918 (mp) cc_final: 0.8650 (mt) REVERT: E 377 MET cc_start: 0.8227 (ttp) cc_final: 0.7194 (ttp) REVERT: E 380 ASN cc_start: 0.8778 (t0) cc_final: 0.8321 (t0) REVERT: E 398 MET cc_start: 0.9201 (mmm) cc_final: 0.8936 (mmt) REVERT: E 431 ASP cc_start: 0.8622 (m-30) cc_final: 0.8322 (t0) REVERT: F 14 ASN cc_start: 0.9139 (m-40) cc_final: 0.8742 (m-40) REVERT: F 21 TRP cc_start: 0.9378 (m100) cc_final: 0.8664 (m100) REVERT: F 45 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8190 (mt-10) REVERT: F 51 TYR cc_start: 0.8549 (m-80) cc_final: 0.8301 (m-80) REVERT: F 91 VAL cc_start: 0.9536 (t) cc_final: 0.9320 (p) REVERT: F 152 ILE cc_start: 0.9377 (mt) cc_final: 0.9147 (mm) REVERT: F 164 MET cc_start: 0.8617 (tpt) cc_final: 0.8010 (tpt) REVERT: F 265 PHE cc_start: 0.9239 (m-80) cc_final: 0.8586 (m-10) REVERT: F 300 MET cc_start: 0.8271 (mtt) cc_final: 0.7962 (mtm) REVERT: F 320 ARG cc_start: 0.7609 (mmt180) cc_final: 0.6895 (mmt180) REVERT: F 323 MET cc_start: 0.8720 (mmp) cc_final: 0.8197 (mmm) REVERT: F 355 ASP cc_start: 0.7762 (m-30) cc_final: 0.7532 (m-30) REVERT: F 363 MET cc_start: 0.8807 (pmm) cc_final: 0.8567 (pmm) REVERT: F 367 PHE cc_start: 0.9073 (t80) cc_final: 0.8802 (t80) REVERT: F 375 GLN cc_start: 0.8785 (pp30) cc_final: 0.8465 (tm-30) REVERT: F 379 LYS cc_start: 0.8900 (mmmm) cc_final: 0.8626 (mmmm) REVERT: F 406 MET cc_start: 0.8456 (tpp) cc_final: 0.8175 (mpp) REVERT: F 427 ASP cc_start: 0.8118 (m-30) cc_final: 0.7614 (t70) REVERT: J 2 ARG cc_start: 0.8608 (mtm180) cc_final: 0.8183 (ptt-90) REVERT: J 21 TRP cc_start: 0.9534 (m100) cc_final: 0.9079 (m100) REVERT: J 24 TYR cc_start: 0.8766 (m-10) cc_final: 0.8441 (m-80) REVERT: J 36 MET cc_start: 0.8756 (ptm) cc_final: 0.8320 (ptm) REVERT: J 85 GLN cc_start: 0.8646 (mm-40) cc_final: 0.8100 (tp40) REVERT: J 121 ARG cc_start: 0.7719 (mmm160) cc_final: 0.7489 (tpt170) REVERT: J 125 LEU cc_start: 0.9442 (mt) cc_final: 0.9192 (tt) REVERT: J 127 ASP cc_start: 0.9006 (m-30) cc_final: 0.8743 (m-30) REVERT: J 129 CYS cc_start: 0.8105 (m) cc_final: 0.7637 (p) REVERT: J 150 THR cc_start: 0.9355 (m) cc_final: 0.9091 (p) REVERT: J 152 LEU cc_start: 0.9093 (tp) cc_final: 0.8719 (tp) REVERT: J 163 LYS cc_start: 0.8727 (mtpp) cc_final: 0.8144 (mmtt) REVERT: J 172 TYR cc_start: 0.8650 (t80) cc_final: 0.8284 (t80) REVERT: J 202 PHE cc_start: 0.9093 (m-80) cc_final: 0.8266 (m-10) REVERT: J 203 MET cc_start: 0.9207 (mmp) cc_final: 0.8656 (mmp) REVERT: J 217 LEU cc_start: 0.9034 (mt) cc_final: 0.8594 (mt) REVERT: J 230 LEU cc_start: 0.9074 (mp) cc_final: 0.8853 (tt) REVERT: J 256 GLN cc_start: 0.9083 (pt0) cc_final: 0.8114 (tm-30) REVERT: J 302 MET cc_start: 0.8984 (mtm) cc_final: 0.8724 (mtp) REVERT: J 313 MET cc_start: 0.7548 (ptp) cc_final: 0.7338 (ptp) REVERT: J 343 PHE cc_start: 0.8639 (m-80) cc_final: 0.8376 (m-10) REVERT: J 345 ASP cc_start: 0.8584 (t70) cc_final: 0.8302 (t0) REVERT: J 368 LEU cc_start: 0.9325 (mp) cc_final: 0.9102 (mp) REVERT: J 380 ASN cc_start: 0.8875 (t0) cc_final: 0.8476 (t0) REVERT: J 382 THR cc_start: 0.9085 (p) cc_final: 0.8819 (p) REVERT: C 2 ARG cc_start: 0.8783 (mtm180) cc_final: 0.8201 (ptt-90) REVERT: C 85 GLN cc_start: 0.8746 (mm-40) cc_final: 0.7741 (mm-40) REVERT: C 88 HIS cc_start: 0.8142 (t-90) cc_final: 0.7468 (t-170) REVERT: C 90 GLU cc_start: 0.9021 (tp30) cc_final: 0.8464 (tp30) REVERT: C 163 LYS cc_start: 0.8517 (mtpp) cc_final: 0.8160 (mptt) REVERT: C 168 GLU cc_start: 0.7996 (mp0) cc_final: 0.7139 (mp0) REVERT: C 209 ILE cc_start: 0.9485 (mt) cc_final: 0.9201 (mm) REVERT: C 256 GLN cc_start: 0.8852 (pt0) cc_final: 0.8512 (pt0) REVERT: C 290 GLU cc_start: 0.8682 (tt0) cc_final: 0.8411 (tt0) REVERT: C 302 MET cc_start: 0.8615 (mtm) cc_final: 0.7965 (mtt) REVERT: C 315 CYS cc_start: 0.8479 (m) cc_final: 0.7575 (m) REVERT: C 380 ASN cc_start: 0.8600 (t0) cc_final: 0.8330 (t0) REVERT: C 401 LYS cc_start: 0.9279 (mmtt) cc_final: 0.9055 (mmmm) REVERT: L 2 ARG cc_start: 0.8721 (mtm180) cc_final: 0.8136 (ptt-90) REVERT: L 85 GLN cc_start: 0.8775 (mm-40) cc_final: 0.7772 (mm-40) REVERT: L 91 GLN cc_start: 0.8549 (mt0) cc_final: 0.8156 (mt0) REVERT: L 163 LYS cc_start: 0.8519 (mtpp) cc_final: 0.8193 (mptt) REVERT: L 172 TYR cc_start: 0.8354 (t80) cc_final: 0.8089 (t80) REVERT: L 187 SER cc_start: 0.9321 (p) cc_final: 0.9114 (p) REVERT: L 202 PHE cc_start: 0.8750 (m-10) cc_final: 0.8454 (m-10) REVERT: L 210 TYR cc_start: 0.8630 (m-80) cc_final: 0.8297 (m-80) REVERT: L 256 GLN cc_start: 0.8832 (pt0) cc_final: 0.8187 (tm-30) REVERT: L 266 HIS cc_start: 0.9034 (p-80) cc_final: 0.8639 (p90) REVERT: L 290 GLU cc_start: 0.8755 (tt0) cc_final: 0.8505 (tt0) REVERT: L 326 LYS cc_start: 0.8945 (tttm) cc_final: 0.8513 (tptt) REVERT: L 347 CYS cc_start: 0.9020 (t) cc_final: 0.8705 (t) REVERT: L 376 CYS cc_start: 0.9244 (t) cc_final: 0.8975 (t) REVERT: L 377 MET cc_start: 0.8214 (ttp) cc_final: 0.6934 (ttm) REVERT: L 378 LEU cc_start: 0.9060 (mt) cc_final: 0.8762 (mt) REVERT: L 380 ASN cc_start: 0.8855 (t0) cc_final: 0.8452 (t0) REVERT: L 430 LYS cc_start: 0.8676 (ptmm) cc_final: 0.8460 (tmtt) REVERT: A 85 GLN cc_start: 0.8437 (mm-40) cc_final: 0.8057 (mm-40) REVERT: A 121 ARG cc_start: 0.8072 (mmm160) cc_final: 0.7733 (tpt170) REVERT: A 129 CYS cc_start: 0.8179 (m) cc_final: 0.7785 (p) REVERT: A 163 LYS cc_start: 0.8655 (mtpp) cc_final: 0.8047 (mptt) REVERT: A 217 LEU cc_start: 0.9170 (mt) cc_final: 0.8631 (mt) REVERT: A 230 LEU cc_start: 0.9090 (mp) cc_final: 0.8834 (tt) REVERT: A 302 MET cc_start: 0.8724 (mtp) cc_final: 0.8341 (mtt) REVERT: K 2 ARG cc_start: 0.8831 (mtm180) cc_final: 0.8626 (mtm180) REVERT: K 85 GLN cc_start: 0.8485 (mm-40) cc_final: 0.7863 (tp-100) REVERT: K 129 CYS cc_start: 0.8119 (m) cc_final: 0.7897 (p) REVERT: K 152 LEU cc_start: 0.9251 (tp) cc_final: 0.8981 (tp) REVERT: K 163 LYS cc_start: 0.8747 (mtpp) cc_final: 0.8319 (mptt) REVERT: K 172 TYR cc_start: 0.8630 (t80) cc_final: 0.7704 (t80) REVERT: K 202 PHE cc_start: 0.9141 (m-80) cc_final: 0.8644 (m-10) REVERT: K 203 MET cc_start: 0.9374 (mmp) cc_final: 0.8452 (mmp) REVERT: K 211 ASP cc_start: 0.8378 (t0) cc_final: 0.7665 (t70) REVERT: K 230 LEU cc_start: 0.9123 (mp) cc_final: 0.8781 (tt) REVERT: K 256 GLN cc_start: 0.8824 (pt0) cc_final: 0.8046 (tm-30) REVERT: K 326 LYS cc_start: 0.8922 (tttm) cc_final: 0.8667 (tptt) REVERT: K 430 LYS cc_start: 0.8870 (ptmm) cc_final: 0.8605 (tmtt) REVERT: G 14 ASN cc_start: 0.9104 (m-40) cc_final: 0.8621 (m-40) REVERT: G 25 SER cc_start: 0.9332 (m) cc_final: 0.8930 (p) REVERT: G 51 TYR cc_start: 0.8572 (m-80) cc_final: 0.8217 (m-80) REVERT: G 81 PHE cc_start: 0.7474 (m-80) cc_final: 0.7198 (m-80) REVERT: G 91 VAL cc_start: 0.9485 (t) cc_final: 0.9235 (p) REVERT: G 115 SER cc_start: 0.9646 (m) cc_final: 0.9359 (p) REVERT: G 122 LYS cc_start: 0.9587 (ttmt) cc_final: 0.9360 (ttmm) REVERT: G 124 SER cc_start: 0.9126 (t) cc_final: 0.8866 (p) REVERT: G 152 ILE cc_start: 0.9281 (mt) cc_final: 0.9064 (mm) REVERT: G 257 MET cc_start: 0.9047 (mmp) cc_final: 0.8729 (mmp) REVERT: G 265 PHE cc_start: 0.9297 (m-80) cc_final: 0.8951 (m-10) REVERT: G 300 MET cc_start: 0.8585 (mtt) cc_final: 0.8096 (mtm) REVERT: G 312 THR cc_start: 0.9256 (p) cc_final: 0.8970 (p) REVERT: G 347 ASN cc_start: 0.9129 (m-40) cc_final: 0.8896 (m-40) REVERT: G 367 PHE cc_start: 0.9167 (t80) cc_final: 0.8901 (t80) REVERT: G 379 LYS cc_start: 0.8981 (mmmm) cc_final: 0.8722 (mmmm) REVERT: G 406 MET cc_start: 0.8505 (tpp) cc_final: 0.8186 (mpp) REVERT: G 427 ASP cc_start: 0.8060 (m-30) cc_final: 0.7606 (t70) REVERT: D 14 ASN cc_start: 0.9222 (m-40) cc_final: 0.8825 (m-40) REVERT: D 65 LEU cc_start: 0.9107 (mt) cc_final: 0.8683 (mp) REVERT: D 81 PHE cc_start: 0.7516 (m-80) cc_final: 0.7261 (m-10) REVERT: D 100 ASN cc_start: 0.9028 (t0) cc_final: 0.8779 (t0) REVERT: D 130 LEU cc_start: 0.9150 (tp) cc_final: 0.8680 (tt) REVERT: D 164 MET cc_start: 0.8344 (tpt) cc_final: 0.8084 (tpt) REVERT: D 199 THR cc_start: 0.8632 (m) cc_final: 0.7955 (p) REVERT: D 203 ASP cc_start: 0.8212 (t0) cc_final: 0.7941 (t0) REVERT: D 265 PHE cc_start: 0.9339 (m-80) cc_final: 0.9040 (m-10) REVERT: D 276 ARG cc_start: 0.8587 (mmm-85) cc_final: 0.8154 (mmp80) REVERT: D 306 ARG cc_start: 0.8789 (mtt90) cc_final: 0.8335 (ttm110) REVERT: D 312 THR cc_start: 0.9135 (p) cc_final: 0.8814 (t) REVERT: D 313 VAL cc_start: 0.9425 (t) cc_final: 0.9182 (m) REVERT: D 323 MET cc_start: 0.8600 (mmm) cc_final: 0.8044 (mmm) REVERT: D 327 ASP cc_start: 0.9012 (m-30) cc_final: 0.8645 (p0) REVERT: D 355 ASP cc_start: 0.8126 (m-30) cc_final: 0.7878 (m-30) REVERT: D 397 TRP cc_start: 0.8544 (m100) cc_final: 0.8148 (m100) REVERT: D 427 ASP cc_start: 0.7859 (m-30) cc_final: 0.7441 (t70) REVERT: I 14 ASN cc_start: 0.9239 (m-40) cc_final: 0.8662 (m-40) REVERT: I 130 LEU cc_start: 0.9283 (tp) cc_final: 0.8897 (tt) REVERT: I 187 LEU cc_start: 0.9427 (mt) cc_final: 0.9214 (mp) REVERT: I 207 LEU cc_start: 0.9443 (mp) cc_final: 0.9105 (mt) REVERT: I 265 PHE cc_start: 0.9322 (m-80) cc_final: 0.8749 (m-10) REVERT: I 276 ARG cc_start: 0.8561 (mmm-85) cc_final: 0.8190 (mmp80) REVERT: I 299 MET cc_start: 0.8981 (mmp) cc_final: 0.8765 (mmp) REVERT: I 306 ARG cc_start: 0.8537 (mpt180) cc_final: 0.8330 (mpt180) REVERT: I 312 THR cc_start: 0.9067 (p) cc_final: 0.8679 (t) REVERT: I 323 MET cc_start: 0.8488 (mmm) cc_final: 0.7922 (mmm) REVERT: I 327 ASP cc_start: 0.8919 (m-30) cc_final: 0.8648 (p0) REVERT: I 379 LYS cc_start: 0.9077 (mtpt) cc_final: 0.8820 (ttmm) REVERT: I 397 TRP cc_start: 0.8371 (m100) cc_final: 0.7967 (m-10) REVERT: I 427 ASP cc_start: 0.7792 (m-30) cc_final: 0.7446 (t70) REVERT: B 14 ASN cc_start: 0.9055 (m-40) cc_final: 0.8681 (m-40) REVERT: B 65 LEU cc_start: 0.9110 (mp) cc_final: 0.8902 (mp) REVERT: B 115 SER cc_start: 0.9591 (m) cc_final: 0.9384 (p) REVERT: B 130 LEU cc_start: 0.8974 (tp) cc_final: 0.8450 (tt) REVERT: B 152 ILE cc_start: 0.9312 (mt) cc_final: 0.9075 (mm) REVERT: B 297 LYS cc_start: 0.8705 (ptpt) cc_final: 0.7705 (mmtt) REVERT: B 306 ARG cc_start: 0.8965 (mtt90) cc_final: 0.8764 (mtm-85) REVERT: B 313 VAL cc_start: 0.9291 (t) cc_final: 0.9064 (m) REVERT: B 323 MET cc_start: 0.8880 (mmp) cc_final: 0.8547 (mmm) REVERT: B 330 MET cc_start: 0.9026 (mmp) cc_final: 0.8728 (mmm) REVERT: B 343 GLU cc_start: 0.8473 (tp30) cc_final: 0.8165 (tp30) REVERT: B 406 MET cc_start: 0.8460 (tpp) cc_final: 0.8022 (mpp) REVERT: B 427 ASP cc_start: 0.8246 (m-30) cc_final: 0.7682 (t70) REVERT: H 14 ASN cc_start: 0.9048 (m-40) cc_final: 0.8633 (m-40) REVERT: H 91 VAL cc_start: 0.9658 (t) cc_final: 0.9406 (p) REVERT: H 111 GLU cc_start: 0.8617 (pp20) cc_final: 0.8333 (pp20) REVERT: H 115 SER cc_start: 0.9597 (m) cc_final: 0.9354 (p) REVERT: H 130 LEU cc_start: 0.9193 (tp) cc_final: 0.8774 (tt) REVERT: H 152 ILE cc_start: 0.9405 (mt) cc_final: 0.9076 (mm) REVERT: H 155 ILE cc_start: 0.9451 (mt) cc_final: 0.9038 (mt) REVERT: H 178 THR cc_start: 0.8271 (m) cc_final: 0.7870 (p) REVERT: H 313 VAL cc_start: 0.9402 (t) cc_final: 0.9172 (m) REVERT: H 323 MET cc_start: 0.8874 (mmp) cc_final: 0.8609 (mmm) REVERT: H 340 TYR cc_start: 0.8654 (m-10) cc_final: 0.8423 (m-80) REVERT: H 397 TRP cc_start: 0.8697 (m100) cc_final: 0.8289 (m-10) REVERT: H 403 MET cc_start: 0.8752 (tpp) cc_final: 0.8270 (mmt) REVERT: H 406 MET cc_start: 0.8562 (tpp) cc_final: 0.8151 (tpp) REVERT: H 423 GLN cc_start: 0.8819 (tp40) cc_final: 0.8604 (tm-30) REVERT: H 427 ASP cc_start: 0.8036 (m-30) cc_final: 0.7654 (t70) outliers start: 1 outliers final: 0 residues processed: 1280 average time/residue: 0.5200 time to fit residues: 1099.8266 Evaluate side-chains 978 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 978 time to evaluate : 4.653 ------------------------------------------------------------------------------- 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: 4.9990 chunk 385 optimal weight: 20.0000 chunk 315 optimal weight: 5.9990 chunk 127 optimal weight: 20.0000 chunk 463 optimal weight: 20.0000 chunk 501 optimal weight: 10.0000 chunk 413 optimal weight: 5.9990 chunk 460 optimal weight: 9.9990 chunk 158 optimal weight: 20.0000 chunk 372 optimal weight: 9.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 293 ASN ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 GLN ** F 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 197 HIS ** C 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 ASN ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 ASN K 128 GLN ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 228 ASN G 134 GLN ** G 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 GLN ** H 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 347 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 41820 Z= 0.315 Angle : 0.620 13.423 56826 Z= 0.315 Chirality : 0.045 0.297 6216 Planarity : 0.004 0.045 7398 Dihedral : 11.179 168.125 5778 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.11), residues: 5130 helix: -0.97 (0.10), residues: 2208 sheet: -0.19 (0.19), residues: 702 loop : -1.67 (0.12), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K 21 HIS 0.015 0.001 HIS J 197 PHE 0.014 0.002 PHE F 92 TYR 0.015 0.002 TYR A 210 ARG 0.007 0.001 ARG B 359 *********************** 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 1155 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1155 time to evaluate : 4.406 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: E 2 ARG cc_start: 0.8649 (mtm180) cc_final: 0.7938 (mtm-85) REVERT: E 21 TRP cc_start: 0.9519 (m100) cc_final: 0.9016 (m100) REVERT: E 24 TYR cc_start: 0.8692 (m-10) cc_final: 0.8410 (m-80) REVERT: E 36 MET cc_start: 0.8815 (ptm) cc_final: 0.8541 (ptm) REVERT: E 85 GLN cc_start: 0.8625 (mm-40) cc_final: 0.8138 (tp40) REVERT: E 127 ASP cc_start: 0.9091 (m-30) cc_final: 0.8823 (m-30) REVERT: E 163 LYS cc_start: 0.8407 (mtpp) cc_final: 0.7924 (mmtt) REVERT: E 202 PHE cc_start: 0.9168 (m-80) cc_final: 0.8353 (m-10) REVERT: E 203 MET cc_start: 0.9194 (mmp) cc_final: 0.8930 (mmp) REVERT: E 266 HIS cc_start: 0.8958 (p90) cc_final: 0.8705 (p90) REVERT: E 380 ASN cc_start: 0.8792 (t0) cc_final: 0.8417 (t0) REVERT: E 398 MET cc_start: 0.9299 (mmm) cc_final: 0.9097 (mmt) REVERT: F 14 ASN cc_start: 0.9253 (m-40) cc_final: 0.8810 (m-40) REVERT: F 45 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8238 (mt-10) REVERT: F 51 TYR cc_start: 0.8462 (m-80) cc_final: 0.8226 (m-80) REVERT: F 152 ILE cc_start: 0.9497 (mt) cc_final: 0.9248 (mm) REVERT: F 164 MET cc_start: 0.8717 (tpt) cc_final: 0.7995 (tpt) REVERT: F 181 GLU cc_start: 0.8958 (pp20) cc_final: 0.8490 (pp20) REVERT: F 257 MET cc_start: 0.8834 (mmm) cc_final: 0.7747 (mmp) REVERT: F 265 PHE cc_start: 0.9288 (m-80) cc_final: 0.8747 (m-10) REVERT: F 300 MET cc_start: 0.8406 (mtt) cc_final: 0.8122 (mtm) REVERT: F 312 THR cc_start: 0.9151 (p) cc_final: 0.7873 (p) REVERT: F 320 ARG cc_start: 0.7475 (mmt180) cc_final: 0.6742 (mmt180) REVERT: F 347 ASN cc_start: 0.9101 (m-40) cc_final: 0.8838 (m-40) REVERT: F 367 PHE cc_start: 0.8955 (t80) cc_final: 0.8731 (t80) REVERT: F 375 GLN cc_start: 0.9019 (pp30) cc_final: 0.8620 (pp30) REVERT: F 379 LYS cc_start: 0.8988 (mmmm) cc_final: 0.8774 (mmmm) REVERT: F 403 MET cc_start: 0.8551 (mmm) cc_final: 0.8209 (mmt) REVERT: F 406 MET cc_start: 0.8434 (tpp) cc_final: 0.8179 (mpp) REVERT: F 427 ASP cc_start: 0.8169 (m-30) cc_final: 0.7694 (t70) REVERT: J 2 ARG cc_start: 0.8608 (mtm180) cc_final: 0.8161 (ptt-90) REVERT: J 21 TRP cc_start: 0.9561 (m100) cc_final: 0.9042 (m100) REVERT: J 36 MET cc_start: 0.8769 (ptm) cc_final: 0.8537 (ptm) REVERT: J 85 GLN cc_start: 0.8638 (mm-40) cc_final: 0.8130 (tp40) REVERT: J 127 ASP cc_start: 0.9094 (m-30) cc_final: 0.8807 (m-30) REVERT: J 163 LYS cc_start: 0.8753 (mtpp) cc_final: 0.8229 (mmtt) REVERT: J 168 GLU cc_start: 0.9027 (mp0) cc_final: 0.8334 (mp0) REVERT: J 172 TYR cc_start: 0.8636 (t80) cc_final: 0.8356 (t80) REVERT: J 203 MET cc_start: 0.9152 (mmp) cc_final: 0.8662 (mmp) REVERT: J 230 LEU cc_start: 0.9040 (mp) cc_final: 0.8739 (tp) REVERT: J 256 GLN cc_start: 0.9162 (pt0) cc_final: 0.8102 (tm-30) REVERT: J 302 MET cc_start: 0.9127 (mtm) cc_final: 0.8416 (mtp) REVERT: J 313 MET cc_start: 0.7508 (ptp) cc_final: 0.7297 (ptp) REVERT: J 343 PHE cc_start: 0.8709 (m-80) cc_final: 0.8486 (m-10) REVERT: J 345 ASP cc_start: 0.8601 (t70) cc_final: 0.8308 (t0) REVERT: J 380 ASN cc_start: 0.8803 (t0) cc_final: 0.8307 (t0) REVERT: C 2 ARG cc_start: 0.8849 (mtm180) cc_final: 0.8606 (mtm180) REVERT: C 85 GLN cc_start: 0.8442 (mm-40) cc_final: 0.8112 (mm-40) REVERT: C 152 LEU cc_start: 0.9466 (tp) cc_final: 0.9151 (tt) REVERT: C 163 LYS cc_start: 0.8560 (mtpp) cc_final: 0.8199 (mptt) REVERT: C 209 ILE cc_start: 0.9543 (mt) cc_final: 0.9316 (mm) REVERT: C 302 MET cc_start: 0.8787 (mtm) cc_final: 0.8003 (mtt) REVERT: C 313 MET cc_start: 0.8084 (pmm) cc_final: 0.7306 (pmm) REVERT: C 377 MET cc_start: 0.8909 (tmm) cc_final: 0.8619 (tmm) REVERT: C 380 ASN cc_start: 0.8744 (t0) cc_final: 0.8283 (t0) REVERT: C 401 LYS cc_start: 0.9321 (mmtt) cc_final: 0.9039 (mmmm) REVERT: L 2 ARG cc_start: 0.8734 (mtm180) cc_final: 0.8190 (ptt-90) REVERT: L 24 TYR cc_start: 0.8468 (m-10) cc_final: 0.8173 (m-80) REVERT: L 85 GLN cc_start: 0.8483 (mm-40) cc_final: 0.8197 (mm-40) REVERT: L 91 GLN cc_start: 0.8476 (mt0) cc_final: 0.8188 (mt0) REVERT: L 152 LEU cc_start: 0.9463 (tp) cc_final: 0.9092 (tt) REVERT: L 163 LYS cc_start: 0.8556 (mtpp) cc_final: 0.8173 (mptt) REVERT: L 210 TYR cc_start: 0.8718 (m-80) cc_final: 0.8491 (m-80) REVERT: L 256 GLN cc_start: 0.8772 (pt0) cc_final: 0.8219 (tm-30) REVERT: L 266 HIS cc_start: 0.8989 (p-80) cc_final: 0.8672 (p90) REVERT: L 302 MET cc_start: 0.9053 (mtt) cc_final: 0.8591 (mtm) REVERT: L 308 ARG cc_start: 0.8794 (mtm-85) cc_final: 0.8410 (mtt90) REVERT: L 313 MET cc_start: 0.8044 (pmm) cc_final: 0.7297 (pmm) REVERT: L 326 LYS cc_start: 0.8977 (tttm) cc_final: 0.8381 (mmtt) REVERT: L 339 ARG cc_start: 0.8060 (mmm160) cc_final: 0.7598 (tpp-160) REVERT: L 347 CYS cc_start: 0.9043 (t) cc_final: 0.8739 (t) REVERT: L 376 CYS cc_start: 0.9385 (t) cc_final: 0.9062 (t) REVERT: L 377 MET cc_start: 0.8637 (ttp) cc_final: 0.8362 (ttm) REVERT: L 378 LEU cc_start: 0.9207 (mt) cc_final: 0.8916 (mt) REVERT: L 380 ASN cc_start: 0.8918 (t0) cc_final: 0.8345 (t0) REVERT: L 398 MET cc_start: 0.9000 (mtp) cc_final: 0.8728 (mmt) REVERT: L 430 LYS cc_start: 0.8771 (ptmm) cc_final: 0.8550 (tmtt) REVERT: A 21 TRP cc_start: 0.9477 (m100) cc_final: 0.9176 (m100) REVERT: A 163 LYS cc_start: 0.8680 (mtpp) cc_final: 0.8088 (mptt) REVERT: A 202 PHE cc_start: 0.8909 (m-10) cc_final: 0.8547 (m-10) REVERT: A 203 MET cc_start: 0.9507 (mmp) cc_final: 0.9265 (mmp) REVERT: A 217 LEU cc_start: 0.9098 (mt) cc_final: 0.8627 (mt) REVERT: A 230 LEU cc_start: 0.9041 (mp) cc_final: 0.8799 (tt) REVERT: A 302 MET cc_start: 0.8919 (mtp) cc_final: 0.8002 (mtp) REVERT: A 313 MET cc_start: 0.8426 (pmm) cc_final: 0.7682 (pmm) REVERT: A 377 MET cc_start: 0.8542 (tmm) cc_final: 0.8227 (tmm) REVERT: A 380 ASN cc_start: 0.8870 (t0) cc_final: 0.8268 (t0) REVERT: K 2 ARG cc_start: 0.8842 (mtm180) cc_final: 0.8623 (mtm180) REVERT: K 21 TRP cc_start: 0.9508 (m100) cc_final: 0.9178 (m100) REVERT: K 85 GLN cc_start: 0.8586 (mm-40) cc_final: 0.7884 (tp-100) REVERT: K 129 CYS cc_start: 0.8285 (m) cc_final: 0.8056 (p) REVERT: K 163 LYS cc_start: 0.8730 (mtpp) cc_final: 0.8271 (mptt) REVERT: K 202 PHE cc_start: 0.9269 (m-80) cc_final: 0.8795 (m-10) REVERT: K 203 MET cc_start: 0.9366 (mmp) cc_final: 0.9070 (mmp) REVERT: K 211 ASP cc_start: 0.8556 (t0) cc_final: 0.7816 (t70) REVERT: K 217 LEU cc_start: 0.9104 (mt) cc_final: 0.8758 (mt) REVERT: K 230 LEU cc_start: 0.9133 (mp) cc_final: 0.8770 (tt) REVERT: K 256 GLN cc_start: 0.8862 (pt0) cc_final: 0.7960 (tm-30) REVERT: K 302 MET cc_start: 0.8847 (mtt) cc_final: 0.8358 (mtt) REVERT: K 313 MET cc_start: 0.8595 (pmm) cc_final: 0.7840 (pmm) REVERT: K 326 LYS cc_start: 0.9101 (tttm) cc_final: 0.8732 (mmtt) REVERT: K 380 ASN cc_start: 0.8891 (t0) cc_final: 0.8190 (t0) REVERT: K 398 MET cc_start: 0.9249 (mmt) cc_final: 0.8960 (mmt) REVERT: K 430 LYS cc_start: 0.8911 (ptmm) cc_final: 0.8639 (tmtt) REVERT: G 14 ASN cc_start: 0.9234 (m-40) cc_final: 0.8708 (m-40) REVERT: G 25 SER cc_start: 0.9425 (m) cc_final: 0.9026 (p) REVERT: G 51 TYR cc_start: 0.8419 (m-80) cc_final: 0.8090 (m-80) REVERT: G 81 PHE cc_start: 0.7472 (m-80) cc_final: 0.7217 (m-80) REVERT: G 124 SER cc_start: 0.9212 (t) cc_final: 0.8971 (p) REVERT: G 265 PHE cc_start: 0.9282 (m-80) cc_final: 0.8928 (m-10) REVERT: G 297 LYS cc_start: 0.8680 (ptpt) cc_final: 0.7781 (mmtt) REVERT: G 300 MET cc_start: 0.8397 (mtt) cc_final: 0.7890 (mtm) REVERT: G 330 MET cc_start: 0.9063 (tpp) cc_final: 0.8796 (tpp) REVERT: G 347 ASN cc_start: 0.9093 (m-40) cc_final: 0.8818 (m-40) REVERT: G 406 MET cc_start: 0.8483 (tpp) cc_final: 0.8173 (mpp) REVERT: G 427 ASP cc_start: 0.8151 (m-30) cc_final: 0.7634 (t70) REVERT: D 14 ASN cc_start: 0.9073 (m-40) cc_final: 0.8679 (m-40) REVERT: D 95 SER cc_start: 0.9238 (m) cc_final: 0.8787 (t) REVERT: D 130 LEU cc_start: 0.9190 (tp) cc_final: 0.8841 (tt) REVERT: D 276 ARG cc_start: 0.8638 (mmm-85) cc_final: 0.8048 (mmp80) REVERT: D 306 ARG cc_start: 0.8748 (mtt90) cc_final: 0.8309 (ttm110) REVERT: D 323 MET cc_start: 0.8589 (mmm) cc_final: 0.8199 (mmm) REVERT: D 327 ASP cc_start: 0.9099 (m-30) cc_final: 0.8733 (p0) REVERT: D 355 ASP cc_start: 0.8361 (m-30) cc_final: 0.7858 (m-30) REVERT: D 397 TRP cc_start: 0.8273 (m100) cc_final: 0.7849 (m100) REVERT: D 427 ASP cc_start: 0.7937 (m-30) cc_final: 0.7497 (t70) REVERT: I 14 ASN cc_start: 0.9056 (m-40) cc_final: 0.8615 (m110) REVERT: I 95 SER cc_start: 0.9087 (m) cc_final: 0.8537 (t) REVERT: I 207 LEU cc_start: 0.9446 (mp) cc_final: 0.9223 (mt) REVERT: I 265 PHE cc_start: 0.9327 (m-80) cc_final: 0.9063 (m-10) REVERT: I 276 ARG cc_start: 0.8640 (mmm-85) cc_final: 0.8157 (mmp80) REVERT: I 306 ARG cc_start: 0.8566 (mpt180) cc_final: 0.8357 (mpt180) REVERT: I 323 MET cc_start: 0.8480 (mmm) cc_final: 0.8099 (mmm) REVERT: I 327 ASP cc_start: 0.8955 (m-30) cc_final: 0.8719 (p0) REVERT: I 427 ASP cc_start: 0.7837 (m-30) cc_final: 0.7478 (t70) REVERT: B 14 ASN cc_start: 0.9104 (m-40) cc_final: 0.8597 (m-40) REVERT: B 37 HIS cc_start: 0.7696 (m90) cc_final: 0.7374 (m90) REVERT: B 95 SER cc_start: 0.9088 (m) cc_final: 0.8791 (t) REVERT: B 115 SER cc_start: 0.9577 (m) cc_final: 0.9377 (p) REVERT: B 130 LEU cc_start: 0.9001 (tp) cc_final: 0.8491 (tt) REVERT: B 257 MET cc_start: 0.8797 (mmm) cc_final: 0.8268 (mmm) REVERT: B 297 LYS cc_start: 0.8771 (ptpt) cc_final: 0.7819 (mmtt) REVERT: B 312 THR cc_start: 0.8984 (p) cc_final: 0.8553 (p) REVERT: B 323 MET cc_start: 0.8820 (mmp) cc_final: 0.8374 (mmm) REVERT: B 330 MET cc_start: 0.9171 (mmp) cc_final: 0.8927 (mmm) REVERT: B 343 GLU cc_start: 0.8604 (tp30) cc_final: 0.8207 (tp30) REVERT: B 368 ILE cc_start: 0.8884 (mm) cc_final: 0.8643 (mm) REVERT: B 388 MET cc_start: 0.9308 (mtm) cc_final: 0.9077 (mtp) REVERT: B 406 MET cc_start: 0.8702 (tpp) cc_final: 0.8276 (tpp) REVERT: B 427 ASP cc_start: 0.8209 (m-30) cc_final: 0.7725 (t70) REVERT: H 14 ASN cc_start: 0.9159 (m-40) cc_final: 0.8645 (m-40) REVERT: H 95 SER cc_start: 0.8940 (m) cc_final: 0.8719 (t) REVERT: H 130 LEU cc_start: 0.9221 (tp) cc_final: 0.8872 (tt) REVERT: H 152 ILE cc_start: 0.9227 (mt) cc_final: 0.8955 (mm) REVERT: H 299 MET cc_start: 0.8611 (mmm) cc_final: 0.8171 (mmp) REVERT: H 312 THR cc_start: 0.9033 (p) cc_final: 0.8691 (t) REVERT: H 313 VAL cc_start: 0.9369 (t) cc_final: 0.9005 (m) REVERT: H 323 MET cc_start: 0.8747 (mmp) cc_final: 0.8329 (mmm) REVERT: H 330 MET cc_start: 0.8811 (mmm) cc_final: 0.8424 (tpp) REVERT: H 397 TRP cc_start: 0.8502 (m100) cc_final: 0.8240 (m-10) REVERT: H 403 MET cc_start: 0.8816 (tpp) cc_final: 0.8594 (mmt) REVERT: H 406 MET cc_start: 0.8578 (tpp) cc_final: 0.8226 (tpp) REVERT: H 415 MET cc_start: 0.8855 (ttm) cc_final: 0.8564 (ttp) REVERT: H 423 GLN cc_start: 0.8886 (tp40) cc_final: 0.8663 (tm-30) REVERT: H 427 ASP cc_start: 0.8128 (m-30) cc_final: 0.7697 (t70) outliers start: 0 outliers final: 0 residues processed: 1155 average time/residue: 0.5042 time to fit residues: 954.7588 Evaluate side-chains 936 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 936 time to evaluate : 4.260 ------------------------------------------------------------------------------- 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: 8.9990 chunk 348 optimal weight: 9.9990 chunk 240 optimal weight: 5.9990 chunk 51 optimal weight: 20.0000 chunk 221 optimal weight: 9.9990 chunk 311 optimal weight: 5.9990 chunk 465 optimal weight: 8.9990 chunk 492 optimal weight: 20.0000 chunk 243 optimal weight: 0.0770 chunk 441 optimal weight: 7.9990 chunk 132 optimal weight: 30.0000 overall best weight: 5.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 GLN ** F 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 228 ASN ** C 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 ASN ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 ASN ** L 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 293 ASN ** A 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 ASN A 356 ASN K 128 GLN ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 206 ASN K 293 ASN ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 ASN ** G 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 GLN D 134 GLN ** D 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 134 GLN ** I 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 375 GLN B 134 GLN ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 GLN ** H 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 41820 Z= 0.257 Angle : 0.574 13.003 56826 Z= 0.288 Chirality : 0.044 0.162 6216 Planarity : 0.004 0.039 7398 Dihedral : 10.879 171.395 5778 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.02 % Allowed : 1.96 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.24 (0.11), residues: 5130 helix: -0.42 (0.11), residues: 2166 sheet: 0.31 (0.20), residues: 690 loop : -1.53 (0.12), residues: 2274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 21 HIS 0.010 0.001 HIS J 197 PHE 0.015 0.001 PHE H 367 TYR 0.017 0.002 TYR E 224 ARG 0.011 0.001 ARG H 359 *********************** 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 1132 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1131 time to evaluate : 4.267 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: E 2 ARG cc_start: 0.8586 (mtm180) cc_final: 0.8106 (mtm-85) REVERT: E 3 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8096 (mm-30) REVERT: E 21 TRP cc_start: 0.9533 (m100) cc_final: 0.8995 (m100) REVERT: E 36 MET cc_start: 0.8762 (ptm) cc_final: 0.8527 (ptm) REVERT: E 85 GLN cc_start: 0.8667 (mm-40) cc_final: 0.7959 (tp-100) REVERT: E 163 LYS cc_start: 0.8395 (mtpp) cc_final: 0.7915 (mmtt) REVERT: E 183 GLU cc_start: 0.8972 (tt0) cc_final: 0.8654 (tt0) REVERT: E 203 MET cc_start: 0.9153 (mmp) cc_final: 0.8913 (mmp) REVERT: E 266 HIS cc_start: 0.8985 (p90) cc_final: 0.8424 (p-80) REVERT: E 295 CYS cc_start: 0.8934 (m) cc_final: 0.8733 (m) REVERT: E 302 MET cc_start: 0.8575 (mtt) cc_final: 0.8016 (mtp) REVERT: E 313 MET cc_start: 0.8577 (pmm) cc_final: 0.7765 (pmm) REVERT: E 367 ASP cc_start: 0.8761 (p0) cc_final: 0.8469 (p0) REVERT: E 377 MET cc_start: 0.8472 (ttp) cc_final: 0.7623 (ttp) REVERT: E 380 ASN cc_start: 0.8725 (t0) cc_final: 0.8427 (t0) REVERT: E 398 MET cc_start: 0.9247 (mmm) cc_final: 0.9028 (mmt) REVERT: F 14 ASN cc_start: 0.9240 (m-40) cc_final: 0.8725 (m-40) REVERT: F 21 TRP cc_start: 0.9422 (m100) cc_final: 0.8715 (m100) REVERT: F 150 LEU cc_start: 0.9629 (tp) cc_final: 0.9404 (tt) REVERT: F 152 ILE cc_start: 0.9483 (mt) cc_final: 0.9264 (mm) REVERT: F 164 MET cc_start: 0.8713 (tpt) cc_final: 0.8017 (tpt) REVERT: F 181 GLU cc_start: 0.8950 (pp20) cc_final: 0.8514 (pp20) REVERT: F 265 PHE cc_start: 0.9284 (m-80) cc_final: 0.8780 (m-10) REVERT: F 320 ARG cc_start: 0.7384 (mmt180) cc_final: 0.6698 (mmt180) REVERT: F 330 MET cc_start: 0.9194 (mmt) cc_final: 0.8915 (tpp) REVERT: F 375 GLN cc_start: 0.9077 (pp30) cc_final: 0.8677 (pp30) REVERT: F 379 LYS cc_start: 0.9030 (mmmm) cc_final: 0.8744 (mmmm) REVERT: F 403 MET cc_start: 0.8634 (mmm) cc_final: 0.8321 (mmt) REVERT: F 427 ASP cc_start: 0.8278 (m-30) cc_final: 0.7780 (t70) REVERT: J 2 ARG cc_start: 0.8478 (mtm180) cc_final: 0.8276 (ptt-90) REVERT: J 21 TRP cc_start: 0.9544 (m100) cc_final: 0.8976 (m100) REVERT: J 24 TYR cc_start: 0.8606 (m-10) cc_final: 0.8390 (m-80) REVERT: J 36 MET cc_start: 0.8744 (ptm) cc_final: 0.8380 (ptm) REVERT: J 85 GLN cc_start: 0.8708 (mm-40) cc_final: 0.7973 (tp-100) REVERT: J 127 ASP cc_start: 0.9091 (m-30) cc_final: 0.8784 (m-30) REVERT: J 163 LYS cc_start: 0.8490 (mtpp) cc_final: 0.8006 (mmtt) REVERT: J 168 GLU cc_start: 0.9058 (mp0) cc_final: 0.8379 (mp0) REVERT: J 203 MET cc_start: 0.9259 (mmp) cc_final: 0.8782 (mmp) REVERT: J 256 GLN cc_start: 0.9144 (pt0) cc_final: 0.8130 (tm-30) REVERT: J 295 CYS cc_start: 0.8924 (m) cc_final: 0.8691 (m) REVERT: J 305 CYS cc_start: 0.8619 (m) cc_final: 0.8390 (m) REVERT: J 320 ARG cc_start: 0.8479 (ptm160) cc_final: 0.8161 (ptm160) REVERT: J 343 PHE cc_start: 0.8729 (m-80) cc_final: 0.8525 (m-10) REVERT: J 345 ASP cc_start: 0.8592 (t70) cc_final: 0.8302 (t0) REVERT: J 367 ASP cc_start: 0.8683 (p0) cc_final: 0.8343 (p0) REVERT: J 377 MET cc_start: 0.8329 (ttm) cc_final: 0.7864 (ttp) REVERT: J 380 ASN cc_start: 0.8828 (t0) cc_final: 0.8126 (t0) REVERT: C 2 ARG cc_start: 0.8810 (mtm180) cc_final: 0.8596 (mtm180) REVERT: C 152 LEU cc_start: 0.9470 (tp) cc_final: 0.9114 (tt) REVERT: C 163 LYS cc_start: 0.8564 (mtpp) cc_final: 0.8168 (mptt) REVERT: C 235 VAL cc_start: 0.8912 (t) cc_final: 0.8690 (t) REVERT: C 266 HIS cc_start: 0.8931 (p90) cc_final: 0.8528 (p-80) REVERT: C 290 GLU cc_start: 0.8554 (tt0) cc_final: 0.8224 (pt0) REVERT: C 302 MET cc_start: 0.8797 (mtm) cc_final: 0.8256 (mtt) REVERT: C 313 MET cc_start: 0.8491 (pmm) cc_final: 0.7770 (pmm) REVERT: C 347 CYS cc_start: 0.9207 (t) cc_final: 0.8760 (t) REVERT: C 377 MET cc_start: 0.8933 (tmm) cc_final: 0.8642 (tmm) REVERT: C 401 LYS cc_start: 0.9348 (mmtt) cc_final: 0.9096 (mmmm) REVERT: L 2 ARG cc_start: 0.8746 (mtm180) cc_final: 0.8325 (ptt-90) REVERT: L 91 GLN cc_start: 0.8441 (mt0) cc_final: 0.7996 (mt0) REVERT: L 129 CYS cc_start: 0.8100 (p) cc_final: 0.7830 (p) REVERT: L 163 LYS cc_start: 0.8426 (mtpp) cc_final: 0.8066 (mptt) REVERT: L 168 GLU cc_start: 0.9012 (mp0) cc_final: 0.7659 (mp0) REVERT: L 169 PHE cc_start: 0.8725 (m-10) cc_final: 0.8524 (m-10) REVERT: L 172 TYR cc_start: 0.8127 (t80) cc_final: 0.7807 (t80) REVERT: L 256 GLN cc_start: 0.8796 (pt0) cc_final: 0.8240 (tm-30) REVERT: L 302 MET cc_start: 0.9056 (mtt) cc_final: 0.8647 (mtm) REVERT: L 313 MET cc_start: 0.8408 (pmm) cc_final: 0.7687 (pmm) REVERT: L 326 LYS cc_start: 0.8902 (tttm) cc_final: 0.8354 (mmtt) REVERT: L 347 CYS cc_start: 0.8994 (t) cc_final: 0.8707 (t) REVERT: L 376 CYS cc_start: 0.9411 (t) cc_final: 0.9122 (t) REVERT: L 380 ASN cc_start: 0.8850 (t0) cc_final: 0.8535 (t0) REVERT: A 2 ARG cc_start: 0.8694 (mtm110) cc_final: 0.7757 (ptt-90) REVERT: A 163 LYS cc_start: 0.8661 (mtpp) cc_final: 0.8061 (mptt) REVERT: A 202 PHE cc_start: 0.8826 (m-10) cc_final: 0.8445 (m-10) REVERT: A 203 MET cc_start: 0.9480 (mmp) cc_final: 0.9162 (mmp) REVERT: A 230 LEU cc_start: 0.9021 (mp) cc_final: 0.8673 (tt) REVERT: A 235 VAL cc_start: 0.8914 (t) cc_final: 0.8546 (t) REVERT: A 302 MET cc_start: 0.8921 (mtp) cc_final: 0.8357 (mtp) REVERT: A 313 MET cc_start: 0.8791 (pmm) cc_final: 0.8090 (pmm) REVERT: A 377 MET cc_start: 0.8556 (tmm) cc_final: 0.8125 (tmm) REVERT: A 380 ASN cc_start: 0.8989 (t0) cc_final: 0.8606 (t0) REVERT: K 2 ARG cc_start: 0.8820 (mtm180) cc_final: 0.8427 (mtm180) REVERT: K 85 GLN cc_start: 0.8612 (mm-40) cc_final: 0.8318 (mm-40) REVERT: K 163 LYS cc_start: 0.8709 (mtpp) cc_final: 0.8271 (mptt) REVERT: K 202 PHE cc_start: 0.9172 (m-80) cc_final: 0.8786 (m-10) REVERT: K 203 MET cc_start: 0.9318 (mmp) cc_final: 0.9082 (mmp) REVERT: K 211 ASP cc_start: 0.8564 (t0) cc_final: 0.7753 (t70) REVERT: K 227 LEU cc_start: 0.9473 (mp) cc_final: 0.9217 (mp) REVERT: K 230 LEU cc_start: 0.9098 (mp) cc_final: 0.8755 (tt) REVERT: K 239 THR cc_start: 0.8435 (p) cc_final: 0.8229 (t) REVERT: K 256 GLN cc_start: 0.8850 (pt0) cc_final: 0.7937 (tm-30) REVERT: K 257 THR cc_start: 0.9180 (m) cc_final: 0.8961 (m) REVERT: K 302 MET cc_start: 0.8820 (mtt) cc_final: 0.8415 (mtt) REVERT: K 313 MET cc_start: 0.8831 (pmm) cc_final: 0.7967 (pmm) REVERT: K 326 LYS cc_start: 0.9081 (tttm) cc_final: 0.8632 (mmtt) REVERT: K 380 ASN cc_start: 0.8958 (t0) cc_final: 0.8317 (t0) REVERT: K 398 MET cc_start: 0.9173 (mmt) cc_final: 0.8863 (mmt) REVERT: K 430 LYS cc_start: 0.8911 (ptmm) cc_final: 0.8635 (tmtt) REVERT: G 14 ASN cc_start: 0.9277 (m-40) cc_final: 0.8737 (m-40) REVERT: G 51 TYR cc_start: 0.8403 (m-80) cc_final: 0.8100 (m-80) REVERT: G 124 SER cc_start: 0.9242 (t) cc_final: 0.9018 (p) REVERT: G 265 PHE cc_start: 0.9340 (m-80) cc_final: 0.8953 (m-10) REVERT: G 297 LYS cc_start: 0.8591 (ptpt) cc_final: 0.7727 (mmtt) REVERT: G 299 MET cc_start: 0.8880 (mmp) cc_final: 0.8674 (mmp) REVERT: G 300 MET cc_start: 0.8285 (mtt) cc_final: 0.7814 (mtm) REVERT: G 330 MET cc_start: 0.9017 (tpp) cc_final: 0.8752 (tpp) REVERT: G 347 ASN cc_start: 0.9126 (m-40) cc_final: 0.8840 (m-40) REVERT: G 404 ASP cc_start: 0.7953 (p0) cc_final: 0.7663 (m-30) REVERT: G 406 MET cc_start: 0.8473 (tpp) cc_final: 0.8202 (mpp) REVERT: G 427 ASP cc_start: 0.8256 (m-30) cc_final: 0.7715 (t70) REVERT: D 14 ASN cc_start: 0.9117 (m-40) cc_final: 0.8809 (m-40) REVERT: D 95 SER cc_start: 0.9285 (m) cc_final: 0.8779 (t) REVERT: D 100 ASN cc_start: 0.9084 (t0) cc_final: 0.8805 (t0) REVERT: D 130 LEU cc_start: 0.9196 (tp) cc_final: 0.8827 (tt) REVERT: D 177 ASP cc_start: 0.7981 (t70) cc_final: 0.7765 (t70) REVERT: D 205 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8342 (mt-10) REVERT: D 209 ASP cc_start: 0.8323 (m-30) cc_final: 0.7908 (m-30) REVERT: D 276 ARG cc_start: 0.8590 (mmm-85) cc_final: 0.8077 (mmp80) REVERT: D 323 MET cc_start: 0.8618 (mmm) cc_final: 0.8330 (mmm) REVERT: D 363 MET cc_start: 0.8570 (pmm) cc_final: 0.8298 (pmm) REVERT: D 397 TRP cc_start: 0.8165 (m100) cc_final: 0.7863 (m100) REVERT: D 427 ASP cc_start: 0.7995 (m-30) cc_final: 0.7529 (t70) REVERT: I 14 ASN cc_start: 0.9078 (m-40) cc_final: 0.8663 (m-40) REVERT: I 95 SER cc_start: 0.9025 (m) cc_final: 0.8532 (t) REVERT: I 265 PHE cc_start: 0.9283 (m-80) cc_final: 0.9007 (m-10) REVERT: I 276 ARG cc_start: 0.8558 (mmm-85) cc_final: 0.8197 (mmp80) REVERT: I 300 MET cc_start: 0.8466 (mtt) cc_final: 0.8206 (mtm) REVERT: I 306 ARG cc_start: 0.8689 (mpt180) cc_final: 0.8475 (mpt180) REVERT: I 323 MET cc_start: 0.8565 (mmm) cc_final: 0.8314 (mmm) REVERT: I 347 ASN cc_start: 0.8861 (m110) cc_final: 0.8457 (m-40) REVERT: I 363 MET cc_start: 0.8546 (pmm) cc_final: 0.8341 (pmm) REVERT: I 376 GLU cc_start: 0.8558 (tp30) cc_final: 0.8338 (tp30) REVERT: I 427 ASP cc_start: 0.7837 (m-30) cc_final: 0.7472 (t70) REVERT: B 14 ASN cc_start: 0.9117 (m-40) cc_final: 0.8666 (m-40) REVERT: B 95 SER cc_start: 0.9115 (m) cc_final: 0.8766 (t) REVERT: B 130 LEU cc_start: 0.9090 (tp) cc_final: 0.8721 (tt) REVERT: B 257 MET cc_start: 0.8833 (mmm) cc_final: 0.8354 (mmm) REVERT: B 300 MET cc_start: 0.8472 (mtt) cc_final: 0.8233 (mtm) REVERT: B 312 THR cc_start: 0.9053 (p) cc_final: 0.8630 (p) REVERT: B 323 MET cc_start: 0.8791 (mmp) cc_final: 0.8344 (mmm) REVERT: B 330 MET cc_start: 0.9197 (mmp) cc_final: 0.8937 (mmm) REVERT: B 340 TYR cc_start: 0.8698 (m-80) cc_final: 0.8355 (m-80) REVERT: B 343 GLU cc_start: 0.8670 (tp30) cc_final: 0.8155 (tp30) REVERT: B 406 MET cc_start: 0.8738 (tpp) cc_final: 0.8295 (tpp) REVERT: B 422 TYR cc_start: 0.8911 (m-80) cc_final: 0.8624 (m-80) REVERT: B 427 ASP cc_start: 0.8238 (m-30) cc_final: 0.7752 (t70) REVERT: H 14 ASN cc_start: 0.9156 (m-40) cc_final: 0.8688 (m-40) REVERT: H 95 SER cc_start: 0.8887 (m) cc_final: 0.8618 (t) REVERT: H 130 LEU cc_start: 0.9150 (tp) cc_final: 0.8830 (tt) REVERT: H 133 PHE cc_start: 0.8508 (m-10) cc_final: 0.8278 (m-80) REVERT: H 152 ILE cc_start: 0.9257 (mt) cc_final: 0.9018 (mm) REVERT: H 299 MET cc_start: 0.8460 (mmm) cc_final: 0.8191 (mmp) REVERT: H 300 MET cc_start: 0.8354 (mtt) cc_final: 0.8103 (mtm) REVERT: H 340 TYR cc_start: 0.8707 (m-80) cc_final: 0.8411 (m-80) REVERT: H 368 ILE cc_start: 0.8936 (mm) cc_final: 0.8694 (mm) REVERT: H 397 TRP cc_start: 0.8501 (m100) cc_final: 0.8222 (m-10) REVERT: H 406 MET cc_start: 0.8547 (tpp) cc_final: 0.8173 (tpp) REVERT: H 427 ASP cc_start: 0.8171 (m-30) cc_final: 0.7711 (t70) outliers start: 1 outliers final: 0 residues processed: 1132 average time/residue: 0.4999 time to fit residues: 934.5674 Evaluate side-chains 915 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 915 time to evaluate : 4.444 ------------------------------------------------------------------------------- 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: 20.0000 chunk 279 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 367 optimal weight: 4.9990 chunk 203 optimal weight: 20.0000 chunk 420 optimal weight: 9.9990 chunk 340 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 251 optimal weight: 9.9990 chunk 442 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 ASN F 134 GLN ** J 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 228 ASN J 293 ASN ** C 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 ASN C 228 ASN C 258 ASN C 380 ASN ** L 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 ASN A 356 ASN K 128 GLN ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 247 ASN ** G 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 GLN ** D 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 GLN H 134 GLN ** H 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.4231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 41820 Z= 0.277 Angle : 0.589 13.345 56826 Z= 0.294 Chirality : 0.044 0.198 6216 Planarity : 0.004 0.038 7398 Dihedral : 10.701 172.240 5778 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.11), residues: 5130 helix: -0.15 (0.11), residues: 2208 sheet: 0.37 (0.20), residues: 708 loop : -1.47 (0.12), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 21 HIS 0.008 0.001 HIS J 197 PHE 0.020 0.001 PHE G 266 TYR 0.033 0.002 TYR K 210 ARG 0.007 0.001 ARG D 156 *********************** 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 1115 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1115 time to evaluate : 5.766 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: E 2 ARG cc_start: 0.8715 (mtm180) cc_final: 0.8280 (ptt-90) REVERT: E 21 TRP cc_start: 0.9542 (m100) cc_final: 0.9066 (m100) REVERT: E 36 MET cc_start: 0.8768 (ptm) cc_final: 0.8548 (ptm) REVERT: E 51 THR cc_start: 0.9036 (p) cc_final: 0.8493 (m) REVERT: E 85 GLN cc_start: 0.8698 (mm-40) cc_final: 0.8055 (tp-100) REVERT: E 127 ASP cc_start: 0.8972 (m-30) cc_final: 0.8702 (m-30) REVERT: E 163 LYS cc_start: 0.8217 (mtpp) cc_final: 0.7804 (mmtt) REVERT: E 183 GLU cc_start: 0.8936 (tt0) cc_final: 0.8709 (tt0) REVERT: E 203 MET cc_start: 0.9311 (mmp) cc_final: 0.9001 (mmp) REVERT: E 256 GLN cc_start: 0.9012 (pt0) cc_final: 0.8628 (pt0) REVERT: E 266 HIS cc_start: 0.9083 (p90) cc_final: 0.8852 (p90) REVERT: E 302 MET cc_start: 0.8591 (mtt) cc_final: 0.8072 (mtp) REVERT: E 313 MET cc_start: 0.8577 (pmm) cc_final: 0.8046 (pmm) REVERT: E 380 ASN cc_start: 0.8717 (t0) cc_final: 0.8369 (t0) REVERT: E 398 MET cc_start: 0.9285 (mmm) cc_final: 0.9073 (mmt) REVERT: F 14 ASN cc_start: 0.9255 (m-40) cc_final: 0.8768 (m-40) REVERT: F 152 ILE cc_start: 0.9458 (mt) cc_final: 0.9219 (mm) REVERT: F 164 MET cc_start: 0.8718 (tpt) cc_final: 0.8045 (tpt) REVERT: F 181 GLU cc_start: 0.8962 (pp20) cc_final: 0.8506 (pp20) REVERT: F 265 PHE cc_start: 0.9278 (m-80) cc_final: 0.8704 (m-10) REVERT: F 320 ARG cc_start: 0.7454 (mmt180) cc_final: 0.6750 (mmt180) REVERT: F 330 MET cc_start: 0.9210 (mmt) cc_final: 0.8618 (mmt) REVERT: F 347 ASN cc_start: 0.8977 (m-40) cc_final: 0.8715 (m-40) REVERT: F 355 ASP cc_start: 0.7640 (m-30) cc_final: 0.7409 (m-30) REVERT: F 375 GLN cc_start: 0.9149 (pp30) cc_final: 0.8669 (pp30) REVERT: F 379 LYS cc_start: 0.9108 (mmmm) cc_final: 0.8790 (mmmm) REVERT: F 403 MET cc_start: 0.8578 (mmm) cc_final: 0.8342 (mmt) REVERT: F 427 ASP cc_start: 0.8297 (m-30) cc_final: 0.7752 (t70) REVERT: J 3 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7987 (mm-30) REVERT: J 21 TRP cc_start: 0.9531 (m100) cc_final: 0.8989 (m100) REVERT: J 36 MET cc_start: 0.8776 (ptm) cc_final: 0.8405 (ptm) REVERT: J 51 THR cc_start: 0.8993 (p) cc_final: 0.8526 (m) REVERT: J 85 GLN cc_start: 0.8751 (mm-40) cc_final: 0.8073 (tp-100) REVERT: J 127 ASP cc_start: 0.9022 (m-30) cc_final: 0.8757 (m-30) REVERT: J 129 CYS cc_start: 0.8050 (m) cc_final: 0.6987 (p) REVERT: J 132 LEU cc_start: 0.8118 (tt) cc_final: 0.7778 (mp) REVERT: J 163 LYS cc_start: 0.8450 (mtpp) cc_final: 0.8016 (mmtt) REVERT: J 168 GLU cc_start: 0.9053 (mp0) cc_final: 0.8374 (mp0) REVERT: J 203 MET cc_start: 0.9214 (mmp) cc_final: 0.8996 (mmp) REVERT: J 256 GLN cc_start: 0.9168 (pt0) cc_final: 0.7976 (tm-30) REVERT: J 264 ARG cc_start: 0.9016 (mmm-85) cc_final: 0.8770 (mmm-85) REVERT: J 295 CYS cc_start: 0.8965 (m) cc_final: 0.8711 (m) REVERT: J 305 CYS cc_start: 0.8666 (m) cc_final: 0.8447 (m) REVERT: J 313 MET cc_start: 0.8691 (pmm) cc_final: 0.8118 (pmm) REVERT: J 345 ASP cc_start: 0.8580 (t70) cc_final: 0.8323 (t0) REVERT: J 367 ASP cc_start: 0.8609 (p0) cc_final: 0.8257 (p0) REVERT: J 377 MET cc_start: 0.8359 (ttm) cc_final: 0.8071 (ttp) REVERT: J 380 ASN cc_start: 0.8890 (t0) cc_final: 0.8227 (t0) REVERT: J 382 THR cc_start: 0.9067 (p) cc_final: 0.8730 (p) REVERT: C 152 LEU cc_start: 0.9484 (tp) cc_final: 0.9068 (tt) REVERT: C 163 LYS cc_start: 0.8398 (mtpp) cc_final: 0.8059 (mptt) REVERT: C 185 TYR cc_start: 0.8791 (m-10) cc_final: 0.8572 (m-10) REVERT: C 205 ASP cc_start: 0.8930 (t0) cc_final: 0.8658 (t0) REVERT: C 256 GLN cc_start: 0.8761 (pt0) cc_final: 0.8444 (pt0) REVERT: C 290 GLU cc_start: 0.8406 (tt0) cc_final: 0.8189 (pt0) REVERT: C 313 MET cc_start: 0.8776 (pmm) cc_final: 0.8109 (pmm) REVERT: C 347 CYS cc_start: 0.9278 (t) cc_final: 0.8869 (t) REVERT: C 358 GLN cc_start: 0.8889 (tp40) cc_final: 0.8667 (tp40) REVERT: C 377 MET cc_start: 0.8955 (tmm) cc_final: 0.8559 (tmm) REVERT: C 378 LEU cc_start: 0.9365 (mp) cc_final: 0.9116 (mm) REVERT: C 380 ASN cc_start: 0.8996 (t0) cc_final: 0.8251 (t0) REVERT: C 401 LYS cc_start: 0.9356 (mmtt) cc_final: 0.9070 (mmmm) REVERT: L 2 ARG cc_start: 0.8777 (mtm180) cc_final: 0.8340 (ptt-90) REVERT: L 24 TYR cc_start: 0.8707 (m-10) cc_final: 0.8448 (m-80) REVERT: L 25 CYS cc_start: 0.8917 (m) cc_final: 0.8706 (m) REVERT: L 129 CYS cc_start: 0.8080 (p) cc_final: 0.7837 (p) REVERT: L 163 LYS cc_start: 0.8373 (mtpp) cc_final: 0.7993 (mptt) REVERT: L 203 MET cc_start: 0.9058 (mmm) cc_final: 0.8687 (mmm) REVERT: L 256 GLN cc_start: 0.8835 (pt0) cc_final: 0.8326 (tm-30) REVERT: L 266 HIS cc_start: 0.9065 (p90) cc_final: 0.8851 (p90) REVERT: L 302 MET cc_start: 0.9076 (mtt) cc_final: 0.8720 (mtm) REVERT: L 313 MET cc_start: 0.8337 (pmm) cc_final: 0.7364 (pmm) REVERT: L 326 LYS cc_start: 0.8880 (tttm) cc_final: 0.8337 (mmtt) REVERT: L 347 CYS cc_start: 0.9017 (t) cc_final: 0.8740 (t) REVERT: L 358 GLN cc_start: 0.8966 (tp40) cc_final: 0.8766 (tp40) REVERT: L 380 ASN cc_start: 0.8798 (t0) cc_final: 0.8251 (t0) REVERT: L 388 TRP cc_start: 0.9191 (m100) cc_final: 0.8965 (m100) REVERT: A 2 ARG cc_start: 0.8715 (mtm110) cc_final: 0.8395 (mtm180) REVERT: A 21 TRP cc_start: 0.9476 (m100) cc_final: 0.9148 (m100) REVERT: A 163 LYS cc_start: 0.8654 (mtpp) cc_final: 0.7966 (mmtt) REVERT: A 202 PHE cc_start: 0.8873 (m-10) cc_final: 0.8389 (m-10) REVERT: A 203 MET cc_start: 0.9468 (mmp) cc_final: 0.9196 (mmp) REVERT: A 217 LEU cc_start: 0.8998 (mt) cc_final: 0.8623 (mt) REVERT: A 230 LEU cc_start: 0.8977 (mp) cc_final: 0.8649 (tt) REVERT: A 302 MET cc_start: 0.8690 (mtp) cc_final: 0.7916 (mtt) REVERT: A 313 MET cc_start: 0.8653 (pmm) cc_final: 0.7651 (pmm) REVERT: A 377 MET cc_start: 0.8583 (tmm) cc_final: 0.8257 (tmm) REVERT: A 380 ASN cc_start: 0.8916 (t0) cc_final: 0.8280 (t0) REVERT: A 401 LYS cc_start: 0.9238 (mmtt) cc_final: 0.9009 (mmtm) REVERT: K 21 TRP cc_start: 0.9538 (m100) cc_final: 0.9120 (m100) REVERT: K 129 CYS cc_start: 0.8269 (m) cc_final: 0.8023 (p) REVERT: K 163 LYS cc_start: 0.8762 (mtpp) cc_final: 0.8173 (mptt) REVERT: K 202 PHE cc_start: 0.9195 (m-80) cc_final: 0.8749 (m-10) REVERT: K 203 MET cc_start: 0.9310 (mmp) cc_final: 0.9048 (mmp) REVERT: K 207 GLU cc_start: 0.8996 (tt0) cc_final: 0.8380 (tt0) REVERT: K 217 LEU cc_start: 0.9269 (mt) cc_final: 0.8829 (mt) REVERT: K 230 LEU cc_start: 0.8973 (mp) cc_final: 0.8587 (tt) REVERT: K 256 GLN cc_start: 0.8886 (pt0) cc_final: 0.7968 (tm-30) REVERT: K 257 THR cc_start: 0.9212 (m) cc_final: 0.9005 (m) REVERT: K 302 MET cc_start: 0.8635 (mtt) cc_final: 0.8175 (mtt) REVERT: K 313 MET cc_start: 0.8605 (pmm) cc_final: 0.7771 (pmm) REVERT: K 326 LYS cc_start: 0.9084 (tttm) cc_final: 0.8624 (mmtt) REVERT: K 380 ASN cc_start: 0.8882 (t0) cc_final: 0.8356 (t0) REVERT: K 401 LYS cc_start: 0.9232 (mmtt) cc_final: 0.9007 (mmtm) REVERT: K 430 LYS cc_start: 0.8938 (ptmm) cc_final: 0.8647 (tmtt) REVERT: G 14 ASN cc_start: 0.9292 (m-40) cc_final: 0.8758 (m-40) REVERT: G 37 HIS cc_start: 0.7834 (m-70) cc_final: 0.7525 (m90) REVERT: G 51 TYR cc_start: 0.8319 (m-80) cc_final: 0.8042 (m-80) REVERT: G 124 SER cc_start: 0.9336 (t) cc_final: 0.9117 (p) REVERT: G 265 PHE cc_start: 0.9271 (m-80) cc_final: 0.8984 (m-10) REVERT: G 297 LYS cc_start: 0.8642 (ptpt) cc_final: 0.7820 (mmtt) REVERT: G 300 MET cc_start: 0.8418 (mtt) cc_final: 0.7991 (mtm) REVERT: G 320 ARG cc_start: 0.7678 (mpt180) cc_final: 0.7266 (mmt180) REVERT: G 347 ASN cc_start: 0.8937 (m-40) cc_final: 0.8733 (m-40) REVERT: G 355 ASP cc_start: 0.8034 (m-30) cc_final: 0.7560 (m-30) REVERT: G 368 ILE cc_start: 0.8790 (mm) cc_final: 0.8583 (mm) REVERT: G 406 MET cc_start: 0.8496 (tpp) cc_final: 0.8212 (mpp) REVERT: G 427 ASP cc_start: 0.8296 (m-30) cc_final: 0.7850 (t70) REVERT: D 14 ASN cc_start: 0.9222 (m-40) cc_final: 0.8815 (m-40) REVERT: D 95 SER cc_start: 0.9370 (m) cc_final: 0.8847 (t) REVERT: D 100 ASN cc_start: 0.9016 (t0) cc_final: 0.8786 (t0) REVERT: D 164 MET cc_start: 0.8496 (mtm) cc_final: 0.8225 (ptp) REVERT: D 177 ASP cc_start: 0.7979 (t70) cc_final: 0.7762 (t70) REVERT: D 209 ASP cc_start: 0.8424 (m-30) cc_final: 0.8028 (m-30) REVERT: D 257 MET cc_start: 0.8769 (mmp) cc_final: 0.8564 (mmm) REVERT: D 276 ARG cc_start: 0.8610 (mmm-85) cc_final: 0.8222 (mmp80) REVERT: D 306 ARG cc_start: 0.8818 (mtt90) cc_final: 0.8293 (ttm110) REVERT: D 312 THR cc_start: 0.9117 (p) cc_final: 0.8896 (p) REVERT: D 320 ARG cc_start: 0.7640 (mpt180) cc_final: 0.7395 (mpt180) REVERT: D 327 ASP cc_start: 0.8966 (m-30) cc_final: 0.8617 (p0) REVERT: D 347 ASN cc_start: 0.8745 (m110) cc_final: 0.8342 (t0) REVERT: D 363 MET cc_start: 0.8685 (pmm) cc_final: 0.8213 (pmm) REVERT: D 397 TRP cc_start: 0.8201 (m100) cc_final: 0.7637 (m100) REVERT: D 403 MET cc_start: 0.8898 (tpp) cc_final: 0.8528 (mmm) REVERT: D 427 ASP cc_start: 0.7964 (m-30) cc_final: 0.7524 (t70) REVERT: I 14 ASN cc_start: 0.9127 (m-40) cc_final: 0.8712 (m-40) REVERT: I 65 LEU cc_start: 0.9237 (mt) cc_final: 0.8874 (mp) REVERT: I 95 SER cc_start: 0.9099 (m) cc_final: 0.8662 (t) REVERT: I 207 LEU cc_start: 0.9527 (mt) cc_final: 0.9306 (mt) REVERT: I 239 CYS cc_start: 0.8107 (t) cc_final: 0.7889 (t) REVERT: I 257 MET cc_start: 0.8942 (mmp) cc_final: 0.8676 (mmm) REVERT: I 265 PHE cc_start: 0.9297 (m-80) cc_final: 0.8993 (m-10) REVERT: I 276 ARG cc_start: 0.8511 (mmm-85) cc_final: 0.8019 (mmp80) REVERT: I 300 MET cc_start: 0.8417 (mtt) cc_final: 0.8111 (mtm) REVERT: I 306 ARG cc_start: 0.8723 (mpt180) cc_final: 0.8466 (mpt180) REVERT: I 312 THR cc_start: 0.9190 (p) cc_final: 0.8946 (p) REVERT: I 347 ASN cc_start: 0.8809 (m110) cc_final: 0.8578 (m-40) REVERT: I 363 MET cc_start: 0.8766 (pmm) cc_final: 0.8194 (pmm) REVERT: I 376 GLU cc_start: 0.8568 (tp30) cc_final: 0.8366 (tp30) REVERT: I 427 ASP cc_start: 0.7910 (m-30) cc_final: 0.7523 (t70) REVERT: B 14 ASN cc_start: 0.9088 (m-40) cc_final: 0.8643 (m-40) REVERT: B 95 SER cc_start: 0.9099 (m) cc_final: 0.8824 (t) REVERT: B 130 LEU cc_start: 0.9149 (tp) cc_final: 0.8792 (tt) REVERT: B 299 MET cc_start: 0.8525 (mmm) cc_final: 0.8147 (mmm) REVERT: B 300 MET cc_start: 0.8647 (mtt) cc_final: 0.8291 (mtm) REVERT: B 312 THR cc_start: 0.9061 (p) cc_final: 0.8764 (p) REVERT: B 323 MET cc_start: 0.8713 (mmp) cc_final: 0.8315 (mmm) REVERT: B 343 GLU cc_start: 0.8747 (tp30) cc_final: 0.8250 (tp30) REVERT: B 347 ASN cc_start: 0.8983 (m-40) cc_final: 0.8485 (m-40) REVERT: B 368 ILE cc_start: 0.8915 (mm) cc_final: 0.8654 (mm) REVERT: B 388 MET cc_start: 0.9340 (mtm) cc_final: 0.9104 (mtp) REVERT: B 406 MET cc_start: 0.8773 (tpp) cc_final: 0.8298 (tpp) REVERT: B 422 TYR cc_start: 0.8888 (m-80) cc_final: 0.8676 (m-80) REVERT: B 427 ASP cc_start: 0.8230 (m-30) cc_final: 0.7819 (t70) REVERT: H 14 ASN cc_start: 0.9100 (m-40) cc_final: 0.8507 (m-40) REVERT: H 95 SER cc_start: 0.8878 (m) cc_final: 0.8627 (t) REVERT: H 130 LEU cc_start: 0.9103 (tp) cc_final: 0.8844 (tt) REVERT: H 246 LEU cc_start: 0.9176 (tt) cc_final: 0.8950 (tt) REVERT: H 257 MET cc_start: 0.8874 (mmm) cc_final: 0.7763 (mmm) REVERT: H 299 MET cc_start: 0.8405 (mmm) cc_final: 0.8124 (mmt) REVERT: H 300 MET cc_start: 0.8485 (mtt) cc_final: 0.8211 (mtm) REVERT: H 323 MET cc_start: 0.8466 (mmm) cc_final: 0.8017 (ttt) REVERT: H 379 LYS cc_start: 0.9084 (ttmt) cc_final: 0.8881 (ttmm) REVERT: H 397 TRP cc_start: 0.8507 (m100) cc_final: 0.8241 (m-10) REVERT: H 406 MET cc_start: 0.8589 (tpp) cc_final: 0.8262 (tpp) REVERT: H 427 ASP cc_start: 0.8233 (m-30) cc_final: 0.7754 (t70) outliers start: 0 outliers final: 0 residues processed: 1115 average time/residue: 0.4971 time to fit residues: 920.3539 Evaluate side-chains 914 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 914 time to evaluate : 5.031 ------------------------------------------------------------------------------- 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: 4.9990 chunk 443 optimal weight: 10.0000 chunk 97 optimal weight: 7.9990 chunk 289 optimal weight: 0.9990 chunk 121 optimal weight: 10.0000 chunk 493 optimal weight: 10.0000 chunk 409 optimal weight: 8.9990 chunk 228 optimal weight: 9.9990 chunk 41 optimal weight: 20.0000 chunk 163 optimal weight: 7.9990 chunk 259 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 GLN ** J 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 GLN C 206 ASN ** L 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 ASN K 128 GLN ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 247 ASN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 GLN ** D 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 GLN H 134 GLN ** H 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 41820 Z= 0.274 Angle : 0.583 14.002 56826 Z= 0.291 Chirality : 0.044 0.244 6216 Planarity : 0.004 0.063 7398 Dihedral : 10.600 173.851 5778 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % 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: -0.78 (0.12), residues: 5130 helix: 0.03 (0.11), residues: 2178 sheet: 0.65 (0.20), residues: 696 loop : -1.41 (0.12), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 21 HIS 0.011 0.001 HIS E 197 PHE 0.020 0.001 PHE H 266 TYR 0.029 0.002 TYR K 172 ARG 0.013 0.001 ARG E 64 *********************** 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 1098 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1098 time to evaluate : 4.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 2 ARG cc_start: 0.8481 (mtm180) cc_final: 0.8141 (ptt-90) REVERT: E 21 TRP cc_start: 0.9501 (m100) cc_final: 0.9000 (m100) REVERT: E 24 TYR cc_start: 0.8746 (m-10) cc_final: 0.8431 (m-80) REVERT: E 36 MET cc_start: 0.8764 (ptm) cc_final: 0.8521 (ptm) REVERT: E 85 GLN cc_start: 0.8654 (mm-40) cc_final: 0.7591 (tp-100) REVERT: E 129 CYS cc_start: 0.8075 (p) cc_final: 0.6747 (p) REVERT: E 132 LEU cc_start: 0.7992 (tt) cc_final: 0.7633 (mp) REVERT: E 163 LYS cc_start: 0.8219 (mtpp) cc_final: 0.7806 (mmtt) REVERT: E 183 GLU cc_start: 0.8943 (tt0) cc_final: 0.8725 (tt0) REVERT: E 203 MET cc_start: 0.9172 (mmp) cc_final: 0.8934 (mmp) REVERT: E 256 GLN cc_start: 0.8954 (pt0) cc_final: 0.8471 (pt0) REVERT: E 302 MET cc_start: 0.8692 (mtt) cc_final: 0.8222 (mtp) REVERT: E 313 MET cc_start: 0.8717 (pmm) cc_final: 0.8034 (pmm) REVERT: E 380 ASN cc_start: 0.8651 (t0) cc_final: 0.8182 (t0) REVERT: F 14 ASN cc_start: 0.9266 (m-40) cc_final: 0.8792 (m-40) REVERT: F 21 TRP cc_start: 0.9393 (m100) cc_final: 0.8900 (m100) REVERT: F 100 ASN cc_start: 0.9097 (t0) cc_final: 0.8788 (t0) REVERT: F 164 MET cc_start: 0.8675 (tpt) cc_final: 0.8000 (tpt) REVERT: F 181 GLU cc_start: 0.8942 (pp20) cc_final: 0.8436 (pp20) REVERT: F 265 PHE cc_start: 0.9215 (m-80) cc_final: 0.8691 (m-10) REVERT: F 320 ARG cc_start: 0.7561 (mmt180) cc_final: 0.6851 (mmt180) REVERT: F 367 PHE cc_start: 0.9127 (t80) cc_final: 0.8589 (t80) REVERT: F 375 GLN cc_start: 0.9135 (pp30) cc_final: 0.8710 (pp30) REVERT: F 379 LYS cc_start: 0.9083 (mmmm) cc_final: 0.8808 (mmmm) REVERT: F 427 ASP cc_start: 0.8299 (m-30) cc_final: 0.7781 (t70) REVERT: J 2 ARG cc_start: 0.8120 (ptt-90) cc_final: 0.7827 (mtm-85) REVERT: J 3 GLU cc_start: 0.8322 (mm-30) cc_final: 0.8020 (mm-30) REVERT: J 21 TRP cc_start: 0.9559 (m100) cc_final: 0.9032 (m100) REVERT: J 36 MET cc_start: 0.8777 (ptm) cc_final: 0.8383 (ptm) REVERT: J 51 THR cc_start: 0.9019 (p) cc_final: 0.8474 (p) REVERT: J 85 GLN cc_start: 0.8718 (mm-40) cc_final: 0.7580 (tp-100) REVERT: J 163 LYS cc_start: 0.8554 (mtpp) cc_final: 0.8025 (mmtt) REVERT: J 168 GLU cc_start: 0.8768 (mp0) cc_final: 0.8238 (mp0) REVERT: J 176 GLN cc_start: 0.8773 (mp10) cc_final: 0.8554 (mp10) REVERT: J 203 MET cc_start: 0.9217 (mmp) cc_final: 0.8992 (mmp) REVERT: J 256 GLN cc_start: 0.9192 (pt0) cc_final: 0.7961 (tm-30) REVERT: J 302 MET cc_start: 0.9110 (mtm) cc_final: 0.8263 (mtp) REVERT: J 305 CYS cc_start: 0.8679 (m) cc_final: 0.8476 (m) REVERT: J 313 MET cc_start: 0.8411 (pmm) cc_final: 0.7783 (pmm) REVERT: J 345 ASP cc_start: 0.8538 (t70) cc_final: 0.8264 (t0) REVERT: J 367 ASP cc_start: 0.8642 (p0) cc_final: 0.8289 (p0) REVERT: J 380 ASN cc_start: 0.8695 (t0) cc_final: 0.8367 (t0) REVERT: J 382 THR cc_start: 0.9100 (p) cc_final: 0.8849 (p) REVERT: C 2 ARG cc_start: 0.8660 (mtm110) cc_final: 0.8022 (ptt-90) REVERT: C 24 TYR cc_start: 0.8735 (m-10) cc_final: 0.8466 (m-80) REVERT: C 152 LEU cc_start: 0.9473 (tp) cc_final: 0.9075 (tt) REVERT: C 163 LYS cc_start: 0.8397 (mtpp) cc_final: 0.8035 (mptt) REVERT: C 185 TYR cc_start: 0.8748 (m-10) cc_final: 0.8526 (m-10) REVERT: C 205 ASP cc_start: 0.8862 (t0) cc_final: 0.8480 (t70) REVERT: C 256 GLN cc_start: 0.8778 (pt0) cc_final: 0.8441 (pt0) REVERT: C 313 MET cc_start: 0.8913 (pmm) cc_final: 0.7929 (pmm) REVERT: C 347 CYS cc_start: 0.9230 (t) cc_final: 0.8822 (t) REVERT: C 377 MET cc_start: 0.8941 (tmm) cc_final: 0.8521 (tmm) REVERT: C 380 ASN cc_start: 0.8916 (t0) cc_final: 0.8224 (t0) REVERT: C 398 MET cc_start: 0.9151 (mmp) cc_final: 0.8902 (mmt) REVERT: C 401 LYS cc_start: 0.9372 (mmtt) cc_final: 0.9094 (mmmm) REVERT: L 2 ARG cc_start: 0.8792 (mtm180) cc_final: 0.8203 (ptt-90) REVERT: L 163 LYS cc_start: 0.8399 (mtpp) cc_final: 0.7976 (mptt) REVERT: L 168 GLU cc_start: 0.8980 (mp0) cc_final: 0.8410 (mp0) REVERT: L 256 GLN cc_start: 0.8817 (pt0) cc_final: 0.8279 (tm-30) REVERT: L 313 MET cc_start: 0.8570 (pmm) cc_final: 0.7806 (pmm) REVERT: L 326 LYS cc_start: 0.8865 (tttm) cc_final: 0.8278 (mmtt) REVERT: L 347 CYS cc_start: 0.8997 (t) cc_final: 0.8743 (t) REVERT: L 376 CYS cc_start: 0.9292 (t) cc_final: 0.9041 (t) REVERT: L 377 MET cc_start: 0.8495 (ttm) cc_final: 0.8251 (ttm) REVERT: L 378 LEU cc_start: 0.9246 (mt) cc_final: 0.8998 (mt) REVERT: L 380 ASN cc_start: 0.8745 (t0) cc_final: 0.8359 (t0) REVERT: A 21 TRP cc_start: 0.9410 (m100) cc_final: 0.9138 (m100) REVERT: A 163 LYS cc_start: 0.8645 (mtpp) cc_final: 0.7988 (mptt) REVERT: A 202 PHE cc_start: 0.8863 (m-10) cc_final: 0.8362 (m-10) REVERT: A 203 MET cc_start: 0.9480 (mmp) cc_final: 0.9150 (mmp) REVERT: A 230 LEU cc_start: 0.9015 (mp) cc_final: 0.8680 (tt) REVERT: A 256 GLN cc_start: 0.8869 (pt0) cc_final: 0.8427 (pt0) REVERT: A 302 MET cc_start: 0.8737 (mtp) cc_final: 0.7946 (mtt) REVERT: A 313 MET cc_start: 0.8865 (pmm) cc_final: 0.8206 (pmm) REVERT: A 377 MET cc_start: 0.8463 (tmm) cc_final: 0.8157 (tmm) REVERT: A 380 ASN cc_start: 0.8928 (t0) cc_final: 0.8370 (t0) REVERT: A 401 LYS cc_start: 0.9243 (mmtt) cc_final: 0.9024 (mmtm) REVERT: K 2 ARG cc_start: 0.8753 (mtm110) cc_final: 0.7911 (ptt-90) REVERT: K 21 TRP cc_start: 0.9491 (m100) cc_final: 0.9182 (m100) REVERT: K 163 LYS cc_start: 0.8750 (mtpp) cc_final: 0.8155 (mptt) REVERT: K 172 TYR cc_start: 0.8683 (t80) cc_final: 0.8482 (t80) REVERT: K 183 GLU cc_start: 0.8843 (tt0) cc_final: 0.8615 (tt0) REVERT: K 202 PHE cc_start: 0.9276 (m-80) cc_final: 0.8777 (m-80) REVERT: K 203 MET cc_start: 0.9297 (mmp) cc_final: 0.8937 (mmp) REVERT: K 205 ASP cc_start: 0.8479 (t70) cc_final: 0.8201 (t70) REVERT: K 217 LEU cc_start: 0.9073 (mt) cc_final: 0.8688 (mt) REVERT: K 230 LEU cc_start: 0.8939 (mp) cc_final: 0.8580 (tt) REVERT: K 256 GLN cc_start: 0.8909 (pt0) cc_final: 0.8089 (tm-30) REVERT: K 302 MET cc_start: 0.8701 (mtt) cc_final: 0.8223 (mtt) REVERT: K 313 MET cc_start: 0.8784 (pmm) cc_final: 0.8059 (pmm) REVERT: K 326 LYS cc_start: 0.9050 (tttm) cc_final: 0.8465 (mmtp) REVERT: K 380 ASN cc_start: 0.8846 (t0) cc_final: 0.8309 (t0) REVERT: K 401 LYS cc_start: 0.9202 (mmtt) cc_final: 0.8958 (mmtm) REVERT: K 430 LYS cc_start: 0.8830 (ptmm) cc_final: 0.8566 (tmtt) REVERT: G 14 ASN cc_start: 0.9301 (m-40) cc_final: 0.8769 (m-40) REVERT: G 21 TRP cc_start: 0.9415 (m100) cc_final: 0.8735 (m100) REVERT: G 37 HIS cc_start: 0.7865 (m-70) cc_final: 0.7362 (m-70) REVERT: G 41 ASP cc_start: 0.8758 (p0) cc_final: 0.8506 (p0) REVERT: G 51 TYR cc_start: 0.8303 (m-80) cc_final: 0.8081 (m-80) REVERT: G 124 SER cc_start: 0.9297 (t) cc_final: 0.8935 (p) REVERT: G 203 ASP cc_start: 0.8172 (t0) cc_final: 0.7789 (t0) REVERT: G 265 PHE cc_start: 0.9268 (m-80) cc_final: 0.8849 (m-10) REVERT: G 297 LYS cc_start: 0.8623 (ptpt) cc_final: 0.7843 (mmtt) REVERT: G 299 MET cc_start: 0.8899 (mmp) cc_final: 0.8594 (mmp) REVERT: G 300 MET cc_start: 0.8373 (mtt) cc_final: 0.7863 (mtm) REVERT: G 320 ARG cc_start: 0.7709 (mpt180) cc_final: 0.7240 (mmt180) REVERT: G 355 ASP cc_start: 0.8017 (m-30) cc_final: 0.7484 (m-30) REVERT: G 403 MET cc_start: 0.8431 (mtp) cc_final: 0.7832 (mmt) REVERT: G 406 MET cc_start: 0.8533 (tpp) cc_final: 0.8268 (mpp) REVERT: G 427 ASP cc_start: 0.8328 (m-30) cc_final: 0.7873 (t70) REVERT: D 14 ASN cc_start: 0.9165 (m-40) cc_final: 0.8854 (m-40) REVERT: D 95 SER cc_start: 0.9328 (m) cc_final: 0.8820 (t) REVERT: D 100 ASN cc_start: 0.9080 (t0) cc_final: 0.8836 (t0) REVERT: D 177 ASP cc_start: 0.8085 (t70) cc_final: 0.7883 (t70) REVERT: D 207 LEU cc_start: 0.9503 (mt) cc_final: 0.9295 (mt) REVERT: D 209 ASP cc_start: 0.8437 (m-30) cc_final: 0.8089 (m-30) REVERT: D 276 ARG cc_start: 0.8569 (mmm-85) cc_final: 0.8152 (mmp80) REVERT: D 300 MET cc_start: 0.8288 (mtm) cc_final: 0.8073 (mtm) REVERT: D 306 ARG cc_start: 0.8869 (mtt90) cc_final: 0.8418 (mtm-85) REVERT: D 347 ASN cc_start: 0.8715 (m110) cc_final: 0.8332 (m-40) REVERT: D 363 MET cc_start: 0.8712 (pmm) cc_final: 0.8337 (pmm) REVERT: D 397 TRP cc_start: 0.8277 (m100) cc_final: 0.7705 (m100) REVERT: D 403 MET cc_start: 0.8879 (tpp) cc_final: 0.8517 (mmm) REVERT: D 427 ASP cc_start: 0.8024 (m-30) cc_final: 0.7565 (t70) REVERT: I 14 ASN cc_start: 0.9208 (m-40) cc_final: 0.8735 (m-40) REVERT: I 65 LEU cc_start: 0.9314 (mt) cc_final: 0.9015 (mp) REVERT: I 95 SER cc_start: 0.9086 (m) cc_final: 0.8632 (t) REVERT: I 150 LEU cc_start: 0.9591 (tp) cc_final: 0.9391 (tp) REVERT: I 207 LEU cc_start: 0.9528 (mt) cc_final: 0.9261 (mt) REVERT: I 265 PHE cc_start: 0.9342 (m-80) cc_final: 0.9001 (m-10) REVERT: I 276 ARG cc_start: 0.8546 (mmm-85) cc_final: 0.8051 (mmp80) REVERT: I 300 MET cc_start: 0.8458 (mtt) cc_final: 0.8178 (mtm) REVERT: I 306 ARG cc_start: 0.8757 (mpt180) cc_final: 0.8474 (mpt180) REVERT: I 320 ARG cc_start: 0.7785 (mpt180) cc_final: 0.7548 (mpt180) REVERT: I 347 ASN cc_start: 0.8800 (m110) cc_final: 0.8458 (m-40) REVERT: I 363 MET cc_start: 0.8684 (pmm) cc_final: 0.8254 (pmm) REVERT: I 376 GLU cc_start: 0.8575 (tp30) cc_final: 0.8372 (tp30) REVERT: I 427 ASP cc_start: 0.7909 (m-30) cc_final: 0.7521 (t70) REVERT: B 14 ASN cc_start: 0.9079 (m-40) cc_final: 0.8615 (m-40) REVERT: B 95 SER cc_start: 0.9086 (m) cc_final: 0.8805 (t) REVERT: B 130 LEU cc_start: 0.9144 (tp) cc_final: 0.8812 (tt) REVERT: B 233 MET cc_start: 0.8563 (ptm) cc_final: 0.8127 (ptm) REVERT: B 299 MET cc_start: 0.8580 (mmm) cc_final: 0.8134 (mmt) REVERT: B 300 MET cc_start: 0.8566 (mtt) cc_final: 0.8301 (mtm) REVERT: B 323 MET cc_start: 0.8745 (mmp) cc_final: 0.8279 (mmm) REVERT: B 343 GLU cc_start: 0.8673 (tp30) cc_final: 0.8173 (tp30) REVERT: B 347 ASN cc_start: 0.8786 (m-40) cc_final: 0.8271 (m-40) REVERT: B 406 MET cc_start: 0.8608 (tpp) cc_final: 0.8369 (tpp) REVERT: B 422 TYR cc_start: 0.8879 (m-80) cc_final: 0.8604 (m-80) REVERT: B 427 ASP cc_start: 0.8235 (m-30) cc_final: 0.7826 (t70) REVERT: H 14 ASN cc_start: 0.9128 (m-40) cc_final: 0.8547 (m-40) REVERT: H 95 SER cc_start: 0.8885 (m) cc_final: 0.8642 (t) REVERT: H 130 LEU cc_start: 0.9109 (tp) cc_final: 0.8800 (tt) REVERT: H 246 LEU cc_start: 0.9261 (tt) cc_final: 0.9025 (tt) REVERT: H 299 MET cc_start: 0.8574 (mmm) cc_final: 0.8362 (mmp) REVERT: H 300 MET cc_start: 0.8495 (mtt) cc_final: 0.8202 (mtm) REVERT: H 312 THR cc_start: 0.9028 (p) cc_final: 0.8721 (p) REVERT: H 321 MET cc_start: 0.8837 (ptp) cc_final: 0.8288 (ptp) REVERT: H 397 TRP cc_start: 0.8519 (m100) cc_final: 0.8241 (m-10) REVERT: H 406 MET cc_start: 0.8591 (tpp) cc_final: 0.8247 (tpp) REVERT: H 416 ASN cc_start: 0.8437 (m-40) cc_final: 0.8167 (m110) REVERT: H 422 TYR cc_start: 0.8936 (m-80) cc_final: 0.8602 (m-80) REVERT: H 427 ASP cc_start: 0.8250 (m-30) cc_final: 0.7754 (t70) outliers start: 0 outliers final: 0 residues processed: 1098 average time/residue: 0.4984 time to fit residues: 907.8053 Evaluate side-chains 903 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 903 time to evaluate : 4.649 ------------------------------------------------------------------------------- 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: 20.0000 chunk 55 optimal weight: 7.9990 chunk 281 optimal weight: 0.2980 chunk 360 optimal weight: 6.9990 chunk 279 optimal weight: 7.9990 chunk 415 optimal weight: 5.9990 chunk 275 optimal weight: 30.0000 chunk 491 optimal weight: 7.9990 chunk 307 optimal weight: 10.0000 chunk 299 optimal weight: 0.2980 chunk 226 optimal weight: 6.9990 overall best weight: 4.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 28 HIS ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 GLN ** J 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 197 HIS ** C 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 ASN ** L 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 192 HIS ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 ASN K 128 GLN ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 247 ASN ** G 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 HIS D 134 GLN I 37 HIS I 134 GLN ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 GLN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 41820 Z= 0.209 Angle : 0.549 11.880 56826 Z= 0.272 Chirality : 0.043 0.255 6216 Planarity : 0.004 0.118 7398 Dihedral : 10.400 174.607 5778 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.05 % Allowed : 0.96 % Favored : 99.00 % 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: -0.52 (0.12), residues: 5130 helix: 0.32 (0.11), residues: 2136 sheet: 0.85 (0.21), residues: 684 loop : -1.33 (0.12), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 21 HIS 0.005 0.001 HIS J 197 PHE 0.020 0.001 PHE I 266 TYR 0.025 0.001 TYR J 24 ARG 0.014 0.000 ARG L 121 *********************** 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 1112 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1110 time to evaluate : 4.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 2 ARG cc_start: 0.8456 (mtm180) cc_final: 0.8178 (ptt-90) REVERT: E 3 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8546 (mm-30) REVERT: E 21 TRP cc_start: 0.9498 (m100) cc_final: 0.9009 (m100) REVERT: E 24 TYR cc_start: 0.8741 (m-10) cc_final: 0.8473 (m-10) REVERT: E 36 MET cc_start: 0.8755 (ptm) cc_final: 0.8507 (ptm) REVERT: E 85 GLN cc_start: 0.8530 (mm-40) cc_final: 0.7333 (tp-100) REVERT: E 163 LYS cc_start: 0.8263 (mtpp) cc_final: 0.7834 (mmtt) REVERT: E 203 MET cc_start: 0.9184 (mmp) cc_final: 0.8884 (mmp) REVERT: E 256 GLN cc_start: 0.8970 (pt0) cc_final: 0.8497 (pt0) REVERT: E 295 CYS cc_start: 0.8947 (m) cc_final: 0.8744 (m) REVERT: E 302 MET cc_start: 0.8654 (mtt) cc_final: 0.8157 (mtp) REVERT: E 313 MET cc_start: 0.8718 (pmm) cc_final: 0.8137 (pmm) REVERT: E 345 ASP cc_start: 0.8333 (t70) cc_final: 0.8104 (t0) REVERT: E 377 MET cc_start: 0.8670 (ttp) cc_final: 0.7741 (ttp) REVERT: E 380 ASN cc_start: 0.8718 (t0) cc_final: 0.8206 (t0) REVERT: E 382 THR cc_start: 0.9159 (p) cc_final: 0.8794 (p) REVERT: F 14 ASN cc_start: 0.9297 (m-40) cc_final: 0.8826 (m-40) REVERT: F 21 TRP cc_start: 0.9400 (m100) cc_final: 0.8907 (m100) REVERT: F 100 ASN cc_start: 0.9002 (t0) cc_final: 0.8729 (t0) REVERT: F 265 PHE cc_start: 0.9189 (m-80) cc_final: 0.8688 (m-10) REVERT: F 320 ARG cc_start: 0.7582 (mmt180) cc_final: 0.6820 (mmt180) REVERT: F 330 MET cc_start: 0.9203 (mmt) cc_final: 0.8871 (tpp) REVERT: F 375 GLN cc_start: 0.9162 (pp30) cc_final: 0.8737 (pp30) REVERT: F 379 LYS cc_start: 0.9084 (mmmm) cc_final: 0.8783 (mmmm) REVERT: F 427 ASP cc_start: 0.8227 (m-30) cc_final: 0.7728 (t70) REVERT: J 21 TRP cc_start: 0.9562 (m100) cc_final: 0.9035 (m100) REVERT: J 36 MET cc_start: 0.8761 (ptm) cc_final: 0.8377 (ptm) REVERT: J 85 GLN cc_start: 0.8588 (mm-40) cc_final: 0.7361 (tp-100) REVERT: J 91 GLN cc_start: 0.8341 (mp10) cc_final: 0.8054 (mp10) REVERT: J 127 ASP cc_start: 0.8927 (m-30) cc_final: 0.8689 (m-30) REVERT: J 156 ARG cc_start: 0.8727 (mmm-85) cc_final: 0.8313 (mmt90) REVERT: J 163 LYS cc_start: 0.8486 (mtpp) cc_final: 0.7922 (mmtt) REVERT: J 168 GLU cc_start: 0.8800 (mp0) cc_final: 0.8243 (mp0) REVERT: J 176 GLN cc_start: 0.8815 (mp10) cc_final: 0.8485 (mp10) REVERT: J 203 MET cc_start: 0.9227 (mmp) cc_final: 0.8767 (mmp) REVERT: J 256 GLN cc_start: 0.9131 (pt0) cc_final: 0.8630 (tm-30) REVERT: J 302 MET cc_start: 0.9144 (mtm) cc_final: 0.8152 (mtp) REVERT: J 305 CYS cc_start: 0.8692 (m) cc_final: 0.8224 (m) REVERT: J 313 MET cc_start: 0.8722 (pmm) cc_final: 0.7933 (pmm) REVERT: J 345 ASP cc_start: 0.8537 (t70) cc_final: 0.8277 (t0) REVERT: J 358 GLN cc_start: 0.8881 (tp40) cc_final: 0.8673 (tp-100) REVERT: J 367 ASP cc_start: 0.8602 (p0) cc_final: 0.8253 (p0) REVERT: J 377 MET cc_start: 0.8713 (ttp) cc_final: 0.7331 (tmm) REVERT: J 380 ASN cc_start: 0.8806 (t0) cc_final: 0.8220 (t0) REVERT: C 2 ARG cc_start: 0.8873 (mtm110) cc_final: 0.7978 (ptt-90) REVERT: C 24 TYR cc_start: 0.8760 (m-10) cc_final: 0.8410 (m-80) REVERT: C 85 GLN cc_start: 0.8590 (mm-40) cc_final: 0.8181 (mm-40) REVERT: C 163 LYS cc_start: 0.8352 (mtpp) cc_final: 0.8005 (mptt) REVERT: C 205 ASP cc_start: 0.8819 (t0) cc_final: 0.8452 (t70) REVERT: C 235 VAL cc_start: 0.8722 (t) cc_final: 0.8513 (t) REVERT: C 256 GLN cc_start: 0.8741 (pt0) cc_final: 0.8429 (pt0) REVERT: C 266 HIS cc_start: 0.8814 (p90) cc_final: 0.8444 (p-80) REVERT: C 302 MET cc_start: 0.8851 (mtt) cc_final: 0.8575 (mtt) REVERT: C 313 MET cc_start: 0.8834 (pmm) cc_final: 0.7861 (pmm) REVERT: C 347 CYS cc_start: 0.9101 (t) cc_final: 0.8755 (t) REVERT: C 377 MET cc_start: 0.8972 (tmm) cc_final: 0.8627 (tmm) REVERT: C 380 ASN cc_start: 0.8925 (t0) cc_final: 0.8170 (t0) REVERT: C 401 LYS cc_start: 0.9340 (mmtt) cc_final: 0.9063 (mmmm) REVERT: L 2 ARG cc_start: 0.8619 (mtm180) cc_final: 0.8187 (ptt-90) REVERT: L 24 TYR cc_start: 0.8705 (m-10) cc_final: 0.8383 (m-80) REVERT: L 129 CYS cc_start: 0.8129 (p) cc_final: 0.7885 (p) REVERT: L 163 LYS cc_start: 0.8360 (mtpp) cc_final: 0.7936 (mptt) REVERT: L 172 TYR cc_start: 0.8205 (t80) cc_final: 0.7999 (t80) REVERT: L 203 MET cc_start: 0.8838 (mmm) cc_final: 0.8381 (mmm) REVERT: L 217 LEU cc_start: 0.9170 (mt) cc_final: 0.8895 (mt) REVERT: L 256 GLN cc_start: 0.8802 (pt0) cc_final: 0.8302 (tm-30) REVERT: L 302 MET cc_start: 0.8781 (mtm) cc_final: 0.7729 (mtm) REVERT: L 313 MET cc_start: 0.8622 (pmm) cc_final: 0.7544 (pmm) REVERT: L 326 LYS cc_start: 0.8824 (tttm) cc_final: 0.8299 (mmtm) REVERT: L 347 CYS cc_start: 0.8952 (t) cc_final: 0.8680 (t) REVERT: L 376 CYS cc_start: 0.9406 (t) cc_final: 0.9165 (t) REVERT: L 377 MET cc_start: 0.8578 (ttm) cc_final: 0.6448 (mtp) REVERT: L 378 LEU cc_start: 0.9218 (mt) cc_final: 0.8883 (mt) REVERT: L 380 ASN cc_start: 0.8767 (t0) cc_final: 0.8100 (t0) REVERT: A 21 TRP cc_start: 0.9396 (m100) cc_final: 0.9121 (m100) REVERT: A 163 LYS cc_start: 0.8615 (mtpp) cc_final: 0.7992 (mptt) REVERT: A 202 PHE cc_start: 0.8793 (m-10) cc_final: 0.8162 (m-10) REVERT: A 203 MET cc_start: 0.9423 (mmp) cc_final: 0.9062 (mmp) REVERT: A 210 TYR cc_start: 0.8870 (m-80) cc_final: 0.8602 (m-80) REVERT: A 217 LEU cc_start: 0.9077 (mt) cc_final: 0.8706 (mt) REVERT: A 230 LEU cc_start: 0.8969 (mp) cc_final: 0.8627 (tt) REVERT: A 256 GLN cc_start: 0.8845 (pt0) cc_final: 0.8428 (pt0) REVERT: A 302 MET cc_start: 0.8782 (mtp) cc_final: 0.8174 (mtt) REVERT: A 313 MET cc_start: 0.8799 (pmm) cc_final: 0.7896 (pmm) REVERT: A 377 MET cc_start: 0.8402 (tmm) cc_final: 0.8104 (tmm) REVERT: A 380 ASN cc_start: 0.8927 (t0) cc_final: 0.8386 (t0) REVERT: A 382 THR cc_start: 0.8753 (p) cc_final: 0.8410 (p) REVERT: A 401 LYS cc_start: 0.9197 (mmtt) cc_final: 0.8955 (mmtm) REVERT: K 2 ARG cc_start: 0.8637 (mtm110) cc_final: 0.7830 (ptt-90) REVERT: K 21 TRP cc_start: 0.9460 (m100) cc_final: 0.9209 (m100) REVERT: K 163 LYS cc_start: 0.8712 (mtpp) cc_final: 0.8140 (mptt) REVERT: K 183 GLU cc_start: 0.8937 (tt0) cc_final: 0.8704 (tt0) REVERT: K 202 PHE cc_start: 0.9221 (m-80) cc_final: 0.8769 (m-80) REVERT: K 203 MET cc_start: 0.9309 (mmp) cc_final: 0.9030 (mmp) REVERT: K 217 LEU cc_start: 0.9106 (mt) cc_final: 0.8708 (mt) REVERT: K 230 LEU cc_start: 0.8917 (mp) cc_final: 0.8579 (tt) REVERT: K 256 GLN cc_start: 0.8891 (pt0) cc_final: 0.8097 (tm-30) REVERT: K 302 MET cc_start: 0.8725 (mtt) cc_final: 0.8342 (mtt) REVERT: K 313 MET cc_start: 0.8709 (pmm) cc_final: 0.7717 (pmm) REVERT: K 326 LYS cc_start: 0.9023 (tttm) cc_final: 0.8476 (mmtp) REVERT: K 380 ASN cc_start: 0.8829 (t0) cc_final: 0.8294 (t0) REVERT: K 401 LYS cc_start: 0.9122 (mmtt) cc_final: 0.8898 (mmtm) REVERT: K 430 LYS cc_start: 0.8814 (ptmm) cc_final: 0.8554 (tmtt) REVERT: G 14 ASN cc_start: 0.9335 (m-40) cc_final: 0.8825 (m-40) REVERT: G 21 TRP cc_start: 0.9396 (m100) cc_final: 0.8774 (m100) REVERT: G 37 HIS cc_start: 0.7823 (m-70) cc_final: 0.7294 (m-70) REVERT: G 51 TYR cc_start: 0.8241 (m-80) cc_final: 0.8019 (m-80) REVERT: G 95 SER cc_start: 0.9011 (m) cc_final: 0.8520 (t) REVERT: G 124 SER cc_start: 0.9389 (t) cc_final: 0.9119 (p) REVERT: G 147 MET cc_start: 0.9536 (mmm) cc_final: 0.9129 (mmp) REVERT: G 203 ASP cc_start: 0.8112 (t0) cc_final: 0.7887 (t0) REVERT: G 265 PHE cc_start: 0.9224 (m-80) cc_final: 0.8816 (m-10) REVERT: G 297 LYS cc_start: 0.8597 (ptpt) cc_final: 0.7774 (mmtt) REVERT: G 300 MET cc_start: 0.8375 (mtt) cc_final: 0.8010 (mtm) REVERT: G 320 ARG cc_start: 0.7715 (mpt180) cc_final: 0.7259 (mmt180) REVERT: G 355 ASP cc_start: 0.8042 (m-30) cc_final: 0.7472 (m-30) REVERT: G 368 ILE cc_start: 0.8855 (mm) cc_final: 0.8626 (mm) REVERT: G 376 GLU cc_start: 0.8872 (tp30) cc_final: 0.8162 (tm-30) REVERT: G 403 MET cc_start: 0.8205 (mtp) cc_final: 0.7689 (mmt) REVERT: G 406 MET cc_start: 0.8590 (tpp) cc_final: 0.8249 (mpp) REVERT: G 427 ASP cc_start: 0.8307 (m-30) cc_final: 0.7869 (t70) REVERT: D 14 ASN cc_start: 0.9277 (m-40) cc_final: 0.8853 (m-40) REVERT: D 95 SER cc_start: 0.9345 (m) cc_final: 0.8806 (t) REVERT: D 100 ASN cc_start: 0.9069 (t0) cc_final: 0.8837 (t0) REVERT: D 207 LEU cc_start: 0.9504 (mt) cc_final: 0.9290 (mt) REVERT: D 209 ASP cc_start: 0.8426 (m-30) cc_final: 0.8087 (m-30) REVERT: D 276 ARG cc_start: 0.8552 (mmm-85) cc_final: 0.7988 (mmp80) REVERT: D 300 MET cc_start: 0.8304 (mtm) cc_final: 0.8092 (mtm) REVERT: D 306 ARG cc_start: 0.8884 (mtt90) cc_final: 0.7930 (mtm-85) REVERT: D 347 ASN cc_start: 0.8755 (m110) cc_final: 0.8377 (m-40) REVERT: D 363 MET cc_start: 0.8693 (pmm) cc_final: 0.8341 (pmm) REVERT: D 374 ILE cc_start: 0.8569 (pt) cc_final: 0.7840 (pt) REVERT: D 397 TRP cc_start: 0.8302 (m100) cc_final: 0.7785 (m100) REVERT: D 403 MET cc_start: 0.8809 (tpp) cc_final: 0.8485 (mmm) REVERT: D 427 ASP cc_start: 0.8024 (m-30) cc_final: 0.7553 (t70) REVERT: I 14 ASN cc_start: 0.9146 (m-40) cc_final: 0.8744 (m-40) REVERT: I 95 SER cc_start: 0.9067 (m) cc_final: 0.8642 (t) REVERT: I 207 LEU cc_start: 0.9547 (mt) cc_final: 0.9260 (mt) REVERT: I 247 ASN cc_start: 0.7970 (t0) cc_final: 0.7570 (t0) REVERT: I 265 PHE cc_start: 0.9288 (m-80) cc_final: 0.8887 (m-10) REVERT: I 276 ARG cc_start: 0.8536 (mmm-85) cc_final: 0.8041 (mmp80) REVERT: I 306 ARG cc_start: 0.8766 (mpt180) cc_final: 0.8465 (mpt180) REVERT: I 347 ASN cc_start: 0.8750 (m110) cc_final: 0.8450 (m-40) REVERT: I 363 MET cc_start: 0.8649 (pmm) cc_final: 0.8254 (pmm) REVERT: I 427 ASP cc_start: 0.7840 (m-30) cc_final: 0.7499 (t70) REVERT: B 14 ASN cc_start: 0.9113 (m-40) cc_final: 0.8653 (m-40) REVERT: B 95 SER cc_start: 0.9104 (m) cc_final: 0.8817 (t) REVERT: B 100 ASN cc_start: 0.9048 (t0) cc_final: 0.8798 (t0) REVERT: B 130 LEU cc_start: 0.9134 (tp) cc_final: 0.8847 (tt) REVERT: B 265 PHE cc_start: 0.9462 (m-10) cc_final: 0.9093 (m-10) REVERT: B 299 MET cc_start: 0.8691 (mmm) cc_final: 0.8299 (mmp) REVERT: B 300 MET cc_start: 0.8612 (mtt) cc_final: 0.8338 (mtm) REVERT: B 343 GLU cc_start: 0.8769 (tp30) cc_final: 0.8319 (tp30) REVERT: B 388 MET cc_start: 0.9325 (mtm) cc_final: 0.9117 (mtp) REVERT: B 422 TYR cc_start: 0.8852 (m-80) cc_final: 0.8576 (m-80) REVERT: B 427 ASP cc_start: 0.8225 (m-30) cc_final: 0.7817 (t70) REVERT: H 14 ASN cc_start: 0.9163 (m-40) cc_final: 0.8582 (m-40) REVERT: H 95 SER cc_start: 0.9043 (m) cc_final: 0.8799 (t) REVERT: H 130 LEU cc_start: 0.9094 (tp) cc_final: 0.8799 (tt) REVERT: H 246 LEU cc_start: 0.9226 (tt) cc_final: 0.8988 (tt) REVERT: H 265 PHE cc_start: 0.9464 (m-10) cc_final: 0.9022 (m-10) REVERT: H 299 MET cc_start: 0.8434 (mmm) cc_final: 0.8031 (mmt) REVERT: H 300 MET cc_start: 0.8533 (mtt) cc_final: 0.8274 (mtm) REVERT: H 321 MET cc_start: 0.8854 (ptp) cc_final: 0.8354 (ptp) REVERT: H 344 TRP cc_start: 0.8819 (p-90) cc_final: 0.8372 (p-90) REVERT: H 397 TRP cc_start: 0.8483 (m100) cc_final: 0.8211 (m-10) REVERT: H 406 MET cc_start: 0.8484 (tpp) cc_final: 0.8202 (mpp) REVERT: H 422 TYR cc_start: 0.8927 (m-80) cc_final: 0.8654 (m-80) REVERT: H 427 ASP cc_start: 0.8230 (m-30) cc_final: 0.7842 (t70) outliers start: 2 outliers final: 1 residues processed: 1111 average time/residue: 0.4862 time to fit residues: 900.2503 Evaluate side-chains 911 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 910 time to evaluate : 4.610 ------------------------------------------------------------------------------- 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: 2.9990 chunk 196 optimal weight: 3.9990 chunk 293 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 312 optimal weight: 9.9990 chunk 334 optimal weight: 7.9990 chunk 243 optimal weight: 0.1980 chunk 45 optimal weight: 6.9990 chunk 386 optimal weight: 9.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN F 134 GLN ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 28 HIS J 35 GLN ** C 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 HIS ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 ASN K 128 GLN ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 GLN ** G 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 GLN D 307 HIS D 335 ASN I 134 GLN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 GLN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 HIS H 134 GLN H 335 ASN H 416 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.4766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 41820 Z= 0.150 Angle : 0.536 9.511 56826 Z= 0.262 Chirality : 0.043 0.292 6216 Planarity : 0.004 0.044 7398 Dihedral : 10.040 176.399 5778 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.02 % Allowed : 0.61 % Favored : 99.36 % 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: -0.21 (0.12), residues: 5130 helix: 0.60 (0.12), residues: 2118 sheet: 1.20 (0.21), residues: 666 loop : -1.22 (0.12), residues: 2346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 21 HIS 0.004 0.001 HIS I 6 PHE 0.020 0.001 PHE G 266 TYR 0.018 0.001 TYR J 24 ARG 0.013 0.000 ARG H 318 *********************** 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 1150 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1149 time to evaluate : 4.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 2 ARG cc_start: 0.8432 (mtm180) cc_final: 0.8204 (ptt-90) REVERT: E 36 MET cc_start: 0.8752 (ptm) cc_final: 0.8505 (ptm) REVERT: E 85 GLN cc_start: 0.8490 (mm-40) cc_final: 0.7295 (tp-100) REVERT: E 163 LYS cc_start: 0.8159 (mtpp) cc_final: 0.7643 (mmtt) REVERT: E 203 MET cc_start: 0.9098 (mmp) cc_final: 0.8839 (mmp) REVERT: E 256 GLN cc_start: 0.8943 (pt0) cc_final: 0.8521 (pt0) REVERT: E 264 ARG cc_start: 0.9011 (mmm-85) cc_final: 0.8670 (mmm-85) REVERT: E 266 HIS cc_start: 0.8842 (p90) cc_final: 0.8273 (p-80) REVERT: E 302 MET cc_start: 0.8645 (mtt) cc_final: 0.8176 (mtp) REVERT: E 313 MET cc_start: 0.8808 (pmm) cc_final: 0.8239 (pmm) REVERT: E 345 ASP cc_start: 0.8300 (t70) cc_final: 0.8068 (t0) REVERT: E 380 ASN cc_start: 0.8715 (t0) cc_final: 0.8141 (t0) REVERT: E 382 THR cc_start: 0.9154 (p) cc_final: 0.8774 (p) REVERT: F 14 ASN cc_start: 0.9385 (m-40) cc_final: 0.8926 (m-40) REVERT: F 21 TRP cc_start: 0.9388 (m100) cc_final: 0.8964 (m100) REVERT: F 86 ARG cc_start: 0.7950 (mtp180) cc_final: 0.5910 (mmt-90) REVERT: F 100 ASN cc_start: 0.9067 (t0) cc_final: 0.8781 (t0) REVERT: F 265 PHE cc_start: 0.9157 (m-80) cc_final: 0.8711 (m-10) REVERT: F 299 MET cc_start: 0.8906 (mmp) cc_final: 0.8698 (mmp) REVERT: F 320 ARG cc_start: 0.7535 (mmt180) cc_final: 0.6784 (mmt180) REVERT: F 330 MET cc_start: 0.9176 (mmt) cc_final: 0.8884 (tpp) REVERT: F 355 ASP cc_start: 0.7599 (m-30) cc_final: 0.7324 (m-30) REVERT: F 367 PHE cc_start: 0.9181 (t80) cc_final: 0.8924 (t80) REVERT: F 375 GLN cc_start: 0.9141 (pp30) cc_final: 0.8671 (pp30) REVERT: F 379 LYS cc_start: 0.9067 (mmmm) cc_final: 0.8751 (mmmm) REVERT: F 427 ASP cc_start: 0.8186 (m-30) cc_final: 0.7717 (t70) REVERT: J 21 TRP cc_start: 0.9492 (m100) cc_final: 0.8899 (m100) REVERT: J 24 TYR cc_start: 0.8806 (m-10) cc_final: 0.8435 (m-80) REVERT: J 36 MET cc_start: 0.8713 (ptm) cc_final: 0.8359 (ptm) REVERT: J 85 GLN cc_start: 0.8534 (mm-40) cc_final: 0.7267 (tp-100) REVERT: J 163 LYS cc_start: 0.8353 (mtpp) cc_final: 0.7795 (mmtt) REVERT: J 168 GLU cc_start: 0.8763 (mp0) cc_final: 0.8105 (mp0) REVERT: J 176 GLN cc_start: 0.8838 (mp10) cc_final: 0.8545 (mp10) REVERT: J 203 MET cc_start: 0.9128 (mmp) cc_final: 0.8864 (mmp) REVERT: J 256 GLN cc_start: 0.9126 (pt0) cc_final: 0.8523 (tm-30) REVERT: J 302 MET cc_start: 0.9202 (mtm) cc_final: 0.8227 (mtp) REVERT: J 313 MET cc_start: 0.8793 (pmm) cc_final: 0.8020 (pmm) REVERT: J 345 ASP cc_start: 0.8621 (t70) cc_final: 0.8306 (t0) REVERT: J 367 ASP cc_start: 0.8569 (p0) cc_final: 0.8189 (p0) REVERT: J 377 MET cc_start: 0.8735 (tmm) cc_final: 0.8080 (tmm) REVERT: J 380 ASN cc_start: 0.8877 (t0) cc_final: 0.8274 (t0) REVERT: J 388 TRP cc_start: 0.9207 (m100) cc_final: 0.8990 (m100) REVERT: C 2 ARG cc_start: 0.8729 (mtm110) cc_final: 0.8060 (ptt-90) REVERT: C 85 GLN cc_start: 0.8574 (mm-40) cc_final: 0.8159 (mm-40) REVERT: C 129 CYS cc_start: 0.7796 (m) cc_final: 0.7066 (p) REVERT: C 163 LYS cc_start: 0.8313 (mtpp) cc_final: 0.7864 (mptt) REVERT: C 203 MET cc_start: 0.9125 (mmm) cc_final: 0.8828 (mmm) REVERT: C 205 ASP cc_start: 0.8901 (t0) cc_final: 0.8258 (t70) REVERT: C 256 GLN cc_start: 0.8765 (pt0) cc_final: 0.8225 (tt0) REVERT: C 266 HIS cc_start: 0.8766 (p90) cc_final: 0.8408 (p-80) REVERT: C 313 MET cc_start: 0.8860 (pmm) cc_final: 0.7922 (pmm) REVERT: C 347 CYS cc_start: 0.9104 (t) cc_final: 0.8738 (t) REVERT: C 377 MET cc_start: 0.8979 (tmm) cc_final: 0.8721 (tmm) REVERT: C 380 ASN cc_start: 0.8831 (t0) cc_final: 0.7904 (t0) REVERT: C 401 LYS cc_start: 0.9258 (mmtt) cc_final: 0.8922 (mmmm) REVERT: L 2 ARG cc_start: 0.8618 (mtm180) cc_final: 0.8142 (ptt-90) REVERT: L 25 CYS cc_start: 0.8850 (m) cc_final: 0.8650 (m) REVERT: L 129 CYS cc_start: 0.8072 (p) cc_final: 0.7857 (p) REVERT: L 163 LYS cc_start: 0.8306 (mtpp) cc_final: 0.7913 (mptt) REVERT: L 203 MET cc_start: 0.8760 (mmm) cc_final: 0.8395 (mmm) REVERT: L 217 LEU cc_start: 0.9151 (mt) cc_final: 0.8890 (mt) REVERT: L 256 GLN cc_start: 0.8767 (pt0) cc_final: 0.8304 (tm-30) REVERT: L 266 HIS cc_start: 0.8899 (p90) cc_final: 0.8492 (p-80) REVERT: L 290 GLU cc_start: 0.8205 (pt0) cc_final: 0.7782 (pt0) REVERT: L 313 MET cc_start: 0.8701 (pmm) cc_final: 0.7563 (pmm) REVERT: L 326 LYS cc_start: 0.8773 (tttm) cc_final: 0.8255 (mmtt) REVERT: L 376 CYS cc_start: 0.9407 (t) cc_final: 0.9112 (t) REVERT: L 378 LEU cc_start: 0.9233 (mt) cc_final: 0.9023 (mt) REVERT: L 380 ASN cc_start: 0.8807 (t0) cc_final: 0.7950 (t0) REVERT: A 21 TRP cc_start: 0.9376 (m100) cc_final: 0.9172 (m100) REVERT: A 163 LYS cc_start: 0.8546 (mtpp) cc_final: 0.7932 (mptt) REVERT: A 202 PHE cc_start: 0.8696 (m-10) cc_final: 0.8195 (m-10) REVERT: A 217 LEU cc_start: 0.9093 (mt) cc_final: 0.8718 (mt) REVERT: A 256 GLN cc_start: 0.8863 (pt0) cc_final: 0.8436 (pt0) REVERT: A 259 LEU cc_start: 0.9086 (mp) cc_final: 0.8771 (mp) REVERT: A 313 MET cc_start: 0.8765 (pmm) cc_final: 0.7944 (pmm) REVERT: A 377 MET cc_start: 0.8492 (tmm) cc_final: 0.8161 (tmm) REVERT: A 380 ASN cc_start: 0.8881 (t0) cc_final: 0.8325 (t0) REVERT: A 382 THR cc_start: 0.8800 (p) cc_final: 0.8465 (p) REVERT: A 401 LYS cc_start: 0.9078 (mmtt) cc_final: 0.8854 (mmtm) REVERT: K 2 ARG cc_start: 0.8548 (mtm110) cc_final: 0.7784 (ptt-90) REVERT: K 21 TRP cc_start: 0.9440 (m100) cc_final: 0.9211 (m100) REVERT: K 163 LYS cc_start: 0.8659 (mtpp) cc_final: 0.8080 (mptt) REVERT: K 183 GLU cc_start: 0.8843 (tt0) cc_final: 0.8565 (tt0) REVERT: K 202 PHE cc_start: 0.9122 (m-80) cc_final: 0.8738 (m-80) REVERT: K 203 MET cc_start: 0.9285 (mmp) cc_final: 0.9029 (mmp) REVERT: K 215 ARG cc_start: 0.8807 (ptp-170) cc_final: 0.8605 (ptp-170) REVERT: K 217 LEU cc_start: 0.9109 (mt) cc_final: 0.8866 (mt) REVERT: K 230 LEU cc_start: 0.8959 (mp) cc_final: 0.8700 (tt) REVERT: K 256 GLN cc_start: 0.8858 (pt0) cc_final: 0.8086 (tm-30) REVERT: K 302 MET cc_start: 0.8813 (mtt) cc_final: 0.8416 (mtt) REVERT: K 313 MET cc_start: 0.8809 (pmm) cc_final: 0.7921 (pmm) REVERT: K 326 LYS cc_start: 0.9025 (tttm) cc_final: 0.8520 (tptm) REVERT: K 380 ASN cc_start: 0.8830 (t0) cc_final: 0.8290 (t0) REVERT: K 401 LYS cc_start: 0.9105 (mmtt) cc_final: 0.8879 (mmtm) REVERT: K 430 LYS cc_start: 0.8782 (ptmm) cc_final: 0.8521 (tmtt) REVERT: G 14 ASN cc_start: 0.9411 (m-40) cc_final: 0.8913 (m-40) REVERT: G 21 TRP cc_start: 0.9406 (m100) cc_final: 0.8871 (m100) REVERT: G 37 HIS cc_start: 0.7803 (m-70) cc_final: 0.7249 (m-70) REVERT: G 95 SER cc_start: 0.8937 (m) cc_final: 0.8420 (t) REVERT: G 122 LYS cc_start: 0.9444 (ttmt) cc_final: 0.9182 (ttmm) REVERT: G 164 MET cc_start: 0.7899 (mmm) cc_final: 0.7518 (mmp) REVERT: G 265 PHE cc_start: 0.9222 (m-80) cc_final: 0.8867 (m-10) REVERT: G 297 LYS cc_start: 0.8532 (ptpt) cc_final: 0.7934 (mmtt) REVERT: G 300 MET cc_start: 0.8467 (mtt) cc_final: 0.8068 (mtm) REVERT: G 368 ILE cc_start: 0.8828 (mm) cc_final: 0.8607 (mm) REVERT: G 403 MET cc_start: 0.8124 (mtp) cc_final: 0.7876 (mmt) REVERT: G 406 MET cc_start: 0.8482 (tpp) cc_final: 0.8169 (mpp) REVERT: G 427 ASP cc_start: 0.8200 (m-30) cc_final: 0.7814 (t70) REVERT: D 14 ASN cc_start: 0.9234 (m-40) cc_final: 0.8917 (m-40) REVERT: D 95 SER cc_start: 0.9314 (m) cc_final: 0.8787 (t) REVERT: D 100 ASN cc_start: 0.9101 (t0) cc_final: 0.8852 (t0) REVERT: D 199 THR cc_start: 0.8587 (m) cc_final: 0.8162 (p) REVERT: D 209 ASP cc_start: 0.8467 (m-30) cc_final: 0.7975 (m-30) REVERT: D 276 ARG cc_start: 0.8546 (mmm-85) cc_final: 0.7980 (mmp80) REVERT: D 300 MET cc_start: 0.8367 (mtm) cc_final: 0.7999 (mtm) REVERT: D 306 ARG cc_start: 0.8881 (mtt90) cc_final: 0.8262 (mtm-85) REVERT: D 347 ASN cc_start: 0.8812 (m110) cc_final: 0.8499 (t0) REVERT: D 363 MET cc_start: 0.8649 (pmm) cc_final: 0.8253 (pmm) REVERT: D 368 ILE cc_start: 0.9057 (mm) cc_final: 0.8664 (mm) REVERT: D 374 ILE cc_start: 0.8567 (pt) cc_final: 0.7761 (pt) REVERT: D 397 TRP cc_start: 0.8299 (m100) cc_final: 0.7637 (m100) REVERT: D 407 GLU cc_start: 0.9167 (tp30) cc_final: 0.8665 (tp30) REVERT: D 427 ASP cc_start: 0.8022 (m-30) cc_final: 0.7565 (t70) REVERT: I 14 ASN cc_start: 0.9288 (m-40) cc_final: 0.8797 (m-40) REVERT: I 95 SER cc_start: 0.9116 (m) cc_final: 0.8807 (t) REVERT: I 207 LEU cc_start: 0.9535 (mt) cc_final: 0.9252 (mt) REVERT: I 265 PHE cc_start: 0.9258 (m-80) cc_final: 0.8854 (m-10) REVERT: I 276 ARG cc_start: 0.8557 (mmm-85) cc_final: 0.8052 (mmp80) REVERT: I 300 MET cc_start: 0.8573 (mtt) cc_final: 0.8331 (mtm) REVERT: I 306 ARG cc_start: 0.8789 (mpt180) cc_final: 0.8435 (mpt180) REVERT: I 330 MET cc_start: 0.8701 (mmm) cc_final: 0.8287 (tpp) REVERT: I 334 GLN cc_start: 0.8952 (tt0) cc_final: 0.8506 (tm-30) REVERT: I 347 ASN cc_start: 0.8845 (m110) cc_final: 0.8453 (m-40) REVERT: I 363 MET cc_start: 0.8739 (pmm) cc_final: 0.8447 (pmm) REVERT: I 407 GLU cc_start: 0.8898 (tp30) cc_final: 0.8246 (tp30) REVERT: I 427 ASP cc_start: 0.7865 (m-30) cc_final: 0.7505 (t70) REVERT: B 14 ASN cc_start: 0.9262 (m-40) cc_final: 0.8694 (m-40) REVERT: B 95 SER cc_start: 0.9022 (m) cc_final: 0.8668 (t) REVERT: B 114 ASP cc_start: 0.8500 (m-30) cc_final: 0.7838 (t0) REVERT: B 130 LEU cc_start: 0.9116 (tp) cc_final: 0.8883 (tt) REVERT: B 199 THR cc_start: 0.8728 (m) cc_final: 0.8513 (p) REVERT: B 233 MET cc_start: 0.8604 (ptm) cc_final: 0.8360 (ptm) REVERT: B 265 PHE cc_start: 0.9433 (m-10) cc_final: 0.9120 (m-10) REVERT: B 299 MET cc_start: 0.8508 (mmm) cc_final: 0.8137 (mmt) REVERT: B 343 GLU cc_start: 0.8727 (tp30) cc_final: 0.8286 (tp30) REVERT: B 344 TRP cc_start: 0.8820 (p-90) cc_final: 0.8383 (p-90) REVERT: B 388 MET cc_start: 0.9311 (mtm) cc_final: 0.9075 (mtp) REVERT: B 406 MET cc_start: 0.8784 (mmp) cc_final: 0.8509 (mpp) REVERT: B 427 ASP cc_start: 0.8193 (m-30) cc_final: 0.7822 (t70) REVERT: H 14 ASN cc_start: 0.9312 (m-40) cc_final: 0.8853 (m-40) REVERT: H 95 SER cc_start: 0.8994 (m) cc_final: 0.8745 (t) REVERT: H 257 MET cc_start: 0.8737 (mmm) cc_final: 0.8292 (mmm) REVERT: H 265 PHE cc_start: 0.9450 (m-10) cc_final: 0.9184 (m-10) REVERT: H 299 MET cc_start: 0.8292 (mmm) cc_final: 0.7983 (mmt) REVERT: H 300 MET cc_start: 0.8396 (mtt) cc_final: 0.8096 (mtm) REVERT: H 321 MET cc_start: 0.8868 (ptp) cc_final: 0.8422 (ptp) REVERT: H 343 GLU cc_start: 0.8504 (tp30) cc_final: 0.8243 (tp30) REVERT: H 344 TRP cc_start: 0.8814 (p-90) cc_final: 0.8280 (p-90) REVERT: H 363 MET cc_start: 0.9040 (pmm) cc_final: 0.8811 (pmm) REVERT: H 397 TRP cc_start: 0.8502 (m100) cc_final: 0.8228 (m-10) REVERT: H 406 MET cc_start: 0.8384 (tpp) cc_final: 0.8153 (mpp) REVERT: H 422 TYR cc_start: 0.8911 (m-80) cc_final: 0.8669 (m-80) REVERT: H 427 ASP cc_start: 0.8182 (m-30) cc_final: 0.7830 (t70) outliers start: 1 outliers final: 0 residues processed: 1149 average time/residue: 0.4911 time to fit residues: 940.4673 Evaluate side-chains 942 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 942 time to evaluate : 4.586 ------------------------------------------------------------------------------- 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: 10.0000 chunk 470 optimal weight: 7.9990 chunk 429 optimal weight: 0.0070 chunk 458 optimal weight: 8.9990 chunk 275 optimal weight: 5.9990 chunk 199 optimal weight: 8.9990 chunk 359 optimal weight: 5.9990 chunk 140 optimal weight: 20.0000 chunk 413 optimal weight: 0.0270 chunk 433 optimal weight: 10.0000 chunk 456 optimal weight: 30.0000 overall best weight: 4.0062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 GLN ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 197 HIS ** C 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 ASN ** L 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 GLN D 335 ASN I 134 GLN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN B 375 GLN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 41820 Z= 0.208 Angle : 0.560 10.314 56826 Z= 0.275 Chirality : 0.044 0.288 6216 Planarity : 0.004 0.052 7398 Dihedral : 9.975 179.417 5778 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.02 % Allowed : 0.41 % Favored : 99.57 % 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: -0.18 (0.12), residues: 5130 helix: 0.57 (0.12), residues: 2124 sheet: 1.12 (0.21), residues: 678 loop : -1.13 (0.13), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 21 HIS 0.007 0.001 HIS A 88 PHE 0.019 0.001 PHE D 266 TYR 0.023 0.001 TYR C 224 ARG 0.012 0.001 ARG B 318 *********************** 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 1084 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1083 time to evaluate : 4.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 2 ARG cc_start: 0.8408 (mtm180) cc_final: 0.8186 (ptt-90) REVERT: E 36 MET cc_start: 0.8759 (ptm) cc_final: 0.8464 (ptm) REVERT: E 85 GLN cc_start: 0.8558 (mm-40) cc_final: 0.7314 (tp-100) REVERT: E 163 LYS cc_start: 0.8076 (mtpp) cc_final: 0.7611 (mmtt) REVERT: E 203 MET cc_start: 0.9129 (mmp) cc_final: 0.8838 (mmp) REVERT: E 256 GLN cc_start: 0.8928 (pt0) cc_final: 0.8526 (pt0) REVERT: E 264 ARG cc_start: 0.9033 (mmm-85) cc_final: 0.8683 (mmm-85) REVERT: E 266 HIS cc_start: 0.8920 (p90) cc_final: 0.8380 (p-80) REVERT: E 302 MET cc_start: 0.8734 (mtt) cc_final: 0.8312 (mtp) REVERT: E 313 MET cc_start: 0.8810 (pmm) cc_final: 0.8209 (pmm) REVERT: E 345 ASP cc_start: 0.8347 (t70) cc_final: 0.8092 (t0) REVERT: E 380 ASN cc_start: 0.8706 (t0) cc_final: 0.8093 (t0) REVERT: E 382 THR cc_start: 0.9207 (p) cc_final: 0.8831 (p) REVERT: E 388 TRP cc_start: 0.9115 (m100) cc_final: 0.8737 (m100) REVERT: F 14 ASN cc_start: 0.9346 (m-40) cc_final: 0.8886 (m-40) REVERT: F 21 TRP cc_start: 0.9396 (m100) cc_final: 0.9019 (m100) REVERT: F 37 HIS cc_start: 0.7942 (m90) cc_final: 0.7609 (m-70) REVERT: F 86 ARG cc_start: 0.7988 (mtp180) cc_final: 0.5901 (mmt-90) REVERT: F 100 ASN cc_start: 0.9128 (t0) cc_final: 0.8825 (t0) REVERT: F 203 ASP cc_start: 0.7853 (t70) cc_final: 0.7446 (t0) REVERT: F 265 PHE cc_start: 0.9158 (m-80) cc_final: 0.8648 (m-10) REVERT: F 320 ARG cc_start: 0.7556 (mmt180) cc_final: 0.7138 (mmt180) REVERT: F 321 MET cc_start: 0.9030 (ptp) cc_final: 0.8828 (pmm) REVERT: F 330 MET cc_start: 0.9172 (mmt) cc_final: 0.8859 (tpp) REVERT: F 355 ASP cc_start: 0.7626 (m-30) cc_final: 0.7361 (m-30) REVERT: F 375 GLN cc_start: 0.9132 (pp30) cc_final: 0.8661 (pp30) REVERT: F 379 LYS cc_start: 0.9080 (mmmm) cc_final: 0.8755 (mmmm) REVERT: F 403 MET cc_start: 0.8663 (tpp) cc_final: 0.8238 (mmm) REVERT: F 427 ASP cc_start: 0.8225 (m-30) cc_final: 0.7720 (t70) REVERT: J 21 TRP cc_start: 0.9530 (m100) cc_final: 0.8923 (m100) REVERT: J 24 TYR cc_start: 0.8854 (m-10) cc_final: 0.8451 (m-80) REVERT: J 36 MET cc_start: 0.8680 (ptm) cc_final: 0.8342 (ptm) REVERT: J 85 GLN cc_start: 0.8603 (mm-40) cc_final: 0.7301 (tp-100) REVERT: J 163 LYS cc_start: 0.8332 (mtpp) cc_final: 0.7814 (mmtt) REVERT: J 176 GLN cc_start: 0.8885 (mp10) cc_final: 0.8593 (mp10) REVERT: J 203 MET cc_start: 0.9141 (mmp) cc_final: 0.8857 (mmp) REVERT: J 256 GLN cc_start: 0.9108 (pt0) cc_final: 0.8543 (tm-30) REVERT: J 302 MET cc_start: 0.8980 (mtm) cc_final: 0.8365 (mtp) REVERT: J 313 MET cc_start: 0.8825 (pmm) cc_final: 0.8200 (pmm) REVERT: J 345 ASP cc_start: 0.8572 (t70) cc_final: 0.8276 (t0) REVERT: J 367 ASP cc_start: 0.8533 (p0) cc_final: 0.8171 (p0) REVERT: J 380 ASN cc_start: 0.8854 (t0) cc_final: 0.8236 (t0) REVERT: C 2 ARG cc_start: 0.8803 (mtm110) cc_final: 0.8066 (ptt-90) REVERT: C 85 GLN cc_start: 0.8618 (mm-40) cc_final: 0.8238 (mm-40) REVERT: C 163 LYS cc_start: 0.8318 (mtpp) cc_final: 0.7882 (mptt) REVERT: C 203 MET cc_start: 0.9100 (mmm) cc_final: 0.8856 (mmm) REVERT: C 205 ASP cc_start: 0.8649 (t0) cc_final: 0.8350 (t70) REVERT: C 256 GLN cc_start: 0.8792 (pt0) cc_final: 0.8274 (tt0) REVERT: C 266 HIS cc_start: 0.8803 (p90) cc_final: 0.8504 (p-80) REVERT: C 313 MET cc_start: 0.8837 (pmm) cc_final: 0.7870 (pmm) REVERT: C 347 CYS cc_start: 0.9052 (t) cc_final: 0.8770 (t) REVERT: C 377 MET cc_start: 0.8939 (tmm) cc_final: 0.8712 (tmm) REVERT: C 380 ASN cc_start: 0.8810 (t0) cc_final: 0.7891 (t0) REVERT: C 401 LYS cc_start: 0.9291 (mmtt) cc_final: 0.8967 (mmmm) REVERT: L 2 ARG cc_start: 0.8628 (mtm180) cc_final: 0.8150 (ptt-90) REVERT: L 24 TYR cc_start: 0.8769 (m-10) cc_final: 0.8511 (m-80) REVERT: L 25 CYS cc_start: 0.8845 (m) cc_final: 0.8641 (m) REVERT: L 129 CYS cc_start: 0.8047 (p) cc_final: 0.7833 (p) REVERT: L 163 LYS cc_start: 0.8344 (mtpp) cc_final: 0.7931 (mptt) REVERT: L 217 LEU cc_start: 0.9154 (mt) cc_final: 0.8909 (mt) REVERT: L 256 GLN cc_start: 0.8811 (pt0) cc_final: 0.8332 (tm-30) REVERT: L 266 HIS cc_start: 0.8937 (p90) cc_final: 0.8593 (p-80) REVERT: L 313 MET cc_start: 0.8736 (pmm) cc_final: 0.7666 (pmm) REVERT: L 326 LYS cc_start: 0.8801 (tttm) cc_final: 0.8245 (mmtt) REVERT: L 347 CYS cc_start: 0.9094 (t) cc_final: 0.8747 (t) REVERT: L 376 CYS cc_start: 0.9451 (t) cc_final: 0.9178 (t) REVERT: L 378 LEU cc_start: 0.9274 (mt) cc_final: 0.9040 (mt) REVERT: L 380 ASN cc_start: 0.8821 (t0) cc_final: 0.7964 (t0) REVERT: A 21 TRP cc_start: 0.9399 (m100) cc_final: 0.9164 (m100) REVERT: A 163 LYS cc_start: 0.8545 (mtpp) cc_final: 0.7950 (mptt) REVERT: A 202 PHE cc_start: 0.8721 (m-10) cc_final: 0.8222 (m-10) REVERT: A 256 GLN cc_start: 0.8898 (pt0) cc_final: 0.8425 (pt0) REVERT: A 313 MET cc_start: 0.8764 (pmm) cc_final: 0.8117 (pmm) REVERT: A 377 MET cc_start: 0.8598 (tmm) cc_final: 0.8207 (tmm) REVERT: A 380 ASN cc_start: 0.8908 (t0) cc_final: 0.8470 (t0) REVERT: A 401 LYS cc_start: 0.9098 (mmtt) cc_final: 0.8885 (mmtm) REVERT: K 2 ARG cc_start: 0.8239 (mtm110) cc_final: 0.7500 (ptt-90) REVERT: K 21 TRP cc_start: 0.9441 (m100) cc_final: 0.9185 (m100) REVERT: K 163 LYS cc_start: 0.8577 (mtpp) cc_final: 0.7959 (mptt) REVERT: K 183 GLU cc_start: 0.8802 (tt0) cc_final: 0.8530 (tt0) REVERT: K 202 PHE cc_start: 0.9154 (m-80) cc_final: 0.8801 (m-80) REVERT: K 203 MET cc_start: 0.9266 (mmp) cc_final: 0.8933 (mmp) REVERT: K 217 LEU cc_start: 0.9251 (mt) cc_final: 0.8843 (mt) REVERT: K 220 GLU cc_start: 0.8122 (tp30) cc_final: 0.7807 (tp30) REVERT: K 230 LEU cc_start: 0.8947 (mp) cc_final: 0.8675 (tt) REVERT: K 256 GLN cc_start: 0.8877 (pt0) cc_final: 0.8055 (tm-30) REVERT: K 302 MET cc_start: 0.8767 (mtt) cc_final: 0.8323 (mtt) REVERT: K 313 MET cc_start: 0.8865 (pmm) cc_final: 0.8115 (pmm) REVERT: K 326 LYS cc_start: 0.8989 (tttm) cc_final: 0.8479 (tptm) REVERT: K 380 ASN cc_start: 0.8838 (t0) cc_final: 0.8397 (t0) REVERT: G 14 ASN cc_start: 0.9408 (m-40) cc_final: 0.8924 (m-40) REVERT: G 21 TRP cc_start: 0.9401 (m100) cc_final: 0.8894 (m100) REVERT: G 37 HIS cc_start: 0.7858 (m-70) cc_final: 0.7318 (m-70) REVERT: G 86 ARG cc_start: 0.7850 (mtp180) cc_final: 0.5863 (mmt-90) REVERT: G 95 SER cc_start: 0.8912 (m) cc_final: 0.8406 (t) REVERT: G 122 LYS cc_start: 0.9435 (ttmt) cc_final: 0.9169 (ttmm) REVERT: G 147 MET cc_start: 0.9539 (mmm) cc_final: 0.9123 (mmp) REVERT: G 265 PHE cc_start: 0.9226 (m-80) cc_final: 0.8899 (m-10) REVERT: G 297 LYS cc_start: 0.8573 (ptpt) cc_final: 0.7923 (mmtt) REVERT: G 300 MET cc_start: 0.8274 (mtt) cc_final: 0.7570 (mtm) REVERT: G 403 MET cc_start: 0.8179 (mtp) cc_final: 0.7902 (mmt) REVERT: G 406 MET cc_start: 0.8504 (tpp) cc_final: 0.8214 (mpp) REVERT: G 427 ASP cc_start: 0.8205 (m-30) cc_final: 0.7787 (t70) REVERT: D 14 ASN cc_start: 0.9303 (m-40) cc_final: 0.8896 (m-40) REVERT: D 95 SER cc_start: 0.9348 (m) cc_final: 0.8878 (t) REVERT: D 100 ASN cc_start: 0.9109 (t0) cc_final: 0.8848 (t0) REVERT: D 199 THR cc_start: 0.8586 (m) cc_final: 0.8250 (p) REVERT: D 209 ASP cc_start: 0.8455 (m-30) cc_final: 0.7935 (m-30) REVERT: D 247 ASN cc_start: 0.7726 (t0) cc_final: 0.7524 (t0) REVERT: D 257 MET cc_start: 0.8713 (mmm) cc_final: 0.7861 (mmm) REVERT: D 276 ARG cc_start: 0.8560 (mmm-85) cc_final: 0.7988 (mmp80) REVERT: D 306 ARG cc_start: 0.8911 (mtt90) cc_final: 0.8295 (mtm-85) REVERT: D 347 ASN cc_start: 0.8840 (m110) cc_final: 0.8501 (m-40) REVERT: D 363 MET cc_start: 0.8678 (pmm) cc_final: 0.8260 (pmm) REVERT: D 368 ILE cc_start: 0.8967 (mm) cc_final: 0.8525 (mm) REVERT: D 397 TRP cc_start: 0.8336 (m100) cc_final: 0.7683 (m100) REVERT: D 406 MET cc_start: 0.8463 (mpp) cc_final: 0.8254 (mpp) REVERT: D 407 GLU cc_start: 0.9023 (tp30) cc_final: 0.8387 (tp30) REVERT: D 427 ASP cc_start: 0.8040 (m-30) cc_final: 0.7581 (t70) REVERT: I 14 ASN cc_start: 0.9255 (m-40) cc_final: 0.8871 (m-40) REVERT: I 95 SER cc_start: 0.9111 (m) cc_final: 0.8862 (t) REVERT: I 207 LEU cc_start: 0.9538 (mt) cc_final: 0.9251 (mt) REVERT: I 209 ASP cc_start: 0.8325 (m-30) cc_final: 0.8048 (m-30) REVERT: I 233 MET cc_start: 0.8860 (ttt) cc_final: 0.8608 (ttp) REVERT: I 265 PHE cc_start: 0.9302 (m-80) cc_final: 0.8853 (m-10) REVERT: I 276 ARG cc_start: 0.8608 (mmm-85) cc_final: 0.8048 (mmp80) REVERT: I 300 MET cc_start: 0.8597 (mtt) cc_final: 0.8334 (mtm) REVERT: I 306 ARG cc_start: 0.8791 (mpt180) cc_final: 0.8481 (mpt180) REVERT: I 330 MET cc_start: 0.8745 (mmm) cc_final: 0.8312 (tpp) REVERT: I 334 GLN cc_start: 0.8948 (tt0) cc_final: 0.8493 (tm-30) REVERT: I 347 ASN cc_start: 0.8830 (m110) cc_final: 0.8464 (m-40) REVERT: I 363 MET cc_start: 0.8723 (pmm) cc_final: 0.8393 (pmm) REVERT: I 407 GLU cc_start: 0.8948 (tp30) cc_final: 0.8272 (tp30) REVERT: I 427 ASP cc_start: 0.7853 (m-30) cc_final: 0.7505 (t70) REVERT: B 14 ASN cc_start: 0.9245 (m-40) cc_final: 0.8757 (m-40) REVERT: B 95 SER cc_start: 0.9059 (m) cc_final: 0.8722 (t) REVERT: B 100 ASN cc_start: 0.9058 (t0) cc_final: 0.8793 (t0) REVERT: B 114 ASP cc_start: 0.8493 (m-30) cc_final: 0.7886 (t0) REVERT: B 130 LEU cc_start: 0.9172 (tp) cc_final: 0.8897 (tt) REVERT: B 265 PHE cc_start: 0.9488 (m-10) cc_final: 0.9222 (m-10) REVERT: B 299 MET cc_start: 0.8581 (mmm) cc_final: 0.8184 (mmt) REVERT: B 321 MET cc_start: 0.9080 (ptp) cc_final: 0.8724 (pmm) REVERT: B 343 GLU cc_start: 0.8677 (tp30) cc_final: 0.8266 (tp30) REVERT: B 347 ASN cc_start: 0.8698 (m-40) cc_final: 0.8278 (m-40) REVERT: B 368 ILE cc_start: 0.8923 (mm) cc_final: 0.8683 (mm) REVERT: B 388 MET cc_start: 0.9339 (mtm) cc_final: 0.9104 (mtp) REVERT: B 406 MET cc_start: 0.8815 (mmp) cc_final: 0.8553 (mpp) REVERT: B 427 ASP cc_start: 0.8237 (m-30) cc_final: 0.7828 (t70) REVERT: H 14 ASN cc_start: 0.9318 (m-40) cc_final: 0.8964 (m-40) REVERT: H 95 SER cc_start: 0.8909 (m) cc_final: 0.8705 (t) REVERT: H 100 ASN cc_start: 0.8910 (t0) cc_final: 0.8702 (t0) REVERT: H 134 GLN cc_start: 0.8566 (tt0) cc_final: 0.8362 (tt0) REVERT: H 199 THR cc_start: 0.8928 (m) cc_final: 0.8470 (p) REVERT: H 265 PHE cc_start: 0.9462 (m-10) cc_final: 0.9198 (m-10) REVERT: H 299 MET cc_start: 0.8302 (mmm) cc_final: 0.7958 (mmt) REVERT: H 300 MET cc_start: 0.8378 (mtt) cc_final: 0.8141 (mtm) REVERT: H 321 MET cc_start: 0.8917 (ptp) cc_final: 0.8406 (ptp) REVERT: H 343 GLU cc_start: 0.8632 (tp30) cc_final: 0.8321 (tp30) REVERT: H 344 TRP cc_start: 0.8831 (p-90) cc_final: 0.8282 (p-90) REVERT: H 397 TRP cc_start: 0.8549 (m100) cc_final: 0.8277 (m-10) REVERT: H 406 MET cc_start: 0.8472 (tpp) cc_final: 0.8155 (mpp) REVERT: H 422 TYR cc_start: 0.8956 (m-80) cc_final: 0.8660 (m-80) REVERT: H 427 ASP cc_start: 0.8238 (m-30) cc_final: 0.7822 (t70) outliers start: 1 outliers final: 1 residues processed: 1083 average time/residue: 0.4927 time to fit residues: 890.1665 Evaluate side-chains 921 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 920 time to evaluate : 4.582 ------------------------------------------------------------------------------- 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: 6.9990 chunk 484 optimal weight: 5.9990 chunk 295 optimal weight: 8.9990 chunk 229 optimal weight: 0.0770 chunk 336 optimal weight: 6.9990 chunk 508 optimal weight: 2.9990 chunk 467 optimal weight: 0.9980 chunk 404 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 312 optimal weight: 7.9990 chunk 248 optimal weight: 10.0000 overall best weight: 3.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 GLN F 347 ASN ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 GLN ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 228 ASN ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 ASN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 GLN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 191 GLN H 335 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.5013 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= 0.182 Angle : 0.558 11.459 56826 Z= 0.272 Chirality : 0.043 0.297 6216 Planarity : 0.004 0.055 7398 Dihedral : 9.837 175.868 5778 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: -0.09 (0.12), residues: 5130 helix: 0.65 (0.12), residues: 2124 sheet: 1.13 (0.21), residues: 684 loop : -1.09 (0.13), residues: 2322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 21 HIS 0.007 0.001 HIS K 88 PHE 0.019 0.001 PHE D 266 TYR 0.015 0.001 TYR D 422 ARG 0.010 0.001 ARG H 320 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10260 Ramachandran restraints generated. 5130 Oldfield, 0 Emsley, 5130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1089 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1089 time to evaluate : 4.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 36 MET cc_start: 0.8742 (ptm) cc_final: 0.8463 (ptm) REVERT: E 85 GLN cc_start: 0.8550 (mm-40) cc_final: 0.7289 (tp-100) REVERT: E 163 LYS cc_start: 0.8050 (mtpp) cc_final: 0.7591 (mmtt) REVERT: E 256 GLN cc_start: 0.8930 (pt0) cc_final: 0.8513 (pt0) REVERT: E 264 ARG cc_start: 0.9013 (mmm-85) cc_final: 0.8675 (mmm-85) REVERT: E 266 HIS cc_start: 0.8885 (p90) cc_final: 0.8327 (p-80) REVERT: E 302 MET cc_start: 0.8727 (mtt) cc_final: 0.8270 (mtp) REVERT: E 313 MET cc_start: 0.8905 (pmm) cc_final: 0.8295 (pmm) REVERT: E 345 ASP cc_start: 0.8361 (t70) cc_final: 0.8127 (t0) REVERT: E 380 ASN cc_start: 0.8674 (t0) cc_final: 0.8147 (t0) REVERT: E 382 THR cc_start: 0.9197 (p) cc_final: 0.8815 (p) REVERT: F 14 ASN cc_start: 0.9372 (m-40) cc_final: 0.8924 (m-40) REVERT: F 21 TRP cc_start: 0.9388 (m100) cc_final: 0.8977 (m100) REVERT: F 37 HIS cc_start: 0.7853 (m90) cc_final: 0.7518 (m-70) REVERT: F 86 ARG cc_start: 0.7958 (mtp180) cc_final: 0.5886 (mmt-90) REVERT: F 100 ASN cc_start: 0.9082 (t0) cc_final: 0.8795 (t0) REVERT: F 205 GLU cc_start: 0.8070 (mp0) cc_final: 0.7615 (mp0) REVERT: F 209 ASP cc_start: 0.8389 (m-30) cc_final: 0.8137 (m-30) REVERT: F 210 ILE cc_start: 0.9300 (mm) cc_final: 0.9057 (mm) REVERT: F 257 MET cc_start: 0.8575 (mmm) cc_final: 0.7273 (mmt) REVERT: F 265 PHE cc_start: 0.9144 (m-80) cc_final: 0.8625 (m-10) REVERT: F 312 THR cc_start: 0.9119 (p) cc_final: 0.7983 (p) REVERT: F 320 ARG cc_start: 0.7515 (mmt180) cc_final: 0.7100 (mmt180) REVERT: F 330 MET cc_start: 0.9179 (mmt) cc_final: 0.8887 (tpp) REVERT: F 355 ASP cc_start: 0.7583 (m-30) cc_final: 0.7264 (m-30) REVERT: F 375 GLN cc_start: 0.9147 (pp30) cc_final: 0.8642 (pp30) REVERT: F 379 LYS cc_start: 0.9022 (mmmm) cc_final: 0.8767 (ttmt) REVERT: F 403 MET cc_start: 0.8665 (tpp) cc_final: 0.8217 (mmm) REVERT: F 427 ASP cc_start: 0.8270 (m-30) cc_final: 0.7716 (t70) REVERT: J 21 TRP cc_start: 0.9519 (m100) cc_final: 0.8930 (m100) REVERT: J 24 TYR cc_start: 0.8771 (m-10) cc_final: 0.8394 (m-80) REVERT: J 36 MET cc_start: 0.8673 (ptm) cc_final: 0.8299 (ptm) REVERT: J 85 GLN cc_start: 0.8566 (mm-40) cc_final: 0.7264 (tp-100) REVERT: J 163 LYS cc_start: 0.8413 (mtpp) cc_final: 0.7909 (mmtt) REVERT: J 176 GLN cc_start: 0.8992 (mp10) cc_final: 0.8667 (mp10) REVERT: J 203 MET cc_start: 0.9178 (mmp) cc_final: 0.8884 (mmp) REVERT: J 256 GLN cc_start: 0.9002 (pt0) cc_final: 0.8391 (tm-30) REVERT: J 302 MET cc_start: 0.8973 (mtm) cc_final: 0.8182 (mtp) REVERT: J 313 MET cc_start: 0.8761 (pmm) cc_final: 0.8165 (pmm) REVERT: J 345 ASP cc_start: 0.8556 (t70) cc_final: 0.8253 (t0) REVERT: J 367 ASP cc_start: 0.8500 (p0) cc_final: 0.8135 (p0) REVERT: J 380 ASN cc_start: 0.8929 (t0) cc_final: 0.8244 (t0) REVERT: C 2 ARG cc_start: 0.8777 (mtm110) cc_final: 0.8062 (ptt-90) REVERT: C 24 TYR cc_start: 0.8756 (m-10) cc_final: 0.8201 (m-10) REVERT: C 85 GLN cc_start: 0.8710 (mm-40) cc_final: 0.8325 (mm-40) REVERT: C 163 LYS cc_start: 0.8255 (mtpp) cc_final: 0.7815 (mptt) REVERT: C 205 ASP cc_start: 0.8803 (t0) cc_final: 0.8204 (t70) REVERT: C 256 GLN cc_start: 0.8796 (pt0) cc_final: 0.8274 (tt0) REVERT: C 266 HIS cc_start: 0.8771 (p90) cc_final: 0.8479 (p-80) REVERT: C 313 MET cc_start: 0.8849 (pmm) cc_final: 0.7855 (pmm) REVERT: C 347 CYS cc_start: 0.9007 (t) cc_final: 0.8732 (t) REVERT: C 377 MET cc_start: 0.9008 (tmm) cc_final: 0.8616 (tmm) REVERT: C 380 ASN cc_start: 0.8864 (t0) cc_final: 0.7854 (t0) REVERT: C 401 LYS cc_start: 0.9258 (mmtt) cc_final: 0.8952 (mmmm) REVERT: L 2 ARG cc_start: 0.8618 (mtm180) cc_final: 0.8151 (ptt-90) REVERT: L 24 TYR cc_start: 0.8766 (m-10) cc_final: 0.8467 (m-80) REVERT: L 25 CYS cc_start: 0.8828 (m) cc_final: 0.8613 (m) REVERT: L 163 LYS cc_start: 0.8298 (mtpp) cc_final: 0.7915 (mptt) REVERT: L 205 ASP cc_start: 0.8880 (t0) cc_final: 0.8668 (t0) REVERT: L 217 LEU cc_start: 0.9126 (mt) cc_final: 0.8880 (mt) REVERT: L 256 GLN cc_start: 0.8802 (pt0) cc_final: 0.8332 (tm-30) REVERT: L 266 HIS cc_start: 0.8934 (p90) cc_final: 0.8598 (p-80) REVERT: L 313 MET cc_start: 0.8722 (pmm) cc_final: 0.7658 (pmm) REVERT: L 326 LYS cc_start: 0.8794 (tttm) cc_final: 0.8267 (mmtt) REVERT: L 347 CYS cc_start: 0.9057 (t) cc_final: 0.8727 (t) REVERT: L 376 CYS cc_start: 0.9427 (t) cc_final: 0.9148 (t) REVERT: L 378 LEU cc_start: 0.9234 (mt) cc_final: 0.9024 (mt) REVERT: L 380 ASN cc_start: 0.8851 (t0) cc_final: 0.7958 (t0) REVERT: A 2 ARG cc_start: 0.8420 (mtm110) cc_final: 0.7633 (ptt-90) REVERT: A 21 TRP cc_start: 0.9437 (m100) cc_final: 0.9135 (m100) REVERT: A 163 LYS cc_start: 0.8483 (mtpp) cc_final: 0.7895 (mptt) REVERT: A 217 LEU cc_start: 0.9129 (mt) cc_final: 0.8832 (mt) REVERT: A 256 GLN cc_start: 0.8868 (pt0) cc_final: 0.8432 (pt0) REVERT: A 313 MET cc_start: 0.8894 (pmm) cc_final: 0.8231 (pmm) REVERT: A 380 ASN cc_start: 0.8936 (t0) cc_final: 0.8560 (t0) REVERT: A 382 THR cc_start: 0.8877 (p) cc_final: 0.8647 (p) REVERT: A 401 LYS cc_start: 0.9010 (mmtt) cc_final: 0.8777 (mmtm) REVERT: A 415 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8026 (tm-30) REVERT: K 2 ARG cc_start: 0.8294 (mtm110) cc_final: 0.7454 (ptt-90) REVERT: K 21 TRP cc_start: 0.9485 (m100) cc_final: 0.9201 (m100) REVERT: K 123 ARG cc_start: 0.7955 (tpp80) cc_final: 0.7736 (tpp80) REVERT: K 163 LYS cc_start: 0.8532 (mtpp) cc_final: 0.7949 (mptt) REVERT: K 168 GLU cc_start: 0.8496 (mp0) cc_final: 0.7970 (mp0) REVERT: K 172 TYR cc_start: 0.8561 (t80) cc_final: 0.7740 (t80) REVERT: K 183 GLU cc_start: 0.8493 (tt0) cc_final: 0.8276 (tt0) REVERT: K 202 PHE cc_start: 0.9137 (m-80) cc_final: 0.8771 (m-80) REVERT: K 203 MET cc_start: 0.9289 (mmp) cc_final: 0.8304 (mmp) REVERT: K 217 LEU cc_start: 0.9219 (mt) cc_final: 0.8790 (mt) REVERT: K 220 GLU cc_start: 0.8106 (tp30) cc_final: 0.7771 (tp30) REVERT: K 256 GLN cc_start: 0.8855 (pt0) cc_final: 0.8236 (tm-30) REVERT: K 302 MET cc_start: 0.8826 (mtt) cc_final: 0.8469 (mtt) REVERT: K 313 MET cc_start: 0.8852 (pmm) cc_final: 0.8091 (pmm) REVERT: K 326 LYS cc_start: 0.8968 (tttm) cc_final: 0.8485 (tptm) REVERT: K 380 ASN cc_start: 0.8843 (t0) cc_final: 0.8386 (t0) REVERT: G 14 ASN cc_start: 0.9393 (m-40) cc_final: 0.8922 (m-40) REVERT: G 21 TRP cc_start: 0.9397 (m100) cc_final: 0.8883 (m100) REVERT: G 37 HIS cc_start: 0.7839 (m-70) cc_final: 0.7304 (m-70) REVERT: G 86 ARG cc_start: 0.7843 (mtp180) cc_final: 0.5835 (mmt-90) REVERT: G 95 SER cc_start: 0.8927 (m) cc_final: 0.8416 (t) REVERT: G 122 LYS cc_start: 0.9418 (ttmt) cc_final: 0.9156 (ttmm) REVERT: G 130 LEU cc_start: 0.8997 (tt) cc_final: 0.8736 (tt) REVERT: G 147 MET cc_start: 0.9563 (mmm) cc_final: 0.9240 (mmp) REVERT: G 257 MET cc_start: 0.8513 (mmm) cc_final: 0.7353 (mmp) REVERT: G 265 PHE cc_start: 0.9197 (m-80) cc_final: 0.8888 (m-10) REVERT: G 297 LYS cc_start: 0.8576 (ptpt) cc_final: 0.7904 (mmtm) REVERT: G 300 MET cc_start: 0.8233 (mtt) cc_final: 0.7705 (mtm) REVERT: G 312 THR cc_start: 0.9188 (p) cc_final: 0.8123 (p) REVERT: G 321 MET cc_start: 0.8935 (pmm) cc_final: 0.8606 (pmm) REVERT: G 368 ILE cc_start: 0.9190 (tp) cc_final: 0.8948 (tp) REVERT: G 406 MET cc_start: 0.8450 (tpp) cc_final: 0.8200 (mpp) REVERT: G 427 ASP cc_start: 0.8207 (m-30) cc_final: 0.7777 (t70) REVERT: D 14 ASN cc_start: 0.9238 (m-40) cc_final: 0.8917 (m-40) REVERT: D 95 SER cc_start: 0.9333 (m) cc_final: 0.8927 (p) REVERT: D 100 ASN cc_start: 0.9104 (t0) cc_final: 0.8844 (t0) REVERT: D 147 MET cc_start: 0.9248 (tpp) cc_final: 0.9027 (mmm) REVERT: D 199 THR cc_start: 0.8592 (m) cc_final: 0.8069 (p) REVERT: D 209 ASP cc_start: 0.8466 (m-30) cc_final: 0.7907 (m-30) REVERT: D 257 MET cc_start: 0.8795 (mmm) cc_final: 0.7885 (mmm) REVERT: D 265 PHE cc_start: 0.9306 (m-10) cc_final: 0.8960 (m-10) REVERT: D 276 ARG cc_start: 0.8559 (mmm-85) cc_final: 0.7980 (mmp80) REVERT: D 306 ARG cc_start: 0.8914 (mtt90) cc_final: 0.8309 (mtm-85) REVERT: D 347 ASN cc_start: 0.8979 (m110) cc_final: 0.8551 (m-40) REVERT: D 363 MET cc_start: 0.8761 (pmm) cc_final: 0.8317 (pmm) REVERT: D 368 ILE cc_start: 0.9089 (mm) cc_final: 0.8722 (mm) REVERT: D 397 TRP cc_start: 0.8297 (m100) cc_final: 0.7635 (m100) REVERT: D 407 GLU cc_start: 0.8991 (tp30) cc_final: 0.8311 (tp30) REVERT: D 427 ASP cc_start: 0.8036 (m-30) cc_final: 0.7544 (t70) REVERT: I 6 HIS cc_start: 0.9108 (t-90) cc_final: 0.8871 (t-170) REVERT: I 14 ASN cc_start: 0.9290 (m-40) cc_final: 0.8873 (m-40) REVERT: I 95 SER cc_start: 0.9105 (m) cc_final: 0.8844 (t) REVERT: I 143 THR cc_start: 0.9234 (m) cc_final: 0.9003 (p) REVERT: I 207 LEU cc_start: 0.9529 (mt) cc_final: 0.9240 (mt) REVERT: I 209 ASP cc_start: 0.8311 (m-30) cc_final: 0.7859 (m-30) REVERT: I 257 MET cc_start: 0.8854 (mmm) cc_final: 0.8262 (mmm) REVERT: I 265 PHE cc_start: 0.9260 (m-80) cc_final: 0.8851 (m-10) REVERT: I 276 ARG cc_start: 0.8630 (mmm-85) cc_final: 0.8055 (mmp80) REVERT: I 300 MET cc_start: 0.8587 (mtt) cc_final: 0.8345 (mtm) REVERT: I 306 ARG cc_start: 0.8812 (mpt180) cc_final: 0.8502 (mpt180) REVERT: I 330 MET cc_start: 0.8702 (mmm) cc_final: 0.8317 (tpp) REVERT: I 334 GLN cc_start: 0.8911 (tt0) cc_final: 0.8489 (tm-30) REVERT: I 347 ASN cc_start: 0.8814 (m110) cc_final: 0.8441 (m-40) REVERT: I 363 MET cc_start: 0.8714 (pmm) cc_final: 0.8346 (pmm) REVERT: I 407 GLU cc_start: 0.8962 (tp30) cc_final: 0.8288 (tp30) REVERT: I 427 ASP cc_start: 0.7920 (m-30) cc_final: 0.7525 (t70) REVERT: B 14 ASN cc_start: 0.9258 (m-40) cc_final: 0.8739 (m-40) REVERT: B 95 SER cc_start: 0.9067 (m) cc_final: 0.8690 (t) REVERT: B 100 ASN cc_start: 0.9114 (t0) cc_final: 0.8814 (t0) REVERT: B 114 ASP cc_start: 0.8483 (m-30) cc_final: 0.7847 (t0) REVERT: B 130 LEU cc_start: 0.9134 (tp) cc_final: 0.8893 (tt) REVERT: B 265 PHE cc_start: 0.9365 (m-10) cc_final: 0.9162 (m-10) REVERT: B 299 MET cc_start: 0.8732 (mmm) cc_final: 0.8381 (mmp) REVERT: B 321 MET cc_start: 0.9135 (ptp) cc_final: 0.8667 (pmm) REVERT: B 343 GLU cc_start: 0.8661 (tp30) cc_final: 0.8270 (tp30) REVERT: B 347 ASN cc_start: 0.8709 (m-40) cc_final: 0.8259 (m-40) REVERT: B 388 MET cc_start: 0.9348 (mtm) cc_final: 0.9088 (mtp) REVERT: B 406 MET cc_start: 0.8901 (mmp) cc_final: 0.8565 (mpp) REVERT: B 427 ASP cc_start: 0.8245 (m-30) cc_final: 0.7818 (t70) REVERT: H 14 ASN cc_start: 0.9294 (m-40) cc_final: 0.8771 (m-40) REVERT: H 95 SER cc_start: 0.8917 (m) cc_final: 0.8710 (t) REVERT: H 114 ASP cc_start: 0.8643 (m-30) cc_final: 0.7967 (t0) REVERT: H 164 MET cc_start: 0.9319 (ttm) cc_final: 0.8865 (ttm) REVERT: H 199 THR cc_start: 0.8852 (m) cc_final: 0.8490 (p) REVERT: H 265 PHE cc_start: 0.9459 (m-10) cc_final: 0.9212 (m-10) REVERT: H 299 MET cc_start: 0.8321 (mmm) cc_final: 0.8051 (mmp) REVERT: H 343 GLU cc_start: 0.8633 (tp30) cc_final: 0.8354 (tp30) REVERT: H 344 TRP cc_start: 0.8849 (p-90) cc_final: 0.8382 (p-90) REVERT: H 362 LYS cc_start: 0.9209 (mtpp) cc_final: 0.8962 (tppp) REVERT: H 397 TRP cc_start: 0.8528 (m100) cc_final: 0.8280 (m-10) REVERT: H 406 MET cc_start: 0.8461 (tpp) cc_final: 0.8135 (mpp) REVERT: H 422 TYR cc_start: 0.8924 (m-80) cc_final: 0.8711 (m-80) REVERT: H 427 ASP cc_start: 0.8227 (m-30) cc_final: 0.7812 (t70) outliers start: 0 outliers final: 0 residues processed: 1089 average time/residue: 0.4927 time to fit residues: 898.8945 Evaluate side-chains 936 residues out of total 4410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 936 time to evaluate : 4.840 ------------------------------------------------------------------------------- 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: 0.9990 chunk 430 optimal weight: 0.4980 chunk 123 optimal weight: 7.9990 chunk 373 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 405 optimal weight: 20.0000 chunk 169 optimal weight: 6.9990 chunk 416 optimal weight: 20.0000 chunk 51 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 GLN ** J 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 ASN ** L 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN D 335 ASN ** I 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 GLN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.093488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.083104 restraints weight = 93076.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.085772 restraints weight = 50980.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.087633 restraints weight = 31621.900| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.5117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 41820 Z= 0.193 Angle : 0.558 10.070 56826 Z= 0.272 Chirality : 0.043 0.292 6216 Planarity : 0.004 0.058 7398 Dihedral : 9.778 178.441 5778 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.02 % Allowed : 0.18 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.12), residues: 5130 helix: 0.69 (0.12), residues: 2160 sheet: 1.11 (0.21), residues: 684 loop : -1.01 (0.13), residues: 2286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 21 HIS 0.006 0.001 HIS K 88 PHE 0.016 0.001 PHE C 202 TYR 0.018 0.001 TYR D 422 ARG 0.009 0.000 ARG B 320 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13286.83 seconds wall clock time: 237 minutes 5.78 seconds (14225.78 seconds total)