Starting phenix.real_space_refine on Sat Feb 24 00:33:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6evw_3961/02_2024/6evw_3961_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6evw_3961/02_2024/6evw_3961.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/6evw_3961/02_2024/6evw_3961.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6evw_3961/02_2024/6evw_3961.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6evw_3961/02_2024/6evw_3961_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6evw_3961/02_2024/6evw_3961_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= 0.013 sd= 0.039 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 12 5.21 5 S 276 5.16 5 C 25464 2.51 5 N 6918 2.21 5 O 7830 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 PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 390": "NH1" <-> "NH2" Residue "J ARG 64": "NH1" <-> "NH2" Residue "J PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 390": "NH1" <-> "NH2" Residue "C ARG 64": "NH1" <-> "NH2" Residue "C PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 390": "NH1" <-> "NH2" Residue "L ARG 64": "NH1" <-> "NH2" Residue "L PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 390": "NH1" <-> "NH2" Residue "A ARG 64": "NH1" <-> "NH2" Residue "A PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 390": "NH1" <-> "NH2" Residue "K ARG 64": "NH1" <-> "NH2" Residue "K PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 390": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 40536 Number of models: 1 Model: "" Number of chains: 24 Chain: "E" Number of atoms: 3322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3322 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 402} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 3322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3322 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 402} Chain breaks: 2 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: 3322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3322 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 402} Chain breaks: 2 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: 3322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3322 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 402} Chain breaks: 2 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: 3322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3322 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 402} Chain breaks: 2 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: 3322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3322 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 402} Chain breaks: 2 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: "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: "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: "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: "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: "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: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 21.17, per 1000 atoms: 0.52 Number of scatterers: 40536 At special positions: 0 Unit cell: (113.98, 169.58, 216.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 276 16.00 P 36 15.00 Mg 12 11.99 O 7830 8.00 N 6918 7.00 C 25464 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: 15.42 Conformation dependent library (CDL) restraints added in 7.1 seconds 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9492 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 216 helices and 42 sheets defined 42.5% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.25 Creating SS restraints... Processing helix chain 'E' and resid 10 through 27 removed outlier: 3.503A pdb=" N GLN E 15 " --> pdb=" O GLN E 11 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA E 19 " --> pdb=" O GLN E 15 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU E 22 " --> pdb=" O ASN E 18 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU E 26 " --> pdb=" O GLU E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 79 Processing helix chain 'E' and resid 103 through 107 Processing helix chain 'E' and resid 115 through 126 removed outlier: 3.504A pdb=" N ILE E 122 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG E 123 " --> pdb=" O LEU E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 160 removed outlier: 4.502A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU E 152 " --> pdb=" O GLY E 148 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU E 155 " --> pdb=" O SER E 151 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG E 156 " --> pdb=" O LEU E 152 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU E 157 " --> pdb=" O LEU E 153 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER E 158 " --> pdb=" O MET E 154 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 189 removed outlier: 3.713A pdb=" N SER E 187 " --> pdb=" O PRO E 184 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILE E 188 " --> pdb=" O TYR E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 194 No H-bonds generated for 'chain 'E' and resid 191 through 194' Processing helix chain 'E' and resid 207 through 214 removed outlier: 4.292A pdb=" N ASP E 211 " --> pdb=" O GLU E 207 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE E 212 " --> pdb=" O ALA E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 240 removed outlier: 3.746A pdb=" N ARG E 229 " --> pdb=" O THR E 225 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU E 230 " --> pdb=" O ASN E 226 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE E 231 " --> pdb=" O LEU E 227 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN E 233 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE E 234 " --> pdb=" O LEU E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 258 removed outlier: 4.140A pdb=" N GLN E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR E 257 " --> pdb=" O THR E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 281 No H-bonds generated for 'chain 'E' and resid 279 through 281' Processing helix chain 'E' and resid 288 through 295 removed outlier: 4.018A pdb=" N THR E 292 " --> pdb=" O VAL E 288 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN E 293 " --> pdb=" O ALA E 289 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA E 294 " --> pdb=" O GLU E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 309 No H-bonds generated for 'chain 'E' and resid 307 through 309' Processing helix chain 'E' and resid 325 through 336 removed outlier: 3.566A pdb=" N ALA E 331 " --> pdb=" O ASP E 327 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE E 335 " --> pdb=" O ALA E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 400 removed outlier: 3.837A pdb=" N GLU E 386 " --> pdb=" O ALA E 383 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TRP E 388 " --> pdb=" O ALA E 385 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP E 392 " --> pdb=" O ALA E 389 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N HIS E 393 " --> pdb=" O ARG E 390 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP E 396 " --> pdb=" O HIS E 393 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU E 397 " --> pdb=" O LYS E 394 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET E 398 " --> pdb=" O PHE E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 411 Processing helix chain 'E' and resid 415 through 436 removed outlier: 3.550A pdb=" N SER E 419 " --> pdb=" O GLU E 415 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU E 423 " --> pdb=" O SER E 419 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP E 424 " --> pdb=" O GLU E 420 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET E 425 " --> pdb=" O ALA E 421 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA E 426 " --> pdb=" O ARG E 422 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP E 431 " --> pdb=" O ALA E 427 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N TYR E 432 " --> pdb=" O LEU E 428 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU E 433 " --> pdb=" O GLU E 429 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 27 removed outlier: 3.502A pdb=" N GLN J 15 " --> pdb=" O GLN J 11 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA J 19 " --> pdb=" O GLN J 15 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU J 22 " --> pdb=" O ASN J 18 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU J 26 " --> pdb=" O GLU J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 79 Processing helix chain 'J' and resid 103 through 107 Processing helix chain 'J' and resid 115 through 126 removed outlier: 3.504A pdb=" N ILE J 122 " --> pdb=" O VAL J 118 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG J 123 " --> pdb=" O LEU J 119 " (cutoff:3.500A) Processing helix chain 'J' and resid 144 through 160 removed outlier: 4.501A pdb=" N THR J 150 " --> pdb=" O GLY J 146 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU J 152 " --> pdb=" O GLY J 148 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU J 155 " --> pdb=" O SER J 151 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG J 156 " --> pdb=" O LEU J 152 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU J 157 " --> pdb=" O LEU J 153 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER J 158 " --> pdb=" O MET J 154 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL J 159 " --> pdb=" O GLU J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 189 removed outlier: 3.714A pdb=" N SER J 187 " --> pdb=" O PRO J 184 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE J 188 " --> pdb=" O TYR J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 191 through 194 No H-bonds generated for 'chain 'J' and resid 191 through 194' Processing helix chain 'J' and resid 207 through 214 removed outlier: 4.293A pdb=" N ASP J 211 " --> pdb=" O GLU J 207 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE J 212 " --> pdb=" O ALA J 208 " (cutoff:3.500A) Processing helix chain 'J' and resid 224 through 240 removed outlier: 3.746A pdb=" N ARG J 229 " --> pdb=" O THR J 225 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU J 230 " --> pdb=" O ASN J 226 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE J 231 " --> pdb=" O LEU J 227 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN J 233 " --> pdb=" O ARG J 229 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE J 234 " --> pdb=" O LEU J 230 " (cutoff:3.500A) Processing helix chain 'J' and resid 252 through 258 removed outlier: 4.140A pdb=" N GLN J 256 " --> pdb=" O LEU J 252 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR J 257 " --> pdb=" O THR J 253 " (cutoff:3.500A) Processing helix chain 'J' and resid 279 through 281 No H-bonds generated for 'chain 'J' and resid 279 through 281' Processing helix chain 'J' and resid 288 through 295 removed outlier: 4.017A pdb=" N THR J 292 " --> pdb=" O VAL J 288 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN J 293 " --> pdb=" O ALA J 289 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA J 294 " --> pdb=" O GLU J 290 " (cutoff:3.500A) Processing helix chain 'J' and resid 307 through 309 No H-bonds generated for 'chain 'J' and resid 307 through 309' Processing helix chain 'J' and resid 325 through 336 removed outlier: 3.566A pdb=" N ALA J 331 " --> pdb=" O ASP J 327 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE J 335 " --> pdb=" O ALA J 331 " (cutoff:3.500A) Processing helix chain 'J' and resid 383 through 400 removed outlier: 3.837A pdb=" N GLU J 386 " --> pdb=" O ALA J 383 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TRP J 388 " --> pdb=" O ALA J 385 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP J 392 " --> pdb=" O ALA J 389 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N HIS J 393 " --> pdb=" O ARG J 390 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP J 396 " --> pdb=" O HIS J 393 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU J 397 " --> pdb=" O LYS J 394 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET J 398 " --> pdb=" O PHE J 395 " (cutoff:3.500A) Processing helix chain 'J' and resid 405 through 411 Processing helix chain 'J' and resid 415 through 436 removed outlier: 3.549A pdb=" N SER J 419 " --> pdb=" O GLU J 415 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU J 423 " --> pdb=" O SER J 419 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP J 424 " --> pdb=" O GLU J 420 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET J 425 " --> pdb=" O ALA J 421 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA J 426 " --> pdb=" O ARG J 422 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP J 431 " --> pdb=" O ALA J 427 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TYR J 432 " --> pdb=" O LEU J 428 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU J 433 " --> pdb=" O GLU J 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 27 removed outlier: 3.502A pdb=" N GLN C 15 " --> pdb=" O GLN C 11 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA C 19 " --> pdb=" O GLN C 15 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU C 22 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 26 " --> pdb=" O GLU C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 79 Processing helix chain 'C' and resid 103 through 107 Processing helix chain 'C' and resid 115 through 126 removed outlier: 3.504A pdb=" N ILE C 122 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ARG C 123 " --> pdb=" O LEU C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 160 removed outlier: 4.501A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU C 152 " --> pdb=" O GLY C 148 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU C 155 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU C 157 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER C 158 " --> pdb=" O MET C 154 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 189 removed outlier: 3.714A pdb=" N SER C 187 " --> pdb=" O PRO C 184 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE C 188 " --> pdb=" O TYR C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 194 No H-bonds generated for 'chain 'C' and resid 191 through 194' Processing helix chain 'C' and resid 207 through 214 removed outlier: 4.294A pdb=" N ASP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 240 removed outlier: 3.747A pdb=" N ARG C 229 " --> pdb=" O THR C 225 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU C 230 " --> pdb=" O ASN C 226 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE C 231 " --> pdb=" O LEU C 227 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN C 233 " --> pdb=" O ARG C 229 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE C 234 " --> pdb=" O LEU C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 258 removed outlier: 4.140A pdb=" N GLN C 256 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR C 257 " --> pdb=" O THR C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 281 No H-bonds generated for 'chain 'C' and resid 279 through 281' Processing helix chain 'C' and resid 288 through 295 removed outlier: 4.018A pdb=" N THR C 292 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 309 No H-bonds generated for 'chain 'C' and resid 307 through 309' Processing helix chain 'C' and resid 325 through 336 removed outlier: 3.566A pdb=" N ALA C 331 " --> pdb=" O ASP C 327 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE C 335 " --> pdb=" O ALA C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 400 removed outlier: 3.837A pdb=" N GLU C 386 " --> pdb=" O ALA C 383 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TRP C 388 " --> pdb=" O ALA C 385 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP C 392 " --> pdb=" O ALA C 389 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N HIS C 393 " --> pdb=" O ARG C 390 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP C 396 " --> pdb=" O HIS C 393 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU C 397 " --> pdb=" O LYS C 394 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET C 398 " --> pdb=" O PHE C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 Processing helix chain 'C' and resid 415 through 436 removed outlier: 3.550A pdb=" N SER C 419 " --> pdb=" O GLU C 415 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU C 423 " --> pdb=" O SER C 419 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP C 424 " --> pdb=" O GLU C 420 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET C 425 " --> pdb=" O ALA C 421 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA C 426 " --> pdb=" O ARG C 422 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP C 431 " --> pdb=" O ALA C 427 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N TYR C 432 " --> pdb=" O LEU C 428 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU C 433 " --> pdb=" O GLU C 429 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 27 removed outlier: 3.502A pdb=" N GLN L 15 " --> pdb=" O GLN L 11 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA L 19 " --> pdb=" O GLN L 15 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU L 22 " --> pdb=" O ASN L 18 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU L 26 " --> pdb=" O GLU L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 79 Processing helix chain 'L' and resid 103 through 107 Processing helix chain 'L' and resid 115 through 126 removed outlier: 3.504A pdb=" N ILE L 122 " --> pdb=" O VAL L 118 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG L 123 " --> pdb=" O LEU L 119 " (cutoff:3.500A) Processing helix chain 'L' and resid 144 through 160 removed outlier: 4.502A pdb=" N THR L 150 " --> pdb=" O GLY L 146 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU L 152 " --> pdb=" O GLY L 148 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU L 155 " --> pdb=" O SER L 151 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG L 156 " --> pdb=" O LEU L 152 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU L 157 " --> pdb=" O LEU L 153 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER L 158 " --> pdb=" O MET L 154 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL L 159 " --> pdb=" O GLU L 155 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 189 removed outlier: 3.714A pdb=" N SER L 187 " --> pdb=" O PRO L 184 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE L 188 " --> pdb=" O TYR L 185 " (cutoff:3.500A) Processing helix chain 'L' and resid 191 through 194 No H-bonds generated for 'chain 'L' and resid 191 through 194' Processing helix chain 'L' and resid 207 through 214 removed outlier: 4.292A pdb=" N ASP L 211 " --> pdb=" O GLU L 207 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE L 212 " --> pdb=" O ALA L 208 " (cutoff:3.500A) Processing helix chain 'L' and resid 224 through 240 removed outlier: 3.746A pdb=" N ARG L 229 " --> pdb=" O THR L 225 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU L 230 " --> pdb=" O ASN L 226 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE L 231 " --> pdb=" O LEU L 227 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN L 233 " --> pdb=" O ARG L 229 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE L 234 " --> pdb=" O LEU L 230 " (cutoff:3.500A) Processing helix chain 'L' and resid 252 through 258 removed outlier: 4.139A pdb=" N GLN L 256 " --> pdb=" O LEU L 252 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR L 257 " --> pdb=" O THR L 253 " (cutoff:3.500A) Processing helix chain 'L' and resid 279 through 281 No H-bonds generated for 'chain 'L' and resid 279 through 281' Processing helix chain 'L' and resid 288 through 295 removed outlier: 4.017A pdb=" N THR L 292 " --> pdb=" O VAL L 288 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN L 293 " --> pdb=" O ALA L 289 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA L 294 " --> pdb=" O GLU L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 307 through 309 No H-bonds generated for 'chain 'L' and resid 307 through 309' Processing helix chain 'L' and resid 325 through 336 removed outlier: 3.566A pdb=" N ALA L 331 " --> pdb=" O ASP L 327 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE L 335 " --> pdb=" O ALA L 331 " (cutoff:3.500A) Processing helix chain 'L' and resid 383 through 400 removed outlier: 3.837A pdb=" N GLU L 386 " --> pdb=" O ALA L 383 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TRP L 388 " --> pdb=" O ALA L 385 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP L 392 " --> pdb=" O ALA L 389 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N HIS L 393 " --> pdb=" O ARG L 390 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP L 396 " --> pdb=" O HIS L 393 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU L 397 " --> pdb=" O LYS L 394 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET L 398 " --> pdb=" O PHE L 395 " (cutoff:3.500A) Processing helix chain 'L' and resid 405 through 411 Processing helix chain 'L' and resid 415 through 436 removed outlier: 3.550A pdb=" N SER L 419 " --> pdb=" O GLU L 415 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU L 423 " --> pdb=" O SER L 419 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP L 424 " --> pdb=" O GLU L 420 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET L 425 " --> pdb=" O ALA L 421 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA L 426 " --> pdb=" O ARG L 422 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP L 431 " --> pdb=" O ALA L 427 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N TYR L 432 " --> pdb=" O LEU L 428 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU L 433 " --> pdb=" O GLU L 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 27 removed outlier: 3.502A pdb=" N GLN A 15 " --> pdb=" O GLN A 11 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU A 22 " --> pdb=" O ASN A 18 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 79 Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 115 through 126 removed outlier: 3.504A pdb=" N ILE A 122 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 160 removed outlier: 4.502A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU A 152 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU A 155 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 189 removed outlier: 3.714A pdb=" N SER A 187 " --> pdb=" O PRO A 184 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILE A 188 " --> pdb=" O TYR A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 194 No H-bonds generated for 'chain 'A' and resid 191 through 194' Processing helix chain 'A' and resid 207 through 214 removed outlier: 4.293A pdb=" N ASP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 212 " --> pdb=" O ALA A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 240 removed outlier: 3.746A pdb=" N ARG A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU A 230 " --> pdb=" O ASN A 226 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN A 233 " --> pdb=" O ARG A 229 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 258 removed outlier: 4.139A pdb=" N GLN A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 281 No H-bonds generated for 'chain 'A' and resid 279 through 281' Processing helix chain 'A' and resid 288 through 295 removed outlier: 4.017A pdb=" N THR A 292 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASN A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA A 294 " --> pdb=" O GLU A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 325 through 336 removed outlier: 3.566A pdb=" N ALA A 331 " --> pdb=" O ASP A 327 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE A 335 " --> pdb=" O ALA A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 400 removed outlier: 3.837A pdb=" N GLU A 386 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N TRP A 388 " --> pdb=" O ALA A 385 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP A 392 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N HIS A 393 " --> pdb=" O ARG A 390 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP A 396 " --> pdb=" O HIS A 393 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU A 397 " --> pdb=" O LYS A 394 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N MET A 398 " --> pdb=" O PHE A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 Processing helix chain 'A' and resid 415 through 436 removed outlier: 3.550A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP A 424 " --> pdb=" O GLU A 420 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET A 425 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA A 426 " --> pdb=" O ARG A 422 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TYR A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 27 removed outlier: 3.502A pdb=" N GLN K 15 " --> pdb=" O GLN K 11 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA K 19 " --> pdb=" O GLN K 15 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU K 22 " --> pdb=" O ASN K 18 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU K 26 " --> pdb=" O GLU K 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 79 Processing helix chain 'K' and resid 103 through 107 Processing helix chain 'K' and resid 115 through 126 removed outlier: 3.504A pdb=" N ILE K 122 " --> pdb=" O VAL K 118 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG K 123 " --> pdb=" O LEU K 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 144 through 160 removed outlier: 4.502A pdb=" N THR K 150 " --> pdb=" O GLY K 146 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU K 152 " --> pdb=" O GLY K 148 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU K 155 " --> pdb=" O SER K 151 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG K 156 " --> pdb=" O LEU K 152 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU K 157 " --> pdb=" O LEU K 153 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER K 158 " --> pdb=" O MET K 154 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL K 159 " --> pdb=" O GLU K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 182 through 189 removed outlier: 3.714A pdb=" N SER K 187 " --> pdb=" O PRO K 184 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILE K 188 " --> pdb=" O TYR K 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 191 through 194 No H-bonds generated for 'chain 'K' and resid 191 through 194' Processing helix chain 'K' and resid 207 through 214 removed outlier: 4.292A pdb=" N ASP K 211 " --> pdb=" O GLU K 207 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE K 212 " --> pdb=" O ALA K 208 " (cutoff:3.500A) Processing helix chain 'K' and resid 224 through 240 removed outlier: 3.746A pdb=" N ARG K 229 " --> pdb=" O THR K 225 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU K 230 " --> pdb=" O ASN K 226 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE K 231 " --> pdb=" O LEU K 227 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN K 233 " --> pdb=" O ARG K 229 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE K 234 " --> pdb=" O LEU K 230 " (cutoff:3.500A) Processing helix chain 'K' and resid 252 through 258 removed outlier: 4.140A pdb=" N GLN K 256 " --> pdb=" O LEU K 252 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR K 257 " --> pdb=" O THR K 253 " (cutoff:3.500A) Processing helix chain 'K' and resid 279 through 281 No H-bonds generated for 'chain 'K' and resid 279 through 281' Processing helix chain 'K' and resid 288 through 295 removed outlier: 4.017A pdb=" N THR K 292 " --> pdb=" O VAL K 288 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN K 293 " --> pdb=" O ALA K 289 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA K 294 " --> pdb=" O GLU K 290 " (cutoff:3.500A) Processing helix chain 'K' and resid 307 through 309 No H-bonds generated for 'chain 'K' and resid 307 through 309' Processing helix chain 'K' and resid 325 through 336 removed outlier: 3.566A pdb=" N ALA K 331 " --> pdb=" O ASP K 327 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE K 335 " --> pdb=" O ALA K 331 " (cutoff:3.500A) Processing helix chain 'K' and resid 383 through 400 removed outlier: 3.837A pdb=" N GLU K 386 " --> pdb=" O ALA K 383 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TRP K 388 " --> pdb=" O ALA K 385 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP K 392 " --> pdb=" O ALA K 389 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N HIS K 393 " --> pdb=" O ARG K 390 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP K 396 " --> pdb=" O HIS K 393 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU K 397 " --> pdb=" O LYS K 394 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N MET K 398 " --> pdb=" O PHE K 395 " (cutoff:3.500A) Processing helix chain 'K' and resid 405 through 411 Processing helix chain 'K' and resid 415 through 436 removed outlier: 3.549A pdb=" N SER K 419 " --> pdb=" O GLU K 415 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU K 423 " --> pdb=" O SER K 419 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP K 424 " --> pdb=" O GLU K 420 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET K 425 " --> pdb=" O ALA K 421 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA K 426 " --> pdb=" O ARG K 422 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP K 431 " --> pdb=" O ALA K 427 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N TYR K 432 " --> pdb=" O LEU K 428 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU K 433 " --> pdb=" O GLU K 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 26 removed outlier: 4.486A pdb=" N GLU B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 49 removed outlier: 4.079A pdb=" N ARG B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ASN B 48 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N VAL B 49 " --> pdb=" O GLU B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 78 Processing helix chain 'B' and resid 101 through 105 Processing helix chain 'B' and resid 109 through 126 removed outlier: 3.749A pdb=" N VAL B 113 " --> pdb=" O GLY B 109 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP B 118 " --> pdb=" O ASP B 114 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL B 119 " --> pdb=" O SER B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 158 removed outlier: 4.380A pdb=" N GLY B 148 " --> pdb=" O GLY B 144 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE B 152 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER B 153 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS B 154 " --> pdb=" O LEU B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 195 removed outlier: 4.321A pdb=" N LEU B 187 " --> pdb=" O TYR B 183 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER B 188 " --> pdb=" O ASN B 184 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN B 195 " --> pdb=" O GLN B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 213 Processing helix chain 'B' and resid 222 through 225 No H-bonds generated for 'chain 'B' and resid 222 through 225' Processing helix chain 'B' and resid 227 through 236 Processing helix chain 'B' and resid 250 through 257 Processing helix chain 'B' and resid 286 through 291 Processing helix chain 'B' and resid 296 through 298 No H-bonds generated for 'chain 'B' and resid 296 through 298' Processing helix chain 'B' and resid 305 through 307 No H-bonds generated for 'chain 'B' and resid 305 through 307' Processing helix chain 'B' and resid 324 through 327 No H-bonds generated for 'chain 'B' and resid 324 through 327' Processing helix chain 'B' and resid 329 through 336 removed outlier: 3.822A pdb=" N VAL B 333 " --> pdb=" O GLN B 329 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N GLN B 334 " --> pdb=" O MET B 330 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 387 removed outlier: 3.702A pdb=" N LYS B 379 " --> pdb=" O GLU B 376 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER B 382 " --> pdb=" O LYS B 379 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA B 387 " --> pdb=" O GLN B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 401 Processing helix chain 'B' and resid 405 through 427 removed outlier: 3.504A pdb=" N ALA B 411 " --> pdb=" O GLU B 407 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN B 424 " --> pdb=" O SER B 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 26 removed outlier: 4.485A pdb=" N GLU F 22 " --> pdb=" O ALA F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 49 removed outlier: 4.079A pdb=" N ARG F 46 " --> pdb=" O LEU F 42 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ASN F 48 " --> pdb=" O LEU F 44 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N VAL F 49 " --> pdb=" O GLU F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 78 Processing helix chain 'F' and resid 101 through 105 Processing helix chain 'F' and resid 109 through 126 removed outlier: 3.749A pdb=" N VAL F 113 " --> pdb=" O GLY F 109 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASP F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER F 115 " --> pdb=" O GLU F 111 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP F 118 " --> pdb=" O ASP F 114 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL F 119 " --> pdb=" O SER F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 158 removed outlier: 4.382A pdb=" N GLY F 148 " --> pdb=" O GLY F 144 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR F 149 " --> pdb=" O SER F 145 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE F 152 " --> pdb=" O GLY F 148 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER F 153 " --> pdb=" O THR F 149 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS F 154 " --> pdb=" O LEU F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 195 removed outlier: 4.321A pdb=" N LEU F 187 " --> pdb=" O TYR F 183 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER F 188 " --> pdb=" O ASN F 184 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS F 190 " --> pdb=" O THR F 186 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLN F 191 " --> pdb=" O LEU F 187 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU F 194 " --> pdb=" O HIS F 190 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN F 195 " --> pdb=" O GLN F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 213 Processing helix chain 'F' and resid 222 through 225 No H-bonds generated for 'chain 'F' and resid 222 through 225' Processing helix chain 'F' and resid 227 through 236 Processing helix chain 'F' and resid 250 through 257 Processing helix chain 'F' and resid 286 through 291 Processing helix chain 'F' and resid 296 through 298 No H-bonds generated for 'chain 'F' and resid 296 through 298' Processing helix chain 'F' and resid 305 through 307 No H-bonds generated for 'chain 'F' and resid 305 through 307' Processing helix chain 'F' and resid 324 through 327 No H-bonds generated for 'chain 'F' and resid 324 through 327' Processing helix chain 'F' and resid 329 through 336 removed outlier: 3.822A pdb=" N VAL F 333 " --> pdb=" O GLN F 329 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N GLN F 334 " --> pdb=" O MET F 330 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASN F 335 " --> pdb=" O LEU F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 387 removed outlier: 3.703A pdb=" N LYS F 379 " --> pdb=" O GLU F 376 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER F 382 " --> pdb=" O LYS F 379 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA F 387 " --> pdb=" O GLN F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 401 Processing helix chain 'F' and resid 405 through 427 removed outlier: 3.504A pdb=" N ALA F 411 " --> pdb=" O GLU F 407 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN F 424 " --> pdb=" O SER F 420 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 26 removed outlier: 4.486A pdb=" N GLU G 22 " --> pdb=" O ALA G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 49 removed outlier: 4.078A pdb=" N ARG G 46 " --> pdb=" O LEU G 42 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ASN G 48 " --> pdb=" O LEU G 44 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL G 49 " --> pdb=" O GLU G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 78 Processing helix chain 'G' and resid 101 through 105 Processing helix chain 'G' and resid 109 through 126 removed outlier: 3.749A pdb=" N VAL G 113 " --> pdb=" O GLY G 109 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ASP G 114 " --> pdb=" O ALA G 110 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER G 115 " --> pdb=" O GLU G 111 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP G 118 " --> pdb=" O ASP G 114 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL G 119 " --> pdb=" O SER G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 158 removed outlier: 4.381A pdb=" N GLY G 148 " --> pdb=" O GLY G 144 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR G 149 " --> pdb=" O SER G 145 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE G 152 " --> pdb=" O GLY G 148 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER G 153 " --> pdb=" O THR G 149 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS G 154 " --> pdb=" O LEU G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 195 removed outlier: 4.321A pdb=" N LEU G 187 " --> pdb=" O TYR G 183 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER G 188 " --> pdb=" O ASN G 184 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS G 190 " --> pdb=" O THR G 186 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLN G 191 " --> pdb=" O LEU G 187 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU G 194 " --> pdb=" O HIS G 190 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN G 195 " --> pdb=" O GLN G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 213 Processing helix chain 'G' and resid 222 through 225 No H-bonds generated for 'chain 'G' and resid 222 through 225' Processing helix chain 'G' and resid 227 through 236 Processing helix chain 'G' and resid 250 through 257 Processing helix chain 'G' and resid 286 through 291 Processing helix chain 'G' and resid 296 through 298 No H-bonds generated for 'chain 'G' and resid 296 through 298' Processing helix chain 'G' and resid 305 through 307 No H-bonds generated for 'chain 'G' and resid 305 through 307' Processing helix chain 'G' and resid 324 through 327 No H-bonds generated for 'chain 'G' and resid 324 through 327' Processing helix chain 'G' and resid 329 through 336 removed outlier: 3.822A pdb=" N VAL G 333 " --> pdb=" O GLN G 329 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N GLN G 334 " --> pdb=" O MET G 330 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASN G 335 " --> pdb=" O LEU G 331 " (cutoff:3.500A) Processing helix chain 'G' and resid 374 through 387 removed outlier: 3.703A pdb=" N LYS G 379 " --> pdb=" O GLU G 376 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER G 382 " --> pdb=" O LYS G 379 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA G 387 " --> pdb=" O GLN G 384 " (cutoff:3.500A) Processing helix chain 'G' and resid 395 through 401 Processing helix chain 'G' and resid 405 through 427 removed outlier: 3.504A pdb=" N ALA G 411 " --> pdb=" O GLU G 407 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN G 424 " --> pdb=" O SER G 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 26 removed outlier: 4.485A pdb=" N GLU D 22 " --> pdb=" O ALA D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 49 removed outlier: 4.079A pdb=" N ARG D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ASN D 48 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL D 49 " --> pdb=" O GLU D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 78 Processing helix chain 'D' and resid 101 through 105 Processing helix chain 'D' and resid 109 through 126 removed outlier: 3.749A pdb=" N VAL D 113 " --> pdb=" O GLY D 109 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ASP D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N SER D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP D 118 " --> pdb=" O ASP D 114 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL D 119 " --> pdb=" O SER D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 158 removed outlier: 4.381A pdb=" N GLY D 148 " --> pdb=" O GLY D 144 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE D 152 " --> pdb=" O GLY D 148 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER D 153 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS D 154 " --> pdb=" O LEU D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 195 removed outlier: 4.320A pdb=" N LEU D 187 " --> pdb=" O TYR D 183 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER D 188 " --> pdb=" O ASN D 184 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLN D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU D 194 " --> pdb=" O HIS D 190 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN D 195 " --> pdb=" O GLN D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 213 Processing helix chain 'D' and resid 222 through 225 No H-bonds generated for 'chain 'D' and resid 222 through 225' Processing helix chain 'D' and resid 227 through 236 Processing helix chain 'D' and resid 250 through 257 Processing helix chain 'D' and resid 286 through 291 Processing helix chain 'D' and resid 296 through 298 No H-bonds generated for 'chain 'D' and resid 296 through 298' Processing helix chain 'D' and resid 305 through 307 No H-bonds generated for 'chain 'D' and resid 305 through 307' Processing helix chain 'D' and resid 324 through 327 No H-bonds generated for 'chain 'D' and resid 324 through 327' Processing helix chain 'D' and resid 329 through 336 removed outlier: 3.823A pdb=" N VAL D 333 " --> pdb=" O GLN D 329 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N GLN D 334 " --> pdb=" O MET D 330 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASN D 335 " --> pdb=" O LEU D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 387 removed outlier: 3.703A pdb=" N LYS D 379 " --> pdb=" O GLU D 376 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER D 382 " --> pdb=" O LYS D 379 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA D 387 " --> pdb=" O GLN D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 401 Processing helix chain 'D' and resid 405 through 427 removed outlier: 3.504A pdb=" N ALA D 411 " --> pdb=" O GLU D 407 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN D 424 " --> pdb=" O SER D 420 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 26 removed outlier: 4.486A pdb=" N GLU I 22 " --> pdb=" O ALA I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 49 removed outlier: 4.079A pdb=" N ARG I 46 " --> pdb=" O LEU I 42 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ASN I 48 " --> pdb=" O LEU I 44 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL I 49 " --> pdb=" O GLU I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 78 Processing helix chain 'I' and resid 101 through 105 Processing helix chain 'I' and resid 109 through 126 removed outlier: 3.750A pdb=" N VAL I 113 " --> pdb=" O GLY I 109 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASP I 114 " --> pdb=" O ALA I 110 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N SER I 115 " --> pdb=" O GLU I 111 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP I 118 " --> pdb=" O ASP I 114 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL I 119 " --> pdb=" O SER I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 143 through 158 removed outlier: 4.381A pdb=" N GLY I 148 " --> pdb=" O GLY I 144 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR I 149 " --> pdb=" O SER I 145 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE I 152 " --> pdb=" O GLY I 148 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER I 153 " --> pdb=" O THR I 149 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS I 154 " --> pdb=" O LEU I 150 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 195 removed outlier: 4.321A pdb=" N LEU I 187 " --> pdb=" O TYR I 183 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER I 188 " --> pdb=" O ASN I 184 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS I 190 " --> pdb=" O THR I 186 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLN I 191 " --> pdb=" O LEU I 187 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU I 194 " --> pdb=" O HIS I 190 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN I 195 " --> pdb=" O GLN I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 204 through 213 Processing helix chain 'I' and resid 222 through 225 No H-bonds generated for 'chain 'I' and resid 222 through 225' Processing helix chain 'I' and resid 227 through 236 Processing helix chain 'I' and resid 250 through 257 Processing helix chain 'I' and resid 286 through 291 Processing helix chain 'I' and resid 296 through 298 No H-bonds generated for 'chain 'I' and resid 296 through 298' Processing helix chain 'I' and resid 305 through 307 No H-bonds generated for 'chain 'I' and resid 305 through 307' Processing helix chain 'I' and resid 324 through 327 No H-bonds generated for 'chain 'I' and resid 324 through 327' Processing helix chain 'I' and resid 329 through 336 removed outlier: 3.822A pdb=" N VAL I 333 " --> pdb=" O GLN I 329 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N GLN I 334 " --> pdb=" O MET I 330 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASN I 335 " --> pdb=" O LEU I 331 " (cutoff:3.500A) Processing helix chain 'I' and resid 374 through 387 removed outlier: 3.703A pdb=" N LYS I 379 " --> pdb=" O GLU I 376 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER I 382 " --> pdb=" O LYS I 379 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA I 387 " --> pdb=" O GLN I 384 " (cutoff:3.500A) Processing helix chain 'I' and resid 395 through 401 Processing helix chain 'I' and resid 405 through 427 removed outlier: 3.504A pdb=" N ALA I 411 " --> pdb=" O GLU I 407 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN I 424 " --> pdb=" O SER I 420 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 26 removed outlier: 4.486A pdb=" N GLU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 49 removed outlier: 4.079A pdb=" N ARG H 46 " --> pdb=" O LEU H 42 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ASN H 48 " --> pdb=" O LEU H 44 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL H 49 " --> pdb=" O GLU H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 78 Processing helix chain 'H' and resid 101 through 105 Processing helix chain 'H' and resid 109 through 126 removed outlier: 3.749A pdb=" N VAL H 113 " --> pdb=" O GLY H 109 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASP H 114 " --> pdb=" O ALA H 110 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N SER H 115 " --> pdb=" O GLU H 111 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP H 118 " --> pdb=" O ASP H 114 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL H 119 " --> pdb=" O SER H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 143 through 158 removed outlier: 4.381A pdb=" N GLY H 148 " --> pdb=" O GLY H 144 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR H 149 " --> pdb=" O SER H 145 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE H 152 " --> pdb=" O GLY H 148 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER H 153 " --> pdb=" O THR H 149 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS H 154 " --> pdb=" O LEU H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 195 removed outlier: 4.320A pdb=" N LEU H 187 " --> pdb=" O TYR H 183 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER H 188 " --> pdb=" O ASN H 184 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N HIS H 190 " --> pdb=" O THR H 186 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLN H 191 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU H 194 " --> pdb=" O HIS H 190 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN H 195 " --> pdb=" O GLN H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 213 Processing helix chain 'H' and resid 222 through 225 No H-bonds generated for 'chain 'H' and resid 222 through 225' Processing helix chain 'H' and resid 227 through 236 Processing helix chain 'H' and resid 250 through 257 Processing helix chain 'H' and resid 286 through 291 Processing helix chain 'H' and resid 296 through 298 No H-bonds generated for 'chain 'H' and resid 296 through 298' Processing helix chain 'H' and resid 305 through 307 No H-bonds generated for 'chain 'H' and resid 305 through 307' Processing helix chain 'H' and resid 324 through 327 No H-bonds generated for 'chain 'H' and resid 324 through 327' Processing helix chain 'H' and resid 329 through 336 removed outlier: 3.822A pdb=" N VAL H 333 " --> pdb=" O GLN H 329 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N GLN H 334 " --> pdb=" O MET H 330 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASN H 335 " --> pdb=" O LEU H 331 " (cutoff:3.500A) Processing helix chain 'H' and resid 374 through 387 removed outlier: 3.703A pdb=" N LYS H 379 " --> pdb=" O GLU H 376 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER H 382 " --> pdb=" O LYS H 379 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA H 387 " --> pdb=" O GLN H 384 " (cutoff:3.500A) Processing helix chain 'H' and resid 395 through 401 Processing helix chain 'H' and resid 405 through 427 removed outlier: 3.504A pdb=" N ALA H 411 " --> pdb=" O GLU H 407 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN H 424 " --> pdb=" O SER H 420 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'E' and resid 135 through 139 removed outlier: 7.116A pdb=" N ILE E 5 " --> pdb=" O LEU E 136 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N PHE E 138 " --> pdb=" O ILE E 5 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ILE E 7 " --> pdb=" O PHE E 138 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'E' and resid 53 through 55 Processing sheet with id= C, first strand: chain 'E' and resid 167 through 169 removed outlier: 7.229A pdb=" N CYS E 200 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET E 203 " --> pdb=" O PRO E 268 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'E' and resid 270 through 273 removed outlier: 6.034A pdb=" N LYS E 352 " --> pdb=" O LEU E 317 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N TYR E 319 " --> pdb=" O LYS E 352 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLY E 354 " --> pdb=" O TYR E 319 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'J' and resid 135 through 139 removed outlier: 7.116A pdb=" N ILE J 5 " --> pdb=" O LEU J 136 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N PHE J 138 " --> pdb=" O ILE J 5 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ILE J 7 " --> pdb=" O PHE J 138 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'J' and resid 53 through 55 Processing sheet with id= G, first strand: chain 'J' and resid 167 through 169 removed outlier: 7.230A pdb=" N CYS J 200 " --> pdb=" O GLU J 168 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET J 203 " --> pdb=" O PRO J 268 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'J' and resid 270 through 273 removed outlier: 6.035A pdb=" N LYS J 352 " --> pdb=" O LEU J 317 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N TYR J 319 " --> pdb=" O LYS J 352 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLY J 354 " --> pdb=" O TYR J 319 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 135 through 139 removed outlier: 7.115A pdb=" N ILE C 5 " --> pdb=" O LEU C 136 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N PHE C 138 " --> pdb=" O ILE C 5 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ILE C 7 " --> pdb=" O PHE C 138 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 53 through 55 Processing sheet with id= K, first strand: chain 'C' and resid 167 through 169 removed outlier: 7.229A pdb=" N CYS C 200 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET C 203 " --> pdb=" O PRO C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'C' and resid 270 through 273 removed outlier: 6.034A pdb=" N LYS C 352 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N TYR C 319 " --> pdb=" O LYS C 352 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLY C 354 " --> pdb=" O TYR C 319 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'L' and resid 135 through 139 removed outlier: 7.116A pdb=" N ILE L 5 " --> pdb=" O LEU L 136 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N PHE L 138 " --> pdb=" O ILE L 5 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ILE L 7 " --> pdb=" O PHE L 138 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'L' and resid 53 through 55 Processing sheet with id= O, first strand: chain 'L' and resid 167 through 169 removed outlier: 7.229A pdb=" N CYS L 200 " --> pdb=" O GLU L 168 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET L 203 " --> pdb=" O PRO L 268 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'L' and resid 270 through 273 removed outlier: 6.034A pdb=" N LYS L 352 " --> pdb=" O LEU L 317 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N TYR L 319 " --> pdb=" O LYS L 352 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLY L 354 " --> pdb=" O TYR L 319 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'A' and resid 135 through 139 removed outlier: 7.115A pdb=" N ILE A 5 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N PHE A 138 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ILE A 7 " --> pdb=" O PHE A 138 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= S, first strand: chain 'A' and resid 167 through 169 removed outlier: 7.230A pdb=" N CYS A 200 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET A 203 " --> pdb=" O PRO A 268 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'A' and resid 270 through 273 removed outlier: 6.035A pdb=" N LYS A 352 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N TYR A 319 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLY A 354 " --> pdb=" O TYR A 319 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'K' and resid 135 through 139 removed outlier: 7.115A pdb=" N ILE K 5 " --> pdb=" O LEU K 136 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N PHE K 138 " --> pdb=" O ILE K 5 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ILE K 7 " --> pdb=" O PHE K 138 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'K' and resid 53 through 55 Processing sheet with id= W, first strand: chain 'K' and resid 167 through 169 removed outlier: 7.230A pdb=" N CYS K 200 " --> pdb=" O GLU K 168 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET K 203 " --> pdb=" O PRO K 268 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'K' and resid 270 through 273 removed outlier: 6.034A pdb=" N LYS K 352 " --> pdb=" O LEU K 317 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N TYR K 319 " --> pdb=" O LYS K 352 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N GLY K 354 " --> pdb=" O TYR K 319 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 65 through 67 removed outlier: 3.880A pdb=" N ASP B 67 " --> pdb=" O VAL B 91 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 198 through 202 removed outlier: 3.773A pdb=" N THR B 166 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE B 202 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE B 163 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N GLU B 3 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE B 133 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL B 5 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ILE B 7 " --> pdb=" O LEU B 135 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'B' and resid 267 through 271 removed outlier: 3.897A pdb=" N THR B 312 " --> pdb=" O ASN B 370 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 65 through 67 removed outlier: 3.879A pdb=" N ASP F 67 " --> pdb=" O VAL F 91 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 198 through 202 removed outlier: 3.774A pdb=" N THR F 166 " --> pdb=" O GLU F 198 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE F 202 " --> pdb=" O SER F 168 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE F 163 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N GLU F 3 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N PHE F 133 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL F 5 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU F 135 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ILE F 7 " --> pdb=" O LEU F 135 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 267 through 271 removed outlier: 3.896A pdb=" N THR F 312 " --> pdb=" O ASN F 370 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'G' and resid 65 through 67 removed outlier: 3.880A pdb=" N ASP G 67 " --> pdb=" O VAL G 91 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'G' and resid 198 through 202 removed outlier: 3.774A pdb=" N THR G 166 " --> pdb=" O GLU G 198 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE G 202 " --> pdb=" O SER G 168 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE G 163 " --> pdb=" O GLN G 131 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N GLU G 3 " --> pdb=" O GLN G 131 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE G 133 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL G 5 " --> pdb=" O PHE G 133 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LEU G 135 " --> pdb=" O VAL G 5 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ILE G 7 " --> pdb=" O LEU G 135 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'G' and resid 267 through 271 removed outlier: 3.897A pdb=" N THR G 312 " --> pdb=" O ASN G 370 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'D' and resid 65 through 67 removed outlier: 3.879A pdb=" N ASP D 67 " --> pdb=" O VAL D 91 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'D' and resid 198 through 202 removed outlier: 3.774A pdb=" N THR D 166 " --> pdb=" O GLU D 198 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE D 202 " --> pdb=" O SER D 168 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE D 163 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N GLU D 3 " --> pdb=" O GLN D 131 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N PHE D 133 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL D 5 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N LEU D 135 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ILE D 7 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'D' and resid 267 through 271 removed outlier: 3.897A pdb=" N THR D 312 " --> pdb=" O ASN D 370 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'I' and resid 65 through 67 removed outlier: 3.879A pdb=" N ASP I 67 " --> pdb=" O VAL I 91 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'I' and resid 198 through 202 removed outlier: 3.774A pdb=" N THR I 166 " --> pdb=" O GLU I 198 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE I 202 " --> pdb=" O SER I 168 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE I 163 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N GLU I 3 " --> pdb=" O GLN I 131 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N PHE I 133 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL I 5 " --> pdb=" O PHE I 133 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU I 135 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ILE I 7 " --> pdb=" O LEU I 135 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'I' and resid 267 through 271 removed outlier: 3.897A pdb=" N THR I 312 " --> pdb=" O ASN I 370 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'H' and resid 65 through 67 removed outlier: 3.880A pdb=" N ASP H 67 " --> pdb=" O VAL H 91 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'H' and resid 198 through 202 removed outlier: 3.774A pdb=" N THR H 166 " --> pdb=" O GLU H 198 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE H 202 " --> pdb=" O SER H 168 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE H 163 " --> pdb=" O GLN H 131 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N GLU H 3 " --> pdb=" O GLN H 131 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE H 133 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL H 5 " --> pdb=" O PHE H 133 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU H 135 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ILE H 7 " --> pdb=" O LEU H 135 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'H' and resid 267 through 271 removed outlier: 3.896A pdb=" N THR H 312 " --> pdb=" O ASN H 370 " (cutoff:3.500A) 1182 hydrogen bonds defined for protein. 3132 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: 13.89 Time building geometry restraints manager: 16.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13215 1.34 - 1.46: 7322 1.46 - 1.57: 20437 1.57 - 1.69: 36 1.69 - 1.81: 444 Bond restraints: 41454 Sorted by residual: bond pdb=" O3B G2P D 501 " pdb=" PG G2P D 501 " ideal model delta sigma weight residual 1.716 1.590 0.126 2.00e-02 2.50e+03 3.97e+01 bond pdb=" O3B G2P B 501 " pdb=" PG G2P B 501 " ideal model delta sigma weight residual 1.716 1.591 0.125 2.00e-02 2.50e+03 3.93e+01 bond pdb=" O3B G2P F 501 " pdb=" PG G2P F 501 " ideal model delta sigma weight residual 1.716 1.591 0.125 2.00e-02 2.50e+03 3.93e+01 bond pdb=" O3B G2P H 501 " pdb=" PG G2P H 501 " ideal model delta sigma weight residual 1.716 1.591 0.125 2.00e-02 2.50e+03 3.92e+01 bond pdb=" O3B G2P G 501 " pdb=" PG G2P G 501 " ideal model delta sigma weight residual 1.716 1.591 0.125 2.00e-02 2.50e+03 3.90e+01 ... (remaining 41449 not shown) Histogram of bond angle deviations from ideal: 99.35 - 106.29: 1351 106.29 - 113.22: 22060 113.22 - 120.16: 15294 120.16 - 127.09: 17137 127.09 - 134.03: 486 Bond angle restraints: 56328 Sorted by residual: angle pdb=" PA GTP L 501 " pdb=" O3A GTP L 501 " pdb=" PB GTP L 501 " ideal model delta sigma weight residual 120.50 132.39 -11.89 3.00e+00 1.11e-01 1.57e+01 angle pdb=" PA GTP C 501 " pdb=" O3A GTP C 501 " pdb=" PB GTP C 501 " ideal model delta sigma weight residual 120.50 132.05 -11.55 3.00e+00 1.11e-01 1.48e+01 angle pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " pdb=" PB GTP A 501 " ideal model delta sigma weight residual 120.50 131.99 -11.49 3.00e+00 1.11e-01 1.47e+01 angle pdb=" PA GTP K 501 " pdb=" O3A GTP K 501 " pdb=" PB GTP K 501 " ideal model delta sigma weight residual 120.50 131.95 -11.45 3.00e+00 1.11e-01 1.46e+01 angle pdb=" PA GTP E 501 " pdb=" O3A GTP E 501 " pdb=" PB GTP E 501 " ideal model delta sigma weight residual 120.50 131.66 -11.16 3.00e+00 1.11e-01 1.38e+01 ... (remaining 56323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.54: 24529 34.54 - 69.08: 178 69.08 - 103.62: 31 103.62 - 138.16: 0 138.16 - 172.70: 18 Dihedral angle restraints: 24756 sinusoidal: 9972 harmonic: 14784 Sorted by residual: dihedral pdb=" C8 GTP L 501 " pdb=" C1' GTP L 501 " pdb=" N9 GTP L 501 " pdb=" O4' GTP L 501 " ideal model delta sinusoidal sigma weight residual 104.59 -68.10 172.70 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C8 GTP J 501 " pdb=" C1' GTP J 501 " pdb=" N9 GTP J 501 " pdb=" O4' GTP J 501 " ideal model delta sinusoidal sigma weight residual 104.59 -67.62 172.22 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C8 GTP K 501 " pdb=" C1' GTP K 501 " pdb=" N9 GTP K 501 " pdb=" O4' GTP K 501 " ideal model delta sinusoidal sigma weight residual 104.59 -66.88 171.47 1 2.00e+01 2.50e-03 4.77e+01 ... (remaining 24753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 4131 0.045 - 0.091: 1544 0.091 - 0.136: 433 0.136 - 0.182: 24 0.182 - 0.227: 30 Chirality restraints: 6162 Sorted by residual: chirality pdb=" C2' GTP C 501 " pdb=" C1' GTP C 501 " pdb=" C3' GTP C 501 " pdb=" O2' GTP C 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.70 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" C2' GTP A 501 " pdb=" C1' GTP A 501 " pdb=" C3' GTP A 501 " pdb=" O2' GTP A 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.69 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" C2' GTP J 501 " pdb=" C1' GTP J 501 " pdb=" C3' GTP J 501 " pdb=" O2' GTP J 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.69 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 6159 not shown) Planarity restraints: 7326 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G2P G 501 " 0.119 2.00e-02 2.50e+03 4.92e-02 7.27e+01 pdb=" C2 G2P G 501 " -0.012 2.00e-02 2.50e+03 pdb=" C4 G2P G 501 " -0.040 2.00e-02 2.50e+03 pdb=" C5 G2P G 501 " -0.035 2.00e-02 2.50e+03 pdb=" C6 G2P G 501 " 0.013 2.00e-02 2.50e+03 pdb=" C8 G2P G 501 " -0.035 2.00e-02 2.50e+03 pdb=" N1 G2P G 501 " 0.018 2.00e-02 2.50e+03 pdb=" N2 G2P G 501 " -0.011 2.00e-02 2.50e+03 pdb=" N3 G2P G 501 " -0.039 2.00e-02 2.50e+03 pdb=" N7 G2P G 501 " -0.043 2.00e-02 2.50e+03 pdb=" N9 G2P G 501 " -0.017 2.00e-02 2.50e+03 pdb=" O6 G2P G 501 " 0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G2P I 501 " -0.119 2.00e-02 2.50e+03 4.91e-02 7.22e+01 pdb=" C2 G2P I 501 " 0.012 2.00e-02 2.50e+03 pdb=" C4 G2P I 501 " 0.043 2.00e-02 2.50e+03 pdb=" C5 G2P I 501 " 0.036 2.00e-02 2.50e+03 pdb=" C6 G2P I 501 " -0.013 2.00e-02 2.50e+03 pdb=" C8 G2P I 501 " 0.032 2.00e-02 2.50e+03 pdb=" N1 G2P I 501 " -0.020 2.00e-02 2.50e+03 pdb=" N2 G2P I 501 " 0.007 2.00e-02 2.50e+03 pdb=" N3 G2P I 501 " 0.043 2.00e-02 2.50e+03 pdb=" N7 G2P I 501 " 0.041 2.00e-02 2.50e+03 pdb=" N9 G2P I 501 " 0.016 2.00e-02 2.50e+03 pdb=" O6 G2P I 501 " -0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G2P D 501 " -0.118 2.00e-02 2.50e+03 4.87e-02 7.13e+01 pdb=" C2 G2P D 501 " 0.013 2.00e-02 2.50e+03 pdb=" C4 G2P D 501 " 0.042 2.00e-02 2.50e+03 pdb=" C5 G2P D 501 " 0.035 2.00e-02 2.50e+03 pdb=" C6 G2P D 501 " -0.014 2.00e-02 2.50e+03 pdb=" C8 G2P D 501 " 0.033 2.00e-02 2.50e+03 pdb=" N1 G2P D 501 " -0.019 2.00e-02 2.50e+03 pdb=" N2 G2P D 501 " 0.007 2.00e-02 2.50e+03 pdb=" N3 G2P D 501 " 0.042 2.00e-02 2.50e+03 pdb=" N7 G2P D 501 " 0.040 2.00e-02 2.50e+03 pdb=" N9 G2P D 501 " 0.017 2.00e-02 2.50e+03 pdb=" O6 G2P D 501 " -0.078 2.00e-02 2.50e+03 ... (remaining 7323 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 720 2.65 - 3.21: 36721 3.21 - 3.78: 62822 3.78 - 4.34: 88685 4.34 - 4.90: 139979 Nonbonded interactions: 328927 Sorted by model distance: nonbonded pdb=" O2B GTP C 501 " pdb="MG MG C 502 " model vdw 2.091 2.170 nonbonded pdb=" O2B GTP A 501 " pdb="MG MG A 502 " model vdw 2.092 2.170 nonbonded pdb=" O2B GTP J 501 " pdb="MG MG J 502 " model vdw 2.095 2.170 nonbonded pdb=" OE1 GLN G 11 " pdb="MG MG G 502 " model vdw 2.099 2.170 nonbonded pdb=" O1B G2P G 501 " pdb="MG MG G 502 " model vdw 2.101 2.170 ... (remaining 328922 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: 0.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 2.870 Check model and map are aligned: 0.570 Set scattering table: 0.340 Process input model: 102.200 Find NCS groups from input model: 2.900 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.126 41454 Z= 0.334 Angle : 0.838 11.892 56328 Z= 0.431 Chirality : 0.051 0.227 6162 Planarity : 0.006 0.056 7326 Dihedral : 11.536 172.697 15264 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % 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: -4.53 (0.09), residues: 5064 helix: -3.66 (0.06), residues: 2052 sheet: -1.81 (0.18), residues: 762 loop : -2.64 (0.11), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP G 101 HIS 0.010 0.002 HIS A 8 PHE 0.018 0.002 PHE J 202 TYR 0.022 0.002 TYR K 24 ARG 0.006 0.001 ARG I 318 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1439 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1439 time to evaluate : 4.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.7252 (ptm) cc_final: 0.6367 (tmm) REVERT: E 120 ASP cc_start: 0.8512 (t70) cc_final: 0.8285 (t70) REVERT: E 172 TYR cc_start: 0.7727 (t80) cc_final: 0.6357 (t80) REVERT: E 192 HIS cc_start: 0.7682 (t-90) cc_final: 0.7331 (t-90) REVERT: E 205 ASP cc_start: 0.7674 (t0) cc_final: 0.6236 (m-30) REVERT: E 301 GLN cc_start: 0.8369 (mt0) cc_final: 0.8162 (mt0) REVERT: E 302 MET cc_start: 0.8303 (mtt) cc_final: 0.7993 (mtt) REVERT: E 313 MET cc_start: 0.8051 (mtm) cc_final: 0.6895 (mtp) REVERT: E 351 PHE cc_start: 0.8166 (m-80) cc_final: 0.7388 (m-80) REVERT: E 391 LEU cc_start: 0.9167 (tp) cc_final: 0.8788 (tp) REVERT: E 398 MET cc_start: 0.7519 (mtp) cc_final: 0.7194 (mtm) REVERT: E 425 MET cc_start: 0.8679 (tpp) cc_final: 0.7975 (mmm) REVERT: J 124 LYS cc_start: 0.8316 (mttm) cc_final: 0.8022 (tptp) REVERT: J 149 PHE cc_start: 0.8577 (t80) cc_final: 0.8270 (t80) REVERT: J 172 TYR cc_start: 0.7670 (t80) cc_final: 0.6202 (t80) REVERT: J 183 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8053 (pp20) REVERT: J 205 ASP cc_start: 0.7452 (t0) cc_final: 0.6383 (m-30) REVERT: J 221 ARG cc_start: 0.8700 (mtt90) cc_final: 0.8447 (mpp-170) REVERT: J 267 PHE cc_start: 0.9043 (m-80) cc_final: 0.8745 (m-80) REVERT: J 313 MET cc_start: 0.7410 (mtm) cc_final: 0.6239 (mtp) REVERT: J 316 CYS cc_start: 0.8439 (t) cc_final: 0.7765 (t) REVERT: J 391 LEU cc_start: 0.9117 (tp) cc_final: 0.8612 (tp) REVERT: J 398 MET cc_start: 0.7304 (mtp) cc_final: 0.6968 (mtm) REVERT: J 425 MET cc_start: 0.8545 (tpp) cc_final: 0.7896 (mmm) REVERT: C 24 TYR cc_start: 0.8374 (m-80) cc_final: 0.8151 (m-80) REVERT: C 36 MET cc_start: 0.7276 (ptm) cc_final: 0.6614 (tmm) REVERT: C 136 LEU cc_start: 0.8533 (mt) cc_final: 0.8332 (mp) REVERT: C 149 PHE cc_start: 0.7882 (t80) cc_final: 0.7568 (t80) REVERT: C 182 VAL cc_start: 0.8535 (m) cc_final: 0.7968 (p) REVERT: C 192 HIS cc_start: 0.8135 (t-90) cc_final: 0.7843 (t-90) REVERT: C 205 ASP cc_start: 0.8280 (t0) cc_final: 0.6866 (m-30) REVERT: C 301 GLN cc_start: 0.8446 (mt0) cc_final: 0.8042 (pt0) REVERT: C 313 MET cc_start: 0.7803 (mtm) cc_final: 0.6548 (mtp) REVERT: C 377 MET cc_start: 0.7876 (ttp) cc_final: 0.7413 (tmm) REVERT: C 425 MET cc_start: 0.8389 (tpp) cc_final: 0.7624 (mmm) REVERT: L 36 MET cc_start: 0.7183 (ptm) cc_final: 0.6238 (tmm) REVERT: L 136 LEU cc_start: 0.8800 (mt) cc_final: 0.8521 (mp) REVERT: L 149 PHE cc_start: 0.8298 (t80) cc_final: 0.8040 (t80) REVERT: L 205 ASP cc_start: 0.8002 (t0) cc_final: 0.6459 (m-30) REVERT: L 301 GLN cc_start: 0.8678 (mt0) cc_final: 0.8007 (pt0) REVERT: L 313 MET cc_start: 0.7719 (mtm) cc_final: 0.6386 (mtp) REVERT: L 377 MET cc_start: 0.7485 (ttp) cc_final: 0.7248 (tmm) REVERT: L 395 PHE cc_start: 0.8848 (t80) cc_final: 0.8165 (t80) REVERT: L 425 MET cc_start: 0.8511 (tpp) cc_final: 0.7604 (mmm) REVERT: A 24 TYR cc_start: 0.8486 (m-80) cc_final: 0.8277 (m-80) REVERT: A 36 MET cc_start: 0.7028 (ptm) cc_final: 0.6398 (tmm) REVERT: A 54 SER cc_start: 0.7385 (p) cc_final: 0.6867 (t) REVERT: A 149 PHE cc_start: 0.8296 (t80) cc_final: 0.8055 (t80) REVERT: A 172 TYR cc_start: 0.7521 (t80) cc_final: 0.6304 (t80) REVERT: A 182 VAL cc_start: 0.8502 (m) cc_final: 0.7815 (p) REVERT: A 196 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8060 (tm-30) REVERT: A 205 ASP cc_start: 0.8003 (t0) cc_final: 0.6276 (m-30) REVERT: A 260 VAL cc_start: 0.8860 (t) cc_final: 0.8621 (t) REVERT: A 267 PHE cc_start: 0.8917 (m-80) cc_final: 0.8550 (m-80) REVERT: A 377 MET cc_start: 0.7915 (ttp) cc_final: 0.7219 (tmm) REVERT: A 380 ASN cc_start: 0.8414 (t0) cc_final: 0.8042 (t0) REVERT: A 391 LEU cc_start: 0.9095 (tp) cc_final: 0.8804 (tp) REVERT: A 398 MET cc_start: 0.7276 (mtp) cc_final: 0.6711 (mtm) REVERT: K 36 MET cc_start: 0.7261 (ptm) cc_final: 0.6639 (tmm) REVERT: K 136 LEU cc_start: 0.8480 (mt) cc_final: 0.8103 (mp) REVERT: K 149 PHE cc_start: 0.8319 (t80) cc_final: 0.7912 (t80) REVERT: K 172 TYR cc_start: 0.7755 (t80) cc_final: 0.6497 (t80) REVERT: K 205 ASP cc_start: 0.8220 (t0) cc_final: 0.6359 (m-30) REVERT: K 212 ILE cc_start: 0.9261 (mt) cc_final: 0.8940 (mt) REVERT: K 316 CYS cc_start: 0.8287 (t) cc_final: 0.7313 (t) REVERT: K 319 TYR cc_start: 0.8183 (m-80) cc_final: 0.7961 (m-10) REVERT: K 377 MET cc_start: 0.7564 (ttp) cc_final: 0.7311 (tmm) REVERT: B 14 ASN cc_start: 0.8491 (m-40) cc_final: 0.8260 (t0) REVERT: B 51 TYR cc_start: 0.8071 (m-80) cc_final: 0.7634 (m-10) REVERT: B 163 ILE cc_start: 0.8678 (pp) cc_final: 0.8214 (mt) REVERT: B 181 GLU cc_start: 0.8938 (pt0) cc_final: 0.8520 (pp20) REVERT: B 200 TYR cc_start: 0.7995 (m-80) cc_final: 0.7519 (m-80) REVERT: B 293 MET cc_start: 0.7126 (mtm) cc_final: 0.6759 (mmm) REVERT: B 297 LYS cc_start: 0.8754 (ptpt) cc_final: 0.8497 (mtmm) REVERT: B 317 PHE cc_start: 0.8738 (m-80) cc_final: 0.8497 (m-80) REVERT: B 355 ASP cc_start: 0.8482 (m-30) cc_final: 0.8109 (m-30) REVERT: B 379 LYS cc_start: 0.8918 (mtpt) cc_final: 0.8079 (mtmm) REVERT: B 383 GLU cc_start: 0.8980 (tt0) cc_final: 0.8732 (mm-30) REVERT: F 6 HIS cc_start: 0.8754 (t70) cc_final: 0.8084 (t-170) REVERT: F 51 TYR cc_start: 0.7823 (m-80) cc_final: 0.7398 (m-10) REVERT: F 117 LEU cc_start: 0.8072 (mt) cc_final: 0.7864 (mm) REVERT: F 163 ILE cc_start: 0.8709 (pp) cc_final: 0.7900 (tp) REVERT: F 197 ASP cc_start: 0.7853 (m-30) cc_final: 0.7651 (m-30) REVERT: F 210 ILE cc_start: 0.9025 (mt) cc_final: 0.8762 (tt) REVERT: F 216 LYS cc_start: 0.8215 (mmtp) cc_final: 0.7784 (mmtm) REVERT: F 233 MET cc_start: 0.9393 (mtp) cc_final: 0.8960 (mtm) REVERT: F 330 MET cc_start: 0.8434 (mmp) cc_final: 0.8090 (mmm) REVERT: F 379 LYS cc_start: 0.9088 (mtpt) cc_final: 0.8621 (pttp) REVERT: G 73 MET cc_start: 0.8235 (mmt) cc_final: 0.8014 (mmt) REVERT: G 163 ILE cc_start: 0.8653 (pp) cc_final: 0.7946 (mt) REVERT: G 178 THR cc_start: 0.8475 (m) cc_final: 0.8249 (m) REVERT: G 233 MET cc_start: 0.9306 (mtp) cc_final: 0.8832 (mtm) REVERT: G 288 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7598 (tm-30) REVERT: G 332 ASN cc_start: 0.8023 (t0) cc_final: 0.7705 (p0) REVERT: D 6 HIS cc_start: 0.8701 (t70) cc_final: 0.8132 (t70) REVERT: D 14 ASN cc_start: 0.8421 (m-40) cc_final: 0.8161 (t0) REVERT: D 21 TRP cc_start: 0.8776 (m100) cc_final: 0.8282 (m100) REVERT: D 51 TYR cc_start: 0.8049 (m-80) cc_final: 0.7147 (m-10) REVERT: D 60 VAL cc_start: 0.8936 (m) cc_final: 0.8736 (m) REVERT: D 163 ILE cc_start: 0.8814 (pp) cc_final: 0.8229 (mt) REVERT: D 181 GLU cc_start: 0.8928 (pt0) cc_final: 0.8642 (pp20) REVERT: D 200 TYR cc_start: 0.8095 (m-80) cc_final: 0.7151 (m-80) REVERT: D 293 MET cc_start: 0.7408 (mtm) cc_final: 0.6882 (mmm) REVERT: D 317 PHE cc_start: 0.8794 (m-80) cc_final: 0.8540 (m-80) REVERT: D 355 ASP cc_start: 0.8403 (m-30) cc_final: 0.8096 (m-30) REVERT: D 379 LYS cc_start: 0.9100 (mtpt) cc_final: 0.8836 (mtmm) REVERT: I 14 ASN cc_start: 0.8403 (m-40) cc_final: 0.8069 (t0) REVERT: I 163 ILE cc_start: 0.8943 (pp) cc_final: 0.8342 (mt) REVERT: I 200 TYR cc_start: 0.7981 (m-80) cc_final: 0.7536 (m-80) REVERT: I 242 PHE cc_start: 0.7765 (m-80) cc_final: 0.7553 (m-10) REVERT: I 250 LEU cc_start: 0.8634 (mt) cc_final: 0.8403 (mp) REVERT: I 297 LYS cc_start: 0.8073 (ptpt) cc_final: 0.7784 (mmtt) REVERT: I 306 ARG cc_start: 0.7348 (mtt90) cc_final: 0.7080 (mpt-90) REVERT: I 353 VAL cc_start: 0.8735 (t) cc_final: 0.8529 (p) REVERT: I 379 LYS cc_start: 0.9109 (mtpt) cc_final: 0.8896 (mttp) REVERT: H 6 HIS cc_start: 0.8621 (t70) cc_final: 0.7975 (t70) REVERT: H 163 ILE cc_start: 0.8682 (pp) cc_final: 0.8222 (mt) REVERT: H 216 LYS cc_start: 0.8658 (mmtp) cc_final: 0.8366 (mtmm) REVERT: H 242 PHE cc_start: 0.8071 (m-80) cc_final: 0.7685 (m-10) REVERT: H 281 TYR cc_start: 0.7661 (m-80) cc_final: 0.7449 (m-80) REVERT: H 293 MET cc_start: 0.7373 (mtm) cc_final: 0.6914 (mmm) REVERT: H 332 ASN cc_start: 0.7871 (t0) cc_final: 0.7575 (p0) REVERT: H 379 LYS cc_start: 0.8913 (mtpt) cc_final: 0.8522 (mttt) outliers start: 0 outliers final: 0 residues processed: 1439 average time/residue: 0.5647 time to fit residues: 1310.7725 Evaluate side-chains 715 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 715 time to evaluate : 4.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 425 optimal weight: 20.0000 chunk 382 optimal weight: 20.0000 chunk 211 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 257 optimal weight: 30.0000 chunk 204 optimal weight: 4.9990 chunk 395 optimal weight: 10.0000 chunk 152 optimal weight: 8.9990 chunk 240 optimal weight: 9.9990 chunk 294 optimal weight: 30.0000 chunk 457 optimal weight: 0.3980 overall best weight: 5.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 88 HIS E 258 ASN E 300 ASN ** E 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 88 HIS J 283 HIS J 300 ASN ** J 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 372 GLN C 88 HIS C 258 ASN ** C 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 HIS ** L 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 HIS A 258 ASN ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 HIS ** K 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN B 256 ASN B 291 GLN ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 HIS B 423 GLN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 57 ASN F 131 GLN F 256 ASN F 292 GLN F 396 HIS F 423 GLN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 GLN G 256 ASN G 292 GLN ** G 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 GLN D 256 ASN ** D 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 HIS ** I 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 131 GLN I 256 ASN ** I 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 GLN H 256 ASN H 291 GLN ** H 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 423 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 41454 Z= 0.246 Angle : 0.602 8.558 56328 Z= 0.319 Chirality : 0.044 0.164 6162 Planarity : 0.005 0.044 7326 Dihedral : 12.590 176.927 5826 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.09 % Allowed : 2.78 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.84 (0.10), residues: 5064 helix: -1.98 (0.09), residues: 2058 sheet: -1.04 (0.19), residues: 714 loop : -1.95 (0.12), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 397 HIS 0.013 0.001 HIS I 28 PHE 0.033 0.002 PHE D 212 TYR 0.048 0.002 TYR J 108 ARG 0.004 0.000 ARG H 262 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 976 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 972 time to evaluate : 4.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 16 ILE cc_start: 0.9202 (mt) cc_final: 0.8873 (mm) REVERT: E 36 MET cc_start: 0.7185 (ptm) cc_final: 0.6263 (tmm) REVERT: E 54 SER cc_start: 0.7617 (p) cc_final: 0.7293 (t) REVERT: E 119 LEU cc_start: 0.9327 (mt) cc_final: 0.9073 (mt) REVERT: E 123 ARG cc_start: 0.8511 (mtm-85) cc_final: 0.8031 (mtp85) REVERT: E 135 PHE cc_start: 0.8859 (m-80) cc_final: 0.8576 (m-10) REVERT: E 136 LEU cc_start: 0.8683 (mp) cc_final: 0.8427 (mp) REVERT: E 253 THR cc_start: 0.8274 (p) cc_final: 0.7525 (t) REVERT: E 267 PHE cc_start: 0.9019 (m-80) cc_final: 0.8755 (m-80) REVERT: E 301 GLN cc_start: 0.8601 (mt0) cc_final: 0.8348 (mt0) REVERT: E 313 MET cc_start: 0.8230 (mtm) cc_final: 0.7070 (mtp) REVERT: E 351 PHE cc_start: 0.8020 (m-80) cc_final: 0.7438 (m-80) REVERT: J 14 VAL cc_start: 0.9170 (t) cc_final: 0.8890 (p) REVERT: J 16 ILE cc_start: 0.9101 (mt) cc_final: 0.8827 (mt) REVERT: J 124 LYS cc_start: 0.8684 (mttm) cc_final: 0.8213 (tptp) REVERT: J 195 LEU cc_start: 0.8015 (mm) cc_final: 0.7745 (mm) REVERT: J 221 ARG cc_start: 0.8704 (mtt90) cc_final: 0.8438 (mpp-170) REVERT: J 267 PHE cc_start: 0.8990 (m-80) cc_final: 0.8780 (m-80) REVERT: J 313 MET cc_start: 0.7793 (mtm) cc_final: 0.6435 (mtp) REVERT: C 36 MET cc_start: 0.7070 (ptm) cc_final: 0.6193 (tmm) REVERT: C 78 VAL cc_start: 0.9171 (t) cc_final: 0.8736 (p) REVERT: C 149 PHE cc_start: 0.7908 (t80) cc_final: 0.7335 (t80) REVERT: C 165 SER cc_start: 0.6660 (t) cc_final: 0.6346 (t) REVERT: C 182 VAL cc_start: 0.8633 (m) cc_final: 0.8123 (p) REVERT: C 192 HIS cc_start: 0.8035 (t-90) cc_final: 0.7658 (p90) REVERT: C 301 GLN cc_start: 0.8842 (mt0) cc_final: 0.8065 (pt0) REVERT: C 313 MET cc_start: 0.7894 (mtm) cc_final: 0.6622 (mtp) REVERT: C 377 MET cc_start: 0.7809 (ttp) cc_final: 0.7257 (tmm) REVERT: L 36 MET cc_start: 0.7172 (ptm) cc_final: 0.6361 (tmm) REVERT: L 149 PHE cc_start: 0.8422 (t80) cc_final: 0.7942 (t80) REVERT: L 195 LEU cc_start: 0.8050 (mm) cc_final: 0.7845 (mm) REVERT: L 256 GLN cc_start: 0.8314 (pt0) cc_final: 0.7603 (tt0) REVERT: L 301 GLN cc_start: 0.8838 (mt0) cc_final: 0.8102 (pt0) REVERT: L 313 MET cc_start: 0.7642 (mtm) cc_final: 0.6333 (mtp) REVERT: L 377 MET cc_start: 0.7271 (ttp) cc_final: 0.7044 (tmm) REVERT: L 395 PHE cc_start: 0.8801 (t80) cc_final: 0.8053 (t80) REVERT: A 36 MET cc_start: 0.6920 (ptm) cc_final: 0.5953 (tmm) REVERT: A 52 PHE cc_start: 0.8494 (m-80) cc_final: 0.8148 (m-10) REVERT: A 119 LEU cc_start: 0.9325 (mt) cc_final: 0.9122 (mm) REVERT: A 149 PHE cc_start: 0.8161 (t80) cc_final: 0.7721 (t80) REVERT: A 192 HIS cc_start: 0.7631 (t-90) cc_final: 0.7291 (p90) REVERT: A 212 ILE cc_start: 0.8959 (mt) cc_final: 0.8662 (mt) REVERT: A 267 PHE cc_start: 0.9101 (m-80) cc_final: 0.8690 (m-80) REVERT: A 316 CYS cc_start: 0.8569 (t) cc_final: 0.8263 (t) REVERT: A 377 MET cc_start: 0.7602 (ttp) cc_final: 0.7085 (tmm) REVERT: K 33 ASP cc_start: 0.7336 (m-30) cc_final: 0.6985 (p0) REVERT: K 36 MET cc_start: 0.7293 (ptm) cc_final: 0.6166 (tmm) REVERT: K 54 SER cc_start: 0.7387 (p) cc_final: 0.6942 (t) REVERT: K 267 PHE cc_start: 0.8984 (m-80) cc_final: 0.8589 (m-80) REVERT: K 301 GLN cc_start: 0.8277 (mt0) cc_final: 0.7519 (pt0) REVERT: K 313 MET cc_start: 0.7381 (mtm) cc_final: 0.6196 (mtp) REVERT: K 377 MET cc_start: 0.7750 (ttp) cc_final: 0.7117 (tmm) REVERT: K 413 MET cc_start: 0.7140 (tpp) cc_final: 0.6555 (tpp) REVERT: K 425 MET cc_start: 0.8627 (mmm) cc_final: 0.8381 (tpp) REVERT: B 6 HIS cc_start: 0.8679 (t70) cc_final: 0.8441 (t70) REVERT: B 51 TYR cc_start: 0.7944 (m-80) cc_final: 0.7319 (m-10) REVERT: B 73 MET cc_start: 0.8420 (mmt) cc_final: 0.8142 (mmt) REVERT: B 163 ILE cc_start: 0.8935 (pt) cc_final: 0.8229 (mt) REVERT: B 164 MET cc_start: 0.7991 (mpp) cc_final: 0.7756 (mpp) REVERT: B 181 GLU cc_start: 0.9115 (pt0) cc_final: 0.8612 (pp20) REVERT: B 257 MET cc_start: 0.8318 (mtm) cc_final: 0.8062 (mtp) REVERT: B 297 LYS cc_start: 0.8944 (ptpt) cc_final: 0.8634 (mtmm) REVERT: B 379 LYS cc_start: 0.8861 (mtpt) cc_final: 0.8109 (mtmm) REVERT: F 51 TYR cc_start: 0.7835 (m-80) cc_final: 0.7129 (m-10) REVERT: F 85 PHE cc_start: 0.8275 (m-80) cc_final: 0.7697 (m-80) REVERT: F 163 ILE cc_start: 0.8623 (pt) cc_final: 0.8009 (mt) REVERT: F 197 ASP cc_start: 0.8052 (m-30) cc_final: 0.7803 (t70) REVERT: F 216 LYS cc_start: 0.8277 (mmtp) cc_final: 0.7858 (mmtm) REVERT: F 233 MET cc_start: 0.9275 (mtp) cc_final: 0.8932 (mtm) REVERT: F 242 PHE cc_start: 0.8058 (m-80) cc_final: 0.7455 (m-10) REVERT: F 250 LEU cc_start: 0.8674 (mt) cc_final: 0.8223 (mp) REVERT: F 267 MET cc_start: 0.7408 (mtm) cc_final: 0.7007 (mtm) REVERT: F 300 MET cc_start: 0.8585 (mtt) cc_final: 0.8216 (mtt) REVERT: G 6 HIS cc_start: 0.8702 (t70) cc_final: 0.8480 (t-170) REVERT: G 83 GLN cc_start: 0.8382 (mp10) cc_final: 0.7950 (mm110) REVERT: G 163 ILE cc_start: 0.8638 (pt) cc_final: 0.8428 (tp) REVERT: G 233 MET cc_start: 0.9169 (mtp) cc_final: 0.8763 (mtm) REVERT: D 51 TYR cc_start: 0.8019 (m-80) cc_final: 0.7113 (m-10) REVERT: D 73 MET cc_start: 0.8375 (mmt) cc_final: 0.8103 (mmt) REVERT: D 163 ILE cc_start: 0.9062 (pt) cc_final: 0.8409 (mt) REVERT: D 164 MET cc_start: 0.7796 (mpp) cc_final: 0.7469 (mpp) REVERT: D 181 GLU cc_start: 0.9031 (pt0) cc_final: 0.8793 (pp20) REVERT: D 200 TYR cc_start: 0.8017 (m-80) cc_final: 0.7687 (m-80) REVERT: D 250 LEU cc_start: 0.8634 (mt) cc_final: 0.8249 (mp) REVERT: D 288 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7943 (tm-30) REVERT: D 317 PHE cc_start: 0.8896 (m-80) cc_final: 0.8538 (m-80) REVERT: D 355 ASP cc_start: 0.8358 (m-30) cc_final: 0.7918 (m-30) REVERT: D 379 LYS cc_start: 0.9146 (mtpt) cc_final: 0.8923 (mtmm) REVERT: I 118 ASP cc_start: 0.8324 (m-30) cc_final: 0.7505 (t0) REVERT: I 163 ILE cc_start: 0.8873 (pt) cc_final: 0.8462 (tp) REVERT: I 164 MET cc_start: 0.7659 (mpp) cc_final: 0.7278 (mpp) REVERT: I 200 TYR cc_start: 0.7896 (m-80) cc_final: 0.7295 (m-80) REVERT: I 228 LEU cc_start: 0.9280 (mm) cc_final: 0.9037 (tt) REVERT: I 242 PHE cc_start: 0.7978 (m-80) cc_final: 0.7531 (m-10) REVERT: I 297 LYS cc_start: 0.8406 (ptpt) cc_final: 0.7981 (mmtm) REVERT: I 306 ARG cc_start: 0.7556 (mtt90) cc_final: 0.7174 (mpt-90) REVERT: I 323 MET cc_start: 0.7731 (mpp) cc_final: 0.7464 (mpp) REVERT: I 328 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8512 (mm-30) REVERT: I 363 MET cc_start: 0.8038 (ptp) cc_final: 0.7705 (ptm) REVERT: I 425 TYR cc_start: 0.8450 (m-80) cc_final: 0.8203 (m-80) REVERT: H 118 ASP cc_start: 0.8514 (m-30) cc_final: 0.8216 (m-30) REVERT: H 147 MET cc_start: 0.8093 (tmm) cc_final: 0.7868 (tmm) REVERT: H 163 ILE cc_start: 0.8927 (pt) cc_final: 0.8483 (mt) REVERT: H 250 LEU cc_start: 0.8283 (mm) cc_final: 0.7739 (mp) REVERT: H 266 PHE cc_start: 0.8387 (m-10) cc_final: 0.8166 (m-10) REVERT: H 363 MET cc_start: 0.8100 (mtp) cc_final: 0.7836 (mtp) REVERT: H 395 LEU cc_start: 0.7259 (tp) cc_final: 0.7056 (tp) REVERT: H 403 MET cc_start: 0.6881 (mtt) cc_final: 0.6351 (mtm) outliers start: 4 outliers final: 1 residues processed: 972 average time/residue: 0.5209 time to fit residues: 827.2419 Evaluate side-chains 654 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 653 time to evaluate : 4.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 254 optimal weight: 20.0000 chunk 142 optimal weight: 20.0000 chunk 380 optimal weight: 20.0000 chunk 311 optimal weight: 30.0000 chunk 126 optimal weight: 40.0000 chunk 458 optimal weight: 0.0670 chunk 495 optimal weight: 20.0000 chunk 408 optimal weight: 7.9990 chunk 454 optimal weight: 30.0000 chunk 156 optimal weight: 5.9990 chunk 367 optimal weight: 20.0000 overall best weight: 10.8130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 226 ASN ** E 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 GLN J 256 GLN ** J 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN C 300 ASN ** C 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 300 ASN ** L 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN K 283 HIS ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 291 GLN ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 ASN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 416 ASN G 256 ASN ** G 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 416 ASN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN ** I 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 GLN I 292 GLN I 307 HIS ** I 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 416 ASN ** H 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 41454 Z= 0.358 Angle : 0.674 9.046 56328 Z= 0.357 Chirality : 0.046 0.176 6162 Planarity : 0.005 0.043 7326 Dihedral : 12.526 178.009 5826 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 0.02 % Allowed : 3.08 % Favored : 96.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.47 (0.11), residues: 5064 helix: -1.45 (0.10), residues: 2148 sheet: -1.05 (0.19), residues: 762 loop : -1.92 (0.13), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP D 397 HIS 0.014 0.002 HIS F 28 PHE 0.037 0.002 PHE H 81 TYR 0.030 0.003 TYR E 172 ARG 0.006 0.001 ARG D 380 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 859 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 858 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.7401 (ptm) cc_final: 0.6104 (tmm) REVERT: E 54 SER cc_start: 0.7902 (p) cc_final: 0.7521 (t) REVERT: E 123 ARG cc_start: 0.8710 (mtm-85) cc_final: 0.8247 (mtp85) REVERT: E 135 PHE cc_start: 0.8907 (m-80) cc_final: 0.8459 (m-10) REVERT: E 149 PHE cc_start: 0.8271 (t80) cc_final: 0.8026 (t80) REVERT: E 267 PHE cc_start: 0.9048 (m-80) cc_final: 0.8740 (m-80) REVERT: E 313 MET cc_start: 0.8324 (mtm) cc_final: 0.7124 (mtp) REVERT: E 351 PHE cc_start: 0.7938 (m-80) cc_final: 0.7318 (m-80) REVERT: J 14 VAL cc_start: 0.9233 (t) cc_final: 0.9030 (p) REVERT: J 16 ILE cc_start: 0.9370 (mt) cc_final: 0.8914 (mm) REVERT: J 124 LYS cc_start: 0.8691 (mttm) cc_final: 0.8265 (tptp) REVERT: J 203 MET cc_start: 0.8713 (tpt) cc_final: 0.8492 (tpp) REVERT: J 260 VAL cc_start: 0.8835 (t) cc_final: 0.8498 (p) REVERT: J 267 PHE cc_start: 0.9040 (m-80) cc_final: 0.8721 (m-80) REVERT: J 301 GLN cc_start: 0.8191 (mt0) cc_final: 0.7415 (pt0) REVERT: J 313 MET cc_start: 0.7866 (mtm) cc_final: 0.6521 (mtp) REVERT: J 425 MET cc_start: 0.8598 (tpt) cc_final: 0.7802 (tpt) REVERT: J 428 LEU cc_start: 0.8934 (tt) cc_final: 0.8638 (tt) REVERT: C 36 MET cc_start: 0.7275 (ptm) cc_final: 0.6315 (tmm) REVERT: C 149 PHE cc_start: 0.8132 (t80) cc_final: 0.7847 (t80) REVERT: C 192 HIS cc_start: 0.8161 (t-90) cc_final: 0.7756 (p90) REVERT: C 203 MET cc_start: 0.8765 (tpp) cc_final: 0.8534 (tpp) REVERT: C 301 GLN cc_start: 0.8906 (mt0) cc_final: 0.8147 (pt0) REVERT: C 313 MET cc_start: 0.7999 (mtm) cc_final: 0.6797 (mtp) REVERT: C 377 MET cc_start: 0.7737 (ttp) cc_final: 0.6837 (tmm) REVERT: L 36 MET cc_start: 0.7473 (ptm) cc_final: 0.6351 (tmm) REVERT: L 123 ARG cc_start: 0.8911 (mtm-85) cc_final: 0.8586 (mtp85) REVERT: L 149 PHE cc_start: 0.8517 (t80) cc_final: 0.8105 (t80) REVERT: L 301 GLN cc_start: 0.8824 (mt0) cc_final: 0.8346 (pt0) REVERT: L 313 MET cc_start: 0.7716 (mtm) cc_final: 0.6387 (mtp) REVERT: L 395 PHE cc_start: 0.9018 (t80) cc_final: 0.8598 (t80) REVERT: A 24 TYR cc_start: 0.8823 (m-80) cc_final: 0.8483 (m-80) REVERT: A 36 MET cc_start: 0.7036 (ptm) cc_final: 0.6017 (tmm) REVERT: A 192 HIS cc_start: 0.7976 (t-90) cc_final: 0.7555 (p90) REVERT: A 255 PHE cc_start: 0.7725 (m-80) cc_final: 0.7505 (m-80) REVERT: A 267 PHE cc_start: 0.9104 (m-80) cc_final: 0.8748 (m-80) REVERT: A 358 GLN cc_start: 0.7912 (pm20) cc_final: 0.7696 (pm20) REVERT: A 377 MET cc_start: 0.7847 (ttp) cc_final: 0.6652 (tmm) REVERT: A 413 MET cc_start: 0.7707 (tpp) cc_final: 0.7179 (mmm) REVERT: K 33 ASP cc_start: 0.7643 (m-30) cc_final: 0.7196 (p0) REVERT: K 36 MET cc_start: 0.7146 (ptm) cc_final: 0.6001 (tmm) REVERT: K 54 SER cc_start: 0.7411 (p) cc_final: 0.6912 (t) REVERT: K 149 PHE cc_start: 0.8390 (t80) cc_final: 0.8119 (t80) REVERT: K 267 PHE cc_start: 0.8988 (m-80) cc_final: 0.8613 (m-80) REVERT: K 313 MET cc_start: 0.7573 (mtm) cc_final: 0.6262 (mtp) REVERT: K 358 GLN cc_start: 0.7804 (pm20) cc_final: 0.7564 (pm20) REVERT: K 377 MET cc_start: 0.7750 (ttp) cc_final: 0.7006 (tmm) REVERT: K 390 ARG cc_start: 0.9128 (tmm160) cc_final: 0.8618 (tmm160) REVERT: K 391 LEU cc_start: 0.9449 (tp) cc_final: 0.9194 (tp) REVERT: B 51 TYR cc_start: 0.7881 (m-80) cc_final: 0.7171 (m-80) REVERT: B 73 MET cc_start: 0.8455 (mmt) cc_final: 0.8240 (mmt) REVERT: B 147 MET cc_start: 0.8561 (tmm) cc_final: 0.8314 (tmm) REVERT: B 163 ILE cc_start: 0.8870 (pt) cc_final: 0.8252 (mp) REVERT: B 164 MET cc_start: 0.7975 (mpp) cc_final: 0.7678 (mpp) REVERT: B 181 GLU cc_start: 0.9145 (pt0) cc_final: 0.8637 (pp20) REVERT: B 200 TYR cc_start: 0.8096 (m-80) cc_final: 0.7796 (m-80) REVERT: B 242 PHE cc_start: 0.8464 (m-10) cc_final: 0.8237 (m-10) REVERT: B 267 MET cc_start: 0.7685 (mtp) cc_final: 0.7423 (mtp) REVERT: B 297 LYS cc_start: 0.8949 (ptpt) cc_final: 0.8589 (mtmm) REVERT: B 379 LYS cc_start: 0.8930 (mtpt) cc_final: 0.8628 (mtmm) REVERT: F 51 TYR cc_start: 0.7823 (m-80) cc_final: 0.6841 (m-80) REVERT: F 85 PHE cc_start: 0.8326 (m-80) cc_final: 0.7810 (m-80) REVERT: F 163 ILE cc_start: 0.8704 (pt) cc_final: 0.8093 (mt) REVERT: F 197 ASP cc_start: 0.8099 (m-30) cc_final: 0.7882 (t70) REVERT: F 198 GLU cc_start: 0.8072 (pt0) cc_final: 0.7745 (pt0) REVERT: F 216 LYS cc_start: 0.8336 (mmtp) cc_final: 0.7921 (mmtm) REVERT: F 233 MET cc_start: 0.9388 (mtp) cc_final: 0.8950 (mtm) REVERT: F 253 LEU cc_start: 0.8955 (pp) cc_final: 0.8730 (pp) REVERT: F 267 MET cc_start: 0.7742 (mtm) cc_final: 0.7328 (mtm) REVERT: F 300 MET cc_start: 0.8619 (mtt) cc_final: 0.8360 (mtm) REVERT: G 6 HIS cc_start: 0.8805 (t70) cc_final: 0.8497 (t-170) REVERT: G 83 GLN cc_start: 0.8472 (mp10) cc_final: 0.7950 (mm110) REVERT: G 163 ILE cc_start: 0.8794 (pt) cc_final: 0.8508 (tp) REVERT: G 164 MET cc_start: 0.7933 (mpp) cc_final: 0.7463 (mpp) REVERT: G 197 ASP cc_start: 0.7840 (m-30) cc_final: 0.6829 (m-30) REVERT: G 216 LYS cc_start: 0.8155 (mmtt) cc_final: 0.7889 (mmtm) REVERT: G 233 MET cc_start: 0.9284 (mtp) cc_final: 0.8807 (mtm) REVERT: G 321 MET cc_start: 0.8447 (ptp) cc_final: 0.7040 (ptp) REVERT: D 57 ASN cc_start: 0.7798 (m110) cc_final: 0.7542 (m110) REVERT: D 73 MET cc_start: 0.8402 (mmt) cc_final: 0.8164 (mmt) REVERT: D 163 ILE cc_start: 0.9033 (pt) cc_final: 0.8529 (mp) REVERT: D 164 MET cc_start: 0.7876 (mpp) cc_final: 0.7451 (mpp) REVERT: D 181 GLU cc_start: 0.8982 (pt0) cc_final: 0.8632 (pp20) REVERT: D 200 TYR cc_start: 0.8147 (m-80) cc_final: 0.7933 (m-80) REVERT: D 288 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8056 (tm-30) REVERT: D 379 LYS cc_start: 0.9135 (mtpt) cc_final: 0.8922 (mtmm) REVERT: D 388 MET cc_start: 0.7373 (mtt) cc_final: 0.7027 (mtt) REVERT: I 22 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7480 (tm-30) REVERT: I 23 VAL cc_start: 0.8131 (t) cc_final: 0.7406 (t) REVERT: I 149 THR cc_start: 0.9536 (p) cc_final: 0.9269 (p) REVERT: I 163 ILE cc_start: 0.9002 (pt) cc_final: 0.8420 (mt) REVERT: I 164 MET cc_start: 0.7964 (mpp) cc_final: 0.7295 (mpp) REVERT: I 242 PHE cc_start: 0.8006 (m-80) cc_final: 0.7534 (m-10) REVERT: I 257 MET cc_start: 0.8477 (mtp) cc_final: 0.8229 (mtp) REVERT: I 297 LYS cc_start: 0.8509 (ptpt) cc_final: 0.7992 (mptt) REVERT: I 306 ARG cc_start: 0.7710 (mtt90) cc_final: 0.7161 (mpt-90) REVERT: I 425 TYR cc_start: 0.8356 (m-80) cc_final: 0.8125 (m-10) REVERT: H 147 MET cc_start: 0.8241 (tmm) cc_final: 0.8023 (tmm) REVERT: H 163 ILE cc_start: 0.8887 (pt) cc_final: 0.8673 (tt) REVERT: H 210 ILE cc_start: 0.9141 (tp) cc_final: 0.8880 (tt) REVERT: H 262 ARG cc_start: 0.7404 (mmp80) cc_final: 0.6564 (mmp80) REVERT: H 266 PHE cc_start: 0.8447 (m-10) cc_final: 0.8200 (m-10) outliers start: 1 outliers final: 1 residues processed: 858 average time/residue: 0.5319 time to fit residues: 746.1742 Evaluate side-chains 582 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 581 time to evaluate : 4.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 453 optimal weight: 9.9990 chunk 344 optimal weight: 0.9980 chunk 237 optimal weight: 8.9990 chunk 50 optimal weight: 0.0270 chunk 218 optimal weight: 20.0000 chunk 307 optimal weight: 9.9990 chunk 460 optimal weight: 6.9990 chunk 487 optimal weight: 10.0000 chunk 240 optimal weight: 8.9990 chunk 436 optimal weight: 10.0000 chunk 131 optimal weight: 7.9990 overall best weight: 5.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 283 HIS ** E 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 226 ASN ** J 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN B 134 GLN B 256 ASN B 291 GLN B 292 GLN ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 GLN ** I 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 256 ASN ** I 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 GLN H 256 ASN ** H 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 292 GLN H 298 ASN ** H 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 416 ASN H 423 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 41454 Z= 0.196 Angle : 0.547 8.389 56328 Z= 0.284 Chirality : 0.044 0.161 6162 Planarity : 0.004 0.041 7326 Dihedral : 12.196 179.884 5826 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % 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: -1.98 (0.11), residues: 5064 helix: -1.03 (0.10), residues: 2160 sheet: -0.63 (0.19), residues: 720 loop : -1.75 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 397 HIS 0.010 0.001 HIS F 28 PHE 0.018 0.001 PHE A 149 TYR 0.031 0.002 TYR L 24 ARG 0.004 0.000 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 875 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 875 time to evaluate : 4.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.7489 (ptm) cc_final: 0.6252 (tmm) REVERT: E 54 SER cc_start: 0.7818 (p) cc_final: 0.7411 (t) REVERT: E 123 ARG cc_start: 0.8633 (mtm-85) cc_final: 0.8322 (mtp85) REVERT: E 135 PHE cc_start: 0.8734 (m-80) cc_final: 0.8365 (m-10) REVERT: E 136 LEU cc_start: 0.8675 (mt) cc_final: 0.8429 (mt) REVERT: E 149 PHE cc_start: 0.8289 (t80) cc_final: 0.7996 (t80) REVERT: E 203 MET cc_start: 0.8995 (tpp) cc_final: 0.8712 (tpp) REVERT: E 250 VAL cc_start: 0.8247 (t) cc_final: 0.7926 (t) REVERT: E 267 PHE cc_start: 0.9003 (m-80) cc_final: 0.8713 (m-80) REVERT: E 293 ASN cc_start: 0.8935 (m110) cc_final: 0.8623 (m110) REVERT: E 301 GLN cc_start: 0.8585 (mt0) cc_final: 0.8218 (mt0) REVERT: E 313 MET cc_start: 0.8318 (mtm) cc_final: 0.7143 (mtp) REVERT: E 351 PHE cc_start: 0.7850 (m-80) cc_final: 0.7235 (m-80) REVERT: J 14 VAL cc_start: 0.9249 (t) cc_final: 0.8826 (p) REVERT: J 16 ILE cc_start: 0.9363 (mt) cc_final: 0.8857 (mm) REVERT: J 18 ASN cc_start: 0.8830 (m-40) cc_final: 0.8613 (m-40) REVERT: J 124 LYS cc_start: 0.8573 (mttm) cc_final: 0.8275 (tptp) REVERT: J 149 PHE cc_start: 0.8576 (t80) cc_final: 0.8319 (t80) REVERT: J 267 PHE cc_start: 0.9014 (m-80) cc_final: 0.8701 (m-80) REVERT: J 301 GLN cc_start: 0.8061 (mt0) cc_final: 0.7265 (pt0) REVERT: J 313 MET cc_start: 0.7826 (mtm) cc_final: 0.6545 (mtp) REVERT: C 36 MET cc_start: 0.7391 (ptm) cc_final: 0.6134 (tmm) REVERT: C 69 ASP cc_start: 0.7837 (t0) cc_final: 0.7467 (m-30) REVERT: C 149 PHE cc_start: 0.8127 (t80) cc_final: 0.7895 (t80) REVERT: C 165 SER cc_start: 0.6046 (t) cc_final: 0.5818 (t) REVERT: C 192 HIS cc_start: 0.8044 (t-90) cc_final: 0.7611 (p90) REVERT: C 301 GLN cc_start: 0.8814 (mt0) cc_final: 0.7961 (pm20) REVERT: C 313 MET cc_start: 0.7904 (mtm) cc_final: 0.6687 (ttt) REVERT: C 377 MET cc_start: 0.7701 (ttp) cc_final: 0.6788 (tmm) REVERT: L 36 MET cc_start: 0.7701 (ptm) cc_final: 0.6330 (tmm) REVERT: L 123 ARG cc_start: 0.8860 (mtm-85) cc_final: 0.8576 (mtp85) REVERT: L 301 GLN cc_start: 0.8837 (mt0) cc_final: 0.8107 (pm20) REVERT: L 313 MET cc_start: 0.7683 (mtm) cc_final: 0.6434 (mtp) REVERT: L 395 PHE cc_start: 0.8976 (t80) cc_final: 0.8557 (t80) REVERT: A 18 ASN cc_start: 0.8722 (m-40) cc_final: 0.8484 (m110) REVERT: A 24 TYR cc_start: 0.8817 (m-80) cc_final: 0.8537 (m-80) REVERT: A 36 MET cc_start: 0.7302 (ptm) cc_final: 0.5974 (tmm) REVERT: A 192 HIS cc_start: 0.7974 (t-90) cc_final: 0.7603 (p90) REVERT: A 205 ASP cc_start: 0.7133 (t70) cc_final: 0.6105 (m-30) REVERT: A 255 PHE cc_start: 0.7621 (m-80) cc_final: 0.7308 (m-80) REVERT: A 267 PHE cc_start: 0.9144 (m-80) cc_final: 0.8791 (m-80) REVERT: A 377 MET cc_start: 0.7950 (ttp) cc_final: 0.7019 (tmm) REVERT: A 413 MET cc_start: 0.7491 (tpp) cc_final: 0.7042 (mmm) REVERT: K 15 GLN cc_start: 0.8819 (mt0) cc_final: 0.8364 (mm-40) REVERT: K 33 ASP cc_start: 0.7542 (m-30) cc_final: 0.7286 (p0) REVERT: K 36 MET cc_start: 0.7057 (ptm) cc_final: 0.5971 (tmm) REVERT: K 54 SER cc_start: 0.7374 (p) cc_final: 0.6869 (t) REVERT: K 149 PHE cc_start: 0.8458 (t80) cc_final: 0.8168 (t80) REVERT: K 172 TYR cc_start: 0.7407 (t80) cc_final: 0.7158 (t80) REVERT: K 203 MET cc_start: 0.8792 (tpp) cc_final: 0.8522 (ttm) REVERT: K 237 SER cc_start: 0.9085 (m) cc_final: 0.8491 (t) REVERT: K 267 PHE cc_start: 0.8972 (m-80) cc_final: 0.8414 (m-80) REVERT: K 313 MET cc_start: 0.7558 (mtm) cc_final: 0.6343 (mtp) REVERT: K 377 MET cc_start: 0.7671 (ttp) cc_final: 0.7123 (tmm) REVERT: K 390 ARG cc_start: 0.8989 (tmm160) cc_final: 0.8718 (tmm160) REVERT: K 391 LEU cc_start: 0.9456 (tp) cc_final: 0.9016 (tp) REVERT: K 413 MET cc_start: 0.7838 (mmm) cc_final: 0.7515 (mmm) REVERT: B 6 HIS cc_start: 0.8859 (t70) cc_final: 0.8205 (t-170) REVERT: B 21 TRP cc_start: 0.8973 (m100) cc_final: 0.8027 (m100) REVERT: B 51 TYR cc_start: 0.8004 (m-80) cc_final: 0.7279 (m-80) REVERT: B 73 MET cc_start: 0.8372 (mmt) cc_final: 0.8167 (mmt) REVERT: B 164 MET cc_start: 0.8063 (mpp) cc_final: 0.7822 (mpp) REVERT: B 181 GLU cc_start: 0.9116 (pt0) cc_final: 0.8563 (pp20) REVERT: B 297 LYS cc_start: 0.8780 (ptpt) cc_final: 0.8400 (mtmm) REVERT: B 379 LYS cc_start: 0.8824 (mtpt) cc_final: 0.8559 (mtmm) REVERT: F 85 PHE cc_start: 0.8318 (m-80) cc_final: 0.7901 (m-80) REVERT: F 90 PHE cc_start: 0.8378 (m-80) cc_final: 0.8156 (m-80) REVERT: F 216 LYS cc_start: 0.8335 (mmtp) cc_final: 0.7951 (mmtm) REVERT: F 233 MET cc_start: 0.9337 (mtp) cc_final: 0.8916 (mtm) REVERT: F 253 LEU cc_start: 0.8977 (pp) cc_final: 0.8758 (pp) REVERT: F 267 MET cc_start: 0.7495 (mtm) cc_final: 0.7274 (mtm) REVERT: F 353 VAL cc_start: 0.8766 (t) cc_final: 0.8485 (p) REVERT: G 83 GLN cc_start: 0.8350 (mp10) cc_final: 0.7753 (pp30) REVERT: G 216 LYS cc_start: 0.8137 (mmtt) cc_final: 0.7839 (mmtm) REVERT: G 228 LEU cc_start: 0.9152 (mm) cc_final: 0.8793 (tp) REVERT: G 233 MET cc_start: 0.9119 (mtp) cc_final: 0.8907 (mtm) REVERT: G 321 MET cc_start: 0.8408 (ptp) cc_final: 0.7953 (ptp) REVERT: D 21 TRP cc_start: 0.8922 (m100) cc_final: 0.8457 (m100) REVERT: D 57 ASN cc_start: 0.7708 (m110) cc_final: 0.7486 (m110) REVERT: D 73 MET cc_start: 0.8370 (mmt) cc_final: 0.8121 (mmt) REVERT: D 163 ILE cc_start: 0.9080 (pt) cc_final: 0.8612 (mp) REVERT: D 164 MET cc_start: 0.7806 (mpp) cc_final: 0.7595 (mpp) REVERT: D 181 GLU cc_start: 0.8909 (pt0) cc_final: 0.8577 (pp20) REVERT: D 288 GLU cc_start: 0.8425 (tm-30) cc_final: 0.8002 (tm-30) REVERT: D 299 MET cc_start: 0.9329 (mmp) cc_final: 0.8774 (mmm) REVERT: D 312 THR cc_start: 0.7924 (t) cc_final: 0.7364 (p) REVERT: D 379 LYS cc_start: 0.9102 (mtpt) cc_final: 0.8819 (mtmm) REVERT: D 388 MET cc_start: 0.7395 (mtt) cc_final: 0.6998 (mtt) REVERT: I 22 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7439 (tm-30) REVERT: I 23 VAL cc_start: 0.8013 (t) cc_final: 0.7338 (t) REVERT: I 164 MET cc_start: 0.7972 (mpp) cc_final: 0.7532 (mpp) REVERT: I 242 PHE cc_start: 0.7912 (m-80) cc_final: 0.7386 (m-10) REVERT: I 297 LYS cc_start: 0.8460 (ptpt) cc_final: 0.7948 (mptt) REVERT: I 299 MET cc_start: 0.9150 (mmp) cc_final: 0.8662 (mmm) REVERT: I 306 ARG cc_start: 0.7952 (mtt90) cc_final: 0.7249 (mpt-90) REVERT: I 362 LYS cc_start: 0.9209 (tptt) cc_final: 0.8410 (tppt) REVERT: I 425 TYR cc_start: 0.8248 (m-80) cc_final: 0.7940 (m-80) REVERT: H 147 MET cc_start: 0.8256 (tmm) cc_final: 0.8027 (tmm) REVERT: H 262 ARG cc_start: 0.7278 (mmp80) cc_final: 0.6690 (mmp80) REVERT: H 355 ASP cc_start: 0.8321 (m-30) cc_final: 0.7864 (m-30) outliers start: 0 outliers final: 0 residues processed: 875 average time/residue: 0.5218 time to fit residues: 752.0568 Evaluate side-chains 620 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 620 time to evaluate : 4.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 405 optimal weight: 5.9990 chunk 276 optimal weight: 9.9990 chunk 7 optimal weight: 30.0000 chunk 362 optimal weight: 20.0000 chunk 201 optimal weight: 8.9990 chunk 415 optimal weight: 9.9990 chunk 336 optimal weight: 0.0970 chunk 0 optimal weight: 40.0000 chunk 248 optimal weight: 20.0000 chunk 437 optimal weight: 0.8980 chunk 122 optimal weight: 20.0000 overall best weight: 5.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 226 ASN ** E 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 226 ASN ** J 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 11 GLN ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN A 283 HIS B 291 GLN B 298 ASN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 423 GLN G 245 GLN ** G 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 ASN ** I 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 329 GLN ** I 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 423 GLN H 298 ASN ** H 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 41454 Z= 0.198 Angle : 0.548 8.914 56328 Z= 0.283 Chirality : 0.044 0.191 6162 Planarity : 0.004 0.050 7326 Dihedral : 12.055 178.685 5826 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % 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: -1.86 (0.11), residues: 5064 helix: -0.95 (0.10), residues: 2262 sheet: -0.47 (0.20), residues: 720 loop : -1.70 (0.14), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 101 HIS 0.007 0.001 HIS D 105 PHE 0.023 0.001 PHE F 265 TYR 0.040 0.002 TYR E 24 ARG 0.007 0.000 ARG J 79 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 845 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 845 time to evaluate : 4.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 18 ASN cc_start: 0.8729 (m-40) cc_final: 0.8512 (m110) REVERT: E 36 MET cc_start: 0.7501 (ptm) cc_final: 0.6269 (tmm) REVERT: E 54 SER cc_start: 0.7552 (p) cc_final: 0.7157 (t) REVERT: E 123 ARG cc_start: 0.8628 (mtm-85) cc_final: 0.8380 (mtp85) REVERT: E 135 PHE cc_start: 0.8678 (m-80) cc_final: 0.8306 (m-10) REVERT: E 149 PHE cc_start: 0.8368 (t80) cc_final: 0.8013 (t80) REVERT: E 203 MET cc_start: 0.9046 (tpp) cc_final: 0.8818 (tpp) REVERT: E 250 VAL cc_start: 0.8119 (t) cc_final: 0.7874 (t) REVERT: E 267 PHE cc_start: 0.9035 (m-80) cc_final: 0.8673 (m-80) REVERT: E 293 ASN cc_start: 0.8911 (m110) cc_final: 0.8584 (m110) REVERT: E 301 GLN cc_start: 0.8633 (mt0) cc_final: 0.8297 (mt0) REVERT: E 313 MET cc_start: 0.8327 (mtm) cc_final: 0.7203 (mtp) REVERT: E 351 PHE cc_start: 0.7810 (m-80) cc_final: 0.7203 (m-80) REVERT: E 398 MET cc_start: 0.6906 (mtm) cc_final: 0.6645 (mtm) REVERT: J 14 VAL cc_start: 0.9264 (t) cc_final: 0.8913 (p) REVERT: J 16 ILE cc_start: 0.9420 (mt) cc_final: 0.8873 (mm) REVERT: J 120 ASP cc_start: 0.8597 (t0) cc_final: 0.8389 (t0) REVERT: J 124 LYS cc_start: 0.8646 (mttm) cc_final: 0.8330 (tptp) REVERT: J 267 PHE cc_start: 0.9042 (m-80) cc_final: 0.8743 (m-80) REVERT: J 301 GLN cc_start: 0.8108 (mt0) cc_final: 0.7208 (pt0) REVERT: J 302 MET cc_start: 0.8648 (mtt) cc_final: 0.8439 (mtm) REVERT: J 313 MET cc_start: 0.7763 (mtm) cc_final: 0.6530 (mtp) REVERT: J 425 MET cc_start: 0.8750 (tpt) cc_final: 0.8311 (tpp) REVERT: C 36 MET cc_start: 0.7649 (ptm) cc_final: 0.6352 (tmm) REVERT: C 69 ASP cc_start: 0.7874 (t0) cc_final: 0.7459 (m-30) REVERT: C 149 PHE cc_start: 0.8131 (t80) cc_final: 0.7903 (t80) REVERT: C 257 THR cc_start: 0.8880 (m) cc_final: 0.8505 (p) REVERT: C 301 GLN cc_start: 0.8812 (mt0) cc_final: 0.8188 (pt0) REVERT: C 313 MET cc_start: 0.7934 (mtm) cc_final: 0.6762 (ttt) REVERT: C 377 MET cc_start: 0.8015 (ttp) cc_final: 0.6915 (tmm) REVERT: C 420 GLU cc_start: 0.8105 (tt0) cc_final: 0.7658 (tp30) REVERT: L 36 MET cc_start: 0.7734 (ptm) cc_final: 0.6544 (tmm) REVERT: L 123 ARG cc_start: 0.8852 (mtm-85) cc_final: 0.8641 (mtp85) REVERT: L 165 SER cc_start: 0.6740 (t) cc_final: 0.6439 (t) REVERT: L 301 GLN cc_start: 0.8855 (mt0) cc_final: 0.8110 (pm20) REVERT: L 313 MET cc_start: 0.7700 (mtm) cc_final: 0.6456 (mtp) REVERT: L 395 PHE cc_start: 0.8965 (t80) cc_final: 0.8588 (t80) REVERT: A 36 MET cc_start: 0.7274 (ptm) cc_final: 0.6043 (tmm) REVERT: A 205 ASP cc_start: 0.7208 (t70) cc_final: 0.6100 (m-30) REVERT: A 255 PHE cc_start: 0.7612 (m-80) cc_final: 0.7291 (m-80) REVERT: A 267 PHE cc_start: 0.9103 (m-80) cc_final: 0.8807 (m-80) REVERT: A 351 PHE cc_start: 0.8075 (m-80) cc_final: 0.7505 (m-80) REVERT: A 377 MET cc_start: 0.8056 (ttp) cc_final: 0.7121 (tmm) REVERT: A 398 MET cc_start: 0.7081 (mtm) cc_final: 0.6818 (mtm) REVERT: A 413 MET cc_start: 0.7608 (tpp) cc_final: 0.7134 (mmm) REVERT: A 420 GLU cc_start: 0.8147 (tt0) cc_final: 0.7597 (tp30) REVERT: K 33 ASP cc_start: 0.7566 (m-30) cc_final: 0.7284 (p0) REVERT: K 36 MET cc_start: 0.7084 (ptm) cc_final: 0.6001 (tmm) REVERT: K 54 SER cc_start: 0.7352 (p) cc_final: 0.6994 (p) REVERT: K 149 PHE cc_start: 0.8473 (t80) cc_final: 0.8137 (t80) REVERT: K 203 MET cc_start: 0.8773 (tpp) cc_final: 0.8456 (ttm) REVERT: K 237 SER cc_start: 0.9101 (m) cc_final: 0.8538 (t) REVERT: K 267 PHE cc_start: 0.9002 (m-80) cc_final: 0.8432 (m-80) REVERT: K 313 MET cc_start: 0.7565 (mtm) cc_final: 0.6327 (mtp) REVERT: K 377 MET cc_start: 0.7619 (ttp) cc_final: 0.6997 (tmm) REVERT: K 413 MET cc_start: 0.7856 (mmm) cc_final: 0.7458 (mmm) REVERT: B 21 TRP cc_start: 0.9067 (m100) cc_final: 0.8188 (m100) REVERT: B 73 MET cc_start: 0.8390 (mmt) cc_final: 0.8161 (mmt) REVERT: B 147 MET cc_start: 0.8470 (tmm) cc_final: 0.8267 (tmm) REVERT: B 164 MET cc_start: 0.8057 (mpp) cc_final: 0.7853 (mpp) REVERT: B 181 GLU cc_start: 0.9067 (pt0) cc_final: 0.8525 (pp20) REVERT: B 297 LYS cc_start: 0.8926 (ptpt) cc_final: 0.8517 (mtmm) REVERT: B 363 MET cc_start: 0.8367 (mtm) cc_final: 0.8101 (mtm) REVERT: B 379 LYS cc_start: 0.8834 (mtpt) cc_final: 0.8627 (mtmm) REVERT: F 85 PHE cc_start: 0.8373 (m-80) cc_final: 0.8005 (m-80) REVERT: F 90 PHE cc_start: 0.8351 (m-80) cc_final: 0.7999 (m-80) REVERT: F 163 ILE cc_start: 0.8785 (pt) cc_final: 0.8442 (pt) REVERT: F 164 MET cc_start: 0.8076 (mpp) cc_final: 0.7731 (mpp) REVERT: F 216 LYS cc_start: 0.8370 (mmtp) cc_final: 0.7950 (mmtm) REVERT: F 233 MET cc_start: 0.9284 (mtp) cc_final: 0.8988 (mtm) REVERT: F 353 VAL cc_start: 0.8764 (t) cc_final: 0.8529 (p) REVERT: G 6 HIS cc_start: 0.8872 (t70) cc_final: 0.8516 (t70) REVERT: G 58 LYS cc_start: 0.7051 (mtpp) cc_final: 0.6656 (mtmt) REVERT: G 83 GLN cc_start: 0.8137 (mp10) cc_final: 0.7480 (tm-30) REVERT: G 163 ILE cc_start: 0.8881 (pt) cc_final: 0.8616 (pt) REVERT: G 164 MET cc_start: 0.8015 (mpp) cc_final: 0.7689 (mpp) REVERT: G 216 LYS cc_start: 0.8221 (mmtt) cc_final: 0.7927 (mmtm) REVERT: G 228 LEU cc_start: 0.9187 (mm) cc_final: 0.8845 (tp) REVERT: G 321 MET cc_start: 0.8313 (ptp) cc_final: 0.7687 (ptp) REVERT: D 21 TRP cc_start: 0.9063 (m100) cc_final: 0.8476 (m100) REVERT: D 73 MET cc_start: 0.8335 (mmt) cc_final: 0.8127 (mmt) REVERT: D 147 MET cc_start: 0.8338 (ppp) cc_final: 0.8092 (ppp) REVERT: D 163 ILE cc_start: 0.9064 (pt) cc_final: 0.8524 (mp) REVERT: D 164 MET cc_start: 0.7806 (mpp) cc_final: 0.7378 (mpp) REVERT: D 288 GLU cc_start: 0.8397 (tm-30) cc_final: 0.7825 (tm-30) REVERT: D 299 MET cc_start: 0.9401 (mmp) cc_final: 0.8820 (mmm) REVERT: D 379 LYS cc_start: 0.9079 (mtpt) cc_final: 0.8818 (mtmm) REVERT: D 388 MET cc_start: 0.7441 (mtt) cc_final: 0.7063 (mtt) REVERT: I 22 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7377 (tm-30) REVERT: I 23 VAL cc_start: 0.7707 (t) cc_final: 0.7031 (t) REVERT: I 164 MET cc_start: 0.7984 (mpp) cc_final: 0.7711 (mpp) REVERT: I 297 LYS cc_start: 0.8322 (ptpt) cc_final: 0.7976 (mmtt) REVERT: I 299 MET cc_start: 0.9268 (mmp) cc_final: 0.8597 (mmm) REVERT: I 306 ARG cc_start: 0.7879 (mtt90) cc_final: 0.7124 (mpt180) REVERT: I 321 MET cc_start: 0.8694 (pmm) cc_final: 0.8478 (pmm) REVERT: I 362 LYS cc_start: 0.9131 (tptt) cc_final: 0.8275 (tppt) REVERT: H 147 MET cc_start: 0.8350 (tmm) cc_final: 0.7932 (tmm) REVERT: H 164 MET cc_start: 0.8000 (mpp) cc_final: 0.7753 (mpp) REVERT: H 266 PHE cc_start: 0.8306 (m-80) cc_final: 0.7993 (m-80) REVERT: H 395 LEU cc_start: 0.7096 (tp) cc_final: 0.6881 (tp) outliers start: 0 outliers final: 0 residues processed: 845 average time/residue: 0.5097 time to fit residues: 713.1697 Evaluate side-chains 606 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 606 time to evaluate : 4.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 163 optimal weight: 9.9990 chunk 438 optimal weight: 3.9990 chunk 96 optimal weight: 30.0000 chunk 286 optimal weight: 20.0000 chunk 120 optimal weight: 10.0000 chunk 487 optimal weight: 7.9990 chunk 404 optimal weight: 30.0000 chunk 225 optimal weight: 0.9980 chunk 40 optimal weight: 20.0000 chunk 161 optimal weight: 0.0060 chunk 256 optimal weight: 10.0000 overall best weight: 4.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 226 ASN ** E 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 226 ASN ** J 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN C 249 ASN ** C 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 226 ASN L 300 ASN ** L 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 11 GLN ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN B 291 GLN ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 291 GLN G 334 GLN ** G 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 131 GLN ** I 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 298 ASN ** H 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.4695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 41454 Z= 0.184 Angle : 0.530 7.426 56328 Z= 0.273 Chirality : 0.043 0.241 6162 Planarity : 0.004 0.051 7326 Dihedral : 11.958 178.383 5826 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.02 % Allowed : 1.17 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.12), residues: 5064 helix: -0.68 (0.11), residues: 2256 sheet: -0.16 (0.20), residues: 744 loop : -1.65 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 101 HIS 0.007 0.001 HIS H 6 PHE 0.023 0.001 PHE K 351 TYR 0.021 0.001 TYR I 425 ARG 0.010 0.000 ARG E 390 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 835 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 834 time to evaluate : 5.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 18 ASN cc_start: 0.8796 (m-40) cc_final: 0.8593 (m110) REVERT: E 36 MET cc_start: 0.7504 (ptm) cc_final: 0.6234 (tmm) REVERT: E 54 SER cc_start: 0.7594 (p) cc_final: 0.7173 (t) REVERT: E 135 PHE cc_start: 0.8627 (m-80) cc_final: 0.8290 (m-10) REVERT: E 149 PHE cc_start: 0.8413 (t80) cc_final: 0.8054 (t80) REVERT: E 250 VAL cc_start: 0.8148 (t) cc_final: 0.7905 (t) REVERT: E 267 PHE cc_start: 0.9019 (m-80) cc_final: 0.8639 (m-80) REVERT: E 293 ASN cc_start: 0.8897 (m110) cc_final: 0.8583 (m110) REVERT: E 313 MET cc_start: 0.8268 (mtm) cc_final: 0.7196 (mtp) REVERT: E 351 PHE cc_start: 0.7797 (m-80) cc_final: 0.7184 (m-80) REVERT: E 398 MET cc_start: 0.6871 (mtm) cc_final: 0.6596 (mtm) REVERT: J 14 VAL cc_start: 0.9281 (t) cc_final: 0.9052 (p) REVERT: J 16 ILE cc_start: 0.9415 (mt) cc_final: 0.9047 (mt) REVERT: J 120 ASP cc_start: 0.8592 (t0) cc_final: 0.8349 (t0) REVERT: J 124 LYS cc_start: 0.8694 (mttm) cc_final: 0.8372 (tptp) REVERT: J 267 PHE cc_start: 0.9026 (m-80) cc_final: 0.8733 (m-80) REVERT: J 313 MET cc_start: 0.7826 (mtm) cc_final: 0.6584 (mtp) REVERT: J 391 LEU cc_start: 0.9439 (tp) cc_final: 0.8974 (pp) REVERT: C 36 MET cc_start: 0.7673 (ptm) cc_final: 0.6393 (tmm) REVERT: C 69 ASP cc_start: 0.7838 (t0) cc_final: 0.7470 (m-30) REVERT: C 149 PHE cc_start: 0.8283 (t80) cc_final: 0.8066 (t80) REVERT: C 257 THR cc_start: 0.8914 (m) cc_final: 0.8496 (p) REVERT: C 301 GLN cc_start: 0.8901 (mt0) cc_final: 0.7992 (pt0) REVERT: C 313 MET cc_start: 0.7910 (mtm) cc_final: 0.6761 (ttt) REVERT: C 420 GLU cc_start: 0.8101 (tt0) cc_final: 0.7659 (tp30) REVERT: L 36 MET cc_start: 0.7767 (ptm) cc_final: 0.6582 (tmm) REVERT: L 165 SER cc_start: 0.6886 (t) cc_final: 0.6561 (t) REVERT: L 203 MET cc_start: 0.8858 (tpp) cc_final: 0.8149 (ttm) REVERT: L 256 GLN cc_start: 0.8104 (pt0) cc_final: 0.7855 (pt0) REVERT: L 301 GLN cc_start: 0.8755 (mt0) cc_final: 0.7999 (pm20) REVERT: L 313 MET cc_start: 0.7696 (mtm) cc_final: 0.6492 (mtp) REVERT: L 395 PHE cc_start: 0.8972 (t80) cc_final: 0.8596 (t80) REVERT: A 36 MET cc_start: 0.7271 (ptm) cc_final: 0.6031 (tmm) REVERT: A 205 ASP cc_start: 0.7037 (t70) cc_final: 0.6140 (m-30) REVERT: A 255 PHE cc_start: 0.7599 (m-80) cc_final: 0.7210 (m-80) REVERT: A 267 PHE cc_start: 0.9103 (m-80) cc_final: 0.8836 (m-80) REVERT: A 316 CYS cc_start: 0.8625 (t) cc_final: 0.8120 (t) REVERT: A 351 PHE cc_start: 0.8105 (m-80) cc_final: 0.7530 (m-80) REVERT: A 413 MET cc_start: 0.7645 (tpp) cc_final: 0.7224 (mmm) REVERT: A 420 GLU cc_start: 0.8150 (tt0) cc_final: 0.7612 (tp30) REVERT: K 33 ASP cc_start: 0.7552 (m-30) cc_final: 0.7320 (p0) REVERT: K 36 MET cc_start: 0.6983 (ptm) cc_final: 0.5946 (tmm) REVERT: K 54 SER cc_start: 0.7389 (p) cc_final: 0.7035 (p) REVERT: K 149 PHE cc_start: 0.8454 (t80) cc_final: 0.8135 (t80) REVERT: K 203 MET cc_start: 0.8851 (tpp) cc_final: 0.8533 (ttm) REVERT: K 237 SER cc_start: 0.9052 (m) cc_final: 0.8518 (t) REVERT: K 267 PHE cc_start: 0.8967 (m-80) cc_final: 0.8429 (m-80) REVERT: K 377 MET cc_start: 0.7802 (ttp) cc_final: 0.7197 (tmm) REVERT: K 380 ASN cc_start: 0.8420 (t0) cc_final: 0.8099 (t0) REVERT: K 390 ARG cc_start: 0.9216 (tmm160) cc_final: 0.8831 (ttp80) REVERT: K 391 LEU cc_start: 0.9415 (tp) cc_final: 0.9129 (tp) REVERT: K 413 MET cc_start: 0.7903 (mmm) cc_final: 0.7514 (mmm) REVERT: K 420 GLU cc_start: 0.8065 (tt0) cc_final: 0.7665 (tp30) REVERT: B 6 HIS cc_start: 0.8891 (t70) cc_final: 0.8553 (t-170) REVERT: B 21 TRP cc_start: 0.8935 (m100) cc_final: 0.8265 (m100) REVERT: B 147 MET cc_start: 0.8537 (tmm) cc_final: 0.8327 (tmm) REVERT: B 164 MET cc_start: 0.8143 (mpp) cc_final: 0.7894 (mpp) REVERT: B 181 GLU cc_start: 0.8983 (pt0) cc_final: 0.8433 (pp20) REVERT: B 293 MET cc_start: 0.7965 (mtp) cc_final: 0.7602 (ptp) REVERT: B 297 LYS cc_start: 0.8930 (ptpt) cc_final: 0.8535 (mtmm) REVERT: B 363 MET cc_start: 0.8377 (mtm) cc_final: 0.8087 (mtm) REVERT: B 379 LYS cc_start: 0.8881 (mtpt) cc_final: 0.8678 (mtmm) REVERT: F 6 HIS cc_start: 0.8838 (t-170) cc_final: 0.8637 (t-170) REVERT: F 90 PHE cc_start: 0.8312 (m-80) cc_final: 0.8061 (m-80) REVERT: F 163 ILE cc_start: 0.8783 (pt) cc_final: 0.8453 (pt) REVERT: F 164 MET cc_start: 0.8104 (mpp) cc_final: 0.7684 (mpp) REVERT: F 216 LYS cc_start: 0.8435 (mmtp) cc_final: 0.7962 (mmtm) REVERT: F 233 MET cc_start: 0.9249 (mtp) cc_final: 0.8964 (mtm) REVERT: F 253 LEU cc_start: 0.9072 (pp) cc_final: 0.8867 (pp) REVERT: G 58 LYS cc_start: 0.7168 (mtpp) cc_final: 0.6772 (mtmt) REVERT: G 83 GLN cc_start: 0.8171 (mp10) cc_final: 0.7462 (tm-30) REVERT: G 163 ILE cc_start: 0.8800 (pt) cc_final: 0.8532 (pt) REVERT: G 164 MET cc_start: 0.8067 (mpp) cc_final: 0.7673 (mpp) REVERT: G 210 ILE cc_start: 0.9178 (tp) cc_final: 0.8907 (tt) REVERT: G 216 LYS cc_start: 0.8206 (mmtt) cc_final: 0.7914 (mmtm) REVERT: G 228 LEU cc_start: 0.9140 (mm) cc_final: 0.8771 (tp) REVERT: G 321 MET cc_start: 0.8252 (ptp) cc_final: 0.7771 (ptp) REVERT: D 21 TRP cc_start: 0.9072 (m100) cc_final: 0.8558 (m100) REVERT: D 147 MET cc_start: 0.8305 (ppp) cc_final: 0.8090 (ppp) REVERT: D 149 THR cc_start: 0.9493 (p) cc_final: 0.9219 (p) REVERT: D 163 ILE cc_start: 0.9079 (pt) cc_final: 0.8512 (mp) REVERT: D 164 MET cc_start: 0.7944 (mpp) cc_final: 0.7529 (mpp) REVERT: D 299 MET cc_start: 0.9334 (mmp) cc_final: 0.8690 (mmm) REVERT: D 323 MET cc_start: 0.8069 (mpp) cc_final: 0.7786 (mpp) REVERT: D 379 LYS cc_start: 0.9058 (mtpt) cc_final: 0.8819 (mtmm) REVERT: D 388 MET cc_start: 0.7424 (mtt) cc_final: 0.7040 (mtt) REVERT: I 22 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7403 (tm-30) REVERT: I 23 VAL cc_start: 0.7864 (t) cc_final: 0.7198 (t) REVERT: I 163 ILE cc_start: 0.9037 (pt) cc_final: 0.8755 (pt) REVERT: I 164 MET cc_start: 0.8118 (mpp) cc_final: 0.7656 (mpp) REVERT: I 297 LYS cc_start: 0.8326 (ptpt) cc_final: 0.7950 (mmtt) REVERT: I 299 MET cc_start: 0.9334 (mmp) cc_final: 0.8938 (mmm) REVERT: I 306 ARG cc_start: 0.7910 (mtt90) cc_final: 0.7148 (mpt180) REVERT: I 321 MET cc_start: 0.8649 (pmm) cc_final: 0.8439 (pmm) REVERT: I 331 LEU cc_start: 0.8387 (mt) cc_final: 0.8178 (pp) REVERT: I 362 LYS cc_start: 0.9131 (tptt) cc_final: 0.8872 (tptp) REVERT: I 363 MET cc_start: 0.8063 (ptp) cc_final: 0.7493 (ptt) REVERT: H 147 MET cc_start: 0.8257 (tmm) cc_final: 0.7904 (tmm) REVERT: H 164 MET cc_start: 0.7946 (mpp) cc_final: 0.7732 (mpp) REVERT: H 266 PHE cc_start: 0.8307 (m-80) cc_final: 0.8026 (m-80) REVERT: H 293 MET cc_start: 0.7746 (mtp) cc_final: 0.7265 (ptp) outliers start: 1 outliers final: 0 residues processed: 834 average time/residue: 0.5057 time to fit residues: 704.0768 Evaluate side-chains 607 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 607 time to evaluate : 4.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 470 optimal weight: 0.4980 chunk 54 optimal weight: 30.0000 chunk 277 optimal weight: 1.9990 chunk 356 optimal weight: 9.9990 chunk 275 optimal weight: 20.0000 chunk 410 optimal weight: 20.0000 chunk 272 optimal weight: 20.0000 chunk 485 optimal weight: 8.9990 chunk 304 optimal weight: 40.0000 chunk 296 optimal weight: 20.0000 chunk 224 optimal weight: 0.9990 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 226 ASN ** E 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 226 ASN ** J 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN ** C 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 11 GLN ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 291 GLN ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 GLN D 291 GLN ** I 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 131 GLN ** I 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 298 ASN ** H 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 41454 Z= 0.180 Angle : 0.525 7.423 56328 Z= 0.271 Chirality : 0.043 0.179 6162 Planarity : 0.004 0.049 7326 Dihedral : 11.904 178.927 5826 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.12), residues: 5064 helix: -0.53 (0.11), residues: 2256 sheet: -0.06 (0.20), residues: 744 loop : -1.61 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP H 101 HIS 0.007 0.001 HIS D 6 PHE 0.026 0.001 PHE B 242 TYR 0.016 0.001 TYR B 200 ARG 0.005 0.000 ARG E 123 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 804 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 804 time to evaluate : 4.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 18 ASN cc_start: 0.8856 (m-40) cc_final: 0.8630 (m110) REVERT: E 36 MET cc_start: 0.7541 (ptm) cc_final: 0.6371 (tmm) REVERT: E 54 SER cc_start: 0.7845 (p) cc_final: 0.7540 (t) REVERT: E 135 PHE cc_start: 0.8345 (m-80) cc_final: 0.7942 (m-10) REVERT: E 149 PHE cc_start: 0.8449 (t80) cc_final: 0.8090 (t80) REVERT: E 250 VAL cc_start: 0.8304 (t) cc_final: 0.7922 (t) REVERT: E 267 PHE cc_start: 0.9049 (m-80) cc_final: 0.8693 (m-80) REVERT: E 293 ASN cc_start: 0.8884 (m110) cc_final: 0.8545 (m110) REVERT: E 313 MET cc_start: 0.8285 (mtm) cc_final: 0.7189 (mtp) REVERT: E 351 PHE cc_start: 0.7792 (m-80) cc_final: 0.7197 (m-80) REVERT: E 391 LEU cc_start: 0.9286 (tp) cc_final: 0.8791 (tp) REVERT: E 398 MET cc_start: 0.6853 (mtm) cc_final: 0.6567 (mtm) REVERT: J 14 VAL cc_start: 0.9257 (t) cc_final: 0.9037 (p) REVERT: J 124 LYS cc_start: 0.8641 (mttm) cc_final: 0.8349 (tptp) REVERT: J 214 ARG cc_start: 0.8797 (ttp80) cc_final: 0.8314 (mmm-85) REVERT: J 267 PHE cc_start: 0.9029 (m-80) cc_final: 0.8748 (m-80) REVERT: J 313 MET cc_start: 0.7727 (mtm) cc_final: 0.6589 (mtp) REVERT: J 391 LEU cc_start: 0.9410 (tp) cc_final: 0.8930 (pp) REVERT: C 36 MET cc_start: 0.7718 (ptm) cc_final: 0.6375 (tmm) REVERT: C 69 ASP cc_start: 0.7806 (t0) cc_final: 0.7506 (m-30) REVERT: C 257 THR cc_start: 0.9017 (m) cc_final: 0.8634 (p) REVERT: C 301 GLN cc_start: 0.8792 (mt0) cc_final: 0.8323 (pm20) REVERT: C 313 MET cc_start: 0.7844 (mtm) cc_final: 0.6675 (ttt) REVERT: L 18 ASN cc_start: 0.8826 (m-40) cc_final: 0.8335 (m110) REVERT: L 36 MET cc_start: 0.7939 (ptm) cc_final: 0.6682 (tmm) REVERT: L 260 VAL cc_start: 0.8872 (t) cc_final: 0.8367 (p) REVERT: L 301 GLN cc_start: 0.8713 (mt0) cc_final: 0.7997 (pm20) REVERT: L 313 MET cc_start: 0.7675 (mtm) cc_final: 0.6493 (mtp) REVERT: L 395 PHE cc_start: 0.8983 (t80) cc_final: 0.8621 (t80) REVERT: A 18 ASN cc_start: 0.8824 (m-40) cc_final: 0.8597 (m110) REVERT: A 36 MET cc_start: 0.7165 (ptm) cc_final: 0.5960 (tmm) REVERT: A 237 SER cc_start: 0.9216 (m) cc_final: 0.8619 (t) REVERT: A 255 PHE cc_start: 0.7710 (m-80) cc_final: 0.7341 (m-80) REVERT: A 267 PHE cc_start: 0.9104 (m-80) cc_final: 0.8857 (m-80) REVERT: A 316 CYS cc_start: 0.8720 (t) cc_final: 0.8175 (t) REVERT: A 351 PHE cc_start: 0.8052 (m-80) cc_final: 0.7464 (m-80) REVERT: A 398 MET cc_start: 0.6984 (mtm) cc_final: 0.6699 (mtm) REVERT: A 413 MET cc_start: 0.7642 (tpp) cc_final: 0.7197 (mmm) REVERT: A 420 GLU cc_start: 0.8195 (tt0) cc_final: 0.7720 (tp30) REVERT: K 33 ASP cc_start: 0.7552 (m-30) cc_final: 0.7340 (p0) REVERT: K 36 MET cc_start: 0.7009 (ptm) cc_final: 0.5993 (tmm) REVERT: K 54 SER cc_start: 0.7439 (p) cc_final: 0.7071 (p) REVERT: K 149 PHE cc_start: 0.8449 (t80) cc_final: 0.8148 (t80) REVERT: K 203 MET cc_start: 0.8907 (tpp) cc_final: 0.8535 (ttm) REVERT: K 214 ARG cc_start: 0.8776 (ttm-80) cc_final: 0.7947 (ttp80) REVERT: K 218 ASP cc_start: 0.8671 (m-30) cc_final: 0.8207 (t0) REVERT: K 237 SER cc_start: 0.9085 (m) cc_final: 0.8586 (t) REVERT: K 267 PHE cc_start: 0.8949 (m-80) cc_final: 0.8438 (m-80) REVERT: K 377 MET cc_start: 0.7847 (ttp) cc_final: 0.7239 (tmm) REVERT: K 413 MET cc_start: 0.8003 (mmm) cc_final: 0.7601 (mmm) REVERT: K 420 GLU cc_start: 0.8077 (tt0) cc_final: 0.7684 (tp30) REVERT: B 6 HIS cc_start: 0.8860 (t70) cc_final: 0.8576 (t-170) REVERT: B 21 TRP cc_start: 0.8991 (m100) cc_final: 0.8247 (m100) REVERT: B 147 MET cc_start: 0.8572 (tmm) cc_final: 0.8330 (tmm) REVERT: B 164 MET cc_start: 0.8020 (mpp) cc_final: 0.7800 (mpp) REVERT: B 181 GLU cc_start: 0.8993 (pt0) cc_final: 0.8421 (pp20) REVERT: B 293 MET cc_start: 0.8005 (mtp) cc_final: 0.7611 (ptp) REVERT: B 297 LYS cc_start: 0.8921 (ptpt) cc_final: 0.8543 (mtmm) REVERT: B 363 MET cc_start: 0.8383 (mtm) cc_final: 0.8097 (mtm) REVERT: B 379 LYS cc_start: 0.8933 (mtpt) cc_final: 0.8727 (mtmm) REVERT: F 6 HIS cc_start: 0.8946 (t-170) cc_final: 0.8664 (t-170) REVERT: F 90 PHE cc_start: 0.8316 (m-80) cc_final: 0.7997 (m-80) REVERT: F 163 ILE cc_start: 0.8830 (pt) cc_final: 0.8528 (pt) REVERT: F 164 MET cc_start: 0.8045 (mpp) cc_final: 0.7559 (mpp) REVERT: F 216 LYS cc_start: 0.8456 (mmtp) cc_final: 0.7974 (mmtm) REVERT: G 6 HIS cc_start: 0.8818 (t70) cc_final: 0.8553 (t70) REVERT: G 58 LYS cc_start: 0.7187 (mtpp) cc_final: 0.6787 (mtmt) REVERT: G 83 GLN cc_start: 0.8194 (mp10) cc_final: 0.7516 (tm-30) REVERT: G 163 ILE cc_start: 0.8775 (pt) cc_final: 0.8473 (pt) REVERT: G 164 MET cc_start: 0.8116 (mpp) cc_final: 0.7540 (mpp) REVERT: G 216 LYS cc_start: 0.8227 (mmtt) cc_final: 0.7914 (mmtm) REVERT: G 228 LEU cc_start: 0.9142 (mm) cc_final: 0.8765 (tp) REVERT: G 321 MET cc_start: 0.8222 (ptp) cc_final: 0.7856 (ptp) REVERT: D 147 MET cc_start: 0.8351 (ppp) cc_final: 0.8117 (ppp) REVERT: D 149 THR cc_start: 0.9475 (p) cc_final: 0.9192 (p) REVERT: D 163 ILE cc_start: 0.9028 (pt) cc_final: 0.8503 (mp) REVERT: D 164 MET cc_start: 0.7928 (mpp) cc_final: 0.7492 (mpp) REVERT: D 299 MET cc_start: 0.9321 (mmp) cc_final: 0.8682 (mmm) REVERT: D 323 MET cc_start: 0.8250 (mpp) cc_final: 0.7990 (mpp) REVERT: D 379 LYS cc_start: 0.9062 (mtpt) cc_final: 0.8819 (mtmm) REVERT: D 388 MET cc_start: 0.7457 (mtt) cc_final: 0.7059 (mtt) REVERT: D 425 TYR cc_start: 0.8359 (m-80) cc_final: 0.7928 (m-10) REVERT: I 22 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7504 (tm-30) REVERT: I 23 VAL cc_start: 0.7940 (t) cc_final: 0.7383 (t) REVERT: I 163 ILE cc_start: 0.8909 (pt) cc_final: 0.8591 (pt) REVERT: I 164 MET cc_start: 0.8177 (mpp) cc_final: 0.7739 (mpp) REVERT: I 242 PHE cc_start: 0.7452 (m-80) cc_final: 0.7239 (m-10) REVERT: I 297 LYS cc_start: 0.8298 (ptpt) cc_final: 0.7968 (mmtt) REVERT: I 299 MET cc_start: 0.9286 (mmp) cc_final: 0.8941 (mmm) REVERT: I 306 ARG cc_start: 0.7961 (mtt90) cc_final: 0.7166 (mpt180) REVERT: I 362 LYS cc_start: 0.9105 (tptt) cc_final: 0.8854 (tptp) REVERT: I 363 MET cc_start: 0.8086 (ptp) cc_final: 0.7563 (ptt) REVERT: H 147 MET cc_start: 0.8227 (tmm) cc_final: 0.7918 (tmm) REVERT: H 164 MET cc_start: 0.7995 (mpp) cc_final: 0.7776 (mpp) REVERT: H 262 ARG cc_start: 0.7122 (mmp80) cc_final: 0.6624 (mmp80) REVERT: H 266 PHE cc_start: 0.8369 (m-80) cc_final: 0.8093 (m-80) REVERT: H 293 MET cc_start: 0.7675 (mtp) cc_final: 0.7200 (ptp) outliers start: 0 outliers final: 0 residues processed: 804 average time/residue: 0.5060 time to fit residues: 674.2272 Evaluate side-chains 602 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 602 time to evaluate : 4.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 300 optimal weight: 8.9990 chunk 193 optimal weight: 8.9990 chunk 290 optimal weight: 3.9990 chunk 146 optimal weight: 20.0000 chunk 95 optimal weight: 0.7980 chunk 94 optimal weight: 6.9990 chunk 308 optimal weight: 40.0000 chunk 330 optimal weight: 0.9990 chunk 240 optimal weight: 20.0000 chunk 45 optimal weight: 0.6980 chunk 381 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 226 ASN ** E 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 226 ASN ** J 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 GLN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN ** C 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 11 GLN ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 ASN K 258 ASN ** K 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 GLN B 291 GLN ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 GLN ** I 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 131 GLN ** I 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 298 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 41454 Z= 0.142 Angle : 0.512 7.815 56328 Z= 0.261 Chirality : 0.043 0.200 6162 Planarity : 0.004 0.053 7326 Dihedral : 11.788 179.395 5826 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % 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: -1.22 (0.12), residues: 5064 helix: -0.37 (0.11), residues: 2262 sheet: -0.16 (0.19), residues: 846 loop : -1.52 (0.15), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 101 HIS 0.008 0.001 HIS H 6 PHE 0.023 0.001 PHE C 149 TYR 0.014 0.001 TYR K 224 ARG 0.007 0.000 ARG C 2 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 823 time to evaluate : 5.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 18 ASN cc_start: 0.8806 (m-40) cc_final: 0.8574 (m110) REVERT: E 36 MET cc_start: 0.7399 (ptm) cc_final: 0.6144 (tmm) REVERT: E 54 SER cc_start: 0.7757 (p) cc_final: 0.7429 (t) REVERT: E 135 PHE cc_start: 0.8339 (m-80) cc_final: 0.7988 (m-10) REVERT: E 149 PHE cc_start: 0.8435 (t80) cc_final: 0.8111 (t80) REVERT: E 218 ASP cc_start: 0.8728 (m-30) cc_final: 0.8011 (t0) REVERT: E 250 VAL cc_start: 0.8201 (t) cc_final: 0.7819 (t) REVERT: E 267 PHE cc_start: 0.9067 (m-80) cc_final: 0.8671 (m-80) REVERT: E 293 ASN cc_start: 0.8871 (m110) cc_final: 0.8489 (m110) REVERT: E 313 MET cc_start: 0.8266 (mtm) cc_final: 0.7158 (mtp) REVERT: E 351 PHE cc_start: 0.7689 (m-80) cc_final: 0.7330 (m-80) REVERT: E 398 MET cc_start: 0.6709 (mtm) cc_final: 0.6465 (mtm) REVERT: J 14 VAL cc_start: 0.9241 (t) cc_final: 0.8997 (p) REVERT: J 124 LYS cc_start: 0.8582 (mttm) cc_final: 0.8345 (tptp) REVERT: J 214 ARG cc_start: 0.8804 (ttp80) cc_final: 0.8317 (mmm-85) REVERT: J 267 PHE cc_start: 0.9005 (m-80) cc_final: 0.8730 (m-80) REVERT: J 313 MET cc_start: 0.7707 (mtm) cc_final: 0.6572 (mtp) REVERT: J 391 LEU cc_start: 0.9437 (tp) cc_final: 0.8874 (pp) REVERT: C 36 MET cc_start: 0.7701 (ptm) cc_final: 0.6535 (tmm) REVERT: C 69 ASP cc_start: 0.7843 (t0) cc_final: 0.7519 (m-30) REVERT: C 256 GLN cc_start: 0.8725 (pt0) cc_final: 0.8194 (pt0) REVERT: C 257 THR cc_start: 0.8986 (m) cc_final: 0.8643 (p) REVERT: C 301 GLN cc_start: 0.8716 (mt0) cc_final: 0.8259 (pm20) REVERT: C 313 MET cc_start: 0.7691 (mtm) cc_final: 0.6584 (ttt) REVERT: L 18 ASN cc_start: 0.8786 (m-40) cc_final: 0.8274 (m110) REVERT: L 36 MET cc_start: 0.7927 (ptm) cc_final: 0.6689 (tmm) REVERT: L 213 CYS cc_start: 0.8917 (t) cc_final: 0.8672 (t) REVERT: L 260 VAL cc_start: 0.8790 (t) cc_final: 0.8289 (p) REVERT: L 301 GLN cc_start: 0.8654 (mt0) cc_final: 0.7968 (pm20) REVERT: L 313 MET cc_start: 0.7648 (mtm) cc_final: 0.6404 (mtp) REVERT: L 395 PHE cc_start: 0.8937 (t80) cc_final: 0.8559 (t80) REVERT: A 18 ASN cc_start: 0.8746 (m-40) cc_final: 0.8516 (m110) REVERT: A 36 MET cc_start: 0.7124 (ptm) cc_final: 0.5915 (tmm) REVERT: A 205 ASP cc_start: 0.7602 (t0) cc_final: 0.6447 (m-30) REVERT: A 237 SER cc_start: 0.9124 (m) cc_final: 0.8676 (t) REVERT: A 255 PHE cc_start: 0.7606 (m-80) cc_final: 0.7273 (m-80) REVERT: A 267 PHE cc_start: 0.9074 (m-80) cc_final: 0.8819 (m-80) REVERT: A 316 CYS cc_start: 0.8736 (t) cc_final: 0.8171 (t) REVERT: A 351 PHE cc_start: 0.7915 (m-80) cc_final: 0.7347 (m-80) REVERT: A 398 MET cc_start: 0.6879 (mtm) cc_final: 0.6673 (mtm) REVERT: A 413 MET cc_start: 0.7437 (tpp) cc_final: 0.7031 (mmm) REVERT: A 420 GLU cc_start: 0.8267 (tt0) cc_final: 0.7785 (tp30) REVERT: K 36 MET cc_start: 0.6871 (ptm) cc_final: 0.5831 (tmm) REVERT: K 54 SER cc_start: 0.7468 (p) cc_final: 0.7102 (p) REVERT: K 149 PHE cc_start: 0.8420 (t80) cc_final: 0.8145 (t80) REVERT: K 205 ASP cc_start: 0.7242 (t70) cc_final: 0.6260 (m-30) REVERT: K 218 ASP cc_start: 0.8604 (m-30) cc_final: 0.8151 (t0) REVERT: K 237 SER cc_start: 0.9045 (m) cc_final: 0.8618 (t) REVERT: K 255 PHE cc_start: 0.7803 (m-80) cc_final: 0.7311 (m-80) REVERT: K 267 PHE cc_start: 0.8979 (m-80) cc_final: 0.8465 (m-80) REVERT: K 276 ILE cc_start: 0.8839 (tp) cc_final: 0.8632 (tp) REVERT: K 280 LYS cc_start: 0.8274 (ttmt) cc_final: 0.7894 (tttt) REVERT: K 377 MET cc_start: 0.7907 (ttp) cc_final: 0.7362 (tmm) REVERT: K 413 MET cc_start: 0.7951 (mmm) cc_final: 0.7584 (mmm) REVERT: K 420 GLU cc_start: 0.7983 (tt0) cc_final: 0.7671 (tp30) REVERT: B 21 TRP cc_start: 0.8988 (m100) cc_final: 0.8363 (m100) REVERT: B 118 ASP cc_start: 0.8330 (m-30) cc_final: 0.7806 (t70) REVERT: B 147 MET cc_start: 0.8579 (tmm) cc_final: 0.8268 (tmm) REVERT: B 181 GLU cc_start: 0.8989 (pt0) cc_final: 0.8518 (pp20) REVERT: B 293 MET cc_start: 0.8199 (mtp) cc_final: 0.7820 (ptp) REVERT: B 297 LYS cc_start: 0.8856 (ptpt) cc_final: 0.8454 (mmtm) REVERT: B 299 MET cc_start: 0.9010 (mmp) cc_final: 0.8725 (mmm) REVERT: B 363 MET cc_start: 0.8352 (mtm) cc_final: 0.8070 (mtm) REVERT: B 379 LYS cc_start: 0.8965 (mtpt) cc_final: 0.8617 (mtmm) REVERT: F 90 PHE cc_start: 0.8321 (m-80) cc_final: 0.8022 (m-80) REVERT: F 163 ILE cc_start: 0.8614 (pt) cc_final: 0.8329 (pt) REVERT: F 164 MET cc_start: 0.8086 (mpp) cc_final: 0.7597 (mpp) REVERT: F 216 LYS cc_start: 0.8435 (mmtp) cc_final: 0.7893 (mmtm) REVERT: F 233 MET cc_start: 0.9309 (mtp) cc_final: 0.8993 (mtm) REVERT: G 6 HIS cc_start: 0.8803 (t70) cc_final: 0.8598 (t70) REVERT: G 58 LYS cc_start: 0.7289 (mtpp) cc_final: 0.6868 (mtmt) REVERT: G 83 GLN cc_start: 0.8163 (mp10) cc_final: 0.7509 (tm-30) REVERT: G 163 ILE cc_start: 0.8750 (pt) cc_final: 0.8470 (pt) REVERT: G 164 MET cc_start: 0.8102 (mpp) cc_final: 0.7530 (mpp) REVERT: G 216 LYS cc_start: 0.8197 (mmtt) cc_final: 0.7796 (mmtm) REVERT: G 228 LEU cc_start: 0.9130 (mm) cc_final: 0.8729 (tp) REVERT: G 300 MET cc_start: 0.7723 (mtm) cc_final: 0.7452 (mtm) REVERT: G 321 MET cc_start: 0.8165 (ptp) cc_final: 0.7943 (ptp) REVERT: D 147 MET cc_start: 0.8480 (ppp) cc_final: 0.8222 (ppp) REVERT: D 164 MET cc_start: 0.7911 (mpp) cc_final: 0.7476 (mpp) REVERT: D 323 MET cc_start: 0.8157 (mpp) cc_final: 0.7887 (mpp) REVERT: D 328 GLU cc_start: 0.8447 (tp30) cc_final: 0.8234 (tp30) REVERT: D 353 VAL cc_start: 0.9059 (p) cc_final: 0.8577 (t) REVERT: D 379 LYS cc_start: 0.9057 (mtpt) cc_final: 0.8806 (mtmm) REVERT: D 388 MET cc_start: 0.7417 (mtt) cc_final: 0.7038 (mtt) REVERT: D 425 TYR cc_start: 0.8361 (m-80) cc_final: 0.8020 (m-10) REVERT: I 22 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7357 (tm-30) REVERT: I 73 MET cc_start: 0.8277 (mmt) cc_final: 0.8067 (mmt) REVERT: I 149 THR cc_start: 0.9387 (p) cc_final: 0.9174 (p) REVERT: I 163 ILE cc_start: 0.8811 (pt) cc_final: 0.8520 (pt) REVERT: I 164 MET cc_start: 0.8172 (mpp) cc_final: 0.7709 (mpp) REVERT: I 297 LYS cc_start: 0.8308 (ptpt) cc_final: 0.7945 (mmtt) REVERT: I 299 MET cc_start: 0.9210 (mmp) cc_final: 0.8984 (mmm) REVERT: I 306 ARG cc_start: 0.7921 (mtt90) cc_final: 0.7145 (mpt180) REVERT: I 362 LYS cc_start: 0.9093 (tptt) cc_final: 0.8846 (tptp) REVERT: I 363 MET cc_start: 0.7926 (ptp) cc_final: 0.7438 (ptt) REVERT: H 101 TRP cc_start: 0.7287 (t60) cc_final: 0.6899 (t60) REVERT: H 147 MET cc_start: 0.8252 (tmm) cc_final: 0.7897 (tmm) REVERT: H 164 MET cc_start: 0.8027 (mpp) cc_final: 0.7773 (mpp) REVERT: H 262 ARG cc_start: 0.7059 (mmp80) cc_final: 0.6587 (mmp80) REVERT: H 266 PHE cc_start: 0.8372 (m-80) cc_final: 0.8035 (m-80) REVERT: H 293 MET cc_start: 0.7673 (mtp) cc_final: 0.7203 (ptp) REVERT: H 300 MET cc_start: 0.7994 (mtt) cc_final: 0.7755 (mtm) REVERT: H 406 MET cc_start: 0.8931 (mmm) cc_final: 0.8575 (mmm) outliers start: 0 outliers final: 0 residues processed: 823 average time/residue: 0.5139 time to fit residues: 703.3780 Evaluate side-chains 620 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 620 time to evaluate : 4.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 441 optimal weight: 9.9990 chunk 465 optimal weight: 8.9990 chunk 424 optimal weight: 0.0060 chunk 452 optimal weight: 20.0000 chunk 272 optimal weight: 9.9990 chunk 197 optimal weight: 5.9990 chunk 355 optimal weight: 6.9990 chunk 138 optimal weight: 30.0000 chunk 409 optimal weight: 30.0000 chunk 428 optimal weight: 0.4980 chunk 451 optimal weight: 6.9990 overall best weight: 4.1002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 358 GLN J 226 ASN ** J 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN ** L 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 11 GLN ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 380 ASN ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 GLN D 291 GLN ** I 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 131 GLN I 291 GLN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 298 ASN ** H 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.5141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 41454 Z= 0.173 Angle : 0.530 8.431 56328 Z= 0.270 Chirality : 0.043 0.201 6162 Planarity : 0.004 0.052 7326 Dihedral : 11.786 179.398 5826 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.13 (0.12), residues: 5064 helix: -0.28 (0.11), residues: 2250 sheet: -0.02 (0.19), residues: 786 loop : -1.49 (0.14), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 101 HIS 0.008 0.001 HIS D 6 PHE 0.031 0.001 PHE D 212 TYR 0.019 0.001 TYR J 172 ARG 0.007 0.000 ARG C 2 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 798 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 798 time to evaluate : 4.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 18 ASN cc_start: 0.8820 (m-40) cc_final: 0.8590 (m110) REVERT: E 36 MET cc_start: 0.7461 (ptm) cc_final: 0.6129 (tmm) REVERT: E 54 SER cc_start: 0.7810 (p) cc_final: 0.7420 (t) REVERT: E 135 PHE cc_start: 0.8296 (m-80) cc_final: 0.8002 (m-10) REVERT: E 205 ASP cc_start: 0.7481 (t70) cc_final: 0.6571 (m-30) REVERT: E 213 CYS cc_start: 0.8757 (t) cc_final: 0.8528 (t) REVERT: E 218 ASP cc_start: 0.8724 (m-30) cc_final: 0.8060 (t0) REVERT: E 250 VAL cc_start: 0.8129 (t) cc_final: 0.7860 (t) REVERT: E 267 PHE cc_start: 0.9049 (m-80) cc_final: 0.8668 (m-80) REVERT: E 293 ASN cc_start: 0.8893 (m110) cc_final: 0.8521 (m110) REVERT: E 313 MET cc_start: 0.8286 (mtm) cc_final: 0.7216 (mtp) REVERT: E 351 PHE cc_start: 0.7731 (m-80) cc_final: 0.7160 (m-80) REVERT: E 398 MET cc_start: 0.6785 (mtm) cc_final: 0.6536 (mtm) REVERT: J 14 VAL cc_start: 0.9243 (t) cc_final: 0.9019 (p) REVERT: J 124 LYS cc_start: 0.8657 (mttm) cc_final: 0.8456 (tptp) REVERT: J 214 ARG cc_start: 0.8797 (ttp80) cc_final: 0.8285 (mmm-85) REVERT: J 267 PHE cc_start: 0.9027 (m-80) cc_final: 0.8685 (m-80) REVERT: J 313 MET cc_start: 0.7698 (mtm) cc_final: 0.6565 (mtp) REVERT: J 377 MET cc_start: 0.7996 (ttt) cc_final: 0.7604 (tmm) REVERT: J 388 TRP cc_start: 0.8348 (m-10) cc_final: 0.8043 (m-10) REVERT: C 36 MET cc_start: 0.7722 (ptm) cc_final: 0.6579 (tmm) REVERT: C 69 ASP cc_start: 0.7816 (t0) cc_final: 0.7532 (m-30) REVERT: C 205 ASP cc_start: 0.7781 (t70) cc_final: 0.6496 (m-30) REVERT: C 257 THR cc_start: 0.9184 (m) cc_final: 0.8876 (p) REVERT: C 301 GLN cc_start: 0.8757 (mt0) cc_final: 0.8284 (pm20) REVERT: C 313 MET cc_start: 0.7839 (mtm) cc_final: 0.6763 (ttt) REVERT: C 351 PHE cc_start: 0.7908 (m-80) cc_final: 0.7428 (m-80) REVERT: L 18 ASN cc_start: 0.8786 (m-40) cc_final: 0.8523 (m110) REVERT: L 36 MET cc_start: 0.7919 (ptm) cc_final: 0.6662 (tmm) REVERT: L 213 CYS cc_start: 0.8932 (t) cc_final: 0.8672 (t) REVERT: L 260 VAL cc_start: 0.8802 (t) cc_final: 0.8321 (p) REVERT: L 301 GLN cc_start: 0.8677 (mt0) cc_final: 0.7985 (pm20) REVERT: L 395 PHE cc_start: 0.8973 (t80) cc_final: 0.8627 (t80) REVERT: A 36 MET cc_start: 0.7040 (ptm) cc_final: 0.5800 (tmm) REVERT: A 205 ASP cc_start: 0.7407 (t0) cc_final: 0.6167 (m-30) REVERT: A 237 SER cc_start: 0.9189 (m) cc_final: 0.8649 (t) REVERT: A 255 PHE cc_start: 0.7654 (m-80) cc_final: 0.7281 (m-80) REVERT: A 267 PHE cc_start: 0.9109 (m-80) cc_final: 0.8872 (m-80) REVERT: A 316 CYS cc_start: 0.8749 (t) cc_final: 0.8141 (t) REVERT: A 351 PHE cc_start: 0.7923 (m-80) cc_final: 0.7349 (m-80) REVERT: A 398 MET cc_start: 0.6971 (mtm) cc_final: 0.6688 (mtm) REVERT: A 413 MET cc_start: 0.7479 (tpp) cc_final: 0.7058 (mmm) REVERT: A 420 GLU cc_start: 0.8225 (tt0) cc_final: 0.7775 (tp30) REVERT: K 36 MET cc_start: 0.7031 (ptm) cc_final: 0.5981 (tmm) REVERT: K 54 SER cc_start: 0.7473 (p) cc_final: 0.6921 (t) REVERT: K 149 PHE cc_start: 0.8471 (t80) cc_final: 0.8066 (t80) REVERT: K 218 ASP cc_start: 0.8605 (m-30) cc_final: 0.8178 (t0) REVERT: K 237 SER cc_start: 0.9038 (m) cc_final: 0.8606 (t) REVERT: K 267 PHE cc_start: 0.9007 (m-80) cc_final: 0.8504 (m-80) REVERT: K 276 ILE cc_start: 0.8925 (tp) cc_final: 0.8715 (tp) REVERT: K 280 LYS cc_start: 0.8207 (ttmt) cc_final: 0.7935 (tttt) REVERT: K 377 MET cc_start: 0.7912 (ttp) cc_final: 0.7363 (tmm) REVERT: K 391 LEU cc_start: 0.9394 (tp) cc_final: 0.9060 (tp) REVERT: K 413 MET cc_start: 0.7986 (mmm) cc_final: 0.7593 (mmm) REVERT: K 420 GLU cc_start: 0.8113 (tt0) cc_final: 0.7790 (tp30) REVERT: B 21 TRP cc_start: 0.9156 (m100) cc_final: 0.8362 (m100) REVERT: B 147 MET cc_start: 0.8502 (tmm) cc_final: 0.8233 (tmm) REVERT: B 181 GLU cc_start: 0.9016 (pt0) cc_final: 0.8512 (pp20) REVERT: B 245 GLN cc_start: 0.8298 (mm-40) cc_final: 0.8018 (mm-40) REVERT: B 293 MET cc_start: 0.8171 (mtp) cc_final: 0.7792 (ptp) REVERT: B 297 LYS cc_start: 0.8720 (ptpt) cc_final: 0.8364 (mmtm) REVERT: B 299 MET cc_start: 0.9053 (mmp) cc_final: 0.8806 (mmm) REVERT: B 363 MET cc_start: 0.8330 (mtm) cc_final: 0.8025 (mtm) REVERT: F 90 PHE cc_start: 0.8360 (m-80) cc_final: 0.8052 (m-80) REVERT: F 163 ILE cc_start: 0.8577 (pt) cc_final: 0.8298 (pt) REVERT: F 164 MET cc_start: 0.8079 (mpp) cc_final: 0.7559 (mpp) REVERT: F 216 LYS cc_start: 0.8437 (mmtp) cc_final: 0.7886 (mmtm) REVERT: F 228 LEU cc_start: 0.8912 (mm) cc_final: 0.8604 (tp) REVERT: F 233 MET cc_start: 0.9289 (mtp) cc_final: 0.8965 (mtm) REVERT: G 6 HIS cc_start: 0.8889 (t70) cc_final: 0.8612 (t-170) REVERT: G 83 GLN cc_start: 0.8216 (mp10) cc_final: 0.7561 (tm-30) REVERT: G 90 PHE cc_start: 0.8170 (m-80) cc_final: 0.7916 (m-80) REVERT: G 163 ILE cc_start: 0.8757 (pt) cc_final: 0.8465 (pt) REVERT: G 164 MET cc_start: 0.8116 (mpp) cc_final: 0.7528 (mpp) REVERT: G 216 LYS cc_start: 0.8218 (mmtt) cc_final: 0.7906 (mmtm) REVERT: G 233 MET cc_start: 0.9123 (mtp) cc_final: 0.8817 (mtm) REVERT: G 276 ARG cc_start: 0.7656 (tpp-160) cc_final: 0.7416 (tpm170) REVERT: G 321 MET cc_start: 0.8187 (ptp) cc_final: 0.7855 (ptp) REVERT: D 21 TRP cc_start: 0.9105 (m100) cc_final: 0.8530 (m100) REVERT: D 127 CYS cc_start: 0.9059 (p) cc_final: 0.8858 (p) REVERT: D 147 MET cc_start: 0.8460 (ppp) cc_final: 0.8149 (ppp) REVERT: D 149 THR cc_start: 0.9460 (p) cc_final: 0.9175 (p) REVERT: D 299 MET cc_start: 0.9090 (mmm) cc_final: 0.8551 (mmm) REVERT: D 300 MET cc_start: 0.7965 (mtt) cc_final: 0.7701 (mtt) REVERT: D 323 MET cc_start: 0.8210 (mpp) cc_final: 0.7970 (mpp) REVERT: D 379 LYS cc_start: 0.9037 (mtpt) cc_final: 0.8777 (mtmm) REVERT: D 388 MET cc_start: 0.7440 (mtt) cc_final: 0.7030 (mtt) REVERT: I 22 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7484 (tm-30) REVERT: I 23 VAL cc_start: 0.7904 (t) cc_final: 0.7357 (t) REVERT: I 73 MET cc_start: 0.8300 (mmt) cc_final: 0.8067 (mmt) REVERT: I 147 MET cc_start: 0.8617 (ppp) cc_final: 0.8317 (tmm) REVERT: I 149 THR cc_start: 0.9411 (p) cc_final: 0.9183 (p) REVERT: I 163 ILE cc_start: 0.8766 (pt) cc_final: 0.8494 (pt) REVERT: I 164 MET cc_start: 0.8188 (mpp) cc_final: 0.7744 (mpp) REVERT: I 297 LYS cc_start: 0.8283 (ptpt) cc_final: 0.7972 (mmtt) REVERT: I 299 MET cc_start: 0.9030 (mmp) cc_final: 0.8765 (mmm) REVERT: I 306 ARG cc_start: 0.7972 (mtt90) cc_final: 0.7176 (mpt180) REVERT: I 328 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8456 (mm-30) REVERT: I 362 LYS cc_start: 0.9078 (tptt) cc_final: 0.8830 (tptp) REVERT: I 363 MET cc_start: 0.7988 (ptp) cc_final: 0.7607 (ptt) REVERT: H 101 TRP cc_start: 0.7522 (t60) cc_final: 0.7231 (t60) REVERT: H 147 MET cc_start: 0.8291 (tmm) cc_final: 0.7948 (tmm) REVERT: H 262 ARG cc_start: 0.7114 (mmp80) cc_final: 0.6636 (mmp80) REVERT: H 293 MET cc_start: 0.7691 (mtp) cc_final: 0.7243 (ptp) REVERT: H 300 MET cc_start: 0.7971 (mtt) cc_final: 0.7694 (mtm) outliers start: 0 outliers final: 0 residues processed: 798 average time/residue: 0.5071 time to fit residues: 673.2364 Evaluate side-chains 601 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 601 time to evaluate : 4.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 297 optimal weight: 9.9990 chunk 478 optimal weight: 7.9990 chunk 292 optimal weight: 10.0000 chunk 227 optimal weight: 7.9990 chunk 332 optimal weight: 6.9990 chunk 502 optimal weight: 9.9990 chunk 462 optimal weight: 0.2980 chunk 399 optimal weight: 0.0570 chunk 41 optimal weight: 5.9990 chunk 308 optimal weight: 50.0000 chunk 245 optimal weight: 0.0570 overall best weight: 2.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 226 ASN ** J 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN C 256 GLN ** L 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 11 GLN ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN B 291 GLN ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 GLN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 GLN ** I 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 131 GLN H 298 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.5225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 41454 Z= 0.153 Angle : 0.530 17.376 56328 Z= 0.268 Chirality : 0.043 0.187 6162 Planarity : 0.004 0.052 7326 Dihedral : 11.744 179.484 5826 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.02 % Allowed : 0.30 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.01 (0.12), residues: 5064 helix: -0.13 (0.11), residues: 2214 sheet: -0.07 (0.19), residues: 852 loop : -1.45 (0.15), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP B 101 HIS 0.008 0.001 HIS J 283 PHE 0.027 0.001 PHE G 378 TYR 0.036 0.001 TYR K 172 ARG 0.007 0.000 ARG C 2 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10128 Ramachandran restraints generated. 5064 Oldfield, 0 Emsley, 5064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 813 time to evaluate : 4.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 18 ASN cc_start: 0.8791 (m-40) cc_final: 0.8561 (m110) REVERT: E 36 MET cc_start: 0.7442 (ptm) cc_final: 0.6137 (tmm) REVERT: E 54 SER cc_start: 0.7787 (p) cc_final: 0.7385 (t) REVERT: E 135 PHE cc_start: 0.8251 (m-80) cc_final: 0.7759 (m-10) REVERT: E 205 ASP cc_start: 0.7498 (t70) cc_final: 0.6469 (m-30) REVERT: E 213 CYS cc_start: 0.8714 (t) cc_final: 0.8482 (t) REVERT: E 218 ASP cc_start: 0.8681 (m-30) cc_final: 0.7993 (t0) REVERT: E 250 VAL cc_start: 0.8266 (t) cc_final: 0.7879 (t) REVERT: E 267 PHE cc_start: 0.8997 (m-80) cc_final: 0.8626 (m-80) REVERT: E 293 ASN cc_start: 0.8888 (m110) cc_final: 0.8497 (m110) REVERT: E 313 MET cc_start: 0.8263 (mtm) cc_final: 0.7184 (mtp) REVERT: E 351 PHE cc_start: 0.7689 (m-80) cc_final: 0.7337 (m-80) REVERT: E 398 MET cc_start: 0.6753 (mtm) cc_final: 0.6505 (mtm) REVERT: J 14 VAL cc_start: 0.9227 (t) cc_final: 0.9003 (p) REVERT: J 214 ARG cc_start: 0.8782 (ttp80) cc_final: 0.8289 (mmm-85) REVERT: J 267 PHE cc_start: 0.8940 (m-80) cc_final: 0.8657 (m-80) REVERT: J 313 MET cc_start: 0.7661 (mtm) cc_final: 0.6552 (mtp) REVERT: J 377 MET cc_start: 0.7992 (ttt) cc_final: 0.7511 (tmm) REVERT: J 391 LEU cc_start: 0.9324 (tp) cc_final: 0.8879 (pp) REVERT: C 36 MET cc_start: 0.7994 (ptm) cc_final: 0.6544 (tmm) REVERT: C 69 ASP cc_start: 0.7735 (t0) cc_final: 0.7521 (m-30) REVERT: C 205 ASP cc_start: 0.7805 (t70) cc_final: 0.6541 (m-30) REVERT: C 257 THR cc_start: 0.9093 (m) cc_final: 0.8766 (p) REVERT: C 301 GLN cc_start: 0.8768 (mt0) cc_final: 0.8278 (pm20) REVERT: C 313 MET cc_start: 0.7778 (mtm) cc_final: 0.6777 (ttt) REVERT: C 351 PHE cc_start: 0.7849 (m-80) cc_final: 0.7424 (m-80) REVERT: L 36 MET cc_start: 0.7916 (ptm) cc_final: 0.6658 (tmm) REVERT: L 203 MET cc_start: 0.8930 (tpp) cc_final: 0.8659 (tpp) REVERT: L 260 VAL cc_start: 0.8756 (t) cc_final: 0.8268 (p) REVERT: L 301 GLN cc_start: 0.8631 (mt0) cc_final: 0.7933 (pm20) REVERT: L 395 PHE cc_start: 0.8958 (t80) cc_final: 0.8620 (t80) REVERT: A 36 MET cc_start: 0.7001 (ptm) cc_final: 0.5779 (tmm) REVERT: A 205 ASP cc_start: 0.7684 (t0) cc_final: 0.6255 (m-30) REVERT: A 237 SER cc_start: 0.9143 (m) cc_final: 0.8670 (t) REVERT: A 255 PHE cc_start: 0.7612 (m-80) cc_final: 0.7257 (m-80) REVERT: A 267 PHE cc_start: 0.9110 (m-80) cc_final: 0.8879 (m-80) REVERT: A 316 CYS cc_start: 0.8765 (t) cc_final: 0.8139 (t) REVERT: A 351 PHE cc_start: 0.7864 (m-80) cc_final: 0.7322 (m-80) REVERT: A 398 MET cc_start: 0.6927 (mtm) cc_final: 0.6661 (mtm) REVERT: A 413 MET cc_start: 0.7471 (tpp) cc_final: 0.7029 (mmm) REVERT: A 420 GLU cc_start: 0.8205 (tt0) cc_final: 0.7690 (tp30) REVERT: K 36 MET cc_start: 0.7042 (ptm) cc_final: 0.5949 (tmm) REVERT: K 149 PHE cc_start: 0.8424 (t80) cc_final: 0.8111 (t80) REVERT: K 218 ASP cc_start: 0.8471 (m-30) cc_final: 0.8150 (t0) REVERT: K 237 SER cc_start: 0.9114 (m) cc_final: 0.8822 (t) REVERT: K 255 PHE cc_start: 0.7756 (m-80) cc_final: 0.7231 (m-80) REVERT: K 267 PHE cc_start: 0.8895 (m-80) cc_final: 0.8507 (m-80) REVERT: K 276 ILE cc_start: 0.8928 (tp) cc_final: 0.8716 (tp) REVERT: K 280 LYS cc_start: 0.8115 (ttmt) cc_final: 0.7908 (tttt) REVERT: K 377 MET cc_start: 0.7970 (ttp) cc_final: 0.7371 (tmm) REVERT: K 391 LEU cc_start: 0.9364 (tp) cc_final: 0.9095 (tp) REVERT: K 420 GLU cc_start: 0.8118 (tt0) cc_final: 0.7794 (tp30) REVERT: B 118 ASP cc_start: 0.8393 (m-30) cc_final: 0.7763 (t70) REVERT: B 147 MET cc_start: 0.8462 (tmm) cc_final: 0.8239 (tmm) REVERT: B 181 GLU cc_start: 0.9043 (pt0) cc_final: 0.8547 (pp20) REVERT: B 245 GLN cc_start: 0.8222 (mm-40) cc_final: 0.7979 (mm-40) REVERT: B 293 MET cc_start: 0.8088 (mtp) cc_final: 0.7737 (ptp) REVERT: B 297 LYS cc_start: 0.8741 (ptpt) cc_final: 0.8399 (mmtm) REVERT: B 323 MET cc_start: 0.7870 (mpp) cc_final: 0.7659 (mpp) REVERT: B 363 MET cc_start: 0.8303 (mtm) cc_final: 0.8007 (mtm) REVERT: B 403 MET cc_start: 0.5793 (mmt) cc_final: 0.5217 (mmt) REVERT: F 90 PHE cc_start: 0.8391 (m-80) cc_final: 0.8083 (m-80) REVERT: F 163 ILE cc_start: 0.8509 (pt) cc_final: 0.8219 (pt) REVERT: F 164 MET cc_start: 0.8097 (mpp) cc_final: 0.7557 (mpp) REVERT: F 216 LYS cc_start: 0.8411 (mmtp) cc_final: 0.7959 (mmtm) REVERT: F 228 LEU cc_start: 0.8923 (mm) cc_final: 0.8584 (tp) REVERT: F 233 MET cc_start: 0.9298 (mtp) cc_final: 0.8954 (mtm) REVERT: F 253 LEU cc_start: 0.9151 (pp) cc_final: 0.8942 (pp) REVERT: F 300 MET cc_start: 0.7496 (mtm) cc_final: 0.7029 (mpp) REVERT: F 353 VAL cc_start: 0.8786 (p) cc_final: 0.8499 (t) REVERT: F 403 MET cc_start: 0.6247 (mmt) cc_final: 0.5784 (mmt) REVERT: G 50 TYR cc_start: 0.7739 (m-10) cc_final: 0.7407 (m-10) REVERT: G 83 GLN cc_start: 0.8210 (mp10) cc_final: 0.7531 (tm-30) REVERT: G 101 TRP cc_start: 0.7573 (t60) cc_final: 0.7245 (t60) REVERT: G 216 LYS cc_start: 0.8245 (mmtt) cc_final: 0.7865 (mmtm) REVERT: G 228 LEU cc_start: 0.9095 (mm) cc_final: 0.8736 (tp) REVERT: G 233 MET cc_start: 0.9063 (mtp) cc_final: 0.8818 (mtm) REVERT: G 276 ARG cc_start: 0.7735 (tpp-160) cc_final: 0.7495 (tpm170) REVERT: G 300 MET cc_start: 0.7214 (mtm) cc_final: 0.6837 (mtm) REVERT: G 321 MET cc_start: 0.8154 (ptp) cc_final: 0.7785 (ptp) REVERT: D 2 ARG cc_start: 0.7024 (mtm180) cc_final: 0.6222 (mtm-85) REVERT: D 6 HIS cc_start: 0.8724 (t70) cc_final: 0.8239 (t-170) REVERT: D 21 TRP cc_start: 0.8988 (m100) cc_final: 0.8399 (m100) REVERT: D 127 CYS cc_start: 0.9052 (p) cc_final: 0.8792 (p) REVERT: D 147 MET cc_start: 0.8457 (ppp) cc_final: 0.8179 (ppp) REVERT: D 200 TYR cc_start: 0.8433 (m-80) cc_final: 0.8149 (m-80) REVERT: D 291 GLN cc_start: 0.8608 (mt0) cc_final: 0.8383 (mt0) REVERT: D 293 MET cc_start: 0.7731 (pmm) cc_final: 0.7485 (pmm) REVERT: D 299 MET cc_start: 0.9082 (mmm) cc_final: 0.8571 (mmm) REVERT: D 300 MET cc_start: 0.7574 (mtt) cc_final: 0.7222 (mtt) REVERT: D 323 MET cc_start: 0.8054 (mpp) cc_final: 0.7815 (mpp) REVERT: D 379 LYS cc_start: 0.9018 (mtpt) cc_final: 0.8743 (mtmm) REVERT: D 388 MET cc_start: 0.7416 (mtt) cc_final: 0.7017 (mtt) REVERT: I 22 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7674 (tm-30) REVERT: I 73 MET cc_start: 0.8285 (mmt) cc_final: 0.8065 (mmt) REVERT: I 147 MET cc_start: 0.8628 (ppp) cc_final: 0.8336 (tmm) REVERT: I 149 THR cc_start: 0.9411 (p) cc_final: 0.9198 (p) REVERT: I 163 ILE cc_start: 0.8687 (pt) cc_final: 0.8413 (pt) REVERT: I 164 MET cc_start: 0.8172 (mpp) cc_final: 0.7762 (mpp) REVERT: I 297 LYS cc_start: 0.8316 (ptpt) cc_final: 0.7978 (mmtt) REVERT: I 299 MET cc_start: 0.8968 (mmp) cc_final: 0.8656 (mmm) REVERT: I 306 ARG cc_start: 0.8130 (mtt90) cc_final: 0.7223 (mpt180) REVERT: I 328 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8411 (mm-30) REVERT: I 362 LYS cc_start: 0.9106 (tptt) cc_final: 0.8877 (tptp) REVERT: I 363 MET cc_start: 0.7928 (ptp) cc_final: 0.7613 (ptt) REVERT: H 101 TRP cc_start: 0.7457 (t60) cc_final: 0.7121 (t60) REVERT: H 147 MET cc_start: 0.8289 (tmm) cc_final: 0.7964 (tmm) REVERT: H 262 ARG cc_start: 0.7097 (mmp80) cc_final: 0.6738 (mmp80) REVERT: H 293 MET cc_start: 0.7794 (mtp) cc_final: 0.7359 (ptp) REVERT: H 300 MET cc_start: 0.7874 (mtt) cc_final: 0.7578 (mtm) outliers start: 1 outliers final: 0 residues processed: 814 average time/residue: 0.5136 time to fit residues: 698.6873 Evaluate side-chains 619 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 619 time to evaluate : 4.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 317 optimal weight: 6.9990 chunk 425 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 368 optimal weight: 10.0000 chunk 59 optimal weight: 0.0050 chunk 111 optimal weight: 20.0000 chunk 400 optimal weight: 20.0000 chunk 167 optimal weight: 10.0000 chunk 411 optimal weight: 0.0050 chunk 50 optimal weight: 7.9990 chunk 73 optimal weight: 0.8980 overall best weight: 2.9812 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 226 ASN ** J 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN ** L 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 11 GLN ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 ASN B 83 GLN B 291 GLN ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 GLN ** F 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 298 ASN H 334 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.094665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.084147 restraints weight = 125512.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.086755 restraints weight = 73013.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.088566 restraints weight = 46718.619| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.5343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 41454 Z= 0.156 Angle : 0.523 8.789 56328 Z= 0.265 Chirality : 0.043 0.181 6162 Planarity : 0.004 0.050 7326 Dihedral : 11.710 179.346 5826 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.02 % Allowed : 0.28 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.12), residues: 5064 helix: -0.04 (0.11), residues: 2208 sheet: 0.02 (0.19), residues: 846 loop : -1.45 (0.14), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP B 101 HIS 0.009 0.001 HIS H 6 PHE 0.023 0.001 PHE E 149 TYR 0.034 0.001 TYR J 24 ARG 0.009 0.000 ARG B 380 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11253.89 seconds wall clock time: 203 minutes 49.87 seconds (12229.87 seconds total)