Starting phenix.real_space_refine on Sun Mar 24 10:01:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dpw_7975/03_2024/6dpw_7975_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dpw_7975/03_2024/6dpw_7975.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dpw_7975/03_2024/6dpw_7975.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dpw_7975/03_2024/6dpw_7975.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dpw_7975/03_2024/6dpw_7975_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dpw_7975/03_2024/6dpw_7975_updated.pdb" } resolution = 3.5 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= -0.022 sd= 0.922 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 6 5.21 5 S 282 5.16 5 C 25620 2.51 5 N 6966 2.21 5 O 7902 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 64": "NH1" <-> "NH2" Residue "A ARG 390": "NH1" <-> "NH2" Residue "C ARG 64": "NH1" <-> "NH2" Residue "C PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 390": "NH1" <-> "NH2" Residue "E ARG 64": "NH1" <-> "NH2" Residue "E PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 390": "NH1" <-> "NH2" Residue "J ARG 64": "NH1" <-> "NH2" Residue "J PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 390": "NH1" <-> "NH2" Residue "K ARG 64": "NH1" <-> "NH2" Residue "K PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 390": "NH1" <-> "NH2" Residue "L ARG 64": "NH1" <-> "NH2" Residue "L PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 390": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 40812 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3369 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 3369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3369 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 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: "E" Number of atoms: 3369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3369 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 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: "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: "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: "J" Number of atoms: 3369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3369 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "K" Number of atoms: 3369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3369 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "L" Number of atoms: 3369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3369 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 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: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GSP': 1} Classifications: {'undetermined': 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: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GSP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GSP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GSP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GSP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GSP': 1} Classifications: {'undetermined': 1} Chain: "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: "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: "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} Time building chain proxies: 19.85, per 1000 atoms: 0.49 Number of scatterers: 40812 At special positions: 0 Unit cell: (171.57, 87.78, 211.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 282 16.00 P 36 15.00 Mg 6 11.99 O 7902 8.00 N 6966 7.00 C 25620 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: 16.16 Conformation dependent library (CDL) restraints added in 6.0 seconds 10236 Ramachandran restraints generated. 5118 Oldfield, 0 Emsley, 5118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9552 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 252 helices and 30 sheets defined 50.1% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.31 Creating SS restraints... Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 48 through 51 removed outlier: 3.888A pdb=" N THR A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 48 through 51' Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.630A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 115 through 128 removed outlier: 3.593A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 161 removed outlier: 4.096A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.557A pdb=" N LEU A 189 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR A 190 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR A 194 " --> pdb=" O THR A 191 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 195 " --> pdb=" O HIS A 192 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N GLU A 196 " --> pdb=" O THR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 217 Processing helix chain 'A' and resid 224 through 243 removed outlier: 4.398A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 removed outlier: 4.436A pdb=" N GLN A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 283 removed outlier: 4.832A pdb=" N HIS A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 296 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 325 through 337 Processing helix chain 'A' and resid 382 through 401 removed outlier: 3.899A pdb=" N ALA A 400 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 415 through 436 removed outlier: 3.568A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 27 Processing helix chain 'B' and resid 41 through 47 removed outlier: 3.558A pdb=" N GLU B 47 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 73 through 80 Processing helix chain 'B' and resid 84 through 86 No H-bonds generated for 'chain 'B' and resid 84 through 86' Processing helix chain 'B' and resid 89 through 91 No H-bonds generated for 'chain 'B' and resid 89 through 91' Processing helix chain 'B' and resid 103 through 107 Processing helix chain 'B' and resid 110 through 128 removed outlier: 4.491A pdb=" N ASP B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N SER B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 160 Processing helix chain 'B' and resid 183 through 197 removed outlier: 3.778A pdb=" N GLU B 196 " --> pdb=" O HIS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 215 Processing helix chain 'B' and resid 224 through 243 removed outlier: 3.648A pdb=" N THR B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N CYS B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N LEU B 242 " --> pdb=" O VAL B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 259 Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 288 through 295 Processing helix chain 'B' and resid 298 through 300 No H-bonds generated for 'chain 'B' and resid 298 through 300' Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 325 through 338 Processing helix chain 'B' and resid 340 through 342 No H-bonds generated for 'chain 'B' and resid 340 through 342' Processing helix chain 'B' and resid 382 through 401 removed outlier: 4.324A pdb=" N ARG B 400 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 4.136A pdb=" N GLU B 411 " --> pdb=" O TRP B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 437 Processing helix chain 'C' and resid 10 through 28 Processing helix chain 'C' and resid 48 through 51 removed outlier: 3.885A pdb=" N THR C 51 " --> pdb=" O SER C 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 48 through 51' Processing helix chain 'C' and resid 73 through 80 removed outlier: 3.633A pdb=" N VAL C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 91 No H-bonds generated for 'chain 'C' and resid 89 through 91' Processing helix chain 'C' and resid 103 through 107 Processing helix chain 'C' and resid 111 through 113 No H-bonds generated for 'chain 'C' and resid 111 through 113' Processing helix chain 'C' and resid 115 through 128 removed outlier: 3.592A pdb=" N GLN C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 161 removed outlier: 4.101A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.563A pdb=" N LEU C 189 " --> pdb=" O ASN C 186 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR C 190 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR C 194 " --> pdb=" O THR C 191 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU C 195 " --> pdb=" O HIS C 192 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N GLU C 196 " --> pdb=" O THR C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 217 Processing helix chain 'C' and resid 224 through 243 removed outlier: 4.396A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LEU C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 259 removed outlier: 4.438A pdb=" N GLN C 256 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR C 257 " --> pdb=" O THR C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 283 removed outlier: 4.836A pdb=" N HIS C 283 " --> pdb=" O GLU C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 296 Processing helix chain 'C' and resid 298 through 300 No H-bonds generated for 'chain 'C' and resid 298 through 300' Processing helix chain 'C' and resid 307 through 309 No H-bonds generated for 'chain 'C' and resid 307 through 309' Processing helix chain 'C' and resid 325 through 337 Processing helix chain 'C' and resid 382 through 401 removed outlier: 3.898A pdb=" N ALA C 400 " --> pdb=" O LEU C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'C' and resid 415 through 436 removed outlier: 3.567A pdb=" N SER C 419 " --> pdb=" O GLU C 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 27 Processing helix chain 'D' and resid 41 through 47 removed outlier: 3.559A pdb=" N GLU D 47 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 51 No H-bonds generated for 'chain 'D' and resid 49 through 51' Processing helix chain 'D' and resid 73 through 80 Processing helix chain 'D' and resid 84 through 86 No H-bonds generated for 'chain 'D' and resid 84 through 86' Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 103 through 107 Processing helix chain 'D' and resid 110 through 128 removed outlier: 4.491A pdb=" N ASP D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N SER D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 160 Processing helix chain 'D' and resid 183 through 197 removed outlier: 3.778A pdb=" N GLU D 196 " --> pdb=" O HIS D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 215 Processing helix chain 'D' and resid 224 through 243 removed outlier: 3.650A pdb=" N THR D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N CYS D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N LEU D 242 " --> pdb=" O VAL D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 259 Processing helix chain 'D' and resid 280 through 283 Processing helix chain 'D' and resid 288 through 295 Processing helix chain 'D' and resid 298 through 300 No H-bonds generated for 'chain 'D' and resid 298 through 300' Processing helix chain 'D' and resid 307 through 309 No H-bonds generated for 'chain 'D' and resid 307 through 309' Processing helix chain 'D' and resid 325 through 338 Processing helix chain 'D' and resid 340 through 342 No H-bonds generated for 'chain 'D' and resid 340 through 342' Processing helix chain 'D' and resid 382 through 401 removed outlier: 4.324A pdb=" N ARG D 400 " --> pdb=" O ALA D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 411 removed outlier: 4.135A pdb=" N GLU D 411 " --> pdb=" O TRP D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 437 Processing helix chain 'E' and resid 10 through 28 Processing helix chain 'E' and resid 48 through 51 removed outlier: 3.887A pdb=" N THR E 51 " --> pdb=" O SER E 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 48 through 51' Processing helix chain 'E' and resid 73 through 80 removed outlier: 3.630A pdb=" N VAL E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 103 through 107 Processing helix chain 'E' and resid 111 through 113 No H-bonds generated for 'chain 'E' and resid 111 through 113' Processing helix chain 'E' and resid 115 through 128 removed outlier: 3.594A pdb=" N GLN E 128 " --> pdb=" O LYS E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 161 removed outlier: 4.096A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 197 removed outlier: 3.555A pdb=" N LEU E 189 " --> pdb=" O ASN E 186 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR E 190 " --> pdb=" O SER E 187 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR E 194 " --> pdb=" O THR E 191 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU E 195 " --> pdb=" O HIS E 192 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N GLU E 196 " --> pdb=" O THR E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 217 Processing helix chain 'E' and resid 224 through 243 removed outlier: 4.399A pdb=" N SER E 241 " --> pdb=" O SER E 237 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N LEU E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 259 removed outlier: 4.437A pdb=" N GLN E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR E 257 " --> pdb=" O THR E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 283 removed outlier: 4.833A pdb=" N HIS E 283 " --> pdb=" O GLU E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 296 Processing helix chain 'E' and resid 298 through 300 No H-bonds generated for 'chain 'E' and resid 298 through 300' Processing helix chain 'E' and resid 307 through 309 No H-bonds generated for 'chain 'E' and resid 307 through 309' Processing helix chain 'E' and resid 325 through 337 Processing helix chain 'E' and resid 382 through 401 removed outlier: 3.900A pdb=" N ALA E 400 " --> pdb=" O LEU E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 Processing helix chain 'E' and resid 415 through 436 removed outlier: 3.568A pdb=" N SER E 419 " --> pdb=" O GLU E 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 27 Processing helix chain 'F' and resid 41 through 47 removed outlier: 3.557A pdb=" N GLU F 47 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 51 No H-bonds generated for 'chain 'F' and resid 49 through 51' Processing helix chain 'F' and resid 73 through 80 Processing helix chain 'F' and resid 84 through 86 No H-bonds generated for 'chain 'F' and resid 84 through 86' Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 103 through 107 Processing helix chain 'F' and resid 110 through 128 removed outlier: 4.490A pdb=" N ASP F 116 " --> pdb=" O ALA F 112 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N SER F 117 " --> pdb=" O GLU F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 160 Processing helix chain 'F' and resid 183 through 197 removed outlier: 3.777A pdb=" N GLU F 196 " --> pdb=" O HIS F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 215 Processing helix chain 'F' and resid 224 through 243 removed outlier: 3.649A pdb=" N THR F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N CYS F 241 " --> pdb=" O GLY F 237 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N LEU F 242 " --> pdb=" O VAL F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 259 Processing helix chain 'F' and resid 280 through 283 Processing helix chain 'F' and resid 288 through 295 Processing helix chain 'F' and resid 298 through 300 No H-bonds generated for 'chain 'F' and resid 298 through 300' Processing helix chain 'F' and resid 307 through 309 No H-bonds generated for 'chain 'F' and resid 307 through 309' Processing helix chain 'F' and resid 325 through 338 Processing helix chain 'F' and resid 340 through 342 No H-bonds generated for 'chain 'F' and resid 340 through 342' Processing helix chain 'F' and resid 382 through 401 removed outlier: 4.325A pdb=" N ARG F 400 " --> pdb=" O ALA F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 411 removed outlier: 4.135A pdb=" N GLU F 411 " --> pdb=" O TRP F 407 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 437 Processing helix chain 'G' and resid 10 through 27 Processing helix chain 'G' and resid 41 through 47 removed outlier: 3.556A pdb=" N GLU G 47 " --> pdb=" O LEU G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 51 No H-bonds generated for 'chain 'G' and resid 49 through 51' Processing helix chain 'G' and resid 73 through 80 Processing helix chain 'G' and resid 84 through 86 No H-bonds generated for 'chain 'G' and resid 84 through 86' Processing helix chain 'G' and resid 89 through 91 No H-bonds generated for 'chain 'G' and resid 89 through 91' Processing helix chain 'G' and resid 103 through 107 Processing helix chain 'G' and resid 110 through 128 removed outlier: 4.492A pdb=" N ASP G 116 " --> pdb=" O ALA G 112 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N SER G 117 " --> pdb=" O GLU G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 160 Processing helix chain 'G' and resid 183 through 197 removed outlier: 3.777A pdb=" N GLU G 196 " --> pdb=" O HIS G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 215 Processing helix chain 'G' and resid 224 through 243 removed outlier: 3.649A pdb=" N THR G 239 " --> pdb=" O MET G 235 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N CYS G 241 " --> pdb=" O GLY G 237 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N LEU G 242 " --> pdb=" O VAL G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 259 Processing helix chain 'G' and resid 280 through 283 Processing helix chain 'G' and resid 288 through 295 Processing helix chain 'G' and resid 298 through 300 No H-bonds generated for 'chain 'G' and resid 298 through 300' Processing helix chain 'G' and resid 307 through 309 No H-bonds generated for 'chain 'G' and resid 307 through 309' Processing helix chain 'G' and resid 325 through 338 Processing helix chain 'G' and resid 340 through 342 No H-bonds generated for 'chain 'G' and resid 340 through 342' Processing helix chain 'G' and resid 382 through 401 removed outlier: 4.324A pdb=" N ARG G 400 " --> pdb=" O ALA G 397 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 411 removed outlier: 4.135A pdb=" N GLU G 411 " --> pdb=" O TRP G 407 " (cutoff:3.500A) Processing helix chain 'G' and resid 415 through 437 Processing helix chain 'H' and resid 10 through 27 Processing helix chain 'H' and resid 41 through 47 removed outlier: 3.557A pdb=" N GLU H 47 " --> pdb=" O LEU H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 51 No H-bonds generated for 'chain 'H' and resid 49 through 51' Processing helix chain 'H' and resid 73 through 80 Processing helix chain 'H' and resid 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' Processing helix chain 'H' and resid 89 through 91 No H-bonds generated for 'chain 'H' and resid 89 through 91' Processing helix chain 'H' and resid 103 through 107 Processing helix chain 'H' and resid 110 through 128 removed outlier: 4.494A pdb=" N ASP H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N SER H 117 " --> pdb=" O GLU H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 160 Processing helix chain 'H' and resid 183 through 197 removed outlier: 3.778A pdb=" N GLU H 196 " --> pdb=" O HIS H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 215 Processing helix chain 'H' and resid 224 through 243 removed outlier: 3.648A pdb=" N THR H 239 " --> pdb=" O MET H 235 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N CYS H 241 " --> pdb=" O GLY H 237 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N LEU H 242 " --> pdb=" O VAL H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 259 Processing helix chain 'H' and resid 280 through 283 Processing helix chain 'H' and resid 288 through 295 Processing helix chain 'H' and resid 298 through 300 No H-bonds generated for 'chain 'H' and resid 298 through 300' Processing helix chain 'H' and resid 307 through 309 No H-bonds generated for 'chain 'H' and resid 307 through 309' Processing helix chain 'H' and resid 325 through 338 Processing helix chain 'H' and resid 340 through 342 No H-bonds generated for 'chain 'H' and resid 340 through 342' Processing helix chain 'H' and resid 382 through 401 removed outlier: 4.325A pdb=" N ARG H 400 " --> pdb=" O ALA H 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 405 through 411 removed outlier: 4.134A pdb=" N GLU H 411 " --> pdb=" O TRP H 407 " (cutoff:3.500A) Processing helix chain 'H' and resid 415 through 437 Processing helix chain 'I' and resid 10 through 27 Processing helix chain 'I' and resid 41 through 47 removed outlier: 3.557A pdb=" N GLU I 47 " --> pdb=" O LEU I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 51 No H-bonds generated for 'chain 'I' and resid 49 through 51' Processing helix chain 'I' and resid 73 through 80 Processing helix chain 'I' and resid 84 through 86 No H-bonds generated for 'chain 'I' and resid 84 through 86' Processing helix chain 'I' and resid 89 through 91 No H-bonds generated for 'chain 'I' and resid 89 through 91' Processing helix chain 'I' and resid 103 through 107 Processing helix chain 'I' and resid 110 through 128 removed outlier: 4.493A pdb=" N ASP I 116 " --> pdb=" O ALA I 112 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N SER I 117 " --> pdb=" O GLU I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 160 Processing helix chain 'I' and resid 183 through 197 removed outlier: 3.778A pdb=" N GLU I 196 " --> pdb=" O HIS I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 215 Processing helix chain 'I' and resid 224 through 243 removed outlier: 3.647A pdb=" N THR I 239 " --> pdb=" O MET I 235 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N CYS I 241 " --> pdb=" O GLY I 237 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N LEU I 242 " --> pdb=" O VAL I 238 " (cutoff:3.500A) Processing helix chain 'I' and resid 252 through 259 Processing helix chain 'I' and resid 280 through 283 Processing helix chain 'I' and resid 288 through 295 Processing helix chain 'I' and resid 298 through 300 No H-bonds generated for 'chain 'I' and resid 298 through 300' Processing helix chain 'I' and resid 307 through 309 No H-bonds generated for 'chain 'I' and resid 307 through 309' Processing helix chain 'I' and resid 325 through 338 Processing helix chain 'I' and resid 340 through 342 No H-bonds generated for 'chain 'I' and resid 340 through 342' Processing helix chain 'I' and resid 382 through 401 removed outlier: 4.325A pdb=" N ARG I 400 " --> pdb=" O ALA I 397 " (cutoff:3.500A) Processing helix chain 'I' and resid 405 through 411 removed outlier: 4.135A pdb=" N GLU I 411 " --> pdb=" O TRP I 407 " (cutoff:3.500A) Processing helix chain 'I' and resid 415 through 437 Processing helix chain 'J' and resid 10 through 28 Processing helix chain 'J' and resid 48 through 51 removed outlier: 3.889A pdb=" N THR J 51 " --> pdb=" O SER J 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 48 through 51' Processing helix chain 'J' and resid 73 through 80 removed outlier: 3.631A pdb=" N VAL J 78 " --> pdb=" O VAL J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 91 No H-bonds generated for 'chain 'J' and resid 89 through 91' Processing helix chain 'J' and resid 103 through 107 Processing helix chain 'J' and resid 111 through 113 No H-bonds generated for 'chain 'J' and resid 111 through 113' Processing helix chain 'J' and resid 115 through 128 removed outlier: 3.593A pdb=" N GLN J 128 " --> pdb=" O LYS J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 144 through 161 removed outlier: 4.096A pdb=" N THR J 150 " --> pdb=" O GLY J 146 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 197 removed outlier: 3.555A pdb=" N LEU J 189 " --> pdb=" O ASN J 186 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR J 190 " --> pdb=" O SER J 187 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR J 194 " --> pdb=" O THR J 191 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU J 195 " --> pdb=" O HIS J 192 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N GLU J 196 " --> pdb=" O THR J 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 217 Processing helix chain 'J' and resid 224 through 243 removed outlier: 4.397A pdb=" N SER J 241 " --> pdb=" O SER J 237 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N LEU J 242 " --> pdb=" O ILE J 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 252 through 259 removed outlier: 4.439A pdb=" N GLN J 256 " --> pdb=" O LEU J 252 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR J 257 " --> pdb=" O THR J 253 " (cutoff:3.500A) Processing helix chain 'J' and resid 278 through 283 removed outlier: 4.832A pdb=" N HIS J 283 " --> pdb=" O GLU J 279 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 296 Processing helix chain 'J' and resid 298 through 300 No H-bonds generated for 'chain 'J' and resid 298 through 300' Processing helix chain 'J' and resid 307 through 309 No H-bonds generated for 'chain 'J' and resid 307 through 309' Processing helix chain 'J' and resid 325 through 337 Processing helix chain 'J' and resid 382 through 401 removed outlier: 3.901A pdb=" N ALA J 400 " --> pdb=" O LEU J 397 " (cutoff:3.500A) Processing helix chain 'J' and resid 405 through 410 Processing helix chain 'J' and resid 415 through 436 removed outlier: 3.568A pdb=" N SER J 419 " --> pdb=" O GLU J 415 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 28 Processing helix chain 'K' and resid 48 through 51 removed outlier: 3.887A pdb=" N THR K 51 " --> pdb=" O SER K 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 48 through 51' Processing helix chain 'K' and resid 73 through 80 removed outlier: 3.634A pdb=" N VAL K 78 " --> pdb=" O VAL K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 91 No H-bonds generated for 'chain 'K' and resid 89 through 91' Processing helix chain 'K' and resid 103 through 107 Processing helix chain 'K' and resid 111 through 113 No H-bonds generated for 'chain 'K' and resid 111 through 113' Processing helix chain 'K' and resid 115 through 128 removed outlier: 3.592A pdb=" N GLN K 128 " --> pdb=" O LYS K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 144 through 161 removed outlier: 4.100A pdb=" N THR K 150 " --> pdb=" O GLY K 146 " (cutoff:3.500A) Processing helix chain 'K' and resid 182 through 197 removed outlier: 3.561A pdb=" N LEU K 189 " --> pdb=" O ASN K 186 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR K 190 " --> pdb=" O SER K 187 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR K 194 " --> pdb=" O THR K 191 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU K 195 " --> pdb=" O HIS K 192 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N GLU K 196 " --> pdb=" O THR K 193 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 217 Processing helix chain 'K' and resid 224 through 243 removed outlier: 4.396A pdb=" N SER K 241 " --> pdb=" O SER K 237 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N LEU K 242 " --> pdb=" O ILE K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 252 through 259 removed outlier: 4.439A pdb=" N GLN K 256 " --> pdb=" O LEU K 252 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR K 257 " --> pdb=" O THR K 253 " (cutoff:3.500A) Processing helix chain 'K' and resid 278 through 283 removed outlier: 4.832A pdb=" N HIS K 283 " --> pdb=" O GLU K 279 " (cutoff:3.500A) Processing helix chain 'K' and resid 288 through 296 Processing helix chain 'K' and resid 298 through 300 No H-bonds generated for 'chain 'K' and resid 298 through 300' Processing helix chain 'K' and resid 307 through 309 No H-bonds generated for 'chain 'K' and resid 307 through 309' Processing helix chain 'K' and resid 325 through 337 Processing helix chain 'K' and resid 382 through 401 removed outlier: 3.901A pdb=" N ALA K 400 " --> pdb=" O LEU K 397 " (cutoff:3.500A) Processing helix chain 'K' and resid 405 through 410 Processing helix chain 'K' and resid 415 through 436 removed outlier: 3.568A pdb=" N SER K 419 " --> pdb=" O GLU K 415 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 28 Processing helix chain 'L' and resid 48 through 51 removed outlier: 3.887A pdb=" N THR L 51 " --> pdb=" O SER L 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 48 through 51' Processing helix chain 'L' and resid 73 through 80 removed outlier: 3.632A pdb=" N VAL L 78 " --> pdb=" O VAL L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 89 through 91 No H-bonds generated for 'chain 'L' and resid 89 through 91' Processing helix chain 'L' and resid 103 through 107 Processing helix chain 'L' and resid 111 through 113 No H-bonds generated for 'chain 'L' and resid 111 through 113' Processing helix chain 'L' and resid 115 through 128 removed outlier: 3.593A pdb=" N GLN L 128 " --> pdb=" O LYS L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 144 through 161 removed outlier: 4.098A pdb=" N THR L 150 " --> pdb=" O GLY L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 197 removed outlier: 3.557A pdb=" N LEU L 189 " --> pdb=" O ASN L 186 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR L 190 " --> pdb=" O SER L 187 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR L 194 " --> pdb=" O THR L 191 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU L 195 " --> pdb=" O HIS L 192 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N GLU L 196 " --> pdb=" O THR L 193 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 217 Processing helix chain 'L' and resid 224 through 243 removed outlier: 4.396A pdb=" N SER L 241 " --> pdb=" O SER L 237 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N LEU L 242 " --> pdb=" O ILE L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 252 through 259 removed outlier: 4.440A pdb=" N GLN L 256 " --> pdb=" O LEU L 252 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR L 257 " --> pdb=" O THR L 253 " (cutoff:3.500A) Processing helix chain 'L' and resid 278 through 283 removed outlier: 4.833A pdb=" N HIS L 283 " --> pdb=" O GLU L 279 " (cutoff:3.500A) Processing helix chain 'L' and resid 288 through 296 Processing helix chain 'L' and resid 298 through 300 No H-bonds generated for 'chain 'L' and resid 298 through 300' Processing helix chain 'L' and resid 307 through 309 No H-bonds generated for 'chain 'L' and resid 307 through 309' Processing helix chain 'L' and resid 325 through 337 Processing helix chain 'L' and resid 382 through 401 removed outlier: 3.901A pdb=" N ALA L 400 " --> pdb=" O LEU L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 405 through 410 Processing helix chain 'L' and resid 415 through 436 removed outlier: 3.568A pdb=" N SER L 419 " --> pdb=" O GLU L 415 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.011A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLY A 134 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ILE A 7 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU A 136 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N VAL A 9 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N PHE A 138 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N SER A 165 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N VAL A 137 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU A 167 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N HIS A 139 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N PHE A 169 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N CYS A 200 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N SER A 170 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N PHE A 202 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TYR A 172 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N VAL A 204 " --> pdb=" O TYR A 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= C, first strand: chain 'A' and resid 269 through 273 removed outlier: 3.589A pdb=" N ALA A 314 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 92 through 94 removed outlier: 7.896A pdb=" N VAL B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU B 67 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N ILE B 66 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N HIS B 6 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL B 68 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLN B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N VAL B 5 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N PHE B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ILE B 7 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ALA B 9 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N HIS B 139 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE B 165 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N LEU B 137 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ASN B 167 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N HIS B 139 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N PHE B 169 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLU B 200 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N SER B 170 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N TYR B 202 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL B 172 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE B 204 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N ASP B 205 " --> pdb=" O PRO B 270 " (cutoff:3.500A) removed outlier: 11.562A pdb=" N PHE B 272 " --> pdb=" O ASP B 205 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N PHE B 267 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N SER B 381 " --> pdb=" O PHE B 267 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 53 through 56 removed outlier: 3.938A pdb=" N LYS B 60 " --> pdb=" O ALA B 56 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 92 through 94 removed outlier: 8.012A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N VAL C 66 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLY C 134 " --> pdb=" O ILE C 5 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ILE C 7 " --> pdb=" O GLY C 134 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU C 136 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N VAL C 9 " --> pdb=" O LEU C 136 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N PHE C 138 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N SER C 165 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N VAL C 137 " --> pdb=" O SER C 165 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU C 167 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N HIS C 139 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N PHE C 169 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N CYS C 200 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N SER C 170 " --> pdb=" O CYS C 200 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N PHE C 202 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N TYR C 172 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N VAL C 204 " --> pdb=" O TYR C 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'C' and resid 53 through 55 Processing sheet with id= H, first strand: chain 'C' and resid 269 through 273 removed outlier: 3.597A pdb=" N ALA C 314 " --> pdb=" O ASN C 380 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 92 through 94 removed outlier: 7.896A pdb=" N VAL D 93 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU D 67 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N ILE D 66 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N HIS D 6 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N VAL D 68 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLN D 8 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N VAL D 5 " --> pdb=" O GLN D 133 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N PHE D 135 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ILE D 7 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU D 137 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ALA D 9 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N HIS D 139 " --> pdb=" O ALA D 9 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE D 165 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N LEU D 137 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ASN D 167 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N HIS D 139 " --> pdb=" O ASN D 167 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N PHE D 169 " --> pdb=" O HIS D 139 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLU D 200 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N SER D 170 " --> pdb=" O GLU D 200 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N TYR D 202 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL D 172 " --> pdb=" O TYR D 202 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE D 204 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ASP D 205 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 11.561A pdb=" N PHE D 272 " --> pdb=" O ASP D 205 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N PHE D 267 " --> pdb=" O SER D 381 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N SER D 381 " --> pdb=" O PHE D 267 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 53 through 56 removed outlier: 3.938A pdb=" N LYS D 60 " --> pdb=" O ALA D 56 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 92 through 94 removed outlier: 8.011A pdb=" N ILE E 93 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N PHE E 67 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N VAL E 66 " --> pdb=" O CYS E 4 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N SER E 6 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N VAL E 68 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N HIS E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLY E 134 " --> pdb=" O ILE E 5 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N ILE E 7 " --> pdb=" O GLY E 134 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU E 136 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N VAL E 9 " --> pdb=" O LEU E 136 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE E 138 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N SER E 165 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N VAL E 137 " --> pdb=" O SER E 165 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU E 167 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N HIS E 139 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N PHE E 169 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N CYS E 200 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N SER E 170 " --> pdb=" O CYS E 200 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N PHE E 202 " --> pdb=" O SER E 170 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TYR E 172 " --> pdb=" O PHE E 202 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL E 204 " --> pdb=" O TYR E 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'E' and resid 53 through 55 Processing sheet with id= M, first strand: chain 'E' and resid 269 through 273 removed outlier: 3.589A pdb=" N ALA E 314 " --> pdb=" O ASN E 380 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 92 through 94 removed outlier: 7.896A pdb=" N VAL F 93 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU F 67 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N ILE F 66 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N HIS F 6 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N VAL F 68 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLN F 8 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N VAL F 5 " --> pdb=" O GLN F 133 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N PHE F 135 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ILE F 7 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU F 137 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ALA F 9 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N HIS F 139 " --> pdb=" O ALA F 9 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE F 165 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N LEU F 137 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ASN F 167 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N HIS F 139 " --> pdb=" O ASN F 167 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N PHE F 169 " --> pdb=" O HIS F 139 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLU F 200 " --> pdb=" O THR F 168 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N SER F 170 " --> pdb=" O GLU F 200 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N TYR F 202 " --> pdb=" O SER F 170 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL F 172 " --> pdb=" O TYR F 202 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE F 204 " --> pdb=" O VAL F 172 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ASP F 205 " --> pdb=" O PRO F 270 " (cutoff:3.500A) removed outlier: 11.563A pdb=" N PHE F 272 " --> pdb=" O ASP F 205 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N PHE F 267 " --> pdb=" O SER F 381 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N SER F 381 " --> pdb=" O PHE F 267 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F' and resid 53 through 56 removed outlier: 3.939A pdb=" N LYS F 60 " --> pdb=" O ALA F 56 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 92 through 94 removed outlier: 7.895A pdb=" N VAL G 93 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU G 67 " --> pdb=" O VAL G 93 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N ILE G 66 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N HIS G 6 " --> pdb=" O ILE G 66 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N VAL G 68 " --> pdb=" O HIS G 6 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLN G 8 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N VAL G 5 " --> pdb=" O GLN G 133 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE G 135 " --> pdb=" O VAL G 5 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ILE G 7 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU G 137 " --> pdb=" O ILE G 7 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ALA G 9 " --> pdb=" O LEU G 137 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N HIS G 139 " --> pdb=" O ALA G 9 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE G 165 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N LEU G 137 " --> pdb=" O ILE G 165 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ASN G 167 " --> pdb=" O LEU G 137 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N HIS G 139 " --> pdb=" O ASN G 167 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N PHE G 169 " --> pdb=" O HIS G 139 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLU G 200 " --> pdb=" O THR G 168 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N SER G 170 " --> pdb=" O GLU G 200 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N TYR G 202 " --> pdb=" O SER G 170 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL G 172 " --> pdb=" O TYR G 202 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE G 204 " --> pdb=" O VAL G 172 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ASP G 205 " --> pdb=" O PRO G 270 " (cutoff:3.500A) removed outlier: 11.560A pdb=" N PHE G 272 " --> pdb=" O ASP G 205 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N PHE G 267 " --> pdb=" O SER G 381 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N SER G 381 " --> pdb=" O PHE G 267 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 53 through 56 removed outlier: 3.939A pdb=" N LYS G 60 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'H' and resid 92 through 94 removed outlier: 7.895A pdb=" N VAL H 93 " --> pdb=" O ALA H 65 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU H 67 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N ILE H 66 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N HIS H 6 " --> pdb=" O ILE H 66 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL H 68 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLN H 8 " --> pdb=" O VAL H 68 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N VAL H 5 " --> pdb=" O GLN H 133 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE H 135 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ILE H 7 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU H 137 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ALA H 9 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N HIS H 139 " --> pdb=" O ALA H 9 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE H 165 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N LEU H 137 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ASN H 167 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N HIS H 139 " --> pdb=" O ASN H 167 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N PHE H 169 " --> pdb=" O HIS H 139 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLU H 200 " --> pdb=" O THR H 168 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N SER H 170 " --> pdb=" O GLU H 200 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N TYR H 202 " --> pdb=" O SER H 170 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL H 172 " --> pdb=" O TYR H 202 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE H 204 " --> pdb=" O VAL H 172 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ASP H 205 " --> pdb=" O PRO H 270 " (cutoff:3.500A) removed outlier: 11.559A pdb=" N PHE H 272 " --> pdb=" O ASP H 205 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N PHE H 267 " --> pdb=" O SER H 381 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N SER H 381 " --> pdb=" O PHE H 267 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'H' and resid 53 through 56 removed outlier: 3.938A pdb=" N LYS H 60 " --> pdb=" O ALA H 56 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 92 through 94 removed outlier: 7.896A pdb=" N VAL I 93 " --> pdb=" O ALA I 65 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU I 67 " --> pdb=" O VAL I 93 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N ILE I 66 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N HIS I 6 " --> pdb=" O ILE I 66 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL I 68 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLN I 8 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N VAL I 5 " --> pdb=" O GLN I 133 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N PHE I 135 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ILE I 7 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU I 137 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ALA I 9 " --> pdb=" O LEU I 137 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N HIS I 139 " --> pdb=" O ALA I 9 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE I 165 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N LEU I 137 " --> pdb=" O ILE I 165 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ASN I 167 " --> pdb=" O LEU I 137 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N HIS I 139 " --> pdb=" O ASN I 167 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N PHE I 169 " --> pdb=" O HIS I 139 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLU I 200 " --> pdb=" O THR I 168 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N SER I 170 " --> pdb=" O GLU I 200 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N TYR I 202 " --> pdb=" O SER I 170 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL I 172 " --> pdb=" O TYR I 202 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE I 204 " --> pdb=" O VAL I 172 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ASP I 205 " --> pdb=" O PRO I 270 " (cutoff:3.500A) removed outlier: 11.559A pdb=" N PHE I 272 " --> pdb=" O ASP I 205 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N PHE I 267 " --> pdb=" O SER I 381 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N SER I 381 " --> pdb=" O PHE I 267 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 53 through 56 removed outlier: 3.938A pdb=" N LYS I 60 " --> pdb=" O ALA I 56 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'J' and resid 92 through 94 removed outlier: 8.011A pdb=" N ILE J 93 " --> pdb=" O ALA J 65 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N PHE J 67 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N VAL J 66 " --> pdb=" O CYS J 4 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N SER J 6 " --> pdb=" O VAL J 66 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N VAL J 68 " --> pdb=" O SER J 6 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N HIS J 8 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLY J 134 " --> pdb=" O ILE J 5 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ILE J 7 " --> pdb=" O GLY J 134 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU J 136 " --> pdb=" O ILE J 7 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N VAL J 9 " --> pdb=" O LEU J 136 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N PHE J 138 " --> pdb=" O VAL J 9 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N SER J 165 " --> pdb=" O PHE J 135 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N VAL J 137 " --> pdb=" O SER J 165 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU J 167 " --> pdb=" O VAL J 137 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N HIS J 139 " --> pdb=" O LEU J 167 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N PHE J 169 " --> pdb=" O HIS J 139 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N CYS J 200 " --> pdb=" O GLU J 168 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N SER J 170 " --> pdb=" O CYS J 200 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N PHE J 202 " --> pdb=" O SER J 170 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N TYR J 172 " --> pdb=" O PHE J 202 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N VAL J 204 " --> pdb=" O TYR J 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'J' and resid 53 through 55 Processing sheet with id= X, first strand: chain 'J' and resid 269 through 273 removed outlier: 3.589A pdb=" N ALA J 314 " --> pdb=" O ASN J 380 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'K' and resid 92 through 94 removed outlier: 8.012A pdb=" N ILE K 93 " --> pdb=" O ALA K 65 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N PHE K 67 " --> pdb=" O ILE K 93 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N VAL K 66 " --> pdb=" O CYS K 4 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N SER K 6 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N VAL K 68 " --> pdb=" O SER K 6 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N HIS K 8 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLY K 134 " --> pdb=" O ILE K 5 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ILE K 7 " --> pdb=" O GLY K 134 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU K 136 " --> pdb=" O ILE K 7 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N VAL K 9 " --> pdb=" O LEU K 136 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N PHE K 138 " --> pdb=" O VAL K 9 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N SER K 165 " --> pdb=" O PHE K 135 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N VAL K 137 " --> pdb=" O SER K 165 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU K 167 " --> pdb=" O VAL K 137 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N HIS K 139 " --> pdb=" O LEU K 167 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N PHE K 169 " --> pdb=" O HIS K 139 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N CYS K 200 " --> pdb=" O GLU K 168 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N SER K 170 " --> pdb=" O CYS K 200 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N PHE K 202 " --> pdb=" O SER K 170 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TYR K 172 " --> pdb=" O PHE K 202 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N VAL K 204 " --> pdb=" O TYR K 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'K' and resid 53 through 55 Processing sheet with id= AA, first strand: chain 'K' and resid 269 through 273 removed outlier: 3.593A pdb=" N ALA K 314 " --> pdb=" O ASN K 380 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'L' and resid 92 through 94 removed outlier: 8.011A pdb=" N ILE L 93 " --> pdb=" O ALA L 65 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N PHE L 67 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N VAL L 66 " --> pdb=" O CYS L 4 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N SER L 6 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N VAL L 68 " --> pdb=" O SER L 6 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N HIS L 8 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLY L 134 " --> pdb=" O ILE L 5 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ILE L 7 " --> pdb=" O GLY L 134 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU L 136 " --> pdb=" O ILE L 7 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N VAL L 9 " --> pdb=" O LEU L 136 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N PHE L 138 " --> pdb=" O VAL L 9 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N SER L 165 " --> pdb=" O PHE L 135 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N VAL L 137 " --> pdb=" O SER L 165 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU L 167 " --> pdb=" O VAL L 137 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N HIS L 139 " --> pdb=" O LEU L 167 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N PHE L 169 " --> pdb=" O HIS L 139 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N CYS L 200 " --> pdb=" O GLU L 168 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N SER L 170 " --> pdb=" O CYS L 200 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N PHE L 202 " --> pdb=" O SER L 170 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TYR L 172 " --> pdb=" O PHE L 202 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N VAL L 204 " --> pdb=" O TYR L 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'L' and resid 53 through 55 Processing sheet with id= AD, first strand: chain 'L' and resid 269 through 273 removed outlier: 3.588A pdb=" N ALA L 314 " --> pdb=" O ASN L 380 " (cutoff:3.500A) 1800 hydrogen bonds defined for protein. 4626 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 15.91 Time building geometry restraints manager: 17.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.35: 13626 1.35 - 1.50: 11303 1.50 - 1.65: 16375 1.65 - 1.80: 215 1.80 - 1.95: 223 Bond restraints: 41742 Sorted by residual: bond pdb=" PG GSP I 501 " pdb=" S1G GSP I 501 " ideal model delta sigma weight residual 1.700 1.948 -0.248 2.00e-02 2.50e+03 1.53e+02 bond pdb=" PG GSP H 501 " pdb=" S1G GSP H 501 " ideal model delta sigma weight residual 1.700 1.947 -0.247 2.00e-02 2.50e+03 1.53e+02 bond pdb=" PG GSP G 501 " pdb=" S1G GSP G 501 " ideal model delta sigma weight residual 1.700 1.947 -0.247 2.00e-02 2.50e+03 1.53e+02 bond pdb=" PG GSP B 501 " pdb=" S1G GSP B 501 " ideal model delta sigma weight residual 1.700 1.939 -0.239 2.00e-02 2.50e+03 1.43e+02 bond pdb=" PG GSP D 501 " pdb=" S1G GSP D 501 " ideal model delta sigma weight residual 1.700 1.937 -0.237 2.00e-02 2.50e+03 1.41e+02 ... (remaining 41737 not shown) Histogram of bond angle deviations from ideal: 96.42 - 104.61: 907 104.61 - 112.81: 19940 112.81 - 121.00: 21732 121.00 - 129.20: 13840 129.20 - 137.39: 299 Bond angle restraints: 56718 Sorted by residual: angle pdb=" C LYS J 338 " pdb=" N ARG J 339 " pdb=" CA ARG J 339 " ideal model delta sigma weight residual 120.38 127.96 -7.58 1.37e+00 5.33e-01 3.06e+01 angle pdb=" C LYS L 338 " pdb=" N ARG L 339 " pdb=" CA ARG L 339 " ideal model delta sigma weight residual 120.38 127.94 -7.56 1.37e+00 5.33e-01 3.05e+01 angle pdb=" C LYS E 338 " pdb=" N ARG E 339 " pdb=" CA ARG E 339 " ideal model delta sigma weight residual 120.38 127.93 -7.55 1.37e+00 5.33e-01 3.03e+01 angle pdb=" C LYS A 338 " pdb=" N ARG A 339 " pdb=" CA ARG A 339 " ideal model delta sigma weight residual 120.38 127.92 -7.54 1.37e+00 5.33e-01 3.03e+01 angle pdb=" N LYS L 338 " pdb=" CA LYS L 338 " pdb=" C LYS L 338 " ideal model delta sigma weight residual 110.24 118.32 -8.08 1.47e+00 4.63e-01 3.02e+01 ... (remaining 56713 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.83: 24095 33.83 - 67.66: 667 67.66 - 101.49: 42 101.49 - 135.32: 0 135.32 - 169.14: 18 Dihedral angle restraints: 24822 sinusoidal: 9930 harmonic: 14892 Sorted by residual: dihedral pdb=" C5' GTP J 501 " pdb=" O5' GTP J 501 " pdb=" PA GTP J 501 " pdb=" O3A GTP J 501 " ideal model delta sinusoidal sigma weight residual 69.27 -121.59 -169.14 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C5' GTP E 501 " pdb=" O5' GTP E 501 " pdb=" PA GTP E 501 " pdb=" O3A GTP E 501 " ideal model delta sinusoidal sigma weight residual 69.27 -121.63 -169.10 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C5' GTP C 501 " pdb=" O5' GTP C 501 " pdb=" PA GTP C 501 " pdb=" O3A GTP C 501 " ideal model delta sinusoidal sigma weight residual 69.27 -121.64 -169.10 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 24819 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 4072 0.069 - 0.139: 1599 0.139 - 0.208: 349 0.208 - 0.278: 159 0.278 - 0.347: 19 Chirality restraints: 6198 Sorted by residual: chirality pdb=" CA ASN G 167 " pdb=" N ASN G 167 " pdb=" C ASN G 167 " pdb=" CB ASN G 167 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CA ASN I 167 " pdb=" N ASN I 167 " pdb=" C ASN I 167 " pdb=" CB ASN I 167 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CA ASN F 167 " pdb=" N ASN F 167 " pdb=" C ASN F 167 " pdb=" CB ASN F 167 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.35 2.00e-01 2.50e+01 2.98e+00 ... (remaining 6195 not shown) Planarity restraints: 7386 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' GTP C 501 " 0.025 2.00e-02 2.50e+03 1.20e-02 4.31e+00 pdb=" C2 GTP C 501 " -0.009 2.00e-02 2.50e+03 pdb=" C4 GTP C 501 " -0.000 2.00e-02 2.50e+03 pdb=" C5 GTP C 501 " -0.005 2.00e-02 2.50e+03 pdb=" C6 GTP C 501 " 0.002 2.00e-02 2.50e+03 pdb=" C8 GTP C 501 " 0.002 2.00e-02 2.50e+03 pdb=" N1 GTP C 501 " 0.007 2.00e-02 2.50e+03 pdb=" N2 GTP C 501 " 0.001 2.00e-02 2.50e+03 pdb=" N3 GTP C 501 " -0.001 2.00e-02 2.50e+03 pdb=" N7 GTP C 501 " -0.002 2.00e-02 2.50e+03 pdb=" N9 GTP C 501 " -0.029 2.00e-02 2.50e+03 pdb=" O6 GTP C 501 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GTP L 501 " 0.023 2.00e-02 2.50e+03 1.12e-02 3.78e+00 pdb=" C2 GTP L 501 " -0.006 2.00e-02 2.50e+03 pdb=" C4 GTP L 501 " 0.001 2.00e-02 2.50e+03 pdb=" C5 GTP L 501 " -0.004 2.00e-02 2.50e+03 pdb=" C6 GTP L 501 " 0.001 2.00e-02 2.50e+03 pdb=" C8 GTP L 501 " 0.003 2.00e-02 2.50e+03 pdb=" N1 GTP L 501 " 0.004 2.00e-02 2.50e+03 pdb=" N2 GTP L 501 " 0.001 2.00e-02 2.50e+03 pdb=" N3 GTP L 501 " -0.002 2.00e-02 2.50e+03 pdb=" N7 GTP L 501 " -0.001 2.00e-02 2.50e+03 pdb=" N9 GTP L 501 " -0.029 2.00e-02 2.50e+03 pdb=" O6 GTP L 501 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 21 " 0.024 2.00e-02 2.50e+03 1.20e-02 3.61e+00 pdb=" CG TRP C 21 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP C 21 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP C 21 " -0.010 2.00e-02 2.50e+03 pdb=" NE1 TRP C 21 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 21 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 21 " -0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 21 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 21 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 21 " 0.008 2.00e-02 2.50e+03 ... (remaining 7383 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 154 2.61 - 3.18: 35639 3.18 - 3.76: 65368 3.76 - 4.33: 91257 4.33 - 4.90: 153779 Nonbonded interactions: 346197 Sorted by model distance: nonbonded pdb=" O1B GTP C 501 " pdb="MG MG C 502 " model vdw 2.040 2.170 nonbonded pdb=" O1G GTP E 501 " pdb="MG MG E 502 " model vdw 2.047 2.170 nonbonded pdb=" O1B GTP J 501 " pdb="MG MG J 502 " model vdw 2.056 2.170 nonbonded pdb=" O1B GTP E 501 " pdb="MG MG E 502 " model vdw 2.060 2.170 nonbonded pdb=" O1B GTP L 501 " pdb="MG MG L 502 " model vdw 2.084 2.170 ... (remaining 346192 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: 8.220 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: 28.990 Check model and map are aligned: 0.640 Set scattering table: 0.380 Process input model: 102.960 Find NCS groups from input model: 2.950 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 147.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 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 : 0.009 0.248 41742 Z= 0.612 Angle : 1.426 12.653 56718 Z= 0.989 Chirality : 0.081 0.347 6198 Planarity : 0.006 0.042 7386 Dihedral : 15.584 169.145 15270 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.33 % Favored : 97.56 % Rotamer: Outliers : 0.82 % Allowed : 5.04 % Favored : 94.14 % 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: 0.22 (0.11), residues: 5118 helix: 0.86 (0.09), residues: 2328 sheet: 0.32 (0.19), residues: 816 loop : -0.71 (0.13), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP C 21 HIS 0.010 0.002 HIS L 8 PHE 0.023 0.002 PHE F 92 TYR 0.020 0.002 TYR J 224 ARG 0.024 0.001 ARG B 2 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10236 Ramachandran restraints generated. 5118 Oldfield, 0 Emsley, 5118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10236 Ramachandran restraints generated. 5118 Oldfield, 0 Emsley, 5118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1463 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 1427 time to evaluate : 4.570 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: A 290 GLU cc_start: 0.7342 (tt0) cc_final: 0.6946 (tt0) REVERT: B 161 TYR cc_start: 0.8672 (m-80) cc_final: 0.8453 (m-80) REVERT: B 224 TYR cc_start: 0.8418 (OUTLIER) cc_final: 0.8181 (m-10) REVERT: B 306 ASP cc_start: 0.8267 (t0) cc_final: 0.7939 (t70) REVERT: B 325 MET cc_start: 0.7378 (mmm) cc_final: 0.7015 (mmm) REVERT: B 329 ASP cc_start: 0.7327 (m-30) cc_final: 0.6804 (m-30) REVERT: B 339 ASN cc_start: 0.7469 (m110) cc_final: 0.6677 (m110) REVERT: B 414 ASP cc_start: 0.7221 (p0) cc_final: 0.6770 (t70) REVERT: B 427 ASP cc_start: 0.8335 (m-30) cc_final: 0.8039 (m-30) REVERT: C 71 GLU cc_start: 0.7616 (pt0) cc_final: 0.7294 (pt0) REVERT: C 84 ARG cc_start: 0.7784 (ttp-110) cc_final: 0.7405 (ptp90) REVERT: C 205 ASP cc_start: 0.7778 (t0) cc_final: 0.7450 (t0) REVERT: C 304 LYS cc_start: 0.8187 (tttt) cc_final: 0.7474 (tptm) REVERT: C 341 ILE cc_start: 0.8807 (mp) cc_final: 0.8545 (mp) REVERT: D 114 LEU cc_start: 0.9440 (tp) cc_final: 0.9100 (tt) REVERT: D 120 ASP cc_start: 0.8047 (m-30) cc_final: 0.7813 (m-30) REVERT: D 138 THR cc_start: 0.9105 (m) cc_final: 0.8893 (p) REVERT: D 210 TYR cc_start: 0.8724 (m-80) cc_final: 0.8256 (m-80) REVERT: D 224 TYR cc_start: 0.8587 (OUTLIER) cc_final: 0.7372 (m-10) REVERT: D 325 MET cc_start: 0.7561 (mmm) cc_final: 0.7341 (tpp) REVERT: D 353 THR cc_start: 0.8765 (m) cc_final: 0.8552 (p) REVERT: E 71 GLU cc_start: 0.7807 (pt0) cc_final: 0.7579 (tt0) REVERT: E 243 ARG cc_start: 0.8611 (mtm110) cc_final: 0.7826 (mtm110) REVERT: E 302 MET cc_start: 0.8127 (mtt) cc_final: 0.7876 (mtt) REVERT: E 304 LYS cc_start: 0.8487 (tttt) cc_final: 0.8054 (ttmm) REVERT: F 138 THR cc_start: 0.8938 (m) cc_final: 0.8667 (p) REVERT: F 179 ASP cc_start: 0.8346 (t70) cc_final: 0.8006 (t0) REVERT: F 210 TYR cc_start: 0.8594 (m-80) cc_final: 0.8106 (m-80) REVERT: F 224 TYR cc_start: 0.8516 (OUTLIER) cc_final: 0.8223 (m-10) REVERT: F 306 ASP cc_start: 0.8002 (t0) cc_final: 0.7200 (t70) REVERT: G 179 ASP cc_start: 0.8277 (t70) cc_final: 0.7823 (t0) REVERT: G 224 TYR cc_start: 0.8406 (OUTLIER) cc_final: 0.8019 (m-80) REVERT: G 228 ASN cc_start: 0.8675 (m-40) cc_final: 0.8249 (m-40) REVERT: G 325 MET cc_start: 0.7560 (mmm) cc_final: 0.7143 (mmm) REVERT: H 131 CYS cc_start: 0.8098 (t) cc_final: 0.7718 (t) REVERT: H 179 ASP cc_start: 0.8025 (t70) cc_final: 0.7691 (t0) REVERT: H 210 TYR cc_start: 0.8366 (m-80) cc_final: 0.8046 (m-80) REVERT: H 325 MET cc_start: 0.7541 (mmm) cc_final: 0.7321 (tpp) REVERT: I 69 ASP cc_start: 0.6708 (t0) cc_final: 0.6301 (t0) REVERT: I 86 ILE cc_start: 0.8292 (tt) cc_final: 0.8018 (tt) REVERT: I 138 THR cc_start: 0.8987 (m) cc_final: 0.8673 (p) REVERT: I 179 ASP cc_start: 0.8166 (t70) cc_final: 0.7846 (t0) REVERT: I 332 MET cc_start: 0.8909 (mmp) cc_final: 0.8516 (mmm) REVERT: J 2 ARG cc_start: 0.7503 (mtm180) cc_final: 0.7097 (mtt90) REVERT: J 115 ILE cc_start: 0.9012 (tp) cc_final: 0.8703 (tp) REVERT: J 176 GLN cc_start: 0.8244 (mt0) cc_final: 0.7901 (mt0) REVERT: J 271 THR cc_start: 0.9014 (m) cc_final: 0.8795 (m) REVERT: J 275 VAL cc_start: 0.8998 (OUTLIER) cc_final: 0.8511 (p) REVERT: K 2 ARG cc_start: 0.7465 (mtm180) cc_final: 0.7132 (mpt180) REVERT: K 71 GLU cc_start: 0.7672 (pt0) cc_final: 0.6684 (tt0) REVERT: K 302 MET cc_start: 0.8066 (mtt) cc_final: 0.7714 (mtt) REVERT: K 417 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7324 (tm-30) REVERT: L 2 ARG cc_start: 0.7515 (mtm180) cc_final: 0.7026 (mtt90) REVERT: L 207 GLU cc_start: 0.7187 (tt0) cc_final: 0.6364 (tt0) REVERT: L 285 GLN cc_start: 0.7793 (pm20) cc_final: 0.6850 (mm110) REVERT: L 417 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7309 (tm-30) outliers start: 36 outliers final: 3 residues processed: 1451 average time/residue: 0.5458 time to fit residues: 1263.3019 Evaluate side-chains 735 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 727 time to evaluate : 4.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 224 TYR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain D residue 224 TYR Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain G residue 224 TYR Chi-restraints excluded: chain J residue 275 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 430 optimal weight: 1.9990 chunk 386 optimal weight: 0.5980 chunk 214 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 260 optimal weight: 2.9990 chunk 206 optimal weight: 2.9990 chunk 399 optimal weight: 0.6980 chunk 154 optimal weight: 0.9990 chunk 243 optimal weight: 2.9990 chunk 297 optimal weight: 5.9990 chunk 463 optimal weight: 5.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 88 HIS A 283 HIS A 358 GLN B 6 HIS B 15 GLN B 192 HIS B 258 ASN B 336 GLN B 406 HIS B 433 GLN C 15 GLN C 88 HIS C 283 HIS C 293 ASN C 358 GLN D 6 HIS D 15 GLN D 192 HIS D 336 GLN D 406 HIS D 433 GLN E 15 GLN E 88 HIS E 283 HIS E 293 ASN E 358 GLN F 6 HIS F 15 GLN F 192 HIS ** F 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 GLN F 406 HIS F 433 GLN G 6 HIS G 15 GLN G 59 ASN G 101 ASN ** G 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 192 HIS ** G 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 349 ASN H 6 HIS H 14 ASN H 15 GLN H 59 ASN ** H 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 339 ASN H 349 ASN H 433 GLN I 6 HIS I 15 GLN I 59 ASN I 101 ASN I 192 HIS ** I 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 309 HIS I 426 ASN I 433 GLN J 15 GLN ** J 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 283 HIS J 358 GLN K 15 GLN ** K 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 283 HIS ** K 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 358 GLN L 15 GLN ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 293 ASN L 358 GLN Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 41742 Z= 0.215 Angle : 0.597 7.235 56718 Z= 0.313 Chirality : 0.044 0.184 6198 Planarity : 0.005 0.044 7386 Dihedral : 11.369 174.413 5781 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.83 % Allowed : 13.36 % Favored : 83.81 % 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: 1.27 (0.12), residues: 5118 helix: 1.89 (0.11), residues: 2304 sheet: 0.41 (0.17), residues: 846 loop : -0.14 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 346 HIS 0.010 0.001 HIS L 309 PHE 0.023 0.002 PHE G 169 TYR 0.017 0.001 TYR E 172 ARG 0.009 0.001 ARG A 390 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10236 Ramachandran restraints generated. 5118 Oldfield, 0 Emsley, 5118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10236 Ramachandran restraints generated. 5118 Oldfield, 0 Emsley, 5118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 898 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 774 time to evaluate : 3.951 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: A 113 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8272 (mm-30) REVERT: A 172 TYR cc_start: 0.8330 (t80) cc_final: 0.7646 (t80) REVERT: A 388 TRP cc_start: 0.8910 (m100) cc_final: 0.8659 (m100) REVERT: B 204 ILE cc_start: 0.9083 (mp) cc_final: 0.8698 (mt) REVERT: B 306 ASP cc_start: 0.8182 (t0) cc_final: 0.7857 (t70) REVERT: B 325 MET cc_start: 0.7786 (mmm) cc_final: 0.7171 (mmm) REVERT: B 329 ASP cc_start: 0.7483 (m-30) cc_final: 0.6890 (m-30) REVERT: C 50 ASN cc_start: 0.8313 (t0) cc_final: 0.8092 (t0) REVERT: C 71 GLU cc_start: 0.7615 (pt0) cc_final: 0.7245 (tt0) REVERT: C 203 MET cc_start: 0.8062 (mmm) cc_final: 0.7773 (mmt) REVERT: C 205 ASP cc_start: 0.8071 (t0) cc_final: 0.7819 (t70) REVERT: D 166 MET cc_start: 0.7699 (tpp) cc_final: 0.7478 (tpp) REVERT: D 210 TYR cc_start: 0.8462 (m-80) cc_final: 0.8008 (m-80) REVERT: D 224 TYR cc_start: 0.8641 (OUTLIER) cc_final: 0.7934 (m-10) REVERT: D 308 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.8359 (mtm-85) REVERT: E 157 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8863 (mp) REVERT: F 138 THR cc_start: 0.8839 (m) cc_final: 0.8615 (p) REVERT: F 179 ASP cc_start: 0.8311 (t70) cc_final: 0.7771 (t0) REVERT: F 204 ILE cc_start: 0.9179 (mp) cc_final: 0.8669 (mt) REVERT: F 205 ASP cc_start: 0.7584 (m-30) cc_final: 0.7315 (m-30) REVERT: F 210 TYR cc_start: 0.8631 (m-80) cc_final: 0.8211 (m-80) REVERT: F 224 TYR cc_start: 0.8592 (OUTLIER) cc_final: 0.8390 (m-10) REVERT: F 334 ASN cc_start: 0.8190 (t0) cc_final: 0.7933 (t0) REVERT: G 41 ASP cc_start: 0.8758 (p0) cc_final: 0.8524 (p0) REVERT: G 179 ASP cc_start: 0.8312 (t70) cc_final: 0.7887 (t0) REVERT: G 204 ILE cc_start: 0.8872 (mp) cc_final: 0.8596 (mt) REVERT: G 224 TYR cc_start: 0.8378 (OUTLIER) cc_final: 0.7819 (m-80) REVERT: G 228 ASN cc_start: 0.8347 (m-40) cc_final: 0.7963 (m-40) REVERT: G 255 LEU cc_start: 0.8485 (mt) cc_final: 0.8223 (mt) REVERT: G 325 MET cc_start: 0.8070 (mmm) cc_final: 0.7739 (mmm) REVERT: H 179 ASP cc_start: 0.8078 (t70) cc_final: 0.7792 (t0) REVERT: H 259 MET cc_start: 0.8543 (mmp) cc_final: 0.8123 (mmp) REVERT: I 179 ASP cc_start: 0.8251 (t70) cc_final: 0.7887 (t0) REVERT: I 426 ASN cc_start: 0.8331 (OUTLIER) cc_final: 0.7810 (m110) REVERT: J 2 ARG cc_start: 0.7439 (mtm180) cc_final: 0.6921 (mpt180) REVERT: J 71 GLU cc_start: 0.7747 (pt0) cc_final: 0.7523 (pt0) REVERT: J 275 VAL cc_start: 0.9012 (OUTLIER) cc_final: 0.8543 (p) REVERT: K 2 ARG cc_start: 0.7591 (mtm180) cc_final: 0.7085 (mpt180) REVERT: K 176 GLN cc_start: 0.8261 (pt0) cc_final: 0.7979 (pm20) REVERT: K 302 MET cc_start: 0.8068 (mtt) cc_final: 0.7650 (mtt) REVERT: L 2 ARG cc_start: 0.7676 (mtm180) cc_final: 0.7300 (mtt90) REVERT: L 285 GLN cc_start: 0.7951 (pm20) cc_final: 0.6614 (mm-40) REVERT: L 378 LEU cc_start: 0.8998 (mt) cc_final: 0.8647 (mt) outliers start: 124 outliers final: 68 residues processed: 859 average time/residue: 0.4901 time to fit residues: 701.1051 Evaluate side-chains 698 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 623 time to evaluate : 4.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 213 CYS Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 224 TYR Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 306 ASP Chi-restraints excluded: chain D residue 308 ARG Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 155 GLU Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 213 CYS Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 126 SER Chi-restraints excluded: chain G residue 217 LEU Chi-restraints excluded: chain G residue 224 TYR Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 356 CYS Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 232 SER Chi-restraints excluded: chain I residue 305 CYS Chi-restraints excluded: chain I residue 356 CYS Chi-restraints excluded: chain I residue 425 MET Chi-restraints excluded: chain I residue 426 ASN Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 199 ASP Chi-restraints excluded: chain J residue 213 CYS Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 353 VAL Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 213 CYS Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 305 CYS Chi-restraints excluded: chain K residue 327 ASP Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 199 ASP Chi-restraints excluded: chain L residue 213 CYS Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 275 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 257 optimal weight: 0.5980 chunk 143 optimal weight: 10.0000 chunk 385 optimal weight: 2.9990 chunk 315 optimal weight: 0.9980 chunk 127 optimal weight: 9.9990 chunk 463 optimal weight: 8.9990 chunk 501 optimal weight: 0.0970 chunk 413 optimal weight: 5.9990 chunk 460 optimal weight: 6.9990 chunk 158 optimal weight: 0.3980 chunk 372 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 HIS A 186 ASN B 8 GLN ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN C 88 HIS C 380 ASN ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 HIS E 186 ASN F 85 GLN ** F 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 167 ASN ** G 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 406 HIS ** H 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 GLN H 406 HIS I 59 ASN I 85 GLN ** I 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 309 HIS I 406 HIS J 88 HIS J 186 ASN K 88 HIS K 186 ASN ** K 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 342 GLN K 380 ASN ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 ASN L 380 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 41742 Z= 0.163 Angle : 0.532 11.744 56718 Z= 0.273 Chirality : 0.042 0.156 6198 Planarity : 0.004 0.039 7386 Dihedral : 10.834 175.850 5775 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.51 % Allowed : 15.57 % Favored : 81.92 % 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: 1.37 (0.12), residues: 5118 helix: 1.80 (0.11), residues: 2340 sheet: 0.81 (0.17), residues: 810 loop : -0.07 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 21 HIS 0.007 0.001 HIS J 88 PHE 0.014 0.001 PHE A 169 TYR 0.020 0.001 TYR I 342 ARG 0.006 0.001 ARG A 390 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10236 Ramachandran restraints generated. 5118 Oldfield, 0 Emsley, 5118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10236 Ramachandran restraints generated. 5118 Oldfield, 0 Emsley, 5118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 701 time to evaluate : 5.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8208 (mm-30) REVERT: A 172 TYR cc_start: 0.8371 (t80) cc_final: 0.7794 (t80) REVERT: A 388 TRP cc_start: 0.8946 (m100) cc_final: 0.8633 (m100) REVERT: B 41 ASP cc_start: 0.8415 (p0) cc_final: 0.7555 (p0) REVERT: B 47 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8329 (mm-30) REVERT: B 299 LYS cc_start: 0.8671 (ptpt) cc_final: 0.8462 (ttpt) REVERT: B 306 ASP cc_start: 0.8195 (t0) cc_final: 0.7777 (t70) REVERT: B 325 MET cc_start: 0.7892 (mmm) cc_final: 0.7099 (mmm) REVERT: B 329 ASP cc_start: 0.7467 (m-30) cc_final: 0.6920 (m-30) REVERT: B 435 TYR cc_start: 0.8434 (m-80) cc_final: 0.8222 (m-80) REVERT: C 50 ASN cc_start: 0.8385 (t0) cc_final: 0.8027 (t0) REVERT: C 109 THR cc_start: 0.7714 (m) cc_final: 0.7475 (m) REVERT: C 203 MET cc_start: 0.8022 (mmm) cc_final: 0.7736 (mmt) REVERT: C 205 ASP cc_start: 0.8108 (t0) cc_final: 0.7869 (t70) REVERT: D 166 MET cc_start: 0.7664 (tpp) cc_final: 0.7463 (tpp) REVERT: D 210 TYR cc_start: 0.8457 (m-80) cc_final: 0.7975 (m-80) REVERT: D 308 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8442 (mtm-85) REVERT: E 157 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8817 (mp) REVERT: F 138 THR cc_start: 0.8861 (m) cc_final: 0.8613 (p) REVERT: F 179 ASP cc_start: 0.8309 (t70) cc_final: 0.7747 (t0) REVERT: F 210 TYR cc_start: 0.8490 (m-80) cc_final: 0.8095 (m-80) REVERT: F 228 ASN cc_start: 0.8604 (m-40) cc_final: 0.8053 (m-40) REVERT: F 259 MET cc_start: 0.8990 (mmp) cc_final: 0.8781 (mmm) REVERT: G 179 ASP cc_start: 0.8369 (t70) cc_final: 0.8032 (t0) REVERT: G 204 ILE cc_start: 0.8927 (mp) cc_final: 0.8641 (mt) REVERT: G 325 MET cc_start: 0.8210 (mmm) cc_final: 0.7729 (tpp) REVERT: H 76 ASP cc_start: 0.8210 (t0) cc_final: 0.7999 (t0) REVERT: H 179 ASP cc_start: 0.8088 (t70) cc_final: 0.7840 (t0) REVERT: H 278 ARG cc_start: 0.7510 (ptp-110) cc_final: 0.7291 (mtm110) REVERT: I 179 ASP cc_start: 0.8235 (t70) cc_final: 0.7905 (t0) REVERT: I 204 ILE cc_start: 0.9039 (mp) cc_final: 0.8709 (mt) REVERT: J 2 ARG cc_start: 0.7601 (mtm180) cc_final: 0.6781 (mpt180) REVERT: J 71 GLU cc_start: 0.7655 (pt0) cc_final: 0.7063 (pt0) REVERT: J 275 VAL cc_start: 0.9019 (OUTLIER) cc_final: 0.8516 (p) REVERT: K 2 ARG cc_start: 0.7717 (mtm180) cc_final: 0.7221 (mpt180) REVERT: K 182 VAL cc_start: 0.8679 (m) cc_final: 0.8398 (p) REVERT: K 302 MET cc_start: 0.8194 (mtt) cc_final: 0.7819 (mtt) REVERT: L 2 ARG cc_start: 0.7742 (mtm180) cc_final: 0.7386 (mpt180) REVERT: L 205 ASP cc_start: 0.7688 (t0) cc_final: 0.7421 (t0) REVERT: L 285 GLN cc_start: 0.8002 (pm20) cc_final: 0.6662 (mm-40) REVERT: L 368 LEU cc_start: 0.8773 (mp) cc_final: 0.8504 (mp) REVERT: L 378 LEU cc_start: 0.9010 (mt) cc_final: 0.8668 (mt) outliers start: 110 outliers final: 72 residues processed: 782 average time/residue: 0.4845 time to fit residues: 638.1721 Evaluate side-chains 671 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 596 time to evaluate : 4.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 308 ARG Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 167 ASN Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 314 THR Chi-restraints excluded: chain H residue 356 CYS Chi-restraints excluded: chain H residue 384 ILE Chi-restraints excluded: chain H residue 428 LEU Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 85 GLN Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 232 SER Chi-restraints excluded: chain I residue 305 CYS Chi-restraints excluded: chain I residue 356 CYS Chi-restraints excluded: chain I residue 425 MET Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 157 LEU Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 353 VAL Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 327 ASP Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 284 GLU Chi-restraints excluded: chain L residue 327 ASP Chi-restraints excluded: chain L residue 353 VAL Chi-restraints excluded: chain L residue 367 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 458 optimal weight: 10.0000 chunk 348 optimal weight: 0.0570 chunk 240 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 221 optimal weight: 0.1980 chunk 311 optimal weight: 8.9990 chunk 465 optimal weight: 2.9990 chunk 492 optimal weight: 0.9990 chunk 243 optimal weight: 10.0000 chunk 441 optimal weight: 0.7980 chunk 132 optimal weight: 9.9990 overall best weight: 0.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 HIS A 293 ASN B 8 GLN B 167 ASN C 88 HIS E 18 ASN E 88 HIS E 380 ASN F 8 GLN ** F 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 436 GLN ** G 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 349 ASN G 426 ASN H 8 GLN ** H 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 300 ASN H 349 ASN ** I 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 258 ASN I 309 HIS ** J 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 8 HIS K 88 HIS ** K 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 HIS L 283 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 41742 Z= 0.161 Angle : 0.509 11.940 56718 Z= 0.259 Chirality : 0.042 0.147 6198 Planarity : 0.004 0.038 7386 Dihedral : 10.512 173.542 5769 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.03 % Allowed : 15.71 % Favored : 81.26 % 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: 1.33 (0.12), residues: 5118 helix: 1.68 (0.11), residues: 2352 sheet: 0.84 (0.17), residues: 834 loop : 0.00 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 21 HIS 0.009 0.001 HIS K 88 PHE 0.024 0.001 PHE A 169 TYR 0.040 0.001 TYR C 24 ARG 0.007 0.000 ARG J 390 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10236 Ramachandran restraints generated. 5118 Oldfield, 0 Emsley, 5118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10236 Ramachandran restraints generated. 5118 Oldfield, 0 Emsley, 5118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 660 time to evaluate : 4.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8236 (mm-30) REVERT: A 172 TYR cc_start: 0.8393 (t80) cc_final: 0.7887 (t80) REVERT: A 306 ASP cc_start: 0.8836 (OUTLIER) cc_final: 0.8572 (t0) REVERT: A 388 TRP cc_start: 0.8918 (m100) cc_final: 0.8653 (m100) REVERT: B 41 ASP cc_start: 0.8473 (p0) cc_final: 0.7585 (p0) REVERT: B 47 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8358 (mm-30) REVERT: B 306 ASP cc_start: 0.8233 (t0) cc_final: 0.7740 (t70) REVERT: B 325 MET cc_start: 0.7991 (mmm) cc_final: 0.7088 (mmm) REVERT: B 329 ASP cc_start: 0.7471 (m-30) cc_final: 0.6938 (m-30) REVERT: B 435 TYR cc_start: 0.8305 (m-80) cc_final: 0.8055 (m-80) REVERT: C 50 ASN cc_start: 0.8481 (t0) cc_final: 0.8067 (t0) REVERT: C 203 MET cc_start: 0.8049 (mmm) cc_final: 0.7724 (mmt) REVERT: D 210 TYR cc_start: 0.8426 (m-80) cc_final: 0.7975 (m-80) REVERT: D 308 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8459 (mtm-85) REVERT: D 433 GLN cc_start: 0.8846 (tp40) cc_final: 0.7841 (tm-30) REVERT: D 437 ASP cc_start: 0.8635 (t70) cc_final: 0.8235 (p0) REVERT: E 157 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8816 (mp) REVERT: E 342 GLN cc_start: 0.7680 (OUTLIER) cc_final: 0.7304 (mp10) REVERT: F 138 THR cc_start: 0.8872 (m) cc_final: 0.8660 (p) REVERT: F 179 ASP cc_start: 0.8198 (t70) cc_final: 0.7623 (t0) REVERT: F 210 TYR cc_start: 0.8505 (m-80) cc_final: 0.8105 (m-80) REVERT: F 228 ASN cc_start: 0.8552 (m-40) cc_final: 0.7990 (m-40) REVERT: F 433 GLN cc_start: 0.8654 (tp40) cc_final: 0.8350 (tp40) REVERT: G 179 ASP cc_start: 0.8289 (t70) cc_final: 0.8018 (t0) REVERT: G 204 ILE cc_start: 0.9064 (mp) cc_final: 0.8649 (mt) REVERT: G 325 MET cc_start: 0.8326 (mmm) cc_final: 0.8046 (tpp) REVERT: H 278 ARG cc_start: 0.7548 (ptp-110) cc_final: 0.7318 (mtm110) REVERT: I 179 ASP cc_start: 0.8123 (t70) cc_final: 0.7784 (t0) REVERT: I 204 ILE cc_start: 0.9047 (mp) cc_final: 0.8746 (mt) REVERT: I 295 MET cc_start: 0.8274 (mtm) cc_final: 0.8059 (mtp) REVERT: J 2 ARG cc_start: 0.7592 (mtm180) cc_final: 0.6903 (mpt180) REVERT: J 275 VAL cc_start: 0.9009 (OUTLIER) cc_final: 0.8482 (p) REVERT: J 327 ASP cc_start: 0.7927 (t0) cc_final: 0.7710 (t0) REVERT: J 371 VAL cc_start: 0.9015 (m) cc_final: 0.8722 (t) REVERT: K 2 ARG cc_start: 0.7808 (mtm180) cc_final: 0.7300 (mpt180) REVERT: K 182 VAL cc_start: 0.8679 (m) cc_final: 0.8410 (p) REVERT: K 302 MET cc_start: 0.8189 (mtt) cc_final: 0.7884 (mtt) REVERT: K 335 ILE cc_start: 0.8127 (mt) cc_final: 0.7837 (mt) REVERT: L 2 ARG cc_start: 0.7763 (mtm180) cc_final: 0.7469 (mpt180) REVERT: L 205 ASP cc_start: 0.7667 (t0) cc_final: 0.7434 (t0) REVERT: L 285 GLN cc_start: 0.7990 (pm20) cc_final: 0.6658 (mm-40) REVERT: L 368 LEU cc_start: 0.8766 (mp) cc_final: 0.8365 (mt) outliers start: 133 outliers final: 85 residues processed: 759 average time/residue: 0.5248 time to fit residues: 676.2533 Evaluate side-chains 687 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 597 time to evaluate : 4.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 306 ASP Chi-restraints excluded: chain D residue 308 ARG Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 113 GLU Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 213 CYS Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 342 GLN Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 436 GLN Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 356 CYS Chi-restraints excluded: chain H residue 384 ILE Chi-restraints excluded: chain H residue 428 LEU Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 232 SER Chi-restraints excluded: chain I residue 305 CYS Chi-restraints excluded: chain I residue 356 CYS Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain K residue 4 CYS Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 327 ASP Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 284 GLU Chi-restraints excluded: chain L residue 327 ASP Chi-restraints excluded: chain L residue 335 ILE Chi-restraints excluded: chain L residue 353 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 367 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 410 optimal weight: 0.5980 chunk 279 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 367 optimal weight: 7.9990 chunk 203 optimal weight: 1.9990 chunk 420 optimal weight: 6.9990 chunk 340 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 251 optimal weight: 0.8980 chunk 442 optimal weight: 2.9990 chunk 124 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 HIS A 88 HIS A 293 ASN B 8 GLN ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 ASN ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 HIS F 8 GLN F 258 ASN ** G 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 339 ASN G 349 ASN G 433 GLN H 8 GLN ** H 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 300 ASN I 85 GLN I 167 ASN I 300 ASN I 309 HIS J 88 HIS K 50 ASN ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 50 ASN ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 41742 Z= 0.147 Angle : 0.497 12.310 56718 Z= 0.251 Chirality : 0.041 0.145 6198 Planarity : 0.004 0.038 7386 Dihedral : 10.296 170.986 5769 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.06 % Allowed : 16.39 % Favored : 80.55 % 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: 1.35 (0.12), residues: 5118 helix: 1.68 (0.11), residues: 2346 sheet: 0.93 (0.17), residues: 834 loop : 0.01 (0.14), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 346 HIS 0.010 0.001 HIS L 88 PHE 0.022 0.001 PHE I 262 TYR 0.023 0.001 TYR I 435 ARG 0.004 0.000 ARG E 156 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10236 Ramachandran restraints generated. 5118 Oldfield, 0 Emsley, 5118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10236 Ramachandran restraints generated. 5118 Oldfield, 0 Emsley, 5118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 637 time to evaluate : 4.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8192 (mm-30) REVERT: B 41 ASP cc_start: 0.8505 (p0) cc_final: 0.7657 (p0) REVERT: B 47 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8333 (mm-30) REVERT: B 196 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7089 (mp0) REVERT: B 204 ILE cc_start: 0.9017 (OUTLIER) cc_final: 0.8692 (mt) REVERT: B 306 ASP cc_start: 0.8251 (t0) cc_final: 0.7767 (t70) REVERT: B 325 MET cc_start: 0.7992 (mmm) cc_final: 0.7123 (mmm) REVERT: B 329 ASP cc_start: 0.7518 (m-30) cc_final: 0.6962 (m-30) REVERT: B 332 MET cc_start: 0.8339 (mmm) cc_final: 0.7509 (mmm) REVERT: B 435 TYR cc_start: 0.8255 (m-80) cc_final: 0.7970 (m-80) REVERT: C 50 ASN cc_start: 0.8593 (OUTLIER) cc_final: 0.8098 (t0) REVERT: C 203 MET cc_start: 0.8074 (mmm) cc_final: 0.7748 (mmt) REVERT: D 210 TYR cc_start: 0.8439 (m-80) cc_final: 0.8037 (m-80) REVERT: D 228 ASN cc_start: 0.8441 (m-40) cc_final: 0.8026 (m-40) REVERT: D 308 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8472 (mtm-85) REVERT: D 433 GLN cc_start: 0.8893 (tp40) cc_final: 0.8447 (tm-30) REVERT: E 157 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8812 (mp) REVERT: E 342 GLN cc_start: 0.7570 (OUTLIER) cc_final: 0.7257 (mp10) REVERT: F 127 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8069 (mp0) REVERT: F 138 THR cc_start: 0.8860 (m) cc_final: 0.8655 (p) REVERT: F 179 ASP cc_start: 0.8194 (t70) cc_final: 0.7668 (t0) REVERT: F 204 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8856 (mt) REVERT: F 210 TYR cc_start: 0.8482 (m-80) cc_final: 0.8090 (m-80) REVERT: F 228 ASN cc_start: 0.8543 (m-40) cc_final: 0.7984 (m-40) REVERT: F 259 MET cc_start: 0.8745 (mmm) cc_final: 0.8414 (mmt) REVERT: F 314 THR cc_start: 0.8824 (OUTLIER) cc_final: 0.8477 (p) REVERT: F 433 GLN cc_start: 0.8634 (tp40) cc_final: 0.8287 (tp40) REVERT: F 437 ASP cc_start: 0.7368 (m-30) cc_final: 0.7133 (m-30) REVERT: G 179 ASP cc_start: 0.8283 (t70) cc_final: 0.8038 (t0) REVERT: G 204 ILE cc_start: 0.9005 (mp) cc_final: 0.8642 (mt) REVERT: G 299 LYS cc_start: 0.8534 (tmmt) cc_final: 0.8333 (ttpp) REVERT: G 325 MET cc_start: 0.8380 (mmm) cc_final: 0.7988 (tpp) REVERT: I 167 ASN cc_start: 0.8214 (OUTLIER) cc_final: 0.7703 (p0) REVERT: I 179 ASP cc_start: 0.8114 (t70) cc_final: 0.7816 (t0) REVERT: I 204 ILE cc_start: 0.9159 (mp) cc_final: 0.8848 (mt) REVERT: J 2 ARG cc_start: 0.7748 (mtm180) cc_final: 0.6980 (mpt180) REVERT: J 275 VAL cc_start: 0.8999 (OUTLIER) cc_final: 0.8393 (p) REVERT: J 327 ASP cc_start: 0.7890 (t0) cc_final: 0.7677 (t0) REVERT: J 371 VAL cc_start: 0.9016 (m) cc_final: 0.8717 (t) REVERT: K 2 ARG cc_start: 0.7839 (mtm180) cc_final: 0.7183 (mpt180) REVERT: K 76 ASP cc_start: 0.8922 (OUTLIER) cc_final: 0.8635 (m-30) REVERT: K 182 VAL cc_start: 0.8669 (m) cc_final: 0.8401 (p) REVERT: K 302 MET cc_start: 0.8195 (mtt) cc_final: 0.7896 (mtt) REVERT: K 335 ILE cc_start: 0.8120 (mt) cc_final: 0.7838 (mt) REVERT: L 2 ARG cc_start: 0.7790 (mtm180) cc_final: 0.7470 (mpt180) REVERT: L 205 ASP cc_start: 0.7697 (t0) cc_final: 0.7421 (t0) REVERT: L 285 GLN cc_start: 0.7997 (pm20) cc_final: 0.6629 (mm-40) REVERT: L 368 LEU cc_start: 0.8769 (mp) cc_final: 0.8372 (mt) outliers start: 134 outliers final: 87 residues processed: 732 average time/residue: 0.4812 time to fit residues: 592.4548 Evaluate side-chains 679 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 581 time to evaluate : 4.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 50 ASN Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 308 ARG Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 113 GLU Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 316 CYS Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 342 GLN Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain G residue 425 MET Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 336 GLN Chi-restraints excluded: chain H residue 356 CYS Chi-restraints excluded: chain H residue 384 ILE Chi-restraints excluded: chain H residue 428 LEU Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 85 GLN Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 167 ASN Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 232 SER Chi-restraints excluded: chain I residue 305 CYS Chi-restraints excluded: chain I residue 356 CYS Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 335 ILE Chi-restraints excluded: chain J residue 353 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 327 ASP Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 415 GLU Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 284 GLU Chi-restraints excluded: chain L residue 335 ILE Chi-restraints excluded: chain L residue 353 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 367 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 165 optimal weight: 0.9980 chunk 443 optimal weight: 8.9990 chunk 97 optimal weight: 0.1980 chunk 289 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 493 optimal weight: 6.9990 chunk 409 optimal weight: 5.9990 chunk 228 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 163 optimal weight: 9.9990 chunk 259 optimal weight: 0.6980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN B 167 ASN ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 HIS ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 GLN E 88 HIS F 8 GLN F 14 ASN F 300 ASN G 167 ASN ** G 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 300 ASN G 349 ASN H 8 GLN ** H 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 300 ASN I 8 GLN I 85 GLN I 300 ASN I 309 HIS ** J 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 50 ASN K 88 HIS ** K 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 206 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 41742 Z= 0.175 Angle : 0.506 12.375 56718 Z= 0.255 Chirality : 0.042 0.148 6198 Planarity : 0.004 0.037 7386 Dihedral : 10.160 168.938 5769 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.31 % Allowed : 16.03 % Favored : 80.67 % 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: 1.33 (0.12), residues: 5118 helix: 1.62 (0.11), residues: 2358 sheet: 0.98 (0.17), residues: 834 loop : 0.01 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 388 HIS 0.008 0.001 HIS J 88 PHE 0.014 0.001 PHE D 377 TYR 0.018 0.001 TYR E 357 ARG 0.006 0.000 ARG F 278 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10236 Ramachandran restraints generated. 5118 Oldfield, 0 Emsley, 5118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10236 Ramachandran restraints generated. 5118 Oldfield, 0 Emsley, 5118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 775 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 630 time to evaluate : 4.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8306 (mm-30) REVERT: A 342 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.7229 (mp10) REVERT: B 41 ASP cc_start: 0.8539 (p0) cc_final: 0.7747 (p0) REVERT: B 47 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8349 (mm-30) REVERT: B 167 ASN cc_start: 0.8166 (OUTLIER) cc_final: 0.7919 (p0) REVERT: B 204 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8692 (mt) REVERT: B 259 MET cc_start: 0.8754 (mmm) cc_final: 0.8489 (mmm) REVERT: B 306 ASP cc_start: 0.8290 (t0) cc_final: 0.7902 (t70) REVERT: B 325 MET cc_start: 0.8002 (mmm) cc_final: 0.7249 (mmm) REVERT: B 329 ASP cc_start: 0.7560 (m-30) cc_final: 0.7025 (m-30) REVERT: B 332 MET cc_start: 0.8294 (mmm) cc_final: 0.7546 (mmm) REVERT: C 50 ASN cc_start: 0.8484 (t0) cc_final: 0.8043 (t0) REVERT: C 203 MET cc_start: 0.8113 (mmm) cc_final: 0.7765 (mmt) REVERT: D 120 ASP cc_start: 0.8010 (m-30) cc_final: 0.7779 (m-30) REVERT: D 210 TYR cc_start: 0.8497 (m-80) cc_final: 0.8003 (m-80) REVERT: D 228 ASN cc_start: 0.8506 (m-40) cc_final: 0.8083 (m-40) REVERT: D 259 MET cc_start: 0.8878 (mmt) cc_final: 0.8654 (mmm) REVERT: D 308 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.8466 (mtm-85) REVERT: D 433 GLN cc_start: 0.8832 (tp40) cc_final: 0.8361 (tm-30) REVERT: E 157 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8840 (mp) REVERT: E 342 GLN cc_start: 0.7604 (OUTLIER) cc_final: 0.7275 (mp10) REVERT: F 127 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8122 (mp0) REVERT: F 179 ASP cc_start: 0.8208 (t70) cc_final: 0.7715 (t0) REVERT: F 204 ILE cc_start: 0.9136 (OUTLIER) cc_final: 0.8886 (mt) REVERT: F 210 TYR cc_start: 0.8515 (m-80) cc_final: 0.7980 (m-80) REVERT: F 228 ASN cc_start: 0.8564 (m-40) cc_final: 0.8020 (m-40) REVERT: G 179 ASP cc_start: 0.8297 (t70) cc_final: 0.8046 (t0) REVERT: G 204 ILE cc_start: 0.9020 (mp) cc_final: 0.8653 (mt) REVERT: G 325 MET cc_start: 0.8309 (mmm) cc_final: 0.7995 (tpp) REVERT: I 149 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7727 (ttm) REVERT: I 179 ASP cc_start: 0.8126 (t70) cc_final: 0.7819 (t0) REVERT: I 204 ILE cc_start: 0.9180 (mp) cc_final: 0.8862 (mt) REVERT: J 2 ARG cc_start: 0.7781 (mtm180) cc_final: 0.7008 (mpt180) REVERT: J 275 VAL cc_start: 0.8961 (OUTLIER) cc_final: 0.8371 (p) REVERT: J 371 VAL cc_start: 0.8977 (m) cc_final: 0.8661 (t) REVERT: K 2 ARG cc_start: 0.7851 (mtm180) cc_final: 0.7173 (mpt180) REVERT: K 76 ASP cc_start: 0.8915 (OUTLIER) cc_final: 0.8635 (m-30) REVERT: K 182 VAL cc_start: 0.8703 (m) cc_final: 0.8435 (p) REVERT: K 248 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7843 (tt) REVERT: K 282 TYR cc_start: 0.8650 (m-10) cc_final: 0.8439 (m-10) REVERT: K 302 MET cc_start: 0.8195 (mtt) cc_final: 0.7893 (mtt) REVERT: K 335 ILE cc_start: 0.8130 (mt) cc_final: 0.7853 (mt) REVERT: L 2 ARG cc_start: 0.7837 (mtm180) cc_final: 0.7484 (mpt180) REVERT: L 35 GLN cc_start: 0.8517 (mp10) cc_final: 0.8266 (mp10) REVERT: L 205 ASP cc_start: 0.7795 (t0) cc_final: 0.7511 (t0) REVERT: L 285 GLN cc_start: 0.8005 (pm20) cc_final: 0.6599 (mm-40) REVERT: L 368 LEU cc_start: 0.8765 (mp) cc_final: 0.8362 (mt) outliers start: 145 outliers final: 97 residues processed: 743 average time/residue: 0.4838 time to fit residues: 607.1274 Evaluate side-chains 703 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 595 time to evaluate : 5.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 302 MET Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 398 MET Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 308 ARG Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain E residue 26 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 113 GLU Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 315 CYS Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 342 GLN Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 204 ILE Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 70 LEU Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain G residue 425 MET Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 356 CYS Chi-restraints excluded: chain H residue 384 ILE Chi-restraints excluded: chain H residue 428 LEU Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 85 GLN Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain I residue 149 MET Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 232 SER Chi-restraints excluded: chain I residue 305 CYS Chi-restraints excluded: chain I residue 356 CYS Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 284 GLU Chi-restraints excluded: chain J residue 335 ILE Chi-restraints excluded: chain J residue 353 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 248 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 327 ASP Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 284 GLU Chi-restraints excluded: chain L residue 335 ILE Chi-restraints excluded: chain L residue 353 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 367 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 475 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 281 optimal weight: 0.0770 chunk 360 optimal weight: 9.9990 chunk 279 optimal weight: 0.0270 chunk 415 optimal weight: 0.5980 chunk 275 optimal weight: 0.9980 chunk 491 optimal weight: 0.8980 chunk 307 optimal weight: 6.9990 chunk 299 optimal weight: 3.9990 chunk 226 optimal weight: 6.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 ASN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 GLN E 88 HIS E 258 ASN F 8 GLN F 14 ASN F 300 ASN G 85 GLN G 167 ASN ** G 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 300 ASN G 349 ASN H 8 GLN ** H 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 309 HIS I 8 GLN I 85 GLN I 197 ASN I 300 ASN I 309 HIS ** J 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 HIS L 88 HIS L 101 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 41742 Z= 0.141 Angle : 0.501 12.588 56718 Z= 0.252 Chirality : 0.041 0.149 6198 Planarity : 0.004 0.042 7386 Dihedral : 9.961 168.811 5769 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.80 % Allowed : 16.92 % Favored : 80.28 % 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: 1.38 (0.12), residues: 5118 helix: 1.60 (0.11), residues: 2364 sheet: 1.12 (0.18), residues: 822 loop : 0.05 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 388 HIS 0.009 0.001 HIS J 88 PHE 0.017 0.001 PHE F 377 TYR 0.014 0.001 TYR E 357 ARG 0.007 0.000 ARG F 278 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10236 Ramachandran restraints generated. 5118 Oldfield, 0 Emsley, 5118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10236 Ramachandran restraints generated. 5118 Oldfield, 0 Emsley, 5118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 775 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 652 time to evaluate : 3.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8262 (mm-30) REVERT: A 154 MET cc_start: 0.8721 (mmp) cc_final: 0.8397 (mmm) REVERT: A 279 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.8007 (pm20) REVERT: A 342 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.7244 (mp10) REVERT: B 41 ASP cc_start: 0.8583 (p0) cc_final: 0.7775 (p0) REVERT: B 47 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8366 (mm-30) REVERT: B 204 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8755 (mt) REVERT: B 259 MET cc_start: 0.8682 (mmm) cc_final: 0.8426 (mmm) REVERT: B 306 ASP cc_start: 0.8346 (t0) cc_final: 0.7877 (t70) REVERT: B 308 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8219 (ttm-80) REVERT: B 325 MET cc_start: 0.8031 (mmm) cc_final: 0.7270 (mmm) REVERT: B 329 ASP cc_start: 0.7631 (m-30) cc_final: 0.7113 (m-30) REVERT: B 332 MET cc_start: 0.8305 (mmm) cc_final: 0.7708 (mmm) REVERT: C 50 ASN cc_start: 0.8447 (t0) cc_final: 0.7986 (t0) REVERT: C 203 MET cc_start: 0.8111 (mmm) cc_final: 0.7759 (mmt) REVERT: D 120 ASP cc_start: 0.8043 (m-30) cc_final: 0.7827 (m-30) REVERT: D 210 TYR cc_start: 0.8458 (m-80) cc_final: 0.8023 (m-80) REVERT: D 433 GLN cc_start: 0.8885 (tp40) cc_final: 0.8428 (tm-30) REVERT: E 215 ARG cc_start: 0.8857 (ttp-110) cc_final: 0.8435 (ttm170) REVERT: F 127 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8165 (mp0) REVERT: F 179 ASP cc_start: 0.8253 (t70) cc_final: 0.7823 (t0) REVERT: F 210 TYR cc_start: 0.8485 (m-80) cc_final: 0.7742 (m-80) REVERT: F 228 ASN cc_start: 0.8511 (m-40) cc_final: 0.7959 (m-40) REVERT: F 417 GLU cc_start: 0.7932 (mp0) cc_final: 0.7152 (mp0) REVERT: G 179 ASP cc_start: 0.8250 (t70) cc_final: 0.8016 (t0) REVERT: G 204 ILE cc_start: 0.9021 (mp) cc_final: 0.8652 (mt) REVERT: G 325 MET cc_start: 0.8388 (mmm) cc_final: 0.8056 (tpp) REVERT: G 433 GLN cc_start: 0.8318 (tp40) cc_final: 0.7763 (tp40) REVERT: I 179 ASP cc_start: 0.8088 (t70) cc_final: 0.7801 (t0) REVERT: I 204 ILE cc_start: 0.9190 (mp) cc_final: 0.8893 (mt) REVERT: J 2 ARG cc_start: 0.7779 (mtm180) cc_final: 0.7237 (mpt180) REVERT: J 275 VAL cc_start: 0.8978 (OUTLIER) cc_final: 0.8411 (p) REVERT: J 371 VAL cc_start: 0.8983 (m) cc_final: 0.8679 (t) REVERT: K 2 ARG cc_start: 0.7962 (mtm180) cc_final: 0.7245 (mpt180) REVERT: K 24 TYR cc_start: 0.8772 (m-80) cc_final: 0.8552 (m-10) REVERT: K 76 ASP cc_start: 0.8894 (OUTLIER) cc_final: 0.8646 (m-30) REVERT: K 182 VAL cc_start: 0.8696 (m) cc_final: 0.8437 (p) REVERT: K 220 GLU cc_start: 0.7493 (pm20) cc_final: 0.7271 (pm20) REVERT: K 248 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7793 (tt) REVERT: K 282 TYR cc_start: 0.8634 (m-10) cc_final: 0.8409 (m-10) REVERT: K 302 MET cc_start: 0.8137 (mtt) cc_final: 0.7913 (mtt) REVERT: K 335 ILE cc_start: 0.7933 (mt) cc_final: 0.7662 (mt) REVERT: L 2 ARG cc_start: 0.7866 (mtm180) cc_final: 0.7511 (mpt180) REVERT: L 35 GLN cc_start: 0.8512 (mp10) cc_final: 0.8236 (mp10) REVERT: L 205 ASP cc_start: 0.7777 (t0) cc_final: 0.7484 (t0) REVERT: L 285 GLN cc_start: 0.8101 (pm20) cc_final: 0.6613 (mm-40) outliers start: 123 outliers final: 86 residues processed: 741 average time/residue: 0.5292 time to fit residues: 662.4173 Evaluate side-chains 692 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 599 time to evaluate : 4.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain E residue 113 GLU Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 315 CYS Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 384 ILE Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 85 GLN Chi-restraints excluded: chain G residue 167 ASN Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain G residue 425 MET Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 356 CYS Chi-restraints excluded: chain H residue 384 ILE Chi-restraints excluded: chain H residue 428 LEU Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 85 GLN Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain I residue 165 ILE Chi-restraints excluded: chain I residue 232 SER Chi-restraints excluded: chain I residue 356 CYS Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 284 GLU Chi-restraints excluded: chain J residue 335 ILE Chi-restraints excluded: chain J residue 353 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 88 HIS Chi-restraints excluded: chain K residue 248 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 327 ASP Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 33 ASP Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 284 GLU Chi-restraints excluded: chain L residue 335 ILE Chi-restraints excluded: chain L residue 353 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 382 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 304 optimal weight: 3.9990 chunk 196 optimal weight: 7.9990 chunk 293 optimal weight: 0.9990 chunk 148 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 312 optimal weight: 1.9990 chunk 334 optimal weight: 4.9990 chunk 243 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 386 optimal weight: 10.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 8 GLN D 258 ASN E 88 HIS F 8 GLN F 300 ASN G 85 GLN ** G 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 300 ASN G 349 ASN H 8 GLN ** H 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 258 ASN I 8 GLN I 300 ASN I 309 HIS J 88 HIS ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 41742 Z= 0.170 Angle : 0.509 12.589 56718 Z= 0.257 Chirality : 0.042 0.150 6198 Planarity : 0.004 0.043 7386 Dihedral : 9.847 169.891 5769 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.06 % Allowed : 16.53 % Favored : 80.41 % 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: 1.35 (0.12), residues: 5118 helix: 1.56 (0.11), residues: 2370 sheet: 1.11 (0.18), residues: 822 loop : 0.06 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 21 HIS 0.015 0.001 HIS K 88 PHE 0.029 0.001 PHE I 169 TYR 0.017 0.001 TYR E 24 ARG 0.007 0.000 ARG F 278 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10236 Ramachandran restraints generated. 5118 Oldfield, 0 Emsley, 5118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10236 Ramachandran restraints generated. 5118 Oldfield, 0 Emsley, 5118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 618 time to evaluate : 4.674 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8269 (mm-30) REVERT: A 154 MET cc_start: 0.8695 (mmp) cc_final: 0.8371 (mmm) REVERT: A 279 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.8013 (pm20) REVERT: A 342 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.7124 (mp10) REVERT: B 41 ASP cc_start: 0.8611 (p0) cc_final: 0.7816 (p0) REVERT: B 47 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8352 (mm-30) REVERT: B 204 ILE cc_start: 0.9164 (OUTLIER) cc_final: 0.8809 (mt) REVERT: B 259 MET cc_start: 0.8681 (mmm) cc_final: 0.8421 (mmm) REVERT: B 306 ASP cc_start: 0.8372 (t0) cc_final: 0.7871 (t70) REVERT: B 325 MET cc_start: 0.8033 (mmm) cc_final: 0.7524 (mmm) REVERT: B 332 MET cc_start: 0.8323 (mmm) cc_final: 0.7729 (mmm) REVERT: B 416 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.8115 (ppp) REVERT: C 50 ASN cc_start: 0.8494 (t0) cc_final: 0.8010 (t0) REVERT: C 90 GLU cc_start: 0.7816 (tp30) cc_final: 0.7611 (tp30) REVERT: C 203 MET cc_start: 0.8126 (mmm) cc_final: 0.7768 (mmt) REVERT: C 269 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8767 (pp) REVERT: C 313 MET cc_start: 0.7959 (mtm) cc_final: 0.7658 (mtm) REVERT: D 120 ASP cc_start: 0.8015 (m-30) cc_final: 0.7662 (m-30) REVERT: D 210 TYR cc_start: 0.8448 (m-80) cc_final: 0.8017 (m-80) REVERT: D 433 GLN cc_start: 0.8837 (tp40) cc_final: 0.8362 (tm-30) REVERT: E 205 ASP cc_start: 0.7555 (t70) cc_final: 0.7064 (t70) REVERT: E 215 ARG cc_start: 0.8826 (ttp-110) cc_final: 0.8336 (ttm170) REVERT: E 342 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.7322 (mp10) REVERT: F 127 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8164 (mp0) REVERT: F 179 ASP cc_start: 0.8279 (t70) cc_final: 0.7850 (t0) REVERT: F 210 TYR cc_start: 0.8445 (m-80) cc_final: 0.7621 (m-80) REVERT: F 228 ASN cc_start: 0.8522 (m-40) cc_final: 0.7988 (m-40) REVERT: F 259 MET cc_start: 0.8957 (mmm) cc_final: 0.8422 (mmt) REVERT: F 417 GLU cc_start: 0.7939 (mp0) cc_final: 0.7147 (mp0) REVERT: F 433 GLN cc_start: 0.9045 (tp40) cc_final: 0.8813 (tp40) REVERT: G 179 ASP cc_start: 0.8254 (t70) cc_final: 0.8024 (t0) REVERT: G 204 ILE cc_start: 0.8973 (mp) cc_final: 0.8603 (mt) REVERT: G 228 ASN cc_start: 0.8076 (m-40) cc_final: 0.7775 (m-40) REVERT: G 325 MET cc_start: 0.8385 (mmm) cc_final: 0.8065 (tpp) REVERT: I 172 VAL cc_start: 0.9389 (t) cc_final: 0.9177 (t) REVERT: I 179 ASP cc_start: 0.8108 (t70) cc_final: 0.7820 (t0) REVERT: I 204 ILE cc_start: 0.9168 (mp) cc_final: 0.8844 (mt) REVERT: J 2 ARG cc_start: 0.7806 (mtm180) cc_final: 0.7256 (mpt180) REVERT: J 275 VAL cc_start: 0.8975 (OUTLIER) cc_final: 0.8365 (p) REVERT: J 367 ASP cc_start: 0.8423 (m-30) cc_final: 0.8223 (m-30) REVERT: J 371 VAL cc_start: 0.8998 (m) cc_final: 0.8704 (t) REVERT: K 2 ARG cc_start: 0.7986 (mtm180) cc_final: 0.7259 (mpt180) REVERT: K 24 TYR cc_start: 0.8781 (m-80) cc_final: 0.8580 (m-10) REVERT: K 76 ASP cc_start: 0.8900 (OUTLIER) cc_final: 0.8664 (m-30) REVERT: K 182 VAL cc_start: 0.8729 (m) cc_final: 0.8481 (p) REVERT: K 248 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7767 (tt) REVERT: K 282 TYR cc_start: 0.8646 (m-10) cc_final: 0.8427 (m-10) REVERT: K 302 MET cc_start: 0.8157 (mtt) cc_final: 0.7947 (mtt) REVERT: K 335 ILE cc_start: 0.7906 (mt) cc_final: 0.7620 (mt) REVERT: L 2 ARG cc_start: 0.7934 (mtm180) cc_final: 0.7572 (mpt180) REVERT: L 35 GLN cc_start: 0.8619 (mp10) cc_final: 0.8330 (mp10) REVERT: L 205 ASP cc_start: 0.7834 (t0) cc_final: 0.7511 (t0) REVERT: L 285 GLN cc_start: 0.8106 (pm20) cc_final: 0.6602 (mm-40) outliers start: 134 outliers final: 102 residues processed: 716 average time/residue: 0.4910 time to fit residues: 589.1977 Evaluate side-chains 707 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 596 time to evaluate : 4.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 215 ARG Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 113 GLU Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 315 CYS Chi-restraints excluded: chain E residue 316 CYS Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 342 GLN Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 384 ILE Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 85 GLN Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 356 CYS Chi-restraints excluded: chain H residue 384 ILE Chi-restraints excluded: chain H residue 428 LEU Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 232 SER Chi-restraints excluded: chain I residue 305 CYS Chi-restraints excluded: chain I residue 356 CYS Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 284 GLU Chi-restraints excluded: chain J residue 335 ILE Chi-restraints excluded: chain J residue 353 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 248 LEU Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 327 ASP Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 33 ASP Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 284 GLU Chi-restraints excluded: chain L residue 295 CYS Chi-restraints excluded: chain L residue 335 ILE Chi-restraints excluded: chain L residue 353 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain L residue 382 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 447 optimal weight: 5.9990 chunk 470 optimal weight: 10.0000 chunk 429 optimal weight: 0.6980 chunk 458 optimal weight: 2.9990 chunk 275 optimal weight: 2.9990 chunk 199 optimal weight: 7.9990 chunk 359 optimal weight: 0.7980 chunk 140 optimal weight: 5.9990 chunk 413 optimal weight: 0.3980 chunk 433 optimal weight: 0.8980 chunk 456 optimal weight: 9.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 300 ASN E 88 HIS ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 300 ASN G 85 GLN G 167 ASN ** G 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 300 ASN H 8 GLN ** H 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 8 GLN ** I 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 300 ASN I 309 HIS ** J 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 HIS ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.4631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 41742 Z= 0.175 Angle : 0.511 13.247 56718 Z= 0.259 Chirality : 0.042 0.170 6198 Planarity : 0.004 0.038 7386 Dihedral : 9.703 172.773 5769 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.01 % Allowed : 16.94 % Favored : 80.05 % 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: 1.34 (0.12), residues: 5118 helix: 1.58 (0.11), residues: 2364 sheet: 1.08 (0.18), residues: 822 loop : 0.03 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 21 HIS 0.011 0.001 HIS K 309 PHE 0.022 0.001 PHE I 169 TYR 0.014 0.001 TYR E 24 ARG 0.012 0.000 ARG C 84 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10236 Ramachandran restraints generated. 5118 Oldfield, 0 Emsley, 5118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10236 Ramachandran restraints generated. 5118 Oldfield, 0 Emsley, 5118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 623 time to evaluate : 4.923 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.8695 (mmp) cc_final: 0.8336 (mmm) REVERT: A 279 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7995 (pm20) REVERT: A 306 ASP cc_start: 0.8800 (OUTLIER) cc_final: 0.8563 (t0) REVERT: A 342 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.7156 (mp10) REVERT: B 41 ASP cc_start: 0.8635 (p0) cc_final: 0.7847 (p0) REVERT: B 204 ILE cc_start: 0.9170 (OUTLIER) cc_final: 0.8820 (mt) REVERT: B 228 ASN cc_start: 0.8543 (m-40) cc_final: 0.8334 (m-40) REVERT: B 259 MET cc_start: 0.8711 (mmm) cc_final: 0.8443 (mmm) REVERT: B 325 MET cc_start: 0.8117 (mmm) cc_final: 0.7836 (mmm) REVERT: B 332 MET cc_start: 0.8325 (mmm) cc_final: 0.7752 (mmm) REVERT: B 416 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.8108 (ppp) REVERT: C 50 ASN cc_start: 0.8583 (t0) cc_final: 0.8084 (t0) REVERT: C 90 GLU cc_start: 0.7835 (tp30) cc_final: 0.7539 (tp30) REVERT: C 203 MET cc_start: 0.8150 (mmm) cc_final: 0.7786 (mmt) REVERT: C 269 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8782 (pp) REVERT: D 120 ASP cc_start: 0.7972 (m-30) cc_final: 0.7646 (m-30) REVERT: D 228 ASN cc_start: 0.8422 (m-40) cc_final: 0.8144 (m-40) REVERT: D 433 GLN cc_start: 0.8860 (tp40) cc_final: 0.8385 (tm-30) REVERT: E 205 ASP cc_start: 0.7550 (t70) cc_final: 0.7046 (t70) REVERT: E 215 ARG cc_start: 0.8820 (ttp-110) cc_final: 0.8324 (ttm170) REVERT: E 342 GLN cc_start: 0.7707 (OUTLIER) cc_final: 0.7349 (mp10) REVERT: F 127 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8172 (mp0) REVERT: F 179 ASP cc_start: 0.8327 (t70) cc_final: 0.7920 (t0) REVERT: F 210 TYR cc_start: 0.8468 (m-80) cc_final: 0.7592 (m-80) REVERT: F 228 ASN cc_start: 0.8529 (m-40) cc_final: 0.7976 (m-40) REVERT: F 259 MET cc_start: 0.8970 (mmm) cc_final: 0.8423 (mmt) REVERT: F 414 ASP cc_start: 0.8555 (t70) cc_final: 0.7764 (t0) REVERT: F 417 GLU cc_start: 0.8017 (mp0) cc_final: 0.7208 (mp0) REVERT: F 433 GLN cc_start: 0.9025 (tp40) cc_final: 0.8546 (tp40) REVERT: G 41 ASP cc_start: 0.8866 (p0) cc_final: 0.8446 (p0) REVERT: G 179 ASP cc_start: 0.8250 (t70) cc_final: 0.8028 (t0) REVERT: G 204 ILE cc_start: 0.8968 (mp) cc_final: 0.8622 (mt) REVERT: G 228 ASN cc_start: 0.8068 (m-40) cc_final: 0.7769 (m-40) REVERT: G 325 MET cc_start: 0.8394 (mmm) cc_final: 0.8094 (tpp) REVERT: G 433 GLN cc_start: 0.8283 (tp40) cc_final: 0.7744 (tp40) REVERT: H 306 ASP cc_start: 0.7641 (OUTLIER) cc_final: 0.7300 (t0) REVERT: I 172 VAL cc_start: 0.9398 (t) cc_final: 0.9198 (t) REVERT: I 179 ASP cc_start: 0.8093 (t70) cc_final: 0.7857 (t0) REVERT: I 204 ILE cc_start: 0.9193 (mp) cc_final: 0.8843 (mt) REVERT: I 372 LYS cc_start: 0.8529 (mmmt) cc_final: 0.8319 (tptt) REVERT: J 2 ARG cc_start: 0.7846 (mtm180) cc_final: 0.7429 (mpt180) REVERT: J 98 ASP cc_start: 0.6913 (p0) cc_final: 0.6654 (p0) REVERT: J 367 ASP cc_start: 0.8417 (m-30) cc_final: 0.8204 (m-30) REVERT: J 371 VAL cc_start: 0.8909 (m) cc_final: 0.8643 (t) REVERT: J 388 TRP cc_start: 0.9021 (m100) cc_final: 0.8807 (m100) REVERT: K 2 ARG cc_start: 0.7983 (mtm180) cc_final: 0.7260 (mpt180) REVERT: K 76 ASP cc_start: 0.8889 (OUTLIER) cc_final: 0.8648 (m-30) REVERT: K 182 VAL cc_start: 0.8754 (m) cc_final: 0.8506 (p) REVERT: K 248 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7752 (tt) REVERT: K 282 TYR cc_start: 0.8658 (m-10) cc_final: 0.8438 (m-10) REVERT: L 2 ARG cc_start: 0.8025 (mtm180) cc_final: 0.7601 (mpt180) REVERT: L 35 GLN cc_start: 0.8658 (mp10) cc_final: 0.8370 (mp10) REVERT: L 205 ASP cc_start: 0.7829 (t0) cc_final: 0.7544 (t0) REVERT: L 285 GLN cc_start: 0.8100 (pm20) cc_final: 0.6524 (mm-40) outliers start: 132 outliers final: 106 residues processed: 722 average time/residue: 0.4929 time to fit residues: 598.5594 Evaluate side-chains 702 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 586 time to evaluate : 4.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 113 GLU Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 316 CYS Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 342 GLN Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 384 ILE Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 167 ASN Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 306 ASP Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 356 CYS Chi-restraints excluded: chain H residue 384 ILE Chi-restraints excluded: chain H residue 428 LEU Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 232 SER Chi-restraints excluded: chain I residue 305 CYS Chi-restraints excluded: chain I residue 356 CYS Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 335 ILE Chi-restraints excluded: chain J residue 353 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 88 HIS Chi-restraints excluded: chain K residue 248 LEU Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 327 ASP Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 33 ASP Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 284 GLU Chi-restraints excluded: chain L residue 295 CYS Chi-restraints excluded: chain L residue 335 ILE Chi-restraints excluded: chain L residue 353 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain L residue 382 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 300 optimal weight: 4.9990 chunk 484 optimal weight: 1.9990 chunk 295 optimal weight: 1.9990 chunk 229 optimal weight: 6.9990 chunk 336 optimal weight: 0.8980 chunk 508 optimal weight: 3.9990 chunk 467 optimal weight: 10.0000 chunk 404 optimal weight: 9.9990 chunk 42 optimal weight: 0.8980 chunk 312 optimal weight: 0.8980 chunk 248 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 ASN D 300 ASN E 88 HIS ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 300 ASN G 167 ASN ** G 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 300 ASN ** G 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 8 GLN ** H 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 8 GLN I 133 GLN ** I 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 300 ASN I 309 HIS J 50 ASN ** J 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.4650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.127 41742 Z= 0.220 Angle : 0.635 59.198 56718 Z= 0.352 Chirality : 0.042 0.431 6198 Planarity : 0.005 0.182 7386 Dihedral : 9.709 172.833 5769 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.76 % Allowed : 17.42 % Favored : 79.82 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.33 (0.12), residues: 5118 helix: 1.58 (0.11), residues: 2364 sheet: 1.06 (0.18), residues: 822 loop : 0.02 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 21 HIS 0.291 0.002 HIS K 88 PHE 0.020 0.001 PHE I 169 TYR 0.024 0.001 TYR K 24 ARG 0.011 0.000 ARG D 278 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10236 Ramachandran restraints generated. 5118 Oldfield, 0 Emsley, 5118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10236 Ramachandran restraints generated. 5118 Oldfield, 0 Emsley, 5118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 586 time to evaluate : 4.646 Fit side-chains revert: symmetry clash REVERT: A 154 MET cc_start: 0.8660 (mmp) cc_final: 0.8339 (mmm) REVERT: A 279 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7993 (pm20) REVERT: A 306 ASP cc_start: 0.8799 (OUTLIER) cc_final: 0.8562 (t0) REVERT: A 342 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.7157 (mp10) REVERT: B 41 ASP cc_start: 0.8427 (p0) cc_final: 0.7857 (p0) REVERT: B 47 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8292 (mm-30) REVERT: B 204 ILE cc_start: 0.9170 (OUTLIER) cc_final: 0.8820 (mt) REVERT: B 211 ASP cc_start: 0.8118 (t0) cc_final: 0.7387 (t0) REVERT: B 215 ARG cc_start: 0.8505 (ptp-110) cc_final: 0.8105 (ptp90) REVERT: B 228 ASN cc_start: 0.8543 (m-40) cc_final: 0.8338 (m-40) REVERT: B 259 MET cc_start: 0.8706 (mmm) cc_final: 0.8442 (mmm) REVERT: B 325 MET cc_start: 0.8090 (mmm) cc_final: 0.7845 (mmm) REVERT: B 332 MET cc_start: 0.8320 (mmm) cc_final: 0.7755 (mmm) REVERT: B 416 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.8109 (ppp) REVERT: C 50 ASN cc_start: 0.8585 (t0) cc_final: 0.8086 (t0) REVERT: C 90 GLU cc_start: 0.7837 (tp30) cc_final: 0.7540 (tp30) REVERT: C 203 MET cc_start: 0.8153 (mmm) cc_final: 0.7786 (mmt) REVERT: C 269 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8783 (pp) REVERT: D 120 ASP cc_start: 0.7972 (m-30) cc_final: 0.7648 (m-30) REVERT: D 433 GLN cc_start: 0.8843 (tp40) cc_final: 0.8353 (tm-30) REVERT: E 205 ASP cc_start: 0.7550 (t70) cc_final: 0.7050 (t70) REVERT: E 215 ARG cc_start: 0.8821 (ttp-110) cc_final: 0.8328 (ttm170) REVERT: E 342 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.7351 (mp10) REVERT: F 127 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8173 (mp0) REVERT: F 179 ASP cc_start: 0.8328 (t70) cc_final: 0.7920 (t0) REVERT: F 210 TYR cc_start: 0.8473 (m-80) cc_final: 0.7594 (m-80) REVERT: F 228 ASN cc_start: 0.8526 (m-40) cc_final: 0.7975 (m-40) REVERT: F 259 MET cc_start: 0.8967 (mmm) cc_final: 0.8430 (mmt) REVERT: F 417 GLU cc_start: 0.8017 (mp0) cc_final: 0.7208 (mp0) REVERT: F 433 GLN cc_start: 0.8984 (tp40) cc_final: 0.8605 (tp40) REVERT: G 179 ASP cc_start: 0.8253 (t70) cc_final: 0.8033 (t0) REVERT: G 204 ILE cc_start: 0.8967 (mp) cc_final: 0.8620 (mt) REVERT: G 228 ASN cc_start: 0.8049 (m-40) cc_final: 0.7745 (m-40) REVERT: G 325 MET cc_start: 0.8387 (mmm) cc_final: 0.8095 (tpp) REVERT: G 433 GLN cc_start: 0.8275 (tp40) cc_final: 0.7740 (tp40) REVERT: H 306 ASP cc_start: 0.7634 (OUTLIER) cc_final: 0.7302 (t0) REVERT: I 179 ASP cc_start: 0.8089 (t70) cc_final: 0.7858 (t0) REVERT: I 204 ILE cc_start: 0.9175 (mp) cc_final: 0.8845 (mt) REVERT: I 372 LYS cc_start: 0.8531 (mmmt) cc_final: 0.8321 (tptt) REVERT: J 2 ARG cc_start: 0.8016 (mtm180) cc_final: 0.7429 (mpt180) REVERT: J 98 ASP cc_start: 0.6911 (p0) cc_final: 0.6657 (p0) REVERT: J 367 ASP cc_start: 0.8416 (m-30) cc_final: 0.8214 (m-30) REVERT: J 371 VAL cc_start: 0.8916 (m) cc_final: 0.8644 (t) REVERT: J 388 TRP cc_start: 0.9012 (m100) cc_final: 0.8807 (m100) REVERT: K 2 ARG cc_start: 0.7995 (mtm180) cc_final: 0.7259 (mpt180) REVERT: K 76 ASP cc_start: 0.8886 (OUTLIER) cc_final: 0.8648 (m-30) REVERT: K 182 VAL cc_start: 0.8753 (m) cc_final: 0.8507 (p) REVERT: K 248 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7752 (tt) REVERT: K 282 TYR cc_start: 0.8656 (m-10) cc_final: 0.8439 (m-10) REVERT: L 2 ARG cc_start: 0.8025 (mtm180) cc_final: 0.7600 (mpt180) REVERT: L 35 GLN cc_start: 0.8658 (mp10) cc_final: 0.8368 (mp10) REVERT: L 205 ASP cc_start: 0.7834 (t0) cc_final: 0.7548 (t0) REVERT: L 285 GLN cc_start: 0.8099 (pm20) cc_final: 0.6524 (mm-40) outliers start: 121 outliers final: 106 residues processed: 676 average time/residue: 0.4863 time to fit residues: 554.8152 Evaluate side-chains 695 residues out of total 4398 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 579 time to evaluate : 4.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 342 GLN Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 149 MET Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 308 ARG Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 416 MET Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain D residue 12 CYS Chi-restraints excluded: chain D residue 41 ASP Chi-restraints excluded: chain D residue 126 SER Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 113 GLU Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 279 GLU Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 316 CYS Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 342 GLN Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 165 ILE Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 384 ILE Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 167 ASN Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain G residue 198 THR Chi-restraints excluded: chain G residue 356 CYS Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 306 ASP Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 356 CYS Chi-restraints excluded: chain H residue 384 ILE Chi-restraints excluded: chain H residue 428 LEU Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 126 SER Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 232 SER Chi-restraints excluded: chain I residue 305 CYS Chi-restraints excluded: chain I residue 356 CYS Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 50 ASN Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 335 ILE Chi-restraints excluded: chain J residue 353 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain K residue 26 LEU Chi-restraints excluded: chain K residue 68 VAL Chi-restraints excluded: chain K residue 76 ASP Chi-restraints excluded: chain K residue 248 LEU Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 327 ASP Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 437 VAL Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 33 ASP Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 284 GLU Chi-restraints excluded: chain L residue 295 CYS Chi-restraints excluded: chain L residue 335 ILE Chi-restraints excluded: chain L residue 353 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain L residue 382 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 321 optimal weight: 0.7980 chunk 430 optimal weight: 0.2980 chunk 123 optimal weight: 0.9980 chunk 373 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 112 optimal weight: 0.0980 chunk 405 optimal weight: 4.9990 chunk 169 optimal weight: 7.9990 chunk 416 optimal weight: 0.0570 chunk 51 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 300 ASN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 300 ASN ** G 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 300 ASN ** G 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 8 GLN ** H 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 8 GLN ** I 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 300 ASN ** J 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.106445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.091508 restraints weight = 67321.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.094938 restraints weight = 32572.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.097282 restraints weight = 19532.949| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.127 41742 Z= 0.222 Angle : 0.610 47.376 56718 Z= 0.337 Chirality : 0.042 0.372 6198 Planarity : 0.005 0.182 7386 Dihedral : 9.709 172.833 5769 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.74 % Allowed : 17.40 % Favored : 79.87 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.33 (0.12), residues: 5118 helix: 1.58 (0.11), residues: 2364 sheet: 1.06 (0.18), residues: 822 loop : 0.02 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 21 HIS 0.291 0.002 HIS K 88 PHE 0.020 0.001 PHE I 169 TYR 0.024 0.001 TYR K 24 ARG 0.011 0.000 ARG D 278 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10840.34 seconds wall clock time: 195 minutes 41.21 seconds (11741.21 seconds total)