Starting phenix.real_space_refine on Sun Mar 17 20:57:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m02_30028/03_2024/6m02_30028.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m02_30028/03_2024/6m02_30028.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m02_30028/03_2024/6m02_30028.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m02_30028/03_2024/6m02_30028.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m02_30028/03_2024/6m02_30028.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m02_30028/03_2024/6m02_30028.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 4 Type Number sf(0) Gaussians S 77 5.16 5 C 12509 2.51 5 N 2996 2.21 5 O 3353 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 81": "OD1" <-> "OD2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ARG 161": "NH1" <-> "NH2" Residue "A TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 310": "OE1" <-> "OE2" Residue "A PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 81": "OD1" <-> "OD2" Residue "B ARG 128": "NH1" <-> "NH2" Residue "B ARG 161": "NH1" <-> "NH2" Residue "B TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 310": "OE1" <-> "OE2" Residue "B PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 81": "OD1" <-> "OD2" Residue "C ARG 128": "NH1" <-> "NH2" Residue "C ARG 161": "NH1" <-> "NH2" Residue "C TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 310": "OE1" <-> "OE2" Residue "C PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 81": "OD1" <-> "OD2" Residue "D ARG 128": "NH1" <-> "NH2" Residue "D ARG 161": "NH1" <-> "NH2" Residue "D TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 310": "OE1" <-> "OE2" Residue "D PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 81": "OD1" <-> "OD2" Residue "E ARG 128": "NH1" <-> "NH2" Residue "E ARG 161": "NH1" <-> "NH2" Residue "E TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 310": "OE1" <-> "OE2" Residue "E PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 81": "OD1" <-> "OD2" Residue "F ARG 128": "NH1" <-> "NH2" Residue "F ARG 161": "NH1" <-> "NH2" Residue "F TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 310": "OE1" <-> "OE2" Residue "F PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 81": "OD1" <-> "OD2" Residue "G ARG 128": "NH1" <-> "NH2" Residue "G ARG 161": "NH1" <-> "NH2" Residue "G TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 310": "OE1" <-> "OE2" Residue "G PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18935 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2705 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain breaks: 3 Chain: "B" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2705 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain breaks: 3 Chain: "C" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2705 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain breaks: 3 Chain: "D" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2705 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain breaks: 3 Chain: "E" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2705 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain breaks: 3 Chain: "F" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2705 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain breaks: 3 Chain: "G" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2705 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 12, 'TRANS': 322} Chain breaks: 3 Time building chain proxies: 9.42, per 1000 atoms: 0.50 Number of scatterers: 18935 At special positions: 0 Unit cell: (109.725, 109.725, 124.355, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 77 16.00 O 3353 8.00 N 2996 7.00 C 12509 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 265 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 265 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 246 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 265 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 246 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 265 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 246 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 265 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 246 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 265 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 246 " distance=2.03 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: 5.85 Conformation dependent library (CDL) restraints added in 3.2 seconds 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4564 Finding SS restraints... Secondary structure from input PDB file: 119 helices and 7 sheets defined 60.6% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 12 through 16 Processing helix chain 'A' and resid 32 through 54 removed outlier: 3.692A pdb=" N LYS A 36 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA A 42 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Proline residue: A 46 - end of helix removed outlier: 3.879A pdb=" N LEU A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 87 removed outlier: 3.711A pdb=" N TRP A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.818A pdb=" N LYS A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 119 removed outlier: 3.948A pdb=" N ALA A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'A' and resid 135 through 155 removed outlier: 3.960A pdb=" N PHE A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU A 144 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 146 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 149 " --> pdb=" O GLU A 145 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A 153 " --> pdb=" O VAL A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 162 removed outlier: 3.916A pdb=" N ARG A 161 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP A 162 " --> pdb=" O LYS A 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 157 through 162' Processing helix chain 'A' and resid 194 through 200 removed outlier: 3.506A pdb=" N LEU A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 237 removed outlier: 4.440A pdb=" N LEU A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY A 232 " --> pdb=" O CYS A 228 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A 236 " --> pdb=" O GLY A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 256 removed outlier: 4.041A pdb=" N ASN A 255 " --> pdb=" O ILE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 283 removed outlier: 3.976A pdb=" N LEU A 275 " --> pdb=" O GLY A 271 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL A 278 " --> pdb=" O GLN A 274 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL A 282 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL A 283 " --> pdb=" O ILE A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 295 Proline residue: A 289 - end of helix removed outlier: 3.548A pdb=" N VAL A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 312 removed outlier: 3.938A pdb=" N ILE A 311 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 339 removed outlier: 4.199A pdb=" N LEU A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU A 336 " --> pdb=" O ASN A 332 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN A 338 " --> pdb=" O PHE A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 353 removed outlier: 4.151A pdb=" N LYS A 346 " --> pdb=" O VAL A 342 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N CYS A 347 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 350 " --> pdb=" O LYS A 346 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU A 351 " --> pdb=" O CYS A 347 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU A 352 " --> pdb=" O LEU A 348 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 removed outlier: 3.569A pdb=" N GLN A 419 " --> pdb=" O LYS A 415 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ARG A 420 " --> pdb=" O ASN A 416 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 421 " --> pdb=" O ALA A 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 16 Processing helix chain 'B' and resid 32 through 54 removed outlier: 3.692A pdb=" N LYS B 36 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA B 42 " --> pdb=" O VAL B 38 " (cutoff:3.500A) Proline residue: B 46 - end of helix removed outlier: 3.879A pdb=" N LEU B 52 " --> pdb=" O LEU B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 87 removed outlier: 3.711A pdb=" N TRP B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.818A pdb=" N LYS B 107 " --> pdb=" O LEU B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 119 removed outlier: 3.948A pdb=" N ALA B 117 " --> pdb=" O LEU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 131 Processing helix chain 'B' and resid 135 through 155 removed outlier: 3.961A pdb=" N PHE B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU B 144 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 146 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B 149 " --> pdb=" O GLU B 145 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR B 150 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA B 153 " --> pdb=" O VAL B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 162 removed outlier: 3.916A pdb=" N ARG B 161 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP B 162 " --> pdb=" O LYS B 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 157 through 162' Processing helix chain 'B' and resid 194 through 200 removed outlier: 3.506A pdb=" N LEU B 200 " --> pdb=" O VAL B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 237 removed outlier: 4.440A pdb=" N LEU B 219 " --> pdb=" O SER B 215 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY B 232 " --> pdb=" O CYS B 228 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER B 236 " --> pdb=" O GLY B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 256 removed outlier: 4.042A pdb=" N ASN B 255 " --> pdb=" O ILE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 283 removed outlier: 3.976A pdb=" N LEU B 275 " --> pdb=" O GLY B 271 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL B 278 " --> pdb=" O GLN B 274 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL B 282 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL B 283 " --> pdb=" O ILE B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 295 Proline residue: B 289 - end of helix removed outlier: 3.547A pdb=" N VAL B 292 " --> pdb=" O ALA B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 312 removed outlier: 3.938A pdb=" N ILE B 311 " --> pdb=" O VAL B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 339 removed outlier: 4.199A pdb=" N LEU B 333 " --> pdb=" O SER B 329 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU B 336 " --> pdb=" O ASN B 332 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU B 337 " --> pdb=" O LEU B 333 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN B 338 " --> pdb=" O PHE B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 353 removed outlier: 4.151A pdb=" N LYS B 346 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N CYS B 347 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 350 " --> pdb=" O LYS B 346 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU B 351 " --> pdb=" O CYS B 347 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU B 352 " --> pdb=" O LEU B 348 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 422 removed outlier: 3.569A pdb=" N GLN B 419 " --> pdb=" O LYS B 415 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ARG B 420 " --> pdb=" O ASN B 416 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU B 421 " --> pdb=" O ALA B 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 16 Processing helix chain 'C' and resid 32 through 54 removed outlier: 3.692A pdb=" N LYS C 36 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA C 42 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Proline residue: C 46 - end of helix removed outlier: 3.879A pdb=" N LEU C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 87 removed outlier: 3.711A pdb=" N TRP C 85 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA C 86 " --> pdb=" O SER C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.818A pdb=" N LYS C 107 " --> pdb=" O LEU C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 119 removed outlier: 3.948A pdb=" N ALA C 117 " --> pdb=" O LEU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 131 Processing helix chain 'C' and resid 135 through 155 removed outlier: 3.960A pdb=" N PHE C 141 " --> pdb=" O SER C 137 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU C 144 " --> pdb=" O LYS C 140 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU C 146 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR C 150 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA C 153 " --> pdb=" O VAL C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 162 removed outlier: 3.916A pdb=" N ARG C 161 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP C 162 " --> pdb=" O LYS C 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 157 through 162' Processing helix chain 'C' and resid 194 through 200 removed outlier: 3.505A pdb=" N LEU C 200 " --> pdb=" O VAL C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 237 removed outlier: 4.440A pdb=" N LEU C 219 " --> pdb=" O SER C 215 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE C 229 " --> pdb=" O LEU C 225 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY C 232 " --> pdb=" O CYS C 228 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER C 236 " --> pdb=" O GLY C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 256 removed outlier: 4.042A pdb=" N ASN C 255 " --> pdb=" O ILE C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 283 removed outlier: 3.976A pdb=" N LEU C 275 " --> pdb=" O GLY C 271 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL C 278 " --> pdb=" O GLN C 274 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL C 282 " --> pdb=" O VAL C 278 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL C 283 " --> pdb=" O ILE C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 295 Proline residue: C 289 - end of helix removed outlier: 3.548A pdb=" N VAL C 292 " --> pdb=" O ALA C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 312 removed outlier: 3.939A pdb=" N ILE C 311 " --> pdb=" O VAL C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 339 removed outlier: 4.199A pdb=" N LEU C 333 " --> pdb=" O SER C 329 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU C 336 " --> pdb=" O ASN C 332 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU C 337 " --> pdb=" O LEU C 333 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN C 338 " --> pdb=" O PHE C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 353 removed outlier: 4.151A pdb=" N LYS C 346 " --> pdb=" O VAL C 342 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N CYS C 347 " --> pdb=" O LYS C 343 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL C 350 " --> pdb=" O LYS C 346 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU C 351 " --> pdb=" O CYS C 347 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU C 352 " --> pdb=" O LEU C 348 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN C 353 " --> pdb=" O LYS C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 422 removed outlier: 3.569A pdb=" N GLN C 419 " --> pdb=" O LYS C 415 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ARG C 420 " --> pdb=" O ASN C 416 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU C 421 " --> pdb=" O ALA C 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 16 Processing helix chain 'D' and resid 32 through 54 removed outlier: 3.692A pdb=" N LYS D 36 " --> pdb=" O LEU D 32 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA D 42 " --> pdb=" O VAL D 38 " (cutoff:3.500A) Proline residue: D 46 - end of helix removed outlier: 3.879A pdb=" N LEU D 52 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 87 removed outlier: 3.711A pdb=" N TRP D 85 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA D 86 " --> pdb=" O SER D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.818A pdb=" N LYS D 107 " --> pdb=" O LEU D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 119 removed outlier: 3.948A pdb=" N ALA D 117 " --> pdb=" O LEU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 131 Processing helix chain 'D' and resid 135 through 155 removed outlier: 3.961A pdb=" N PHE D 141 " --> pdb=" O SER D 137 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU D 144 " --> pdb=" O LYS D 140 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU D 146 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL D 149 " --> pdb=" O GLU D 145 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR D 150 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA D 153 " --> pdb=" O VAL D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 162 removed outlier: 3.916A pdb=" N ARG D 161 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP D 162 " --> pdb=" O LYS D 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 157 through 162' Processing helix chain 'D' and resid 194 through 200 removed outlier: 3.506A pdb=" N LEU D 200 " --> pdb=" O VAL D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 237 removed outlier: 4.440A pdb=" N LEU D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE D 229 " --> pdb=" O LEU D 225 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY D 232 " --> pdb=" O CYS D 228 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER D 236 " --> pdb=" O GLY D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 256 removed outlier: 4.041A pdb=" N ASN D 255 " --> pdb=" O ILE D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 283 removed outlier: 3.976A pdb=" N LEU D 275 " --> pdb=" O GLY D 271 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL D 278 " --> pdb=" O GLN D 274 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL D 282 " --> pdb=" O VAL D 278 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL D 283 " --> pdb=" O ILE D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 295 Proline residue: D 289 - end of helix removed outlier: 3.548A pdb=" N VAL D 292 " --> pdb=" O ALA D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 312 removed outlier: 3.938A pdb=" N ILE D 311 " --> pdb=" O VAL D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 339 removed outlier: 4.199A pdb=" N LEU D 333 " --> pdb=" O SER D 329 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU D 336 " --> pdb=" O ASN D 332 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU D 337 " --> pdb=" O LEU D 333 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN D 338 " --> pdb=" O PHE D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 353 removed outlier: 4.151A pdb=" N LYS D 346 " --> pdb=" O VAL D 342 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N CYS D 347 " --> pdb=" O LYS D 343 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL D 350 " --> pdb=" O LYS D 346 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU D 351 " --> pdb=" O CYS D 347 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU D 352 " --> pdb=" O LEU D 348 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN D 353 " --> pdb=" O LYS D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 removed outlier: 3.569A pdb=" N GLN D 419 " --> pdb=" O LYS D 415 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ARG D 420 " --> pdb=" O ASN D 416 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU D 421 " --> pdb=" O ALA D 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 16 Processing helix chain 'E' and resid 32 through 54 removed outlier: 3.692A pdb=" N LYS E 36 " --> pdb=" O LEU E 32 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA E 42 " --> pdb=" O VAL E 38 " (cutoff:3.500A) Proline residue: E 46 - end of helix removed outlier: 3.878A pdb=" N LEU E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 87 removed outlier: 3.711A pdb=" N TRP E 85 " --> pdb=" O ASP E 81 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA E 86 " --> pdb=" O SER E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 108 removed outlier: 3.818A pdb=" N LYS E 107 " --> pdb=" O LEU E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 119 removed outlier: 3.948A pdb=" N ALA E 117 " --> pdb=" O LEU E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'E' and resid 135 through 155 removed outlier: 3.960A pdb=" N PHE E 141 " --> pdb=" O SER E 137 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU E 144 " --> pdb=" O LYS E 140 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU E 146 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL E 149 " --> pdb=" O GLU E 145 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR E 150 " --> pdb=" O LEU E 146 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA E 153 " --> pdb=" O VAL E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 162 removed outlier: 3.916A pdb=" N ARG E 161 " --> pdb=" O ALA E 157 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP E 162 " --> pdb=" O LYS E 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 157 through 162' Processing helix chain 'E' and resid 194 through 200 removed outlier: 3.506A pdb=" N LEU E 200 " --> pdb=" O VAL E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 237 removed outlier: 4.440A pdb=" N LEU E 219 " --> pdb=" O SER E 215 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE E 229 " --> pdb=" O LEU E 225 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY E 232 " --> pdb=" O CYS E 228 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER E 236 " --> pdb=" O GLY E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 256 removed outlier: 4.041A pdb=" N ASN E 255 " --> pdb=" O ILE E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 283 removed outlier: 3.976A pdb=" N LEU E 275 " --> pdb=" O GLY E 271 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL E 278 " --> pdb=" O GLN E 274 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL E 282 " --> pdb=" O VAL E 278 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL E 283 " --> pdb=" O ILE E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 295 Proline residue: E 289 - end of helix removed outlier: 3.547A pdb=" N VAL E 292 " --> pdb=" O ALA E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 312 removed outlier: 3.938A pdb=" N ILE E 311 " --> pdb=" O VAL E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 339 removed outlier: 4.199A pdb=" N LEU E 333 " --> pdb=" O SER E 329 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU E 336 " --> pdb=" O ASN E 332 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU E 337 " --> pdb=" O LEU E 333 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN E 338 " --> pdb=" O PHE E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 353 removed outlier: 4.151A pdb=" N LYS E 346 " --> pdb=" O VAL E 342 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N CYS E 347 " --> pdb=" O LYS E 343 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL E 350 " --> pdb=" O LYS E 346 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU E 351 " --> pdb=" O CYS E 347 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLU E 352 " --> pdb=" O LEU E 348 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN E 353 " --> pdb=" O LYS E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 422 removed outlier: 3.570A pdb=" N GLN E 419 " --> pdb=" O LYS E 415 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ARG E 420 " --> pdb=" O ASN E 416 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU E 421 " --> pdb=" O ALA E 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 16 Processing helix chain 'F' and resid 32 through 54 removed outlier: 3.692A pdb=" N LYS F 36 " --> pdb=" O LEU F 32 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA F 42 " --> pdb=" O VAL F 38 " (cutoff:3.500A) Proline residue: F 46 - end of helix removed outlier: 3.879A pdb=" N LEU F 52 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 87 removed outlier: 3.711A pdb=" N TRP F 85 " --> pdb=" O ASP F 81 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA F 86 " --> pdb=" O SER F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 108 removed outlier: 3.818A pdb=" N LYS F 107 " --> pdb=" O LEU F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 119 removed outlier: 3.948A pdb=" N ALA F 117 " --> pdb=" O LEU F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 131 Processing helix chain 'F' and resid 135 through 155 removed outlier: 3.960A pdb=" N PHE F 141 " --> pdb=" O SER F 137 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU F 144 " --> pdb=" O LYS F 140 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU F 146 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL F 149 " --> pdb=" O GLU F 145 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR F 150 " --> pdb=" O LEU F 146 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA F 153 " --> pdb=" O VAL F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 162 removed outlier: 3.916A pdb=" N ARG F 161 " --> pdb=" O ALA F 157 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP F 162 " --> pdb=" O LYS F 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 157 through 162' Processing helix chain 'F' and resid 194 through 200 removed outlier: 3.506A pdb=" N LEU F 200 " --> pdb=" O VAL F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 237 removed outlier: 4.441A pdb=" N LEU F 219 " --> pdb=" O SER F 215 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE F 229 " --> pdb=" O LEU F 225 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY F 232 " --> pdb=" O CYS F 228 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER F 236 " --> pdb=" O GLY F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 256 removed outlier: 4.040A pdb=" N ASN F 255 " --> pdb=" O ILE F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 283 removed outlier: 3.976A pdb=" N LEU F 275 " --> pdb=" O GLY F 271 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL F 278 " --> pdb=" O GLN F 274 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL F 282 " --> pdb=" O VAL F 278 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL F 283 " --> pdb=" O ILE F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 295 Proline residue: F 289 - end of helix removed outlier: 3.547A pdb=" N VAL F 292 " --> pdb=" O ALA F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 312 removed outlier: 3.938A pdb=" N ILE F 311 " --> pdb=" O VAL F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 339 removed outlier: 4.199A pdb=" N LEU F 333 " --> pdb=" O SER F 329 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU F 336 " --> pdb=" O ASN F 332 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU F 337 " --> pdb=" O LEU F 333 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN F 338 " --> pdb=" O PHE F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 353 removed outlier: 4.151A pdb=" N LYS F 346 " --> pdb=" O VAL F 342 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N CYS F 347 " --> pdb=" O LYS F 343 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL F 350 " --> pdb=" O LYS F 346 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU F 351 " --> pdb=" O CYS F 347 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU F 352 " --> pdb=" O LEU F 348 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN F 353 " --> pdb=" O LYS F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 422 removed outlier: 3.569A pdb=" N GLN F 419 " --> pdb=" O LYS F 415 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ARG F 420 " --> pdb=" O ASN F 416 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU F 421 " --> pdb=" O ALA F 417 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 16 Processing helix chain 'G' and resid 32 through 54 removed outlier: 3.692A pdb=" N LYS G 36 " --> pdb=" O LEU G 32 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA G 42 " --> pdb=" O VAL G 38 " (cutoff:3.500A) Proline residue: G 46 - end of helix removed outlier: 3.879A pdb=" N LEU G 52 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 87 removed outlier: 3.710A pdb=" N TRP G 85 " --> pdb=" O ASP G 81 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA G 86 " --> pdb=" O SER G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 108 removed outlier: 3.819A pdb=" N LYS G 107 " --> pdb=" O LEU G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 119 removed outlier: 3.948A pdb=" N ALA G 117 " --> pdb=" O LEU G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 131 Processing helix chain 'G' and resid 135 through 155 removed outlier: 3.961A pdb=" N PHE G 141 " --> pdb=" O SER G 137 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU G 144 " --> pdb=" O LYS G 140 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU G 146 " --> pdb=" O ILE G 142 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL G 149 " --> pdb=" O GLU G 145 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR G 150 " --> pdb=" O LEU G 146 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA G 153 " --> pdb=" O VAL G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 157 through 162 removed outlier: 3.916A pdb=" N ARG G 161 " --> pdb=" O ALA G 157 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP G 162 " --> pdb=" O LYS G 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 157 through 162' Processing helix chain 'G' and resid 194 through 200 removed outlier: 3.506A pdb=" N LEU G 200 " --> pdb=" O VAL G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 237 removed outlier: 4.440A pdb=" N LEU G 219 " --> pdb=" O SER G 215 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE G 229 " --> pdb=" O LEU G 225 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY G 232 " --> pdb=" O CYS G 228 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER G 236 " --> pdb=" O GLY G 232 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 256 removed outlier: 4.041A pdb=" N ASN G 255 " --> pdb=" O ILE G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 283 removed outlier: 3.976A pdb=" N LEU G 275 " --> pdb=" O GLY G 271 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL G 278 " --> pdb=" O GLN G 274 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL G 282 " --> pdb=" O VAL G 278 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL G 283 " --> pdb=" O ILE G 279 " (cutoff:3.500A) Processing helix chain 'G' and resid 283 through 295 Proline residue: G 289 - end of helix removed outlier: 3.548A pdb=" N VAL G 292 " --> pdb=" O ALA G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 312 removed outlier: 3.938A pdb=" N ILE G 311 " --> pdb=" O VAL G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 339 removed outlier: 4.199A pdb=" N LEU G 333 " --> pdb=" O SER G 329 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU G 336 " --> pdb=" O ASN G 332 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU G 337 " --> pdb=" O LEU G 333 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN G 338 " --> pdb=" O PHE G 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 353 removed outlier: 4.150A pdb=" N LYS G 346 " --> pdb=" O VAL G 342 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N CYS G 347 " --> pdb=" O LYS G 343 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL G 350 " --> pdb=" O LYS G 346 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU G 351 " --> pdb=" O CYS G 347 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU G 352 " --> pdb=" O LEU G 348 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN G 353 " --> pdb=" O LYS G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 422 removed outlier: 3.569A pdb=" N GLN G 419 " --> pdb=" O LYS G 415 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ARG G 420 " --> pdb=" O ASN G 416 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU G 421 " --> pdb=" O ALA G 417 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 removed outlier: 3.609A pdb=" N PHE A 244 " --> pdb=" O CYS A 265 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 66 removed outlier: 3.609A pdb=" N PHE B 244 " --> pdb=" O CYS B 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 66 removed outlier: 3.609A pdb=" N PHE C 244 " --> pdb=" O CYS C 265 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 66 removed outlier: 3.608A pdb=" N PHE D 244 " --> pdb=" O CYS D 265 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 66 removed outlier: 3.608A pdb=" N PHE E 244 " --> pdb=" O CYS E 265 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 66 removed outlier: 3.609A pdb=" N PHE F 244 " --> pdb=" O CYS F 265 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 66 removed outlier: 3.609A pdb=" N PHE G 244 " --> pdb=" O CYS G 265 " (cutoff:3.500A) 679 hydrogen bonds defined for protein. 1890 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: 5.41 Time building geometry restraints manager: 6.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5660 1.34 - 1.46: 4040 1.46 - 1.57: 9564 1.57 - 1.69: 0 1.69 - 1.81: 91 Bond restraints: 19355 Sorted by residual: bond pdb=" C PRO G 123 " pdb=" N PRO G 124 " ideal model delta sigma weight residual 1.337 1.356 -0.020 1.06e-02 8.90e+03 3.56e+00 bond pdb=" C PRO F 123 " pdb=" N PRO F 124 " ideal model delta sigma weight residual 1.337 1.356 -0.020 1.06e-02 8.90e+03 3.51e+00 bond pdb=" C PRO A 123 " pdb=" N PRO A 124 " ideal model delta sigma weight residual 1.337 1.356 -0.020 1.06e-02 8.90e+03 3.39e+00 bond pdb=" C PRO E 123 " pdb=" N PRO E 124 " ideal model delta sigma weight residual 1.337 1.356 -0.019 1.06e-02 8.90e+03 3.37e+00 bond pdb=" C PRO C 123 " pdb=" N PRO C 124 " ideal model delta sigma weight residual 1.337 1.356 -0.019 1.06e-02 8.90e+03 3.34e+00 ... (remaining 19350 not shown) Histogram of bond angle deviations from ideal: 100.24 - 107.30: 494 107.30 - 114.35: 11265 114.35 - 121.40: 10315 121.40 - 128.46: 4015 128.46 - 135.51: 126 Bond angle restraints: 26215 Sorted by residual: angle pdb=" CA PRO E 123 " pdb=" C PRO E 123 " pdb=" N PRO E 124 " ideal model delta sigma weight residual 117.93 122.19 -4.26 1.20e+00 6.94e-01 1.26e+01 angle pdb=" CA PRO F 123 " pdb=" C PRO F 123 " pdb=" N PRO F 124 " ideal model delta sigma weight residual 117.93 122.19 -4.26 1.20e+00 6.94e-01 1.26e+01 angle pdb=" CA PRO A 123 " pdb=" C PRO A 123 " pdb=" N PRO A 124 " ideal model delta sigma weight residual 117.93 122.19 -4.26 1.20e+00 6.94e-01 1.26e+01 angle pdb=" CA PRO B 123 " pdb=" C PRO B 123 " pdb=" N PRO B 124 " ideal model delta sigma weight residual 117.93 122.18 -4.25 1.20e+00 6.94e-01 1.26e+01 angle pdb=" CA PRO C 123 " pdb=" C PRO C 123 " pdb=" N PRO C 124 " ideal model delta sigma weight residual 117.93 122.18 -4.25 1.20e+00 6.94e-01 1.25e+01 ... (remaining 26210 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 10023 17.97 - 35.93: 1292 35.93 - 53.90: 284 53.90 - 71.86: 7 71.86 - 89.83: 28 Dihedral angle restraints: 11634 sinusoidal: 4634 harmonic: 7000 Sorted by residual: dihedral pdb=" CA ARG A 75 " pdb=" C ARG A 75 " pdb=" N GLN A 76 " pdb=" CA GLN A 76 " ideal model delta harmonic sigma weight residual 180.00 156.98 23.02 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA ARG D 75 " pdb=" C ARG D 75 " pdb=" N GLN D 76 " pdb=" CA GLN D 76 " ideal model delta harmonic sigma weight residual 180.00 156.98 23.02 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA ARG G 75 " pdb=" C ARG G 75 " pdb=" N GLN G 76 " pdb=" CA GLN G 76 " ideal model delta harmonic sigma weight residual 180.00 156.99 23.01 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 11631 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2086 0.045 - 0.089: 687 0.089 - 0.134: 205 0.134 - 0.179: 61 0.179 - 0.223: 20 Chirality restraints: 3059 Sorted by residual: chirality pdb=" CB VAL E 278 " pdb=" CA VAL E 278 " pdb=" CG1 VAL E 278 " pdb=" CG2 VAL E 278 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CB VAL F 278 " pdb=" CA VAL F 278 " pdb=" CG1 VAL F 278 " pdb=" CG2 VAL F 278 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CB VAL C 278 " pdb=" CA VAL C 278 " pdb=" CG1 VAL C 278 " pdb=" CG2 VAL C 278 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 3056 not shown) Planarity restraints: 3206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 122 " -0.047 5.00e-02 4.00e+02 7.01e-02 7.87e+00 pdb=" N PRO A 123 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 123 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 123 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 122 " -0.047 5.00e-02 4.00e+02 7.01e-02 7.85e+00 pdb=" N PRO C 123 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO C 123 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 123 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 122 " 0.047 5.00e-02 4.00e+02 7.01e-02 7.85e+00 pdb=" N PRO E 123 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO E 123 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 123 " 0.039 5.00e-02 4.00e+02 ... (remaining 3203 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 5282 2.79 - 3.32: 16628 3.32 - 3.85: 30005 3.85 - 4.37: 35740 4.37 - 4.90: 58553 Nonbonded interactions: 146208 Sorted by model distance: nonbonded pdb=" OH TYR G 83 " pdb=" OG SER G 250 " model vdw 2.263 2.440 nonbonded pdb=" OH TYR A 83 " pdb=" OG SER A 250 " model vdw 2.263 2.440 nonbonded pdb=" OH TYR C 83 " pdb=" OG SER C 250 " model vdw 2.263 2.440 nonbonded pdb=" OH TYR F 83 " pdb=" OG SER F 250 " model vdw 2.263 2.440 nonbonded pdb=" OH TYR D 83 " pdb=" OG SER D 250 " model vdw 2.264 2.440 ... (remaining 146203 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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 individual isotropic 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: 1.390 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: 0.020 Extract box with map and model: 7.860 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 45.410 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 19355 Z= 0.352 Angle : 0.955 10.512 26215 Z= 0.526 Chirality : 0.052 0.223 3059 Planarity : 0.007 0.070 3206 Dihedral : 16.354 89.826 7028 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 1.64 % Allowed : 12.83 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -6.29 (0.12), residues: 2289 helix: -4.88 (0.05), residues: 1365 sheet: -4.13 (0.33), residues: 126 loop : -2.27 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 74 HIS 0.003 0.001 HIS D 106 PHE 0.018 0.002 PHE E 15 TYR 0.014 0.002 TYR B 193 ARG 0.006 0.001 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 323 time to evaluate : 2.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ILE cc_start: 0.7723 (mm) cc_final: 0.7503 (mm) REVERT: A 212 LYS cc_start: 0.8057 (mmtt) cc_final: 0.7801 (mtmm) REVERT: A 295 LEU cc_start: 0.8040 (mt) cc_final: 0.7548 (mt) REVERT: A 339 ILE cc_start: 0.8466 (mm) cc_final: 0.8239 (mm) REVERT: A 422 LEU cc_start: 0.7115 (OUTLIER) cc_final: 0.6652 (mm) REVERT: B 63 GLN cc_start: 0.7704 (mm110) cc_final: 0.7395 (mm110) REVERT: B 212 LYS cc_start: 0.7855 (mmtt) cc_final: 0.7573 (mtmm) REVERT: B 295 LEU cc_start: 0.7931 (mt) cc_final: 0.7560 (mt) REVERT: B 422 LEU cc_start: 0.6908 (OUTLIER) cc_final: 0.6520 (mm) REVERT: C 50 ILE cc_start: 0.7788 (mm) cc_final: 0.7573 (mm) REVERT: C 212 LYS cc_start: 0.8109 (mmtt) cc_final: 0.7794 (mtmm) REVERT: C 339 ILE cc_start: 0.8528 (mm) cc_final: 0.8155 (mm) REVERT: C 422 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6870 (mm) REVERT: D 295 LEU cc_start: 0.8162 (mt) cc_final: 0.7809 (mt) REVERT: D 310 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7538 (tm-30) REVERT: D 339 ILE cc_start: 0.8446 (mm) cc_final: 0.8193 (mm) REVERT: D 422 LEU cc_start: 0.7073 (OUTLIER) cc_final: 0.6671 (mm) REVERT: E 48 LEU cc_start: 0.9015 (mm) cc_final: 0.8800 (mm) REVERT: E 50 ILE cc_start: 0.7608 (mm) cc_final: 0.7398 (mm) REVERT: E 212 LYS cc_start: 0.8016 (mmtt) cc_final: 0.7649 (mtmm) REVERT: E 295 LEU cc_start: 0.7866 (mt) cc_final: 0.7436 (mt) REVERT: E 339 ILE cc_start: 0.8443 (mm) cc_final: 0.8096 (mm) REVERT: E 418 ARG cc_start: 0.6420 (tpm170) cc_final: 0.6119 (tpp-160) REVERT: E 419 GLN cc_start: 0.5070 (pt0) cc_final: 0.4342 (tt0) REVERT: E 422 LEU cc_start: 0.7178 (OUTLIER) cc_final: 0.6263 (mm) REVERT: F 212 LYS cc_start: 0.8032 (mmtt) cc_final: 0.7767 (mtmm) REVERT: F 295 LEU cc_start: 0.7731 (mt) cc_final: 0.7358 (mt) REVERT: F 339 ILE cc_start: 0.8387 (mm) cc_final: 0.8044 (mm) REVERT: F 422 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.7080 (mm) REVERT: G 212 LYS cc_start: 0.8031 (mmtt) cc_final: 0.7643 (mtmm) REVERT: G 295 LEU cc_start: 0.8079 (mt) cc_final: 0.7631 (mt) REVERT: G 310 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7565 (tm-30) REVERT: G 339 ILE cc_start: 0.8370 (mm) cc_final: 0.8132 (mm) REVERT: G 422 LEU cc_start: 0.6995 (OUTLIER) cc_final: 0.6686 (mm) outliers start: 35 outliers final: 0 residues processed: 344 average time/residue: 0.3928 time to fit residues: 188.6103 Evaluate side-chains 206 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 199 time to evaluate : 2.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain E residue 422 LEU Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain G residue 422 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 0.0010 chunk 175 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 118 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 181 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 134 optimal weight: 0.2980 chunk 209 optimal weight: 1.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 95 GLN A 134 HIS A 198 GLN ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN B 95 GLN B 134 HIS B 198 GLN ** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN C 95 GLN C 134 HIS C 198 GLN ** C 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 GLN D 95 GLN D 134 HIS D 198 GLN ** D 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN E 95 GLN E 134 HIS E 198 GLN ** E 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN F 95 GLN F 134 HIS ** F 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 GLN G 95 GLN G 134 HIS G 198 GLN ** G 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 19355 Z= 0.150 Angle : 0.637 11.652 26215 Z= 0.327 Chirality : 0.038 0.140 3059 Planarity : 0.005 0.043 3206 Dihedral : 5.981 58.872 2520 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.81 % Allowed : 14.43 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.78 (0.15), residues: 2289 helix: -3.60 (0.10), residues: 1414 sheet: -3.15 (0.38), residues: 126 loop : -1.68 (0.23), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 74 HIS 0.001 0.000 HIS G 190 PHE 0.012 0.001 PHE F 15 TYR 0.016 0.002 TYR E 345 ARG 0.007 0.001 ARG F 152 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 191 time to evaluate : 2.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8708 (mt) cc_final: 0.8240 (pp) REVERT: A 212 LYS cc_start: 0.7924 (mmtt) cc_final: 0.7573 (mtmm) REVERT: B 63 GLN cc_start: 0.7467 (mm110) cc_final: 0.7179 (mm110) REVERT: B 74 TRP cc_start: 0.7372 (OUTLIER) cc_final: 0.6630 (t60) REVERT: B 339 ILE cc_start: 0.8809 (tp) cc_final: 0.8474 (tp) REVERT: C 128 ARG cc_start: 0.7562 (ttm170) cc_final: 0.7279 (tmm-80) REVERT: C 212 LYS cc_start: 0.7929 (mmtt) cc_final: 0.7667 (mtmm) REVERT: C 418 ARG cc_start: 0.7076 (tpp-160) cc_final: 0.6178 (tpp-160) REVERT: D 128 ARG cc_start: 0.7662 (ttm170) cc_final: 0.7346 (tmm-80) REVERT: D 209 LEU cc_start: 0.6622 (tp) cc_final: 0.6352 (tt) REVERT: E 49 LEU cc_start: 0.8639 (mt) cc_final: 0.8090 (pp) REVERT: E 212 LYS cc_start: 0.7914 (mmtt) cc_final: 0.7558 (mtmm) REVERT: E 295 LEU cc_start: 0.7863 (mt) cc_final: 0.7478 (mt) REVERT: F 49 LEU cc_start: 0.8573 (mt) cc_final: 0.8188 (pp) REVERT: F 128 ARG cc_start: 0.7776 (ttm170) cc_final: 0.7412 (tmm-80) REVERT: F 212 LYS cc_start: 0.7829 (mmtt) cc_final: 0.7627 (mtmm) REVERT: G 212 LYS cc_start: 0.7918 (mmtt) cc_final: 0.7533 (mtmm) REVERT: G 234 TYR cc_start: 0.7735 (t80) cc_final: 0.7495 (t80) REVERT: G 310 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7523 (tm-30) REVERT: G 418 ARG cc_start: 0.7102 (tpp-160) cc_final: 0.6865 (tpp-160) outliers start: 81 outliers final: 36 residues processed: 252 average time/residue: 0.3453 time to fit residues: 126.4585 Evaluate side-chains 201 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 164 time to evaluate : 2.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 74 TRP Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 422 LEU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 74 TRP Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 299 PHE Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 420 ARG Chi-restraints excluded: chain F residue 422 LEU Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 422 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 116 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 174 optimal weight: 0.2980 chunk 142 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 210 optimal weight: 5.9990 chunk 227 optimal weight: 0.9980 chunk 187 optimal weight: 1.9990 chunk 208 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 168 optimal weight: 0.0770 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 GLN ** F 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19355 Z= 0.133 Angle : 0.567 10.123 26215 Z= 0.287 Chirality : 0.037 0.122 3059 Planarity : 0.004 0.040 3206 Dihedral : 5.110 31.332 2516 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 4.23 % Allowed : 13.86 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.82 (0.16), residues: 2289 helix: -2.70 (0.12), residues: 1442 sheet: -2.32 (0.38), residues: 126 loop : -1.67 (0.24), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 74 HIS 0.001 0.000 HIS D 106 PHE 0.013 0.001 PHE F 15 TYR 0.016 0.001 TYR D 234 ARG 0.005 0.000 ARG C 152 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 171 time to evaluate : 2.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8671 (mt) cc_final: 0.8218 (pp) REVERT: A 212 LYS cc_start: 0.7943 (mmtt) cc_final: 0.7587 (mtmm) REVERT: B 63 GLN cc_start: 0.7663 (mm110) cc_final: 0.7419 (mm110) REVERT: B 74 TRP cc_start: 0.7554 (OUTLIER) cc_final: 0.6664 (t60) REVERT: C 37 MET cc_start: 0.8100 (tpp) cc_final: 0.7682 (tpp) REVERT: C 128 ARG cc_start: 0.7692 (ttm170) cc_final: 0.7384 (tmm-80) REVERT: C 212 LYS cc_start: 0.7954 (mmtt) cc_final: 0.7596 (mtmm) REVERT: C 418 ARG cc_start: 0.7109 (tpp-160) cc_final: 0.6232 (tpp-160) REVERT: D 128 ARG cc_start: 0.7805 (ttm170) cc_final: 0.7442 (tmm-80) REVERT: D 209 LEU cc_start: 0.6417 (tp) cc_final: 0.6144 (tt) REVERT: E 49 LEU cc_start: 0.8639 (mt) cc_final: 0.8163 (pp) REVERT: E 212 LYS cc_start: 0.7923 (mmtt) cc_final: 0.7542 (mtmm) REVERT: E 295 LEU cc_start: 0.7894 (mt) cc_final: 0.7495 (mt) REVERT: E 310 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7718 (tm-30) REVERT: F 49 LEU cc_start: 0.8588 (mt) cc_final: 0.8055 (pp) REVERT: F 128 ARG cc_start: 0.7822 (ttm170) cc_final: 0.7550 (tmm-80) REVERT: F 212 LYS cc_start: 0.7904 (mmtt) cc_final: 0.7609 (mtmm) REVERT: F 351 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.7156 (mt) REVERT: G 212 LYS cc_start: 0.8001 (mmtt) cc_final: 0.7495 (mtmm) REVERT: G 310 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7577 (tm-30) REVERT: G 351 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7389 (mt) REVERT: G 418 ARG cc_start: 0.7129 (tpp-160) cc_final: 0.6902 (tpp-160) outliers start: 90 outliers final: 68 residues processed: 239 average time/residue: 0.3238 time to fit residues: 115.4890 Evaluate side-chains 215 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 144 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 74 TRP Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 74 TRP Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 74 TRP Chi-restraints excluded: chain D residue 207 ASN Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 74 TRP Chi-restraints excluded: chain E residue 207 ASN Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 299 PHE Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 351 LEU Chi-restraints excluded: chain F residue 420 ARG Chi-restraints excluded: chain F residue 423 ASP Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 207 ASN Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 351 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 207 optimal weight: 0.6980 chunk 158 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 141 optimal weight: 0.7980 chunk 210 optimal weight: 4.9990 chunk 223 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 199 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 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 56 GLN ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 GLN ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 GLN ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 ASN ** E 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 GLN ** G 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 19355 Z= 0.140 Angle : 0.566 8.792 26215 Z= 0.282 Chirality : 0.037 0.113 3059 Planarity : 0.003 0.040 3206 Dihedral : 4.640 15.571 2506 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.04 % Allowed : 16.35 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.17), residues: 2289 helix: -2.09 (0.13), residues: 1407 sheet: -1.88 (0.39), residues: 126 loop : -1.34 (0.24), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 74 HIS 0.001 0.000 HIS A 319 PHE 0.013 0.001 PHE F 15 TYR 0.016 0.001 TYR B 234 ARG 0.003 0.000 ARG D 29 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 154 time to evaluate : 2.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8638 (mt) cc_final: 0.8184 (pp) REVERT: A 212 LYS cc_start: 0.8013 (mmtt) cc_final: 0.7609 (mtmm) REVERT: B 74 TRP cc_start: 0.7599 (OUTLIER) cc_final: 0.6735 (t60) REVERT: B 310 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7550 (tm-30) REVERT: C 37 MET cc_start: 0.8029 (tpp) cc_final: 0.7691 (tpp) REVERT: C 49 LEU cc_start: 0.8634 (mt) cc_final: 0.8177 (pp) REVERT: C 128 ARG cc_start: 0.7849 (ttm170) cc_final: 0.7565 (tmm-80) REVERT: C 212 LYS cc_start: 0.7904 (mmtt) cc_final: 0.7401 (mtmm) REVERT: C 418 ARG cc_start: 0.7217 (tpp-160) cc_final: 0.6290 (tpp-160) REVERT: D 49 LEU cc_start: 0.8588 (mt) cc_final: 0.8142 (pp) REVERT: D 128 ARG cc_start: 0.7870 (ttm170) cc_final: 0.7486 (tmm-80) REVERT: D 209 LEU cc_start: 0.6532 (tp) cc_final: 0.6265 (tt) REVERT: E 49 LEU cc_start: 0.8698 (mt) cc_final: 0.8164 (pp) REVERT: E 212 LYS cc_start: 0.7852 (mmtt) cc_final: 0.7470 (mtmm) REVERT: E 310 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7640 (tm-30) REVERT: F 49 LEU cc_start: 0.8638 (mt) cc_final: 0.8130 (pp) REVERT: F 128 ARG cc_start: 0.7844 (ttm170) cc_final: 0.7569 (tmm-80) REVERT: F 212 LYS cc_start: 0.7914 (mmtt) cc_final: 0.7558 (mtmm) REVERT: G 212 LYS cc_start: 0.7986 (mmtt) cc_final: 0.7432 (mtmm) REVERT: G 310 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7612 (tm-30) REVERT: G 418 ARG cc_start: 0.7175 (tpp-160) cc_final: 0.6879 (tpp-160) outliers start: 86 outliers final: 72 residues processed: 222 average time/residue: 0.3343 time to fit residues: 110.8731 Evaluate side-chains 214 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 141 time to evaluate : 2.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 74 TRP Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 74 TRP Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 74 TRP Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 207 ASN Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 74 TRP Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 207 ASN Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 299 PHE Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 74 TRP Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 207 ASN Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 278 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 185 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 166 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 190 optimal weight: 0.0270 chunk 154 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 114 optimal weight: 0.2980 chunk 200 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 ASN C 280 ASN ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 ASN ** D 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 19355 Z= 0.120 Angle : 0.534 7.810 26215 Z= 0.267 Chirality : 0.036 0.120 3059 Planarity : 0.003 0.040 3206 Dihedral : 4.409 15.969 2506 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.67 % Allowed : 18.70 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.18), residues: 2289 helix: -1.77 (0.14), residues: 1400 sheet: -1.67 (0.39), residues: 126 loop : -1.29 (0.24), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 74 HIS 0.001 0.000 HIS D 106 PHE 0.012 0.001 PHE E 79 TYR 0.015 0.001 TYR D 230 ARG 0.004 0.000 ARG B 152 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 152 time to evaluate : 2.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8647 (mt) cc_final: 0.8332 (pp) REVERT: A 128 ARG cc_start: 0.7938 (ttm170) cc_final: 0.7672 (tmm-80) REVERT: A 212 LYS cc_start: 0.7998 (mmtt) cc_final: 0.7562 (mtmm) REVERT: A 280 ASN cc_start: 0.7869 (OUTLIER) cc_final: 0.7179 (t0) REVERT: B 49 LEU cc_start: 0.8512 (mt) cc_final: 0.8103 (pp) REVERT: B 74 TRP cc_start: 0.7552 (OUTLIER) cc_final: 0.6674 (t60) REVERT: B 212 LYS cc_start: 0.7920 (mmtt) cc_final: 0.7411 (mtmm) REVERT: B 243 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7481 (pp20) REVERT: B 310 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7577 (tm-30) REVERT: C 37 MET cc_start: 0.8026 (tpp) cc_final: 0.7706 (tpp) REVERT: C 49 LEU cc_start: 0.8593 (mt) cc_final: 0.8168 (pp) REVERT: C 128 ARG cc_start: 0.7869 (ttm170) cc_final: 0.7581 (tmm-80) REVERT: C 212 LYS cc_start: 0.7891 (mmtt) cc_final: 0.7256 (mtmm) REVERT: C 418 ARG cc_start: 0.7228 (tpp-160) cc_final: 0.6184 (tpp-160) REVERT: D 49 LEU cc_start: 0.8508 (mt) cc_final: 0.8085 (pp) REVERT: D 128 ARG cc_start: 0.7882 (ttm170) cc_final: 0.7577 (tmm-80) REVERT: E 49 LEU cc_start: 0.8635 (mt) cc_final: 0.8145 (pp) REVERT: F 37 MET cc_start: 0.7959 (tpp) cc_final: 0.7681 (tpp) REVERT: F 49 LEU cc_start: 0.8627 (mt) cc_final: 0.8156 (pp) REVERT: F 128 ARG cc_start: 0.7832 (ttm170) cc_final: 0.7583 (tmm-80) REVERT: G 43 VAL cc_start: 0.8097 (t) cc_final: 0.7844 (m) REVERT: G 49 LEU cc_start: 0.8581 (mt) cc_final: 0.8071 (pp) REVERT: G 212 LYS cc_start: 0.7961 (mmtt) cc_final: 0.7338 (mtmm) REVERT: G 310 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7662 (tm-30) REVERT: G 418 ARG cc_start: 0.7221 (tpp-160) cc_final: 0.6900 (tpp-160) outliers start: 78 outliers final: 69 residues processed: 214 average time/residue: 0.3319 time to fit residues: 106.5449 Evaluate side-chains 210 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 138 time to evaluate : 2.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 74 TRP Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 74 TRP Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 74 TRP Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 207 ASN Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 74 TRP Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 207 ASN Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 299 PHE Chi-restraints excluded: chain E residue 423 ASP Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 74 TRP Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 420 ARG Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 207 ASN Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 299 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 75 optimal weight: 0.9990 chunk 201 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 131 optimal weight: 0.6980 chunk 55 optimal weight: 0.0370 chunk 223 optimal weight: 0.8980 chunk 185 optimal weight: 8.9990 chunk 103 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 73 optimal weight: 0.0870 chunk 117 optimal weight: 1.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 ASN E 411 ASN ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 GLN ** G 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19355 Z= 0.119 Angle : 0.528 9.263 26215 Z= 0.264 Chirality : 0.036 0.122 3059 Planarity : 0.003 0.040 3206 Dihedral : 4.312 15.143 2506 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.90 % Allowed : 19.50 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.18), residues: 2289 helix: -1.56 (0.14), residues: 1400 sheet: -1.59 (0.38), residues: 126 loop : -1.20 (0.24), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 74 HIS 0.000 0.000 HIS D 106 PHE 0.012 0.001 PHE D 15 TYR 0.019 0.001 TYR D 10 ARG 0.004 0.000 ARG B 152 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 141 time to evaluate : 2.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8651 (mt) cc_final: 0.8316 (pp) REVERT: A 128 ARG cc_start: 0.7938 (ttm170) cc_final: 0.7678 (tmm-80) REVERT: A 212 LYS cc_start: 0.7965 (mmtt) cc_final: 0.7514 (mtmm) REVERT: A 243 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7563 (tm-30) REVERT: B 49 LEU cc_start: 0.8495 (mt) cc_final: 0.8115 (pp) REVERT: B 74 TRP cc_start: 0.7548 (OUTLIER) cc_final: 0.6672 (t60) REVERT: B 154 ILE cc_start: 0.7059 (tp) cc_final: 0.6702 (mm) REVERT: B 212 LYS cc_start: 0.7936 (mmtt) cc_final: 0.7401 (mtmm) REVERT: B 310 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7604 (tm-30) REVERT: C 37 MET cc_start: 0.8021 (tpp) cc_final: 0.7718 (tpp) REVERT: C 49 LEU cc_start: 0.8602 (mt) cc_final: 0.8193 (pp) REVERT: C 128 ARG cc_start: 0.7887 (ttm170) cc_final: 0.7606 (tmm-80) REVERT: C 418 ARG cc_start: 0.7186 (tpp-160) cc_final: 0.6263 (tpp-160) REVERT: D 49 LEU cc_start: 0.8507 (mt) cc_final: 0.8120 (pp) REVERT: D 128 ARG cc_start: 0.7889 (ttm170) cc_final: 0.7587 (tmm-80) REVERT: D 243 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7516 (pp20) REVERT: E 49 LEU cc_start: 0.8588 (mt) cc_final: 0.8155 (pp) REVERT: E 212 LYS cc_start: 0.7811 (mmtt) cc_final: 0.7272 (mtmm) REVERT: F 37 MET cc_start: 0.7954 (tpp) cc_final: 0.7692 (tpp) REVERT: F 49 LEU cc_start: 0.8564 (mt) cc_final: 0.8172 (pp) REVERT: F 128 ARG cc_start: 0.7848 (ttm170) cc_final: 0.7593 (tmm-80) REVERT: G 43 VAL cc_start: 0.8125 (t) cc_final: 0.7840 (m) REVERT: G 49 LEU cc_start: 0.8589 (mt) cc_final: 0.8108 (pp) REVERT: G 310 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7677 (tm-30) REVERT: G 418 ARG cc_start: 0.7265 (tpp-160) cc_final: 0.6955 (tpp-160) outliers start: 83 outliers final: 73 residues processed: 210 average time/residue: 0.3287 time to fit residues: 103.3677 Evaluate side-chains 214 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 138 time to evaluate : 2.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 74 TRP Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 74 TRP Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 74 TRP Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 207 ASN Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 74 TRP Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 207 ASN Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 299 PHE Chi-restraints excluded: chain E residue 423 ASP Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 74 TRP Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 299 PHE Chi-restraints excluded: chain F residue 423 ASP Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 207 ASN Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 299 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 215 optimal weight: 0.4980 chunk 25 optimal weight: 0.3980 chunk 127 optimal weight: 0.9990 chunk 163 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 188 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 222 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 135 optimal weight: 0.6980 chunk 102 optimal weight: 0.0980 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 ASN C 280 ASN ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 ASN ** D 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 56 GLN ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 264 GLN ** F 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 19355 Z= 0.117 Angle : 0.524 8.694 26215 Z= 0.262 Chirality : 0.036 0.151 3059 Planarity : 0.003 0.040 3206 Dihedral : 4.214 15.091 2506 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.85 % Allowed : 20.11 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.18), residues: 2289 helix: -1.37 (0.14), residues: 1400 sheet: -1.56 (0.37), residues: 126 loop : -1.19 (0.24), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 74 HIS 0.000 0.000 HIS D 106 PHE 0.011 0.001 PHE F 15 TYR 0.016 0.001 TYR D 230 ARG 0.004 0.000 ARG B 152 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 142 time to evaluate : 2.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8667 (mt) cc_final: 0.8354 (pp) REVERT: A 128 ARG cc_start: 0.7943 (ttm170) cc_final: 0.7682 (tmm-80) REVERT: A 212 LYS cc_start: 0.7958 (mmtt) cc_final: 0.7499 (mtmm) REVERT: A 243 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7513 (tm-30) REVERT: B 43 VAL cc_start: 0.8223 (t) cc_final: 0.7930 (m) REVERT: B 49 LEU cc_start: 0.8466 (mt) cc_final: 0.8063 (pp) REVERT: B 74 TRP cc_start: 0.7541 (OUTLIER) cc_final: 0.6668 (t60) REVERT: B 154 ILE cc_start: 0.7012 (tp) cc_final: 0.6763 (mm) REVERT: B 212 LYS cc_start: 0.7892 (mmtt) cc_final: 0.7317 (mtmm) REVERT: B 243 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7469 (pp20) REVERT: B 310 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7600 (tm-30) REVERT: C 37 MET cc_start: 0.7977 (tpp) cc_final: 0.7683 (tpp) REVERT: C 49 LEU cc_start: 0.8658 (mt) cc_final: 0.8228 (pp) REVERT: C 128 ARG cc_start: 0.7893 (ttm170) cc_final: 0.7608 (tmm-80) REVERT: C 418 ARG cc_start: 0.7117 (tpp-160) cc_final: 0.6102 (tpp-160) REVERT: D 49 LEU cc_start: 0.8501 (mt) cc_final: 0.8122 (pp) REVERT: D 128 ARG cc_start: 0.7873 (ttm170) cc_final: 0.7580 (tmm-80) REVERT: D 243 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7165 (tm-30) REVERT: E 49 LEU cc_start: 0.8547 (mt) cc_final: 0.8160 (pp) REVERT: E 212 LYS cc_start: 0.7738 (mmtt) cc_final: 0.7136 (mtmm) REVERT: E 243 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7504 (pp20) REVERT: F 37 MET cc_start: 0.7979 (tpp) cc_final: 0.7724 (tpp) REVERT: F 49 LEU cc_start: 0.8514 (mt) cc_final: 0.8154 (pp) REVERT: F 128 ARG cc_start: 0.7867 (ttm170) cc_final: 0.7666 (tmm-80) REVERT: G 43 VAL cc_start: 0.8120 (t) cc_final: 0.7764 (m) REVERT: G 49 LEU cc_start: 0.8602 (mt) cc_final: 0.8136 (pp) REVERT: G 243 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7527 (pp20) REVERT: G 310 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7695 (tm-30) REVERT: G 418 ARG cc_start: 0.7255 (tpp-160) cc_final: 0.6359 (tpp-160) outliers start: 82 outliers final: 72 residues processed: 208 average time/residue: 0.3358 time to fit residues: 104.5761 Evaluate side-chains 215 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 137 time to evaluate : 2.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 74 TRP Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 74 TRP Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 207 ASN Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 74 TRP Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 207 ASN Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 299 PHE Chi-restraints excluded: chain E residue 423 ASP Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 74 TRP Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 299 PHE Chi-restraints excluded: chain F residue 420 ARG Chi-restraints excluded: chain F residue 423 ASP Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 207 ASN Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain G residue 243 GLU Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 299 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 137 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 132 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 175 optimal weight: 1.9990 chunk 202 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 HIS ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN B 319 HIS ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 HIS ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 ASN D 319 HIS D 411 ASN ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 319 HIS F 280 ASN F 319 HIS ** F 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 280 ASN G 319 HIS ** G 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 19355 Z= 0.352 Angle : 0.731 9.257 26215 Z= 0.363 Chirality : 0.044 0.201 3059 Planarity : 0.004 0.061 3206 Dihedral : 5.472 20.132 2506 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 4.75 % Allowed : 20.82 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.17), residues: 2289 helix: -1.68 (0.14), residues: 1386 sheet: -1.85 (0.38), residues: 126 loop : -1.40 (0.23), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP A 74 HIS 0.002 0.001 HIS A 106 PHE 0.029 0.002 PHE A 15 TYR 0.023 0.002 TYR A 10 ARG 0.005 0.001 ARG E 152 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 144 time to evaluate : 2.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8739 (mt) cc_final: 0.8416 (pp) REVERT: A 212 LYS cc_start: 0.7955 (mmtt) cc_final: 0.7367 (mtmm) REVERT: A 243 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7735 (tm-30) REVERT: B 49 LEU cc_start: 0.8561 (mt) cc_final: 0.8194 (pp) REVERT: B 74 TRP cc_start: 0.7555 (OUTLIER) cc_final: 0.6821 (t60) REVERT: B 154 ILE cc_start: 0.7028 (tp) cc_final: 0.6755 (mm) REVERT: B 212 LYS cc_start: 0.7998 (mmtt) cc_final: 0.7430 (mtmm) REVERT: B 243 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7163 (tm-30) REVERT: B 310 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7625 (tm-30) REVERT: C 37 MET cc_start: 0.7904 (tpp) cc_final: 0.7655 (tpp) REVERT: C 49 LEU cc_start: 0.8690 (mt) cc_final: 0.8279 (pp) REVERT: C 243 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7366 (tm-30) REVERT: C 418 ARG cc_start: 0.7233 (tpp-160) cc_final: 0.6367 (tpp-160) REVERT: D 49 LEU cc_start: 0.8565 (mt) cc_final: 0.8221 (pp) REVERT: D 128 ARG cc_start: 0.7981 (ttm170) cc_final: 0.7556 (tmm-80) REVERT: D 243 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7350 (tm-30) REVERT: E 49 LEU cc_start: 0.8647 (mt) cc_final: 0.8334 (pp) REVERT: E 212 LYS cc_start: 0.7801 (mmtt) cc_final: 0.7140 (mtmm) REVERT: E 242 ASP cc_start: 0.8038 (OUTLIER) cc_final: 0.7566 (m-30) REVERT: E 295 LEU cc_start: 0.7958 (mt) cc_final: 0.7419 (mt) REVERT: F 37 MET cc_start: 0.7891 (tpp) cc_final: 0.7575 (tpp) REVERT: F 49 LEU cc_start: 0.8595 (mt) cc_final: 0.8312 (pp) REVERT: F 128 ARG cc_start: 0.7882 (ttm170) cc_final: 0.7564 (tmm-80) REVERT: G 49 LEU cc_start: 0.8717 (mt) cc_final: 0.8376 (pp) REVERT: G 243 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7356 (tm-30) REVERT: G 310 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7779 (tm-30) REVERT: G 418 ARG cc_start: 0.7340 (tpp-160) cc_final: 0.7133 (tpp-160) outliers start: 101 outliers final: 79 residues processed: 230 average time/residue: 0.3081 time to fit residues: 107.7299 Evaluate side-chains 225 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 139 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 74 TRP Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 74 TRP Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 207 ASN Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 74 TRP Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 207 ASN Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 299 PHE Chi-restraints excluded: chain E residue 423 ASP Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 74 TRP Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 224 ILE Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 299 PHE Chi-restraints excluded: chain F residue 420 ARG Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 207 ASN Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 243 GLU Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 285 VAL Chi-restraints excluded: chain G residue 299 PHE Chi-restraints excluded: chain G residue 336 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 213 optimal weight: 0.9980 chunk 194 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 162 optimal weight: 0.0060 chunk 63 optimal weight: 10.0000 chunk 187 optimal weight: 0.9980 chunk 196 optimal weight: 0.9990 chunk 206 optimal weight: 7.9990 chunk 136 optimal weight: 3.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 ASN C 280 ASN ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 ASN ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 19355 Z= 0.143 Angle : 0.557 9.634 26215 Z= 0.279 Chirality : 0.037 0.159 3059 Planarity : 0.003 0.042 3206 Dihedral : 4.703 16.999 2506 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.18 % Allowed : 21.48 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.18), residues: 2289 helix: -1.44 (0.14), residues: 1421 sheet: -1.71 (0.39), residues: 126 loop : -1.34 (0.24), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 74 HIS 0.001 0.000 HIS D 106 PHE 0.012 0.001 PHE A 108 TYR 0.021 0.001 TYR A 10 ARG 0.004 0.000 ARG B 152 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 147 time to evaluate : 2.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8672 (mt) cc_final: 0.8369 (pp) REVERT: A 128 ARG cc_start: 0.7951 (ttm170) cc_final: 0.7537 (tmm-80) REVERT: A 212 LYS cc_start: 0.7981 (mmtt) cc_final: 0.7468 (mtmm) REVERT: A 243 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7714 (tm-30) REVERT: B 49 LEU cc_start: 0.8549 (mt) cc_final: 0.8169 (pp) REVERT: B 74 TRP cc_start: 0.7466 (OUTLIER) cc_final: 0.6712 (t60) REVERT: B 243 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7048 (tm-30) REVERT: B 310 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7653 (tm-30) REVERT: C 37 MET cc_start: 0.7955 (tpp) cc_final: 0.7710 (tpp) REVERT: C 49 LEU cc_start: 0.8692 (mt) cc_final: 0.8292 (pp) REVERT: C 128 ARG cc_start: 0.7860 (ttm170) cc_final: 0.7470 (tmm-80) REVERT: C 243 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7275 (tm-30) REVERT: C 418 ARG cc_start: 0.7314 (tpp-160) cc_final: 0.6399 (tpp-160) REVERT: D 49 LEU cc_start: 0.8499 (mt) cc_final: 0.8108 (pp) REVERT: D 128 ARG cc_start: 0.7915 (ttm170) cc_final: 0.7605 (tmm-80) REVERT: D 243 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7286 (tm-30) REVERT: E 49 LEU cc_start: 0.8586 (mt) cc_final: 0.8249 (pp) REVERT: E 243 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7662 (pp20) REVERT: E 295 LEU cc_start: 0.7897 (mt) cc_final: 0.7511 (mt) REVERT: E 299 PHE cc_start: 0.7589 (OUTLIER) cc_final: 0.6914 (t80) REVERT: F 128 ARG cc_start: 0.7864 (ttm170) cc_final: 0.7456 (tmm-80) REVERT: G 49 LEU cc_start: 0.8694 (mt) cc_final: 0.8348 (pp) REVERT: G 212 LYS cc_start: 0.7920 (mmtt) cc_final: 0.7211 (mtmm) REVERT: G 310 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7731 (tm-30) outliers start: 89 outliers final: 70 residues processed: 223 average time/residue: 0.3173 time to fit residues: 107.3843 Evaluate side-chains 206 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 129 time to evaluate : 2.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 40 CYS Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 74 TRP Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 74 TRP Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 207 ASN Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 243 GLU Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain D residue 351 LEU Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 74 TRP Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 207 ASN Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 299 PHE Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 74 TRP Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 299 PHE Chi-restraints excluded: chain F residue 420 ARG Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 207 ASN Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 285 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 219 optimal weight: 0.8980 chunk 133 optimal weight: 0.0770 chunk 104 optimal weight: 0.0030 chunk 152 optimal weight: 3.9990 chunk 230 optimal weight: 9.9990 chunk 211 optimal weight: 5.9990 chunk 183 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 141 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 overall best weight: 1.1952 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 411 ASN ** G 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 19355 Z= 0.166 Angle : 0.617 14.245 26215 Z= 0.295 Chirality : 0.038 0.131 3059 Planarity : 0.003 0.043 3206 Dihedral : 4.700 16.707 2506 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.90 % Allowed : 21.80 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.18), residues: 2289 helix: -1.33 (0.14), residues: 1421 sheet: -1.68 (0.40), residues: 126 loop : -1.32 (0.24), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 74 HIS 0.001 0.000 HIS D 106 PHE 0.013 0.001 PHE A 108 TYR 0.019 0.001 TYR B 10 ARG 0.004 0.000 ARG B 152 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4578 Ramachandran restraints generated. 2289 Oldfield, 0 Emsley, 2289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 135 time to evaluate : 2.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 LEU cc_start: 0.8677 (mt) cc_final: 0.8384 (pp) REVERT: A 128 ARG cc_start: 0.7959 (ttm170) cc_final: 0.7547 (tmm-80) REVERT: A 212 LYS cc_start: 0.7887 (mmtt) cc_final: 0.7339 (mtmm) REVERT: A 243 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7678 (tm-30) REVERT: A 418 ARG cc_start: 0.7218 (tpp-160) cc_final: 0.6851 (tpp-160) REVERT: B 43 VAL cc_start: 0.8148 (t) cc_final: 0.7743 (m) REVERT: B 49 LEU cc_start: 0.8546 (mt) cc_final: 0.8179 (pp) REVERT: B 74 TRP cc_start: 0.7512 (OUTLIER) cc_final: 0.6717 (t60) REVERT: B 243 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7093 (tm-30) REVERT: B 310 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7680 (tm-30) REVERT: C 37 MET cc_start: 0.7915 (tpp) cc_final: 0.7688 (tpp) REVERT: C 49 LEU cc_start: 0.8686 (mt) cc_final: 0.8307 (pp) REVERT: C 128 ARG cc_start: 0.7878 (ttm170) cc_final: 0.7493 (tmm-80) REVERT: C 243 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7371 (tm-30) REVERT: C 418 ARG cc_start: 0.7279 (tpp-160) cc_final: 0.6326 (tpp-160) REVERT: D 49 LEU cc_start: 0.8508 (mt) cc_final: 0.8114 (pp) REVERT: D 128 ARG cc_start: 0.7915 (ttm170) cc_final: 0.7592 (tmm-80) REVERT: E 37 MET cc_start: 0.8167 (tpp) cc_final: 0.7942 (tpp) REVERT: E 49 LEU cc_start: 0.8501 (mt) cc_final: 0.8192 (pp) REVERT: E 243 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7623 (pp20) REVERT: E 299 PHE cc_start: 0.7579 (OUTLIER) cc_final: 0.6928 (t80) REVERT: F 74 TRP cc_start: 0.7569 (OUTLIER) cc_final: 0.6953 (t60) REVERT: F 128 ARG cc_start: 0.7871 (ttm170) cc_final: 0.7463 (tmm-80) REVERT: G 49 LEU cc_start: 0.8646 (mt) cc_final: 0.8361 (pp) REVERT: G 310 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7727 (tm-30) outliers start: 83 outliers final: 69 residues processed: 205 average time/residue: 0.3333 time to fit residues: 102.5033 Evaluate side-chains 209 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 133 time to evaluate : 2.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 THR Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 74 TRP Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 74 TRP Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 207 ASN Chi-restraints excluded: chain B residue 214 ILE Chi-restraints excluded: chain B residue 224 ILE Chi-restraints excluded: chain B residue 243 GLU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 207 ASN Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 246 CYS Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 299 PHE Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 74 TRP Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 207 ASN Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 224 ILE Chi-restraints excluded: chain D residue 278 VAL Chi-restraints excluded: chain D residue 285 VAL Chi-restraints excluded: chain D residue 299 PHE Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 74 TRP Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 207 ASN Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 299 PHE Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 74 TRP Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 207 ASN Chi-restraints excluded: chain F residue 214 ILE Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 299 PHE Chi-restraints excluded: chain F residue 420 ARG Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 74 TRP Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 207 ASN Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain G residue 224 ILE Chi-restraints excluded: chain G residue 246 CYS Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 285 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 0.0070 chunk 56 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 50 optimal weight: 4.9990 chunk 183 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 chunk 188 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 33 optimal weight: 10.0000 chunk 161 optimal weight: 1.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 ASN C 280 ASN C 411 ASN ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 264 GLN E 207 ASN E 280 ASN ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 411 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.132509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.112929 restraints weight = 41148.906| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 3.16 r_work: 0.3843 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 19355 Z= 0.125 Angle : 0.582 12.873 26215 Z= 0.279 Chirality : 0.037 0.112 3059 Planarity : 0.003 0.043 3206 Dihedral : 4.364 15.705 2506 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.71 % Allowed : 22.18 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.18), residues: 2289 helix: -1.16 (0.14), residues: 1421 sheet: -1.81 (0.38), residues: 126 loop : -1.26 (0.24), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 74 HIS 0.001 0.000 HIS D 106 PHE 0.011 0.001 PHE E 79 TYR 0.019 0.001 TYR B 10 ARG 0.004 0.000 ARG G 128 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3687.28 seconds wall clock time: 67 minutes 52.80 seconds (4072.80 seconds total)