Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 00:19:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m02_30028/04_2023/6m02_30028.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m02_30028/04_2023/6m02_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_30028/04_2023/6m02_30028.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m02_30028/04_2023/6m02_30028.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m02_30028/04_2023/6m02_30028.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m02_30028/04_2023/6m02_30028.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 9.80, per 1000 atoms: 0.52 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: 7.48 Conformation dependent library (CDL) restraints added in 2.8 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: 0.76 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: 5.34 Time building geometry restraints manager: 7.97 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: 1.870 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: 8.660 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 46.590 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.970 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 2.354 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 outliers start: 35 outliers final: 0 residues processed: 344 average time/residue: 0.4083 time to fit residues: 196.1415 Evaluate side-chains 188 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 2.123 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 0.8980 chunk 175 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 59 optimal weight: 0.0170 chunk 118 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 181 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 chunk 134 optimal weight: 0.2980 chunk 209 optimal weight: 1.9990 overall best weight: 0.7820 ------------------------------------------------------------------------------- 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 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 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: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 19355 Z= 0.167 Angle : 0.672 10.704 26215 Z= 0.340 Chirality : 0.039 0.160 3059 Planarity : 0.005 0.045 3206 Dihedral : 5.820 22.224 2506 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer Outliers : 4.32 % 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: -4.82 (0.15), residues: 2289 helix: -3.64 (0.10), residues: 1414 sheet: -3.26 (0.37), residues: 126 loop : -1.67 (0.23), residues: 749 *********************** 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 277 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 185 time to evaluate : 2.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 92 outliers final: 39 residues processed: 255 average time/residue: 0.3436 time to fit residues: 129.3568 Evaluate side-chains 193 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 154 time to evaluate : 2.456 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.1883 time to fit residues: 16.6267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 20.0000 chunk 174 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 210 optimal weight: 3.9990 chunk 227 optimal weight: 0.8980 chunk 187 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 168 optimal weight: 0.0050 overall best weight: 1.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 198 GLN ** 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 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 GLN F 207 ASN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.2994 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= 0.168 Angle : 0.624 10.726 26215 Z= 0.310 Chirality : 0.039 0.179 3059 Planarity : 0.004 0.041 3206 Dihedral : 5.262 18.361 2506 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer Outliers : 2.40 % 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: -3.92 (0.16), residues: 2289 helix: -2.76 (0.12), residues: 1442 sheet: -2.54 (0.37), residues: 126 loop : -1.70 (0.25), residues: 721 *********************** 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 217 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 166 time to evaluate : 2.396 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 outliers start: 51 outliers final: 33 residues processed: 210 average time/residue: 0.3301 time to fit residues: 104.8220 Evaluate side-chains 172 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 139 time to evaluate : 2.330 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.1685 time to fit residues: 13.7958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 207 optimal weight: 0.7980 chunk 158 optimal weight: 0.0040 chunk 109 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 100 optimal weight: 0.2980 chunk 141 optimal weight: 0.9990 chunk 210 optimal weight: 3.9990 chunk 223 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 199 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 ASN B 411 ASN 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 ** D 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 19355 Z= 0.130 Angle : 0.572 10.185 26215 Z= 0.286 Chirality : 0.038 0.197 3059 Planarity : 0.003 0.040 3206 Dihedral : 4.801 17.173 2506 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer Outliers : 1.64 % 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: -3.19 (0.17), residues: 2289 helix: -2.17 (0.13), residues: 1442 sheet: -2.06 (0.39), residues: 126 loop : -1.49 (0.25), residues: 721 *********************** 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 181 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 146 time to evaluate : 2.966 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 outliers start: 35 outliers final: 18 residues processed: 167 average time/residue: 0.3834 time to fit residues: 95.0987 Evaluate side-chains 154 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 136 time to evaluate : 2.287 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1785 time to fit residues: 9.1942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 185 optimal weight: 0.0010 chunk 126 optimal weight: 6.9990 chunk 3 optimal weight: 0.6980 chunk 166 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 190 optimal weight: 0.5980 chunk 154 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 114 optimal weight: 0.5980 chunk 200 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN C 207 ASN ** C 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 ASN E 280 ASN ** E 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 56 GLN F 207 ASN ** F 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 207 ASN ** G 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 19355 Z= 0.129 Angle : 0.570 11.216 26215 Z= 0.281 Chirality : 0.038 0.232 3059 Planarity : 0.003 0.056 3206 Dihedral : 4.600 15.186 2506 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer Outliers : 1.46 % 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: -2.67 (0.17), residues: 2289 helix: -1.78 (0.14), residues: 1400 sheet: -1.76 (0.40), residues: 126 loop : -1.33 (0.24), residues: 763 *********************** 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 171 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 140 time to evaluate : 2.156 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 outliers start: 31 outliers final: 20 residues processed: 162 average time/residue: 0.3537 time to fit residues: 85.7901 Evaluate side-chains 148 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 128 time to evaluate : 2.227 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1855 time to fit residues: 9.8226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 44 optimal weight: 4.9990 chunk 131 optimal weight: 0.0770 chunk 55 optimal weight: 0.8980 chunk 223 optimal weight: 3.9990 chunk 185 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- 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 264 GLN C 207 ASN C 411 ASN ** D 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.3868 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= 0.131 Angle : 0.559 9.921 26215 Z= 0.276 Chirality : 0.038 0.224 3059 Planarity : 0.003 0.041 3206 Dihedral : 4.477 16.184 2506 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer Outliers : 1.46 % 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: -2.35 (0.18), residues: 2289 helix: -1.51 (0.14), residues: 1400 sheet: -1.69 (0.38), residues: 126 loop : -1.23 (0.24), residues: 763 *********************** 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 170 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 139 time to evaluate : 2.353 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 outliers start: 31 outliers final: 15 residues processed: 164 average time/residue: 0.3556 time to fit residues: 87.6930 Evaluate side-chains 138 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 123 time to evaluate : 2.287 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1829 time to fit residues: 8.3097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 215 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 127 optimal weight: 7.9990 chunk 163 optimal weight: 3.9990 chunk 126 optimal weight: 0.7980 chunk 188 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 222 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 135 optimal weight: 0.7980 chunk 102 optimal weight: 0.0770 overall best weight: 0.8940 ------------------------------------------------------------------------------- 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** D 264 GLN D 411 ASN E 264 GLN ** E 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 264 GLN ** F 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 264 GLN ** 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: 0.6791 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 19355 Z= 0.144 Angle : 0.566 11.880 26215 Z= 0.279 Chirality : 0.038 0.192 3059 Planarity : 0.003 0.041 3206 Dihedral : 4.478 16.138 2506 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer Outliers : 0.89 % 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: -2.26 (0.18), residues: 2289 helix: -1.36 (0.14), residues: 1435 sheet: -1.82 (0.37), residues: 126 loop : -1.33 (0.25), residues: 728 *********************** 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 145 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 126 time to evaluate : 2.402 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 outliers start: 19 outliers final: 10 residues processed: 140 average time/residue: 0.3695 time to fit residues: 77.4799 Evaluate side-chains 136 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 126 time to evaluate : 2.212 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1846 time to fit residues: 6.3203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0030 chunk 132 optimal weight: 20.0000 chunk 67 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 110 optimal weight: 0.7980 chunk 20 optimal weight: 7.9990 chunk 175 optimal weight: 4.9990 chunk 202 optimal weight: 0.8980 overall best weight: 0.9394 ------------------------------------------------------------------------------- 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 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 264 GLN D 416 ASN E 264 GLN E 411 ASN F 280 ASN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 19355 Z= 0.145 Angle : 0.566 9.890 26215 Z= 0.279 Chirality : 0.038 0.190 3059 Planarity : 0.003 0.042 3206 Dihedral : 4.447 16.720 2506 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer Outliers : 0.42 % 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: -2.08 (0.18), residues: 2289 helix: -1.27 (0.14), residues: 1393 sheet: -1.90 (0.36), residues: 126 loop : -1.12 (0.24), residues: 770 *********************** 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 147 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 138 time to evaluate : 2.280 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 outliers start: 9 outliers final: 3 residues processed: 146 average time/residue: 0.3609 time to fit residues: 79.1427 Evaluate side-chains 131 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 128 time to evaluate : 2.264 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1916 time to fit residues: 4.1862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 213 optimal weight: 0.4980 chunk 194 optimal weight: 0.6980 chunk 207 optimal weight: 6.9990 chunk 124 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 162 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 chunk 187 optimal weight: 0.2980 chunk 196 optimal weight: 0.9980 chunk 206 optimal weight: 0.7980 chunk 136 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 416 ASN ** F 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 ASN ** F 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 264 GLN ** 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: 0.6781 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 19355 Z= 0.128 Angle : 0.563 10.884 26215 Z= 0.278 Chirality : 0.037 0.204 3059 Planarity : 0.003 0.041 3206 Dihedral : 4.345 16.330 2506 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer Outliers : 0.75 % 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: -1.95 (0.18), residues: 2289 helix: -1.15 (0.14), residues: 1393 sheet: -1.87 (0.36), residues: 126 loop : -1.08 (0.24), residues: 770 *********************** 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 153 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 137 time to evaluate : 2.464 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 outliers start: 16 outliers final: 7 residues processed: 151 average time/residue: 0.3624 time to fit residues: 82.1078 Evaluate side-chains 139 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 132 time to evaluate : 2.197 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2080 time to fit residues: 5.5999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 219 optimal weight: 3.9990 chunk 133 optimal weight: 9.9990 chunk 104 optimal weight: 3.9990 chunk 152 optimal weight: 0.1980 chunk 230 optimal weight: 7.9990 chunk 211 optimal weight: 0.6980 chunk 183 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 141 optimal weight: 0.0030 chunk 112 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- 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 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 ASN C 264 GLN ** D 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 264 GLN F 280 ASN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 19355 Z= 0.134 Angle : 0.566 10.514 26215 Z= 0.279 Chirality : 0.037 0.167 3059 Planarity : 0.003 0.041 3206 Dihedral : 4.320 16.474 2506 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer Outliers : 0.23 % 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: -1.82 (0.18), residues: 2289 helix: -1.03 (0.14), residues: 1379 sheet: -1.85 (0.36), residues: 126 loop : -1.07 (0.24), residues: 784 ********************** 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 140 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 135 time to evaluate : 2.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 140 average time/residue: 0.3821 time to fit residues: 78.2595 Evaluate side-chains 128 residues out of total 2128 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 125 time to evaluate : 2.277 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2283 time to fit residues: 4.3204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 27 optimal weight: 0.0000 chunk 50 optimal weight: 7.9990 chunk 183 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 33 optimal weight: 10.0000 chunk 161 optimal weight: 3.9990 overall best weight: 1.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 ASN F 411 ASN ** G 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.132702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.112760 restraints weight = 41128.690| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 3.12 r_work: 0.3839 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.4537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 19355 Z= 0.155 Angle : 0.585 11.101 26215 Z= 0.287 Chirality : 0.038 0.172 3059 Planarity : 0.003 0.042 3206 Dihedral : 4.393 17.476 2506 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer Outliers : 0.42 % 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: -1.79 (0.18), residues: 2289 helix: -0.96 (0.14), residues: 1372 sheet: -1.90 (0.36), residues: 126 loop : -1.15 (0.24), residues: 791 =============================================================================== Job complete usr+sys time: 3290.14 seconds wall clock time: 61 minutes 34.03 seconds (3694.03 seconds total)