Starting phenix.real_space_refine on Tue Nov 19 11:26:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8atd_15646/11_2024/8atd_15646.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8atd_15646/11_2024/8atd_15646.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8atd_15646/11_2024/8atd_15646.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8atd_15646/11_2024/8atd_15646.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8atd_15646/11_2024/8atd_15646.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8atd_15646/11_2024/8atd_15646.cif" } resolution = 3.1 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= 0.009 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 72 5.16 5 C 12617 2.51 5 N 3362 2.21 5 O 3602 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 19653 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 3316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3316 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 400} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 4, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 38 Chain: "E" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3264 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 400} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "F" Number of atoms: 3265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3265 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 400} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 160 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 59 Chain: "D" Number of atoms: 3314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3314 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 400} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 37 Chain: "B" Number of atoms: 3262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3262 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 400} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 162 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 6, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 54 Chain: "A" Number of atoms: 3232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3232 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 400} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 165 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 8, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 85 Time building chain proxies: 12.81, per 1000 atoms: 0.65 Number of scatterers: 19653 At special positions: 0 Unit cell: (138.43, 105.73, 119.9, 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 72 16.00 O 3602 8.00 N 3362 7.00 C 12617 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 4.65 Conformation dependent library (CDL) restraints added in 2.6 seconds 5148 Ramachandran restraints generated. 2574 Oldfield, 0 Emsley, 2574 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4872 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 31 sheets defined 32.6% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.27 Creating SS restraints... Processing helix chain 'C' and resid 10 through 15 Processing helix chain 'C' and resid 34 through 46 Processing helix chain 'C' and resid 47 through 49 No H-bonds generated for 'chain 'C' and resid 47 through 49' Processing helix chain 'C' and resid 72 through 85 Processing helix chain 'C' and resid 99 through 109 removed outlier: 6.115A pdb=" N LEU C 105 " --> pdb=" O PHE C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 131 removed outlier: 3.783A pdb=" N LYS C 129 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER C 130 " --> pdb=" O GLU C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 160 Processing helix chain 'C' and resid 169 through 171 No H-bonds generated for 'chain 'C' and resid 169 through 171' Processing helix chain 'C' and resid 211 through 226 Processing helix chain 'C' and resid 241 through 246 Processing helix chain 'C' and resid 248 through 255 Processing helix chain 'C' and resid 266 through 277 removed outlier: 4.450A pdb=" N TRP C 271 " --> pdb=" O PRO C 267 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ASP C 272 " --> pdb=" O LYS C 268 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR C 277 " --> pdb=" O GLN C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 293 Processing helix chain 'C' and resid 315 through 327 Processing helix chain 'C' and resid 336 through 340 Processing helix chain 'C' and resid 398 through 406 Processing helix chain 'E' and resid 10 through 15 Processing helix chain 'E' and resid 34 through 46 Processing helix chain 'E' and resid 53 through 57 removed outlier: 3.990A pdb=" N GLY E 57 " --> pdb=" O PRO E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 85 Processing helix chain 'E' and resid 97 through 109 Processing helix chain 'E' and resid 127 through 135 Processing helix chain 'E' and resid 156 through 160 Processing helix chain 'E' and resid 169 through 171 No H-bonds generated for 'chain 'E' and resid 169 through 171' Processing helix chain 'E' and resid 211 through 226 Processing helix chain 'E' and resid 241 through 246 Processing helix chain 'E' and resid 248 through 255 removed outlier: 3.506A pdb=" N THR E 255 " --> pdb=" O SER E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 277 removed outlier: 4.403A pdb=" N TRP E 271 " --> pdb=" O PRO E 267 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ASP E 272 " --> pdb=" O LYS E 268 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL E 275 " --> pdb=" O TRP E 271 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS E 276 " --> pdb=" O ASP E 272 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR E 277 " --> pdb=" O GLN E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 293 Processing helix chain 'E' and resid 315 through 327 Processing helix chain 'E' and resid 398 through 406 Processing helix chain 'F' and resid 10 through 15 Processing helix chain 'F' and resid 34 through 46 removed outlier: 3.917A pdb=" N PHE F 44 " --> pdb=" O MET F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 85 Processing helix chain 'F' and resid 97 through 109 Processing helix chain 'F' and resid 125 through 135 removed outlier: 4.321A pdb=" N LYS F 129 " --> pdb=" O SER F 125 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N SER F 130 " --> pdb=" O GLU F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 160 Processing helix chain 'F' and resid 169 through 171 No H-bonds generated for 'chain 'F' and resid 169 through 171' Processing helix chain 'F' and resid 211 through 226 removed outlier: 3.969A pdb=" N SER F 217 " --> pdb=" O ASN F 213 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ASN F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 246 Processing helix chain 'F' and resid 248 through 255 Processing helix chain 'F' and resid 266 through 277 removed outlier: 4.484A pdb=" N TRP F 271 " --> pdb=" O PRO F 267 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ASP F 272 " --> pdb=" O LYS F 268 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL F 275 " --> pdb=" O TRP F 271 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS F 276 " --> pdb=" O ASP F 272 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TYR F 277 " --> pdb=" O GLN F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 293 Processing helix chain 'F' and resid 315 through 327 Processing helix chain 'F' and resid 336 through 340 Processing helix chain 'F' and resid 398 through 405 Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 34 through 42 Processing helix chain 'D' and resid 44 through 48 Processing helix chain 'D' and resid 72 through 85 Processing helix chain 'D' and resid 97 through 109 Processing helix chain 'D' and resid 125 through 135 removed outlier: 3.653A pdb=" N LYS D 129 " --> pdb=" O SER D 125 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER D 130 " --> pdb=" O GLU D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 160 Processing helix chain 'D' and resid 169 through 171 No H-bonds generated for 'chain 'D' and resid 169 through 171' Processing helix chain 'D' and resid 211 through 225 Processing helix chain 'D' and resid 241 through 246 Processing helix chain 'D' and resid 248 through 255 Processing helix chain 'D' and resid 266 through 277 removed outlier: 4.440A pdb=" N TRP D 271 " --> pdb=" O PRO D 267 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ASP D 272 " --> pdb=" O LYS D 268 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR D 277 " --> pdb=" O GLN D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 293 Processing helix chain 'D' and resid 315 through 327 Processing helix chain 'D' and resid 398 through 406 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 34 through 45 Processing helix chain 'B' and resid 72 through 85 Processing helix chain 'B' and resid 97 through 109 Processing helix chain 'B' and resid 127 through 135 Processing helix chain 'B' and resid 156 through 160 removed outlier: 3.510A pdb=" N ASP B 159 " --> pdb=" O SER B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 171 No H-bonds generated for 'chain 'B' and resid 169 through 171' Processing helix chain 'B' and resid 211 through 226 Processing helix chain 'B' and resid 241 through 246 Processing helix chain 'B' and resid 248 through 255 removed outlier: 3.520A pdb=" N THR B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 277 removed outlier: 4.318A pdb=" N TRP B 271 " --> pdb=" O PRO B 267 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ASP B 272 " --> pdb=" O LYS B 268 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL B 275 " --> pdb=" O TRP B 271 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR B 277 " --> pdb=" O GLN B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 293 Processing helix chain 'B' and resid 315 through 327 Processing helix chain 'B' and resid 398 through 406 removed outlier: 3.630A pdb=" N PHE B 406 " --> pdb=" O ASN B 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 15 Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.990A pdb=" N MET A 47 " --> pdb=" O HIS A 43 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N PHE A 48 " --> pdb=" O PHE A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 85 Processing helix chain 'A' and resid 97 through 109 Processing helix chain 'A' and resid 125 through 135 removed outlier: 4.341A pdb=" N LYS A 129 " --> pdb=" O SER A 125 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N SER A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 removed outlier: 3.789A pdb=" N ASP A 159 " --> pdb=" O SER A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 171 No H-bonds generated for 'chain 'A' and resid 169 through 171' Processing helix chain 'A' and resid 211 through 226 Processing helix chain 'A' and resid 241 through 246 Processing helix chain 'A' and resid 248 through 255 Processing helix chain 'A' and resid 266 through 277 removed outlier: 4.420A pdb=" N TRP A 271 " --> pdb=" O PRO A 267 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ASP A 272 " --> pdb=" O LYS A 268 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 275 " --> pdb=" O TRP A 271 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TYR A 277 " --> pdb=" O GLN A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 293 Processing helix chain 'A' and resid 315 through 327 Processing helix chain 'A' and resid 336 through 340 Processing helix chain 'A' and resid 398 through 405 removed outlier: 3.506A pdb=" N LYS A 403 " --> pdb=" O PRO A 399 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 30 through 33 Processing sheet with id=AA2, first strand: chain 'C' and resid 88 through 91 removed outlier: 7.436A pdb=" N THR C 64 " --> pdb=" O ALA C 112 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N CYS C 114 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ALA C 66 " --> pdb=" O CYS C 114 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE C 113 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N LEU C 141 " --> pdb=" O ILE C 113 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL C 115 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N PHE C 143 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR C 166 " --> pdb=" O ILE C 154 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 191 through 196 Processing sheet with id=AA4, first strand: chain 'C' and resid 281 through 284 removed outlier: 3.770A pdb=" N PHE C 282 " --> pdb=" O PHE C 306 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE C 307 " --> pdb=" O LEU C 331 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ALA C 333 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N SER C 309 " --> pdb=" O ALA C 333 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 365 through 369 removed outlier: 5.031A pdb=" N ASP C 417 " --> pdb=" O VAL C 384 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N ILE C 386 " --> pdb=" O THR C 415 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N THR C 415 " --> pdb=" O ILE C 386 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY C 431 " --> pdb=" O GLN C 418 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N TYR C 420 " --> pdb=" O LEU C 429 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LEU C 429 " --> pdb=" O TYR C 420 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 30 through 33 removed outlier: 6.084A pdb=" N ALA E 22 " --> pdb=" O VAL E 259 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 88 through 91 removed outlier: 7.416A pdb=" N THR E 64 " --> pdb=" O ALA E 112 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N CYS E 114 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA E 66 " --> pdb=" O CYS E 114 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE E 113 " --> pdb=" O VAL E 139 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N LEU E 141 " --> pdb=" O ILE E 113 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL E 115 " --> pdb=" O LEU E 141 " (cutoff:3.500A) removed outlier: 8.982A pdb=" N PHE E 143 " --> pdb=" O VAL E 115 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TYR E 166 " --> pdb=" O ILE E 154 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 191 through 196 removed outlier: 4.862A pdb=" N LEU E 193 " --> pdb=" O LEU E 209 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU E 209 " --> pdb=" O LEU E 193 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 282 through 283 removed outlier: 6.754A pdb=" N PHE E 282 " --> pdb=" O ARG E 308 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE E 307 " --> pdb=" O LEU E 331 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ALA E 333 " --> pdb=" O ILE E 307 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N SER E 309 " --> pdb=" O ALA E 333 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR E 344 " --> pdb=" O TYR E 334 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 366 through 369 removed outlier: 6.697A pdb=" N GLY E 382 " --> pdb=" O ASP E 417 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ASP E 417 " --> pdb=" O GLY E 382 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N VAL E 384 " --> pdb=" O THR E 415 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY E 431 " --> pdb=" O GLN E 418 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N TYR E 420 " --> pdb=" O LEU E 429 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N LEU E 429 " --> pdb=" O TYR E 420 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 30 through 33 removed outlier: 3.537A pdb=" N VAL F 23 " --> pdb=" O VAL F 32 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 64 through 65 Processing sheet with id=AB4, first strand: chain 'F' and resid 112 through 114 removed outlier: 6.424A pdb=" N ILE F 113 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR F 166 " --> pdb=" O ILE F 154 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 142 through 143 Processing sheet with id=AB6, first strand: chain 'F' and resid 191 through 196 Processing sheet with id=AB7, first strand: chain 'F' and resid 282 through 284 removed outlier: 6.616A pdb=" N ILE F 307 " --> pdb=" O LEU F 331 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ALA F 333 " --> pdb=" O ILE F 307 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N SER F 309 " --> pdb=" O ALA F 333 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR F 344 " --> pdb=" O TYR F 334 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN F 360 " --> pdb=" O SER F 345 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 365 through 369 removed outlier: 6.637A pdb=" N GLY F 382 " --> pdb=" O ASP F 417 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ASP F 417 " --> pdb=" O GLY F 382 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL F 384 " --> pdb=" O THR F 415 " (cutoff:3.500A) removed outlier: 9.045A pdb=" N GLY F 416 " --> pdb=" O ARG F 432 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ARG F 432 " --> pdb=" O GLY F 416 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLN F 418 " --> pdb=" O THR F 430 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 30 through 33 Processing sheet with id=AC1, first strand: chain 'D' and resid 88 through 91 removed outlier: 8.713A pdb=" N CYS D 114 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ALA D 66 " --> pdb=" O CYS D 114 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ILE D 113 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LEU D 141 " --> pdb=" O ILE D 113 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL D 115 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 8.992A pdb=" N PHE D 143 " --> pdb=" O VAL D 115 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR D 166 " --> pdb=" O ILE D 154 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 191 through 196 Processing sheet with id=AC3, first strand: chain 'D' and resid 281 through 284 removed outlier: 3.753A pdb=" N PHE D 282 " --> pdb=" O PHE D 306 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE D 307 " --> pdb=" O LEU D 331 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ALA D 333 " --> pdb=" O ILE D 307 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N SER D 309 " --> pdb=" O ALA D 333 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 365 through 369 removed outlier: 5.002A pdb=" N ASP D 417 " --> pdb=" O VAL D 384 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N ILE D 386 " --> pdb=" O THR D 415 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N THR D 415 " --> pdb=" O ILE D 386 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY D 431 " --> pdb=" O GLN D 418 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N TYR D 420 " --> pdb=" O LEU D 429 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N LEU D 429 " --> pdb=" O TYR D 420 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 30 through 33 removed outlier: 6.089A pdb=" N ALA B 22 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N SER B 233 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TRP B 281 " --> pdb=" O ARG B 232 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N PHE B 282 " --> pdb=" O ARG B 308 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE B 307 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ALA B 333 " --> pdb=" O ILE B 307 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N SER B 309 " --> pdb=" O ALA B 333 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 88 through 91 removed outlier: 7.430A pdb=" N THR B 64 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N CYS B 114 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ALA B 66 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE B 113 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N LEU B 141 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL B 115 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 9.018A pdb=" N PHE B 143 " --> pdb=" O VAL B 115 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N TYR B 166 " --> pdb=" O ILE B 154 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 191 through 196 Processing sheet with id=AC8, first strand: chain 'B' and resid 365 through 369 removed outlier: 6.801A pdb=" N GLY B 382 " --> pdb=" O ASP B 417 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ASP B 417 " --> pdb=" O GLY B 382 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N VAL B 384 " --> pdb=" O THR B 415 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY B 431 " --> pdb=" O GLN B 418 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N TYR B 420 " --> pdb=" O LEU B 429 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N LEU B 429 " --> pdb=" O TYR B 420 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 30 through 33 removed outlier: 3.594A pdb=" N VAL A 23 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N SER A 233 " --> pdb=" O VAL A 260 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 88 through 92 removed outlier: 4.790A pdb=" N ALA A 112 " --> pdb=" O THR A 64 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ILE A 113 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU A 141 " --> pdb=" O ILE A 113 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL A 115 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 9.022A pdb=" N PHE A 143 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR A 166 " --> pdb=" O ILE A 154 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 191 through 196 Processing sheet with id=AD3, first strand: chain 'A' and resid 281 through 284 removed outlier: 3.753A pdb=" N PHE A 282 " --> pdb=" O PHE A 306 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE A 307 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ALA A 333 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N SER A 309 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 365 through 369 removed outlier: 6.548A pdb=" N GLY A 382 " --> pdb=" O ASP A 417 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ASP A 417 " --> pdb=" O GLY A 382 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL A 384 " --> pdb=" O THR A 415 " (cutoff:3.500A) removed outlier: 9.027A pdb=" N GLY A 416 " --> pdb=" O ARG A 432 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ARG A 432 " --> pdb=" O GLY A 416 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLN A 418 " --> pdb=" O THR A 430 " (cutoff:3.500A) 669 hydrogen bonds defined for protein. 1860 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: 5.79 Time building geometry restraints manager: 5.34 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: 6380 1.34 - 1.46: 3623 1.46 - 1.57: 10039 1.57 - 1.69: 0 1.69 - 1.81: 116 Bond restraints: 20158 Sorted by residual: bond pdb=" N ASN E 390 " pdb=" CA ASN E 390 " ideal model delta sigma weight residual 1.457 1.473 -0.015 1.29e-02 6.01e+03 1.39e+00 bond pdb=" N THR D 337 " pdb=" CA THR D 337 " ideal model delta sigma weight residual 1.457 1.470 -0.012 1.29e-02 6.01e+03 9.39e-01 bond pdb=" C PRO D 300 " pdb=" N PHE D 301 " ideal model delta sigma weight residual 1.331 1.351 -0.020 2.07e-02 2.33e+03 9.20e-01 bond pdb=" CA GLN A 342 " pdb=" C GLN A 342 " ideal model delta sigma weight residual 1.532 1.523 0.009 9.60e-03 1.09e+04 8.92e-01 bond pdb=" N PHE D 137 " pdb=" CA PHE D 137 " ideal model delta sigma weight residual 1.457 1.469 -0.012 1.29e-02 6.01e+03 8.59e-01 ... (remaining 20153 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 27063 1.69 - 3.38: 395 3.38 - 5.07: 38 5.07 - 6.76: 18 6.76 - 8.45: 5 Bond angle restraints: 27519 Sorted by residual: angle pdb=" N VAL C 236 " pdb=" CA VAL C 236 " pdb=" C VAL C 236 " ideal model delta sigma weight residual 113.53 108.23 5.30 9.80e-01 1.04e+00 2.92e+01 angle pdb=" N VAL D 236 " pdb=" CA VAL D 236 " pdb=" C VAL D 236 " ideal model delta sigma weight residual 113.53 108.28 5.25 9.80e-01 1.04e+00 2.87e+01 angle pdb=" N ARG F 216 " pdb=" CA ARG F 216 " pdb=" C ARG F 216 " ideal model delta sigma weight residual 112.97 107.47 5.50 1.06e+00 8.90e-01 2.69e+01 angle pdb=" N SER F 217 " pdb=" CA SER F 217 " pdb=" C SER F 217 " ideal model delta sigma weight residual 113.43 107.64 5.79 1.26e+00 6.30e-01 2.11e+01 angle pdb=" C PRO D 296 " pdb=" N LYS D 297 " pdb=" CA LYS D 297 " ideal model delta sigma weight residual 120.68 127.64 -6.96 1.52e+00 4.33e-01 2.10e+01 ... (remaining 27514 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 11334 17.59 - 35.17: 538 35.17 - 52.76: 46 52.76 - 70.35: 21 70.35 - 87.93: 13 Dihedral angle restraints: 11952 sinusoidal: 4413 harmonic: 7539 Sorted by residual: dihedral pdb=" CA SER C 132 " pdb=" C SER C 132 " pdb=" N THR C 133 " pdb=" CA THR C 133 " ideal model delta harmonic sigma weight residual 180.00 151.29 28.71 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA THR A 146 " pdb=" C THR A 146 " pdb=" N ARG A 147 " pdb=" CA ARG A 147 " ideal model delta harmonic sigma weight residual 180.00 154.84 25.16 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA CYS D 136 " pdb=" C CYS D 136 " pdb=" N PHE D 137 " pdb=" CA PHE D 137 " ideal model delta harmonic sigma weight residual -180.00 -156.64 -23.36 0 5.00e+00 4.00e-02 2.18e+01 ... (remaining 11949 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2600 0.053 - 0.107: 436 0.107 - 0.160: 118 0.160 - 0.213: 0 0.213 - 0.266: 1 Chirality restraints: 3155 Sorted by residual: chirality pdb=" CB THR A 357 " pdb=" CA THR A 357 " pdb=" OG1 THR A 357 " pdb=" CG2 THR A 357 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CA GLU D 100 " pdb=" N GLU D 100 " pdb=" C GLU D 100 " pdb=" CB GLU D 100 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.36e-01 chirality pdb=" CA ASN E 390 " pdb=" N ASN E 390 " pdb=" C ASN E 390 " pdb=" CB ASN E 390 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.95e-01 ... (remaining 3152 not shown) Planarity restraints: 3590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 102 " 0.019 2.00e-02 2.50e+03 3.80e-02 1.45e+01 pdb=" C ASN C 102 " -0.066 2.00e-02 2.50e+03 pdb=" O ASN C 102 " 0.024 2.00e-02 2.50e+03 pdb=" N PHE C 103 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 348 " -0.044 5.00e-02 4.00e+02 6.56e-02 6.87e+00 pdb=" N PRO C 349 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 349 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 349 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 101 " -0.022 2.00e-02 2.50e+03 1.91e-02 6.37e+00 pdb=" CG PHE D 101 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE D 101 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE D 101 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE D 101 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 101 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE D 101 " -0.002 2.00e-02 2.50e+03 ... (remaining 3587 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 336 2.68 - 3.24: 18961 3.24 - 3.79: 30226 3.79 - 4.35: 42349 4.35 - 4.90: 71142 Nonbonded interactions: 163014 Sorted by model distance: nonbonded pdb=" OH TYR A 334 " pdb=" OD2 ASP A 417 " model vdw 2.129 3.040 nonbonded pdb=" O LYS D 226 " pdb=" NH1 ARG D 305 " model vdw 2.226 3.120 nonbonded pdb=" O THR B 46 " pdb=" ND2 ASN B 50 " model vdw 2.230 3.120 nonbonded pdb=" OG1 THR B 357 " pdb=" O LEU B 427 " model vdw 2.232 3.040 nonbonded pdb=" O GLY B 388 " pdb=" NH1 ARG A 187 " model vdw 2.258 3.120 ... (remaining 163009 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 28 or (resid 29 and (name N or name \ CA or name C or name O or name CB )) or resid 30 through 58 or (resid 59 and (n \ ame N or name CA or name C or name O or name CB )) or resid 60 through 69 or (re \ sid 70 and (name N or name CA or name C or name O or name CB )) or resid 71 thro \ ugh 75 or (resid 76 and (name N or name CA or name C or name O or name CB )) or \ resid 77 through 118 or (resid 119 and (name N or name CA or name C or name O or \ name CB )) or resid 120 through 127 or (resid 128 through 129 and (name N or na \ me CA or name C or name O or name CB )) or resid 130 through 153 or (resid 154 a \ nd (name N or name CA or name C or name O or name CB )) or resid 155 through 163 \ or (resid 164 and (name N or name CA or name C or name O or name CB )) or resid \ 165 through 180 or (resid 181 and (name N or name CA or name C or name O or nam \ e CB )) or resid 182 through 205 or (resid 206 and (name N or name CA or name C \ or name O or name CB )) or resid 207 through 216 or (resid 217 and (name N or na \ me CA or name C or name O or name CB )) or resid 218 through 236 or (resid 237 t \ hrough 238 and (name N or name CA or name C or name O or name CB )) or resid 239 \ through 242 or (resid 243 and (name N or name CA or name C or name O or name CB \ )) or resid 244 through 282 or (resid 283 and (name N or name CA or name C or n \ ame O or name CB )) or resid 284 through 285 or (resid 286 and (name N or name C \ A or name C or name O or name CB )) or resid 287 through 289 or (resid 290 and ( \ name N or name CA or name C or name O or name CB )) or resid 291 or (resid 292 t \ hrough 293 and (name N or name CA or name C or name O or name CB )) or resid 294 \ through 296 or (resid 297 and (name N or name CA or name C or name O or name CB \ )) or resid 298 or (resid 299 and (name N or name CA or name C or name O or nam \ e CB )) or resid 300 through 306 or (resid 307 and (name N or name CA or name C \ or name O or name CB )) or resid 308 through 309 or (resid 310 through 313 and ( \ name N or name CA or name C or name O or name CB )) or resid 314 through 324 or \ (resid 325 and (name N or name CA or name C or name O or name CB )) or resid 326 \ through 335 or (resid 336 and (name N or name CA or name C or name O or name CB \ )) or resid 337 through 343 or (resid 344 and (name N or name CA or name C or n \ ame O or name CB )) or resid 345 through 347 or (resid 348 through 350 and (name \ N or name CA or name C or name O or name CB )) or resid 351 or (resid 352 and ( \ name N or name CA or name C or name O or name CB )) or resid 353 or (resid 354 a \ nd (name N or name CA or name C or name O or name CB )) or resid 355 through 356 \ or (resid 357 and (name N or name CA or name C or name O or name CB )) or resid \ 358 through 360 or (resid 361 and (name N or name CA or name C or name O or nam \ e CB )) or resid 362 through 365 or (resid 366 and (name N or name CA or name C \ or name O or name CB )) or resid 367 through 372 or (resid 373 and (name N or na \ me CA or name C or name O or name CB )) or resid 374 through 376 or (resid 377 a \ nd (name N or name CA or name C or name O or name CB )) or resid 378 through 385 \ or (resid 386 and (name N or name CA or name C or name O or name CB )) or resid \ 387 through 389 or (resid 390 and (name N or name CA or name C or name O or nam \ e CB )) or resid 391 through 406 or (resid 407 and (name N or name CA or name C \ or name O or name CB )) or resid 408 or (resid 409 through 411 and (name N or na \ me CA or name C or name O or name CB )) or resid 412 through 414 or (resid 415 a \ nd (name N or name CA or name C or name O or name CB )) or resid 416 or (resid 4 \ 17 and (name N or name CA or name C or name O or name CB )) or resid 418 through \ 422 or (resid 423 through 424 and (name N or name CA or name C or name O or nam \ e CB )) or resid 425 or (resid 426 and (name N or name CA or name C or name O or \ name CB )) or resid 427 through 432 or (resid 433 and (name N or name CA or nam \ e C or name O or name CB )) or resid 434 through 436)) selection = (chain 'B' and (resid 6 through 7 or (resid 8 through 9 and (name N or name CA o \ r name C or name O or name CB )) or resid 10 through 13 or (resid 14 and (name N \ or name CA or name C or name O or name CB )) or resid 15 through 46 or (resid 4 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 48 through 6 \ 0 or (resid 61 and (name N or name CA or name C or name O or name CB )) or resid \ 62 through 69 or (resid 70 and (name N or name CA or name C or name O or name C \ B )) or resid 71 through 73 or (resid 74 and (name N or name CA or name C or nam \ e O or name CB )) or resid 75 or (resid 76 and (name N or name CA or name C or n \ ame O or name CB )) or resid 77 through 95 or (resid 96 through 100 and (name N \ or name CA or name C or name O or name CB )) or resid 101 through 108 or (resid \ 109 and (name N or name CA or name C or name O or name CB )) or resid 110 throug \ h 118 or (resid 119 and (name N or name CA or name C or name O or name CB )) or \ resid 120 through 121 or (resid 122 and (name N or name CA or name C or name O o \ r name CB )) or resid 123 through 127 or (resid 128 through 129 and (name N or n \ ame CA or name C or name O or name CB )) or resid 130 through 139 or (resid 140 \ and (name N or name CA or name C or name O or name CB )) or resid 141 through 14 \ 3 or (resid 144 through 145 and (name N or name CA or name C or name O or name C \ B )) or resid 146 through 153 or (resid 154 and (name N or name CA or name C or \ name O or name CB )) or resid 155 through 160 or (resid 161 through 162 and (nam \ e N or name CA or name C or name O or name CB )) or resid 163 through 180 or (re \ sid 181 and (name N or name CA or name C or name O or name CB )) or resid 182 th \ rough 199 or (resid 200 through 202 and (name N or name CA or name C or name O o \ r name CB )) or resid 203 through 216 or (resid 217 and (name N or name CA or na \ me C or name O or name CB )) or resid 218 through 235 or (resid 236 through 238 \ and (name N or name CA or name C or name O or name CB )) or resid 239 through 26 \ 2 or (resid 263 and (name N or name CA or name C or name O or name CB )) or resi \ d 264 through 271 or (resid 272 and (name N or name CA or name C or name O or na \ me CB )) or resid 273 through 285 or (resid 286 and (name N or name CA or name C \ or name O or name CB )) or resid 287 through 296 or (resid 297 and (name N or n \ ame CA or name C or name O or name CB )) or resid 298 or (resid 299 and (name N \ or name CA or name C or name O or name CB )) or resid 300 through 306 or (resid \ 307 and (name N or name CA or name C or name O or name CB )) or resid 308 throug \ h 309 or (resid 310 through 313 and (name N or name CA or name C or name O or na \ me CB )) or resid 314 through 315 or (resid 316 through 317 and (name N or name \ CA or name C or name O or name CB )) or resid 318 through 319 or (resid 320 thro \ ugh 322 and (name N or name CA or name C or name O or name CB )) or resid 323 th \ rough 335 or (resid 336 and (name N or name CA or name C or name O or name CB )) \ or resid 337 through 347 or (resid 348 through 350 and (name N or name CA or na \ me C or name O or name CB )) or resid 351 or (resid 352 and (name N or name CA o \ r name C or name O or name CB )) or resid 353 through 356 or (resid 357 and (nam \ e N or name CA or name C or name O or name CB )) or resid 358 through 369 or (re \ sid 370 and (name N or name CA or name C or name O or name CB )) or resid 371 th \ rough 376 or (resid 377 and (name N or name CA or name C or name O or name CB )) \ or resid 378 through 382 or (resid 383 and (name N or name CA or name C or name \ O or name CB )) or resid 384 or (resid 385 through 386 and (name N or name CA o \ r name C or name O or name CB )) or resid 387 through 389 or (resid 390 and (nam \ e N or name CA or name C or name O or name CB )) or resid 391 through 396 or (re \ sid 397 and (name N or name CA or name C or name O or name CB )) or resid 398 th \ rough 410 or (resid 411 and (name N or name CA or name C or name O or name CB )) \ or resid 412 through 421 or (resid 422 through 424 and (name N or name CA or na \ me C or name O or name CB )) or resid 425 or (resid 426 and (name N or name CA o \ r name C or name O or name CB )) or resid 427 through 436)) selection = (chain 'C' and (resid 6 through 7 or (resid 8 through 9 and (name N or name CA o \ r name C or name O or name CB )) or resid 10 through 13 or (resid 14 and (name N \ or name CA or name C or name O or name CB )) or resid 15 through 45 or (resid 4 \ 6 through 47 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 8 through 58 or (resid 59 and (name N or name CA or name C or name O or name CB \ )) or resid 60 or (resid 61 and (name N or name CA or name C or name O or name C \ B )) or resid 62 through 73 or (resid 74 and (name N or name CA or name C or nam \ e O or name CB )) or resid 75 or (resid 76 and (name N or name CA or name C or n \ ame O or name CB )) or resid 77 through 95 or (resid 96 through 100 and (name N \ or name CA or name C or name O or name CB )) or resid 101 through 108 or (resid \ 109 and (name N or name CA or name C or name O or name CB )) or resid 110 throug \ h 116 or (resid 117 and (name N or name CA or name C or name O or name CB )) or \ resid 118 or (resid 119 and (name N or name CA or name C or name O or name CB )) \ or resid 120 through 121 or (resid 122 and (name N or name CA or name C or name \ O or name CB )) or resid 123 through 128 or (resid 129 and (name N or name CA o \ r name C or name O or name CB )) or resid 130 through 139 or (resid 140 and (nam \ e N or name CA or name C or name O or name CB )) or resid 141 through 143 or (re \ sid 144 through 145 and (name N or name CA or name C or name O or name CB )) or \ resid 146 through 150 or (resid 151 and (name N or name CA or name C or name O o \ r name CB )) or resid 152 through 153 or (resid 154 and (name N or name CA or na \ me C or name O or name CB )) or resid 155 through 160 or (resid 161 through 162 \ and (name N or name CA or name C or name O or name CB )) or resid 163 or (resid \ 164 and (name N or name CA or name C or name O or name CB )) or resid 165 throug \ h 167 or (resid 168 and (name N or name CA or name C or name O or name CB )) or \ resid 169 through 180 or (resid 181 and (name N or name CA or name C or name O o \ r name CB )) or resid 182 through 199 or (resid 200 through 202 and (name N or n \ ame CA or name C or name O or name CB )) or resid 203 through 205 or (resid 206 \ and (name N or name CA or name C or name O or name CB )) or resid 207 through 21 \ 6 or (resid 217 and (name N or name CA or name C or name O or name CB )) or resi \ d 218 through 235 or (resid 236 through 238 and (name N or name CA or name C or \ name O or name CB )) or resid 239 through 242 or (resid 243 and (name N or name \ CA or name C or name O or name CB )) or resid 244 through 262 or (resid 263 and \ (name N or name CA or name C or name O or name CB )) or resid 264 through 271 or \ (resid 272 and (name N or name CA or name C or name O or name CB )) or resid 27 \ 3 through 282 or (resid 283 and (name N or name CA or name C or name O or name C \ B )) or resid 284 through 285 or (resid 286 and (name N or name CA or name C or \ name O or name CB )) or resid 287 through 291 or (resid 292 through 293 and (nam \ e N or name CA or name C or name O or name CB )) or resid 294 through 296 or (re \ sid 297 and (name N or name CA or name C or name O or name CB )) or resid 298 or \ (resid 299 and (name N or name CA or name C or name O or name CB )) or resid 30 \ 0 through 306 or (resid 307 and (name N or name CA or name C or name O or name C \ B )) or resid 308 through 310 or (resid 311 through 313 and (name N or name CA o \ r name C or name O or name CB )) or resid 314 through 315 or (resid 316 through \ 317 and (name N or name CA or name C or name O or name CB )) or resid 318 throug \ h 335 or (resid 336 and (name N or name CA or name C or name O or name CB )) or \ resid 337 through 343 or (resid 344 and (name N or name CA or name C or name O o \ r name CB )) or resid 345 through 348 or (resid 349 through 350 and (name N or n \ ame CA or name C or name O or name CB )) or resid 351 or (resid 352 and (name N \ or name CA or name C or name O or name CB )) or resid 353 or (resid 354 and (nam \ e N or name CA or name C or name O or name CB )) or resid 355 through 356 or (re \ sid 357 and (name N or name CA or name C or name O or name CB )) or resid 358 th \ rough 360 or (resid 361 and (name N or name CA or name C or name O or name CB )) \ or resid 362 through 365 or (resid 366 and (name N or name CA or name C or name \ O or name CB )) or resid 367 through 369 or (resid 370 and (name N or name CA o \ r name C or name O or name CB )) or resid 371 through 376 or (resid 377 and (nam \ e N or name CA or name C or name O or name CB )) or resid 378 through 384 or (re \ sid 385 through 386 and (name N or name CA or name C or name O or name CB )) or \ resid 387 through 389 or (resid 390 and (name N or name CA or name C or name O o \ r name CB )) or resid 391 through 396 or (resid 397 and (name N or name CA or na \ me C or name O or name CB )) or resid 398 through 406 or (resid 407 and (name N \ or name CA or name C or name O or name CB )) or resid 408 or (resid 409 through \ 411 and (name N or name CA or name C or name O or name CB )) or resid 412 throug \ h 414 or (resid 415 and (name N or name CA or name C or name O or name CB )) or \ resid 416 or (resid 417 and (name N or name CA or name C or name O or name CB )) \ or resid 418 through 421 or (resid 422 through 424 and (name N or name CA or na \ me C or name O or name CB )) or resid 425 or (resid 426 and (name N or name CA o \ r name C or name O or name CB )) or resid 427 through 431 or (resid 432 through \ 433 and (name N or name CA or name C or name O or name CB )) or resid 434 throug \ h 436)) selection = (chain 'D' and (resid 6 through 7 or (resid 8 through 9 and (name N or name CA o \ r name C or name O or name CB )) or resid 10 through 13 or (resid 14 and (name N \ or name CA or name C or name O or name CB )) or resid 15 through 45 or (resid 4 \ 6 through 47 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 8 through 58 or (resid 59 and (name N or name CA or name C or name O or name CB \ )) or resid 60 or (resid 61 and (name N or name CA or name C or name O or name C \ B )) or resid 62 through 69 or (resid 70 and (name N or name CA or name C or nam \ e O or name CB )) or resid 71 through 73 or (resid 74 and (name N or name CA or \ name C or name O or name CB )) or resid 75 or (resid 76 and (name N or name CA o \ r name C or name O or name CB )) or resid 77 through 95 or (resid 96 through 100 \ and (name N or name CA or name C or name O or name CB )) or resid 101 through 1 \ 08 or (resid 109 and (name N or name CA or name C or name O or name CB )) or res \ id 110 through 116 or (resid 117 and (name N or name CA or name C or name O or n \ ame CB )) or resid 118 through 128 or (resid 129 and (name N or name CA or name \ C or name O or name CB )) or resid 130 through 139 or (resid 140 and (name N or \ name CA or name C or name O or name CB )) or resid 141 through 143 or (resid 144 \ through 145 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 46 through 150 or (resid 151 and (name N or name CA or name C or name O or name \ CB )) or resid 152 through 153 or (resid 154 and (name N or name CA or name C or \ name O or name CB )) or resid 155 through 160 or (resid 161 through 162 and (na \ me N or name CA or name C or name O or name CB )) or resid 163 or (resid 164 and \ (name N or name CA or name C or name O or name CB )) or resid 165 through 167 o \ r (resid 168 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 69 through 180 or (resid 181 and (name N or name CA or name C or name O or name \ CB )) or resid 182 through 189 or (resid 190 and (name N or name CA or name C or \ name O or name CB )) or resid 191 through 199 or (resid 200 through 202 and (na \ me N or name CA or name C or name O or name CB )) or resid 203 through 205 or (r \ esid 206 and (name N or name CA or name C or name O or name CB )) or resid 207 t \ hrough 235 or (resid 236 through 238 and (name N or name CA or name C or name O \ or name CB )) or resid 239 through 242 or (resid 243 and (name N or name CA or n \ ame C or name O or name CB )) or resid 244 through 262 or (resid 263 and (name N \ or name CA or name C or name O or name CB )) or resid 264 through 271 or (resid \ 272 and (name N or name CA or name C or name O or name CB )) or resid 273 throu \ gh 282 or (resid 283 and (name N or name CA or name C or name O or name CB )) or \ resid 284 through 285 or (resid 286 and (name N or name CA or name C or name O \ or name CB )) or resid 287 through 289 or (resid 290 and (name N or name CA or n \ ame C or name O or name CB )) or resid 291 or (resid 292 through 293 and (name N \ or name CA or name C or name O or name CB )) or resid 294 through 306 or (resid \ 307 and (name N or name CA or name C or name O or name CB )) or resid 308 throu \ gh 310 or (resid 311 through 313 and (name N or name CA or name C or name O or n \ ame CB )) or resid 314 through 315 or (resid 316 through 317 and (name N or name \ CA or name C or name O or name CB )) or resid 318 through 321 or (resid 322 and \ (name N or name CA or name C or name O or name CB )) or resid 323 through 335 o \ r (resid 336 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 37 through 343 or (resid 344 and (name N or name CA or name C or name O or name \ CB )) or resid 345 through 347 or (resid 348 through 350 and (name N or name CA \ or name C or name O or name CB )) or resid 351 or (resid 352 and (name N or name \ CA or name C or name O or name CB )) or resid 353 or (resid 354 and (name N or \ name CA or name C or name O or name CB )) or resid 355 through 356 or (resid 357 \ and (name N or name CA or name C or name O or name CB )) or resid 358 through 3 \ 60 or (resid 361 and (name N or name CA or name C or name O or name CB )) or res \ id 362 through 365 or (resid 366 and (name N or name CA or name C or name O or n \ ame CB )) or resid 367 through 369 or (resid 370 and (name N or name CA or name \ C or name O or name CB )) or resid 371 through 376 or (resid 377 and (name N or \ name CA or name C or name O or name CB )) or resid 378 through 384 or (resid 385 \ through 386 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 87 through 389 or (resid 390 and (name N or name CA or name C or name O or name \ CB )) or resid 391 through 396 or (resid 397 and (name N or name CA or name C or \ name O or name CB )) or resid 398 through 406 or (resid 407 and (name N or name \ CA or name C or name O or name CB )) or resid 408 or (resid 409 through 411 and \ (name N or name CA or name C or name O or name CB )) or resid 412 through 414 o \ r (resid 415 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 16 through 421 or (resid 422 through 424 and (name N or name CA or name C or nam \ e O or name CB )) or resid 425 or (resid 426 and (name N or name CA or name C or \ name O or name CB )) or resid 427 through 432 or (resid 433 and (name N or name \ CA or name C or name O or name CB )) or resid 434 through 436)) selection = (chain 'E' and (resid 6 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 28 or (resid 29 and (name N or name \ CA or name C or name O or name CB )) or resid 30 through 46 or (resid 47 and (n \ ame N or name CA or name C or name O or name CB )) or resid 48 through 58 or (re \ sid 59 and (name N or name CA or name C or name O or name CB )) or resid 60 or ( \ resid 61 and (name N or name CA or name C or name O or name CB )) or resid 62 th \ rough 69 or (resid 70 and (name N or name CA or name C or name O or name CB )) o \ r resid 71 through 73 or (resid 74 and (name N or name CA or name C or name O or \ name CB )) or resid 75 or (resid 76 and (name N or name CA or name C or name O \ or name CB )) or resid 77 through 95 or (resid 96 through 100 and (name N or nam \ e CA or name C or name O or name CB )) or resid 101 through 108 or (resid 109 an \ d (name N or name CA or name C or name O or name CB )) or resid 110 through 118 \ or (resid 119 and (name N or name CA or name C or name O or name CB )) or resid \ 120 through 121 or (resid 122 and (name N or name CA or name C or name O or name \ CB )) or resid 123 through 127 or (resid 128 through 129 and (name N or name CA \ or name C or name O or name CB )) or resid 130 through 139 or (resid 140 and (n \ ame N or name CA or name C or name O or name CB )) or resid 141 through 143 or ( \ resid 144 through 145 and (name N or name CA or name C or name O or name CB )) o \ r resid 146 through 150 or (resid 151 and (name N or name CA or name C or name O \ or name CB )) or resid 152 through 153 or (resid 154 and (name N or name CA or \ name C or name O or name CB )) or resid 155 through 160 or (resid 161 through 16 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 163 through \ 180 or (resid 181 and (name N or name CA or name C or name O or name CB )) or re \ sid 182 through 199 or (resid 200 through 202 and (name N or name CA or name C o \ r name O or name CB )) or resid 203 through 216 or (resid 217 and (name N or nam \ e CA or name C or name O or name CB )) or resid 218 through 235 or (resid 236 th \ rough 238 and (name N or name CA or name C or name O or name CB )) or resid 239 \ through 262 or (resid 263 and (name N or name CA or name C or name O or name CB \ )) or resid 264 through 271 or (resid 272 and (name N or name CA or name C or na \ me O or name CB )) or resid 273 through 285 or (resid 286 and (name N or name CA \ or name C or name O or name CB )) or resid 287 through 291 or (resid 292 throug \ h 293 and (name N or name CA or name C or name O or name CB )) or resid 294 thro \ ugh 296 or (resid 297 and (name N or name CA or name C or name O or name CB )) o \ r resid 298 or (resid 299 and (name N or name CA or name C or name O or name CB \ )) or resid 300 through 309 or (resid 310 through 313 and (name N or name CA or \ name C or name O or name CB )) or resid 314 through 315 or (resid 316 through 31 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 318 through \ 319 or (resid 320 through 322 and (name N or name CA or name C or name O or name \ CB )) or resid 323 through 347 or (resid 348 through 350 and (name N or name CA \ or name C or name O or name CB )) or resid 351 through 353 or (resid 354 and (n \ ame N or name CA or name C or name O or name CB )) or resid 355 through 360 or ( \ resid 361 and (name N or name CA or name C or name O or name CB )) or resid 362 \ through 369 or (resid 370 and (name N or name CA or name C or name O or name CB \ )) or resid 371 through 382 or (resid 383 and (name N or name CA or name C or na \ me O or name CB )) or resid 384 or (resid 385 through 386 and (name N or name CA \ or name C or name O or name CB )) or resid 387 through 389 or (resid 390 and (n \ ame N or name CA or name C or name O or name CB )) or resid 391 through 396 or ( \ resid 397 and (name N or name CA or name C or name O or name CB )) or resid 398 \ through 406 or (resid 407 and (name N or name CA or name C or name O or name CB \ )) or resid 408 or (resid 409 through 411 and (name N or name CA or name C or na \ me O or name CB )) or resid 412 through 414 or (resid 415 and (name N or name CA \ or name C or name O or name CB )) or resid 416 or (resid 417 and (name N or nam \ e CA or name C or name O or name CB )) or resid 418 through 436)) selection = (chain 'F' and (resid 6 through 28 or (resid 29 and (name N or name CA or name C \ or name O or name CB )) or resid 30 through 58 or (resid 59 and (name N or name \ CA or name C or name O or name CB )) or resid 60 through 69 or (resid 70 and (n \ ame N or name CA or name C or name O or name CB )) or resid 71 through 97 or (re \ sid 98 through 100 and (name N or name CA or name C or name O or name CB )) or r \ esid 101 through 108 or (resid 109 and (name N or name CA or name C or name O or \ name CB )) or resid 110 through 116 or (resid 117 and (name N or name CA or nam \ e C or name O or name CB )) or resid 118 or (resid 119 and (name N or name CA or \ name C or name O or name CB )) or resid 120 through 127 or (resid 128 through 1 \ 29 and (name N or name CA or name C or name O or name CB )) or resid 130 through \ 139 or (resid 140 and (name N or name CA or name C or name O or name CB )) or r \ esid 141 through 143 or (resid 144 through 145 and (name N or name CA or name C \ or name O or name CB )) or resid 146 through 150 or (resid 151 and (name N or na \ me CA or name C or name O or name CB )) or resid 152 through 160 or (resid 161 t \ hrough 162 and (name N or name CA or name C or name O or name CB )) or resid 163 \ or (resid 164 and (name N or name CA or name C or name O or name CB )) or resid \ 165 through 199 or (resid 200 through 202 and (name N or name CA or name C or n \ ame O or name CB )) or resid 203 through 205 or (resid 206 and (name N or name C \ A or name C or name O or name CB )) or resid 207 through 216 or (resid 217 and ( \ name N or name CA or name C or name O or name CB )) or resid 218 through 235 or \ (resid 236 through 238 and (name N or name CA or name C or name O or name CB )) \ or resid 239 through 242 or (resid 243 and (name N or name CA or name C or name \ O or name CB )) or resid 244 through 262 or (resid 263 and (name N or name CA or \ name C or name O or name CB )) or resid 264 through 282 or (resid 283 and (name \ N or name CA or name C or name O or name CB )) or resid 284 through 289 or (res \ id 290 and (name N or name CA or name C or name O or name CB )) or resid 291 or \ (resid 292 through 293 and (name N or name CA or name C or name O or name CB )) \ or resid 294 through 296 or (resid 297 and (name N or name CA or name C or name \ O or name CB )) or resid 298 or (resid 299 and (name N or name CA or name C or n \ ame O or name CB )) or resid 300 through 306 or (resid 307 and (name N or name C \ A or name C or name O or name CB )) or resid 308 through 309 or (resid 310 throu \ gh 313 and (name N or name CA or name C or name O or name CB )) or resid 314 thr \ ough 315 or (resid 316 through 317 and (name N or name CA or name C or name O or \ name CB )) or resid 318 through 324 or (resid 325 and (name N or name CA or nam \ e C or name O or name CB )) or resid 326 through 335 or (resid 336 and (name N o \ r name CA or name C or name O or name CB )) or resid 337 through 343 or (resid 3 \ 44 and (name N or name CA or name C or name O or name CB )) or resid 345 through \ 347 or (resid 348 through 350 and (name N or name CA or name C or name O or nam \ e CB )) or resid 351 or (resid 352 and (name N or name CA or name C or name O or \ name CB )) or resid 353 or (resid 354 and (name N or name CA or name C or name \ O or name CB )) or resid 355 through 356 or (resid 357 and (name N or name CA or \ name C or name O or name CB )) or resid 358 through 360 or (resid 361 and (name \ N or name CA or name C or name O or name CB )) or resid 362 through 365 or (res \ id 366 and (name N or name CA or name C or name O or name CB )) or resid 367 thr \ ough 376 or (resid 377 and (name N or name CA or name C or name O or name CB )) \ or resid 378 through 384 or (resid 385 through 386 and (name N or name CA or nam \ e C or name O or name CB )) or resid 387 through 396 or (resid 397 and (name N o \ r name CA or name C or name O or name CB )) or resid 398 through 406 or (resid 4 \ 07 and (name N or name CA or name C or name O or name CB )) or resid 408 or (res \ id 409 through 411 and (name N or name CA or name C or name O or name CB )) or r \ esid 412 through 414 or (resid 415 and (name N or name CA or name C or name O or \ name CB )) or resid 416 through 421 or (resid 422 through 424 and (name N or na \ me CA or name C or name O or name CB )) or resid 425 or (resid 426 and (name N o \ r name CA or name C or name O or name CB )) or resid 427 through 436)) } 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: 0.000 Extract box with map and model: 0.900 Check model and map are aligned: 0.040 Set scattering table: 0.200 Process input model: 42.890 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.070 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:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.0000 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: