Starting phenix.real_space_refine on Thu Mar 5 23:18:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l9p_23244/03_2026/7l9p_23244.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l9p_23244/03_2026/7l9p_23244.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7l9p_23244/03_2026/7l9p_23244.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l9p_23244/03_2026/7l9p_23244.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7l9p_23244/03_2026/7l9p_23244.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l9p_23244/03_2026/7l9p_23244.map" } resolution = 3.6 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 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= 0.002 sd= 1.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5328 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 76 5.16 5 C 14015 2.51 5 N 3699 2.21 5 O 4103 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 205 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21908 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 2301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2301 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 9, 'TRANS': 298} Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 8, 'GLN:plan1': 2, 'GLU:plan': 5, 'ASP:plan': 3, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 83 Chain: "B" Number of atoms: 3037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3037 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 11, 'TRANS': 386} Chain breaks: 2 Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 3, 'GLU:plan': 7, 'ARG:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 77 Chain: "C" Number of atoms: 2995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 2995 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 386} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 12, 'GLN:plan1': 2, 'ARG:plan': 4, 'ASP:plan': 5, 'ASN:plan1': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 107 Chain: "D" Number of atoms: 3043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 3043 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 11, 'TRANS': 386} Chain breaks: 2 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 5, 'ASP:plan': 4, 'ASN:plan1': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 74 Chain: "E" Number of atoms: 2982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 398, 2982 Classifications: {'peptide': 398} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 386} Chain breaks: 2 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 215 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 8, 'ASN:plan1': 4, 'ASP:plan': 4, 'GLU:plan': 11, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 121 Chain: "F" Number of atoms: 2007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2007 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 264} Chain breaks: 3 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 4, 'ASN:plan1': 3, 'PHE:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 77 Chain: "G" Number of atoms: 1199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1199 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 9, 'TRANS': 162} Chain breaks: 2 Unresolved non-hydrogen bonds: 234 Unresolved non-hydrogen angles: 289 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PHE:plan': 4, 'GLU:plan': 5, 'HIS:plan': 4, 'TYR:plan': 3, 'ARG:plan': 7, 'GLN:plan1': 4, 'ASP:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 148 Chain: "I" Number of atoms: 1325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1325 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 11, 'TRANS': 177} Chain breaks: 2 Unresolved non-hydrogen bonds: 234 Unresolved non-hydrogen angles: 288 Unresolved non-hydrogen dihedrals: 202 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ARG:plan': 8, 'GLN:plan1': 4, 'ASP:plan': 4, 'GLU:plan': 7, 'PHE:plan': 2, 'TYR:plan': 3, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 143 Chain: "J" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 945 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain breaks: 3 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 4, 'HIS:plan': 2, 'ARG:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 67 Chain: "K" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 929 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain breaks: 3 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'HIS:plan': 2, 'TYR:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 64 Chain: "Y" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 522 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 12, 'TRANS': 56} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "X" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 468 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 11, 'TRANS': 51} Chain breaks: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 3, 'ASP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.99, per 1000 atoms: 0.23 Number of scatterers: 21908 At special positions: 0 Unit cell: (147.896, 134.064, 192.584, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 76 16.00 P 15 15.00 O 4103 8.00 N 3699 7.00 C 14015 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: 1.72 Conformation dependent library (CDL) restraints added in 1.1 seconds 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5654 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 20 sheets defined 45.5% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 144 through 163 Processing helix chain 'A' and resid 184 through 200 Processing helix chain 'A' and resid 214 through 218 removed outlier: 3.676A pdb=" N LEU A 217 " --> pdb=" O SER A 214 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE A 218 " --> pdb=" O HIS A 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 214 through 218' Processing helix chain 'A' and resid 221 through 242 removed outlier: 3.524A pdb=" N SER A 225 " --> pdb=" O TRP A 221 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LYS A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ASP A 242 " --> pdb=" O ASP A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 263 removed outlier: 3.715A pdb=" N THR A 258 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ALA A 260 " --> pdb=" O SER A 256 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 288 removed outlier: 4.434A pdb=" N ARG A 275 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N VAL A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP A 285 " --> pdb=" O LEU A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 341 removed outlier: 4.074A pdb=" N PHE A 328 " --> pdb=" O ALA A 324 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS A 329 " --> pdb=" O ALA A 325 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N CYS A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 360 removed outlier: 3.537A pdb=" N LEU A 356 " --> pdb=" O THR A 352 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY A 360 " --> pdb=" O LEU A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 380 Processing helix chain 'A' and resid 386 through 400 Proline residue: A 392 - end of helix removed outlier: 3.763A pdb=" N VAL A 400 " --> pdb=" O HIS A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 428 removed outlier: 3.797A pdb=" N GLN A 412 " --> pdb=" O GLU A 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 Processing helix chain 'B' and resid 63 through 69 Processing helix chain 'B' and resid 129 through 133 Processing helix chain 'B' and resid 134 through 139 Processing helix chain 'B' and resid 145 through 162 Processing helix chain 'B' and resid 184 through 200 removed outlier: 4.113A pdb=" N CYS B 189 " --> pdb=" O LYS B 185 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N LYS B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA B 191 " --> pdb=" O SER B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 203 No H-bonds generated for 'chain 'B' and resid 201 through 203' Processing helix chain 'B' and resid 213 through 217 Processing helix chain 'B' and resid 223 through 241 removed outlier: 4.032A pdb=" N LYS B 227 " --> pdb=" O SER B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 257 Processing helix chain 'B' and resid 262 through 266 Processing helix chain 'B' and resid 270 through 274 removed outlier: 3.689A pdb=" N ALA B 273 " --> pdb=" O PRO B 270 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ILE B 274 " --> pdb=" O SER B 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 270 through 274' Processing helix chain 'B' and resid 276 through 288 removed outlier: 3.590A pdb=" N LYS B 288 " --> pdb=" O ILE B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 341 Processing helix chain 'B' and resid 352 through 359 removed outlier: 3.900A pdb=" N MET B 358 " --> pdb=" O ARG B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 380 Processing helix chain 'B' and resid 386 through 401 Proline residue: B 392 - end of helix removed outlier: 4.191A pdb=" N GLN B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 428 removed outlier: 3.823A pdb=" N PHE B 410 " --> pdb=" O THR B 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 50 Processing helix chain 'C' and resid 63 through 69 Processing helix chain 'C' and resid 134 through 139 removed outlier: 3.509A pdb=" N LEU C 139 " --> pdb=" O LEU C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 162 removed outlier: 4.109A pdb=" N HIS C 148 " --> pdb=" O GLU C 144 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL C 153 " --> pdb=" O LEU C 149 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET C 154 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS C 162 " --> pdb=" O LEU C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 200 removed outlier: 4.575A pdb=" N THR C 197 " --> pdb=" O ALA C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 218 removed outlier: 3.840A pdb=" N LEU C 217 " --> pdb=" O ASN C 213 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE C 218 " --> pdb=" O SER C 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 213 through 218' Processing helix chain 'C' and resid 228 through 241 Processing helix chain 'C' and resid 253 through 257 Processing helix chain 'C' and resid 271 through 276 removed outlier: 3.817A pdb=" N ARG C 275 " --> pdb=" O SER C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 281 removed outlier: 3.649A pdb=" N LEU C 281 " --> pdb=" O VAL C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 removed outlier: 3.812A pdb=" N LYS C 304 " --> pdb=" O ILE C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 342 Processing helix chain 'C' and resid 352 through 360 Processing helix chain 'C' and resid 366 through 380 removed outlier: 4.296A pdb=" N SER C 370 " --> pdb=" O VAL C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 398 Proline residue: C 392 - end of helix Processing helix chain 'C' and resid 406 through 427 removed outlier: 5.166A pdb=" N GLN C 412 " --> pdb=" O GLU C 408 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA C 417 " --> pdb=" O ALA C 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 50 Processing helix chain 'D' and resid 63 through 70 Processing helix chain 'D' and resid 134 through 139 removed outlier: 3.635A pdb=" N SER D 138 " --> pdb=" O GLY D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 161 removed outlier: 3.822A pdb=" N SER D 147 " --> pdb=" O VAL D 143 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N HIS D 148 " --> pdb=" O GLU D 144 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU D 149 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL D 153 " --> pdb=" O LEU D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 200 Processing helix chain 'D' and resid 225 through 241 Processing helix chain 'D' and resid 253 through 257 Processing helix chain 'D' and resid 271 through 287 removed outlier: 4.475A pdb=" N VAL D 277 " --> pdb=" O ALA D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 311 Processing helix chain 'D' and resid 323 through 341 Processing helix chain 'D' and resid 352 through 359 Processing helix chain 'D' and resid 364 through 380 removed outlier: 4.522A pdb=" N LEU D 369 " --> pdb=" O ASN D 365 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N SER D 370 " --> pdb=" O VAL D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 389 Processing helix chain 'D' and resid 390 through 395 Processing helix chain 'D' and resid 410 through 428 removed outlier: 3.765A pdb=" N LEU D 428 " --> pdb=" O GLU D 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 50 Processing helix chain 'E' and resid 63 through 70 Processing helix chain 'E' and resid 129 through 133 Processing helix chain 'E' and resid 134 through 139 removed outlier: 3.525A pdb=" N LEU E 139 " --> pdb=" O LEU E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 162 removed outlier: 4.485A pdb=" N VAL E 153 " --> pdb=" O LEU E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 200 removed outlier: 3.631A pdb=" N LYS E 190 " --> pdb=" O THR E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 242 removed outlier: 4.687A pdb=" N THR E 230 " --> pdb=" O GLY E 226 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS E 231 " --> pdb=" O LYS E 227 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET E 232 " --> pdb=" O LEU E 228 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASP E 242 " --> pdb=" O ASP E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 258 removed outlier: 3.789A pdb=" N LEU E 257 " --> pdb=" O GLN E 253 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR E 258 " --> pdb=" O VAL E 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 253 through 258' Processing helix chain 'E' and resid 271 through 276 removed outlier: 3.532A pdb=" N VAL E 276 " --> pdb=" O ASP E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 288 removed outlier: 3.539A pdb=" N ILE E 287 " --> pdb=" O GLN E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 341 Processing helix chain 'E' and resid 352 through 360 Processing helix chain 'E' and resid 367 through 380 Processing helix chain 'E' and resid 384 through 396 Proline residue: E 392 - end of helix Processing helix chain 'E' and resid 409 through 428 removed outlier: 4.194A pdb=" N ASP E 419 " --> pdb=" O SER E 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 139 Processing helix chain 'F' and resid 147 through 162 removed outlier: 4.245A pdb=" N VAL F 153 " --> pdb=" O LEU F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 199 Processing helix chain 'F' and resid 230 through 239 Processing helix chain 'F' and resid 280 through 288 Processing helix chain 'F' and resid 306 through 311 removed outlier: 3.741A pdb=" N VAL F 310 " --> pdb=" O ASP F 306 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASP F 311 " --> pdb=" O VAL F 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 306 through 311' Processing helix chain 'F' and resid 323 through 341 removed outlier: 3.805A pdb=" N CYS F 341 " --> pdb=" O GLU F 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 352 through 360 Processing helix chain 'F' and resid 368 through 376 removed outlier: 4.290A pdb=" N LEU F 372 " --> pdb=" O LYS F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 379 through 383 removed outlier: 4.019A pdb=" N GLY F 382 " --> pdb=" O LYS F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 399 removed outlier: 3.849A pdb=" N LEU F 388 " --> pdb=" O SER F 384 " (cutoff:3.500A) Proline residue: F 392 - end of helix Processing helix chain 'F' and resid 407 through 424 removed outlier: 3.984A pdb=" N GLU F 424 " --> pdb=" O LYS F 420 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 34 removed outlier: 4.405A pdb=" N ARG G 34 " --> pdb=" O ILE G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 42 removed outlier: 3.674A pdb=" N ILE G 41 " --> pdb=" O PRO G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 78 Proline residue: G 73 - end of helix Processing helix chain 'G' and resid 118 through 132 removed outlier: 4.318A pdb=" N LEU G 122 " --> pdb=" O HIS G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 164 Processing helix chain 'I' and resid 14 through 34 removed outlier: 4.327A pdb=" N LEU I 19 " --> pdb=" O VAL I 15 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N CYS I 20 " --> pdb=" O ALA I 16 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU I 21 " --> pdb=" O ASP I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 68 Processing helix chain 'I' and resid 118 through 134 removed outlier: 4.270A pdb=" N ALA I 125 " --> pdb=" O GLN I 121 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASP I 134 " --> pdb=" O ILE I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 164 removed outlier: 3.896A pdb=" N ILE I 163 " --> pdb=" O ASN I 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 35 removed outlier: 4.663A pdb=" N GLU J 21 " --> pdb=" O ASP J 17 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 72 Processing helix chain 'J' and resid 120 through 137 removed outlier: 3.940A pdb=" N VAL J 136 " --> pdb=" O VAL J 132 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU J 137 " --> pdb=" O CYS J 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 33 Processing helix chain 'K' and resid 57 through 77 Proline residue: K 73 - end of helix Processing helix chain 'K' and resid 120 through 137 removed outlier: 4.766A pdb=" N ILE K 127 " --> pdb=" O LEU K 123 " (cutoff:3.500A) Processing helix chain 'Y' and resid 50 through 59 removed outlier: 3.612A pdb=" N GLN Y 59 " --> pdb=" O GLU Y 55 " (cutoff:3.500A) Processing helix chain 'X' and resid 41 through 45 Processing helix chain 'X' and resid 50 through 59 removed outlier: 3.597A pdb=" N LYS X 56 " --> pdb=" O LYS X 52 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA X 57 " --> pdb=" O ILE X 53 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE X 58 " --> pdb=" O ALA X 54 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN X 59 " --> pdb=" O GLU X 55 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 123 through 125 removed outlier: 6.509A pdb=" N GLN A 208 " --> pdb=" O PHE A 248 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N LEU A 250 " --> pdb=" O GLN A 208 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ILE A 210 " --> pdb=" O LEU A 250 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ASP A 252 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL A 247 " --> pdb=" O VAL A 294 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N LEU A 296 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N VAL A 249 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N THR A 298 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ILE A 251 " --> pdb=" O THR A 298 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE A 315 " --> pdb=" O VAL A 174 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 57 through 58 removed outlier: 6.823A pdb=" N HIS B 26 " --> pdb=" O GLN B 71 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N VAL B 73 " --> pdb=" O GLU B 24 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLU B 24 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ILE B 75 " --> pdb=" O HIS B 22 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N HIS B 22 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE B 100 " --> pdb=" O VAL B 25 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLN B 27 " --> pdb=" O PHE B 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 108 through 110 removed outlier: 3.521A pdb=" N HIS B 124 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA B 122 " --> pdb=" O GLU B 110 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 210 through 211 removed outlier: 6.187A pdb=" N ILE B 210 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR B 298 " --> pdb=" O ILE B 251 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 57 through 59 removed outlier: 6.530A pdb=" N HIS C 26 " --> pdb=" O GLN C 71 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL C 73 " --> pdb=" O GLU C 24 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLU C 24 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ILE C 75 " --> pdb=" O HIS C 22 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N HIS C 22 " --> pdb=" O ILE C 75 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 122 through 125 removed outlier: 6.277A pdb=" N ILE C 210 " --> pdb=" O LEU C 250 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 56 through 58 removed outlier: 4.072A pdb=" N SER D 72 " --> pdb=" O HIS D 26 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N HIS D 22 " --> pdb=" O ILE D 76 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 123 through 125 removed outlier: 3.792A pdb=" N GLY D 179 " --> pdb=" O SER D 299 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE D 315 " --> pdb=" O VAL D 174 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 57 through 58 removed outlier: 3.789A pdb=" N SER E 72 " --> pdb=" O HIS E 26 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N HIS E 22 " --> pdb=" O ILE E 76 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL E 21 " --> pdb=" O ALA E 96 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N HIS E 98 " --> pdb=" O VAL E 21 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL E 23 " --> pdb=" O HIS E 98 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N PHE E 100 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL E 25 " --> pdb=" O PHE E 100 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 108 through 110 removed outlier: 3.516A pdb=" N GLY E 207 " --> pdb=" O LEU E 127 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP E 252 " --> pdb=" O ILE E 212 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL E 247 " --> pdb=" O VAL E 294 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N LEU E 296 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N VAL E 249 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N THR E 298 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE E 251 " --> pdb=" O THR E 298 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL E 175 " --> pdb=" O THR E 297 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N SER E 299 " --> pdb=" O VAL E 175 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU E 177 " --> pdb=" O SER E 299 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE E 315 " --> pdb=" O VAL E 174 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 206 through 212 removed outlier: 7.254A pdb=" N TYR F 206 " --> pdb=" O LEU F 246 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N PHE F 248 " --> pdb=" O TYR F 206 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N GLN F 208 " --> pdb=" O PHE F 248 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU F 250 " --> pdb=" O GLN F 208 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ILE F 210 " --> pdb=" O LEU F 250 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ASP F 252 " --> pdb=" O ILE F 210 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ILE F 212 " --> pdb=" O ASP F 252 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N VAL F 294 " --> pdb=" O ALA F 245 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL F 247 " --> pdb=" O VAL F 294 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N LEU F 296 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N VAL F 249 " --> pdb=" O LEU F 296 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N THR F 298 " --> pdb=" O VAL F 249 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE F 251 " --> pdb=" O THR F 298 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL F 175 " --> pdb=" O THR F 297 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE F 315 " --> pdb=" O VAL F 174 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 344 through 345 Processing sheet with id=AB4, first strand: chain 'G' and resid 43 through 47 Processing sheet with id=AB5, first strand: chain 'G' and resid 146 through 152 removed outlier: 5.708A pdb=" N GLU G 81 " --> pdb=" O ILE G 102 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE G 102 " --> pdb=" O GLU G 81 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLU G 96 " --> pdb=" O ILE G 87 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 171 through 173 Processing sheet with id=AB7, first strand: chain 'I' and resid 42 through 44 Processing sheet with id=AB8, first strand: chain 'I' and resid 171 through 172 removed outlier: 4.157A pdb=" N ARG Y 83 " --> pdb=" O ILE I 172 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N VAL I 148 " --> pdb=" O PRO Y 84 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL I 83 " --> pdb=" O VAL I 99 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N VAL I 99 " --> pdb=" O VAL I 83 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL I 85 " --> pdb=" O LYS I 97 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N LYS I 97 " --> pdb=" O VAL I 85 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE I 87 " --> pdb=" O VAL I 95 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL I 203 " --> pdb=" O ILE I 187 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE I 187 " --> pdb=" O VAL I 203 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 146 through 151 removed outlier: 3.831A pdb=" N GLU J 96 " --> pdb=" O ILE J 87 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 42 through 47 Processing sheet with id=AC2, first strand: chain 'K' and resid 85 through 86 removed outlier: 3.935A pdb=" N VAL K 86 " --> pdb=" O THR K 147 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL K 150 " --> pdb=" O HIS X 5 " (cutoff:3.500A) 997 hydrogen bonds defined for protein. 2862 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: 3.86 Time building geometry restraints manager: 2.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.36: 7310 1.36 - 1.54: 14690 1.54 - 1.72: 207 1.72 - 1.90: 100 1.90 - 2.07: 5 Bond restraints: 22312 Sorted by residual: bond pdb=" C3' AGS A 901 " pdb=" C4' AGS A 901 " ideal model delta sigma weight residual 1.526 1.318 0.208 1.10e-02 8.26e+03 3.56e+02 bond pdb=" C4 AGS D 901 " pdb=" N9 AGS D 901 " ideal model delta sigma weight residual 1.374 1.186 0.188 1.00e-02 1.00e+04 3.52e+02 bond pdb=" C5 AGS D 901 " pdb=" N7 AGS D 901 " ideal model delta sigma weight residual 1.387 1.201 0.186 1.00e-02 1.00e+04 3.47e+02 bond pdb=" C4' AGS A 901 " pdb=" O4' AGS A 901 " ideal model delta sigma weight residual 1.444 1.626 -0.182 1.20e-02 6.94e+03 2.29e+02 bond pdb=" C5 AGS E 901 " pdb=" N7 AGS E 901 " ideal model delta sigma weight residual 1.387 1.236 0.151 1.00e-02 1.00e+04 2.27e+02 ... (remaining 22307 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.38: 30302 5.38 - 10.76: 157 10.76 - 16.14: 28 16.14 - 21.52: 10 21.52 - 26.90: 5 Bond angle restraints: 30502 Sorted by residual: angle pdb=" C5 AGS E 901 " pdb=" C4 AGS E 901 " pdb=" N3 AGS E 901 " ideal model delta sigma weight residual 126.80 114.99 11.81 7.41e-01 1.82e+00 2.54e+02 angle pdb=" C4 AGS D 901 " pdb=" C5 AGS D 901 " pdb=" N7 AGS D 901 " ideal model delta sigma weight residual 110.73 103.84 6.89 4.52e-01 4.89e+00 2.32e+02 angle pdb=" C5 AGS D 901 " pdb=" C4 AGS D 901 " pdb=" N9 AGS D 901 " ideal model delta sigma weight residual 105.77 112.17 -6.40 4.43e-01 5.10e+00 2.09e+02 angle pdb=" C5 AGS A 901 " pdb=" C6 AGS A 901 " pdb=" N6 AGS A 901 " ideal model delta sigma weight residual 123.61 138.16 -14.55 1.03e+00 9.46e-01 2.00e+02 angle pdb=" N1 AGS A 901 " pdb=" C6 AGS A 901 " pdb=" N6 AGS A 901 " ideal model delta sigma weight residual 118.30 101.59 16.71 1.19e+00 7.01e-01 1.96e+02 ... (remaining 30497 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.07: 12628 27.07 - 54.13: 692 54.13 - 81.20: 64 81.20 - 108.26: 13 108.26 - 135.33: 5 Dihedral angle restraints: 13402 sinusoidal: 4802 harmonic: 8600 Sorted by residual: dihedral pdb=" CA LEU I 197 " pdb=" C LEU I 197 " pdb=" N LYS I 198 " pdb=" CA LYS I 198 " ideal model delta harmonic sigma weight residual 180.00 150.19 29.81 0 5.00e+00 4.00e-02 3.56e+01 dihedral pdb=" CA PRO I 94 " pdb=" C PRO I 94 " pdb=" N VAL I 95 " pdb=" CA VAL I 95 " ideal model delta harmonic sigma weight residual 180.00 151.10 28.90 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" C LYS D 316 " pdb=" N LYS D 316 " pdb=" CA LYS D 316 " pdb=" CB LYS D 316 " ideal model delta harmonic sigma weight residual -122.60 -108.61 -13.99 0 2.50e+00 1.60e-01 3.13e+01 ... (remaining 13399 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.192: 3738 0.192 - 0.385: 35 0.385 - 0.577: 3 0.577 - 0.770: 0 0.770 - 0.962: 3 Chirality restraints: 3779 Sorted by residual: chirality pdb=" PA AGS D 901 " pdb=" O2A AGS D 901 " pdb=" O3A AGS D 901 " pdb=" O5' AGS D 901 " both_signs ideal model delta sigma weight residual True 3.18 2.22 0.96 2.00e-01 2.50e+01 2.31e+01 chirality pdb=" PB AGS C 901 " pdb=" O2B AGS C 901 " pdb=" O3A AGS C 901 " pdb=" O3B AGS C 901 " both_signs ideal model delta sigma weight residual True 3.18 -2.29 0.89 2.00e-01 2.50e+01 1.99e+01 chirality pdb=" PA AGS C 901 " pdb=" O2A AGS C 901 " pdb=" O3A AGS C 901 " pdb=" O5' AGS C 901 " both_signs ideal model delta sigma weight residual True 3.18 2.33 0.85 2.00e-01 2.50e+01 1.82e+01 ... (remaining 3776 not shown) Planarity restraints: 3833 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN I 7 " 0.027 2.00e-02 2.50e+03 5.22e-02 2.73e+01 pdb=" C GLN I 7 " -0.090 2.00e-02 2.50e+03 pdb=" O GLN I 7 " 0.034 2.00e-02 2.50e+03 pdb=" N ASP I 8 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 125 " -0.018 2.00e-02 2.50e+03 2.09e-02 1.09e+01 pdb=" CG TRP B 125 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP B 125 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP B 125 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 125 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 125 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 125 " -0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 125 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 125 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 125 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA K 26 " 0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C ALA K 26 " -0.055 2.00e-02 2.50e+03 pdb=" O ALA K 26 " 0.021 2.00e-02 2.50e+03 pdb=" N VAL K 27 " 0.019 2.00e-02 2.50e+03 ... (remaining 3830 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 356 2.61 - 3.18: 21013 3.18 - 3.76: 33240 3.76 - 4.33: 43875 4.33 - 4.90: 70945 Nonbonded interactions: 169429 Sorted by model distance: nonbonded pdb=" O2B AGS C 901 " pdb=" O2G AGS C 901 " model vdw 2.041 3.040 nonbonded pdb=" O1B AGS D 901 " pdb=" O2G AGS D 901 " model vdw 2.046 3.040 nonbonded pdb=" O PRO B 181 " pdb=" OG SER B 384 " model vdw 2.161 3.040 nonbonded pdb=" O1B AGS E 901 " pdb=" O2G AGS E 901 " model vdw 2.192 3.040 nonbonded pdb=" O GLN D 253 " pdb=" OG SER D 256 " model vdw 2.207 3.040 ... (remaining 169424 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 122 through 145 or (resid 146 and (name N or name CA or na \ me C or name O or name CB )) or resid 147 through 184 or (resid 185 and (name N \ or name CA or name C or name O or name CB )) or resid 186 or (resid 187 and (nam \ e N or name CA or name C or name O or name CB )) or resid 188 through 194 or (re \ sid 195 and (name N or name CA or name C or name O or name CB )) or resid 196 th \ rough 216 or resid 229 through 236 or (resid 237 and (name N or name CA or name \ C or name O or name CB )) or resid 238 through 245 or (resid 246 and (name N or \ name CA or name C or name O or name CB )) or resid 247 through 254 or (resid 273 \ through 277 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 78 through 280 or (resid 281 and (name N or name CA or name C or name O or name \ CB )) or resid 282 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 (na \ me N or name CA or name C or name O or name CB )) or resid 294 through 304 or (r \ esid 305 through 308 and (name N or name CA or name C or name O or name CB )) or \ resid 309 through 327 or (resid 328 through 329 and (name N or name CA or name \ C or name O or name CB )) or resid 330 through 335 or (resid 336 through 337 and \ (name N or name CA or name C or name O or name CB )) or resid 338 or (resid 339 \ through 340 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 41 or (resid 342 through 343 and (name N or name CA or name C or name O or name \ CB )) or resid 344 through 345 or resid 347 or (resid 348 and (name N or name CA \ or name C or name O or name CB )) or resid 349 through 360 or (resid 361 and (n \ ame N or name CA or name C or name O or name CB )) or resid 362 through 367 or ( \ resid 368 through 369 and (name N or name CA or name C or name O or name CB )) o \ r resid 370 or (resid 371 and (name N or name CA or name C or name O or name CB \ )) or resid 372 through 373 or (resid 374 and (name N or name CA or name C or na \ me O or name CB )) or resid 375 or (resid 376 and (name N or name CA or name C o \ r name O or name CB )) or resid 377 through 382 or (resid 383 and (name N or nam \ e CA or name C or name O or name CB )) or resid 384 through 385 or (resid 386 an \ d (name N or name CA or name C or name O or name CB )) or resid 387 through 388 \ or (resid 389 through 390 and (name N or name CA or name C or name O or name CB \ )) or resid 391 through 400 or (resid 401 through 402 and (name N or name CA or \ name C or name O or name CB )) or resid 403 through 419 or (resid 420 through 42 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 422 through \ 424)) selection = (chain 'F' and (resid 122 through 167 or (resid 168 and (name N or name CA or na \ me C or name O or name CB )) or resid 169 through 172 or (resid 173 and (name N \ or name CA or name C or name O or name CB )) or resid 174 through 193 or (resid \ 194 through 195 and (name N or name CA or name C or name O or name CB )) or resi \ d 196 through 204 or (resid 205 and (name N or name CA or name C or name O or na \ me CB )) or resid 206 through 230 or (resid 231 and (name N or name CA or name C \ or name O or name CB )) or resid 232 through 234 or (resid 235 and (name N or n \ ame CA or name C or name O or name CB )) or resid 236 through 251 or (resid 252 \ and (name N or name CA or name C or name O or name CB )) or resid 253 through 30 \ 5 or (resid 306 through 308 and (name N or name CA or name C or name O or name C \ B )) or resid 309 through 311 or (resid 312 through 313 and (name N or name CA o \ r name C or name O or name CB )) or resid 314 through 326 or (resid 327 through \ 329 and (name N or name CA or name C or name O or name CB )) or resid 330 throug \ h 356 or (resid 357 through 359 and (name N or name CA or name C or name O or na \ me CB )) or resid 360 through 377 or (resid 378 and (name N or name CA or name C \ or name O or name CB )) or resid 379 through 380 or (resid 381 and (name N or n \ ame CA or name C or name O or name CB )) or resid 382 through 407 or (resid 408 \ and (name N or name CA or name C or name O or name CB )) or resid 409 through 42 \ 4)) } ncs_group { reference = (chain 'B' and (resid 19 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 27 or (resid 28 and (name N or nam \ e CA or name C or name O or name CB )) or resid 29 through 30 or (resid 31 and ( \ name N or name CA or name C or name O or name CB )) or resid 32 through 33 or (r \ esid 34 through 36 and (name N or name CA or name C or name O or name CB )) or r \ esid 37 through 42 or (resid 43 through 45 and (name N or name CA or name C or n \ ame O or name CB )) or resid 46 or (resid 47 through 48 and (name N or name CA o \ r name C or name O or name CB )) or resid 49 or (resid 50 and (name N or name CA \ or name C or name O or name CB )) or resid 51 through 59 or (resid 60 and (name \ N or name CA or name C or name O or name CB )) or resid 61 or (resid 62 through \ 63 and (name N or name CA or name C or name O or name CB )) or resid 64 through \ 70 or (resid 71 and (name N or name CA or name C or name O or name CB )) or res \ id 72 through 104 or (resid 105 and (name N or name CA or name C or name O or na \ me CB )) or resid 106 or (resid 107 through 122 and (name N or name CA or name C \ or name O or name CB )) or resid 123 through 130 or (resid 131 and (name N or n \ ame CA or name C or name O or name CB )) or resid 132 through 160 or (resid 161 \ and (name N or name CA or name C or name O or name CB )) or resid 162 through 17 \ 1 or (resid 172 through 173 and (name N or name CA or name C or name O or name C \ B )) or resid 174 through 210 or (resid 211 and (name N or name CA or name C or \ name O or name CB )) or resid 212 through 214 or (resid 215 and (name N or name \ CA or name C or name O or name CB )) or resid 216 through 219 or (resid 220 and \ (name N or name CA or name C or name O or name CB )) or resid 221 through 240 or \ (resid 241 through 243 and (name N or name CA or name C or name O or name CB )) \ or resid 244 through 261 or (resid 262 through 266 and (name N or name CA or na \ me C or name O or name CB )) or resid 267 or (resid 268 through 269 and (name N \ or name CA or name C or name O or name CB )) or resid 270 through 271 or (resid \ 272 through 273 and (name N or name CA or name C or name O or name CB )) or resi \ d 274 or (resid 275 and (name N or name CA or name C or name O or name CB )) or \ resid 276 through 287 or (resid 288 and (name N or name CA or name C or name O o \ r name CB )) or resid 289 through 300 or (resid 301 and (name N or name CA or na \ me C or name O or name CB )) or resid 302 or (resid 303 through 304 and (name N \ or name CA or name C or name O or name CB )) or resid 305 through 313 or (resid \ 314 and (name N or name CA or name C or name O or name CB )) or resid 315 throug \ h 326 or (resid 327 and (name N or name CA or name C or name O or name CB )) or \ resid 328 through 340 or (resid 341 through 342 and (name N or name CA or name C \ or name O or name CB )) or resid 343 through 346 or (resid 347 and (name N or n \ ame CA or name C or name O or name CB )) or resid 348 or (resid 349 and (name N \ or name CA or name C or name O or name CB )) or resid 350 through 356 or (resid \ 357 through 358 and (name N or name CA or name C or name O or name CB )) or resi \ d 359 through 362 or (resid 363 through 365 and (name N or name CA or name C or \ name O or name CB )) or resid 366 through 367 or (resid 368 and (name N or name \ CA or name C or name O or name CB )) or resid 369 through 371 or (resid 372 and \ (name N or name CA or name C or name O or name CB )) or resid 373 through 376 or \ (resid 377 through 379 and (name N or name CA or name C or name O or name CB )) \ or resid 380 through 389 or (resid 390 and (name N or name CA or name C or name \ O or name CB )) or resid 391 through 400 or (resid 401 through 402 and (name N \ or name CA or name C or name O or name CB )) or resid 403 through 407 or (resid \ 408 and (name N or name CA or name C or name O or name CB )) or resid 409 throug \ h 411 or (resid 412 through 413 and (name N or name CA or name C or name O or na \ me CB )) or resid 414 through 423 or (resid 424 through 429 and (name N or name \ CA or name C or name O or name CB )) or resid 901)) selection = (chain 'C' and (resid 19 through 27 or (resid 28 and (name N or name CA or name \ C or name O or name CB )) or resid 29 through 30 or (resid 31 and (name N or nam \ e CA or name C or name O or name CB )) or resid 32 through 42 or (resid 43 throu \ gh 45 and (name N or name CA or name C or name O or name CB )) or resid 46 or (r \ esid 47 through 48 and (name N or name CA or name C or name O or name CB )) or r \ esid 49 or (resid 50 and (name N or name CA or name C or name O or name CB )) or \ resid 51 through 70 or (resid 71 and (name N or name CA or name C or name O or \ name CB )) or resid 72 through 100 or (resid 101 and (name N or name CA or name \ C or name O or name CB )) or resid 102 through 104 or (resid 105 and (name N or \ name CA or name C or name O or name CB )) or (resid 106 through 122 and (name N \ or name CA or name C or name O or name CB )) or resid 123 through 130 or (resid \ 131 and (name N or name CA or name C or name O or name CB )) or resid 132 throug \ h 171 or (resid 172 through 173 and (name N or name CA or name C or name O or na \ me CB )) or resid 174 through 204 or (resid 205 and (name N or name CA or name C \ or name O or name CB )) or resid 206 through 210 or (resid 211 and (name N or n \ ame CA or name C or name O or name CB )) or resid 212 through 214 or (resid 215 \ and (name N or name CA or name C or name O or name CB )) or resid 216 through 21 \ 9 or (resid 220 and (name N or name CA or name C or name O or name CB )) or resi \ d 221 through 240 or (resid 241 through 243 and (name N or name CA or name C or \ name O or name CB )) or resid 244 through 251 or (resid 252 and (name N or name \ CA or name C or name O or name CB )) or resid 253 through 254 or (resid 255 and \ (name N or name CA or name C or name O or name CB )) or resid 256 through 261 or \ (resid 262 through 266 and (name N or name CA or name C or name O or name CB )) \ or resid 267 or (resid 268 through 269 and (name N or name CA or name C or name \ O or name CB )) or resid 270 through 271 or (resid 272 through 273 and (name N \ or name CA or name C or name O or name CB )) or resid 274 or (resid 275 and (nam \ e N or name CA or name C or name O or name CB )) or resid 276 through 284 or (re \ sid 285 and (name N or name CA or name C or name O or name CB )) or resid 286 th \ rough 287 or (resid 288 and (name N or name CA or name C or name O or name CB )) \ or resid 289 through 300 or (resid 301 and (name N or name CA or name C or name \ O or name CB )) or resid 302 or (resid 303 through 304 and (name N or name CA o \ r name C or name O or name CB )) or resid 305 through 328 or (resid 329 and (nam \ e N or name CA or name C or name O or name CB )) or resid 330 through 340 or (re \ sid 341 through 342 and (name N or name CA or name C or name O or name CB )) or \ resid 343 through 346 or (resid 347 and (name N or name CA or name C or name O o \ r name CB )) or resid 348 or (resid 349 and (name N or name CA or name C or name \ O or name CB )) or resid 350 or (resid 351 and (name N or name CA or name C or \ name O or name CB )) or resid 352 through 357 or (resid 358 and (name N or name \ CA or name C or name O or name CB )) or resid 359 through 361 or (resid 362 thro \ ugh 365 and (name N or name CA or name C or name O or name CB )) or resid 366 th \ rough 367 or (resid 368 and (name N or name CA or name C or name O or name CB )) \ or resid 369 through 371 or (resid 372 and (name N or name CA or name C or name \ O or name CB )) or resid 373 through 376 or (resid 377 through 379 and (name N \ or name CA or name C or name O or name CB )) or resid 380 through 389 or (resid \ 390 and (name N or name CA or name C or name O or name CB )) or resid 391 throug \ h 400 or (resid 401 through 402 and (name N or name CA or name C or name O or na \ me CB )) or resid 403 through 419 or (resid 420 and (name N or name CA or name C \ or name O or name CB )) or resid 421 through 424 or (resid 425 through 429 and \ (name N or name CA or name C or name O or name CB )) or resid 901)) selection = (chain 'D' and (resid 19 through 26 or (resid 27 through 28 and (name N or name \ CA or name C or name O or name CB )) or resid 29 through 30 or (resid 31 and (na \ me N or name CA or name C or name O or name CB )) or resid 32 through 34 or (res \ id 35 through 36 and (name N or name CA or name C or name O or name CB )) or res \ id 37 through 44 or (resid 45 and (name N or name CA or name C or name O or name \ CB )) or resid 46 or (resid 47 through 48 and (name N or name CA or name C or n \ ame O or name CB )) or resid 49 or (resid 50 and (name N or name CA or name C or \ name O or name CB )) or resid 51 through 59 or (resid 60 and (name N or name CA \ or name C or name O or name CB )) or resid 61 through 67 or (resid 68 and (name \ N or name CA or name C or name O or name CB )) or resid 69 through 70 or (resid \ 71 and (name N or name CA or name C or name O or name CB )) or resid 72 through \ 100 or (resid 101 and (name N or name CA or name C or name O or name CB )) or r \ esid 102 through 106 or (resid 107 through 122 and (name N or name CA or name C \ or name O or name CB )) or resid 123 through 130 or (resid 131 and (name N or na \ me CA or name C or name O or name CB )) or resid 132 through 160 or (resid 161 a \ nd (name N or name CA or name C or name O or name CB )) or resid 162 through 210 \ or (resid 211 and (name N or name CA or name C or name O or name CB )) or resid \ 212 through 214 or (resid 215 and (name N or name CA or name C or name O or nam \ e CB )) or resid 216 through 219 or (resid 220 and (name N or name CA or name C \ or name O or name CB )) or resid 221 through 241 or (resid 242 through 243 and ( \ name N or name CA or name C or name O or name CB )) or resid 244 through 251 or \ (resid 252 and (name N or name CA or name C or name O or name CB )) or resid 253 \ through 254 or (resid 255 and (name N or name CA or name C or name O or name CB \ )) or resid 256 through 261 or (resid 262 through 266 and (name N or name CA or \ name C or name O or name CB )) or resid 267 through 271 or (resid 272 through 2 \ 73 and (name N or name CA or name C or name O or name CB )) or resid 274 through \ 284 or (resid 285 and (name N or name CA or name C or name O or name CB )) or r \ esid 286 through 303 or (resid 304 and (name N or name CA or name C or name O or \ name CB )) or resid 305 through 313 or (resid 314 and (name N or name CA or nam \ e C or name O or name CB )) or resid 315 through 326 or (resid 327 and (name N o \ r name CA or name C or name O or name CB )) or resid 328 or (resid 329 and (name \ N or name CA or name C or name O or name CB )) or resid 330 through 341 or (res \ id 342 and (name N or name CA or name C or name O or name CB )) or resid 343 thr \ ough 344 or (resid 345 and (name N or name CA or name C or name O or name CB )) \ or resid 346 or (resid 347 and (name N or name CA or name C or name O or name CB \ )) or resid 348 or (resid 349 and (name N or name CA or name C or name O or nam \ e CB )) or resid 350 or (resid 351 and (name N or name CA or name C or name O or \ name CB )) or resid 352 through 356 or (resid 357 through 358 and (name N or na \ me CA or name C or name O or name CB )) or resid 359 through 361 or (resid 362 t \ hrough 365 and (name N or name CA or name C or name O or name CB )) or resid 366 \ through 371 or (resid 372 and (name N or name CA or name C or name O or name CB \ )) or resid 373 through 376 or (resid 377 through 379 and (name N or name CA or \ name C or name O or name CB )) or resid 380 through 389 or (resid 390 and (name \ N or name CA or name C or name O or name CB )) or resid 391 through 407 or (res \ id 408 and (name N or name CA or name C or name O or name CB )) or resid 409 thr \ ough 411 or (resid 412 through 413 and (name N or name CA or name C or name O or \ name CB )) or resid 414 through 419 or (resid 420 and (name N or name CA or nam \ e C or name O or name CB )) or resid 421 through 423 or (resid 424 through 429 a \ nd (name N or name CA or name C or name O or name CB )) or resid 901)) selection = (chain 'E' and (resid 19 through 23 or (resid 24 and (name N or name CA or name \ C or name O or name CB )) or resid 25 through 26 or (resid 27 through 28 and (na \ me N or name CA or name C or name O or name CB )) or resid 29 through 33 or (res \ id 34 through 36 and (name N or name CA or name C or name O or name CB )) or res \ id 37 through 42 or (resid 43 through 45 and (name N or name CA or name C or nam \ e O or name CB )) or resid 46 through 47 or (resid 48 and (name N or name CA or \ name C or name O or name CB )) or resid 49 through 100 or (resid 101 and (name N \ or name CA or name C or name O or name CB )) or resid 102 through 106 or (resid \ 107 through 122 and (name N or name CA or name C or name O or name CB )) or res \ id 123 through 126 or (resid 127 and (name N or name CA or name C or name O or n \ ame CB )) or resid 128 through 160 or (resid 161 and (name N or name CA or name \ C or name O or name CB )) or resid 162 through 171 or (resid 172 through 173 and \ (name N or name CA or name C or name O or name CB )) or resid 174 through 240 o \ r (resid 241 through 243 and (name N or name CA or name C or name O or name CB ) \ ) or resid 244 through 251 or (resid 252 and (name N or name CA or name C or nam \ e O or name CB )) or resid 253 through 254 or (resid 255 and (name N or name CA \ or name C or name O or name CB )) or resid 256 through 267 or (resid 268 through \ 269 and (name N or name CA or name C or name O or name CB )) or resid 270 or (r \ esid 271 through 273 and (name N or name CA or name C or name O or name CB )) or \ resid 274 through 284 or (resid 285 and (name N or name CA or name C or name O \ or name CB )) or resid 286 through 287 or (resid 288 and (name N or name CA or n \ ame C or name O or name CB )) or resid 289 through 300 or (resid 301 and (name N \ or name CA or name C or name O or name CB )) or resid 302 through 309 or (resid \ 310 and (name N or name CA or name C or name O or name CB )) or resid 311 throu \ gh 313 or (resid 314 and (name N or name CA or name C or name O or name CB )) or \ resid 315 through 326 or (resid 327 and (name N or name CA or name C or name O \ or name CB )) or resid 328 or (resid 329 and (name N or name CA or name C or nam \ e O or name CB )) or resid 330 through 340 or (resid 341 through 342 and (name N \ or name CA or name C or name O or name CB )) or resid 343 through 344 or (resid \ 345 and (name N or name CA or name C or name O or name CB )) or resid 346 throu \ gh 350 or (resid 351 and (name N or name CA or name C or name O or name CB )) or \ resid 352 through 356 or (resid 357 through 358 and (name N or name CA or name \ C or name O or name CB )) or resid 359 through 362 or (resid 363 through 365 and \ (name N or name CA or name C or name O or name CB )) or resid 366 through 367 o \ r (resid 368 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 69 through 378 or (resid 379 and (name N or name CA or name C or name O or name \ CB )) or resid 380 through 400 or (resid 401 through 402 and (name N or name CA \ or name C or name O or name CB )) or resid 403 through 411 or (resid 412 through \ 413 and (name N or name CA or name C or name O or name CB )) or resid 414 throu \ gh 419 or (resid 420 and (name N or name CA or name C or name O or name CB )) or \ resid 421 through 423 or (resid 424 through 429 and (name N or name CA or name \ C or name O or name CB )) or resid 901)) } ncs_group { reference = (chain 'G' and (resid 15 through 16 or (resid 17 and (name N or name CA or name \ C or name O or name CB )) or resid 18 through 20 or (resid 21 through 22 and (na \ me N or name CA or name C or name O or name CB )) or resid 23 through 26 or (res \ id 27 through 29 and (name N or name CA or name C or name O or name CB )) or res \ id 30 through 37 or resid 40 through 41 or (resid 42 and (name N or name CA or n \ ame C or name O or name CB )) or resid 43 through 44 or (resid 45 and (name N or \ name CA or name C or name O or name CB )) or resid 46 or (resid 47 through 48 a \ nd (name N or name CA or name C or name O or name CB )) or resid 49 through 73 o \ r (resid 74 and (name N or name CA or name C or name O or name CB )) or resid 75 \ or (resid 76 through 77 and (name N or name CA or name C or name O or name CB ) \ ) or resid 78 through 80 or (resid 81 through 82 and (name N or name CA or name \ C or name O or name CB )) or resid 83 through 87 or (resid 88 through 93 and (na \ me N or name CA or name C or name O or name CB )) or resid 94 through 120 or (re \ sid 121 and (name N or name CA or name C or name O or name CB )) or resid 122 th \ rough 126 or (resid 127 and (name N or name CA or name C or name O or name CB )) \ or resid 128 through 156 or (resid 157 through 158 and (name N or name CA or na \ me C or name O or name CB )) or resid 159 through 165 or (resid 166 through 168 \ and (name N or name CA or name C or name O or name CB )) or resid 169 through 17 \ 2 or (resid 173 through 174 and (name N or name CA or name C or name O or name C \ B )) or resid 175 or (resid 176 through 177 and (name N or name CA or name C or \ name O or name CB )) or resid 178 through 180 or (resid 181 and (name N or name \ CA or name C or name O or name CB )) or resid 182 or (resid 183 and (name N or n \ ame CA or name C or name O or name CB )) or resid 184 through 200 or (resid 201 \ and (name N or name CA or name C or name O or name CB )) or resid 202 through 20 \ 6)) selection = (chain 'I' and (resid 15 through 27 or (resid 28 through 29 and (name N or name \ CA or name C or name O or name CB )) or resid 30 through 64 or (resid 65 and (na \ me N or name CA or name C or name O or name CB )) or resid 66 through 68 or (res \ id 69 and (name N or name CA or name C or name O or name CB )) or resid 70 throu \ gh 81 or (resid 82 and (name N or name CA or name C or name O or name CB )) or r \ esid 83 through 85 or (resid 86 through 93 and (name N or name CA or name C or n \ ame O or name CB )) or resid 94 through 95 or (resid 96 through 98 and (name N o \ r name CA or name C or name O or name CB )) or resid 99 through 105 or resid 117 \ through 122 or (resid 123 through 127 and (name N or name CA or name C or name \ O or name CB )) or resid 128 through 133 or resid 145 or (resid 146 and (name N \ or name CA or name C or name O or name CB )) or resid 147 through 159 or (resid \ 160 through 162 and (name N or name CA or name C or name O or name CB )) or resi \ d 163 through 164 or (resid 165 through 168 and (name N or name CA or name C or \ name O or name CB )) or resid 169 through 179 or (resid 180 through 181 and (nam \ e N or name CA or name C or name O or name CB )) or resid 182 through 184 or (re \ sid 185 and (name N or name CA or name C or name O or name CB )) or resid 186 th \ rough 188 or (resid 189 through 190 and (name N or name CA or name C or name O o \ r name CB )) or resid 191 through 198 or (resid 199 through 201 and (name N or n \ ame CA or name C or name O or name CB )) or resid 202 through 206)) } ncs_group { reference = (chain 'J' and (resid 15 through 29 or (resid 30 and (name N or name CA or name \ C or name O or name CB )) or resid 31 or (resid 32 and (name N or name CA or nam \ e C or name O or name CB )) or resid 33 or resid 39 through 51 or (resid 52 thro \ ugh 54 and (name N or name CA or name C or name O or name CB )) or resid 55 thro \ ugh 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or \ resid 65 through 73 or (resid 74 and (name N or name CA or name C or name O or n \ ame 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 87 or (resid 88 and (name N or name CA or name C \ or name O or name CB )) or resid 89 or (resid 90 through 93 and (name N or name \ CA or name C or name O or name CB )) or resid 94 through 97 or (resid 98 and (n \ ame N or name CA or name C or name O or name CB )) or resid 99 through 137 or (r \ esid 138 and (name N or name CA or name C or name O or name CB )) or resid 145 t \ hrough 151 or resid 199 through 203 or (resid 204 and (name N or name CA or name \ C or name O or name CB )) or resid 205)) selection = (chain 'K' and (resid 15 through 16 or (resid 17 and (name N or name CA or name \ C or name O or name CB )) or resid 18 through 40 or (resid 41 and (name N or nam \ e CA or name C or name O or name CB )) or resid 42 through 47 or (resid 48 throu \ gh 50 and (name N or name CA or name C or name O or name CB )) or resid 51 throu \ gh 53 or (resid 54 and (name N or name CA or name C or name O or name CB )) or r \ esid 55 through 80 or (resid 81 through 82 and (name N or name CA or name C or n \ ame O or name CB )) or resid 83 through 91 or (resid 92 through 93 and (name N o \ r name CA or name C or name O or name CB )) or resid 94 through 104 or resid 119 \ or (resid 120 and (name N or name CA or name C or name O or name CB )) or resid \ 121 through 125 or (resid 126 and (name N or name CA or name C or name O or nam \ e CB )) or resid 127 through 128 or (resid 129 and (name N or name CA or name C \ or name O or name CB )) or resid 130 through 135 or (resid 136 and (name N or na \ me CA or name C or name O or name CB )) or resid 137 through 138 or resid 145 th \ rough 151 or resid 199 through 205)) } ncs_group { reference = (chain 'X' and ((resid 3 through 4 and (name N or name CA or name C or name O or \ name CB )) or resid 5 through 48 or (resid 49 through 50 and (name N or name CA \ or name C or name O or name CB )) or resid 51 through 67 or (resid 68 through 7 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 71 through 7 \ 8 or (resid 79 through 80 and (name N or name CA or name C or name O or name CB \ )) or resid 81 or (resid 82 through 83 and (name N or name CA or name C or name \ O or name CB )) or resid 84 through 89)) selection = (chain 'Y' and (resid 3 through 8 or resid 34 through 35 or (resid 36 and (name \ N or name CA or name C or name O or name CB )) or resid 37 through 39 or (resid \ 40 through 41 and (name N or name CA or name C or name O or name CB )) or resid \ 42 through 45 or (resid 46 and (name N or name CA or name C or name O or name CB \ )) or resid 47 or (resid 48 through 50 and (name N or name CA or name C or name \ O or name CB )) or resid 51 or (resid 52 through 54 and (name N or name CA or n \ ame C or name O or name CB )) or resid 55 or (resid 56 through 57 and (name N or \ name CA or name C or name O or name CB )) or resid 58 through 63 or (resid 64 a \ nd (name N or name CA or name C or name O or name CB )) or resid 65 through 68 o \ r (resid 69 through 70 and (name N or name CA or name C or name O or name CB )) \ or resid 71 through 74 or (resid 75 and (name N or name CA or name C or name O o \ r name CB )) or resid 76 through 85 or (resid 86 and (name N or name CA or name \ C or name O or name CB )) or resid 87 through 89)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.850 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 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 : 0.008 0.208 22312 Z= 0.559 Angle : 1.240 26.899 30502 Z= 0.728 Chirality : 0.066 0.962 3779 Planarity : 0.006 0.059 3833 Dihedral : 17.038 135.327 7748 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 20.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.44 % Favored : 90.49 % Rotamer: Outliers : 0.54 % Allowed : 1.65 % Favored : 97.81 % Cbeta Deviations : 0.18 % Peptide Plane: Cis-proline : 2.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.83 (0.15), residues: 2849 helix: -1.24 (0.14), residues: 1201 sheet: -0.98 (0.28), residues: 330 loop : -2.74 (0.16), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.002 ARG C 205 TYR 0.033 0.002 TYR J 32 PHE 0.053 0.003 PHE I 11 TRP 0.056 0.003 TRP B 125 HIS 0.021 0.001 HIS Y 5 Details of bonding type rmsd covalent geometry : bond 0.00814 (22312) covalent geometry : angle 1.24015 (30502) hydrogen bonds : bond 0.17772 ( 997) hydrogen bonds : angle 7.59710 ( 2862) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 331 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 58 TRP cc_start: 0.8051 (m-90) cc_final: 0.7633 (m-90) REVERT: B 354 ARG cc_start: 0.7645 (ppt170) cc_final: 0.7436 (ppt170) REVERT: B 376 ILE cc_start: 0.9109 (mm) cc_final: 0.8721 (mt) REVERT: D 26 HIS cc_start: 0.8059 (OUTLIER) cc_final: 0.7643 (t-90) REVERT: D 354 ARG cc_start: 0.7757 (ttt180) cc_final: 0.7536 (ttt180) REVERT: F 379 LYS cc_start: 0.5726 (ttmt) cc_final: 0.4822 (ttpp) REVERT: J 97 LYS cc_start: 0.7473 (mtpp) cc_final: 0.7152 (mtpp) outliers start: 12 outliers final: 5 residues processed: 340 average time/residue: 0.1589 time to fit residues: 84.4257 Evaluate side-chains 270 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 264 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 ARG Chi-restraints excluded: chain B residue 124 HIS Chi-restraints excluded: chain D residue 26 HIS Chi-restraints excluded: chain F residue 278 ASN Chi-restraints excluded: chain F residue 347 ARG Chi-restraints excluded: chain K residue 54 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 8.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 ASN B 98 HIS B 292 ASN B 300 ASN C 283 GLN D 49 HIS D 348 GLN E 163 ASN E 292 ASN ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 GLN F 123 ASN G 53 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.148981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.117517 restraints weight = 46605.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.118420 restraints weight = 33087.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.118802 restraints weight = 26452.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.119027 restraints weight = 19095.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.119390 restraints weight = 17780.179| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 22312 Z= 0.206 Angle : 0.782 10.627 30502 Z= 0.405 Chirality : 0.050 0.319 3779 Planarity : 0.005 0.050 3833 Dihedral : 9.448 118.301 3142 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.39 % Favored : 91.58 % Rotamer: Outliers : 2.19 % Allowed : 14.48 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.15), residues: 2849 helix: -0.74 (0.14), residues: 1243 sheet: -0.87 (0.27), residues: 367 loop : -2.57 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 205 TYR 0.018 0.002 TYR K 63 PHE 0.018 0.002 PHE B 248 TRP 0.034 0.002 TRP B 125 HIS 0.015 0.001 HIS Y 5 Details of bonding type rmsd covalent geometry : bond 0.00471 (22312) covalent geometry : angle 0.78227 (30502) hydrogen bonds : bond 0.05521 ( 997) hydrogen bonds : angle 6.06727 ( 2862) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 285 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 TRP cc_start: 0.7671 (p-90) cc_final: 0.7295 (p-90) REVERT: B 58 TRP cc_start: 0.8382 (m-90) cc_final: 0.8130 (m-90) REVERT: B 376 ILE cc_start: 0.9092 (mm) cc_final: 0.8767 (mt) REVERT: C 375 ASP cc_start: 0.8128 (m-30) cc_final: 0.7895 (m-30) REVERT: E 332 LEU cc_start: 0.9133 (mt) cc_final: 0.8681 (mt) REVERT: E 336 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7809 (mp0) REVERT: F 344 ILE cc_start: 0.3547 (mm) cc_final: 0.3162 (mm) REVERT: F 358 MET cc_start: 0.6050 (mtt) cc_final: 0.5823 (mtt) REVERT: F 379 LYS cc_start: 0.5461 (ttmt) cc_final: 0.4588 (ttpp) REVERT: J 97 LYS cc_start: 0.7361 (mtpp) cc_final: 0.6855 (mtpp) REVERT: J 199 MET cc_start: 0.5732 (mmm) cc_final: 0.5520 (mmm) REVERT: K 199 MET cc_start: 0.7143 (pmm) cc_final: 0.6889 (pmm) outliers start: 49 outliers final: 34 residues processed: 307 average time/residue: 0.1498 time to fit residues: 72.5727 Evaluate side-chains 289 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 254 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 368 LYS Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 290 HIS Chi-restraints excluded: chain F residue 298 THR Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain J residue 79 ASP Chi-restraints excluded: chain J residue 87 ILE Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain Y residue 58 ILE Chi-restraints excluded: chain X residue 5 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 215 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 85 optimal weight: 0.0270 chunk 223 optimal weight: 8.9990 chunk 44 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 234 optimal weight: 7.9990 chunk 23 optimal weight: 20.0000 chunk 202 optimal weight: 9.9990 chunk 191 optimal weight: 6.9990 overall best weight: 5.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN A 365 ASN B 194 GLN ** B 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 HIS E 163 ASN ** E 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 28 HIS I 140 ASN ** J 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.144698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.113471 restraints weight = 47447.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.113234 restraints weight = 36337.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.114155 restraints weight = 30745.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.114095 restraints weight = 22488.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.114509 restraints weight = 20568.467| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 22312 Z= 0.303 Angle : 0.812 9.962 30502 Z= 0.426 Chirality : 0.052 0.373 3779 Planarity : 0.006 0.069 3833 Dihedral : 9.174 124.057 3125 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.53 % Favored : 89.40 % Rotamer: Outliers : 4.47 % Allowed : 19.48 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.15), residues: 2849 helix: -0.85 (0.14), residues: 1260 sheet: -0.93 (0.27), residues: 363 loop : -2.69 (0.17), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 275 TYR 0.027 0.002 TYR K 63 PHE 0.051 0.003 PHE F 410 TRP 0.034 0.002 TRP E 221 HIS 0.012 0.002 HIS I 151 Details of bonding type rmsd covalent geometry : bond 0.00702 (22312) covalent geometry : angle 0.81202 (30502) hydrogen bonds : bond 0.05745 ( 997) hydrogen bonds : angle 6.04641 ( 2862) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 256 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 TRP cc_start: 0.7760 (p-90) cc_final: 0.7407 (p-90) REVERT: B 58 TRP cc_start: 0.8471 (m-90) cc_final: 0.8173 (m-90) REVERT: B 283 GLN cc_start: 0.7374 (OUTLIER) cc_final: 0.6723 (mp-120) REVERT: C 206 TYR cc_start: 0.8201 (p90) cc_final: 0.7992 (p90) REVERT: C 375 ASP cc_start: 0.8134 (m-30) cc_final: 0.7865 (m-30) REVERT: D 49 HIS cc_start: 0.8048 (OUTLIER) cc_final: 0.7748 (m-70) REVERT: D 327 ILE cc_start: 0.8542 (mt) cc_final: 0.8172 (mt) REVERT: E 332 LEU cc_start: 0.9133 (mt) cc_final: 0.8726 (mt) REVERT: E 336 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7849 (mp0) REVERT: E 389 ARG cc_start: 0.7101 (ttt90) cc_final: 0.6695 (ttt90) REVERT: F 154 MET cc_start: 0.7834 (mmm) cc_final: 0.7469 (mmm) REVERT: F 357 GLU cc_start: 0.5997 (OUTLIER) cc_final: 0.5637 (mp0) REVERT: F 379 LYS cc_start: 0.5501 (ttmt) cc_final: 0.4537 (ttpp) REVERT: J 198 LYS cc_start: 0.6705 (tptt) cc_final: 0.6251 (tptt) REVERT: J 199 MET cc_start: 0.6097 (mmm) cc_final: 0.5865 (mmm) REVERT: X 5 HIS cc_start: 0.6586 (OUTLIER) cc_final: 0.5740 (m170) outliers start: 100 outliers final: 63 residues processed: 322 average time/residue: 0.1499 time to fit residues: 76.7004 Evaluate side-chains 309 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 241 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 124 HIS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 249 VAL Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 405 VAL Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 315 ILE Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 368 LYS Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 290 HIS Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 298 THR Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain I residue 9 LEU Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 23 LEU Chi-restraints excluded: chain I residue 69 HIS Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain J residue 23 LEU Chi-restraints excluded: chain J residue 79 ASP Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain X residue 5 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 18 optimal weight: 0.0770 chunk 218 optimal weight: 20.0000 chunk 32 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 9 optimal weight: 9.9990 chunk 156 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 174 optimal weight: 0.8980 chunk 197 optimal weight: 20.0000 chunk 108 optimal weight: 9.9990 overall best weight: 1.3540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 ASN B 194 GLN ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 ASN E 348 GLN I 28 HIS ** J 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.149834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.118399 restraints weight = 45439.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.117002 restraints weight = 32367.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.117929 restraints weight = 28147.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.118544 restraints weight = 20128.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.118708 restraints weight = 18239.019| |-----------------------------------------------------------------------------| r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22312 Z= 0.137 Angle : 0.666 10.279 30502 Z= 0.343 Chirality : 0.046 0.182 3779 Planarity : 0.004 0.043 3833 Dihedral : 8.493 117.075 3125 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.06 % Favored : 92.91 % Rotamer: Outliers : 3.84 % Allowed : 21.18 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % Cis-general : 0.00 % Twisted Proline : 0.87 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.16), residues: 2849 helix: -0.33 (0.15), residues: 1262 sheet: -0.64 (0.27), residues: 361 loop : -2.38 (0.17), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 48 TYR 0.017 0.001 TYR J 202 PHE 0.035 0.001 PHE F 410 TRP 0.021 0.002 TRP E 221 HIS 0.019 0.001 HIS D 49 Details of bonding type rmsd covalent geometry : bond 0.00303 (22312) covalent geometry : angle 0.66641 (30502) hydrogen bonds : bond 0.04267 ( 997) hydrogen bonds : angle 5.51468 ( 2862) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 289 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 TRP cc_start: 0.7670 (p-90) cc_final: 0.7466 (p-90) REVERT: B 58 TRP cc_start: 0.8430 (m-90) cc_final: 0.8175 (m-90) REVERT: B 240 ILE cc_start: 0.8367 (mt) cc_final: 0.8159 (mt) REVERT: B 283 GLN cc_start: 0.7240 (OUTLIER) cc_final: 0.6650 (mp-120) REVERT: C 206 TYR cc_start: 0.8108 (p90) cc_final: 0.7841 (p90) REVERT: D 327 ILE cc_start: 0.8353 (mt) cc_final: 0.8051 (mt) REVERT: D 357 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8377 (mp0) REVERT: E 65 PHE cc_start: 0.5063 (OUTLIER) cc_final: 0.4604 (t80) REVERT: E 332 LEU cc_start: 0.9048 (mt) cc_final: 0.8605 (mt) REVERT: E 336 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.8059 (mp0) REVERT: F 154 MET cc_start: 0.7814 (mmm) cc_final: 0.7395 (mmm) REVERT: F 232 MET cc_start: 0.5655 (mpp) cc_final: 0.4819 (mtp) REVERT: F 379 LYS cc_start: 0.5293 (ttmt) cc_final: 0.4449 (ttpp) REVERT: G 184 PRO cc_start: 0.5546 (Cg_endo) cc_final: 0.5332 (Cg_exo) REVERT: I 132 VAL cc_start: 0.6548 (m) cc_final: 0.6246 (p) REVERT: J 198 LYS cc_start: 0.6479 (tptt) cc_final: 0.6087 (tptt) outliers start: 86 outliers final: 57 residues processed: 346 average time/residue: 0.1512 time to fit residues: 83.2066 Evaluate side-chains 304 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 243 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 124 HIS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain E residue 65 PHE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 368 LYS Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 290 HIS Chi-restraints excluded: chain F residue 298 THR Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 202 TYR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain I residue 9 LEU Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 129 LYS Chi-restraints excluded: chain J residue 79 ASP Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 96 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 0 optimal weight: 20.0000 chunk 85 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 135 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 260 optimal weight: 8.9990 chunk 161 optimal weight: 0.7980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 ASN ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 ASN ** G 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 28 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.148778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.117528 restraints weight = 45397.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.117237 restraints weight = 32338.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.117607 restraints weight = 30261.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.118342 restraints weight = 21948.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.118547 restraints weight = 18991.785| |-----------------------------------------------------------------------------| r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22312 Z= 0.157 Angle : 0.665 12.602 30502 Z= 0.340 Chirality : 0.046 0.324 3779 Planarity : 0.004 0.039 3833 Dihedral : 8.368 120.232 3125 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.21 % Favored : 91.75 % Rotamer: Outliers : 4.56 % Allowed : 22.03 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.16), residues: 2849 helix: -0.17 (0.15), residues: 1262 sheet: -0.73 (0.27), residues: 384 loop : -2.33 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 312 TYR 0.016 0.001 TYR C 399 PHE 0.040 0.001 PHE F 410 TRP 0.020 0.001 TRP E 221 HIS 0.005 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00364 (22312) covalent geometry : angle 0.66451 (30502) hydrogen bonds : bond 0.04247 ( 997) hydrogen bonds : angle 5.39314 ( 2862) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 260 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 TRP cc_start: 0.8403 (m-90) cc_final: 0.8175 (m-90) REVERT: B 283 GLN cc_start: 0.7268 (OUTLIER) cc_final: 0.6631 (mp-120) REVERT: D 327 ILE cc_start: 0.8374 (mt) cc_final: 0.8117 (mt) REVERT: E 65 PHE cc_start: 0.5142 (OUTLIER) cc_final: 0.4587 (t80) REVERT: E 332 LEU cc_start: 0.9009 (mt) cc_final: 0.8560 (mt) REVERT: E 336 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7963 (mp0) REVERT: E 411 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.6913 (tt) REVERT: F 154 MET cc_start: 0.7834 (mmm) cc_final: 0.7400 (mmm) REVERT: F 379 LYS cc_start: 0.5384 (ttmt) cc_final: 0.4509 (ttpp) REVERT: G 184 PRO cc_start: 0.5499 (Cg_endo) cc_final: 0.5292 (Cg_exo) REVERT: J 198 LYS cc_start: 0.6405 (tptt) cc_final: 0.6078 (tptt) outliers start: 102 outliers final: 74 residues processed: 328 average time/residue: 0.1435 time to fit residues: 75.8744 Evaluate side-chains 317 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 239 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 124 HIS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 376 ILE Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 65 PHE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 368 LYS Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 132 PHE Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 290 HIS Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 298 THR Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 202 TYR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain I residue 9 LEU Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 129 LYS Chi-restraints excluded: chain J residue 79 ASP Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 66 ASP Chi-restraints excluded: chain K residue 96 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 124 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 202 optimal weight: 20.0000 chunk 63 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 178 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 283 optimal weight: 5.9990 chunk 206 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 ASN B 194 GLN D 49 HIS E 163 ASN G 121 GLN ** G 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 28 HIS X 5 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.147634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.115787 restraints weight = 46112.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.114785 restraints weight = 31863.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.115818 restraints weight = 28642.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.115842 restraints weight = 21102.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.116305 restraints weight = 18971.740| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22312 Z= 0.187 Angle : 0.672 11.854 30502 Z= 0.345 Chirality : 0.047 0.274 3779 Planarity : 0.004 0.039 3833 Dihedral : 8.345 122.169 3125 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.42 % Favored : 91.54 % Rotamer: Outliers : 5.27 % Allowed : 22.79 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.16), residues: 2849 helix: -0.16 (0.15), residues: 1269 sheet: -0.65 (0.27), residues: 365 loop : -2.32 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 312 TYR 0.018 0.002 TYR E 318 PHE 0.041 0.002 PHE F 410 TRP 0.023 0.002 TRP E 221 HIS 0.007 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00435 (22312) covalent geometry : angle 0.67223 (30502) hydrogen bonds : bond 0.04310 ( 997) hydrogen bonds : angle 5.37440 ( 2862) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 253 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 TRP cc_start: 0.8456 (m-90) cc_final: 0.8222 (m-90) REVERT: B 283 GLN cc_start: 0.7272 (OUTLIER) cc_final: 0.6611 (mp-120) REVERT: C 275 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7701 (ptp-170) REVERT: C 288 LYS cc_start: 0.8034 (tttm) cc_final: 0.7827 (tptm) REVERT: D 49 HIS cc_start: 0.7834 (OUTLIER) cc_final: 0.7421 (m-70) REVERT: D 327 ILE cc_start: 0.8430 (mt) cc_final: 0.8230 (mt) REVERT: E 65 PHE cc_start: 0.5014 (OUTLIER) cc_final: 0.4508 (t80) REVERT: E 199 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.8227 (ttt90) REVERT: E 332 LEU cc_start: 0.9084 (mt) cc_final: 0.8637 (mt) REVERT: E 336 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8025 (mp0) REVERT: E 411 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.6927 (tt) REVERT: F 154 MET cc_start: 0.7895 (mmm) cc_final: 0.7659 (mmm) REVERT: F 379 LYS cc_start: 0.5575 (ttmt) cc_final: 0.4721 (ttpp) REVERT: G 181 MET cc_start: -0.1373 (mmp) cc_final: -0.1977 (mmp) REVERT: G 184 PRO cc_start: 0.5628 (Cg_endo) cc_final: 0.5400 (Cg_exo) REVERT: I 199 MET cc_start: 0.7441 (mmm) cc_final: 0.7217 (mmm) REVERT: J 198 LYS cc_start: 0.6394 (tptt) cc_final: 0.6168 (tptt) REVERT: X 5 HIS cc_start: 0.6278 (OUTLIER) cc_final: 0.5720 (m-70) outliers start: 118 outliers final: 83 residues processed: 344 average time/residue: 0.1438 time to fit residues: 79.3402 Evaluate side-chains 330 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 239 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain B residue 124 HIS Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 275 ARG Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 142 ASP Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 285 ASP Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 65 PHE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 199 ARG Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 368 LYS Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 132 PHE Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 290 HIS Chi-restraints excluded: chain F residue 298 THR Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 202 TYR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain I residue 9 LEU Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 23 LEU Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 129 LYS Chi-restraints excluded: chain J residue 23 LEU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 79 ASP Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 66 ASP Chi-restraints excluded: chain K residue 96 GLU Chi-restraints excluded: chain K residue 152 THR Chi-restraints excluded: chain X residue 5 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 162 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 chunk 271 optimal weight: 9.9990 chunk 115 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 214 optimal weight: 0.7980 chunk 217 optimal weight: 30.0000 chunk 117 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 ASN B 194 GLN ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 HIS E 163 ASN F 148 HIS ** G 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 28 HIS ** Y 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 3 GLN X 5 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.150237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.118982 restraints weight = 45262.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.117801 restraints weight = 31887.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.118592 restraints weight = 32344.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.118791 restraints weight = 21648.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.119196 restraints weight = 19181.865| |-----------------------------------------------------------------------------| r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22312 Z= 0.129 Angle : 0.643 12.810 30502 Z= 0.326 Chirality : 0.045 0.263 3779 Planarity : 0.004 0.035 3833 Dihedral : 8.076 118.264 3125 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.06 % Favored : 92.91 % Rotamer: Outliers : 4.60 % Allowed : 24.13 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.16), residues: 2849 helix: 0.03 (0.15), residues: 1272 sheet: -0.81 (0.27), residues: 390 loop : -2.15 (0.18), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 203 TYR 0.019 0.001 TYR E 318 PHE 0.030 0.001 PHE F 410 TRP 0.027 0.002 TRP A 171 HIS 0.015 0.001 HIS D 49 Details of bonding type rmsd covalent geometry : bond 0.00292 (22312) covalent geometry : angle 0.64280 (30502) hydrogen bonds : bond 0.03853 ( 997) hydrogen bonds : angle 5.17842 ( 2862) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 268 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7973 (tm-30) REVERT: B 58 TRP cc_start: 0.8439 (m-90) cc_final: 0.8177 (m-90) REVERT: B 283 GLN cc_start: 0.7200 (OUTLIER) cc_final: 0.6523 (mp-120) REVERT: D 49 HIS cc_start: 0.7773 (OUTLIER) cc_final: 0.7531 (m90) REVERT: E 65 PHE cc_start: 0.5123 (OUTLIER) cc_final: 0.4628 (t80) REVERT: E 332 LEU cc_start: 0.9020 (mt) cc_final: 0.8605 (mt) REVERT: E 336 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7948 (mp0) REVERT: E 411 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.6935 (tt) REVERT: F 154 MET cc_start: 0.7846 (mmm) cc_final: 0.7596 (mmm) REVERT: F 357 GLU cc_start: 0.5908 (OUTLIER) cc_final: 0.5615 (mp0) REVERT: F 379 LYS cc_start: 0.5644 (ttmt) cc_final: 0.4709 (ttpp) REVERT: G 181 MET cc_start: -0.1448 (mmp) cc_final: -0.1987 (mmp) REVERT: I 199 MET cc_start: 0.7445 (mmm) cc_final: 0.7198 (mmm) REVERT: X 5 HIS cc_start: 0.5957 (OUTLIER) cc_final: 0.5230 (m-70) outliers start: 103 outliers final: 73 residues processed: 343 average time/residue: 0.1387 time to fit residues: 77.3118 Evaluate side-chains 325 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 245 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 285 ASP Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 65 PHE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 221 TRP Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 132 PHE Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 298 THR Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 202 TYR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain I residue 9 LEU Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 23 LEU Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 129 LYS Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 66 ASP Chi-restraints excluded: chain K residue 96 GLU Chi-restraints excluded: chain X residue 5 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 23 optimal weight: 20.0000 chunk 269 optimal weight: 5.9990 chunk 140 optimal weight: 6.9990 chunk 110 optimal weight: 10.0000 chunk 277 optimal weight: 0.6980 chunk 208 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 207 optimal weight: 0.0870 overall best weight: 2.5362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 ASN ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 ASN F 412 GLN ** G 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 28 HIS ** Y 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 5 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.149043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.117689 restraints weight = 45627.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.117102 restraints weight = 31947.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.117878 restraints weight = 30133.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.118101 restraints weight = 21450.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.118487 restraints weight = 19167.363| |-----------------------------------------------------------------------------| r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22312 Z= 0.161 Angle : 0.661 12.691 30502 Z= 0.335 Chirality : 0.046 0.241 3779 Planarity : 0.004 0.056 3833 Dihedral : 8.118 120.665 3125 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.55 % Favored : 92.42 % Rotamer: Outliers : 5.00 % Allowed : 24.62 % Favored : 70.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % Cis-general : 0.00 % Twisted Proline : 0.87 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.16), residues: 2849 helix: 0.04 (0.15), residues: 1272 sheet: -0.71 (0.27), residues: 393 loop : -2.17 (0.18), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 203 TYR 0.017 0.001 TYR E 318 PHE 0.032 0.001 PHE F 410 TRP 0.025 0.002 TRP A 171 HIS 0.010 0.001 HIS D 49 Details of bonding type rmsd covalent geometry : bond 0.00376 (22312) covalent geometry : angle 0.66130 (30502) hydrogen bonds : bond 0.04009 ( 997) hydrogen bonds : angle 5.21313 ( 2862) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 250 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7961 (tm-30) REVERT: B 58 TRP cc_start: 0.8432 (m-90) cc_final: 0.8186 (m-90) REVERT: B 283 GLN cc_start: 0.7242 (OUTLIER) cc_final: 0.6576 (mp-120) REVERT: B 386 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.8068 (ttm170) REVERT: E 65 PHE cc_start: 0.5044 (OUTLIER) cc_final: 0.4530 (t80) REVERT: E 332 LEU cc_start: 0.9048 (mt) cc_final: 0.8603 (mt) REVERT: E 336 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7978 (mp0) REVERT: E 411 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.6968 (tt) REVERT: F 379 LYS cc_start: 0.5594 (ttmt) cc_final: 0.4719 (ttpp) REVERT: I 199 MET cc_start: 0.7471 (mmm) cc_final: 0.7240 (mmm) REVERT: X 5 HIS cc_start: 0.5897 (OUTLIER) cc_final: 0.5316 (m-70) outliers start: 112 outliers final: 86 residues processed: 333 average time/residue: 0.1462 time to fit residues: 78.2598 Evaluate side-chains 332 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 240 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 222 PHE Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 386 ARG Chi-restraints excluded: chain B residue 405 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 142 ASP Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 285 ASP Chi-restraints excluded: chain D residue 296 LEU Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 375 ASP Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 65 PHE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 353 LEU Chi-restraints excluded: chain E residue 368 LYS Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 132 PHE Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 290 HIS Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 298 THR Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 358 MET Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 202 TYR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 23 LEU Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 129 LYS Chi-restraints excluded: chain J residue 23 LEU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 66 ASP Chi-restraints excluded: chain K residue 96 GLU Chi-restraints excluded: chain X residue 5 HIS Chi-restraints excluded: chain X residue 63 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 108 optimal weight: 5.9990 chunk 270 optimal weight: 0.8980 chunk 253 optimal weight: 0.9990 chunk 233 optimal weight: 4.9990 chunk 141 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 chunk 216 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 203 optimal weight: 0.0070 chunk 177 optimal weight: 8.9990 chunk 143 optimal weight: 0.8980 overall best weight: 0.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 ASN C 69 ASN ** C 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 ASN ** G 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 28 HIS J 151 HIS X 5 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.151830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.120641 restraints weight = 45128.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.121213 restraints weight = 32397.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.121378 restraints weight = 33505.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.121954 restraints weight = 21386.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.122267 restraints weight = 18411.933| |-----------------------------------------------------------------------------| r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22312 Z= 0.120 Angle : 0.648 14.113 30502 Z= 0.323 Chirality : 0.045 0.237 3779 Planarity : 0.004 0.038 3833 Dihedral : 7.897 117.906 3125 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.18 % Favored : 93.79 % Rotamer: Outliers : 4.02 % Allowed : 25.25 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.16), residues: 2849 helix: 0.22 (0.15), residues: 1281 sheet: -0.67 (0.27), residues: 393 loop : -2.11 (0.18), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 203 TYR 0.019 0.001 TYR E 318 PHE 0.034 0.001 PHE F 410 TRP 0.038 0.002 TRP A 171 HIS 0.016 0.001 HIS X 5 Details of bonding type rmsd covalent geometry : bond 0.00270 (22312) covalent geometry : angle 0.64780 (30502) hydrogen bonds : bond 0.03632 ( 997) hydrogen bonds : angle 5.06863 ( 2862) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 270 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 GLU cc_start: 0.6799 (pp20) cc_final: 0.6052 (pm20) REVERT: A 424 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7923 (tm-30) REVERT: B 58 TRP cc_start: 0.8416 (m-90) cc_final: 0.8209 (m-90) REVERT: B 217 LEU cc_start: 0.7912 (tp) cc_final: 0.7497 (mt) REVERT: B 283 GLN cc_start: 0.7156 (OUTLIER) cc_final: 0.6459 (mp-120) REVERT: B 386 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7998 (ttm170) REVERT: E 65 PHE cc_start: 0.5123 (OUTLIER) cc_final: 0.4649 (t80) REVERT: E 154 MET cc_start: 0.7553 (mmp) cc_final: 0.7261 (mmp) REVERT: E 199 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.8248 (ttm-80) REVERT: E 332 LEU cc_start: 0.8950 (mt) cc_final: 0.8508 (mt) REVERT: E 336 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7919 (mp0) REVERT: E 411 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.6856 (tt) REVERT: F 154 MET cc_start: 0.7836 (mmm) cc_final: 0.7294 (mmm) REVERT: F 239 LEU cc_start: 0.6071 (OUTLIER) cc_final: 0.5834 (mm) REVERT: F 357 GLU cc_start: 0.5948 (OUTLIER) cc_final: 0.5449 (mp0) REVERT: F 379 LYS cc_start: 0.5584 (ttmt) cc_final: 0.4688 (ttpp) REVERT: I 11 PHE cc_start: 0.7847 (t80) cc_final: 0.7646 (t80) REVERT: I 23 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7592 (mm) REVERT: I 199 MET cc_start: 0.7408 (mmm) cc_final: 0.7190 (mmm) REVERT: J 97 LYS cc_start: 0.7198 (mtpp) cc_final: 0.6433 (mmmt) REVERT: Y 5 HIS cc_start: 0.7536 (OUTLIER) cc_final: 0.7045 (m170) outliers start: 90 outliers final: 64 residues processed: 334 average time/residue: 0.1468 time to fit residues: 79.0222 Evaluate side-chains 327 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 253 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 386 ARG Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 285 ASP Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 65 PHE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 199 ARG Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 368 LYS Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 132 PHE Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 290 HIS Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 298 THR Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 358 MET Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 122 LEU Chi-restraints excluded: chain G residue 202 TYR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain I residue 9 LEU Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 23 LEU Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 129 LYS Chi-restraints excluded: chain J residue 23 LEU Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 96 GLU Chi-restraints excluded: chain K residue 152 THR Chi-restraints excluded: chain Y residue 5 HIS Chi-restraints excluded: chain X residue 5 HIS Chi-restraints excluded: chain X residue 63 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 73 optimal weight: 3.9990 chunk 142 optimal weight: 0.6980 chunk 220 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 271 optimal weight: 3.9990 chunk 277 optimal weight: 0.9990 chunk 6 optimal weight: 10.0000 chunk 231 optimal weight: 0.0770 chunk 22 optimal weight: 0.0870 chunk 96 optimal weight: 8.9990 chunk 112 optimal weight: 5.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 ASN C 290 HIS E 163 ASN ** G 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 28 HIS X 5 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.153200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.121572 restraints weight = 45906.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.121917 restraints weight = 31653.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.122379 restraints weight = 31375.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.122693 restraints weight = 21966.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.123104 restraints weight = 19327.128| |-----------------------------------------------------------------------------| r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22312 Z= 0.116 Angle : 0.654 13.841 30502 Z= 0.324 Chirality : 0.045 0.276 3779 Planarity : 0.004 0.051 3833 Dihedral : 7.766 117.991 3125 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.14 % Favored : 93.82 % Rotamer: Outliers : 3.26 % Allowed : 26.50 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.16), residues: 2849 helix: 0.36 (0.15), residues: 1281 sheet: -0.62 (0.26), residues: 403 loop : -2.06 (0.18), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 203 TYR 0.017 0.001 TYR E 345 PHE 0.033 0.001 PHE F 410 TRP 0.028 0.002 TRP A 171 HIS 0.015 0.001 HIS X 5 Details of bonding type rmsd covalent geometry : bond 0.00259 (22312) covalent geometry : angle 0.65381 (30502) hydrogen bonds : bond 0.03498 ( 997) hydrogen bonds : angle 4.94338 ( 2862) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5698 Ramachandran restraints generated. 2849 Oldfield, 0 Emsley, 2849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 277 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 GLU cc_start: 0.6818 (pp20) cc_final: 0.6110 (pm20) REVERT: A 424 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7806 (tm-30) REVERT: B 56 TYR cc_start: 0.7817 (t80) cc_final: 0.7157 (t80) REVERT: B 58 TRP cc_start: 0.8399 (m-90) cc_final: 0.8109 (m-90) REVERT: B 217 LEU cc_start: 0.7890 (tp) cc_final: 0.7461 (mt) REVERT: B 283 GLN cc_start: 0.7164 (OUTLIER) cc_final: 0.6591 (mp-120) REVERT: B 386 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.8031 (ttm170) REVERT: E 65 PHE cc_start: 0.5058 (OUTLIER) cc_final: 0.4552 (t80) REVERT: E 199 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.8096 (ttt90) REVERT: E 250 LEU cc_start: 0.8295 (tp) cc_final: 0.8017 (tp) REVERT: E 411 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.6779 (tt) REVERT: F 154 MET cc_start: 0.7817 (mmm) cc_final: 0.7222 (mmm) REVERT: F 239 LEU cc_start: 0.6072 (OUTLIER) cc_final: 0.5848 (mm) REVERT: F 379 LYS cc_start: 0.5529 (ttmt) cc_final: 0.4688 (ttpp) REVERT: I 23 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7500 (mm) REVERT: J 60 LEU cc_start: 0.4115 (mt) cc_final: 0.3674 (tt) REVERT: J 97 LYS cc_start: 0.7155 (mtpp) cc_final: 0.6810 (mmtp) REVERT: Y 5 HIS cc_start: 0.7397 (OUTLIER) cc_final: 0.6893 (m170) outliers start: 73 outliers final: 57 residues processed: 329 average time/residue: 0.1469 time to fit residues: 78.1420 Evaluate side-chains 322 residues out of total 2649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 257 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 319 ILE Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 386 ARG Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 285 ASP Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 65 PHE Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 199 ARG Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 391 LEU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 418 VAL Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 132 PHE Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 239 LEU Chi-restraints excluded: chain F residue 296 LEU Chi-restraints excluded: chain F residue 298 THR Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 357 GLU Chi-restraints excluded: chain F residue 358 MET Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 202 TYR Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain I residue 9 LEU Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 23 LEU Chi-restraints excluded: chain I residue 122 LEU Chi-restraints excluded: chain I residue 129 LYS Chi-restraints excluded: chain J residue 23 LEU Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 96 GLU Chi-restraints excluded: chain Y residue 5 HIS Chi-restraints excluded: chain X residue 5 HIS Chi-restraints excluded: chain X residue 63 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 109 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 205 optimal weight: 6.9990 chunk 148 optimal weight: 8.9990 chunk 171 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 chunk 223 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 138 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 95 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 HIS A 365 ASN B 194 GLN D 49 HIS E 163 ASN ** G 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 28 HIS J 104 GLN X 5 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.150490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.119219 restraints weight = 46465.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.118240 restraints weight = 34928.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.119011 restraints weight = 31425.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.119691 restraints weight = 22112.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.120117 restraints weight = 19779.832| |-----------------------------------------------------------------------------| r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 22312 Z= 0.157 Angle : 0.680 15.117 30502 Z= 0.340 Chirality : 0.046 0.232 3779 Planarity : 0.004 0.052 3833 Dihedral : 7.892 120.661 3125 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.95 % Favored : 93.02 % Rotamer: Outliers : 3.35 % Allowed : 26.50 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.16), residues: 2849 helix: 0.32 (0.15), residues: 1278 sheet: -0.56 (0.27), residues: 397 loop : -2.08 (0.18), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 203 TYR 0.018 0.001 TYR E 318 PHE 0.073 0.002 PHE F 410 TRP 0.028 0.002 TRP B 171 HIS 0.020 0.001 HIS X 5 Details of bonding type rmsd covalent geometry : bond 0.00370 (22312) covalent geometry : angle 0.67985 (30502) hydrogen bonds : bond 0.03797 ( 997) hydrogen bonds : angle 4.99380 ( 2862) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4494.02 seconds wall clock time: 78 minutes 6.42 seconds (4686.42 seconds total)