Starting phenix.real_space_refine on Sun Sep 13 16:55:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6caj_7442/09_2026/6caj_7442.cif Found real_map, /net/cci-nas-00/data/ceres_data/6caj_7442/09_2026/6caj_7442.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6caj_7442/09_2026/6caj_7442.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6caj_7442/09_2026/6caj_7442.cif" model { file = "/net/cci-nas-00/data/ceres_data/6caj_7442/09_2026/6caj_7442.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6caj_7442/09_2026/6caj_7442.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6caj_7442/09_2026/6caj_7442.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6caj_7442/09_2026/6caj_7442.map" } resolution = 2.8 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= 0.055 sd= 1.469 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 122 5.16 5 Cl 4 4.86 5 C 15461 2.51 5 N 4238 2.21 5 O 4470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24295 Number of models: 1 Model: "" Number of chains: 11 Chain: "B" Number of atoms: 3201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3201 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 402} Chain breaks: 1 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 4, 'ASN:plan1': 3, 'GLN:plan1': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 85 Chain: "J" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1753 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 11, 'TRANS': 232} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 191 Unresolved non-hydrogen angles: 238 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASN:plan1': 3, 'ARG:plan': 3, 'ASP:plan': 10, 'GLU:plan': 3, 'PHE:plan': 1, 'GLN:plan1': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 94 Chain: "H" Number of atoms: 1916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 1916 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 9, 'TRANS': 255} Chain breaks: 3 Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLU:plan': 6, 'PHE:plan': 2, 'ARG:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 70 Chain: "C" Number of atoms: 2472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2472 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "F" Number of atoms: 2776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2776 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 338} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 3201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3201 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 402} Chain breaks: 1 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 4, 'ASN:plan1': 3, 'GLN:plan1': 3, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 85 Chain: "I" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1753 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 11, 'TRANS': 232} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 191 Unresolved non-hydrogen angles: 238 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASN:plan1': 3, 'ARG:plan': 3, 'ASP:plan': 10, 'GLU:plan': 3, 'PHE:plan': 1, 'GLN:plan1': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 94 Chain: "G" Number of atoms: 1916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 1916 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 9, 'TRANS': 255} Chain breaks: 3 Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLU:plan': 6, 'PHE:plan': 2, 'ARG:plan': 5, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 70 Chain: "D" Number of atoms: 2472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2472 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 2775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2775 Classifications: {'peptide': 357} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 338} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 60 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 30 Unusual residues: {'C7B': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 30 Unusual residues: {'C7B': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C09AC7B C 401 " occ=0.50 ... (58 atoms not shown) pdb="CL2 BC7B C 401 " occ=0.50 Time building chain proxies: 5.15, per 1000 atoms: 0.21 Number of scatterers: 24295 At special positions: 0 Unit cell: (134.918, 171.79, 118.996, 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) Cl 4 17.00 S 122 16.00 O 4470 8.00 N 4238 7.00 C 15461 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: 1.92 Conformation dependent library (CDL) restraints added in 1.2 seconds 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6090 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 36 sheets defined 43.4% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'B' and resid 64 through 68 Processing helix chain 'B' and resid 74 through 87 removed outlier: 3.511A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 108 removed outlier: 4.235A pdb=" N LYS B 108 " --> pdb=" O GLU B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 113 removed outlier: 3.838A pdb=" N CYS B 112 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 142 Processing helix chain 'B' and resid 161 through 176 Processing helix chain 'B' and resid 228 through 234 removed outlier: 3.576A pdb=" N GLN B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 263 removed outlier: 3.845A pdb=" N ALA B 257 " --> pdb=" O SER B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 278 Processing helix chain 'B' and resid 302 through 315 Processing helix chain 'B' and resid 339 through 341 No H-bonds generated for 'chain 'B' and resid 339 through 341' Processing helix chain 'J' and resid 36 through 46 removed outlier: 3.831A pdb=" N LEU J 40 " --> pdb=" O ILE J 36 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL J 46 " --> pdb=" O LEU J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 68 Processing helix chain 'J' and resid 85 through 93 Processing helix chain 'J' and resid 94 through 97 Processing helix chain 'J' and resid 114 through 124 removed outlier: 3.691A pdb=" N VAL J 118 " --> pdb=" O LEU J 114 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TYR J 124 " --> pdb=" O LEU J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 190 Processing helix chain 'J' and resid 208 through 218 removed outlier: 3.654A pdb=" N VAL J 212 " --> pdb=" O LYS J 208 " (cutoff:3.500A) Processing helix chain 'J' and resid 223 through 227 Processing helix chain 'J' and resid 283 through 288 removed outlier: 3.673A pdb=" N GLY J 287 " --> pdb=" O ASN J 283 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP J 288 " --> pdb=" O ALA J 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 283 through 288' Processing helix chain 'H' and resid 5 through 16 removed outlier: 3.632A pdb=" N GLU H 16 " --> pdb=" O SER H 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 36 removed outlier: 3.831A pdb=" N ALA H 25 " --> pdb=" O ALA H 21 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG H 36 " --> pdb=" O GLU H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 56 Processing helix chain 'H' and resid 62 through 77 removed outlier: 3.878A pdb=" N SER H 66 " --> pdb=" O SER H 62 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER H 77 " --> pdb=" O LEU H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 106 Processing helix chain 'H' and resid 106 through 116 removed outlier: 3.857A pdb=" N LYS H 110 " --> pdb=" O LEU H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 144 Processing helix chain 'H' and resid 160 through 170 Processing helix chain 'H' and resid 179 through 183 removed outlier: 4.258A pdb=" N VAL H 183 " --> pdb=" O ASP H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 222 removed outlier: 3.790A pdb=" N MET H 215 " --> pdb=" O GLY H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 252 removed outlier: 3.812A pdb=" N TYR H 252 " --> pdb=" O ASP H 248 " (cutoff:3.500A) Processing helix chain 'H' and resid 277 through 281 Processing helix chain 'H' and resid 293 through 304 removed outlier: 4.542A pdb=" N SER H 297 " --> pdb=" O PRO H 293 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP H 298 " --> pdb=" O SER H 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 25 Processing helix chain 'C' and resid 30 through 48 removed outlier: 3.536A pdb=" N ASP C 48 " --> pdb=" O GLN C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 72 removed outlier: 3.620A pdb=" N LEU C 57 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG C 67 " --> pdb=" O ARG C 63 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN C 72 " --> pdb=" O MET C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 96 removed outlier: 4.542A pdb=" N GLY C 79 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 146 removed outlier: 3.624A pdb=" N GLN C 130 " --> pdb=" O TYR C 126 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY C 146 " --> pdb=" O VAL C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 154 Processing helix chain 'C' and resid 155 through 159 removed outlier: 3.587A pdb=" N HIS C 158 " --> pdb=" O ALA C 155 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE C 159 " --> pdb=" O LEU C 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 155 through 159' Processing helix chain 'C' and resid 171 through 182 Processing helix chain 'C' and resid 199 through 209 removed outlier: 3.809A pdb=" N MET C 203 " --> pdb=" O GLN C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 220 No H-bonds generated for 'chain 'C' and resid 218 through 220' Processing helix chain 'C' and resid 221 through 226 Processing helix chain 'C' and resid 227 through 229 No H-bonds generated for 'chain 'C' and resid 227 through 229' Processing helix chain 'C' and resid 250 through 261 Processing helix chain 'C' and resid 296 through 304 removed outlier: 3.621A pdb=" N GLU C 299 " --> pdb=" O PRO C 296 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLY C 300 " --> pdb=" O PHE C 297 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ASP C 301 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ILE C 302 " --> pdb=" O GLU C 299 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 303 " --> pdb=" O GLY C 300 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU C 304 " --> pdb=" O ASP C 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 296 through 304' Processing helix chain 'C' and resid 317 through 321 Processing helix chain 'C' and resid 332 through 334 No H-bonds generated for 'chain 'C' and resid 332 through 334' Processing helix chain 'C' and resid 335 through 344 removed outlier: 3.613A pdb=" N LEU C 339 " --> pdb=" O TYR C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 349 removed outlier: 3.979A pdb=" N HIS C 349 " --> pdb=" O PRO C 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 196 removed outlier: 4.056A pdb=" N GLN F 194 " --> pdb=" O SER F 191 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE F 195 " --> pdb=" O LEU F 192 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N MET F 196 " --> pdb=" O THR F 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 191 through 196' Processing helix chain 'F' and resid 204 through 216 Processing helix chain 'F' and resid 221 through 239 removed outlier: 3.773A pdb=" N CYS F 226 " --> pdb=" O SER F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 267 removed outlier: 4.653A pdb=" N VAL F 253 " --> pdb=" O SER F 249 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS F 257 " --> pdb=" O VAL F 253 " (cutoff:3.500A) Proline residue: F 258 - end of helix Processing helix chain 'F' and resid 270 through 286 Processing helix chain 'F' and resid 292 through 325 removed outlier: 5.619A pdb=" N ALA F 315 " --> pdb=" O LYS F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 352 removed outlier: 3.574A pdb=" N GLU F 352 " --> pdb=" O GLU F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 379 removed outlier: 4.179A pdb=" N THR F 372 " --> pdb=" O GLU F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 395 removed outlier: 4.055A pdb=" N SER F 392 " --> pdb=" O ILE F 388 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N TYR F 393 " --> pdb=" O PRO F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 430 Processing helix chain 'F' and resid 439 through 443 removed outlier: 3.614A pdb=" N PHE F 443 " --> pdb=" O THR F 440 " (cutoff:3.500A) Processing helix chain 'F' and resid 459 through 463 removed outlier: 3.961A pdb=" N LEU F 463 " --> pdb=" O PRO F 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 508 through 510 No H-bonds generated for 'chain 'F' and resid 508 through 510' Processing helix chain 'F' and resid 511 through 520 Processing helix chain 'A' and resid 64 through 68 Processing helix chain 'A' and resid 74 through 87 removed outlier: 3.511A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 108 removed outlier: 4.234A pdb=" N LYS A 108 " --> pdb=" O GLU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 113 removed outlier: 3.845A pdb=" N CYS A 112 " --> pdb=" O SER A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 142 Processing helix chain 'A' and resid 161 through 176 Processing helix chain 'A' and resid 228 through 234 removed outlier: 3.566A pdb=" N GLN A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 263 removed outlier: 3.847A pdb=" N ALA A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 278 Processing helix chain 'A' and resid 302 through 315 Processing helix chain 'A' and resid 339 through 341 No H-bonds generated for 'chain 'A' and resid 339 through 341' Processing helix chain 'I' and resid 36 through 46 removed outlier: 3.830A pdb=" N LEU I 40 " --> pdb=" O ILE I 36 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL I 46 " --> pdb=" O LEU I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 68 Processing helix chain 'I' and resid 85 through 93 Processing helix chain 'I' and resid 94 through 97 Processing helix chain 'I' and resid 114 through 124 removed outlier: 3.691A pdb=" N VAL I 118 " --> pdb=" O LEU I 114 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TYR I 124 " --> pdb=" O LEU I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 190 Processing helix chain 'I' and resid 208 through 218 removed outlier: 3.654A pdb=" N VAL I 212 " --> pdb=" O LYS I 208 " (cutoff:3.500A) Processing helix chain 'I' and resid 223 through 227 Processing helix chain 'I' and resid 283 through 288 removed outlier: 3.674A pdb=" N GLY I 287 " --> pdb=" O ASN I 283 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP I 288 " --> pdb=" O ALA I 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 283 through 288' Processing helix chain 'G' and resid 5 through 16 removed outlier: 3.631A pdb=" N GLU G 16 " --> pdb=" O SER G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 36 removed outlier: 3.831A pdb=" N ALA G 25 " --> pdb=" O ALA G 21 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG G 36 " --> pdb=" O GLU G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 56 Processing helix chain 'G' and resid 62 through 77 removed outlier: 3.878A pdb=" N SER G 66 " --> pdb=" O SER G 62 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER G 77 " --> pdb=" O LEU G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 106 Processing helix chain 'G' and resid 106 through 116 removed outlier: 3.857A pdb=" N LYS G 110 " --> pdb=" O LEU G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 144 Processing helix chain 'G' and resid 160 through 170 Processing helix chain 'G' and resid 179 through 183 removed outlier: 4.258A pdb=" N VAL G 183 " --> pdb=" O ASP G 180 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 222 removed outlier: 3.790A pdb=" N MET G 215 " --> pdb=" O GLY G 211 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 252 removed outlier: 3.813A pdb=" N TYR G 252 " --> pdb=" O ASP G 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 277 through 281 Processing helix chain 'G' and resid 293 through 304 removed outlier: 4.542A pdb=" N SER G 297 " --> pdb=" O PRO G 293 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP G 298 " --> pdb=" O SER G 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 25 Processing helix chain 'D' and resid 30 through 48 removed outlier: 3.537A pdb=" N ASP D 48 " --> pdb=" O GLN D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 72 removed outlier: 3.620A pdb=" N LEU D 57 " --> pdb=" O ASN D 53 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG D 67 " --> pdb=" O ARG D 63 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N MET D 68 " --> pdb=" O GLU D 64 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN D 72 " --> pdb=" O MET D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 96 removed outlier: 4.542A pdb=" N GLY D 79 " --> pdb=" O GLU D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 146 removed outlier: 3.626A pdb=" N GLN D 130 " --> pdb=" O TYR D 126 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY D 146 " --> pdb=" O VAL D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 154 Processing helix chain 'D' and resid 155 through 159 removed outlier: 3.587A pdb=" N HIS D 158 " --> pdb=" O ALA D 155 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE D 159 " --> pdb=" O LEU D 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 155 through 159' Processing helix chain 'D' and resid 171 through 182 Processing helix chain 'D' and resid 199 through 209 removed outlier: 3.808A pdb=" N MET D 203 " --> pdb=" O GLN D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 220 No H-bonds generated for 'chain 'D' and resid 218 through 220' Processing helix chain 'D' and resid 221 through 226 Processing helix chain 'D' and resid 227 through 229 No H-bonds generated for 'chain 'D' and resid 227 through 229' Processing helix chain 'D' and resid 250 through 261 Processing helix chain 'D' and resid 296 through 304 removed outlier: 3.622A pdb=" N GLU D 299 " --> pdb=" O PRO D 296 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLY D 300 " --> pdb=" O PHE D 297 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ASP D 301 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ILE D 302 " --> pdb=" O GLU D 299 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU D 303 " --> pdb=" O GLY D 300 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU D 304 " --> pdb=" O ASP D 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 296 through 304' Processing helix chain 'D' and resid 317 through 321 Processing helix chain 'D' and resid 332 through 334 No H-bonds generated for 'chain 'D' and resid 332 through 334' Processing helix chain 'D' and resid 335 through 344 removed outlier: 3.611A pdb=" N LEU D 339 " --> pdb=" O TYR D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 349 removed outlier: 3.979A pdb=" N HIS D 349 " --> pdb=" O PRO D 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 196 removed outlier: 4.057A pdb=" N GLN E 194 " --> pdb=" O SER E 191 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE E 195 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET E 196 " --> pdb=" O THR E 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 191 through 196' Processing helix chain 'E' and resid 204 through 216 Processing helix chain 'E' and resid 221 through 239 removed outlier: 3.774A pdb=" N CYS E 226 " --> pdb=" O SER E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 267 removed outlier: 4.655A pdb=" N VAL E 253 " --> pdb=" O SER E 249 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS E 257 " --> pdb=" O VAL E 253 " (cutoff:3.500A) Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 270 through 286 Processing helix chain 'E' and resid 292 through 325 removed outlier: 5.620A pdb=" N ALA E 315 " --> pdb=" O LYS E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 352 removed outlier: 3.574A pdb=" N GLU E 352 " --> pdb=" O GLU E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 379 removed outlier: 4.178A pdb=" N THR E 372 " --> pdb=" O GLU E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 395 removed outlier: 4.046A pdb=" N SER E 392 " --> pdb=" O ILE E 388 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N TYR E 393 " --> pdb=" O PRO E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 430 Processing helix chain 'E' and resid 439 through 443 removed outlier: 3.613A pdb=" N PHE E 443 " --> pdb=" O THR E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 459 through 463 removed outlier: 3.962A pdb=" N LEU E 463 " --> pdb=" O PRO E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 510 No H-bonds generated for 'chain 'E' and resid 508 through 510' Processing helix chain 'E' and resid 511 through 520 Processing sheet with id=AA1, first strand: chain 'B' and resid 119 through 123 removed outlier: 6.872A pdb=" N THR B 91 " --> pdb=" O ARG B 121 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ILE B 123 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL B 93 " --> pdb=" O ILE B 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 119 through 123 removed outlier: 6.872A pdb=" N THR B 91 " --> pdb=" O ARG B 121 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ILE B 123 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL B 93 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N SER B 179 " --> pdb=" O GLN B 286 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N HIS B 288 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N MET B 181 " --> pdb=" O HIS B 288 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N HIS B 290 " --> pdb=" O MET B 181 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N MET B 183 " --> pdb=" O HIS B 290 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N THR B 292 " --> pdb=" O MET B 183 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE B 185 " --> pdb=" O THR B 292 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 155 through 157 Processing sheet with id=AA4, first strand: chain 'B' and resid 211 through 212 removed outlier: 3.738A pdb=" N ARG B 211 " --> pdb=" O ASP B 206 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL B 202 " --> pdb=" O GLN B 216 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLN B 216 " --> pdb=" O VAL B 202 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 211 through 212 removed outlier: 3.738A pdb=" N ARG B 211 " --> pdb=" O ASP B 206 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL B 238 " --> pdb=" O PHE J 195 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE J 193 " --> pdb=" O VAL B 240 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N PHE J 157 " --> pdb=" O MET J 170 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N MET J 170 " --> pdb=" O PHE J 157 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLY J 159 " --> pdb=" O LEU J 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 223 through 226 Processing sheet with id=AA7, first strand: chain 'B' and resid 336 through 337 removed outlier: 6.835A pdb=" N TYR B 343 " --> pdb=" O LEU B 362 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N LEU B 361 " --> pdb=" O ILE B 379 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N VAL B 378 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TYR B 395 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU B 412 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL B 430 " --> pdb=" O ILE B 449 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 355 through 356 removed outlier: 6.390A pdb=" N ILE B 355 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N VAL B 390 " --> pdb=" O ILE B 408 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 367 through 368 removed outlier: 6.374A pdb=" N VAL B 367 " --> pdb=" O ILE B 385 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 418 through 419 removed outlier: 7.696A pdb=" N GLU B 418 " --> pdb=" O VAL B 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'J' and resid 76 through 78 removed outlier: 8.824A pdb=" N ILE J 52 " --> pdb=" O PHE J 3 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ALA J 5 " --> pdb=" O ILE J 52 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N VAL J 54 " --> pdb=" O ALA J 5 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL J 7 " --> pdb=" O VAL J 54 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLN J 4 " --> pdb=" O LEU J 102 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU J 104 " --> pdb=" O GLN J 4 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL J 6 " --> pdb=" O LEU J 104 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 200 through 201 removed outlier: 6.312A pdb=" N LEU J 128 " --> pdb=" O TYR J 264 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N PHE J 266 " --> pdb=" O LEU J 128 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N MET J 130 " --> pdb=" O PHE J 266 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N THR J 272 " --> pdb=" O MET J 130 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N MET J 132 " --> pdb=" O THR J 272 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 175 through 178 removed outlier: 6.955A pdb=" N VAL H 150 " --> pdb=" O THR H 176 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N VAL H 178 " --> pdb=" O VAL H 150 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL H 152 " --> pdb=" O VAL H 178 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE H 125 " --> pdb=" O TYR H 151 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N THR H 153 " --> pdb=" O ILE H 125 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N THR H 127 " --> pdb=" O THR H 153 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N THR H 124 " --> pdb=" O LEU H 192 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ILE H 194 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N LEU H 126 " --> pdb=" O ILE H 194 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL H 193 " --> pdb=" O TYR H 227 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU H 283 " --> pdb=" O PHE H 226 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 199 through 200 removed outlier: 4.089A pdb=" N ASN H 208 " --> pdb=" O ASP H 274 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 329 through 331 removed outlier: 3.525A pdb=" N SER C 326 " --> pdb=" O GLY C 329 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU C 265 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ILE C 325 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL C 267 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL C 232 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N CYS C 268 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE C 234 " --> pdb=" O CYS C 268 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL C 164 " --> pdb=" O LYS C 231 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ILE C 233 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N MET C 166 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE C 165 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ALA C 192 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N THR C 167 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N MET C 217 " --> pdb=" O VAL C 191 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 238 through 239 removed outlier: 3.795A pdb=" N ALA C 247 " --> pdb=" O ASP C 314 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP C 314 " --> pdb=" O ALA C 247 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 306 through 307 removed outlier: 6.461A pdb=" N ILE F 333 " --> pdb=" O VAL F 359 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N VAL F 361 " --> pdb=" O ILE F 333 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N VAL F 335 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL F 332 " --> pdb=" O LYS F 400 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N LEU F 402 " --> pdb=" O VAL F 332 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N LEU F 334 " --> pdb=" O LEU F 402 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N GLY F 404 " --> pdb=" O LEU F 334 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N TYR F 336 " --> pdb=" O GLY F 404 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL F 434 " --> pdb=" O LEU F 499 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N ILE F 501 " --> pdb=" O VAL F 434 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N VAL F 436 " --> pdb=" O ILE F 501 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR F 502 " --> pdb=" O GLY F 505 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 407 through 408 removed outlier: 3.657A pdb=" N SER F 416 " --> pdb=" O ASP F 490 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP F 490 " --> pdb=" O SER F 416 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 119 through 123 removed outlier: 6.872A pdb=" N THR A 91 " --> pdb=" O ARG A 121 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE A 123 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL A 93 " --> pdb=" O ILE A 123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 119 through 123 removed outlier: 6.872A pdb=" N THR A 91 " --> pdb=" O ARG A 121 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE A 123 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N VAL A 93 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N SER A 179 " --> pdb=" O GLN A 286 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N HIS A 288 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N MET A 181 " --> pdb=" O HIS A 288 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N HIS A 290 " --> pdb=" O MET A 181 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N MET A 183 " --> pdb=" O HIS A 290 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N THR A 292 " --> pdb=" O MET A 183 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N PHE A 185 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 155 through 157 Processing sheet with id=AC4, first strand: chain 'A' and resid 211 through 212 removed outlier: 3.746A pdb=" N ARG A 211 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL A 202 " --> pdb=" O GLN A 216 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN A 216 " --> pdb=" O VAL A 202 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 211 through 212 removed outlier: 3.746A pdb=" N ARG A 211 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL A 238 " --> pdb=" O PHE I 195 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE I 193 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N PHE I 157 " --> pdb=" O MET I 170 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N MET I 170 " --> pdb=" O PHE I 157 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLY I 159 " --> pdb=" O LEU I 168 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 223 through 226 Processing sheet with id=AC7, first strand: chain 'A' and resid 336 through 337 removed outlier: 6.835A pdb=" N TYR A 343 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N LEU A 361 " --> pdb=" O ILE A 379 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N VAL A 378 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TYR A 395 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU A 412 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL A 430 " --> pdb=" O ILE A 449 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 355 through 356 removed outlier: 6.389A pdb=" N ILE A 355 " --> pdb=" O ILE A 374 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N VAL A 390 " --> pdb=" O ILE A 408 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 367 through 368 removed outlier: 6.375A pdb=" N VAL A 367 " --> pdb=" O ILE A 385 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'A' and resid 418 through 419 removed outlier: 7.695A pdb=" N GLU A 418 " --> pdb=" O VAL A 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'I' and resid 76 through 78 removed outlier: 8.826A pdb=" N ILE I 52 " --> pdb=" O PHE I 3 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA I 5 " --> pdb=" O ILE I 52 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N VAL I 54 " --> pdb=" O ALA I 5 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N VAL I 7 " --> pdb=" O VAL I 54 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLN I 4 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU I 104 " --> pdb=" O GLN I 4 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL I 6 " --> pdb=" O LEU I 104 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 200 through 201 removed outlier: 6.314A pdb=" N LEU I 128 " --> pdb=" O TYR I 264 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N PHE I 266 " --> pdb=" O LEU I 128 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N MET I 130 " --> pdb=" O PHE I 266 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 175 through 178 removed outlier: 6.955A pdb=" N VAL G 150 " --> pdb=" O THR G 176 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N VAL G 178 " --> pdb=" O VAL G 150 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL G 152 " --> pdb=" O VAL G 178 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE G 125 " --> pdb=" O TYR G 151 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N THR G 153 " --> pdb=" O ILE G 125 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N THR G 127 " --> pdb=" O THR G 153 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N THR G 124 " --> pdb=" O LEU G 192 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE G 194 " --> pdb=" O THR G 124 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N LEU G 126 " --> pdb=" O ILE G 194 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL G 193 " --> pdb=" O TYR G 227 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU G 283 " --> pdb=" O PHE G 226 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 199 through 200 removed outlier: 4.088A pdb=" N ASN G 208 " --> pdb=" O ASP G 274 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 329 through 331 removed outlier: 3.527A pdb=" N SER D 326 " --> pdb=" O GLY D 329 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU D 265 " --> pdb=" O LEU D 323 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ILE D 325 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL D 267 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL D 232 " --> pdb=" O ILE D 266 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N CYS D 268 " --> pdb=" O VAL D 232 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE D 234 " --> pdb=" O CYS D 268 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL D 164 " --> pdb=" O LYS D 231 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ILE D 233 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N MET D 166 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE D 165 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ALA D 192 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N THR D 167 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET D 217 " --> pdb=" O VAL D 191 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 238 through 239 removed outlier: 3.792A pdb=" N ALA D 247 " --> pdb=" O ASP D 314 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP D 314 " --> pdb=" O ALA D 247 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 306 through 307 removed outlier: 6.464A pdb=" N ILE E 333 " --> pdb=" O VAL E 359 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL E 361 " --> pdb=" O ILE E 333 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL E 335 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL E 332 " --> pdb=" O LYS E 400 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N LEU E 402 " --> pdb=" O VAL E 332 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N LEU E 334 " --> pdb=" O LEU E 402 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N GLY E 404 " --> pdb=" O LEU E 334 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N TYR E 336 " --> pdb=" O GLY E 404 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N VAL E 434 " --> pdb=" O LEU E 499 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N ILE E 501 " --> pdb=" O VAL E 434 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL E 436 " --> pdb=" O ILE E 501 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR E 502 " --> pdb=" O GLY E 505 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 407 through 408 removed outlier: 3.657A pdb=" N SER E 416 " --> pdb=" O ASP E 490 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP E 490 " --> pdb=" O SER E 416 " (cutoff:3.500A) 972 hydrogen bonds defined for protein. 2742 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.31 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.41: 9872 1.41 - 1.65: 14681 1.65 - 1.88: 190 1.88 - 2.11: 0 2.11 - 2.35: 1 Bond restraints: 24744 Sorted by residual: bond pdb=" C ILE J 267 " pdb=" N THR J 272 " ideal model delta sigma weight residual 1.329 2.346 -1.017 1.44e-02 4.82e+03 4.99e+03 bond pdb=" C16BC7B C 401 " pdb=" N08BC7B C 401 " ideal model delta sigma weight residual 1.341 1.442 -0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" C15AC7B C 401 " pdb=" N07AC7B C 401 " ideal model delta sigma weight residual 1.341 1.441 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" C16AC7B C 401 " pdb=" N08AC7B C 401 " ideal model delta sigma weight residual 1.341 1.441 -0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" C15BC7B C 401 " pdb=" N07BC7B C 401 " ideal model delta sigma weight residual 1.341 1.439 -0.098 2.00e-02 2.50e+03 2.40e+01 ... (remaining 24739 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.28: 33519 5.28 - 10.55: 109 10.55 - 15.83: 2 15.83 - 21.11: 0 21.11 - 26.39: 1 Bond angle restraints: 33631 Sorted by residual: angle pdb=" C ILE J 267 " pdb=" N THR J 272 " pdb=" CA THR J 272 " ideal model delta sigma weight residual 122.64 96.25 26.39 1.70e+00 3.46e-01 2.41e+02 angle pdb=" O ILE J 267 " pdb=" C ILE J 267 " pdb=" N THR J 272 " ideal model delta sigma weight residual 122.76 114.16 8.60 1.47e+00 4.63e-01 3.42e+01 angle pdb=" C LEU E 387 " pdb=" N ILE E 388 " pdb=" CA ILE E 388 " ideal model delta sigma weight residual 120.33 124.77 -4.44 8.00e-01 1.56e+00 3.08e+01 angle pdb=" C LEU F 387 " pdb=" N ILE F 388 " pdb=" CA ILE F 388 " ideal model delta sigma weight residual 120.33 124.73 -4.40 8.00e-01 1.56e+00 3.02e+01 angle pdb=" C THR A 209 " pdb=" N ASN A 210 " pdb=" CA ASN A 210 " ideal model delta sigma weight residual 122.46 129.43 -6.97 1.41e+00 5.03e-01 2.45e+01 ... (remaining 33626 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.00: 14837 34.00 - 68.00: 58 68.00 - 102.00: 14 102.00 - 136.00: 4 136.00 - 170.00: 2 Dihedral angle restraints: 14915 sinusoidal: 5554 harmonic: 9361 Sorted by residual: dihedral pdb=" CA GLN G 156 " pdb=" C GLN G 156 " pdb=" N PRO G 157 " pdb=" CA PRO G 157 " ideal model delta harmonic sigma weight residual 180.00 140.39 39.61 0 5.00e+00 4.00e-02 6.27e+01 dihedral pdb=" CA GLN H 156 " pdb=" C GLN H 156 " pdb=" N PRO H 157 " pdb=" CA PRO H 157 " ideal model delta harmonic sigma weight residual 180.00 140.49 39.51 0 5.00e+00 4.00e-02 6.24e+01 dihedral pdb=" CA ALA C 195 " pdb=" C ALA C 195 " pdb=" N PRO C 196 " pdb=" CA PRO C 196 " ideal model delta harmonic sigma weight residual 180.00 142.84 37.16 0 5.00e+00 4.00e-02 5.52e+01 ... (remaining 14912 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.018: 4003 1.018 - 2.036: 0 2.036 - 3.054: 0 3.054 - 4.072: 0 4.072 - 5.090: 4 Chirality restraints: 4007 Sorted by residual: chirality pdb=" C09AC7B C 401 " pdb=" C13AC7B C 401 " pdb=" C14AC7B C 401 " pdb=" N07AC7B C 401 " both_signs ideal model delta sigma weight residual False 2.47 -2.62 5.09 2.00e-01 2.50e+01 6.48e+02 chirality pdb=" C09BC7B C 401 " pdb=" C13BC7B C 401 " pdb=" C14BC7B C 401 " pdb=" N07BC7B C 401 " both_signs ideal model delta sigma weight residual False 2.47 -2.62 5.09 2.00e-01 2.50e+01 6.48e+02 chirality pdb=" C10BC7B C 401 " pdb=" C11BC7B C 401 " pdb=" C12BC7B C 401 " pdb=" N08BC7B C 401 " both_signs ideal model delta sigma weight residual False 2.47 -2.50 4.97 2.00e-01 2.50e+01 6.18e+02 ... (remaining 4004 not shown) Planarity restraints: 4297 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE J 267 " -0.079 2.00e-02 2.50e+03 1.31e-01 1.72e+02 pdb=" C ILE J 267 " 0.225 2.00e-02 2.50e+03 pdb=" O ILE J 267 " -0.100 2.00e-02 2.50e+03 pdb=" N THR J 272 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN H 156 " 0.042 5.00e-02 4.00e+02 6.43e-02 6.62e+00 pdb=" N PRO H 157 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO H 157 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO H 157 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN G 156 " -0.042 5.00e-02 4.00e+02 6.41e-02 6.58e+00 pdb=" N PRO G 157 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO G 157 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO G 157 " -0.036 5.00e-02 4.00e+02 ... (remaining 4294 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.15: 3 2.15 - 2.84: 7542 2.84 - 3.53: 31921 3.53 - 4.21: 56930 4.21 - 4.90: 97487 Nonbonded interactions: 193883 Sorted by model distance: nonbonded pdb=" CD2 PHE I 266 " pdb=" CG2 THR I 272 " model vdw 1.467 3.760 nonbonded pdb=" CE2 PHE I 266 " pdb=" CG2 THR I 272 " model vdw 1.474 3.760 nonbonded pdb=" O ILE I 267 " pdb=" CB THR I 272 " model vdw 2.063 3.470 nonbonded pdb=" CE2 PHE I 266 " pdb=" OG1 THR I 272 " model vdw 2.273 3.340 nonbonded pdb=" CE2 PHE I 266 " pdb=" CB THR I 272 " model vdw 2.292 3.770 ... (remaining 193878 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' selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 8 through 351) selection = chain 'D' } ncs_group { reference = chain 'E' selection = (chain 'F' and (resid 166 through 521 or (resid 522 and (name N or name CA or na \ me C or name O )))) } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 23.240 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1524 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 1.017 24744 Z= 0.501 Angle : 0.879 26.386 33631 Z= 0.490 Chirality : 0.167 5.090 4007 Planarity : 0.007 0.131 4297 Dihedral : 9.838 170.000 8825 Min Nonbonded Distance : 1.467 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.24 % Allowed : 1.81 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -3.63 (0.12), residues: 3150 helix: -2.59 (0.10), residues: 1204 sheet: -2.05 (0.22), residues: 410 loop : -2.29 (0.14), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 517 TYR 0.018 0.002 TYR A 78 PHE 0.019 0.002 PHE C 272 TRP 0.017 0.001 TRP G 272 HIS 0.006 0.001 HIS F 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00763 / 0.50 (24744) covalent geometry : angle 0.87945 / 0.49 (33631) hydrogen bonds : bond 0.16987 / 11.23 ( 946) hydrogen bonds : angle 6.92517 / 4.88 ( 2742) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6300 Ramachandran restraints generated. 3150 Oldfield, 0 Emsley, 3150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 2800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 828 time to evaluate : 0.922 Fit side-chains revert: symmetry clash REVERT: B 53 ASP cc_start: 0.4412 (t0) cc_final: 0.4161 (p0) REVERT: B 104 GLU cc_start: 0.5600 (tt0) cc_final: 0.5291 (tm-30) REVERT: B 269 ARG cc_start: 0.1374 (ttp80) cc_final: 0.1152 (ttp-170) REVERT: B 339 ARG cc_start: 0.1236 (mtp85) cc_final: 0.1032 (ttm-80) REVERT: B 352 HIS cc_start: 0.5278 (m-70) cc_final: 0.5007 (t70) REVERT: J 99 THR cc_start: 0.0757 (t) cc_final: -0.0026 (t) REVERT: H 270 HIS cc_start: 0.3595 (m-70) cc_final: 0.3321 (m170) REVERT: H 292 THR cc_start: 0.1763 (t) cc_final: 0.1558 (p) REVERT: C 149 GLU cc_start: 0.5583 (mt-10) cc_final: 0.5264 (tm-30) REVERT: C 203 MET cc_start: 0.3078 (ttt) cc_final: 0.2629 (tpp) REVERT: C 206 ASN cc_start: 0.4851 (m-40) cc_final: 0.4529 (m110) REVERT: C 251 THR cc_start: 0.3240 (t) cc_final: 0.2800 (t) REVERT: C 309 HIS cc_start: 0.0332 (m90) cc_final: -0.0504 (m-70) REVERT: C 342 GLU cc_start: 0.5093 (mt-10) cc_final: 0.4836 (mt-10) REVERT: F 248 LEU cc_start: 0.3485 (tt) cc_final: 0.3276 (tp) REVERT: F 277 ILE cc_start: 0.4718 (mt) cc_final: 0.4367 (mt) REVERT: F 362 ASP cc_start: 0.4420 (t0) cc_final: 0.4099 (t0) REVERT: F 461 ASP cc_start: 0.2855 (m-30) cc_final: 0.2646 (m-30) REVERT: A 53 ASP cc_start: 0.4342 (t0) cc_final: 0.4009 (p0) REVERT: A 104 GLU cc_start: 0.5504 (tt0) cc_final: 0.5241 (tm-30) REVERT: A 264 PHE cc_start: 0.3768 (t80) cc_final: 0.3566 (t80) REVERT: A 269 ARG cc_start: 0.1298 (ttp80) cc_final: 0.1071 (ttp-170) REVERT: A 352 HIS cc_start: 0.5286 (m-70) cc_final: 0.5014 (t70) REVERT: I 1 MET cc_start: 0.4147 (mmm) cc_final: 0.3931 (ttp) REVERT: I 99 THR cc_start: 0.0479 (t) cc_final: -0.0843 (t) REVERT: G 270 HIS cc_start: 0.3603 (m-70) cc_final: 0.3339 (m170) REVERT: G 292 THR cc_start: 0.1850 (t) cc_final: 0.1641 (p) REVERT: D 149 GLU cc_start: 0.5607 (mt-10) cc_final: 0.5295 (tm-30) REVERT: D 203 MET cc_start: 0.2943 (ttt) cc_final: 0.2502 (tpp) REVERT: D 206 ASN cc_start: 0.4809 (m-40) cc_final: 0.4467 (m110) REVERT: D 251 THR cc_start: 0.3224 (t) cc_final: 0.2786 (t) REVERT: D 309 HIS cc_start: 0.0388 (m90) cc_final: -0.0487 (m-70) REVERT: D 342 GLU cc_start: 0.5034 (mt-10) cc_final: 0.4816 (mt-10) REVERT: E 273 MET cc_start: 0.3322 (mtp) cc_final: 0.3028 (mtp) REVERT: E 324 TYR cc_start: 0.1569 (t80) cc_final: 0.1358 (t80) REVERT: E 362 ASP cc_start: 0.4382 (t0) cc_final: 0.4085 (t0) outliers start: 6 outliers final: 2 residues processed: 832 average time/residue: 0.6552 time to fit residues: 627.0946 Evaluate side-chains 450 residues out of total 2800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 448 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain A residue 57 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 197 optimal weight: 0.0670 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 2.9990 overall best weight: 0.7922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 63 GLN B 101 GLN B 255 GLN B 258 GLN B 263 ASN B 409 HIS B 410 GLN J 196 HIS J 218 ASN H 213 ASN H 243 GLN H 244 GLN C 160 HIS C 252 HIS C 286 HIS F 275 ASN F 422 GLN F 430 HIS A 63 GLN A 101 GLN A 255 GLN A 258 GLN A 263 ASN ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 HIS A 410 GLN I 203 HIS I 218 ASN G 213 ASN G 243 GLN G 244 GLN D 160 HIS D 252 HIS D 286 HIS E 275 ASN E 422 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.187536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.163721 restraints weight = 32779.337| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 1.58 r_work: 0.3784 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3690 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3682 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3682 r_free = 0.3682 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3682 r_free = 0.3682 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3682 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 24744 Z= 0.181 Angle : 0.684 13.021 33631 Z= 0.344 Chirality : 0.047 0.153 4007 Planarity : 0.006 0.073 4297 Dihedral : 6.703 166.950 3455 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.81 % Allowed : 13.55 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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 (0.14), residues: 3152 helix: -0.49 (0.14), residues: 1244 sheet: -1.71 (0.24), residues: 451 loop : -1.44 (0.15), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 36 TYR 0.016 0.002 TYR J 210 PHE 0.024 0.002 PHE I 266 TRP 0.013 0.002 TRP I 37 HIS 0.011 0.002 HIS A 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (24744) covalent geometry : angle 0.68384 / 0.34 (33631) hydrogen bonds : bond 0.03811 / 2.53 ( 946) hydrogen bonds : angle 4.36126 / 3.06 ( 2742) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 2800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 475 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 303 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8256 (mp) REVERT: B 324 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.6826 (pp20) REVERT: J 88 ASP cc_start: 0.7391 (m-30) cc_final: 0.7060 (m-30) REVERT: J 232 LEU cc_start: 0.6106 (OUTLIER) cc_final: 0.5726 (mp) REVERT: H 220 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.7663 (tppt) REVERT: H 252 TYR cc_start: 0.5783 (m-80) cc_final: 0.5524 (m-80) REVERT: C 32 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7784 (tp30) REVERT: F 386 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8332 (pp) REVERT: F 444 CYS cc_start: 0.8282 (m) cc_final: 0.7859 (m) REVERT: F 506 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.6466 (mpp) REVERT: A 300 VAL cc_start: 0.7836 (m) cc_final: 0.7506 (t) REVERT: A 324 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.6793 (pp20) REVERT: I 38 TYR cc_start: 0.5246 (m-10) cc_final: 0.5036 (m-10) REVERT: I 88 ASP cc_start: 0.7386 (m-30) cc_final: 0.7061 (m-30) REVERT: I 125 ASP cc_start: 0.8075 (t0) cc_final: 0.7794 (t0) REVERT: I 232 LEU cc_start: 0.6094 (OUTLIER) cc_final: 0.5662 (mp) REVERT: G 220 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.7659 (tppt) REVERT: D 32 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7838 (tp30) REVERT: E 386 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8372 (pp) REVERT: E 444 CYS cc_start: 0.8195 (m) cc_final: 0.7749 (m) REVERT: E 506 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.6556 (mpp) outliers start: 122 outliers final: 37 residues processed: 551 average time/residue: 0.6314 time to fit residues: 401.6403 Evaluate side-chains 386 residues out of total 2800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 338 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 232 LEU Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 220 LYS Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 506 MET Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 232 LEU Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 220 LYS Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 506 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 99 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 240 optimal weight: 1.9990 chunk 231 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 chunk 243 optimal weight: 0.9980 chunk 241 optimal weight: 1.9990 chunk 120 optimal weight: 0.4980 chunk 102 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 244 GLN C 44 GLN C 158 HIS C 206 ASN F 254 ASN F 325 GLN F 406 HIS ** F 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 431 ASN A 44 GLN ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN D 158 HIS D 162 ASN D 206 ASN E 254 ASN E 325 GLN E 406 HIS E 430 HIS E 431 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.174490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.148383 restraints weight = 37198.299| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 1.64 r_work: 0.3618 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3523 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3509 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3509 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 24744 Z= 0.192 Angle : 0.681 10.597 33631 Z= 0.341 Chirality : 0.048 0.179 4007 Planarity : 0.005 0.057 4297 Dihedral : 6.859 177.104 3453 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 5.12 % Allowed : 16.43 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -1.01 (0.15), residues: 3152 helix: 0.22 (0.14), residues: 1224 sheet: -1.46 (0.23), residues: 481 loop : -1.08 (0.16), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 136 TYR 0.018 0.002 TYR I 210 PHE 0.021 0.002 PHE D 177 TRP 0.017 0.002 TRP I 37 HIS 0.010 0.002 HIS B 288 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.19 (24744) covalent geometry : angle 0.68065 / 0.34 (33631) hydrogen bonds : bond 0.04032 / 2.67 ( 946) hydrogen bonds : angle 4.31217 / 3.03 ( 2742) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 354 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 303 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8598 (mp) REVERT: B 305 MET cc_start: 0.9000 (mmm) cc_final: 0.8632 (mmm) REVERT: C 32 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7721 (tp30) REVERT: C 143 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7424 (tp30) REVERT: C 186 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8041 (mptt) REVERT: F 368 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.8019 (mt-10) REVERT: F 386 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8367 (pp) REVERT: A 183 MET cc_start: 0.8671 (mtp) cc_final: 0.8380 (mtt) REVERT: I 116 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6768 (tp30) REVERT: D 32 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7751 (tp30) REVERT: D 34 MET cc_start: 0.7291 (OUTLIER) cc_final: 0.6979 (tpp) REVERT: D 143 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7416 (tp30) REVERT: E 368 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8042 (mt-10) REVERT: E 386 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8355 (pp) outliers start: 130 outliers final: 53 residues processed: 434 average time/residue: 0.6538 time to fit residues: 326.8072 Evaluate side-chains 354 residues out of total 2800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 293 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 302 ASN Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 226 SER Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 242 ASN Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 186 LYS Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 368 GLU Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 116 GLU Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 166 LYS Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 242 ASN Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 368 GLU Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 388 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 239 optimal weight: 0.7980 chunk 309 optimal weight: 2.9990 chunk 297 optimal weight: 0.5980 chunk 269 optimal weight: 0.0980 chunk 264 optimal weight: 1.9990 chunk 263 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 chunk 312 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 44 GLN B 255 GLN ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 325 GLN A 101 GLN ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 244 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.174978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.149426 restraints weight = 38596.200| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 1.76 r_work: 0.3615 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3502 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3502 r_free = 0.3502 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3502 r_free = 0.3502 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3502 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.5035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 24744 Z= 0.135 Angle : 0.592 9.325 33631 Z= 0.298 Chirality : 0.045 0.220 4007 Planarity : 0.004 0.056 4297 Dihedral : 6.490 170.610 3453 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 5.28 % Allowed : 17.42 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -0.58 (0.15), residues: 3152 helix: 0.70 (0.15), residues: 1234 sheet: -1.44 (0.23), residues: 481 loop : -0.88 (0.17), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 274 TYR 0.018 0.001 TYR A 128 PHE 0.016 0.002 PHE C 177 TRP 0.007 0.001 TRP E 366 HIS 0.007 0.001 HIS B 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.13 (24744) covalent geometry : angle 0.59242 / 0.30 (33631) hydrogen bonds : bond 0.03285 / 2.18 ( 946) hydrogen bonds : angle 4.07037 / 2.85 ( 2742) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 330 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 98 LYS cc_start: 0.8274 (mttm) cc_final: 0.7723 (mttt) REVERT: B 303 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8573 (mp) REVERT: H 194 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8336 (mt) REVERT: C 32 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7672 (tp30) REVERT: C 33 GLU cc_start: 0.8056 (tt0) cc_final: 0.7487 (mm-30) REVERT: C 34 MET cc_start: 0.7250 (OUTLIER) cc_final: 0.6965 (tpp) REVERT: F 171 LYS cc_start: 0.7750 (pptt) cc_final: 0.7259 (mtmm) REVERT: F 386 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8355 (pp) REVERT: F 445 GLU cc_start: 0.7398 (mp0) cc_final: 0.7110 (mm-30) REVERT: A 98 LYS cc_start: 0.8294 (mttm) cc_final: 0.7740 (mttt) REVERT: A 183 MET cc_start: 0.8741 (mtp) cc_final: 0.8410 (mtt) REVERT: I 116 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6653 (tp30) REVERT: I 232 LEU cc_start: 0.6360 (OUTLIER) cc_final: 0.5915 (mp) REVERT: G 194 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8345 (mt) REVERT: D 32 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7795 (tp30) REVERT: D 33 GLU cc_start: 0.8065 (tt0) cc_final: 0.7486 (mm-30) REVERT: E 171 LYS cc_start: 0.7677 (pptt) cc_final: 0.7210 (mtmm) REVERT: E 368 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7994 (mt-10) REVERT: E 386 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8369 (pp) REVERT: E 445 GLU cc_start: 0.7383 (mp0) cc_final: 0.7105 (mm-30) outliers start: 134 outliers final: 58 residues processed: 421 average time/residue: 0.6722 time to fit residues: 325.3026 Evaluate side-chains 362 residues out of total 2800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 295 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 116 GLU Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 189 LYS Chi-restraints excluded: chain J residue 197 THR Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain J residue 203 HIS Chi-restraints excluded: chain J residue 226 SER Chi-restraints excluded: chain J residue 272 THR Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 166 LYS Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 242 ASN Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 467 ARG Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 116 GLU Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain I residue 232 LEU Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 242 ASN Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 368 GLU Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 388 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 10 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 175 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 165 optimal weight: 0.5980 chunk 240 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 222 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 325 GLN F 422 GLN A 255 GLN ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 HIS ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 HIS E 422 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.169700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.145049 restraints weight = 47422.103| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 2.44 r_work: 0.3526 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3407 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3407 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.5578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 24744 Z= 0.210 Angle : 0.683 13.520 33631 Z= 0.342 Chirality : 0.048 0.266 4007 Planarity : 0.005 0.050 4297 Dihedral : 6.858 174.457 3453 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 6.19 % Allowed : 17.57 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -0.56 (0.15), residues: 3152 helix: 0.69 (0.15), residues: 1232 sheet: -1.41 (0.22), residues: 487 loop : -0.85 (0.17), residues: 1433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 274 TYR 0.025 0.002 TYR B 128 PHE 0.024 0.002 PHE C 177 TRP 0.008 0.001 TRP I 37 HIS 0.007 0.001 HIS B 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.21 (24744) covalent geometry : angle 0.68336 / 0.34 (33631) hydrogen bonds : bond 0.03981 / 2.63 ( 946) hydrogen bonds : angle 4.24418 / 2.98 ( 2742) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 2800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 313 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 89 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7978 (mt0) REVERT: B 324 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7044 (pp20) REVERT: J 44 GLU cc_start: 0.6151 (mm-30) cc_final: 0.5925 (mm-30) REVERT: H 111 ILE cc_start: 0.7671 (mm) cc_final: 0.7404 (mm) REVERT: H 194 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8453 (mt) REVERT: H 220 LYS cc_start: 0.9057 (OUTLIER) cc_final: 0.7844 (tppt) REVERT: C 14 ARG cc_start: 0.6859 (ttt90) cc_final: 0.6412 (ttt-90) REVERT: C 32 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7856 (tp30) REVERT: C 34 MET cc_start: 0.7504 (OUTLIER) cc_final: 0.7290 (tpp) REVERT: F 247 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.5837 (mp0) REVERT: F 368 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8078 (mt-10) REVERT: F 386 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8471 (pp) REVERT: F 506 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8289 (tpp) REVERT: A 89 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7948 (mt0) REVERT: A 324 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7099 (pp20) REVERT: I 44 GLU cc_start: 0.6146 (mm-30) cc_final: 0.5926 (mm-30) REVERT: I 189 LYS cc_start: 0.7647 (OUTLIER) cc_final: 0.7328 (ttmm) REVERT: G 111 ILE cc_start: 0.7648 (mm) cc_final: 0.7401 (mm) REVERT: G 158 ASP cc_start: 0.7567 (p0) cc_final: 0.7332 (p0) REVERT: G 194 ILE cc_start: 0.8908 (OUTLIER) cc_final: 0.8367 (mt) REVERT: G 220 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.7867 (tppt) REVERT: D 14 ARG cc_start: 0.6907 (ttt90) cc_final: 0.6645 (ttt-90) REVERT: D 32 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7877 (tp30) REVERT: D 34 MET cc_start: 0.7755 (tpp) cc_final: 0.7474 (tpp) REVERT: D 43 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7895 (ttp80) REVERT: D 67 ARG cc_start: 0.7221 (OUTLIER) cc_final: 0.5974 (mmm160) REVERT: D 81 MET cc_start: 0.8435 (mmp) cc_final: 0.8227 (mmm) REVERT: E 368 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8112 (mt-10) REVERT: E 386 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8481 (pp) REVERT: E 506 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.8273 (tpp) outliers start: 157 outliers final: 78 residues processed: 418 average time/residue: 0.6589 time to fit residues: 317.8013 Evaluate side-chains 383 residues out of total 2800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 286 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 116 GLU Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 197 THR Chi-restraints excluded: chain J residue 199 LEU Chi-restraints excluded: chain J residue 226 SER Chi-restraints excluded: chain J residue 272 THR Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 166 LYS Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 220 LYS Chi-restraints excluded: chain H residue 242 ASN Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain F residue 247 GLU Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 368 GLU Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 467 ARG Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain F residue 506 MET Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 114 LEU Chi-restraints excluded: chain I residue 116 GLU Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 189 LYS Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 166 LYS Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 220 LYS Chi-restraints excluded: chain G residue 242 ASN Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 285 THR Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 368 GLU Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 502 THR Chi-restraints excluded: chain E residue 506 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 12 optimal weight: 0.8980 chunk 234 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 132 optimal weight: 0.5980 chunk 214 optimal weight: 1.9990 chunk 45 optimal weight: 0.1980 chunk 251 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 135 optimal weight: 0.0980 chunk 37 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 371 HIS F 422 GLN ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.171304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.146836 restraints weight = 52121.167| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.57 r_work: 0.3541 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3416 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3416 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.5596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 24744 Z= 0.146 Angle : 0.621 12.590 33631 Z= 0.309 Chirality : 0.046 0.290 4007 Planarity : 0.005 0.063 4297 Dihedral : 6.581 171.965 3453 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 5.12 % Allowed : 19.07 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -0.29 (0.15), residues: 3152 helix: 1.00 (0.15), residues: 1234 sheet: -1.37 (0.23), residues: 455 loop : -0.77 (0.17), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 274 TYR 0.022 0.002 TYR A 128 PHE 0.019 0.002 PHE C 177 TRP 0.008 0.001 TRP E 366 HIS 0.007 0.001 HIS B 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (24744) covalent geometry : angle 0.62069 / 0.31 (33631) hydrogen bonds : bond 0.03392 / 2.25 ( 946) hydrogen bonds : angle 4.08945 / 2.86 ( 2742) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 301 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 89 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7965 (mt0) REVERT: B 98 LYS cc_start: 0.8395 (mttm) cc_final: 0.7942 (mttp) REVERT: B 104 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7435 (tm-30) REVERT: B 270 ASP cc_start: 0.7249 (p0) cc_final: 0.6929 (t0) REVERT: J 44 GLU cc_start: 0.6163 (mm-30) cc_final: 0.5913 (mm-30) REVERT: J 189 LYS cc_start: 0.7687 (OUTLIER) cc_final: 0.7384 (ttmm) REVERT: J 232 LEU cc_start: 0.6331 (OUTLIER) cc_final: 0.5914 (mp) REVERT: H 111 ILE cc_start: 0.7557 (mm) cc_final: 0.7295 (mm) REVERT: H 194 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8425 (mt) REVERT: H 220 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.7860 (tppt) REVERT: C 14 ARG cc_start: 0.6941 (ttt90) cc_final: 0.6509 (mtp180) REVERT: C 31 SER cc_start: 0.8179 (OUTLIER) cc_final: 0.7820 (m) REVERT: C 32 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7821 (tp30) REVERT: C 34 MET cc_start: 0.7509 (OUTLIER) cc_final: 0.7301 (tpp) REVERT: C 67 ARG cc_start: 0.7275 (OUTLIER) cc_final: 0.6719 (mmm160) REVERT: F 171 LYS cc_start: 0.7883 (pptt) cc_final: 0.7333 (mtmm) REVERT: F 386 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8417 (pp) REVERT: F 415 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8243 (tmm) REVERT: A 98 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.7918 (mttp) REVERT: A 270 ASP cc_start: 0.7173 (p0) cc_final: 0.6930 (t0) REVERT: I 44 GLU cc_start: 0.6156 (mm-30) cc_final: 0.5919 (mm-30) REVERT: I 116 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6685 (tp30) REVERT: I 189 LYS cc_start: 0.7659 (OUTLIER) cc_final: 0.7407 (ttmm) REVERT: G 158 ASP cc_start: 0.7394 (p0) cc_final: 0.7179 (p0) REVERT: G 178 VAL cc_start: 0.8517 (OUTLIER) cc_final: 0.8210 (m) REVERT: G 194 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8426 (mt) REVERT: G 220 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.7862 (tppt) REVERT: D 14 ARG cc_start: 0.6879 (ttt90) cc_final: 0.6669 (ttp-170) REVERT: D 31 SER cc_start: 0.8197 (OUTLIER) cc_final: 0.7855 (m) REVERT: D 32 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7825 (tp30) REVERT: D 34 MET cc_start: 0.7787 (tpp) cc_final: 0.7476 (tpp) REVERT: D 43 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7874 (ttp80) REVERT: D 67 ARG cc_start: 0.7182 (OUTLIER) cc_final: 0.5950 (mmm160) REVERT: D 81 MET cc_start: 0.8431 (mmp) cc_final: 0.8227 (mmm) REVERT: E 368 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8106 (mt-10) REVERT: E 386 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8433 (pp) REVERT: E 415 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8245 (tmm) outliers start: 130 outliers final: 64 residues processed: 395 average time/residue: 0.6432 time to fit residues: 293.0535 Evaluate side-chains 365 residues out of total 2800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 278 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 116 GLU Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 189 LYS Chi-restraints excluded: chain J residue 197 THR Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 232 LEU Chi-restraints excluded: chain J residue 272 THR Chi-restraints excluded: chain H residue 139 GLU Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 166 LYS Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 220 LYS Chi-restraints excluded: chain H residue 242 ASN Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 415 MET Chi-restraints excluded: chain F residue 467 ARG Chi-restraints excluded: chain F residue 499 LEU Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 116 GLU Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 189 LYS Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 220 LYS Chi-restraints excluded: chain G residue 242 ASN Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 43 ARG Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 368 GLU Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 415 MET Chi-restraints excluded: chain E residue 502 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 168 optimal weight: 2.9990 chunk 253 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 96 optimal weight: 0.0470 chunk 277 optimal weight: 0.0030 chunk 10 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 257 optimal weight: 0.9980 chunk 280 optimal weight: 2.9990 chunk 273 optimal weight: 0.7980 chunk 278 optimal weight: 0.5980 overall best weight: 0.4888 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN E 422 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.172534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.148748 restraints weight = 44410.202| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.27 r_work: 0.3572 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3456 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3456 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.5620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 24744 Z= 0.122 Angle : 0.591 11.965 33631 Z= 0.296 Chirality : 0.044 0.263 4007 Planarity : 0.005 0.064 4297 Dihedral : 6.449 170.551 3453 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 4.89 % Allowed : 19.50 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -0.08 (0.15), residues: 3152 helix: 1.17 (0.15), residues: 1236 sheet: -1.27 (0.24), residues: 441 loop : -0.64 (0.17), residues: 1475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 274 TYR 0.022 0.001 TYR I 210 PHE 0.017 0.001 PHE C 177 TRP 0.007 0.001 TRP E 366 HIS 0.007 0.001 HIS B 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (24744) covalent geometry : angle 0.59110 / 0.30 (33631) hydrogen bonds : bond 0.03143 / 2.08 ( 946) hydrogen bonds : angle 3.98354 / 2.79 ( 2742) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 305 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 98 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7881 (mttt) REVERT: B 270 ASP cc_start: 0.7140 (p0) cc_final: 0.6897 (t0) REVERT: B 305 MET cc_start: 0.9094 (mmm) cc_final: 0.8778 (mmm) REVERT: B 324 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7040 (pp20) REVERT: J 44 GLU cc_start: 0.6110 (mm-30) cc_final: 0.5882 (mm-30) REVERT: J 189 LYS cc_start: 0.7600 (OUTLIER) cc_final: 0.7305 (ttmm) REVERT: J 232 LEU cc_start: 0.6177 (OUTLIER) cc_final: 0.5771 (mp) REVERT: H 194 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8382 (mt) REVERT: H 220 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.7799 (tppt) REVERT: C 31 SER cc_start: 0.8171 (OUTLIER) cc_final: 0.7873 (m) REVERT: C 32 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7769 (tp30) REVERT: C 34 MET cc_start: 0.7402 (OUTLIER) cc_final: 0.7158 (tpp) REVERT: C 157 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8354 (pm20) REVERT: F 171 LYS cc_start: 0.7847 (pptt) cc_final: 0.7281 (mtmm) REVERT: F 386 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8384 (pp) REVERT: F 415 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.8177 (tmm) REVERT: F 428 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.7941 (ttm-80) REVERT: F 445 GLU cc_start: 0.7678 (mp0) cc_final: 0.7277 (mm-30) REVERT: A 89 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7969 (mt0) REVERT: A 98 LYS cc_start: 0.8397 (mttm) cc_final: 0.7932 (mttt) REVERT: A 238 VAL cc_start: 0.7726 (p) cc_final: 0.7502 (t) REVERT: A 270 ASP cc_start: 0.7181 (p0) cc_final: 0.6946 (t0) REVERT: I 8 MET cc_start: 0.8130 (mmt) cc_final: 0.7888 (mmt) REVERT: I 44 GLU cc_start: 0.6103 (mm-30) cc_final: 0.5894 (mm-30) REVERT: I 116 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6576 (tp30) REVERT: I 189 LYS cc_start: 0.7573 (OUTLIER) cc_final: 0.7357 (ttmm) REVERT: I 232 LEU cc_start: 0.6159 (OUTLIER) cc_final: 0.5744 (mp) REVERT: G 156 GLN cc_start: 0.6185 (tm130) cc_final: 0.4642 (tp-100) REVERT: G 178 VAL cc_start: 0.8488 (OUTLIER) cc_final: 0.8175 (m) REVERT: G 194 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8454 (mt) REVERT: G 220 LYS cc_start: 0.9000 (OUTLIER) cc_final: 0.7757 (tppt) REVERT: D 31 SER cc_start: 0.8149 (OUTLIER) cc_final: 0.7873 (m) REVERT: D 32 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7787 (tp30) REVERT: D 34 MET cc_start: 0.7703 (tpp) cc_final: 0.7387 (tpp) REVERT: D 41 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7904 (mt) REVERT: D 67 ARG cc_start: 0.7149 (OUTLIER) cc_final: 0.5931 (mmm160) REVERT: D 81 MET cc_start: 0.8380 (mmp) cc_final: 0.8164 (mmm) REVERT: D 157 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8375 (pm20) REVERT: E 171 LYS cc_start: 0.7895 (pptt) cc_final: 0.7274 (mtmm) REVERT: E 368 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8001 (mt-10) REVERT: E 386 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8397 (pp) REVERT: E 415 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8172 (tmm) REVERT: E 428 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.7960 (ttm-80) REVERT: E 445 GLU cc_start: 0.7684 (mp0) cc_final: 0.7240 (mm-30) outliers start: 124 outliers final: 63 residues processed: 393 average time/residue: 0.6115 time to fit residues: 278.3994 Evaluate side-chains 370 residues out of total 2800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 280 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 176 LEU Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 189 LYS Chi-restraints excluded: chain J residue 197 THR Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 226 SER Chi-restraints excluded: chain J residue 232 LEU Chi-restraints excluded: chain J residue 272 THR Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 220 LYS Chi-restraints excluded: chain H residue 242 ASN Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 157 GLU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 415 MET Chi-restraints excluded: chain F residue 428 ARG Chi-restraints excluded: chain F residue 467 ARG Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 116 GLU Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 189 LYS Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain I residue 232 LEU Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 220 LYS Chi-restraints excluded: chain G residue 242 ASN Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 368 GLU Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 415 MET Chi-restraints excluded: chain E residue 428 ARG Chi-restraints excluded: chain E residue 502 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 120 optimal weight: 0.9990 chunk 204 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 284 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 136 optimal weight: 0.8980 chunk 258 optimal weight: 4.9990 chunk 279 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 101 GLN ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.170661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.146163 restraints weight = 50646.304| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.56 r_work: 0.3525 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3395 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3395 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.5739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 24744 Z= 0.158 Angle : 0.625 11.533 33631 Z= 0.314 Chirality : 0.046 0.277 4007 Planarity : 0.005 0.081 4297 Dihedral : 6.573 171.350 3453 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 4.93 % Allowed : 19.78 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -0.06 (0.15), residues: 3152 helix: 1.17 (0.15), residues: 1238 sheet: -1.36 (0.23), residues: 443 loop : -0.59 (0.17), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 274 TYR 0.022 0.002 TYR A 128 PHE 0.021 0.002 PHE C 177 TRP 0.007 0.001 TRP E 366 HIS 0.008 0.001 HIS B 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (24744) covalent geometry : angle 0.62477 / 0.31 (33631) hydrogen bonds : bond 0.03466 / 2.29 ( 946) hydrogen bonds : angle 4.03901 / 2.82 ( 2742) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 305 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 89 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.8022 (mt0) REVERT: B 98 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.7920 (mttt) REVERT: B 270 ASP cc_start: 0.7255 (p0) cc_final: 0.6870 (t0) REVERT: B 324 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7165 (pp20) REVERT: J 44 GLU cc_start: 0.6224 (mm-30) cc_final: 0.5941 (mm-30) REVERT: J 189 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.7380 (ttmm) REVERT: H 103 ARG cc_start: 0.6466 (mmm-85) cc_final: 0.5781 (tpt170) REVERT: H 111 ILE cc_start: 0.7564 (mm) cc_final: 0.7307 (mm) REVERT: H 194 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8522 (mt) REVERT: H 220 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.7863 (tppt) REVERT: C 31 SER cc_start: 0.8178 (OUTLIER) cc_final: 0.7850 (m) REVERT: C 32 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7809 (tp30) REVERT: C 34 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.7384 (tpp) REVERT: C 67 ARG cc_start: 0.7298 (OUTLIER) cc_final: 0.6701 (mmm160) REVERT: F 171 LYS cc_start: 0.7899 (pptt) cc_final: 0.7457 (ptpp) REVERT: F 386 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8430 (pp) REVERT: F 415 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.8315 (tmm) REVERT: F 428 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.7993 (ttm-80) REVERT: F 445 GLU cc_start: 0.7769 (mp0) cc_final: 0.7318 (mm-30) REVERT: A 89 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.8026 (mt0) REVERT: A 98 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.7911 (mttt) REVERT: I 44 GLU cc_start: 0.6183 (mm-30) cc_final: 0.5918 (mm-30) REVERT: G 103 ARG cc_start: 0.6483 (mmm-85) cc_final: 0.5734 (tpt170) REVERT: G 156 GLN cc_start: 0.6257 (tm130) cc_final: 0.4656 (tp-100) REVERT: G 194 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8558 (mt) REVERT: G 220 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.7885 (tppt) REVERT: D 31 SER cc_start: 0.8190 (OUTLIER) cc_final: 0.7888 (m) REVERT: D 32 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7792 (tp30) REVERT: D 34 MET cc_start: 0.7832 (tpp) cc_final: 0.7516 (tpp) REVERT: D 41 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8004 (mt) REVERT: D 67 ARG cc_start: 0.7250 (OUTLIER) cc_final: 0.6060 (mmm160) REVERT: E 171 LYS cc_start: 0.7973 (pptt) cc_final: 0.7338 (mtmm) REVERT: E 368 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8106 (mt-10) REVERT: E 386 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8432 (pp) REVERT: E 415 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8312 (tmm) REVERT: E 428 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8023 (ttm-80) REVERT: E 445 GLU cc_start: 0.7755 (mp0) cc_final: 0.7268 (mm-30) outliers start: 125 outliers final: 70 residues processed: 394 average time/residue: 0.6906 time to fit residues: 312.3115 Evaluate side-chains 388 residues out of total 2800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 295 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 88 ASP Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 189 LYS Chi-restraints excluded: chain J residue 197 THR Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 226 SER Chi-restraints excluded: chain J residue 272 THR Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 166 LYS Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 220 LYS Chi-restraints excluded: chain H residue 242 ASN Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 415 MET Chi-restraints excluded: chain F residue 428 ARG Chi-restraints excluded: chain F residue 467 ARG Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 220 LYS Chi-restraints excluded: chain G residue 242 ASN Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 368 GLU Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 415 MET Chi-restraints excluded: chain E residue 428 ARG Chi-restraints excluded: chain E residue 502 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 168 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 309 optimal weight: 0.9980 chunk 127 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 246 optimal weight: 0.4980 chunk 268 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 187 optimal weight: 1.9990 chunk 226 optimal weight: 0.9980 chunk 154 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.170920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.146624 restraints weight = 59839.050| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 3.27 r_work: 0.3510 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3495 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3495 r_free = 0.3495 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3495 r_free = 0.3495 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3495 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.5825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 24744 Z= 0.149 Angle : 0.620 11.430 33631 Z= 0.310 Chirality : 0.046 0.271 4007 Planarity : 0.005 0.078 4297 Dihedral : 6.546 171.466 3453 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 4.29 % Allowed : 20.72 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: -0.01 (0.15), residues: 3152 helix: 1.21 (0.15), residues: 1238 sheet: -1.38 (0.23), residues: 431 loop : -0.54 (0.17), residues: 1483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 274 TYR 0.023 0.002 TYR J 210 PHE 0.020 0.002 PHE C 177 TRP 0.008 0.001 TRP E 366 HIS 0.008 0.001 HIS B 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (24744) covalent geometry : angle 0.62016 / 0.31 (33631) hydrogen bonds : bond 0.03391 / 2.24 ( 946) hydrogen bonds : angle 4.03591 / 2.82 ( 2742) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 298 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 98 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7884 (mttt) REVERT: B 324 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7033 (pp20) REVERT: J 189 LYS cc_start: 0.7494 (OUTLIER) cc_final: 0.7287 (ttmm) REVERT: H 103 ARG cc_start: 0.6479 (mmm-85) cc_final: 0.5847 (tpt170) REVERT: H 108 ARG cc_start: 0.4218 (OUTLIER) cc_final: 0.3622 (ptm160) REVERT: H 111 ILE cc_start: 0.7608 (mm) cc_final: 0.7327 (mm) REVERT: H 194 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8531 (mt) REVERT: H 220 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.7777 (tppt) REVERT: C 31 SER cc_start: 0.8077 (OUTLIER) cc_final: 0.7767 (m) REVERT: C 67 ARG cc_start: 0.7219 (OUTLIER) cc_final: 0.6036 (mmm160) REVERT: F 171 LYS cc_start: 0.7864 (pptt) cc_final: 0.7465 (ptpp) REVERT: F 386 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8370 (pp) REVERT: F 415 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.8126 (tmm) REVERT: F 428 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.7792 (ttm-80) REVERT: F 445 GLU cc_start: 0.7551 (mp0) cc_final: 0.7170 (mm-30) REVERT: A 89 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7931 (mt0) REVERT: A 98 LYS cc_start: 0.8354 (mttm) cc_final: 0.7897 (mttt) REVERT: G 103 ARG cc_start: 0.6511 (mmm-85) cc_final: 0.5814 (tpt170) REVERT: G 156 GLN cc_start: 0.6153 (tm130) cc_final: 0.4629 (tp-100) REVERT: G 178 VAL cc_start: 0.8443 (OUTLIER) cc_final: 0.8194 (m) REVERT: G 194 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8585 (mt) REVERT: G 220 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.7780 (tppt) REVERT: D 31 SER cc_start: 0.8100 (OUTLIER) cc_final: 0.7814 (m) REVERT: D 32 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7674 (tp30) REVERT: D 34 MET cc_start: 0.7612 (tpp) cc_final: 0.7352 (tpp) REVERT: D 67 ARG cc_start: 0.7130 (OUTLIER) cc_final: 0.5971 (mmm160) REVERT: E 171 LYS cc_start: 0.7916 (pptt) cc_final: 0.7343 (mtmm) REVERT: E 368 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7966 (mt-10) REVERT: E 386 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8370 (pp) REVERT: E 415 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.8126 (tmm) REVERT: E 428 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.7826 (ttm-80) REVERT: E 445 GLU cc_start: 0.7553 (mp0) cc_final: 0.7168 (mm-30) outliers start: 109 outliers final: 68 residues processed: 377 average time/residue: 0.6752 time to fit residues: 292.2976 Evaluate side-chains 382 residues out of total 2800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 293 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 189 LYS Chi-restraints excluded: chain J residue 197 THR Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 226 SER Chi-restraints excluded: chain J residue 272 THR Chi-restraints excluded: chain H residue 108 ARG Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 220 LYS Chi-restraints excluded: chain H residue 242 ASN Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 415 MET Chi-restraints excluded: chain F residue 428 ARG Chi-restraints excluded: chain F residue 467 ARG Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 220 LYS Chi-restraints excluded: chain G residue 242 ASN Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 238 GLN Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 368 GLU Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 415 MET Chi-restraints excluded: chain E residue 428 ARG Chi-restraints excluded: chain E residue 502 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 12 optimal weight: 0.8980 chunk 41 optimal weight: 9.9990 chunk 201 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 44 optimal weight: 0.0040 chunk 255 optimal weight: 0.9990 chunk 264 optimal weight: 2.9990 chunk 151 optimal weight: 0.6980 chunk 289 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.171843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.147631 restraints weight = 47501.405| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.33 r_work: 0.3550 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3431 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3431 r_free = 0.3431 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3431 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.5811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24744 Z= 0.132 Angle : 0.609 11.175 33631 Z= 0.305 Chirality : 0.045 0.254 4007 Planarity : 0.005 0.081 4297 Dihedral : 6.447 170.628 3453 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 4.14 % Allowed : 20.96 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: 0.05 (0.15), residues: 3152 helix: 1.26 (0.15), residues: 1242 sheet: -1.33 (0.24), residues: 427 loop : -0.52 (0.17), residues: 1483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 274 TYR 0.020 0.001 TYR B 128 PHE 0.018 0.001 PHE C 177 TRP 0.008 0.001 TRP E 366 HIS 0.008 0.001 HIS A 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 (24744) covalent geometry : angle 0.60909 / 0.30 (33631) hydrogen bonds : bond 0.03232 / 2.14 ( 946) hydrogen bonds : angle 4.00472 / 2.80 ( 2742) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6304 Ramachandran restraints generated. 3152 Oldfield, 0 Emsley, 3152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 299 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 89 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.8047 (mt0) REVERT: B 98 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7889 (mttt) REVERT: J 44 GLU cc_start: 0.6284 (mm-30) cc_final: 0.6048 (mm-30) REVERT: J 189 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.7330 (ttmm) REVERT: J 217 GLU cc_start: 0.5982 (mm-30) cc_final: 0.5446 (mt-10) REVERT: H 103 ARG cc_start: 0.6478 (mmm-85) cc_final: 0.5791 (tpt170) REVERT: H 108 ARG cc_start: 0.3991 (OUTLIER) cc_final: 0.3387 (ptm160) REVERT: H 111 ILE cc_start: 0.7460 (mm) cc_final: 0.7213 (mm) REVERT: H 220 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.7832 (tppt) REVERT: C 67 ARG cc_start: 0.7262 (OUTLIER) cc_final: 0.6106 (mmm160) REVERT: C 246 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.8274 (ptp90) REVERT: F 171 LYS cc_start: 0.7851 (pptt) cc_final: 0.7304 (mtmm) REVERT: F 386 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8375 (pp) REVERT: F 415 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8256 (tmm) REVERT: F 428 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.7927 (ttm-80) REVERT: F 445 GLU cc_start: 0.7713 (mp0) cc_final: 0.7240 (mm-30) REVERT: A 89 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.8029 (mt0) REVERT: A 98 LYS cc_start: 0.8416 (mttm) cc_final: 0.7953 (mttt) REVERT: I 8 MET cc_start: 0.8073 (mmt) cc_final: 0.7845 (mmt) REVERT: I 217 GLU cc_start: 0.5938 (mm-30) cc_final: 0.5400 (mt-10) REVERT: G 103 ARG cc_start: 0.6497 (mmm-85) cc_final: 0.5750 (tpt170) REVERT: G 156 GLN cc_start: 0.6234 (tm130) cc_final: 0.4530 (tp-100) REVERT: G 178 VAL cc_start: 0.8442 (OUTLIER) cc_final: 0.8148 (m) REVERT: G 194 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8471 (mt) REVERT: G 220 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.7849 (tppt) REVERT: D 31 SER cc_start: 0.8163 (OUTLIER) cc_final: 0.7886 (m) REVERT: D 32 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7768 (tp30) REVERT: D 34 MET cc_start: 0.7829 (tpp) cc_final: 0.7531 (tpp) REVERT: D 67 ARG cc_start: 0.7178 (OUTLIER) cc_final: 0.6006 (mmm160) REVERT: D 246 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.8311 (ptp90) REVERT: E 171 LYS cc_start: 0.7916 (pptt) cc_final: 0.7307 (mtmm) REVERT: E 368 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8066 (mt-10) REVERT: E 386 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8407 (pp) REVERT: E 415 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8247 (tmm) REVERT: E 428 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.7947 (ttm-80) REVERT: E 445 GLU cc_start: 0.7725 (mp0) cc_final: 0.7249 (mm-30) outliers start: 105 outliers final: 66 residues processed: 377 average time/residue: 0.7095 time to fit residues: 305.8765 Evaluate side-chains 386 residues out of total 2800 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 299 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 180 LEU Chi-restraints excluded: chain J residue 186 ILE Chi-restraints excluded: chain J residue 189 LYS Chi-restraints excluded: chain J residue 197 THR Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 226 SER Chi-restraints excluded: chain J residue 272 THR Chi-restraints excluded: chain H residue 108 ARG Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 177 VAL Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 220 LYS Chi-restraints excluded: chain H residue 242 ASN Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 67 ARG Chi-restraints excluded: chain C residue 246 ARG Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 415 MET Chi-restraints excluded: chain F residue 428 ARG Chi-restraints excluded: chain F residue 467 ARG Chi-restraints excluded: chain F residue 502 THR Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 89 GLN Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain I residue 52 ILE Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 212 VAL Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain G residue 120 LYS Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 220 LYS Chi-restraints excluded: chain G residue 242 ASN Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain D residue 16 GLU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain D residue 67 ARG Chi-restraints excluded: chain D residue 246 ARG Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 238 GLN Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 368 GLU Chi-restraints excluded: chain E residue 386 LEU Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 415 MET Chi-restraints excluded: chain E residue 428 ARG Chi-restraints excluded: chain E residue 502 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 29 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 135 optimal weight: 0.8980 chunk 115 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 36 optimal weight: 0.0030 chunk 103 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 ASN ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.171061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.146744 restraints weight = 57345.730| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.94 r_work: 0.3515 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3506 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3506 r_free = 0.3506 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3506 r_free = 0.3506 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3506 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.5881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 24744 Z= 0.146 Angle : 0.621 11.201 33631 Z= 0.311 Chirality : 0.045 0.243 4007 Planarity : 0.005 0.080 4297 Dihedral : 6.496 170.840 3453 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 4.06 % Allowed : 20.88 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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: 0.06 (0.15), residues: 3152 helix: 1.26 (0.15), residues: 1234 sheet: -1.37 (0.24), residues: 431 loop : -0.49 (0.17), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 274 TYR 0.024 0.002 TYR I 210 PHE 0.020 0.002 PHE C 177 TRP 0.007 0.001 TRP E 366 HIS 0.008 0.001 HIS B 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (24744) covalent geometry : angle 0.62107 / 0.31 (33631) hydrogen bonds : bond 0.03380 / 2.23 ( 946) hydrogen bonds : angle 4.05128 / 2.83 ( 2742) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10385.86 seconds wall clock time: 177 minutes 28.66 seconds (10648.66 seconds total)