Starting phenix.real_space_refine on Fri Mar 6 05:22:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f64_31472/03_2026/7f64_31472.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f64_31472/03_2026/7f64_31472.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7f64_31472/03_2026/7f64_31472.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f64_31472/03_2026/7f64_31472.map" model { file = "/net/cci-nas-00/data/ceres_data/7f64_31472/03_2026/7f64_31472.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f64_31472/03_2026/7f64_31472.cif" } resolution = 2.42 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= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 158 5.16 5 C 18274 2.51 5 N 4994 2.21 5 O 5326 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 75 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28752 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2268 Classifications: {'peptide': 292} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 9, 'TRANS': 282} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 2268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2268 Classifications: {'peptide': 292} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 9, 'TRANS': 282} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 2613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2613 Classifications: {'peptide': 333} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain breaks: 2 Chain: "D" Number of atoms: 2613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2613 Classifications: {'peptide': 333} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain breaks: 2 Chain: "E" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1802 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 9, 'TRANS': 232} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 8, 'GLN:plan1': 1, 'GLU:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 2, 'TYR:plan': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 93 Chain: "F" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1802 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 9, 'TRANS': 232} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 183 Unresolved non-hydrogen dihedrals: 130 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 8, 'GLN:plan1': 1, 'GLU:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 2, 'TYR:plan': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 93 Chain: "G" Number of atoms: 2771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2771 Classifications: {'peptide': 356} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 337} Chain: "H" Number of atoms: 2771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2771 Classifications: {'peptide': 356} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 337} Chain: "I" Number of atoms: 3333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3333 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 407} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "J" Number of atoms: 3333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3333 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 407} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "K" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1589 Classifications: {'peptide': 197} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 188} Chain breaks: 1 Chain: "L" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1589 Classifications: {'peptide': 197} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 188} Chain breaks: 1 Time building chain proxies: 6.63, per 1000 atoms: 0.23 Number of scatterers: 28752 At special positions: 0 Unit cell: (152.536, 168.287, 181.551, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 158 16.00 O 5326 8.00 N 4994 7.00 C 18274 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: 2.62 Conformation dependent library (CDL) restraints added in 1.5 seconds 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7012 Finding SS restraints... Secondary structure from input PDB file: 164 helices and 32 sheets defined 47.3% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 2 through 17 removed outlier: 3.571A pdb=" N ASP A 17 " --> pdb=" O GLN A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 36 Processing helix chain 'A' and resid 42 through 60 WARNING: missing atoms! Processing helix chain 'A' and resid 62 through 83 removed outlier: 3.735A pdb=" N SER A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 116 removed outlier: 4.030A pdb=" N LYS A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ARG A 108 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ASN A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 131 through 144 Processing helix chain 'A' and resid 159 through 171 removed outlier: 3.578A pdb=" N LYS A 163 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU A 171 " --> pdb=" O ALA A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 211 through 222 removed outlier: 3.552A pdb=" N MET A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 247 through 252 removed outlier: 3.726A pdb=" N LYS A 251 " --> pdb=" O PRO A 247 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR A 252 " --> pdb=" O ASP A 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 247 through 252' Processing helix chain 'A' and resid 277 through 281 Processing helix chain 'A' and resid 292 through 304 removed outlier: 4.133A pdb=" N VAL A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N SER A 297 " --> pdb=" O PRO A 293 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP A 298 " --> pdb=" O SER A 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 17 removed outlier: 3.785A pdb=" N ASP B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 36 removed outlier: 3.642A pdb=" N ARG B 36 " --> pdb=" O GLU B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 60 WARNING: missing atoms! Processing helix chain 'B' and resid 62 through 83 removed outlier: 3.773A pdb=" N SER B 66 " --> pdb=" O SER B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 106 removed outlier: 3.672A pdb=" N LEU B 106 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 116 removed outlier: 3.547A pdb=" N LYS B 110 " --> pdb=" O LEU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 119 No H-bonds generated for 'chain 'B' and resid 117 through 119' Processing helix chain 'B' and resid 131 through 144 Processing helix chain 'B' and resid 159 through 170 removed outlier: 3.507A pdb=" N LYS B 163 " --> pdb=" O LEU B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 187 Processing helix chain 'B' and resid 211 through 222 removed outlier: 3.640A pdb=" N MET B 215 " --> pdb=" O GLY B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 Processing helix chain 'B' and resid 247 through 252 removed outlier: 3.724A pdb=" N LYS B 251 " --> pdb=" O PRO B 247 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR B 252 " --> pdb=" O ASP B 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 247 through 252' Processing helix chain 'B' and resid 277 through 281 Processing helix chain 'B' and resid 292 through 304 removed outlier: 3.924A pdb=" N VAL B 296 " --> pdb=" O THR B 292 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER B 297 " --> pdb=" O PRO B 293 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP B 298 " --> pdb=" O SER B 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 24 Processing helix chain 'C' and resid 30 through 49 Processing helix chain 'C' and resid 53 through 72 removed outlier: 3.680A pdb=" N GLN C 72 " --> pdb=" O MET C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 98 removed outlier: 4.619A pdb=" N GLY C 79 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 115 Processing helix chain 'C' and resid 128 through 146 removed outlier: 3.955A pdb=" N ASN C 132 " --> pdb=" O GLN C 128 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY C 146 " --> pdb=" O VAL C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 153 Processing helix chain 'C' and resid 171 through 182 Processing helix chain 'C' and resid 199 through 210 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 270 through 274 Processing helix chain 'C' and resid 290 through 294 removed outlier: 3.502A pdb=" N GLU C 293 " --> pdb=" O ALA C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 304 removed outlier: 3.684A pdb=" N GLY C 300 " --> pdb=" O PHE C 297 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASP C 301 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ILE C 302 " --> pdb=" O GLU C 299 " (cutoff:3.500A) 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: 3.532A pdb=" N LEU C 339 " --> pdb=" O TYR C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 349 removed outlier: 3.597A pdb=" N HIS C 349 " --> pdb=" O PRO C 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 25 Processing helix chain 'D' and resid 30 through 49 Processing helix chain 'D' and resid 53 through 72 removed outlier: 3.599A pdb=" N LEU D 57 " --> pdb=" O ASN D 53 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN D 72 " --> pdb=" O MET D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 98 removed outlier: 4.365A pdb=" N GLY D 79 " --> pdb=" O GLU D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 115 Processing helix chain 'D' and resid 128 through 146 removed outlier: 3.625A pdb=" N GLY D 146 " --> pdb=" O VAL D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 153 Processing helix chain 'D' and resid 171 through 182 Processing helix chain 'D' and resid 199 through 210 removed outlier: 3.502A 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 227 removed outlier: 4.175A pdb=" N SER D 227 " --> pdb=" O PHE D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 261 Processing helix chain 'D' and resid 270 through 274 Processing helix chain 'D' and resid 290 through 294 removed outlier: 3.501A pdb=" N GLU D 293 " --> pdb=" O ALA D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 304 removed outlier: 3.913A pdb=" N GLY D 300 " --> pdb=" O PHE D 297 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ASP D 301 " --> pdb=" O THR D 298 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ILE D 302 " --> pdb=" O GLU D 299 " (cutoff:3.500A) 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 Processing helix chain 'D' and resid 345 through 349 removed outlier: 3.848A pdb=" N HIS D 349 " --> pdb=" O PRO D 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 47 Processing helix chain 'E' and resid 62 through 68 Processing helix chain 'E' and resid 85 through 93 Processing helix chain 'E' and resid 94 through 97 Processing helix chain 'E' and resid 114 through 124 removed outlier: 4.584A pdb=" N LEU E 120 " --> pdb=" O GLU E 116 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TYR E 124 " --> pdb=" O LEU E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 190 Processing helix chain 'E' and resid 208 through 218 removed outlier: 3.757A pdb=" N VAL E 212 " --> pdb=" O LYS E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 236 Processing helix chain 'E' and resid 277 through 279 No H-bonds generated for 'chain 'E' and resid 277 through 279' Processing helix chain 'E' and resid 280 through 293 removed outlier: 3.537A pdb=" N ALA E 284 " --> pdb=" O ALA E 280 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N CYS E 285 " --> pdb=" O CYS E 281 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG E 289 " --> pdb=" O CYS E 285 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N TRP E 290 " --> pdb=" O ARG E 286 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU E 293 " --> pdb=" O ARG E 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 47 removed outlier: 3.713A pdb=" N LEU F 40 " --> pdb=" O ILE F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 68 Processing helix chain 'F' and resid 85 through 93 removed outlier: 3.577A pdb=" N ILE F 93 " --> pdb=" O SER F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 97 Processing helix chain 'F' and resid 114 through 124 removed outlier: 4.492A pdb=" N LEU F 120 " --> pdb=" O GLU F 116 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TYR F 124 " --> pdb=" O LEU F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 190 Processing helix chain 'F' and resid 208 through 218 removed outlier: 3.716A pdb=" N VAL F 212 " --> pdb=" O LYS F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 236 Processing helix chain 'F' and resid 277 through 279 No H-bonds generated for 'chain 'F' and resid 277 through 279' Processing helix chain 'F' and resid 280 through 292 removed outlier: 3.613A pdb=" N ARG F 289 " --> pdb=" O CYS F 285 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TRP F 290 " --> pdb=" O ARG F 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 181 Processing helix chain 'G' and resid 191 through 196 removed outlier: 4.012A pdb=" N GLN G 194 " --> pdb=" O SER G 191 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE G 195 " --> pdb=" O LEU G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 216 Processing helix chain 'G' and resid 221 through 240 Processing helix chain 'G' and resid 247 through 267 removed outlier: 4.121A pdb=" N VAL G 253 " --> pdb=" O SER G 249 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS G 257 " --> pdb=" O VAL G 253 " (cutoff:3.500A) Proline residue: G 258 - end of helix Processing helix chain 'G' and resid 270 through 286 Processing helix chain 'G' and resid 292 through 325 removed outlier: 4.101A pdb=" N LEU G 314 " --> pdb=" O GLU G 310 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ALA G 315 " --> pdb=" O LYS G 311 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN G 325 " --> pdb=" O ARG G 321 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 353 removed outlier: 3.575A pdb=" N GLY G 353 " --> pdb=" O ALA G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 379 removed outlier: 3.820A pdb=" N THR G 372 " --> pdb=" O GLU G 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 390 through 395 removed outlier: 3.646A pdb=" N VAL G 394 " --> pdb=" O ALA G 390 " (cutoff:3.500A) Processing helix chain 'G' and resid 396 through 398 No H-bonds generated for 'chain 'G' and resid 396 through 398' Processing helix chain 'G' and resid 419 through 430 Processing helix chain 'G' and resid 439 through 443 Processing helix chain 'G' and resid 459 through 464 Processing helix chain 'G' and resid 475 through 479 Processing helix chain 'G' and resid 493 through 497 Processing helix chain 'G' and resid 508 through 510 No H-bonds generated for 'chain 'G' and resid 508 through 510' Processing helix chain 'G' and resid 511 through 521 Processing helix chain 'H' and resid 177 through 181 Processing helix chain 'H' and resid 191 through 196 removed outlier: 3.693A pdb=" N GLN H 194 " --> pdb=" O SER H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 216 Processing helix chain 'H' and resid 221 through 240 Processing helix chain 'H' and resid 247 through 267 removed outlier: 4.176A pdb=" N VAL H 253 " --> pdb=" O SER H 249 " (cutoff:3.500A) Proline residue: H 258 - end of helix Processing helix chain 'H' and resid 270 through 286 Processing helix chain 'H' and resid 292 through 325 removed outlier: 4.568A pdb=" N LEU H 314 " --> pdb=" O GLU H 310 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ALA H 315 " --> pdb=" O LYS H 311 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN H 325 " --> pdb=" O ARG H 321 " (cutoff:3.500A) Processing helix chain 'H' and resid 339 through 353 removed outlier: 3.517A pdb=" N GLY H 353 " --> pdb=" O ALA H 349 " (cutoff:3.500A) Processing helix chain 'H' and resid 368 through 379 removed outlier: 3.868A pdb=" N THR H 372 " --> pdb=" O GLU H 368 " (cutoff:3.500A) Processing helix chain 'H' and resid 390 through 395 removed outlier: 3.614A pdb=" N VAL H 394 " --> pdb=" O ALA H 390 " (cutoff:3.500A) Processing helix chain 'H' and resid 396 through 398 No H-bonds generated for 'chain 'H' and resid 396 through 398' Processing helix chain 'H' and resid 419 through 430 Processing helix chain 'H' and resid 439 through 443 Processing helix chain 'H' and resid 459 through 464 Processing helix chain 'H' and resid 475 through 479 Processing helix chain 'H' and resid 493 through 497 Processing helix chain 'H' and resid 508 through 510 No H-bonds generated for 'chain 'H' and resid 508 through 510' Processing helix chain 'H' and resid 511 through 521 removed outlier: 3.567A pdb=" N SER H 520 " --> pdb=" O LEU H 516 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER H 521 " --> pdb=" O ARG H 517 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 62 removed outlier: 3.627A pdb=" N ASP I 62 " --> pdb=" O ILE I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 68 Processing helix chain 'I' and resid 74 through 86 Processing helix chain 'I' and resid 98 through 108 removed outlier: 3.640A pdb=" N ILE I 102 " --> pdb=" O LYS I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 142 Processing helix chain 'I' and resid 161 through 175 Processing helix chain 'I' and resid 228 through 234 Processing helix chain 'I' and resid 253 through 263 removed outlier: 3.774A pdb=" N ALA I 257 " --> pdb=" O SER I 253 " (cutoff:3.500A) Processing helix chain 'I' and resid 268 through 279 removed outlier: 3.568A pdb=" N ASN I 279 " --> pdb=" O GLY I 275 " (cutoff:3.500A) Processing helix chain 'I' and resid 302 through 315 Processing helix chain 'I' and resid 330 through 334 removed outlier: 3.560A pdb=" N GLN I 333 " --> pdb=" O SER I 330 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER I 334 " --> pdb=" O THR I 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 330 through 334' Processing helix chain 'J' and resid 58 through 63 removed outlier: 4.258A pdb=" N ASP J 62 " --> pdb=" O PRO J 58 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN J 63 " --> pdb=" O ILE J 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 58 through 63' Processing helix chain 'J' and resid 64 through 68 Processing helix chain 'J' and resid 74 through 87 Processing helix chain 'J' and resid 98 through 109 removed outlier: 3.611A pdb=" N ILE J 102 " --> pdb=" O LYS J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 110 through 113 Processing helix chain 'J' and resid 130 through 142 Processing helix chain 'J' and resid 161 through 175 Processing helix chain 'J' and resid 196 through 199 Processing helix chain 'J' and resid 228 through 234 Processing helix chain 'J' and resid 253 through 263 removed outlier: 3.662A pdb=" N ALA J 257 " --> pdb=" O SER J 253 " (cutoff:3.500A) Processing helix chain 'J' and resid 268 through 279 Processing helix chain 'J' and resid 302 through 315 Processing helix chain 'J' and resid 330 through 334 Processing helix chain 'K' and resid 1 through 3 No H-bonds generated for 'chain 'K' and resid 1 through 3' Processing helix chain 'K' and resid 61 through 66 Processing helix chain 'K' and resid 90 through 99 removed outlier: 4.187A pdb=" N ARG K 99 " --> pdb=" O SER K 95 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 119 removed outlier: 4.223A pdb=" N TRP K 119 " --> pdb=" O LYS K 115 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 133 removed outlier: 3.836A pdb=" N SER K 130 " --> pdb=" O CYS K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 154 Processing helix chain 'K' and resid 158 through 177 Processing helix chain 'K' and resid 188 through 204 Processing helix chain 'L' and resid 1 through 3 No H-bonds generated for 'chain 'L' and resid 1 through 3' Processing helix chain 'L' and resid 61 through 66 Processing helix chain 'L' and resid 90 through 98 Processing helix chain 'L' and resid 112 through 118 Processing helix chain 'L' and resid 126 through 133 removed outlier: 3.860A pdb=" N SER L 130 " --> pdb=" O CYS L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 142 through 154 Processing helix chain 'L' and resid 158 through 178 Processing helix chain 'L' and resid 188 through 204 Processing sheet with id=AA1, first strand: chain 'A' and resid 175 through 178 removed outlier: 6.726A pdb=" N VAL A 150 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N VAL A 178 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL A 152 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE A 125 " --> pdb=" O TYR A 151 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N THR A 153 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N THR A 124 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N ILE A 194 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N LEU A 126 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N GLY A 196 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N VAL A 193 " --> pdb=" O TYR A 227 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N VAL A 229 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL A 195 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N PHE A 226 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N PHE A 285 " --> pdb=" O PHE A 226 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL A 228 " --> pdb=" O PHE A 285 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 199 through 200 Processing sheet with id=AA3, first strand: chain 'B' and resid 175 through 178 removed outlier: 6.795A pdb=" N VAL B 150 " --> pdb=" O THR B 176 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N VAL B 178 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL B 152 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE B 125 " --> pdb=" O TYR B 151 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N THR B 153 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N THR B 127 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N THR B 124 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE B 194 " --> pdb=" O THR B 124 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU B 126 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL B 193 " --> pdb=" O TYR B 227 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL B 229 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL B 195 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE B 226 " --> pdb=" O LEU B 283 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N PHE B 285 " --> pdb=" O PHE B 226 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL B 228 " --> pdb=" O PHE B 285 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 199 through 200 Processing sheet with id=AA5, first strand: chain 'C' and resid 329 through 331 removed outlier: 6.709A pdb=" N LEU C 265 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ILE C 325 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL C 267 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL C 232 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N CYS C 268 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE C 234 " --> pdb=" O CYS C 268 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N VAL C 164 " --> pdb=" O LYS C 231 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ILE C 233 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N MET C 166 " --> pdb=" O ILE C 233 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 238 through 239 Processing sheet with id=AA7, first strand: chain 'C' and resid 306 through 308 removed outlier: 6.430A pdb=" N ILE H 333 " --> pdb=" O VAL H 359 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N VAL H 361 " --> pdb=" O ILE H 333 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL H 335 " --> pdb=" O VAL H 361 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL H 332 " --> pdb=" O LYS H 400 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LEU H 402 " --> pdb=" O VAL H 332 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N LEU H 334 " --> pdb=" O LEU H 402 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N GLY H 404 " --> pdb=" O LEU H 334 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N TYR H 336 " --> pdb=" O GLY H 404 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N VAL H 401 " --> pdb=" O LEU H 435 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N CYS H 437 " --> pdb=" O VAL H 401 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU H 403 " --> pdb=" O CYS H 437 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL H 434 " --> pdb=" O LEU H 499 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ILE H 501 " --> pdb=" O VAL H 434 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL H 436 " --> pdb=" O ILE H 501 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 329 through 331 removed outlier: 6.202A pdb=" N VAL D 232 " --> pdb=" O ILE D 266 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N CYS D 268 " --> pdb=" O VAL D 232 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE D 234 " --> pdb=" O CYS D 268 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL D 164 " --> pdb=" O LYS D 231 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ILE D 233 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N MET D 166 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE D 165 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ALA D 192 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR D 167 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR D 214 " --> pdb=" O ARG G 483 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 238 through 239 Processing sheet with id=AB1, first strand: chain 'D' and resid 306 through 308 removed outlier: 6.409A pdb=" N SER D 307 " --> pdb=" O TYR G 385 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N LEU G 387 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE G 333 " --> pdb=" O VAL G 359 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VAL G 361 " --> pdb=" O ILE G 333 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL G 335 " --> pdb=" O VAL G 361 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL G 332 " --> pdb=" O LYS G 400 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LEU G 402 " --> pdb=" O VAL G 332 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N LEU G 334 " --> pdb=" O LEU G 402 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N GLY G 404 " --> pdb=" O LEU G 334 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N TYR G 336 " --> pdb=" O GLY G 404 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL G 401 " --> pdb=" O LEU G 435 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N CYS G 437 " --> pdb=" O VAL G 401 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU G 403 " --> pdb=" O CYS G 437 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL G 434 " --> pdb=" O LEU G 499 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ILE G 501 " --> pdb=" O VAL G 434 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL G 436 " --> pdb=" O ILE G 501 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 74 through 79 removed outlier: 3.675A pdb=" N VAL E 51 " --> pdb=" O ASP E 74 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ALA E 5 " --> pdb=" O GLU E 50 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLN E 4 " --> pdb=" O LEU E 102 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LEU E 104 " --> pdb=" O GLN E 4 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL E 6 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER E 105 " --> pdb=" O HIS E 203 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N HIS E 203 " --> pdb=" O SER E 105 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU E 131 " --> pdb=" O ALA E 202 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU E 204 " --> pdb=" O ALA E 129 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA E 129 " --> pdb=" O LEU E 204 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 167 through 172 removed outlier: 4.172A pdb=" N VAL I 238 " --> pdb=" O PHE E 195 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASP I 206 " --> pdb=" O VAL I 212 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL I 212 " --> pdb=" O ASP I 206 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ILE I 287 " --> pdb=" O VAL I 212 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N MET I 181 " --> pdb=" O HIS I 288 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N HIS I 290 " --> pdb=" O MET I 181 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N MET I 183 " --> pdb=" O HIS I 290 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N THR I 292 " --> pdb=" O MET I 183 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N PHE I 185 " --> pdb=" O THR I 292 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N THR I 182 " --> pdb=" O ILE I 249 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ILE I 249 " --> pdb=" O THR I 182 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ILE I 184 " --> pdb=" O CYS I 247 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N CYS I 247 " --> pdb=" O ILE I 184 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N HIS I 248 " --> pdb=" O TYR I 152 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N TYR I 152 " --> pdb=" O HIS I 248 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 179 through 183 Processing sheet with id=AB5, first strand: chain 'F' and resid 75 through 79 removed outlier: 3.511A pdb=" N THR F 55 " --> pdb=" O ILE F 78 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLN F 4 " --> pdb=" O LEU F 102 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU F 104 " --> pdb=" O GLN F 4 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N VAL F 6 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N SER F 105 " --> pdb=" O HIS F 203 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N HIS F 203 " --> pdb=" O SER F 105 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N LEU F 131 " --> pdb=" O ALA F 202 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU F 204 " --> pdb=" O ALA F 129 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA F 129 " --> pdb=" O LEU F 204 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 167 through 172 removed outlier: 6.348A pdb=" N GLY F 159 " --> pdb=" O LEU F 168 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N MET F 170 " --> pdb=" O PHE F 157 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N PHE F 157 " --> pdb=" O MET F 170 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N VAL J 238 " --> pdb=" O PHE F 195 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASP J 206 " --> pdb=" O VAL J 212 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL J 212 " --> pdb=" O ASP J 206 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ILE J 287 " --> pdb=" O VAL J 212 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N THR J 182 " --> pdb=" O ILE J 249 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ILE J 249 " --> pdb=" O THR J 182 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ILE J 184 " --> pdb=" O CYS J 247 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N CYS J 247 " --> pdb=" O ILE J 184 " (cutoff:3.500A) removed outlier: 9.111A pdb=" N HIS J 248 " --> pdb=" O TYR J 152 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TYR J 152 " --> pdb=" O HIS J 248 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N GLN J 44 " --> pdb=" O LEU J 149 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N VAL J 151 " --> pdb=" O GLN J 44 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N VAL J 46 " --> pdb=" O VAL J 151 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N THR J 91 " --> pdb=" O ARG J 121 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ILE J 123 " --> pdb=" O THR J 91 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N VAL J 93 " --> pdb=" O ILE J 123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 179 through 183 Processing sheet with id=AB8, first strand: chain 'G' and resid 407 through 408 Processing sheet with id=AB9, first strand: chain 'H' and resid 407 through 408 Processing sheet with id=AC1, first strand: chain 'I' and resid 155 through 157 Processing sheet with id=AC2, first strand: chain 'I' and resid 336 through 338 removed outlier: 6.204A pdb=" N LEU I 361 " --> pdb=" O ILE I 379 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL I 378 " --> pdb=" O LEU I 396 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TYR I 395 " --> pdb=" O LEU I 413 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU I 412 " --> pdb=" O LEU I 431 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL I 430 " --> pdb=" O ILE I 449 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 355 through 356 removed outlier: 6.417A pdb=" N ILE I 355 " --> pdb=" O ILE I 374 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N PHE I 373 " --> pdb=" O LEU I 391 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL I 390 " --> pdb=" O ILE I 408 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLN I 407 " --> pdb=" O LEU I 425 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N THR I 424 " --> pdb=" O LEU I 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'I' and resid 367 through 368 removed outlier: 6.525A pdb=" N VAL I 367 " --> pdb=" O ILE I 385 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N HIS I 384 " --> pdb=" O VAL I 402 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ARG I 401 " --> pdb=" O VAL I 419 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N GLU I 418 " --> pdb=" O VAL I 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'J' and resid 155 through 157 Processing sheet with id=AC6, first strand: chain 'J' and resid 336 through 338 removed outlier: 6.231A pdb=" N LEU J 361 " --> pdb=" O ILE J 379 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL J 378 " --> pdb=" O LEU J 396 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N TYR J 395 " --> pdb=" O LEU J 413 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 355 through 356 removed outlier: 6.389A pdb=" N ILE J 355 " --> pdb=" O ILE J 374 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLN J 407 " --> pdb=" O LEU J 425 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N THR J 424 " --> pdb=" O LEU J 443 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 384 through 385 removed outlier: 6.494A pdb=" N HIS J 384 " --> pdb=" O VAL J 402 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ARG J 401 " --> pdb=" O VAL J 419 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N GLU J 418 " --> pdb=" O VAL J 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'K' and resid 5 through 13 removed outlier: 6.693A pdb=" N ASP K 8 " --> pdb=" O TYR K 30 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N TYR K 30 " --> pdb=" O ASP K 8 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL K 28 " --> pdb=" O PRO K 10 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ILE K 12 " --> pdb=" O SER K 26 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N SER K 26 " --> pdb=" O ILE K 12 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 38 through 41 Processing sheet with id=AD2, first strand: chain 'K' and resid 52 through 54 Processing sheet with id=AD3, first strand: chain 'L' and resid 5 through 13 removed outlier: 4.895A pdb=" N TYR L 5 " --> pdb=" O LYS L 32 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LYS L 32 " --> pdb=" O TYR L 5 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N PHE L 7 " --> pdb=" O TYR L 30 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 44 through 47 removed outlier: 9.088A pdb=" N TRP L 74 " --> pdb=" O VAL L 38 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N THR L 40 " --> pdb=" O TRP L 74 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 52 through 54 1284 hydrogen bonds defined for protein. 3582 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: 6.81 Time building geometry restraints manager: 3.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 9522 1.35 - 1.46: 6392 1.46 - 1.58: 13138 1.58 - 1.70: 0 1.70 - 1.82: 240 Bond restraints: 29292 Sorted by residual: bond pdb=" CB PRO H 243 " pdb=" CG PRO H 243 " ideal model delta sigma weight residual 1.492 1.562 -0.070 5.00e-02 4.00e+02 1.95e+00 bond pdb=" CB LYS I 176 " pdb=" CG LYS I 176 " ideal model delta sigma weight residual 1.520 1.560 -0.040 3.00e-02 1.11e+03 1.81e+00 bond pdb=" CG PRO B 157 " pdb=" CD PRO B 157 " ideal model delta sigma weight residual 1.503 1.545 -0.042 3.40e-02 8.65e+02 1.55e+00 bond pdb=" CB GLU C 64 " pdb=" CG GLU C 64 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.50e+00 bond pdb=" C PRO J 453 " pdb=" N PRO J 454 " ideal model delta sigma weight residual 1.334 1.362 -0.028 2.34e-02 1.83e+03 1.44e+00 ... (remaining 29287 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 39294 2.18 - 4.37: 347 4.37 - 6.55: 48 6.55 - 8.74: 6 8.74 - 10.92: 5 Bond angle restraints: 39700 Sorted by residual: angle pdb=" CB LYS I 176 " pdb=" CG LYS I 176 " pdb=" CD LYS I 176 " ideal model delta sigma weight residual 111.30 120.11 -8.81 2.30e+00 1.89e-01 1.47e+01 angle pdb=" CB MET K 87 " pdb=" CG MET K 87 " pdb=" SD MET K 87 " ideal model delta sigma weight residual 112.70 123.62 -10.92 3.00e+00 1.11e-01 1.32e+01 angle pdb=" C GLU D 282 " pdb=" N ASP D 283 " pdb=" CA ASP D 283 " ideal model delta sigma weight residual 121.54 128.16 -6.62 1.91e+00 2.74e-01 1.20e+01 angle pdb=" CA LEU F 27 " pdb=" CB LEU F 27 " pdb=" CG LEU F 27 " ideal model delta sigma weight residual 116.30 127.20 -10.90 3.50e+00 8.16e-02 9.70e+00 angle pdb=" CA LEU B 171 " pdb=" CB LEU B 171 " pdb=" CG LEU B 171 " ideal model delta sigma weight residual 116.30 127.09 -10.79 3.50e+00 8.16e-02 9.50e+00 ... (remaining 39695 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.31: 15505 18.31 - 36.62: 1703 36.62 - 54.94: 471 54.94 - 73.25: 66 73.25 - 91.56: 39 Dihedral angle restraints: 17784 sinusoidal: 6990 harmonic: 10794 Sorted by residual: dihedral pdb=" CA THR J 432 " pdb=" C THR J 432 " pdb=" N SER J 433 " pdb=" CA SER J 433 " ideal model delta harmonic sigma weight residual 180.00 156.52 23.48 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA THR I 432 " pdb=" C THR I 432 " pdb=" N SER I 433 " pdb=" CA SER I 433 " ideal model delta harmonic sigma weight residual 180.00 158.73 21.27 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA LEU J 431 " pdb=" C LEU J 431 " pdb=" N THR J 432 " pdb=" CA THR J 432 " ideal model delta harmonic sigma weight residual 180.00 -159.73 -20.27 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 17781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 3091 0.033 - 0.066: 991 0.066 - 0.098: 319 0.098 - 0.131: 217 0.131 - 0.164: 16 Chirality restraints: 4634 Sorted by residual: chirality pdb=" CA ILE L 123 " pdb=" N ILE L 123 " pdb=" C ILE L 123 " pdb=" CB ILE L 123 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.72e-01 chirality pdb=" CA ILE J 156 " pdb=" N ILE J 156 " pdb=" C ILE J 156 " pdb=" CB ILE J 156 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.44e-01 chirality pdb=" CA GLU C 64 " pdb=" N GLU C 64 " pdb=" C GLU C 64 " pdb=" CB GLU C 64 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.13e-01 ... (remaining 4631 not shown) Planarity restraints: 5072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 156 " 0.055 5.00e-02 4.00e+02 8.21e-02 1.08e+01 pdb=" N PRO B 157 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO B 157 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 157 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU G 395 " -0.041 5.00e-02 4.00e+02 6.15e-02 6.06e+00 pdb=" N PRO G 396 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO G 396 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO G 396 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 395 " 0.040 5.00e-02 4.00e+02 6.09e-02 5.94e+00 pdb=" N PRO H 396 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO H 396 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO H 396 " 0.034 5.00e-02 4.00e+02 ... (remaining 5069 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 681 2.70 - 3.25: 27798 3.25 - 3.80: 46591 3.80 - 4.35: 61892 4.35 - 4.90: 101941 Nonbonded interactions: 238903 Sorted by model distance: nonbonded pdb=" OG SER J 51 " pdb=" OD1 ASP J 53 " model vdw 2.154 3.040 nonbonded pdb=" OG SER B 61 " pdb=" O LYS B 249 " model vdw 2.164 3.040 nonbonded pdb=" OG SER K 39 " pdb=" O PRO K 71 " model vdw 2.197 3.040 nonbonded pdb=" NZ LYS I 61 " pdb=" OD2 ASP I 455 " model vdw 2.221 3.120 nonbonded pdb=" OG SER A 61 " pdb=" O LYS A 249 " model vdw 2.221 3.040 ... (remaining 238898 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.040 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: 0.600 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 29.730 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.090 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:10.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 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 : 0.003 0.070 29292 Z= 0.115 Angle : 0.533 10.920 39700 Z= 0.281 Chirality : 0.042 0.164 4634 Planarity : 0.004 0.082 5072 Dihedral : 16.817 91.561 10772 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.67 % Allowed : 21.82 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.14), residues: 3642 helix: 1.47 (0.14), residues: 1476 sheet: 0.12 (0.24), residues: 462 loop : 0.28 (0.16), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 194 TYR 0.011 0.001 TYR K 65 PHE 0.017 0.001 PHE L 190 TRP 0.016 0.001 TRP L 119 HIS 0.007 0.001 HIS I 304 Details of bonding type rmsd covalent geometry : bond 0.00254 (29292) covalent geometry : angle 0.53349 (39700) hydrogen bonds : bond 0.14216 ( 1284) hydrogen bonds : angle 5.55980 ( 3582) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 327 time to evaluate : 0.971 Fit side-chains REVERT: B 91 LYS cc_start: 0.8367 (pttt) cc_final: 0.8083 (ptpp) REVERT: D 135 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7436 (tt0) REVERT: E 173 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7343 (mp0) REVERT: F 222 THR cc_start: 0.7949 (OUTLIER) cc_final: 0.7684 (m) REVERT: J 433 SER cc_start: 0.7684 (OUTLIER) cc_final: 0.7445 (m) REVERT: K 93 MET cc_start: 0.7315 (ptm) cc_final: 0.4954 (mpt) REVERT: L 42 GLU cc_start: 0.6300 (mm-30) cc_final: 0.6096 (tm-30) REVERT: L 86 MET cc_start: 0.6346 (ptp) cc_final: 0.5496 (ptp) REVERT: L 87 MET cc_start: 0.6292 (ppp) cc_final: 0.5711 (tpt) outliers start: 84 outliers final: 58 residues processed: 405 average time/residue: 0.6850 time to fit residues: 321.0477 Evaluate side-chains 361 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 301 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain F residue 188 GLN Chi-restraints excluded: chain F residue 220 SER Chi-restraints excluded: chain F residue 222 THR Chi-restraints excluded: chain F residue 260 SER Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain H residue 178 SER Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 305 ASP Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain I residue 51 SER Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 174 LEU Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 389 VAL Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 447 SER Chi-restraints excluded: chain J residue 62 ASP Chi-restraints excluded: chain J residue 95 CYS Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 265 ASP Chi-restraints excluded: chain J residue 318 VAL Chi-restraints excluded: chain J residue 324 GLU Chi-restraints excluded: chain J residue 332 THR Chi-restraints excluded: chain J residue 429 SER Chi-restraints excluded: chain J residue 433 SER Chi-restraints excluded: chain K residue 80 PHE Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 95 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.3980 chunk 248 optimal weight: 0.0030 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 3.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 214 GLN A 222 GLN B 13 GLN ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 GLN F 172 ASN G 265 GLN H 317 GLN H 347 GLN ** I 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 145 GLN K 183 HIS L 145 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.149334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.110829 restraints weight = 39729.315| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.19 r_work: 0.3319 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.0750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 29292 Z= 0.110 Angle : 0.512 11.321 39700 Z= 0.265 Chirality : 0.042 0.158 4634 Planarity : 0.004 0.061 5072 Dihedral : 5.690 52.966 4080 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.11 % Allowed : 20.58 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.14), residues: 3642 helix: 1.84 (0.14), residues: 1474 sheet: 0.12 (0.24), residues: 448 loop : 0.41 (0.16), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 223 TYR 0.016 0.001 TYR K 65 PHE 0.016 0.001 PHE L 190 TRP 0.010 0.001 TRP E 37 HIS 0.008 0.001 HIS J 304 Details of bonding type rmsd covalent geometry : bond 0.00247 (29292) covalent geometry : angle 0.51202 (39700) hydrogen bonds : bond 0.03804 ( 1284) hydrogen bonds : angle 4.28483 ( 3582) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 325 time to evaluate : 0.985 Fit side-chains REVERT: B 91 LYS cc_start: 0.8138 (pttt) cc_final: 0.7833 (ptpp) REVERT: B 244 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7784 (tm-30) REVERT: C 16 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6944 (mp0) REVERT: C 124 PHE cc_start: 0.7343 (t80) cc_final: 0.6935 (m-80) REVERT: D 341 SER cc_start: 0.8737 (m) cc_final: 0.8436 (p) REVERT: F 132 MET cc_start: 0.7950 (mtp) cc_final: 0.7545 (mtt) REVERT: H 344 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.7965 (ttt-90) REVERT: H 506 MET cc_start: 0.8980 (OUTLIER) cc_final: 0.8449 (mtp) REVERT: I 156 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.8228 (mm) REVERT: I 176 LYS cc_start: 0.8281 (tppt) cc_final: 0.7654 (mmmt) REVERT: I 222 ARG cc_start: 0.8144 (mpp80) cc_final: 0.7516 (mmm-85) REVERT: I 230 LEU cc_start: 0.6676 (OUTLIER) cc_final: 0.6237 (mt) REVERT: I 357 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7709 (tt0) REVERT: I 418 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7860 (tm-30) REVERT: J 121 ARG cc_start: 0.6577 (OUTLIER) cc_final: 0.6140 (mtt-85) REVERT: J 431 LEU cc_start: 0.7686 (tt) cc_final: 0.7410 (mp) REVERT: K 93 MET cc_start: 0.7442 (ptm) cc_final: 0.5075 (mpt) REVERT: K 175 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.7151 (mpt-90) REVERT: L 42 GLU cc_start: 0.6387 (mm-30) cc_final: 0.6121 (tm-30) REVERT: L 86 MET cc_start: 0.6310 (ptp) cc_final: 0.5634 (ptp) REVERT: L 87 MET cc_start: 0.6574 (ppp) cc_final: 0.5686 (tpt) outliers start: 98 outliers final: 40 residues processed: 390 average time/residue: 0.6954 time to fit residues: 313.4225 Evaluate side-chains 345 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 295 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 188 GLN Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 235 GLN Chi-restraints excluded: chain H residue 344 ARG Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain H residue 453 VAL Chi-restraints excluded: chain H residue 506 MET Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 357 GLU Chi-restraints excluded: chain I residue 389 VAL Chi-restraints excluded: chain I residue 418 GLU Chi-restraints excluded: chain I residue 435 VAL Chi-restraints excluded: chain J residue 62 ASP Chi-restraints excluded: chain J residue 121 ARG Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 318 VAL Chi-restraints excluded: chain J residue 400 VAL Chi-restraints excluded: chain K residue 80 PHE Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 175 ARG Chi-restraints excluded: chain K residue 195 SER Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 142 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 116 optimal weight: 0.9990 chunk 299 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 206 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 226 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 174 optimal weight: 6.9990 chunk 301 optimal weight: 0.1980 chunk 2 optimal weight: 3.9990 chunk 343 optimal weight: 10.0000 overall best weight: 1.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN B 13 GLN ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 GLN F 172 ASN G 265 GLN G 422 GLN H 317 GLN H 347 GLN H 477 GLN I 177 ASN K 183 HIS L 91 GLN L 145 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.147408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.108543 restraints weight = 39618.698| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.18 r_work: 0.3286 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29292 Z= 0.142 Angle : 0.525 12.437 39700 Z= 0.274 Chirality : 0.044 0.159 4634 Planarity : 0.004 0.061 5072 Dihedral : 5.110 56.539 4029 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.03 % Allowed : 19.92 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.14), residues: 3642 helix: 1.79 (0.14), residues: 1488 sheet: -0.01 (0.23), residues: 472 loop : 0.28 (0.16), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 223 TYR 0.014 0.001 TYR B 304 PHE 0.018 0.001 PHE L 190 TRP 0.010 0.001 TRP E 37 HIS 0.008 0.001 HIS J 304 Details of bonding type rmsd covalent geometry : bond 0.00335 (29292) covalent geometry : angle 0.52524 (39700) hydrogen bonds : bond 0.04113 ( 1284) hydrogen bonds : angle 4.16374 ( 3582) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 313 time to evaluate : 1.194 Fit side-chains REVERT: B 1 MET cc_start: 0.5910 (ttt) cc_final: 0.5539 (ttm) REVERT: B 32 GLU cc_start: 0.5896 (OUTLIER) cc_final: 0.4790 (tm-30) REVERT: B 91 LYS cc_start: 0.8205 (pttt) cc_final: 0.7887 (ptpp) REVERT: B 121 ASP cc_start: 0.8411 (OUTLIER) cc_final: 0.8135 (t0) REVERT: B 244 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.7816 (tm-30) REVERT: C 16 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6905 (mp0) REVERT: C 20 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7293 (mp0) REVERT: D 139 GLU cc_start: 0.7690 (tp30) cc_final: 0.7390 (mp0) REVERT: D 180 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8121 (tp30) REVERT: D 202 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7763 (mp0) REVERT: D 240 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8388 (mm) REVERT: D 341 SER cc_start: 0.8714 (m) cc_final: 0.8422 (p) REVERT: E 173 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7069 (mp0) REVERT: E 227 GLU cc_start: 0.7222 (mp0) cc_final: 0.6914 (mp0) REVERT: F 172 ASN cc_start: 0.6529 (t0) cc_final: 0.6315 (t0) REVERT: F 194 ARG cc_start: 0.6968 (tpt90) cc_final: 0.6681 (tpt90) REVERT: F 225 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7508 (ttm170) REVERT: G 261 SER cc_start: 0.7804 (OUTLIER) cc_final: 0.7594 (m) REVERT: H 344 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7975 (ttt-90) REVERT: H 506 MET cc_start: 0.9021 (OUTLIER) cc_final: 0.8441 (mtp) REVERT: I 176 LYS cc_start: 0.8348 (tppt) cc_final: 0.7682 (mmmt) REVERT: I 222 ARG cc_start: 0.8162 (mpp80) cc_final: 0.7579 (mmm-85) REVERT: I 230 LEU cc_start: 0.6807 (OUTLIER) cc_final: 0.6317 (mt) REVERT: I 357 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7698 (tt0) REVERT: I 418 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7891 (tm-30) REVERT: J 121 ARG cc_start: 0.6674 (OUTLIER) cc_final: 0.6223 (mtt-85) REVERT: J 181 MET cc_start: 0.8256 (ttm) cc_final: 0.8025 (ttm) REVERT: J 199 ASP cc_start: 0.7847 (m-30) cc_final: 0.6997 (t0) REVERT: J 282 ILE cc_start: 0.7062 (OUTLIER) cc_final: 0.6735 (pt) REVERT: K 93 MET cc_start: 0.7512 (ptm) cc_final: 0.5087 (mpt) REVERT: L 42 GLU cc_start: 0.6417 (mm-30) cc_final: 0.6139 (tm-30) REVERT: L 86 MET cc_start: 0.6315 (ptp) cc_final: 0.5724 (ptp) outliers start: 127 outliers final: 49 residues processed: 399 average time/residue: 0.6517 time to fit residues: 301.8980 Evaluate side-chains 369 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 303 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 106 CYS Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 188 GLN Chi-restraints excluded: chain F residue 225 ARG Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 261 SER Chi-restraints excluded: chain H residue 305 ASP Chi-restraints excluded: chain H residue 344 ARG Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain H residue 506 MET Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 357 GLU Chi-restraints excluded: chain I residue 389 VAL Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 418 GLU Chi-restraints excluded: chain I residue 435 VAL Chi-restraints excluded: chain J residue 62 ASP Chi-restraints excluded: chain J residue 95 CYS Chi-restraints excluded: chain J residue 121 ARG Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 282 ILE Chi-restraints excluded: chain J residue 318 VAL Chi-restraints excluded: chain J residue 400 VAL Chi-restraints excluded: chain K residue 80 PHE Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 195 SER Chi-restraints excluded: chain L residue 14 ILE Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 142 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 180 optimal weight: 3.9990 chunk 197 optimal weight: 2.9990 chunk 238 optimal weight: 0.8980 chunk 159 optimal weight: 7.9990 chunk 301 optimal weight: 5.9990 chunk 250 optimal weight: 5.9990 chunk 332 optimal weight: 7.9990 chunk 246 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 272 optimal weight: 0.8980 chunk 130 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN B 13 GLN ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 GLN F 188 GLN G 265 GLN H 317 GLN H 347 GLN H 477 GLN ** I 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 183 HIS L 2 ASN L 145 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.147901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.109151 restraints weight = 39402.070| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.17 r_work: 0.3295 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29292 Z= 0.127 Angle : 0.512 11.005 39700 Z= 0.265 Chirality : 0.043 0.157 4634 Planarity : 0.004 0.060 5072 Dihedral : 5.003 56.408 4024 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.19 % Allowed : 19.73 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.14), residues: 3642 helix: 1.90 (0.14), residues: 1476 sheet: -0.01 (0.24), residues: 452 loop : 0.28 (0.16), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 223 TYR 0.014 0.001 TYR K 65 PHE 0.020 0.001 PHE D 272 TRP 0.008 0.001 TRP E 37 HIS 0.007 0.001 HIS J 304 Details of bonding type rmsd covalent geometry : bond 0.00296 (29292) covalent geometry : angle 0.51249 (39700) hydrogen bonds : bond 0.03746 ( 1284) hydrogen bonds : angle 4.05609 ( 3582) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 323 time to evaluate : 1.089 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.6049 (ttt) cc_final: 0.5647 (ttm) REVERT: B 32 GLU cc_start: 0.5897 (OUTLIER) cc_final: 0.4789 (tm-30) REVERT: B 91 LYS cc_start: 0.8175 (pttt) cc_final: 0.7777 (pttm) REVERT: B 244 GLN cc_start: 0.8324 (OUTLIER) cc_final: 0.7812 (tm-30) REVERT: C 16 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6951 (mp0) REVERT: C 20 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7299 (mp0) REVERT: C 64 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7479 (mp0) REVERT: C 124 PHE cc_start: 0.7507 (OUTLIER) cc_final: 0.6696 (t80) REVERT: C 167 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8338 (t) REVERT: D 139 GLU cc_start: 0.7688 (tp30) cc_final: 0.7355 (mp0) REVERT: D 180 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8106 (tp30) REVERT: D 202 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7758 (mp0) REVERT: D 240 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8348 (mm) REVERT: D 341 SER cc_start: 0.8634 (m) cc_final: 0.8338 (p) REVERT: E 173 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7137 (mp0) REVERT: E 227 GLU cc_start: 0.7145 (mp0) cc_final: 0.6770 (mp0) REVERT: F 194 ARG cc_start: 0.6904 (tpt90) cc_final: 0.6562 (tpt90) REVERT: F 225 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7542 (ttm170) REVERT: G 348 GLU cc_start: 0.8327 (mt-10) cc_final: 0.8071 (mt-10) REVERT: G 352 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7956 (mp0) REVERT: H 344 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7970 (ttt-90) REVERT: H 368 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8468 (mt-10) REVERT: H 477 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7828 (mt0) REVERT: H 506 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8448 (mtp) REVERT: I 156 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8221 (mm) REVERT: I 176 LYS cc_start: 0.8453 (tppt) cc_final: 0.7784 (mmmt) REVERT: I 222 ARG cc_start: 0.8185 (mpp80) cc_final: 0.7602 (mmm-85) REVERT: I 230 LEU cc_start: 0.6838 (OUTLIER) cc_final: 0.6354 (mt) REVERT: I 357 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7663 (tt0) REVERT: I 418 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7870 (tm-30) REVERT: I 458 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7587 (mp0) REVERT: J 121 ARG cc_start: 0.6691 (OUTLIER) cc_final: 0.6230 (mtt-85) REVERT: J 177 ASN cc_start: 0.6194 (p0) cc_final: 0.5919 (p0) REVERT: J 181 MET cc_start: 0.8290 (ttm) cc_final: 0.8058 (ttm) REVERT: J 199 ASP cc_start: 0.7909 (m-30) cc_final: 0.7019 (t0) REVERT: J 222 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7516 (mtt-85) REVERT: K 93 MET cc_start: 0.7514 (ptm) cc_final: 0.5115 (mpt) REVERT: K 175 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.7163 (mpt-90) REVERT: L 42 GLU cc_start: 0.6453 (mm-30) cc_final: 0.6180 (tm-30) REVERT: L 87 MET cc_start: 0.6660 (ppp) cc_final: 0.5781 (tpt) outliers start: 132 outliers final: 53 residues processed: 411 average time/residue: 0.6839 time to fit residues: 323.7875 Evaluate side-chains 378 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 303 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 106 CYS Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 188 GLN Chi-restraints excluded: chain F residue 225 ARG Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 511 SER Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 305 ASP Chi-restraints excluded: chain H residue 344 ARG Chi-restraints excluded: chain H residue 368 GLU Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain H residue 453 VAL Chi-restraints excluded: chain H residue 477 GLN Chi-restraints excluded: chain H residue 506 MET Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 357 GLU Chi-restraints excluded: chain I residue 389 VAL Chi-restraints excluded: chain I residue 418 GLU Chi-restraints excluded: chain I residue 435 VAL Chi-restraints excluded: chain I residue 458 GLU Chi-restraints excluded: chain J residue 95 CYS Chi-restraints excluded: chain J residue 121 ARG Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 222 ARG Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 318 VAL Chi-restraints excluded: chain J residue 331 THR Chi-restraints excluded: chain J residue 400 VAL Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 175 ARG Chi-restraints excluded: chain K residue 195 SER Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 142 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 331 optimal weight: 2.9990 chunk 163 optimal weight: 5.9990 chunk 357 optimal weight: 0.8980 chunk 314 optimal weight: 4.9990 chunk 266 optimal weight: 7.9990 chunk 292 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 305 optimal weight: 0.9990 chunk 273 optimal weight: 5.9990 chunk 203 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 GLN D 252 HIS F 172 ASN G 265 GLN H 317 GLN H 347 GLN ** I 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 177 ASN L 145 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.146092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.107136 restraints weight = 39432.106| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.18 r_work: 0.3267 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 29292 Z= 0.175 Angle : 0.554 9.871 39700 Z= 0.288 Chirality : 0.045 0.163 4634 Planarity : 0.004 0.061 5072 Dihedral : 5.108 59.532 4019 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.10 % Allowed : 19.89 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.14), residues: 3642 helix: 1.71 (0.13), residues: 1488 sheet: -0.14 (0.23), residues: 466 loop : 0.17 (0.16), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 223 TYR 0.016 0.001 TYR E 210 PHE 0.020 0.002 PHE F 266 TRP 0.009 0.001 TRP E 37 HIS 0.007 0.001 HIS J 168 Details of bonding type rmsd covalent geometry : bond 0.00420 (29292) covalent geometry : angle 0.55427 (39700) hydrogen bonds : bond 0.04304 ( 1284) hydrogen bonds : angle 4.15831 ( 3582) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 310 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: A 5 GLU cc_start: 0.7561 (pt0) cc_final: 0.7271 (pt0) REVERT: A 91 LYS cc_start: 0.8504 (mmpt) cc_final: 0.8087 (mmmt) REVERT: B 1 MET cc_start: 0.6316 (ttt) cc_final: 0.5892 (ttm) REVERT: B 32 GLU cc_start: 0.5935 (OUTLIER) cc_final: 0.4771 (tm-30) REVERT: B 91 LYS cc_start: 0.8212 (pttt) cc_final: 0.7777 (pttm) REVERT: B 92 ILE cc_start: 0.7846 (OUTLIER) cc_final: 0.7559 (mp) REVERT: B 121 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.8095 (t0) REVERT: B 244 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7826 (tm-30) REVERT: C 16 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6938 (mp0) REVERT: C 20 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7310 (mp0) REVERT: C 49 HIS cc_start: 0.7223 (OUTLIER) cc_final: 0.6564 (m-70) REVERT: C 64 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7506 (mp0) REVERT: C 124 PHE cc_start: 0.7531 (OUTLIER) cc_final: 0.7326 (t80) REVERT: D 139 GLU cc_start: 0.7720 (tp30) cc_final: 0.7419 (mp0) REVERT: D 180 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8127 (tp30) REVERT: D 202 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7802 (mp0) REVERT: D 240 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8472 (mm) REVERT: D 293 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8438 (mm-30) REVERT: D 341 SER cc_start: 0.8616 (m) cc_final: 0.8315 (p) REVERT: E 173 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7132 (mp0) REVERT: E 227 GLU cc_start: 0.7217 (mp0) cc_final: 0.6909 (mp0) REVERT: F 194 ARG cc_start: 0.6929 (tpt90) cc_final: 0.6541 (tpt90) REVERT: F 225 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7567 (ttm170) REVERT: H 344 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8008 (ttt-90) REVERT: H 477 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7944 (mt0) REVERT: H 506 MET cc_start: 0.9034 (OUTLIER) cc_final: 0.8457 (mtp) REVERT: I 63 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7839 (mm-40) REVERT: I 176 LYS cc_start: 0.8452 (tppt) cc_final: 0.7857 (mmmt) REVERT: I 222 ARG cc_start: 0.8191 (mpp80) cc_final: 0.7620 (mmm-85) REVERT: I 230 LEU cc_start: 0.6877 (OUTLIER) cc_final: 0.6354 (mt) REVERT: I 357 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7686 (tt0) REVERT: I 418 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7829 (tm-30) REVERT: J 121 ARG cc_start: 0.6716 (OUTLIER) cc_final: 0.6246 (mtt-85) REVERT: J 177 ASN cc_start: 0.6242 (p0) cc_final: 0.5951 (p0) REVERT: J 181 MET cc_start: 0.8314 (ttm) cc_final: 0.8106 (ttm) REVERT: J 199 ASP cc_start: 0.8013 (m-30) cc_final: 0.7098 (t0) REVERT: J 222 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7546 (mtt-85) REVERT: K 93 MET cc_start: 0.7558 (ptm) cc_final: 0.5150 (mpt) REVERT: L 42 GLU cc_start: 0.6415 (mm-30) cc_final: 0.6145 (tm-30) REVERT: L 86 MET cc_start: 0.6295 (ptp) cc_final: 0.6051 (ptp) outliers start: 129 outliers final: 64 residues processed: 399 average time/residue: 0.6835 time to fit residues: 314.1934 Evaluate side-chains 382 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 296 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 197 PHE Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 106 CYS Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 188 GLN Chi-restraints excluded: chain F residue 225 ARG Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 511 SER Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 305 ASP Chi-restraints excluded: chain H residue 344 ARG Chi-restraints excluded: chain H residue 368 GLU Chi-restraints excluded: chain H residue 394 VAL Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain H residue 477 GLN Chi-restraints excluded: chain H residue 506 MET Chi-restraints excluded: chain I residue 63 GLN Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 331 THR Chi-restraints excluded: chain I residue 357 GLU Chi-restraints excluded: chain I residue 389 VAL Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 418 GLU Chi-restraints excluded: chain J residue 95 CYS Chi-restraints excluded: chain J residue 121 ARG Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 222 ARG Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 318 VAL Chi-restraints excluded: chain J residue 331 THR Chi-restraints excluded: chain J residue 400 VAL Chi-restraints excluded: chain K residue 80 PHE Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 195 SER Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain L residue 150 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 59 optimal weight: 5.9990 chunk 128 optimal weight: 9.9990 chunk 121 optimal weight: 0.6980 chunk 222 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 262 optimal weight: 4.9990 chunk 181 optimal weight: 0.5980 chunk 89 optimal weight: 0.9980 chunk 346 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 GLN G 265 GLN H 317 GLN H 347 GLN H 477 GLN ** I 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 2 ASN ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.146568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.107929 restraints weight = 39468.513| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.10 r_work: 0.3274 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29292 Z= 0.142 Angle : 0.532 11.295 39700 Z= 0.274 Chirality : 0.044 0.158 4634 Planarity : 0.004 0.060 5072 Dihedral : 5.055 57.587 4019 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.72 % Allowed : 20.68 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.14), residues: 3642 helix: 1.82 (0.14), residues: 1476 sheet: -0.07 (0.21), residues: 610 loop : 0.18 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 223 TYR 0.014 0.001 TYR E 210 PHE 0.017 0.001 PHE C 272 TRP 0.008 0.001 TRP J 111 HIS 0.007 0.001 HIS J 304 Details of bonding type rmsd covalent geometry : bond 0.00337 (29292) covalent geometry : angle 0.53227 (39700) hydrogen bonds : bond 0.03912 ( 1284) hydrogen bonds : angle 4.09207 ( 3582) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 304 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.7568 (pt0) cc_final: 0.7348 (pt0) REVERT: A 91 LYS cc_start: 0.8505 (mmpt) cc_final: 0.8095 (mmmt) REVERT: B 1 MET cc_start: 0.6208 (ttt) cc_final: 0.5822 (ttm) REVERT: B 32 GLU cc_start: 0.5820 (OUTLIER) cc_final: 0.4729 (tm-30) REVERT: B 91 LYS cc_start: 0.8203 (pttt) cc_final: 0.7759 (pttm) REVERT: B 92 ILE cc_start: 0.7847 (OUTLIER) cc_final: 0.7559 (mp) REVERT: B 244 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7813 (tm-30) REVERT: C 16 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6929 (mp0) REVERT: C 20 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7279 (mp0) REVERT: C 64 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7579 (mp0) REVERT: C 167 THR cc_start: 0.8613 (OUTLIER) cc_final: 0.8397 (t) REVERT: D 139 GLU cc_start: 0.7686 (tp30) cc_final: 0.7393 (mp0) REVERT: D 180 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8124 (tp30) REVERT: D 202 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7774 (mp0) REVERT: D 240 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8416 (mm) REVERT: D 293 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8446 (mm-30) REVERT: D 341 SER cc_start: 0.8610 (m) cc_final: 0.8316 (p) REVERT: E 173 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7178 (mp0) REVERT: E 227 GLU cc_start: 0.7256 (mp0) cc_final: 0.6934 (mp0) REVERT: F 194 ARG cc_start: 0.6862 (tpt90) cc_final: 0.6439 (tpt90) REVERT: F 225 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7607 (ttm170) REVERT: H 344 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.8007 (ttt-90) REVERT: H 477 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7709 (mt0) REVERT: H 506 MET cc_start: 0.9023 (OUTLIER) cc_final: 0.8463 (mtp) REVERT: I 63 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7881 (mm-40) REVERT: I 176 LYS cc_start: 0.8453 (tppt) cc_final: 0.7854 (mmmt) REVERT: I 222 ARG cc_start: 0.8165 (mpp80) cc_final: 0.7598 (mmm-85) REVERT: I 230 LEU cc_start: 0.6883 (OUTLIER) cc_final: 0.6358 (mt) REVERT: I 357 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7688 (tt0) REVERT: I 418 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7824 (tm-30) REVERT: J 121 ARG cc_start: 0.6712 (OUTLIER) cc_final: 0.6247 (mtt-85) REVERT: J 177 ASN cc_start: 0.6236 (p0) cc_final: 0.6031 (p0) REVERT: J 181 MET cc_start: 0.8326 (ttm) cc_final: 0.8123 (ttm) REVERT: J 199 ASP cc_start: 0.8038 (m-30) cc_final: 0.7784 (m-30) REVERT: J 222 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.7525 (mtt-85) REVERT: K 93 MET cc_start: 0.7550 (ptm) cc_final: 0.5166 (mpt) REVERT: L 42 GLU cc_start: 0.6371 (mm-30) cc_final: 0.6120 (tm-30) outliers start: 117 outliers final: 54 residues processed: 382 average time/residue: 0.7016 time to fit residues: 308.3656 Evaluate side-chains 375 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 301 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 170 HIS Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain E residue 106 CYS Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain F residue 188 GLN Chi-restraints excluded: chain F residue 225 ARG Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 511 SER Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 305 ASP Chi-restraints excluded: chain H residue 344 ARG Chi-restraints excluded: chain H residue 368 GLU Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain H residue 477 GLN Chi-restraints excluded: chain H residue 506 MET Chi-restraints excluded: chain I residue 63 GLN Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 331 THR Chi-restraints excluded: chain I residue 357 GLU Chi-restraints excluded: chain I residue 389 VAL Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 418 GLU Chi-restraints excluded: chain J residue 95 CYS Chi-restraints excluded: chain J residue 121 ARG Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 222 ARG Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 318 VAL Chi-restraints excluded: chain J residue 331 THR Chi-restraints excluded: chain J residue 400 VAL Chi-restraints excluded: chain K residue 80 PHE Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 195 SER Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain L residue 150 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 91 optimal weight: 8.9990 chunk 351 optimal weight: 3.9990 chunk 151 optimal weight: 0.7980 chunk 175 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 195 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 348 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 GLN G 166 GLN G 265 GLN H 317 GLN H 347 GLN H 477 GLN ** I 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.146873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.108196 restraints weight = 39362.785| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.11 r_work: 0.3278 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29292 Z= 0.135 Angle : 0.524 10.039 39700 Z= 0.270 Chirality : 0.043 0.158 4634 Planarity : 0.004 0.061 5072 Dihedral : 4.976 56.886 4017 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.88 % Allowed : 20.74 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.14), residues: 3642 helix: 1.85 (0.14), residues: 1476 sheet: -0.05 (0.24), residues: 442 loop : 0.20 (0.15), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 223 TYR 0.013 0.001 TYR K 65 PHE 0.020 0.001 PHE D 272 TRP 0.008 0.001 TRP J 111 HIS 0.007 0.001 HIS J 304 Details of bonding type rmsd covalent geometry : bond 0.00318 (29292) covalent geometry : angle 0.52350 (39700) hydrogen bonds : bond 0.03819 ( 1284) hydrogen bonds : angle 4.06155 ( 3582) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 314 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.7575 (pt0) cc_final: 0.7277 (pt0) REVERT: A 91 LYS cc_start: 0.8504 (mmpt) cc_final: 0.8079 (mmmt) REVERT: B 1 MET cc_start: 0.6151 (ttt) cc_final: 0.5799 (ttm) REVERT: B 32 GLU cc_start: 0.5826 (OUTLIER) cc_final: 0.4760 (tm-30) REVERT: B 91 LYS cc_start: 0.8201 (pttt) cc_final: 0.7750 (pttm) REVERT: B 92 ILE cc_start: 0.7843 (OUTLIER) cc_final: 0.7524 (mp) REVERT: B 121 ASP cc_start: 0.8375 (OUTLIER) cc_final: 0.8059 (t0) REVERT: B 244 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7805 (tm-30) REVERT: C 16 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6923 (mp0) REVERT: C 20 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7263 (mp0) REVERT: C 64 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7596 (mp0) REVERT: C 167 THR cc_start: 0.8603 (OUTLIER) cc_final: 0.8389 (t) REVERT: D 59 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7767 (mt-10) REVERT: D 139 GLU cc_start: 0.7693 (tp30) cc_final: 0.7396 (mp0) REVERT: D 180 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8119 (tp30) REVERT: D 202 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7793 (mp0) REVERT: D 240 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8401 (mm) REVERT: D 293 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8432 (mm-30) REVERT: D 341 SER cc_start: 0.8601 (m) cc_final: 0.8304 (p) REVERT: E 227 GLU cc_start: 0.7275 (mp0) cc_final: 0.6939 (mp0) REVERT: F 194 ARG cc_start: 0.6855 (tpt90) cc_final: 0.6393 (tpt90) REVERT: F 225 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7603 (ttm170) REVERT: G 348 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8090 (mt-10) REVERT: G 352 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7965 (mp0) REVERT: H 344 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7997 (ttt-90) REVERT: H 477 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7580 (mt0) REVERT: H 506 MET cc_start: 0.9026 (OUTLIER) cc_final: 0.8466 (mtp) REVERT: I 63 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7805 (mm-40) REVERT: I 156 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8249 (mm) REVERT: I 176 LYS cc_start: 0.8423 (tppt) cc_final: 0.7860 (mmmt) REVERT: I 222 ARG cc_start: 0.8173 (mpp80) cc_final: 0.7609 (mmm-85) REVERT: I 230 LEU cc_start: 0.6882 (OUTLIER) cc_final: 0.6356 (mt) REVERT: I 357 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7678 (tt0) REVERT: I 418 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7903 (tm-30) REVERT: J 121 ARG cc_start: 0.6703 (OUTLIER) cc_final: 0.6237 (mtt-85) REVERT: J 177 ASN cc_start: 0.6252 (p0) cc_final: 0.6039 (p0) REVERT: J 181 MET cc_start: 0.8323 (ttm) cc_final: 0.8110 (ttm) REVERT: J 199 ASP cc_start: 0.8039 (m-30) cc_final: 0.7820 (m-30) REVERT: J 222 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7519 (mtt-85) REVERT: K 93 MET cc_start: 0.7551 (ptm) cc_final: 0.5119 (mpt) REVERT: K 141 GLN cc_start: 0.8058 (mm-40) cc_final: 0.7810 (mp10) REVERT: L 42 GLU cc_start: 0.6438 (mm-30) cc_final: 0.6185 (tm-30) outliers start: 122 outliers final: 64 residues processed: 403 average time/residue: 0.6990 time to fit residues: 324.3926 Evaluate side-chains 385 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 299 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 170 HIS Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 293 GLU Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 106 CYS Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain F residue 63 LEU Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain F residue 225 ARG Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 235 GLN Chi-restraints excluded: chain G residue 511 SER Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 305 ASP Chi-restraints excluded: chain H residue 344 ARG Chi-restraints excluded: chain H residue 368 GLU Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain H residue 453 VAL Chi-restraints excluded: chain H residue 477 GLN Chi-restraints excluded: chain H residue 506 MET Chi-restraints excluded: chain I residue 63 GLN Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 331 THR Chi-restraints excluded: chain I residue 357 GLU Chi-restraints excluded: chain I residue 389 VAL Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 418 GLU Chi-restraints excluded: chain J residue 95 CYS Chi-restraints excluded: chain J residue 121 ARG Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 222 ARG Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 318 VAL Chi-restraints excluded: chain J residue 331 THR Chi-restraints excluded: chain J residue 400 VAL Chi-restraints excluded: chain K residue 80 PHE Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 195 SER Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 142 THR Chi-restraints excluded: chain L residue 150 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 336 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 214 optimal weight: 5.9990 chunk 354 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 351 optimal weight: 0.8980 chunk 192 optimal weight: 0.9980 chunk 316 optimal weight: 3.9990 chunk 304 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 252 optimal weight: 5.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 GLN G 265 GLN H 317 GLN H 347 GLN H 477 GLN ** I 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.145340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.106407 restraints weight = 39400.900| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.11 r_work: 0.3252 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 29292 Z= 0.193 Angle : 0.580 11.349 39700 Z= 0.299 Chirality : 0.046 0.184 4634 Planarity : 0.004 0.061 5072 Dihedral : 5.075 55.449 4014 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.68 % Allowed : 20.84 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.14), residues: 3642 helix: 1.64 (0.13), residues: 1488 sheet: -0.15 (0.23), residues: 442 loop : 0.11 (0.15), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 223 TYR 0.016 0.002 TYR E 210 PHE 0.023 0.002 PHE D 272 TRP 0.008 0.001 TRP I 111 HIS 0.007 0.001 HIS J 168 Details of bonding type rmsd covalent geometry : bond 0.00464 (29292) covalent geometry : angle 0.57957 (39700) hydrogen bonds : bond 0.04455 ( 1284) hydrogen bonds : angle 4.18621 ( 3582) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 301 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.7588 (pt0) cc_final: 0.7365 (pt0) REVERT: A 91 LYS cc_start: 0.8515 (mmpt) cc_final: 0.8097 (mmmt) REVERT: B 1 MET cc_start: 0.6327 (ttt) cc_final: 0.5888 (ttm) REVERT: B 32 GLU cc_start: 0.5874 (OUTLIER) cc_final: 0.4736 (tm-30) REVERT: B 91 LYS cc_start: 0.8242 (pttt) cc_final: 0.7913 (ptmm) REVERT: B 92 ILE cc_start: 0.7843 (OUTLIER) cc_final: 0.7546 (mp) REVERT: B 121 ASP cc_start: 0.8392 (OUTLIER) cc_final: 0.8077 (t0) REVERT: B 244 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7821 (tm-30) REVERT: C 16 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6698 (mp0) REVERT: C 20 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7308 (mp0) REVERT: C 49 HIS cc_start: 0.7236 (OUTLIER) cc_final: 0.6598 (m-70) REVERT: C 64 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7597 (mp0) REVERT: D 59 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7747 (mt-10) REVERT: D 139 GLU cc_start: 0.7712 (tp30) cc_final: 0.7408 (mp0) REVERT: D 180 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8140 (tp30) REVERT: D 202 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7802 (mp0) REVERT: D 240 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8495 (mm) REVERT: D 341 SER cc_start: 0.8622 (m) cc_final: 0.8326 (p) REVERT: E 173 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7050 (mp0) REVERT: E 227 GLU cc_start: 0.7342 (mp0) cc_final: 0.6962 (mp0) REVERT: F 194 ARG cc_start: 0.6900 (tpt90) cc_final: 0.6398 (tpt90) REVERT: F 225 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7633 (ttm170) REVERT: H 344 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8046 (ttt-90) REVERT: H 506 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.8480 (mtp) REVERT: I 63 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7872 (mm-40) REVERT: I 176 LYS cc_start: 0.8425 (tppt) cc_final: 0.7856 (mmmt) REVERT: I 222 ARG cc_start: 0.8179 (mpp80) cc_final: 0.7630 (mmm-85) REVERT: I 230 LEU cc_start: 0.6919 (OUTLIER) cc_final: 0.6340 (mt) REVERT: I 276 LEU cc_start: 0.8426 (tp) cc_final: 0.8219 (tp) REVERT: I 357 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7683 (tt0) REVERT: I 418 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7847 (tm-30) REVERT: J 121 ARG cc_start: 0.6706 (OUTLIER) cc_final: 0.6254 (mtt-85) REVERT: J 145 ARG cc_start: 0.7130 (mtp180) cc_final: 0.6904 (mmp80) REVERT: J 177 ASN cc_start: 0.6323 (p0) cc_final: 0.6115 (p0) REVERT: J 181 MET cc_start: 0.8324 (ttm) cc_final: 0.8106 (ttm) REVERT: J 199 ASP cc_start: 0.8085 (m-30) cc_final: 0.7876 (m-30) REVERT: J 222 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7528 (mtt-85) REVERT: K 93 MET cc_start: 0.7428 (ptm) cc_final: 0.5019 (mpt) REVERT: K 141 GLN cc_start: 0.8096 (mm-40) cc_final: 0.7804 (mp10) REVERT: L 42 GLU cc_start: 0.6346 (mm-30) cc_final: 0.6100 (tm-30) outliers start: 116 outliers final: 66 residues processed: 380 average time/residue: 0.7022 time to fit residues: 306.6544 Evaluate side-chains 389 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 304 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 170 HIS Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 135 GLU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 106 CYS Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 188 GLN Chi-restraints excluded: chain F residue 225 ARG Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 511 SER Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 305 ASP Chi-restraints excluded: chain H residue 344 ARG Chi-restraints excluded: chain H residue 368 GLU Chi-restraints excluded: chain H residue 394 VAL Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain H residue 453 VAL Chi-restraints excluded: chain H residue 506 MET Chi-restraints excluded: chain I residue 63 GLN Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 331 THR Chi-restraints excluded: chain I residue 357 GLU Chi-restraints excluded: chain I residue 368 ILE Chi-restraints excluded: chain I residue 389 VAL Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 418 GLU Chi-restraints excluded: chain J residue 95 CYS Chi-restraints excluded: chain J residue 121 ARG Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 222 ARG Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 318 VAL Chi-restraints excluded: chain J residue 331 THR Chi-restraints excluded: chain J residue 400 VAL Chi-restraints excluded: chain K residue 80 PHE Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 177 LEU Chi-restraints excluded: chain K residue 195 SER Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 142 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 157 optimal weight: 9.9990 chunk 27 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 319 optimal weight: 0.9980 chunk 267 optimal weight: 3.9990 chunk 200 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 328 optimal weight: 6.9990 chunk 250 optimal weight: 6.9990 chunk 207 optimal weight: 4.9990 chunk 163 optimal weight: 0.9980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 GLN ** G 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 317 GLN H 347 GLN ** I 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.146812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.108143 restraints weight = 39527.614| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.11 r_work: 0.3277 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29292 Z= 0.128 Angle : 0.533 10.314 39700 Z= 0.273 Chirality : 0.043 0.165 4634 Planarity : 0.004 0.061 5072 Dihedral : 4.881 57.160 4014 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.02 % Allowed : 21.73 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.14), residues: 3642 helix: 1.85 (0.14), residues: 1476 sheet: -0.08 (0.24), residues: 442 loop : 0.18 (0.15), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 223 TYR 0.014 0.001 TYR K 65 PHE 0.017 0.001 PHE C 272 TRP 0.009 0.001 TRP L 119 HIS 0.006 0.001 HIS J 304 Details of bonding type rmsd covalent geometry : bond 0.00301 (29292) covalent geometry : angle 0.53270 (39700) hydrogen bonds : bond 0.03762 ( 1284) hydrogen bonds : angle 4.06825 ( 3582) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 309 time to evaluate : 0.888 Fit side-chains revert: symmetry clash REVERT: A 2 ASP cc_start: 0.7446 (t70) cc_final: 0.7119 (t0) REVERT: A 14 MET cc_start: 0.7043 (ttp) cc_final: 0.6725 (ttp) REVERT: A 91 LYS cc_start: 0.8510 (mmpt) cc_final: 0.8105 (mmmt) REVERT: B 1 MET cc_start: 0.6292 (ttt) cc_final: 0.5873 (ttm) REVERT: B 32 GLU cc_start: 0.5811 (OUTLIER) cc_final: 0.4758 (tm-30) REVERT: B 67 SER cc_start: 0.7850 (OUTLIER) cc_final: 0.7522 (t) REVERT: B 91 LYS cc_start: 0.8185 (pttt) cc_final: 0.7731 (pttm) REVERT: B 92 ILE cc_start: 0.7841 (OUTLIER) cc_final: 0.7495 (mp) REVERT: B 121 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.8049 (t0) REVERT: B 244 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7808 (tm-30) REVERT: C 16 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6972 (mp0) REVERT: C 20 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7237 (mp0) REVERT: C 49 HIS cc_start: 0.7256 (OUTLIER) cc_final: 0.6599 (m-70) REVERT: C 64 GLU cc_start: 0.8091 (mm-30) cc_final: 0.7616 (mp0) REVERT: C 167 THR cc_start: 0.8594 (OUTLIER) cc_final: 0.8384 (t) REVERT: D 59 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7733 (mt-10) REVERT: D 139 GLU cc_start: 0.7691 (tp30) cc_final: 0.7367 (mp0) REVERT: D 180 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8117 (tp30) REVERT: D 202 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7783 (mp0) REVERT: D 240 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8397 (mm) REVERT: D 341 SER cc_start: 0.8611 (m) cc_final: 0.8321 (p) REVERT: E 173 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7101 (mp0) REVERT: E 227 GLU cc_start: 0.7337 (mp0) cc_final: 0.6996 (mp0) REVERT: F 194 ARG cc_start: 0.6824 (tpt90) cc_final: 0.6317 (tpt90) REVERT: F 225 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7624 (ttm170) REVERT: G 171 LYS cc_start: 0.8005 (mtmm) cc_final: 0.7403 (mmpt) REVERT: H 344 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.8021 (ttt-90) REVERT: H 506 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8460 (mtp) REVERT: I 63 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7812 (mm-40) REVERT: I 176 LYS cc_start: 0.8417 (tppt) cc_final: 0.7841 (mmmt) REVERT: I 222 ARG cc_start: 0.8185 (mpp80) cc_final: 0.7636 (mmm-85) REVERT: I 230 LEU cc_start: 0.6876 (OUTLIER) cc_final: 0.6332 (mt) REVERT: I 357 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7667 (tt0) REVERT: I 418 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7910 (tm-30) REVERT: J 121 ARG cc_start: 0.6715 (OUTLIER) cc_final: 0.6249 (mtt-85) REVERT: J 145 ARG cc_start: 0.7097 (mtp180) cc_final: 0.6888 (mmp80) REVERT: J 177 ASN cc_start: 0.6283 (p0) cc_final: 0.6071 (p0) REVERT: J 181 MET cc_start: 0.8316 (ttm) cc_final: 0.8109 (ttm) REVERT: J 199 ASP cc_start: 0.8066 (m-30) cc_final: 0.7852 (m-30) REVERT: J 222 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7499 (mtt-85) REVERT: K 93 MET cc_start: 0.7500 (ptm) cc_final: 0.5043 (mpt) REVERT: K 141 GLN cc_start: 0.8086 (mm-40) cc_final: 0.7809 (mp10) REVERT: K 155 ASP cc_start: 0.7855 (p0) cc_final: 0.7615 (p0) REVERT: L 42 GLU cc_start: 0.6338 (mm-30) cc_final: 0.6101 (tm-30) outliers start: 95 outliers final: 59 residues processed: 378 average time/residue: 0.7253 time to fit residues: 313.6897 Evaluate side-chains 373 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 293 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 170 HIS Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 95 ARG Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 202 GLU Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 106 CYS Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 188 GLN Chi-restraints excluded: chain F residue 225 ARG Chi-restraints excluded: chain F residue 273 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 511 SER Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 305 ASP Chi-restraints excluded: chain H residue 344 ARG Chi-restraints excluded: chain H residue 368 GLU Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain H residue 453 VAL Chi-restraints excluded: chain H residue 506 MET Chi-restraints excluded: chain I residue 63 GLN Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 95 CYS Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 331 THR Chi-restraints excluded: chain I residue 357 GLU Chi-restraints excluded: chain I residue 389 VAL Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 418 GLU Chi-restraints excluded: chain J residue 95 CYS Chi-restraints excluded: chain J residue 121 ARG Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 222 ARG Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 318 VAL Chi-restraints excluded: chain J residue 400 VAL Chi-restraints excluded: chain K residue 80 PHE Chi-restraints excluded: chain K residue 142 THR Chi-restraints excluded: chain K residue 195 SER Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 142 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 109 optimal weight: 4.9990 chunk 190 optimal weight: 0.7980 chunk 330 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 218 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 246 optimal weight: 0.9990 chunk 209 optimal weight: 8.9990 chunk 126 optimal weight: 0.0970 chunk 4 optimal weight: 0.8980 chunk 337 optimal weight: 0.3980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 GLN G 265 GLN G 422 GLN H 317 GLN H 347 GLN ** I 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 145 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.150207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.111929 restraints weight = 39219.687| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.14 r_work: 0.3371 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 29292 Z= 0.104 Angle : 0.518 13.985 39700 Z= 0.262 Chirality : 0.042 0.173 4634 Planarity : 0.004 0.061 5072 Dihedral : 4.607 56.680 4014 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.32 % Allowed : 22.49 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.14), residues: 3642 helix: 2.02 (0.14), residues: 1476 sheet: 0.06 (0.21), residues: 616 loop : 0.17 (0.16), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 223 TYR 0.019 0.001 TYR L 187 PHE 0.022 0.001 PHE D 272 TRP 0.011 0.001 TRP L 119 HIS 0.006 0.001 HIS J 304 Details of bonding type rmsd covalent geometry : bond 0.00239 (29292) covalent geometry : angle 0.51758 (39700) hydrogen bonds : bond 0.03273 ( 1284) hydrogen bonds : angle 3.94707 ( 3582) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7284 Ramachandran restraints generated. 3642 Oldfield, 0 Emsley, 3642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 321 time to evaluate : 1.225 Fit side-chains REVERT: A 91 LYS cc_start: 0.8466 (mmpt) cc_final: 0.8059 (mmmt) REVERT: B 1 MET cc_start: 0.6243 (ttt) cc_final: 0.5904 (ttm) REVERT: B 76 ILE cc_start: 0.7153 (OUTLIER) cc_final: 0.6897 (mp) REVERT: B 91 LYS cc_start: 0.8258 (pttt) cc_final: 0.7756 (pttm) REVERT: B 92 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7581 (mp) REVERT: B 121 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.8052 (t0) REVERT: B 223 ASN cc_start: 0.8430 (OUTLIER) cc_final: 0.8190 (t0) REVERT: B 244 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.7898 (tm-30) REVERT: C 16 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7077 (mp0) REVERT: C 20 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7299 (mp0) REVERT: C 49 HIS cc_start: 0.7260 (OUTLIER) cc_final: 0.6622 (m-70) REVERT: C 64 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7667 (mp0) REVERT: D 20 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7659 (mm-30) REVERT: D 59 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7757 (mt-10) REVERT: D 139 GLU cc_start: 0.7778 (tp30) cc_final: 0.7468 (mp0) REVERT: D 180 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8204 (tp30) REVERT: D 240 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8324 (mm) REVERT: D 341 SER cc_start: 0.8612 (m) cc_final: 0.8353 (p) REVERT: E 173 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7240 (mp0) REVERT: E 227 GLU cc_start: 0.7399 (mp0) cc_final: 0.7069 (mp0) REVERT: F 188 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8296 (mt0) REVERT: F 194 ARG cc_start: 0.6909 (tpt90) cc_final: 0.6418 (tpt90) REVERT: F 225 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7652 (ttm170) REVERT: F 227 GLU cc_start: 0.7407 (mt-10) cc_final: 0.7106 (mp0) REVERT: G 171 LYS cc_start: 0.8019 (mtmm) cc_final: 0.7412 (mmpt) REVERT: G 348 GLU cc_start: 0.8473 (mt-10) cc_final: 0.7849 (mt-10) REVERT: H 344 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.7794 (ttt-90) REVERT: H 506 MET cc_start: 0.8972 (OUTLIER) cc_final: 0.8486 (mtp) REVERT: I 63 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7848 (mm-40) REVERT: I 176 LYS cc_start: 0.8465 (tppt) cc_final: 0.7809 (mmmt) REVERT: I 222 ARG cc_start: 0.8193 (mpp80) cc_final: 0.7672 (mmm-85) REVERT: I 230 LEU cc_start: 0.6956 (OUTLIER) cc_final: 0.6444 (mt) REVERT: I 357 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7699 (tt0) REVERT: I 418 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7858 (tm-30) REVERT: J 177 ASN cc_start: 0.6290 (p0) cc_final: 0.6079 (p0) REVERT: J 199 ASP cc_start: 0.8037 (m-30) cc_final: 0.7797 (m-30) REVERT: J 222 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7496 (mtt-85) REVERT: K 93 MET cc_start: 0.7519 (ptm) cc_final: 0.5029 (mpp) REVERT: K 141 GLN cc_start: 0.8070 (mm-40) cc_final: 0.7832 (mp10) REVERT: L 87 MET cc_start: 0.6686 (ppp) cc_final: 0.5890 (tpt) outliers start: 73 outliers final: 36 residues processed: 372 average time/residue: 0.7011 time to fit residues: 300.2543 Evaluate side-chains 352 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 297 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 170 HIS Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 244 GLN Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 20 GLU Chi-restraints excluded: chain C residue 49 HIS Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 286 HIS Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 106 CYS Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain F residue 116 GLU Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 188 GLN Chi-restraints excluded: chain F residue 225 ARG Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 511 SER Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 305 ASP Chi-restraints excluded: chain H residue 344 ARG Chi-restraints excluded: chain H residue 432 VAL Chi-restraints excluded: chain H residue 453 VAL Chi-restraints excluded: chain H residue 506 MET Chi-restraints excluded: chain I residue 63 GLN Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain I residue 331 THR Chi-restraints excluded: chain I residue 357 GLU Chi-restraints excluded: chain I residue 389 VAL Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 418 GLU Chi-restraints excluded: chain J residue 95 CYS Chi-restraints excluded: chain J residue 222 ARG Chi-restraints excluded: chain J residue 256 VAL Chi-restraints excluded: chain J residue 318 VAL Chi-restraints excluded: chain K residue 195 SER Chi-restraints excluded: chain L residue 28 VAL Chi-restraints excluded: chain L residue 38 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 38 optimal weight: 1.9990 chunk 112 optimal weight: 0.0870 chunk 71 optimal weight: 0.6980 chunk 353 optimal weight: 7.9990 chunk 185 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 327 optimal weight: 0.0020 chunk 220 optimal weight: 6.9990 chunk 310 optimal weight: 0.6980 chunk 169 optimal weight: 0.9980 chunk 215 optimal weight: 1.9990 overall best weight: 0.4966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 GLN F 172 ASN G 265 GLN H 317 GLN H 347 GLN H 422 GLN ** I 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 145 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.150782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.112475 restraints weight = 39385.419| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.15 r_work: 0.3380 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 29292 Z= 0.101 Angle : 0.520 14.872 39700 Z= 0.261 Chirality : 0.042 0.162 4634 Planarity : 0.004 0.061 5072 Dihedral : 4.475 57.326 4013 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.16 % Allowed : 22.55 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.14), residues: 3642 helix: 2.09 (0.14), residues: 1476 sheet: 0.01 (0.24), residues: 472 loop : 0.28 (0.16), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 223 TYR 0.018 0.001 TYR L 187 PHE 0.013 0.001 PHE C 272 TRP 0.016 0.001 TRP L 119 HIS 0.008 0.001 HIS I 304 Details of bonding type rmsd covalent geometry : bond 0.00231 (29292) covalent geometry : angle 0.51953 (39700) hydrogen bonds : bond 0.03205 ( 1284) hydrogen bonds : angle 3.89252 ( 3582) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14031.74 seconds wall clock time: 238 minutes 21.30 seconds (14301.30 seconds total)