Starting phenix.real_space_refine on Fri Mar 6 04:22:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d44_30569/03_2026/7d44_30569.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d44_30569/03_2026/7d44_30569.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7d44_30569/03_2026/7d44_30569.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d44_30569/03_2026/7d44_30569.map" model { file = "/net/cci-nas-00/data/ceres_data/7d44_30569/03_2026/7d44_30569.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d44_30569/03_2026/7d44_30569.cif" } resolution = 4.0 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 142 5.16 5 C 17918 2.51 5 N 4998 2.21 5 O 5331 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 115 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28391 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2262 Classifications: {'peptide': 293} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 283} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2247 Classifications: {'peptide': 291} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 281} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 2476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2476 Classifications: {'peptide': 317} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 302} Chain breaks: 1 Chain: "D" Number of atoms: 2538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2538 Classifications: {'peptide': 324} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 309} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2430 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 10, 'TRANS': 332} Chain breaks: 4 Unresolved non-hydrogen bonds: 248 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASP:plan': 4, 'GLU:plan': 7, 'ARG:plan': 4, 'ASN:plan1': 6} Unresolved non-hydrogen planarities: 99 Chain: "F" Number of atoms: 2429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2429 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 10, 'TRANS': 332} Chain breaks: 4 Unresolved non-hydrogen bonds: 249 Unresolved non-hydrogen angles: 313 Unresolved non-hydrogen dihedrals: 188 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASP:plan': 4, 'GLU:plan': 7, 'ARG:plan': 4, 'ASN:plan1': 6} Unresolved non-hydrogen planarities: 100 Chain: "G" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2750 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 334} Chain: "H" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2750 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 334} Chain: "I" Number of atoms: 3358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3358 Classifications: {'peptide': 427} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 408} Chain: "J" Number of atoms: 3373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3373 Classifications: {'peptide': 429} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 409} Chain: "K" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 889 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 158} Link IDs: {'PTRANS': 4, 'TRANS': 171} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 585 Unresolved non-hydrogen angles: 743 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'ARG:plan': 14, 'PHE:plan': 6, 'TYR:plan': 9, 'GLN:plan1': 3, 'HIS:plan': 3, 'GLU:plan': 18, 'ASP:plan': 12, 'ASN:plan1': 9, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 340 Chain: "L" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 889 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 158} Link IDs: {'PTRANS': 4, 'TRANS': 171} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 585 Unresolved non-hydrogen angles: 743 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'ARG:plan': 14, 'PHE:plan': 6, 'TYR:plan': 9, 'GLN:plan1': 3, 'HIS:plan': 3, 'GLU:plan': 18, 'ASP:plan': 12, 'ASN:plan1': 9, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 340 Time building chain proxies: 5.91, per 1000 atoms: 0.21 Number of scatterers: 28391 At special positions: 0 Unit cell: (164.64, 169.05, 191.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 142 16.00 P 2 15.00 O 5331 8.00 N 4998 7.00 C 17918 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: 2.20 Conformation dependent library (CDL) restraints added in 1.1 seconds 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7258 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 41 sheets defined 42.1% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 3 through 16 Processing helix chain 'A' and resid 21 through 36 removed outlier: 3.558A pdb=" N ALA A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 58 WARNING: missing atoms! Processing helix chain 'A' and resid 62 through 77 removed outlier: 4.035A pdb=" N SER A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 116 removed outlier: 3.608A pdb=" N LYS A 90 " --> pdb=" O TYR A 86 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ARG A 108 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ASN A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N HIS A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 143 Processing helix chain 'A' and resid 159 through 170 Processing helix chain 'A' and resid 179 through 181 No H-bonds generated for 'chain 'A' and resid 179 through 181' Processing helix chain 'A' and resid 182 through 187 Processing helix chain 'A' and resid 212 through 222 Processing helix chain 'A' and resid 242 through 246 removed outlier: 3.622A pdb=" N VAL A 246 " --> pdb=" O GLN A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 252 removed outlier: 3.882A pdb=" N TYR A 252 " --> pdb=" O ASP A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 304 removed outlier: 3.853A pdb=" N VAL A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER A 297 " --> pdb=" O PRO A 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 17 removed outlier: 5.019A pdb=" N GLU B 8 " --> pdb=" O LYS B 4 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASP B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 35 removed outlier: 3.616A pdb=" N ALA B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 47 Processing helix chain 'B' and resid 47 through 60 removed outlier: 4.295A pdb=" N GLY B 58 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL B 59 " --> pdb=" O THR B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 77 removed outlier: 3.831A pdb=" N SER B 66 " --> pdb=" O SER B 62 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 116 removed outlier: 4.105A pdb=" N ARG B 108 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ASN B 109 " --> pdb=" O SER B 105 " (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 removed outlier: 4.002A pdb=" N ALA B 140 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA B 144 " --> pdb=" O ALA B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 170 Processing helix chain 'B' and resid 185 through 190 removed outlier: 3.923A pdb=" N ALA B 190 " --> pdb=" O MET B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 222 removed outlier: 3.893A pdb=" N MET B 215 " --> pdb=" O GLY B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 252 removed outlier: 3.805A pdb=" N TYR B 252 " --> pdb=" O ASP B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 305 removed outlier: 3.549A pdb=" N VAL B 296 " --> pdb=" O THR B 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 24 Processing helix chain 'C' and resid 30 through 48 Processing helix chain 'C' and resid 53 through 72 removed outlier: 3.883A pdb=" N LEU C 57 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLN C 72 " --> pdb=" O MET C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 96 Processing helix chain 'C' and resid 128 through 145 removed outlier: 3.774A pdb=" N ASN C 132 " --> pdb=" O GLN C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 156 removed outlier: 4.300A pdb=" N LEU C 156 " --> pdb=" O ALA C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 182 Processing helix chain 'C' and resid 198 through 207 removed outlier: 3.874A pdb=" N GLU C 202 " --> pdb=" O CYS C 198 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N MET C 203 " --> pdb=" O GLN C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 211 removed outlier: 3.709A pdb=" N GLY C 211 " --> pdb=" O SER C 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 208 through 211' Processing helix chain 'C' and resid 221 through 227 removed outlier: 4.257A pdb=" N SER C 227 " --> pdb=" O PHE C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 261 removed outlier: 3.582A pdb=" N HIS C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 274 removed outlier: 3.720A pdb=" N LEU C 274 " --> pdb=" O MET C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 305 removed outlier: 3.815A pdb=" N GLY C 300 " --> pdb=" O PHE C 297 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ASP C 301 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ILE C 302 " --> pdb=" O GLU C 299 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS C 305 " --> pdb=" O ILE C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 321 removed outlier: 3.675A pdb=" N LEU C 320 " --> pdb=" O PRO C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 343 removed outlier: 4.284A pdb=" N ARG C 338 " --> pdb=" O SER C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 351 removed outlier: 4.034A pdb=" N HIS C 349 " --> pdb=" O PRO C 346 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL C 350 " --> pdb=" O ASP C 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 25 Processing helix chain 'D' and resid 30 through 48 Processing helix chain 'D' and resid 53 through 72 Processing helix chain 'D' and resid 75 through 96 removed outlier: 4.027A pdb=" N GLY D 79 " --> pdb=" O GLU D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 146 removed outlier: 3.879A pdb=" N GLY D 146 " --> pdb=" O VAL D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 156 removed outlier: 3.888A pdb=" N ASN D 150 " --> pdb=" O GLY D 146 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N GLN D 154 " --> pdb=" O ASN D 150 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 159 No H-bonds generated for 'chain 'D' and resid 157 through 159' Processing helix chain 'D' and resid 171 through 181 Processing helix chain 'D' and resid 199 through 209 removed outlier: 4.156A pdb=" N MET D 203 " --> pdb=" O GLN D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 226 Processing helix chain 'D' and resid 227 through 229 No H-bonds generated for 'chain 'D' and resid 227 through 229' Processing helix chain 'D' and resid 250 through 261 Processing helix chain 'D' and resid 270 through 274 removed outlier: 3.642A pdb=" N LYS D 273 " --> pdb=" O PRO D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 282 removed outlier: 4.217A pdb=" N GLU D 282 " --> pdb=" O PRO D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 294 Processing helix chain 'D' and resid 300 through 305 removed outlier: 3.725A pdb=" N LYS D 305 " --> pdb=" O ILE D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 321 removed outlier: 4.151A pdb=" N LEU D 320 " --> pdb=" O PRO D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 344 Processing helix chain 'D' and resid 345 through 349 removed outlier: 3.726A pdb=" N ASP D 348 " --> pdb=" O HIS D 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 44 removed outlier: 4.042A pdb=" N LEU E 40 " --> pdb=" O ILE E 36 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU E 42 " --> pdb=" O TYR E 38 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU E 43 " --> pdb=" O PRO E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 67 Processing helix chain 'E' and resid 85 through 94 Processing helix chain 'E' and resid 95 through 97 No H-bonds generated for 'chain 'E' and resid 95 through 97' Processing helix chain 'E' and resid 113 through 124 removed outlier: 3.842A pdb=" N VAL E 117 " --> pdb=" O ALA E 113 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR E 124 " --> pdb=" O LEU E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 217 Processing helix chain 'E' and resid 223 through 228 Processing helix chain 'E' and resid 228 through 236 Processing helix chain 'E' and resid 277 through 292 removed outlier: 4.329A pdb=" N TRP E 290 " --> pdb=" O ARG E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 295 No H-bonds generated for 'chain 'E' and resid 293 through 295' Processing helix chain 'F' and resid 36 through 46 Processing helix chain 'F' and resid 62 through 68 removed outlier: 4.529A pdb=" N GLU F 66 " --> pdb=" O ALA F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 94 Processing helix chain 'F' and resid 113 through 123 removed outlier: 3.747A pdb=" N VAL F 117 " --> pdb=" O ALA F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 190 removed outlier: 3.691A pdb=" N LEU F 187 " --> pdb=" O LYS F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 218 Processing helix chain 'F' and resid 223 through 236 removed outlier: 5.256A pdb=" N ILE F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) Proline residue: F 230 - end of helix Processing helix chain 'F' and resid 278 through 292 removed outlier: 3.776A pdb=" N ASN F 283 " --> pdb=" O ASP F 279 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP F 290 " --> pdb=" O ARG F 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 181 removed outlier: 3.840A pdb=" N SER G 181 " --> pdb=" O SER G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 195 Processing helix chain 'G' and resid 204 through 216 Processing helix chain 'G' and resid 221 through 238 Processing helix chain 'G' and resid 247 through 267 removed outlier: 4.991A pdb=" N VAL G 253 " --> pdb=" O SER G 249 " (cutoff:3.500A) Proline residue: G 258 - end of helix Processing helix chain 'G' and resid 270 through 287 Processing helix chain 'G' and resid 292 through 311 Processing helix chain 'G' and resid 312 through 324 Processing helix chain 'G' and resid 339 through 352 removed outlier: 3.553A pdb=" N GLU G 352 " --> pdb=" O GLU G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 378 removed outlier: 4.092A pdb=" N THR G 372 " --> pdb=" O GLU G 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 389 through 394 removed outlier: 4.674A pdb=" N SER G 392 " --> pdb=" O PRO G 389 " (cutoff:3.500A) Processing helix chain 'G' and resid 418 through 431 removed outlier: 4.621A pdb=" N GLN G 422 " --> pdb=" O VAL G 418 " (cutoff:3.500A) Processing helix chain 'G' and resid 459 through 463 removed outlier: 3.787A pdb=" N ASP G 462 " --> pdb=" O ASP G 459 " (cutoff:3.500A) 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 516 removed outlier: 3.606A pdb=" N VAL G 515 " --> pdb=" O SER G 511 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU G 516 " --> pdb=" O VAL G 512 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 511 through 516' Processing helix chain 'H' and resid 177 through 181 removed outlier: 3.545A pdb=" N SER H 181 " --> pdb=" O SER H 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 196 removed outlier: 3.949A pdb=" N MET H 196 " --> pdb=" O THR H 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 216 Processing helix chain 'H' and resid 221 through 238 removed outlier: 3.666A pdb=" N ARG H 225 " --> pdb=" O GLY H 221 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 267 removed outlier: 3.579A pdb=" N ASP H 251 " --> pdb=" O GLU H 247 " (cutoff:3.500A) removed outlier: 4.573A 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 287 Processing helix chain 'H' and resid 292 through 311 Processing helix chain 'H' and resid 312 through 324 Processing helix chain 'H' and resid 325 through 327 No H-bonds generated for 'chain 'H' and resid 325 through 327' Processing helix chain 'H' and resid 339 through 350 removed outlier: 3.589A pdb=" N SER H 343 " --> pdb=" O SER H 339 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 378 Processing helix chain 'H' and resid 390 through 395 removed outlier: 4.048A pdb=" N VAL H 394 " --> pdb=" O ALA H 390 " (cutoff:3.500A) Processing helix chain 'H' and resid 419 through 430 Processing helix chain 'H' and resid 459 through 463 removed outlier: 3.802A pdb=" N ASP H 462 " --> pdb=" O ASP H 459 " (cutoff:3.500A) Processing helix chain 'H' and resid 508 through 511 Processing helix chain 'H' and resid 512 through 517 Processing helix chain 'I' and resid 58 through 63 removed outlier: 3.861A pdb=" N ASP I 62 " --> pdb=" O PRO I 58 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN I 63 " --> pdb=" O ILE I 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 58 through 63' Processing helix chain 'I' and resid 74 through 87 removed outlier: 3.760A pdb=" N TYR I 78 " --> pdb=" O ALA I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 108 removed outlier: 3.797A pdb=" N ILE I 102 " --> pdb=" O LYS I 98 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS I 108 " --> pdb=" O GLU I 104 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 141 removed outlier: 3.587A pdb=" N VAL I 134 " --> pdb=" O SER I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 175 Processing helix chain 'I' and resid 227 through 233 removed outlier: 3.558A pdb=" N PHE I 231 " --> pdb=" O PRO I 227 " (cutoff:3.500A) Processing helix chain 'I' and resid 253 through 262 removed outlier: 4.252A pdb=" N ALA I 257 " --> pdb=" O SER I 253 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP I 262 " --> pdb=" O GLN I 258 " (cutoff:3.500A) Processing helix chain 'I' and resid 268 through 279 Processing helix chain 'I' and resid 302 through 314 Processing helix chain 'I' and resid 330 through 334 removed outlier: 3.935A pdb=" N SER I 334 " --> pdb=" O THR I 331 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 342 removed outlier: 3.643A pdb=" N ASN I 341 " --> pdb=" O SER I 338 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 62 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 107 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 200 removed outlier: 3.792A pdb=" N ASN J 200 " --> pdb=" O HIS J 197 " (cutoff:3.500A) Processing helix chain 'J' and resid 228 through 234 Processing helix chain 'J' and resid 253 through 261 removed outlier: 3.801A 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 314 Processing helix chain 'J' and resid 330 through 334 removed outlier: 4.149A pdb=" N SER J 334 " --> pdb=" O THR J 331 " (cutoff:3.500A) Processing helix chain 'J' and resid 338 through 342 Processing helix chain 'K' and resid 53 through 57 Processing helix chain 'K' and resid 60 through 65 removed outlier: 3.564A pdb=" N ILE K 64 " --> pdb=" O LYS K 60 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY K 65 " --> pdb=" O LEU K 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 60 through 65' Processing helix chain 'K' and resid 90 through 118 Processing helix chain 'K' and resid 122 through 141 removed outlier: 3.611A pdb=" N LEU K 126 " --> pdb=" O LYS K 122 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N TYR K 141 " --> pdb=" O PHE K 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 155 Processing helix chain 'K' and resid 168 through 179 Processing helix chain 'L' and resid 51 through 57 removed outlier: 3.575A pdb=" N ILE L 55 " --> pdb=" O ARG L 52 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG L 56 " --> pdb=" O ARG L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 90 through 116 Processing helix chain 'L' and resid 122 through 141 removed outlier: 3.575A pdb=" N LEU L 126 " --> pdb=" O LYS L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 147 through 155 Processing helix chain 'L' and resid 162 through 166 Processing helix chain 'L' and resid 168 through 179 removed outlier: 3.616A pdb=" N ARG L 172 " --> pdb=" O ASN L 168 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 123 through 126 removed outlier: 6.268A pdb=" N ALA A 123 " --> pdb=" O SER A 149 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N TYR A 151 " --> pdb=" O ALA A 123 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE A 125 " --> pdb=" O TYR A 151 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N THR A 153 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 9.541A pdb=" N THR A 176 " --> pdb=" O PHE A 148 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL A 150 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N VAL A 178 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N VAL A 152 " --> pdb=" O VAL A 178 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 196 removed outlier: 6.049A pdb=" N VAL A 193 " --> pdb=" O TYR A 227 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N VAL A 229 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL A 195 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N PHE A 226 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N PHE A 285 " --> pdb=" O PHE A 226 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL A 228 " --> pdb=" O PHE A 285 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 206 through 209 Processing sheet with id=AA4, first strand: chain 'B' and resid 175 through 176 removed outlier: 8.381A pdb=" N THR B 176 " --> pdb=" O PHE B 148 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL B 150 " --> pdb=" O THR B 176 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ALA B 123 " --> pdb=" O SER B 149 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N TYR B 151 " --> pdb=" O ALA B 123 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ILE B 125 " --> pdb=" O TYR B 151 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N THR B 124 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE B 194 " --> pdb=" O THR B 124 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N LEU B 126 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N GLY B 196 " --> pdb=" O LEU B 126 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N VAL B 193 " --> pdb=" O TYR B 227 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N VAL B 229 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N VAL B 195 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N PHE B 226 " --> pdb=" O LEU B 283 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N PHE B 285 " --> pdb=" O PHE B 226 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL B 228 " --> pdb=" O PHE B 285 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 207 through 209 Processing sheet with id=AA6, first strand: chain 'C' and resid 329 through 331 removed outlier: 6.063A pdb=" N LEU C 265 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE C 325 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL C 267 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL C 232 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N CYS C 268 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE C 234 " --> pdb=" O CYS C 268 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS C 231 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE C 168 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE C 165 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ALA C 192 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N THR C 167 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL C 189 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N MET C 217 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL C 191 " --> pdb=" O MET C 217 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N THR C 214 " --> pdb=" O ARG G 483 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 238 through 239 removed outlier: 3.698A pdb=" N THR C 238 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 164 through 165 removed outlier: 6.149A pdb=" N ILE D 165 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALA D 192 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL D 189 " --> pdb=" O THR D 215 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N MET D 217 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL D 191 " --> pdb=" O MET D 217 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N THR D 214 " --> pdb=" O ARG H 483 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 232 through 234 removed outlier: 6.224A pdb=" N VAL D 232 " --> pdb=" O ILE D 266 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU D 323 " --> pdb=" O LEU D 265 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 246 through 248 Processing sheet with id=AB2, first strand: chain 'E' and resid 78 through 79 removed outlier: 7.544A pdb=" N ILE E 78 " --> pdb=" O VAL E 51 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL E 53 " --> pdb=" O ILE E 78 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ILE E 52 " --> pdb=" O PHE E 3 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N ALA E 5 " --> pdb=" O ILE E 52 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL E 54 " --> pdb=" O ALA E 5 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL E 7 " --> pdb=" O VAL E 54 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 200 through 201 removed outlier: 3.582A pdb=" N MET E 130 " --> pdb=" O TYR E 264 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE E 266 " --> pdb=" O MET E 130 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET E 132 " --> pdb=" O PHE E 266 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 167 through 172 removed outlier: 6.265A pdb=" N GLY E 159 " --> pdb=" O LEU E 168 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N MET E 170 " --> pdb=" O PHE E 157 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N PHE E 157 " --> pdb=" O MET E 170 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL J 202 " --> pdb=" O PHE J 215 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N PHE J 215 " --> pdb=" O VAL J 202 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ALA J 204 " --> pdb=" O LEU J 213 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 391 through 392 removed outlier: 6.405A pdb=" N LEU E 391 " --> pdb=" O ILE E 409 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'E' and resid 402 through 403 removed outlier: 6.784A pdb=" N ALA E 419 " --> pdb=" O ASN E 403 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'F' and resid 52 through 54 removed outlier: 3.507A pdb=" N ILE F 78 " --> pdb=" O VAL F 53 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 101 through 103 Processing sheet with id=AB9, first strand: chain 'F' and resid 169 through 171 Processing sheet with id=AC1, first strand: chain 'F' and resid 380 through 381 removed outlier: 7.303A pdb=" N LEU F 380 " --> pdb=" O VAL F 398 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'G' and resid 333 through 334 removed outlier: 6.791A pdb=" N ILE G 333 " --> pdb=" O VAL G 359 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N VAL G 361 " --> pdb=" O ILE G 333 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU G 386 " --> pdb=" O VAL G 360 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP G 362 " --> pdb=" O LEU G 386 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'G' and resid 414 through 417 Processing sheet with id=AC4, first strand: chain 'G' and resid 436 through 437 removed outlier: 7.592A pdb=" N VAL G 436 " --> pdb=" O ILE G 501 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 361 through 362 removed outlier: 3.669A pdb=" N ASP H 362 " --> pdb=" O LEU H 386 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'H' and resid 401 through 404 removed outlier: 6.038A pdb=" N VAL H 401 " --> pdb=" O LEU H 435 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N CYS H 437 " --> pdb=" O VAL H 401 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU H 403 " --> pdb=" O CYS H 437 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N ILE H 501 " --> pdb=" O VAL H 434 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL H 436 " --> pdb=" O ILE H 501 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 414 through 416 Processing sheet with id=AC8, first strand: chain 'I' and resid 119 through 121 Processing sheet with id=AC9, first strand: chain 'I' and resid 119 through 121 Processing sheet with id=AD1, first strand: chain 'I' and resid 155 through 156 Processing sheet with id=AD2, first strand: chain 'I' and resid 373 through 375 removed outlier: 6.471A pdb=" N PHE I 373 " --> pdb=" O LEU I 391 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N VAL I 390 " --> pdb=" O ILE I 408 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'I' and resid 384 through 385 removed outlier: 6.642A pdb=" N HIS I 384 " --> pdb=" O VAL I 402 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ARG I 401 " --> pdb=" O VAL I 419 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'J' and resid 44 through 48 removed outlier: 7.647A pdb=" N ALA J 45 " --> pdb=" O PHE J 92 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N PHE J 94 " --> pdb=" O ALA J 45 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU J 47 " --> pdb=" O PHE J 94 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR J 91 " --> pdb=" O VAL J 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'J' and resid 44 through 48 removed outlier: 7.647A pdb=" N ALA J 45 " --> pdb=" O PHE J 92 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N PHE J 94 " --> pdb=" O ALA J 45 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU J 47 " --> pdb=" O PHE J 94 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 244 through 246 removed outlier: 6.427A pdb=" N PHE J 185 " --> pdb=" O THR J 292 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 355 through 356 removed outlier: 6.637A pdb=" N ILE J 355 " --> pdb=" O ILE J 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'J' and resid 384 through 385 removed outlier: 6.268A pdb=" N HIS J 384 " --> pdb=" O VAL J 402 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'J' and resid 390 through 392 removed outlier: 6.330A pdb=" N VAL J 390 " --> pdb=" O ILE J 408 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N THR J 424 " --> pdb=" O ILE J 441 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 395 through 396 removed outlier: 5.917A pdb=" N TYR J 395 " --> pdb=" O LEU J 413 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'J' and resid 430 through 431 removed outlier: 7.205A pdb=" N VAL J 430 " --> pdb=" O ILE J 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'K' and resid 18 through 26 removed outlier: 6.944A pdb=" N TYR K 32 " --> pdb=" O ARG K 24 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N GLU K 42 " --> pdb=" O ILE K 82 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N LEU K 84 " --> pdb=" O GLU K 42 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N MET K 44 " --> pdb=" O LEU K 84 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ASP K 83 " --> pdb=" O ILE K 73 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 42 through 46 removed outlier: 3.531A pdb=" N SER L 34 " --> pdb=" O ASN L 22 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 74 through 76 1115 hydrogen bonds defined for protein. 3117 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.15 Time building geometry restraints manager: 2.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9599 1.34 - 1.46: 5112 1.46 - 1.58: 13932 1.58 - 1.70: 8 1.70 - 1.81: 216 Bond restraints: 28867 Sorted by residual: bond pdb=" C SER J 188 " pdb=" N SER J 189 " ideal model delta sigma weight residual 1.329 1.252 0.077 1.86e-02 2.89e+03 1.71e+01 bond pdb=" CA LEU D 303 " pdb=" C LEU D 303 " ideal model delta sigma weight residual 1.523 1.481 0.042 1.34e-02 5.57e+03 9.89e+00 bond pdb=" CA GLU D 157 " pdb=" C GLU D 157 " ideal model delta sigma weight residual 1.524 1.483 0.040 1.29e-02 6.01e+03 9.65e+00 bond pdb=" CA SER H 481 " pdb=" C SER H 481 " ideal model delta sigma weight residual 1.523 1.488 0.035 1.34e-02 5.57e+03 6.98e+00 bond pdb=" CA HIS D 260 " pdb=" C HIS D 260 " ideal model delta sigma weight residual 1.522 1.489 0.033 1.40e-02 5.10e+03 5.71e+00 ... (remaining 28862 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 38148 2.24 - 4.47: 967 4.47 - 6.71: 93 6.71 - 8.94: 12 8.94 - 11.18: 5 Bond angle restraints: 39225 Sorted by residual: angle pdb=" C PHE K 12 " pdb=" N PRO K 13 " pdb=" CA PRO K 13 " ideal model delta sigma weight residual 119.84 131.02 -11.18 1.25e+00 6.40e-01 8.00e+01 angle pdb=" N GLU K 14 " pdb=" CA GLU K 14 " pdb=" C GLU K 14 " ideal model delta sigma weight residual 108.74 116.72 -7.98 1.38e+00 5.25e-01 3.35e+01 angle pdb=" C GLU K 14 " pdb=" N VAL K 15 " pdb=" CA VAL K 15 " ideal model delta sigma weight residual 120.35 128.24 -7.89 1.39e+00 5.18e-01 3.22e+01 angle pdb=" C LEU C 178 " pdb=" N LYS C 179 " pdb=" CA LYS C 179 " ideal model delta sigma weight residual 121.94 111.23 10.71 2.00e+00 2.50e-01 2.87e+01 angle pdb=" N VAL C 225 " pdb=" CA VAL C 225 " pdb=" C VAL C 225 " ideal model delta sigma weight residual 113.20 108.63 4.57 9.60e-01 1.09e+00 2.26e+01 ... (remaining 39220 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 15567 17.51 - 35.03: 1610 35.03 - 52.54: 288 52.54 - 70.06: 34 70.06 - 87.57: 22 Dihedral angle restraints: 17521 sinusoidal: 6374 harmonic: 11147 Sorted by residual: dihedral pdb=" CA GLU K 14 " pdb=" C GLU K 14 " pdb=" N VAL K 15 " pdb=" CA VAL K 15 " ideal model delta harmonic sigma weight residual -180.00 -137.21 -42.79 0 5.00e+00 4.00e-02 7.32e+01 dihedral pdb=" CA HIS D 125 " pdb=" C HIS D 125 " pdb=" N TYR D 126 " pdb=" CA TYR D 126 " ideal model delta harmonic sigma weight residual -180.00 -153.91 -26.09 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA SER C 284 " pdb=" C SER C 284 " pdb=" N PHE C 285 " pdb=" CA PHE C 285 " ideal model delta harmonic sigma weight residual 180.00 -154.08 -25.92 0 5.00e+00 4.00e-02 2.69e+01 ... (remaining 17518 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2669 0.036 - 0.073: 1333 0.073 - 0.109: 493 0.109 - 0.145: 151 0.145 - 0.182: 11 Chirality restraints: 4657 Sorted by residual: chirality pdb=" CA PRO A 293 " pdb=" N PRO A 293 " pdb=" C PRO A 293 " pdb=" CB PRO A 293 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.24e-01 chirality pdb=" CA VAL I 238 " pdb=" N VAL I 238 " pdb=" C VAL I 238 " pdb=" CB VAL I 238 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.05e-01 chirality pdb=" CA ILE A 207 " pdb=" N ILE A 207 " pdb=" C ILE A 207 " pdb=" CB ILE A 207 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.87e-01 ... (remaining 4654 not shown) Planarity restraints: 5083 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 345 " 0.047 5.00e-02 4.00e+02 7.17e-02 8.22e+00 pdb=" N PRO D 346 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO D 346 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 346 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 395 " 0.045 5.00e-02 4.00e+02 6.82e-02 7.44e+00 pdb=" N PRO H 396 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO H 396 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO H 396 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU G 395 " -0.043 5.00e-02 4.00e+02 6.53e-02 6.82e+00 pdb=" N PRO G 396 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO G 396 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO G 396 " -0.037 5.00e-02 4.00e+02 ... (remaining 5080 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 528 2.62 - 3.19: 28571 3.19 - 3.76: 43757 3.76 - 4.33: 59038 4.33 - 4.90: 95789 Nonbonded interactions: 227683 Sorted by model distance: nonbonded pdb=" OG SER G 416 " pdb=" OG1 THR G 420 " model vdw 2.049 3.040 nonbonded pdb=" OD2 ASP F 161 " pdb=" OG1 THR F 163 " model vdw 2.089 3.040 nonbonded pdb=" OG SER J 130 " pdb=" OE1 GLN J 267 " model vdw 2.113 3.040 nonbonded pdb=" ND2 ASN A 203 " pdb=" OH TYR A 275 " model vdw 2.123 3.120 nonbonded pdb=" O GLU A 202 " pdb=" OG SER A 297 " model vdw 2.148 3.040 ... (remaining 227678 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ )) or resid 29 \ through 253 or resid 268 through 305)) selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 8 through 343 or (resid 344 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name C \ E2 or name CZ )) or resid 345 through 351)) selection = (chain 'D' and (resid 8 through 98 or resid 126 through 351)) } ncs_group { reference = (chain 'E' and (resid 1 through 263 or (resid 264 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name C \ E2 or name CZ )) or resid 265 through 444)) selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = (chain 'J' and resid 41 through 467) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 24.170 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 28867 Z= 0.277 Angle : 0.857 11.180 39225 Z= 0.504 Chirality : 0.049 0.182 4657 Planarity : 0.005 0.072 5083 Dihedral : 14.780 87.573 10263 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 20.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 16.34 % Favored : 83.61 % Rotamer: Outliers : 0.28 % Allowed : 9.91 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -5.25 (0.11), residues: 3771 helix: -2.48 (0.11), residues: 1365 sheet: -4.09 (0.20), residues: 409 loop : -4.24 (0.11), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 185 TYR 0.020 0.002 TYR E 231 PHE 0.021 0.002 PHE D 177 TRP 0.021 0.002 TRP A 272 HIS 0.010 0.001 HIS B 128 Details of bonding type rmsd covalent geometry : bond 0.00602 (28867) covalent geometry : angle 0.85749 (39225) hydrogen bonds : bond 0.14266 ( 1100) hydrogen bonds : angle 6.82812 ( 3117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 366 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 ILE cc_start: 0.9101 (pt) cc_final: 0.8858 (mm) REVERT: A 187 MET cc_start: 0.7955 (tpp) cc_final: 0.7141 (tpp) REVERT: B 93 MET cc_start: 0.7170 (mmp) cc_final: 0.6474 (mmp) REVERT: C 34 MET cc_start: 0.7750 (mtm) cc_final: 0.7328 (mtm) REVERT: C 148 MET cc_start: 0.7762 (ttm) cc_final: 0.7426 (ttm) REVERT: C 217 MET cc_start: 0.6672 (ptt) cc_final: 0.6414 (ptt) REVERT: C 340 MET cc_start: 0.8157 (tmm) cc_final: 0.7881 (tmm) REVERT: D 226 MET cc_start: 0.8454 (tpt) cc_final: 0.7886 (tpp) REVERT: D 259 LYS cc_start: 0.8611 (ttpp) cc_final: 0.8074 (tptt) REVERT: E 69 MET cc_start: 0.6604 (tmm) cc_final: 0.6186 (tmm) REVERT: E 274 ASN cc_start: 0.7604 (m-40) cc_final: 0.7302 (m110) REVERT: F 84 MET cc_start: 0.5746 (mtt) cc_final: 0.5188 (mtt) REVERT: F 210 TYR cc_start: 0.7562 (p90) cc_final: 0.5286 (t80) REVERT: F 267 ILE cc_start: 0.7302 (pt) cc_final: 0.7087 (pt) REVERT: G 212 LEU cc_start: 0.8562 (tp) cc_final: 0.8318 (tt) REVERT: G 214 TYR cc_start: 0.8666 (OUTLIER) cc_final: 0.8171 (m-10) REVERT: G 216 GLN cc_start: 0.8084 (mm110) cc_final: 0.7617 (mp10) REVERT: G 467 ARG cc_start: 0.5816 (tpm170) cc_final: 0.4822 (tpp-160) REVERT: H 172 ASP cc_start: 0.7068 (t0) cc_final: 0.6809 (t0) REVERT: J 183 MET cc_start: 0.8035 (mtp) cc_final: 0.7658 (ttt) outliers start: 8 outliers final: 5 residues processed: 373 average time/residue: 0.1844 time to fit residues: 109.3057 Evaluate side-chains 254 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 248 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain G residue 214 TYR Chi-restraints excluded: chain G residue 394 VAL Chi-restraints excluded: chain J residue 133 ASP Chi-restraints excluded: chain J residue 400 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.4980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 40.0000 chunk 298 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 ASN B 214 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 HIS C 252 HIS C 261 HIS D 97 HIS D 125 HIS D 158 HIS ** D 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 HIS E 274 ASN F 60 GLN ** F 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN F 283 ASN G 166 GLN G 189 GLN G 213 GLN G 254 ASN G 265 GLN G 325 GLN G 430 HIS G 455 ASN G 479 HIS H 194 GLN H 216 GLN H 265 GLN H 274 HIS H 430 HIS I 214 HIS ** I 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 255 GLN ** I 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 388 ASN J 44 GLN ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 158 ASN J 279 ASN ** J 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.114491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.096619 restraints weight = 62493.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.096026 restraints weight = 70215.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.097087 restraints weight = 62133.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.097381 restraints weight = 44905.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.098122 restraints weight = 40290.236| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 28867 Z= 0.146 Angle : 0.668 9.480 39225 Z= 0.346 Chirality : 0.046 0.181 4657 Planarity : 0.005 0.069 5083 Dihedral : 5.907 54.149 4099 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.75 % Favored : 91.22 % Rotamer: Outliers : 2.24 % Allowed : 16.32 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.44 % 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: -3.72 (0.12), residues: 3771 helix: -0.95 (0.13), residues: 1405 sheet: -3.73 (0.20), residues: 414 loop : -3.45 (0.12), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 171 TYR 0.015 0.002 TYR G 324 PHE 0.019 0.002 PHE E 48 TRP 0.013 0.001 TRP E 282 HIS 0.005 0.001 HIS B 128 Details of bonding type rmsd covalent geometry : bond 0.00338 (28867) covalent geometry : angle 0.66764 (39225) hydrogen bonds : bond 0.04116 ( 1100) hydrogen bonds : angle 5.15547 ( 3117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 312 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 MET cc_start: 0.7313 (mmp) cc_final: 0.6380 (mmp) REVERT: B 223 ASN cc_start: 0.8272 (m-40) cc_final: 0.8027 (m-40) REVERT: B 244 GLN cc_start: 0.7686 (tp40) cc_final: 0.7369 (tp40) REVERT: C 34 MET cc_start: 0.7510 (mtm) cc_final: 0.7181 (mtm) REVERT: C 271 MET cc_start: 0.8270 (ttp) cc_final: 0.7918 (ttp) REVERT: C 340 MET cc_start: 0.8107 (tmm) cc_final: 0.7796 (tmm) REVERT: D 259 LYS cc_start: 0.8371 (ttpp) cc_final: 0.7968 (tptt) REVERT: E 69 MET cc_start: 0.6582 (tmm) cc_final: 0.5929 (tmm) REVERT: F 210 TYR cc_start: 0.7368 (p90) cc_final: 0.5189 (t80) REVERT: G 376 LEU cc_start: 0.8991 (mt) cc_final: 0.8753 (mt) REVERT: G 386 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7607 (pp) REVERT: G 467 ARG cc_start: 0.5571 (tpm170) cc_final: 0.4735 (tpp-160) REVERT: H 499 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8113 (mm) REVERT: I 285 ASN cc_start: 0.7730 (OUTLIER) cc_final: 0.7524 (t0) REVERT: J 173 LYS cc_start: 0.6716 (ptmm) cc_final: 0.6174 (tptp) REVERT: J 183 MET cc_start: 0.8104 (mtp) cc_final: 0.7631 (ttt) REVERT: J 224 PHE cc_start: 0.8010 (m-80) cc_final: 0.7316 (m-80) REVERT: J 305 MET cc_start: 0.7997 (ttm) cc_final: 0.7729 (ttt) outliers start: 64 outliers final: 27 residues processed: 353 average time/residue: 0.1515 time to fit residues: 90.8337 Evaluate side-chains 295 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 265 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 203 HIS Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain G residue 166 GLN Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 394 VAL Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain G residue 435 LEU Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 220 SER Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 499 LEU Chi-restraints excluded: chain I residue 285 ASN Chi-restraints excluded: chain J residue 203 VAL Chi-restraints excluded: chain J residue 236 ASP Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 342 ILE Chi-restraints excluded: chain J residue 400 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 150 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 352 optimal weight: 8.9990 chunk 327 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 303 optimal weight: 1.9990 chunk 266 optimal weight: 0.7980 chunk 162 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 281 optimal weight: 0.0030 chunk 122 optimal weight: 8.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 ASN B 13 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 HIS C 277 GLN D 125 HIS ** D 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 236 GLN E 274 ASN F 236 GLN F 274 ASN ** G 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 265 GLN ** I 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 359 ASN I 376 ASN ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 341 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.116295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.098222 restraints weight = 62267.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.098060 restraints weight = 65373.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.099461 restraints weight = 57119.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.099362 restraints weight = 37884.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.099620 restraints weight = 36491.993| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28867 Z= 0.125 Angle : 0.615 7.620 39225 Z= 0.317 Chirality : 0.045 0.154 4657 Planarity : 0.005 0.063 5083 Dihedral : 5.453 55.853 4093 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 2.42 % Allowed : 19.57 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.93 (0.13), residues: 3771 helix: -0.17 (0.14), residues: 1393 sheet: -3.43 (0.21), residues: 416 loop : -3.05 (0.13), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 170 TYR 0.014 0.001 TYR A 185 PHE 0.020 0.001 PHE C 177 TRP 0.014 0.001 TRP E 37 HIS 0.005 0.001 HIS A 116 Details of bonding type rmsd covalent geometry : bond 0.00284 (28867) covalent geometry : angle 0.61470 (39225) hydrogen bonds : bond 0.03634 ( 1100) hydrogen bonds : angle 4.75944 ( 3117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 307 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 MET cc_start: 0.7387 (mmp) cc_final: 0.6358 (mmp) REVERT: B 223 ASN cc_start: 0.8070 (m110) cc_final: 0.7824 (m-40) REVERT: B 244 GLN cc_start: 0.7535 (tp40) cc_final: 0.7214 (tp40) REVERT: C 18 PHE cc_start: 0.8393 (t80) cc_final: 0.7972 (t80) REVERT: C 34 MET cc_start: 0.7665 (mtm) cc_final: 0.7094 (mtm) REVERT: C 128 GLN cc_start: 0.7690 (pm20) cc_final: 0.7188 (pp30) REVERT: C 148 MET cc_start: 0.7900 (ttm) cc_final: 0.7638 (ttm) REVERT: C 271 MET cc_start: 0.8207 (ttp) cc_final: 0.7896 (ttp) REVERT: C 286 HIS cc_start: 0.7452 (OUTLIER) cc_final: 0.7216 (m-70) REVERT: C 340 MET cc_start: 0.8024 (tmm) cc_final: 0.7721 (tmm) REVERT: D 229 VAL cc_start: 0.8145 (t) cc_final: 0.7888 (m) REVERT: E 69 MET cc_start: 0.6576 (tmm) cc_final: 0.6039 (tmm) REVERT: E 203 HIS cc_start: 0.6978 (OUTLIER) cc_final: 0.6099 (m-70) REVERT: E 290 TRP cc_start: 0.7139 (t60) cc_final: 0.6824 (p90) REVERT: F 36 ILE cc_start: 0.7244 (mp) cc_final: 0.6547 (mm) REVERT: F 210 TYR cc_start: 0.7285 (p90) cc_final: 0.5067 (t80) REVERT: G 376 LEU cc_start: 0.9012 (mt) cc_final: 0.8783 (mt) REVERT: G 467 ARG cc_start: 0.5659 (tpm170) cc_final: 0.4850 (tpp-160) REVERT: H 207 MET cc_start: 0.7765 (mmp) cc_final: 0.7300 (mmp) REVERT: H 490 ASP cc_start: 0.6917 (t0) cc_final: 0.6716 (t70) REVERT: J 173 LYS cc_start: 0.6827 (ptmm) cc_final: 0.6359 (tptp) REVERT: J 224 PHE cc_start: 0.8024 (m-80) cc_final: 0.7388 (m-80) REVERT: J 289 MET cc_start: 0.7541 (tmm) cc_final: 0.6863 (tmm) REVERT: J 305 MET cc_start: 0.8053 (ttm) cc_final: 0.7828 (ttt) outliers start: 69 outliers final: 33 residues processed: 359 average time/residue: 0.1568 time to fit residues: 95.3507 Evaluate side-chains 305 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 270 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 203 HIS Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 292 ASP Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 394 VAL Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain H residue 220 SER Chi-restraints excluded: chain H residue 287 VAL Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain I residue 191 SER Chi-restraints excluded: chain I residue 377 SER Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 203 VAL Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 400 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 42 optimal weight: 0.9990 chunk 251 optimal weight: 0.0270 chunk 222 optimal weight: 0.7980 chunk 87 optimal weight: 0.0870 chunk 6 optimal weight: 6.9990 chunk 224 optimal weight: 10.0000 chunk 211 optimal weight: 0.6980 chunk 283 optimal weight: 0.8980 chunk 237 optimal weight: 0.9990 chunk 339 optimal weight: 4.9990 chunk 219 optimal weight: 1.9990 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 ASN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 HIS ** D 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN H 213 GLN ** I 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 285 ASN I 304 HIS I 410 GLN ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 393 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.116921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.099386 restraints weight = 61897.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.099451 restraints weight = 60093.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.100298 restraints weight = 56218.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.100417 restraints weight = 38380.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.100646 restraints weight = 36363.615| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28867 Z= 0.120 Angle : 0.599 8.223 39225 Z= 0.305 Chirality : 0.044 0.147 4657 Planarity : 0.004 0.064 5083 Dihedral : 5.225 55.809 4093 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 2.98 % Allowed : 21.22 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.13), residues: 3771 helix: 0.24 (0.14), residues: 1388 sheet: -3.18 (0.22), residues: 415 loop : -2.79 (0.13), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 225 TYR 0.015 0.001 TYR A 185 PHE 0.027 0.001 PHE G 443 TRP 0.014 0.001 TRP E 37 HIS 0.008 0.001 HIS I 192 Details of bonding type rmsd covalent geometry : bond 0.00271 (28867) covalent geometry : angle 0.59866 (39225) hydrogen bonds : bond 0.03411 ( 1100) hydrogen bonds : angle 4.54732 ( 3117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 301 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 MET cc_start: 0.7499 (mmp) cc_final: 0.6903 (mmp) REVERT: B 223 ASN cc_start: 0.8081 (m110) cc_final: 0.7773 (m-40) REVERT: B 244 GLN cc_start: 0.7480 (tp40) cc_final: 0.7217 (tp40) REVERT: B 304 TYR cc_start: 0.7496 (OUTLIER) cc_final: 0.5896 (m-10) REVERT: C 18 PHE cc_start: 0.8358 (t80) cc_final: 0.7898 (t80) REVERT: C 34 MET cc_start: 0.7559 (mtm) cc_final: 0.7047 (mtm) REVERT: C 68 MET cc_start: 0.8038 (mtp) cc_final: 0.7732 (mtm) REVERT: C 128 GLN cc_start: 0.7703 (pm20) cc_final: 0.7408 (pp30) REVERT: C 271 MET cc_start: 0.8204 (ttp) cc_final: 0.7900 (ttp) REVERT: C 286 HIS cc_start: 0.7571 (OUTLIER) cc_final: 0.7323 (m-70) REVERT: C 340 MET cc_start: 0.8008 (tmm) cc_final: 0.7664 (tmm) REVERT: D 278 PHE cc_start: 0.7990 (m-80) cc_final: 0.7784 (m-10) REVERT: E 44 GLU cc_start: 0.6569 (mm-30) cc_final: 0.6293 (mm-30) REVERT: E 69 MET cc_start: 0.6552 (tmm) cc_final: 0.6320 (tmm) REVERT: E 124 TYR cc_start: 0.7543 (m-10) cc_final: 0.7193 (m-10) REVERT: E 132 MET cc_start: 0.7664 (mmm) cc_final: 0.7253 (mmm) REVERT: E 170 MET cc_start: 0.4282 (ppp) cc_final: 0.3904 (ppp) REVERT: E 216 MET cc_start: 0.7217 (tmm) cc_final: 0.6822 (tmm) REVERT: E 273 LEU cc_start: 0.3472 (OUTLIER) cc_final: 0.2821 (tt) REVERT: E 290 TRP cc_start: 0.7132 (t60) cc_final: 0.6837 (p90) REVERT: F 36 ILE cc_start: 0.7127 (mp) cc_final: 0.6502 (mm) REVERT: F 210 TYR cc_start: 0.7242 (p90) cc_final: 0.4952 (t80) REVERT: G 255 LYS cc_start: 0.8412 (mmtp) cc_final: 0.8050 (tptt) REVERT: G 362 ASP cc_start: 0.8387 (t0) cc_final: 0.7972 (m-30) REVERT: G 376 LEU cc_start: 0.9011 (mt) cc_final: 0.8752 (mt) REVERT: G 467 ARG cc_start: 0.5658 (tpm170) cc_final: 0.4780 (tpp-160) REVERT: H 207 MET cc_start: 0.7672 (mmp) cc_final: 0.7330 (mmp) REVERT: H 499 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8251 (mm) REVERT: I 250 SER cc_start: 0.5558 (m) cc_final: 0.5206 (t) REVERT: J 173 LYS cc_start: 0.6929 (ptmm) cc_final: 0.6427 (tptp) REVERT: J 224 PHE cc_start: 0.8010 (m-80) cc_final: 0.7402 (m-80) REVERT: J 289 MET cc_start: 0.7430 (tmm) cc_final: 0.6886 (tmm) REVERT: J 305 MET cc_start: 0.7993 (ttm) cc_final: 0.7771 (ttt) outliers start: 85 outliers final: 47 residues processed: 364 average time/residue: 0.1602 time to fit residues: 98.1040 Evaluate side-chains 316 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 265 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 304 TYR Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 119 ASP Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 394 VAL Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain H residue 195 PHE Chi-restraints excluded: chain H residue 287 VAL Chi-restraints excluded: chain H residue 308 VAL Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 449 THR Chi-restraints excluded: chain H residue 499 LEU Chi-restraints excluded: chain I residue 43 LEU Chi-restraints excluded: chain I residue 191 SER Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain I residue 377 SER Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 203 VAL Chi-restraints excluded: chain J residue 279 ASN Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 342 ILE Chi-restraints excluded: chain J residue 393 GLN Chi-restraints excluded: chain J residue 400 VAL Chi-restraints excluded: chain J residue 421 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 12 optimal weight: 2.9990 chunk 53 optimal weight: 0.0170 chunk 331 optimal weight: 0.0970 chunk 215 optimal weight: 0.9990 chunk 246 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 197 optimal weight: 0.2980 chunk 351 optimal weight: 20.0000 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 ASN B 13 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 HIS ** D 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN G 411 ASN H 213 GLN ** I 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 384 HIS ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.116798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.099157 restraints weight = 61987.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.099044 restraints weight = 60849.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.099976 restraints weight = 57510.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.100132 restraints weight = 39774.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.100409 restraints weight = 39118.547| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28867 Z= 0.124 Angle : 0.594 9.283 39225 Z= 0.303 Chirality : 0.044 0.168 4657 Planarity : 0.004 0.064 5083 Dihedral : 5.123 55.252 4093 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 3.47 % Allowed : 22.41 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.14), residues: 3771 helix: 0.35 (0.14), residues: 1402 sheet: -3.04 (0.22), residues: 428 loop : -2.67 (0.13), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 172 TYR 0.018 0.001 TYR E 38 PHE 0.041 0.001 PHE A 72 TRP 0.015 0.001 TRP E 37 HIS 0.005 0.001 HIS I 192 Details of bonding type rmsd covalent geometry : bond 0.00288 (28867) covalent geometry : angle 0.59352 (39225) hydrogen bonds : bond 0.03367 ( 1100) hydrogen bonds : angle 4.46233 ( 3117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 281 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7314 (tt) REVERT: A 164 MET cc_start: 0.8630 (tpt) cc_final: 0.8283 (tpt) REVERT: A 187 MET cc_start: 0.7896 (tpp) cc_final: 0.7110 (tpp) REVERT: B 93 MET cc_start: 0.7479 (mmp) cc_final: 0.6880 (mmp) REVERT: B 223 ASN cc_start: 0.8039 (m110) cc_final: 0.7748 (m-40) REVERT: B 244 GLN cc_start: 0.7528 (tp40) cc_final: 0.7225 (tp40) REVERT: B 304 TYR cc_start: 0.7549 (OUTLIER) cc_final: 0.5964 (m-10) REVERT: C 34 MET cc_start: 0.7573 (mtm) cc_final: 0.7103 (mtm) REVERT: C 68 MET cc_start: 0.8038 (mtp) cc_final: 0.7746 (mtm) REVERT: C 201 HIS cc_start: 0.7363 (OUTLIER) cc_final: 0.6706 (m170) REVERT: C 271 MET cc_start: 0.8203 (ttp) cc_final: 0.7912 (ttp) REVERT: C 286 HIS cc_start: 0.7329 (OUTLIER) cc_final: 0.7083 (m-70) REVERT: C 299 GLU cc_start: 0.8094 (tp30) cc_final: 0.7778 (tp30) REVERT: C 340 MET cc_start: 0.8086 (tmm) cc_final: 0.7735 (tmm) REVERT: D 226 MET cc_start: 0.8854 (tpp) cc_final: 0.8629 (tpp) REVERT: E 69 MET cc_start: 0.6504 (tmm) cc_final: 0.6292 (tmm) REVERT: E 124 TYR cc_start: 0.7409 (m-10) cc_final: 0.7204 (m-10) REVERT: E 131 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8051 (tt) REVERT: E 132 MET cc_start: 0.7917 (mmm) cc_final: 0.7442 (mmm) REVERT: E 170 MET cc_start: 0.4331 (ppp) cc_final: 0.3868 (ppp) REVERT: E 216 MET cc_start: 0.7314 (tmm) cc_final: 0.6894 (tmm) REVERT: E 268 LYS cc_start: 0.6924 (tppt) cc_final: 0.6600 (pttm) REVERT: E 273 LEU cc_start: 0.3492 (OUTLIER) cc_final: 0.2857 (tt) REVERT: F 36 ILE cc_start: 0.7184 (mp) cc_final: 0.6535 (mm) REVERT: F 210 TYR cc_start: 0.7208 (p90) cc_final: 0.4656 (t80) REVERT: G 189 GLN cc_start: 0.8231 (pm20) cc_final: 0.7439 (pp30) REVERT: G 255 LYS cc_start: 0.8413 (mmtp) cc_final: 0.8061 (tptt) REVERT: G 260 MET cc_start: 0.8578 (mmm) cc_final: 0.7966 (mmp) REVERT: G 273 MET cc_start: 0.7188 (mtp) cc_final: 0.6800 (ttp) REVERT: G 376 LEU cc_start: 0.9029 (mt) cc_final: 0.8761 (mt) REVERT: G 467 ARG cc_start: 0.6011 (tpm170) cc_final: 0.5230 (tpp-160) REVERT: H 422 GLN cc_start: 0.7944 (tt0) cc_final: 0.7714 (tt0) REVERT: H 499 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8266 (mm) REVERT: I 250 SER cc_start: 0.5515 (m) cc_final: 0.4803 (t) REVERT: I 289 MET cc_start: 0.7624 (tmm) cc_final: 0.7404 (tmm) REVERT: J 173 LYS cc_start: 0.6898 (ptmm) cc_final: 0.6471 (tptp) REVERT: J 224 PHE cc_start: 0.8008 (m-80) cc_final: 0.7445 (m-80) REVERT: J 289 MET cc_start: 0.7456 (tmm) cc_final: 0.7004 (tmm) REVERT: J 431 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.7963 (pp) outliers start: 99 outliers final: 58 residues processed: 359 average time/residue: 0.1512 time to fit residues: 92.4607 Evaluate side-chains 329 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 263 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 304 TYR Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 119 ASP Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 292 ASP Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 394 VAL Chi-restraints excluded: chain H residue 195 PHE Chi-restraints excluded: chain H residue 220 SER Chi-restraints excluded: chain H residue 287 VAL Chi-restraints excluded: chain H residue 308 VAL Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 449 THR Chi-restraints excluded: chain H residue 499 LEU Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 191 SER Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain I residue 377 SER Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 203 VAL Chi-restraints excluded: chain J residue 279 ASN Chi-restraints excluded: chain J residue 342 ILE Chi-restraints excluded: chain J residue 400 VAL Chi-restraints excluded: chain J residue 421 GLU Chi-restraints excluded: chain J residue 430 VAL Chi-restraints excluded: chain J residue 431 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 37 optimal weight: 0.1980 chunk 35 optimal weight: 5.9990 chunk 139 optimal weight: 7.9990 chunk 227 optimal weight: 0.0170 chunk 345 optimal weight: 0.0970 chunk 342 optimal weight: 0.0070 chunk 252 optimal weight: 0.0170 chunk 1 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 overall best weight: 0.0672 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 ASN B 13 GLN D 125 HIS ** D 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN I 177 ASN ** I 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 285 ASN J 72 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.120648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.101425 restraints weight = 61152.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.101787 restraints weight = 57868.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.102943 restraints weight = 47255.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.103274 restraints weight = 33539.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.103438 restraints weight = 30604.301| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.100 28867 Z= 0.107 Angle : 0.579 9.563 39225 Z= 0.294 Chirality : 0.044 0.161 4657 Planarity : 0.004 0.064 5083 Dihedral : 4.852 55.908 4093 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.91 % Allowed : 23.21 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.44 % 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: -1.93 (0.14), residues: 3771 helix: 0.67 (0.14), residues: 1382 sheet: -2.81 (0.23), residues: 425 loop : -2.47 (0.14), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 286 TYR 0.016 0.001 TYR A 185 PHE 0.031 0.001 PHE D 278 TRP 0.030 0.001 TRP E 290 HIS 0.023 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00235 (28867) covalent geometry : angle 0.57860 (39225) hydrogen bonds : bond 0.03090 ( 1100) hydrogen bonds : angle 4.31878 ( 3117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 315 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 MET cc_start: 0.8532 (tpt) cc_final: 0.8077 (tpt) REVERT: A 187 MET cc_start: 0.7803 (tpp) cc_final: 0.7160 (tpp) REVERT: B 223 ASN cc_start: 0.7933 (m110) cc_final: 0.7653 (m-40) REVERT: B 304 TYR cc_start: 0.7485 (OUTLIER) cc_final: 0.5885 (m-10) REVERT: C 34 MET cc_start: 0.7469 (mtm) cc_final: 0.7208 (mtm) REVERT: C 68 MET cc_start: 0.8378 (mtp) cc_final: 0.8034 (mtm) REVERT: C 128 GLN cc_start: 0.7471 (pm20) cc_final: 0.7118 (pp30) REVERT: C 299 GLU cc_start: 0.8010 (tp30) cc_final: 0.7785 (tp30) REVERT: C 340 MET cc_start: 0.8041 (tmm) cc_final: 0.7619 (tmm) REVERT: E 69 MET cc_start: 0.7007 (tmm) cc_final: 0.6550 (tmm) REVERT: E 132 MET cc_start: 0.7955 (mmm) cc_final: 0.7668 (mmm) REVERT: E 170 MET cc_start: 0.4048 (ppp) cc_final: 0.3639 (ppp) REVERT: F 36 ILE cc_start: 0.7326 (mp) cc_final: 0.6666 (mm) REVERT: F 128 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7863 (tp) REVERT: F 210 TYR cc_start: 0.7123 (p90) cc_final: 0.4424 (t80) REVERT: G 189 GLN cc_start: 0.8264 (pm20) cc_final: 0.7537 (pp30) REVERT: G 255 LYS cc_start: 0.8422 (mmtp) cc_final: 0.8113 (mttm) REVERT: G 260 MET cc_start: 0.8754 (mmm) cc_final: 0.8333 (mmp) REVERT: G 376 LEU cc_start: 0.9081 (mt) cc_final: 0.8824 (mt) REVERT: G 467 ARG cc_start: 0.5759 (tpm170) cc_final: 0.4644 (tpp-160) REVERT: H 207 MET cc_start: 0.7244 (mmp) cc_final: 0.6906 (mmp) REVERT: H 499 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8281 (mm) REVERT: I 250 SER cc_start: 0.4487 (m) cc_final: 0.4197 (t) REVERT: J 122 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8337 (tt) REVERT: J 173 LYS cc_start: 0.7182 (ptmm) cc_final: 0.6724 (tptp) REVERT: J 224 PHE cc_start: 0.7982 (m-80) cc_final: 0.7400 (m-80) REVERT: J 289 MET cc_start: 0.7329 (tmm) cc_final: 0.6853 (tmm) REVERT: J 424 THR cc_start: 0.7851 (OUTLIER) cc_final: 0.7588 (p) REVERT: J 431 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7831 (pp) outliers start: 83 outliers final: 56 residues processed: 378 average time/residue: 0.1524 time to fit residues: 98.4001 Evaluate side-chains 331 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 269 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 304 TYR Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 305 LYS Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 292 ASP Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 335 VAL Chi-restraints excluded: chain G residue 394 VAL Chi-restraints excluded: chain H residue 195 PHE Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 212 LEU Chi-restraints excluded: chain H residue 220 SER Chi-restraints excluded: chain H residue 287 VAL Chi-restraints excluded: chain H residue 308 VAL Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 449 THR Chi-restraints excluded: chain H residue 499 LEU Chi-restraints excluded: chain H residue 518 VAL Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 191 SER Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain I residue 377 SER Chi-restraints excluded: chain I residue 437 VAL Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain J residue 203 VAL Chi-restraints excluded: chain J residue 279 ASN Chi-restraints excluded: chain J residue 342 ILE Chi-restraints excluded: chain J residue 400 VAL Chi-restraints excluded: chain J residue 421 GLU Chi-restraints excluded: chain J residue 424 THR Chi-restraints excluded: chain J residue 431 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 274 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 252 optimal weight: 3.9990 chunk 230 optimal weight: 0.9990 chunk 267 optimal weight: 0.7980 chunk 223 optimal weight: 3.9990 chunk 148 optimal weight: 30.0000 chunk 123 optimal weight: 0.3980 chunk 339 optimal weight: 4.9990 chunk 311 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 HIS A 214 GLN B 13 GLN B 214 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 196 HIS F 274 ASN G 422 GLN ** I 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 197 HIS J 393 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.118210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.098972 restraints weight = 61673.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.099248 restraints weight = 56195.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.100642 restraints weight = 47497.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.100659 restraints weight = 34029.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.100927 restraints weight = 33394.559| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 28867 Z= 0.131 Angle : 0.603 14.483 39225 Z= 0.305 Chirality : 0.045 0.187 4657 Planarity : 0.004 0.064 5083 Dihedral : 4.899 54.136 4093 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.22 % Allowed : 23.91 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.44 % 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: -1.90 (0.14), residues: 3771 helix: 0.69 (0.14), residues: 1389 sheet: -2.78 (0.23), residues: 428 loop : -2.45 (0.14), residues: 1954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 228 TYR 0.016 0.001 TYR F 205 PHE 0.023 0.001 PHE C 177 TRP 0.027 0.002 TRP E 290 HIS 0.016 0.001 HIS D 125 Details of bonding type rmsd covalent geometry : bond 0.00309 (28867) covalent geometry : angle 0.60281 (39225) hydrogen bonds : bond 0.03230 ( 1100) hydrogen bonds : angle 4.31218 ( 3117) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 281 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7502 (tt) REVERT: A 187 MET cc_start: 0.7871 (tpp) cc_final: 0.7167 (tpp) REVERT: B 14 MET cc_start: 0.6880 (tpp) cc_final: 0.5897 (ttt) REVERT: B 223 ASN cc_start: 0.7980 (m110) cc_final: 0.7681 (m-40) REVERT: B 304 TYR cc_start: 0.7509 (OUTLIER) cc_final: 0.5935 (m-10) REVERT: C 34 MET cc_start: 0.7702 (mtm) cc_final: 0.7377 (mtm) REVERT: C 38 THR cc_start: 0.8826 (p) cc_final: 0.8558 (t) REVERT: C 68 MET cc_start: 0.8047 (mtp) cc_final: 0.7803 (mtm) REVERT: C 271 MET cc_start: 0.8073 (ptm) cc_final: 0.7820 (ptm) REVERT: C 286 HIS cc_start: 0.7577 (OUTLIER) cc_final: 0.7368 (m-70) REVERT: C 340 MET cc_start: 0.8057 (tmm) cc_final: 0.7702 (tmm) REVERT: D 226 MET cc_start: 0.8532 (tpp) cc_final: 0.8228 (tpt) REVERT: E 69 MET cc_start: 0.6908 (tmm) cc_final: 0.6341 (tmm) REVERT: E 170 MET cc_start: 0.4247 (ppp) cc_final: 0.3708 (ppp) REVERT: E 268 LYS cc_start: 0.6987 (tppt) cc_final: 0.6575 (pttm) REVERT: F 36 ILE cc_start: 0.7406 (mp) cc_final: 0.6740 (mm) REVERT: F 128 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7863 (tp) REVERT: F 210 TYR cc_start: 0.7091 (p90) cc_final: 0.4363 (t80) REVERT: G 255 LYS cc_start: 0.8434 (mmtp) cc_final: 0.8087 (mttm) REVERT: G 273 MET cc_start: 0.7299 (mtp) cc_final: 0.6863 (ttp) REVERT: G 362 ASP cc_start: 0.8384 (t0) cc_final: 0.7935 (m-30) REVERT: G 467 ARG cc_start: 0.6044 (tpm170) cc_final: 0.5035 (tpp-160) REVERT: H 499 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8334 (mm) REVERT: I 250 SER cc_start: 0.4586 (m) cc_final: 0.3929 (t) REVERT: J 173 LYS cc_start: 0.7143 (ptmm) cc_final: 0.6658 (tptp) REVERT: J 224 PHE cc_start: 0.8026 (m-80) cc_final: 0.7463 (m-80) REVERT: J 289 MET cc_start: 0.7517 (tmm) cc_final: 0.7063 (tmm) REVERT: J 424 THR cc_start: 0.7883 (OUTLIER) cc_final: 0.7630 (p) REVERT: J 431 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8000 (pp) outliers start: 92 outliers final: 64 residues processed: 351 average time/residue: 0.1513 time to fit residues: 91.2970 Evaluate side-chains 335 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 264 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 MET Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 304 TYR Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 305 LYS Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 292 ASP Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 394 VAL Chi-restraints excluded: chain H residue 195 PHE Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 212 LEU Chi-restraints excluded: chain H residue 220 SER Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 287 VAL Chi-restraints excluded: chain H residue 308 VAL Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 449 THR Chi-restraints excluded: chain H residue 499 LEU Chi-restraints excluded: chain H residue 518 VAL Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 191 SER Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain I residue 377 SER Chi-restraints excluded: chain I residue 437 VAL Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 147 ASP Chi-restraints excluded: chain J residue 203 VAL Chi-restraints excluded: chain J residue 279 ASN Chi-restraints excluded: chain J residue 342 ILE Chi-restraints excluded: chain J residue 400 VAL Chi-restraints excluded: chain J residue 424 THR Chi-restraints excluded: chain J residue 431 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 242 optimal weight: 4.9990 chunk 159 optimal weight: 0.0040 chunk 356 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 275 optimal weight: 3.9990 chunk 253 optimal weight: 0.7980 chunk 327 optimal weight: 0.6980 chunk 10 optimal weight: 0.3980 chunk 177 optimal weight: 0.3980 chunk 353 optimal weight: 5.9990 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN B 13 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 HIS ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN ** I 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 197 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.119500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.100281 restraints weight = 61688.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.100384 restraints weight = 56747.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.101783 restraints weight = 50134.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.101998 restraints weight = 33634.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.102185 restraints weight = 31195.025| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 28867 Z= 0.113 Angle : 0.600 13.007 39225 Z= 0.300 Chirality : 0.044 0.158 4657 Planarity : 0.004 0.064 5083 Dihedral : 4.803 53.508 4093 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.87 % Allowed : 24.47 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.44 % 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: -1.77 (0.14), residues: 3771 helix: 0.79 (0.14), residues: 1388 sheet: -2.64 (0.23), residues: 422 loop : -2.38 (0.14), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 269 TYR 0.014 0.001 TYR B 185 PHE 0.023 0.001 PHE D 223 TRP 0.035 0.001 TRP E 290 HIS 0.004 0.001 HIS J 192 Details of bonding type rmsd covalent geometry : bond 0.00263 (28867) covalent geometry : angle 0.59967 (39225) hydrogen bonds : bond 0.03073 ( 1100) hydrogen bonds : angle 4.28159 ( 3117) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 293 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7510 (tt) REVERT: A 164 MET cc_start: 0.8524 (tpt) cc_final: 0.8120 (tpt) REVERT: A 187 MET cc_start: 0.7780 (tpp) cc_final: 0.7028 (tpp) REVERT: B 14 MET cc_start: 0.7028 (tpp) cc_final: 0.5624 (ttt) REVERT: B 223 ASN cc_start: 0.7945 (m110) cc_final: 0.7647 (m-40) REVERT: B 304 TYR cc_start: 0.7472 (OUTLIER) cc_final: 0.5933 (m-10) REVERT: C 34 MET cc_start: 0.7659 (mtm) cc_final: 0.7253 (mtm) REVERT: C 37 GLU cc_start: 0.7274 (tm-30) cc_final: 0.7064 (tp30) REVERT: C 38 THR cc_start: 0.8751 (p) cc_final: 0.8396 (t) REVERT: C 68 MET cc_start: 0.8038 (mtp) cc_final: 0.7772 (mtm) REVERT: C 128 GLN cc_start: 0.7538 (pm20) cc_final: 0.7147 (pp30) REVERT: C 271 MET cc_start: 0.8037 (ptm) cc_final: 0.7773 (ptm) REVERT: C 299 GLU cc_start: 0.8173 (tp30) cc_final: 0.7909 (tp30) REVERT: C 340 MET cc_start: 0.8035 (tmm) cc_final: 0.7658 (tmm) REVERT: D 226 MET cc_start: 0.8503 (tpp) cc_final: 0.8233 (tpt) REVERT: D 340 MET cc_start: 0.7824 (mmp) cc_final: 0.7537 (mmp) REVERT: E 69 MET cc_start: 0.6910 (tmm) cc_final: 0.6246 (tmm) REVERT: E 132 MET cc_start: 0.7659 (mmm) cc_final: 0.7125 (mmm) REVERT: E 170 MET cc_start: 0.4233 (ppp) cc_final: 0.3655 (ppp) REVERT: E 268 LYS cc_start: 0.7167 (tppt) cc_final: 0.6752 (pttm) REVERT: F 36 ILE cc_start: 0.7332 (mp) cc_final: 0.6649 (mm) REVERT: F 128 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7843 (tp) REVERT: F 210 TYR cc_start: 0.7024 (p90) cc_final: 0.4319 (t80) REVERT: F 211 ILE cc_start: 0.7732 (OUTLIER) cc_final: 0.7239 (tp) REVERT: G 255 LYS cc_start: 0.8399 (mmtp) cc_final: 0.8054 (mttm) REVERT: G 260 MET cc_start: 0.8698 (mmm) cc_final: 0.8318 (mmp) REVERT: G 273 MET cc_start: 0.7275 (mtp) cc_final: 0.6738 (ttp) REVERT: H 207 MET cc_start: 0.7488 (mmp) cc_final: 0.7133 (mmp) REVERT: H 499 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8315 (mm) REVERT: J 173 LYS cc_start: 0.7178 (ptmm) cc_final: 0.6740 (tptp) REVERT: J 224 PHE cc_start: 0.8001 (m-80) cc_final: 0.7316 (m-80) REVERT: J 289 MET cc_start: 0.7429 (tmm) cc_final: 0.7120 (tmm) REVERT: J 424 THR cc_start: 0.7873 (OUTLIER) cc_final: 0.7622 (p) REVERT: J 431 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7957 (pp) REVERT: K 63 ARG cc_start: 0.6613 (mtp-110) cc_final: 0.6176 (mmp-170) outliers start: 82 outliers final: 64 residues processed: 358 average time/residue: 0.1464 time to fit residues: 90.3324 Evaluate side-chains 343 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 272 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 MET Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 304 TYR Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 292 ASP Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 394 VAL Chi-restraints excluded: chain G residue 499 LEU Chi-restraints excluded: chain H residue 195 PHE Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 212 LEU Chi-restraints excluded: chain H residue 220 SER Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 287 VAL Chi-restraints excluded: chain H residue 308 VAL Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 449 THR Chi-restraints excluded: chain H residue 499 LEU Chi-restraints excluded: chain H residue 518 VAL Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 191 SER Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain I residue 377 SER Chi-restraints excluded: chain I residue 437 VAL Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 203 VAL Chi-restraints excluded: chain J residue 279 ASN Chi-restraints excluded: chain J residue 342 ILE Chi-restraints excluded: chain J residue 400 VAL Chi-restraints excluded: chain J residue 421 GLU Chi-restraints excluded: chain J residue 424 THR Chi-restraints excluded: chain J residue 431 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 310 optimal weight: 0.4980 chunk 288 optimal weight: 8.9990 chunk 291 optimal weight: 4.9990 chunk 328 optimal weight: 1.9990 chunk 146 optimal weight: 30.0000 chunk 284 optimal weight: 2.9990 chunk 316 optimal weight: 0.0030 chunk 201 optimal weight: 0.3980 chunk 36 optimal weight: 2.9990 chunk 31 optimal weight: 0.3980 chunk 144 optimal weight: 6.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 ASN ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN H 422 GLN ** I 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 197 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.118941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.099620 restraints weight = 61435.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.099516 restraints weight = 59832.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.101253 restraints weight = 51036.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.101260 restraints weight = 34206.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.101634 restraints weight = 32024.321| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 28867 Z= 0.123 Angle : 0.606 11.543 39225 Z= 0.303 Chirality : 0.044 0.165 4657 Planarity : 0.004 0.067 5083 Dihedral : 4.801 52.055 4093 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.91 % Allowed : 24.58 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.14), residues: 3771 helix: 0.82 (0.14), residues: 1393 sheet: -2.61 (0.23), residues: 424 loop : -2.32 (0.14), residues: 1954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 269 TYR 0.034 0.001 TYR F 94 PHE 0.022 0.001 PHE C 177 TRP 0.035 0.001 TRP E 290 HIS 0.008 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00290 (28867) covalent geometry : angle 0.60604 (39225) hydrogen bonds : bond 0.03113 ( 1100) hydrogen bonds : angle 4.26044 ( 3117) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 270 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6285 (tpt) cc_final: 0.5227 (ptt) REVERT: A 101 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7513 (tt) REVERT: A 164 MET cc_start: 0.8502 (tpt) cc_final: 0.8124 (tpt) REVERT: A 187 MET cc_start: 0.7822 (tpp) cc_final: 0.7097 (tpp) REVERT: B 14 MET cc_start: 0.6874 (tpp) cc_final: 0.5812 (ttt) REVERT: B 223 ASN cc_start: 0.8049 (m110) cc_final: 0.7774 (m-40) REVERT: B 304 TYR cc_start: 0.7494 (OUTLIER) cc_final: 0.5908 (m-10) REVERT: C 34 MET cc_start: 0.7682 (mtm) cc_final: 0.7263 (mtm) REVERT: C 38 THR cc_start: 0.8737 (p) cc_final: 0.8431 (t) REVERT: C 68 MET cc_start: 0.8061 (mtp) cc_final: 0.7831 (mtm) REVERT: C 128 GLN cc_start: 0.7573 (pm20) cc_final: 0.7172 (pp30) REVERT: C 271 MET cc_start: 0.8053 (ptm) cc_final: 0.7795 (ptm) REVERT: C 286 HIS cc_start: 0.7736 (OUTLIER) cc_final: 0.7523 (m-70) REVERT: C 299 GLU cc_start: 0.8099 (tp30) cc_final: 0.7793 (tp30) REVERT: C 340 MET cc_start: 0.8076 (tmm) cc_final: 0.7707 (tmm) REVERT: D 226 MET cc_start: 0.8609 (tpp) cc_final: 0.8224 (tpt) REVERT: E 37 TRP cc_start: 0.7967 (t60) cc_final: 0.7399 (t-100) REVERT: E 69 MET cc_start: 0.6967 (tmm) cc_final: 0.6110 (tmm) REVERT: E 132 MET cc_start: 0.7837 (mmm) cc_final: 0.7332 (mmm) REVERT: E 170 MET cc_start: 0.4238 (ppp) cc_final: 0.3725 (ppp) REVERT: E 268 LYS cc_start: 0.7163 (tppt) cc_final: 0.6750 (pttm) REVERT: E 273 LEU cc_start: 0.2866 (OUTLIER) cc_final: 0.2203 (tp) REVERT: F 36 ILE cc_start: 0.7355 (mp) cc_final: 0.6662 (mm) REVERT: F 128 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7851 (tp) REVERT: F 210 TYR cc_start: 0.7042 (p90) cc_final: 0.4304 (t80) REVERT: F 211 ILE cc_start: 0.7781 (OUTLIER) cc_final: 0.7226 (tp) REVERT: F 216 MET cc_start: 0.8460 (mtm) cc_final: 0.7870 (mtm) REVERT: G 255 LYS cc_start: 0.8414 (mmtp) cc_final: 0.8071 (mttm) REVERT: G 260 MET cc_start: 0.8669 (mmm) cc_final: 0.8272 (mmp) REVERT: G 273 MET cc_start: 0.7320 (mtp) cc_final: 0.6789 (ttp) REVERT: H 438 CYS cc_start: 0.8514 (t) cc_final: 0.7943 (t) REVERT: H 459 ASP cc_start: 0.7455 (t70) cc_final: 0.7159 (t0) REVERT: H 499 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8355 (mm) REVERT: J 122 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8302 (tt) REVERT: J 173 LYS cc_start: 0.7138 (ptmm) cc_final: 0.6743 (tptp) REVERT: J 224 PHE cc_start: 0.8074 (m-80) cc_final: 0.7409 (m-80) REVERT: J 289 MET cc_start: 0.7575 (tmm) cc_final: 0.7216 (tmm) REVERT: J 424 THR cc_start: 0.7854 (OUTLIER) cc_final: 0.7596 (p) REVERT: J 431 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7960 (pp) outliers start: 83 outliers final: 67 residues processed: 337 average time/residue: 0.1441 time to fit residues: 84.3564 Evaluate side-chains 332 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 255 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 304 TYR Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 292 ASP Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 394 VAL Chi-restraints excluded: chain G residue 499 LEU Chi-restraints excluded: chain H residue 195 PHE Chi-restraints excluded: chain H residue 212 LEU Chi-restraints excluded: chain H residue 220 SER Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 287 VAL Chi-restraints excluded: chain H residue 308 VAL Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 422 GLN Chi-restraints excluded: chain H residue 449 THR Chi-restraints excluded: chain H residue 499 LEU Chi-restraints excluded: chain H residue 518 VAL Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 191 SER Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain I residue 377 SER Chi-restraints excluded: chain I residue 437 VAL Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain J residue 203 VAL Chi-restraints excluded: chain J residue 279 ASN Chi-restraints excluded: chain J residue 342 ILE Chi-restraints excluded: chain J residue 354 SER Chi-restraints excluded: chain J residue 400 VAL Chi-restraints excluded: chain J residue 421 GLU Chi-restraints excluded: chain J residue 424 THR Chi-restraints excluded: chain J residue 431 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 316 optimal weight: 0.8980 chunk 211 optimal weight: 0.0570 chunk 262 optimal weight: 0.8980 chunk 222 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 188 optimal weight: 40.0000 chunk 27 optimal weight: 0.6980 chunk 237 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 358 optimal weight: 9.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN H 422 GLN ** I 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 197 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.118958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.099527 restraints weight = 61089.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.099667 restraints weight = 57564.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.101007 restraints weight = 46961.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.101380 restraints weight = 33871.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.101618 restraints weight = 32767.638| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 28867 Z= 0.125 Angle : 0.618 13.949 39225 Z= 0.308 Chirality : 0.044 0.164 4657 Planarity : 0.004 0.070 5083 Dihedral : 4.804 51.640 4093 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 3.12 % Allowed : 24.79 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.44 % 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: -1.64 (0.14), residues: 3771 helix: 0.82 (0.14), residues: 1393 sheet: -2.53 (0.24), residues: 423 loop : -2.26 (0.14), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 269 TYR 0.029 0.001 TYR F 94 PHE 0.025 0.001 PHE D 223 TRP 0.037 0.001 TRP E 290 HIS 0.007 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00295 (28867) covalent geometry : angle 0.61791 (39225) hydrogen bonds : bond 0.03082 ( 1100) hydrogen bonds : angle 4.26676 ( 3117) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 261 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7546 (tt) REVERT: A 164 MET cc_start: 0.8502 (tpt) cc_final: 0.8131 (tpt) REVERT: A 187 MET cc_start: 0.7827 (tpp) cc_final: 0.7089 (tpp) REVERT: A 287 ASP cc_start: 0.6777 (p0) cc_final: 0.6016 (t0) REVERT: B 14 MET cc_start: 0.6805 (tpp) cc_final: 0.5756 (ttt) REVERT: B 223 ASN cc_start: 0.8061 (m110) cc_final: 0.7791 (m-40) REVERT: B 304 TYR cc_start: 0.7508 (OUTLIER) cc_final: 0.5907 (m-10) REVERT: C 34 MET cc_start: 0.7625 (mtm) cc_final: 0.7241 (mtm) REVERT: C 38 THR cc_start: 0.8699 (p) cc_final: 0.8408 (t) REVERT: C 68 MET cc_start: 0.8051 (mtp) cc_final: 0.7824 (mtm) REVERT: C 271 MET cc_start: 0.8052 (ptm) cc_final: 0.7796 (ptm) REVERT: C 286 HIS cc_start: 0.7762 (OUTLIER) cc_final: 0.7547 (m-70) REVERT: C 299 GLU cc_start: 0.8144 (tp30) cc_final: 0.7774 (tp30) REVERT: C 340 MET cc_start: 0.8097 (tmm) cc_final: 0.7704 (tmm) REVERT: D 226 MET cc_start: 0.8547 (tpp) cc_final: 0.8201 (tpt) REVERT: E 37 TRP cc_start: 0.7930 (t60) cc_final: 0.7343 (t-100) REVERT: E 69 MET cc_start: 0.7001 (tmm) cc_final: 0.6321 (tmm) REVERT: E 131 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8405 (tt) REVERT: E 132 MET cc_start: 0.7875 (mmm) cc_final: 0.7339 (mmm) REVERT: E 170 MET cc_start: 0.4278 (ppp) cc_final: 0.3810 (ppp) REVERT: E 268 LYS cc_start: 0.7141 (tppt) cc_final: 0.6709 (pttm) REVERT: E 273 LEU cc_start: 0.2897 (OUTLIER) cc_final: 0.2142 (tp) REVERT: F 36 ILE cc_start: 0.7330 (mp) cc_final: 0.6648 (mm) REVERT: F 210 TYR cc_start: 0.7079 (p90) cc_final: 0.4243 (t80) REVERT: F 211 ILE cc_start: 0.7780 (OUTLIER) cc_final: 0.7212 (tp) REVERT: G 255 LYS cc_start: 0.8400 (mmtp) cc_final: 0.7975 (tptt) REVERT: G 273 MET cc_start: 0.7307 (mtp) cc_final: 0.6815 (ttp) REVERT: H 207 MET cc_start: 0.7651 (mmp) cc_final: 0.7189 (mmp) REVERT: H 438 CYS cc_start: 0.8525 (t) cc_final: 0.7939 (t) REVERT: H 499 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8330 (mm) REVERT: J 122 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8296 (tt) REVERT: J 173 LYS cc_start: 0.7103 (ptmm) cc_final: 0.6738 (tptp) REVERT: J 224 PHE cc_start: 0.8069 (m-80) cc_final: 0.7415 (m-80) REVERT: J 289 MET cc_start: 0.7371 (tmm) cc_final: 0.7051 (tmm) REVERT: J 424 THR cc_start: 0.7865 (OUTLIER) cc_final: 0.7614 (p) REVERT: J 431 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7995 (pp) outliers start: 89 outliers final: 70 residues processed: 330 average time/residue: 0.1497 time to fit residues: 85.7534 Evaluate side-chains 339 residues out of total 3352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 259 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 304 TYR Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 272 THR Chi-restraints excluded: chain F residue 292 ASP Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 394 VAL Chi-restraints excluded: chain G residue 499 LEU Chi-restraints excluded: chain H residue 195 PHE Chi-restraints excluded: chain H residue 212 LEU Chi-restraints excluded: chain H residue 220 SER Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 287 VAL Chi-restraints excluded: chain H residue 308 VAL Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 422 GLN Chi-restraints excluded: chain H residue 449 THR Chi-restraints excluded: chain H residue 499 LEU Chi-restraints excluded: chain H residue 518 VAL Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 191 SER Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain I residue 377 SER Chi-restraints excluded: chain I residue 437 VAL Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain J residue 203 VAL Chi-restraints excluded: chain J residue 279 ASN Chi-restraints excluded: chain J residue 342 ILE Chi-restraints excluded: chain J residue 354 SER Chi-restraints excluded: chain J residue 400 VAL Chi-restraints excluded: chain J residue 421 GLU Chi-restraints excluded: chain J residue 424 THR Chi-restraints excluded: chain J residue 430 VAL Chi-restraints excluded: chain J residue 431 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 143 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 181 optimal weight: 20.0000 chunk 226 optimal weight: 0.8980 chunk 210 optimal weight: 2.9990 chunk 257 optimal weight: 0.8980 chunk 153 optimal weight: 40.0000 chunk 115 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 HIS ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN H 422 GLN ** I 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 197 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.118066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.098628 restraints weight = 61670.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.098521 restraints weight = 59228.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.100168 restraints weight = 52057.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.100270 restraints weight = 35186.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.100584 restraints weight = 32865.671| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 28867 Z= 0.137 Angle : 0.626 13.201 39225 Z= 0.313 Chirality : 0.045 0.159 4657 Planarity : 0.004 0.072 5083 Dihedral : 4.863 50.481 4093 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 3.08 % Allowed : 24.96 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.44 % 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: -1.62 (0.14), residues: 3771 helix: 0.81 (0.14), residues: 1391 sheet: -2.48 (0.24), residues: 419 loop : -2.24 (0.14), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 269 TYR 0.036 0.002 TYR F 231 PHE 0.024 0.001 PHE D 223 TRP 0.048 0.002 TRP E 290 HIS 0.007 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00326 (28867) covalent geometry : angle 0.62602 (39225) hydrogen bonds : bond 0.03239 ( 1100) hydrogen bonds : angle 4.28778 ( 3117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3730.40 seconds wall clock time: 65 minutes 47.95 seconds (3947.95 seconds total)