Starting phenix.real_space_refine on Mon Aug 25 17:00:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c9z_45377/08_2025/9c9z_45377_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c9z_45377/08_2025/9c9z_45377.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9c9z_45377/08_2025/9c9z_45377_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c9z_45377/08_2025/9c9z_45377_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9c9z_45377/08_2025/9c9z_45377.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c9z_45377/08_2025/9c9z_45377.map" } resolution = 2.55 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= 0.001 sd= 0.035 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 12 5.49 5 S 95 5.16 5 C 18010 2.51 5 N 4929 2.21 5 O 5586 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28632 Number of models: 1 Model: "" Number of chains: 16 Chain: "Q" Number of atoms: 3372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3372 Classifications: {'peptide': 419} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 22, 'TRANS': 396} Chain breaks: 5 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "R" Number of atoms: 3519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3519 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 28, 'TRANS': 413} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "S" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1015 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 118} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 17 Chain: "T" Number of atoms: 3351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3351 Classifications: {'peptide': 437} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 17, 'TRANS': 419} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 4 Chain: "U" Number of atoms: 3421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3421 Classifications: {'peptide': 445} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 434} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "V" Number of atoms: 3394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3394 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 423} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 3398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3398 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 431} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "X" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3404 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 18, 'TRANS': 424} Chain: "Y" Number of atoms: 3351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3351 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 425} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Z" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 245 Classifications: {'peptide': 28} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 25} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.95, per 1000 atoms: 0.24 Number of scatterers: 28632 At special positions: 0 Unit cell: (126.929, 155.591, 195.717, 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 95 16.00 P 12 15.00 O 5586 8.00 N 4929 7.00 C 18010 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: 2.50 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 476.8 nanoseconds 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6832 Finding SS restraints... Secondary structure from input PDB file: 145 helices and 36 sheets defined 43.6% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'Q' and resid 957 through 972 Processing helix chain 'Q' and resid 974 through 985 removed outlier: 3.551A pdb=" N ASP Q 985 " --> pdb=" O ALA Q 981 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1000 through 1013 removed outlier: 3.616A pdb=" N VAL Q1004 " --> pdb=" O LEU Q1000 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1013 through 1018 removed outlier: 3.842A pdb=" N PHE Q1017 " --> pdb=" O HIS Q1013 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU Q1018 " --> pdb=" O PRO Q1014 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 1013 through 1018' Processing helix chain 'Q' and resid 1086 through 1094 removed outlier: 3.697A pdb=" N TYR Q1090 " --> pdb=" O PRO Q1086 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1101 through 1111 Processing helix chain 'Q' and resid 1121 through 1133 Processing helix chain 'Q' and resid 1138 through 1145 Processing helix chain 'Q' and resid 1147 through 1154 Processing helix chain 'Q' and resid 1169 through 1178 removed outlier: 3.668A pdb=" N THR Q1178 " --> pdb=" O LEU Q1174 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1185 through 1191 removed outlier: 3.643A pdb=" N LEU Q1191 " --> pdb=" O MET Q1187 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1193 through 1201 Processing helix chain 'Q' and resid 1226 through 1238 removed outlier: 3.938A pdb=" N THR Q1230 " --> pdb=" O SER Q1226 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1239 through 1246 Processing helix chain 'Q' and resid 1250 through 1259 Processing helix chain 'Q' and resid 1264 through 1268 Processing helix chain 'Q' and resid 1290 through 1298 removed outlier: 3.555A pdb=" N ILE Q1295 " --> pdb=" O MET Q1291 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR Q1296 " --> pdb=" O ASP Q1292 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N SER Q1298 " --> pdb=" O PHE Q1294 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1298 through 1311 Processing helix chain 'Q' and resid 1326 through 1335 removed outlier: 3.626A pdb=" N LEU Q1330 " --> pdb=" O LYS Q1326 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1357 through 1364 Processing helix chain 'Q' and resid 1397 through 1406 removed outlier: 4.098A pdb=" N ASP Q1401 " --> pdb=" O ASN Q1397 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1427 through 1435 Processing helix chain 'R' and resid 83 through 88 removed outlier: 3.556A pdb=" N THR R 86 " --> pdb=" O GLY R 83 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU R 88 " --> pdb=" O ASP R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 89 through 95 removed outlier: 4.188A pdb=" N GLN R 95 " --> pdb=" O ALA R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 107 through 122 removed outlier: 3.585A pdb=" N THR R 111 " --> pdb=" O ASN R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 143 through 159 removed outlier: 4.520A pdb=" N THR R 157 " --> pdb=" O ILE R 153 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 177 Processing helix chain 'R' and resid 206 through 209 Processing helix chain 'R' and resid 216 through 231 Processing helix chain 'R' and resid 239 through 251 removed outlier: 3.629A pdb=" N ASP R 249 " --> pdb=" O THR R 245 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N CYS R 251 " --> pdb=" O TYR R 247 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 274 removed outlier: 3.606A pdb=" N ASP R 274 " --> pdb=" O LEU R 270 " (cutoff:3.500A) Processing helix chain 'R' and resid 589 through 597 Processing helix chain 'R' and resid 605 through 610 removed outlier: 3.506A pdb=" N GLN R 609 " --> pdb=" O ASN R 605 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS R 610 " --> pdb=" O ILE R 606 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 605 through 610' Processing helix chain 'R' and resid 619 through 624 removed outlier: 3.765A pdb=" N VAL R 624 " --> pdb=" O ARG R 620 " (cutoff:3.500A) Processing helix chain 'R' and resid 625 through 626 No H-bonds generated for 'chain 'R' and resid 625 through 626' Processing helix chain 'R' and resid 627 through 631 Processing helix chain 'R' and resid 637 through 649 removed outlier: 3.728A pdb=" N LYS R 649 " --> pdb=" O ILE R 645 " (cutoff:3.500A) Processing helix chain 'R' and resid 658 through 666 Processing helix chain 'R' and resid 672 through 677 removed outlier: 4.120A pdb=" N LYS R 676 " --> pdb=" O GLY R 673 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL R 677 " --> pdb=" O ASN R 674 " (cutoff:3.500A) Processing helix chain 'R' and resid 679 through 692 removed outlier: 3.747A pdb=" N PHE R 691 " --> pdb=" O GLU R 687 " (cutoff:3.500A) Processing helix chain 'R' and resid 708 through 720 removed outlier: 3.579A pdb=" N LYS R 712 " --> pdb=" O LEU R 708 " (cutoff:3.500A) Processing helix chain 'R' and resid 720 through 725 Processing helix chain 'R' and resid 731 through 738 Processing helix chain 'S' and resid 29 through 38 Processing helix chain 'S' and resid 64 through 83 removed outlier: 3.878A pdb=" N SER S 68 " --> pdb=" O ARG S 64 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS S 83 " --> pdb=" O THR S 79 " (cutoff:3.500A) Processing helix chain 'S' and resid 136 through 143 Processing helix chain 'S' and resid 151 through 159 removed outlier: 3.793A pdb=" N TYR S 155 " --> pdb=" O VAL S 151 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG S 159 " --> pdb=" O TYR S 155 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 68 removed outlier: 3.808A pdb=" N LYS T 68 " --> pdb=" O LEU T 64 " (cutoff:3.500A) Processing helix chain 'T' and resid 84 through 97 Processing helix chain 'T' and resid 108 through 111 Processing helix chain 'T' and resid 116 through 127 Processing helix chain 'T' and resid 182 through 192 Processing helix chain 'T' and resid 217 through 219 No H-bonds generated for 'chain 'T' and resid 217 through 219' Processing helix chain 'T' and resid 249 through 256 removed outlier: 3.721A pdb=" N ASN T 256 " --> pdb=" O LEU T 252 " (cutoff:3.500A) Processing helix chain 'T' and resid 281 through 298 removed outlier: 3.513A pdb=" N ARG T 285 " --> pdb=" O THR T 281 " (cutoff:3.500A) Processing helix chain 'T' and resid 312 through 316 Processing helix chain 'T' and resid 317 through 328 Processing helix chain 'T' and resid 360 through 365 Processing helix chain 'T' and resid 376 through 391 Processing helix chain 'T' and resid 396 through 410 Processing helix chain 'T' and resid 411 through 429 removed outlier: 3.685A pdb=" N ALA T 415 " --> pdb=" O SER T 411 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ALA T 420 " --> pdb=" O LEU T 416 " (cutoff:3.500A) Proline residue: T 421 - end of helix removed outlier: 3.562A pdb=" N SER T 429 " --> pdb=" O LEU T 425 " (cutoff:3.500A) Processing helix chain 'T' and resid 435 through 446 Processing helix chain 'T' and resid 448 through 459 Processing helix chain 'U' and resid 47 through 64 Processing helix chain 'U' and resid 80 through 92 Processing helix chain 'U' and resid 104 through 106 No H-bonds generated for 'chain 'U' and resid 104 through 106' Processing helix chain 'U' and resid 112 through 123 Processing helix chain 'U' and resid 172 through 182 removed outlier: 3.644A pdb=" N GLU U 182 " --> pdb=" O GLY U 178 " (cutoff:3.500A) Processing helix chain 'U' and resid 241 through 250 removed outlier: 3.887A pdb=" N ARG U 250 " --> pdb=" O VAL U 246 " (cutoff:3.500A) Processing helix chain 'U' and resid 255 through 260 Processing helix chain 'U' and resid 266 through 283 removed outlier: 3.772A pdb=" N ARG U 270 " --> pdb=" O ARG U 266 " (cutoff:3.500A) Processing helix chain 'U' and resid 302 through 313 Processing helix chain 'U' and resid 344 through 350 removed outlier: 3.590A pdb=" N ARG U 350 " --> pdb=" O ASP U 346 " (cutoff:3.500A) Processing helix chain 'U' and resid 360 through 375 Processing helix chain 'U' and resid 380 through 394 Processing helix chain 'U' and resid 395 through 413 removed outlier: 3.605A pdb=" N SER U 399 " --> pdb=" O SER U 395 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N SER U 404 " --> pdb=" O SER U 400 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL U 405 " --> pdb=" O ASN U 401 " (cutoff:3.500A) Processing helix chain 'U' and resid 419 through 430 Processing helix chain 'U' and resid 432 through 443 Processing helix chain 'V' and resid 51 through 67 Processing helix chain 'V' and resid 84 through 97 Processing helix chain 'V' and resid 108 through 111 removed outlier: 3.531A pdb=" N TYR V 111 " --> pdb=" O SER V 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 108 through 111' Processing helix chain 'V' and resid 116 through 127 Processing helix chain 'V' and resid 184 through 192 removed outlier: 4.301A pdb=" N SER V 188 " --> pdb=" O THR V 184 " (cutoff:3.500A) Processing helix chain 'V' and resid 249 through 258 Processing helix chain 'V' and resid 264 through 273 Processing helix chain 'V' and resid 281 through 298 Processing helix chain 'V' and resid 312 through 316 Processing helix chain 'V' and resid 317 through 328 Processing helix chain 'V' and resid 360 through 366 Processing helix chain 'V' and resid 376 through 391 Processing helix chain 'V' and resid 396 through 410 Processing helix chain 'V' and resid 411 through 418 removed outlier: 3.524A pdb=" N ALA V 415 " --> pdb=" O SER V 411 " (cutoff:3.500A) Processing helix chain 'V' and resid 418 through 428 Processing helix chain 'V' and resid 435 through 446 Processing helix chain 'V' and resid 448 through 459 Processing helix chain 'W' and resid 47 through 64 Processing helix chain 'W' and resid 80 through 92 Processing helix chain 'W' and resid 112 through 123 Processing helix chain 'W' and resid 172 through 181 removed outlier: 3.514A pdb=" N LYS W 181 " --> pdb=" O ASP W 177 " (cutoff:3.500A) Processing helix chain 'W' and resid 241 through 250 removed outlier: 4.122A pdb=" N ARG W 250 " --> pdb=" O VAL W 246 " (cutoff:3.500A) Processing helix chain 'W' and resid 252 through 260 removed outlier: 3.534A pdb=" N ALA W 256 " --> pdb=" O GLN W 252 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE W 258 " --> pdb=" O PHE W 254 " (cutoff:3.500A) Processing helix chain 'W' and resid 266 through 283 removed outlier: 3.549A pdb=" N ARG W 270 " --> pdb=" O ARG W 266 " (cutoff:3.500A) Processing helix chain 'W' and resid 298 through 301 Processing helix chain 'W' and resid 302 through 313 Processing helix chain 'W' and resid 344 through 350 removed outlier: 3.598A pdb=" N ARG W 350 " --> pdb=" O ASP W 346 " (cutoff:3.500A) Processing helix chain 'W' and resid 360 through 375 Processing helix chain 'W' and resid 380 through 394 Processing helix chain 'W' and resid 395 through 413 removed outlier: 4.424A pdb=" N SER W 404 " --> pdb=" O SER W 400 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL W 405 " --> pdb=" O ASN W 401 " (cutoff:3.500A) Processing helix chain 'W' and resid 419 through 430 removed outlier: 3.512A pdb=" N VAL W 423 " --> pdb=" O GLU W 419 " (cutoff:3.500A) Processing helix chain 'W' and resid 432 through 443 Processing helix chain 'W' and resid 444 through 447 Processing helix chain 'X' and resid 51 through 68 removed outlier: 3.727A pdb=" N LYS X 68 " --> pdb=" O LEU X 64 " (cutoff:3.500A) Processing helix chain 'X' and resid 84 through 97 Processing helix chain 'X' and resid 108 through 111 Processing helix chain 'X' and resid 116 through 128 Processing helix chain 'X' and resid 182 through 191 Processing helix chain 'X' and resid 249 through 258 Processing helix chain 'X' and resid 264 through 273 removed outlier: 3.622A pdb=" N LEU X 272 " --> pdb=" O MET X 268 " (cutoff:3.500A) Processing helix chain 'X' and resid 281 through 298 Processing helix chain 'X' and resid 312 through 316 Processing helix chain 'X' and resid 317 through 328 Processing helix chain 'X' and resid 360 through 365 Processing helix chain 'X' and resid 376 through 391 Processing helix chain 'X' and resid 396 through 410 Processing helix chain 'X' and resid 411 through 418 Processing helix chain 'X' and resid 418 through 429 Processing helix chain 'X' and resid 435 through 446 Processing helix chain 'X' and resid 448 through 458 Processing helix chain 'Y' and resid 47 through 64 Processing helix chain 'Y' and resid 80 through 93 removed outlier: 4.028A pdb=" N GLY Y 93 " --> pdb=" O SER Y 89 " (cutoff:3.500A) Processing helix chain 'Y' and resid 104 through 107 removed outlier: 3.674A pdb=" N PHE Y 107 " --> pdb=" O SER Y 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 104 through 107' Processing helix chain 'Y' and resid 112 through 123 Processing helix chain 'Y' and resid 172 through 181 Processing helix chain 'Y' and resid 241 through 249 Processing helix chain 'Y' and resid 255 through 260 Processing helix chain 'Y' and resid 266 through 283 removed outlier: 3.746A pdb=" N ARG Y 270 " --> pdb=" O ARG Y 266 " (cutoff:3.500A) Processing helix chain 'Y' and resid 298 through 301 removed outlier: 3.541A pdb=" N LEU Y 301 " --> pdb=" O VAL Y 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 298 through 301' Processing helix chain 'Y' and resid 302 through 313 Processing helix chain 'Y' and resid 340 through 343 Processing helix chain 'Y' and resid 344 through 350 removed outlier: 3.545A pdb=" N ARG Y 350 " --> pdb=" O ASP Y 346 " (cutoff:3.500A) Processing helix chain 'Y' and resid 360 through 375 Processing helix chain 'Y' and resid 380 through 394 Processing helix chain 'Y' and resid 395 through 413 removed outlier: 4.426A pdb=" N SER Y 404 " --> pdb=" O SER Y 400 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL Y 405 " --> pdb=" O ASN Y 401 " (cutoff:3.500A) Processing helix chain 'Y' and resid 419 through 430 removed outlier: 3.541A pdb=" N VAL Y 423 " --> pdb=" O GLU Y 419 " (cutoff:3.500A) Processing helix chain 'Y' and resid 432 through 443 removed outlier: 3.515A pdb=" N ASN Y 443 " --> pdb=" O TYR Y 439 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Q' and resid 952 through 954 removed outlier: 5.936A pdb=" N VAL Q 952 " --> pdb=" O LEU Q1423 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'Q' and resid 1026 through 1027 removed outlier: 6.018A pdb=" N PHE Q1026 " --> pdb=" O SER Q1215 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'Q' and resid 1071 through 1073 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 1071 through 1073 current: chain 'X' and resid 163 through 172 removed outlier: 3.617A pdb=" N GLY X 175 " --> pdb=" O SER X 172 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 175 through 181 current: chain 'X' and resid 209 through 215 removed outlier: 6.038A pdb=" N VAL X 230 " --> pdb=" O VAL X 212 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ARG X 214 " --> pdb=" O VAL X 230 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Q' and resid 1082 through 1084 removed outlier: 6.084A pdb=" N TYR Q1083 " --> pdb=" O GLU Q1222 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'Q' and resid 1317 through 1318 removed outlier: 6.878A pdb=" N ARG Q1317 " --> pdb=" O ILE Q1390 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'R' and resid 61 through 63 removed outlier: 4.025A pdb=" N THR R 137 " --> pdb=" O ILE R 42 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N PHE R 44 " --> pdb=" O THR R 137 " (cutoff:3.500A) removed outlier: 9.175A pdb=" N GLY R 166 " --> pdb=" O ILE R 134 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LEU R 136 " --> pdb=" O GLY R 166 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'R' and resid 162 through 163 Processing sheet with id=AA8, first strand: chain 'R' and resid 184 through 189 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 203 through 204 current: chain 'R' and resid 700 through 701 Processing sheet with id=AA9, first strand: chain 'R' and resid 277 through 278 Processing sheet with id=AB1, first strand: chain 'S' and resid 125 through 126 removed outlier: 3.610A pdb=" N TYR S 125 " --> pdb=" O TYR S 134 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'T' and resid 44 through 45 Processing sheet with id=AB3, first strand: chain 'T' and resid 102 through 106 removed outlier: 6.230A pdb=" N CYS T 103 " --> pdb=" O PHE T 309 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ASP T 311 " --> pdb=" O CYS T 103 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU T 105 " --> pdb=" O ASP T 311 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY T 79 " --> pdb=" O SER T 340 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ALA T 74 " --> pdb=" O LEU T 368 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N VAL T 370 " --> pdb=" O ALA T 74 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU T 76 " --> pdb=" O VAL T 370 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N THR T 372 " --> pdb=" O LEU T 76 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ALA T 78 " --> pdb=" O THR T 372 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'T' and resid 129 through 150 removed outlier: 6.384A pdb=" N GLY T 169 " --> pdb=" O THR T 145 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU T 147 " --> pdb=" O ILE T 167 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE T 167 " --> pdb=" O LEU T 147 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N HIS T 165 " --> pdb=" O PRO T 149 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 175 through 181 current: chain 'T' and resid 209 through 215 removed outlier: 6.047A pdb=" N VAL T 230 " --> pdb=" O VAL T 212 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ARG T 214 " --> pdb=" O VAL T 230 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'T' and resid 344 through 346 Processing sheet with id=AB6, first strand: chain 'T' and resid 394 through 395 removed outlier: 7.206A pdb=" N GLN T 394 " --> pdb=" O ILE T 434 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'U' and resid 40 through 41 Processing sheet with id=AB8, first strand: chain 'U' and resid 98 through 102 removed outlier: 6.397A pdb=" N THR U 99 " --> pdb=" O PHE U 294 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ASP U 296 " --> pdb=" O THR U 99 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE U 101 " --> pdb=" O ASP U 296 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'U' and resid 125 through 146 removed outlier: 5.389A pdb=" N VAL U 140 " --> pdb=" O LYS U 161 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LYS U 161 " --> pdb=" O VAL U 140 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU U 142 " --> pdb=" O THR U 159 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN U 155 " --> pdb=" O ASP U 146 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE U 160 " --> pdb=" O THR U 167 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR U 167 " --> pdb=" O ILE U 160 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 166 through 171 current: chain 'U' and resid 203 through 205 removed outlier: 5.597A pdb=" N ARG U 204 " --> pdb=" O VAL U 222 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'U' and resid 329 through 331 Processing sheet with id=AC2, first strand: chain 'V' and resid 44 through 45 removed outlier: 3.570A pdb=" N PHE V 48 " --> pdb=" O GLU V 45 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'V' and resid 102 through 106 removed outlier: 6.234A pdb=" N ILE V 75 " --> pdb=" O LEU V 338 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N SER V 340 " --> pdb=" O ILE V 75 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU V 77 " --> pdb=" O SER V 340 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ALA V 74 " --> pdb=" O LEU V 368 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N VAL V 370 " --> pdb=" O ALA V 74 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU V 76 " --> pdb=" O VAL V 370 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'V' and resid 129 through 151 removed outlier: 6.397A pdb=" N GLY V 169 " --> pdb=" O THR V 145 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU V 147 " --> pdb=" O ILE V 167 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE V 167 " --> pdb=" O LEU V 147 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N HIS V 165 " --> pdb=" O PRO V 149 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASP V 151 " --> pdb=" O ILE V 163 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE V 163 " --> pdb=" O ASP V 151 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 176 through 181 current: chain 'V' and resid 213 through 215 removed outlier: 5.511A pdb=" N ARG V 214 " --> pdb=" O VAL V 230 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'V' and resid 344 through 346 Processing sheet with id=AC6, first strand: chain 'V' and resid 394 through 395 removed outlier: 7.526A pdb=" N GLN V 394 " --> pdb=" O ILE V 434 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'W' and resid 40 through 41 Processing sheet with id=AC8, first strand: chain 'W' and resid 98 through 102 removed outlier: 6.070A pdb=" N LEU W 293 " --> pdb=" O MET W 322 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ALA W 324 " --> pdb=" O LEU W 293 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE W 295 " --> pdb=" O ALA W 324 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ALA W 70 " --> pdb=" O ILE W 352 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ILE W 354 " --> pdb=" O ALA W 70 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU W 72 " --> pdb=" O ILE W 354 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'W' and resid 126 through 147 removed outlier: 5.131A pdb=" N VAL W 140 " --> pdb=" O LYS W 161 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LYS W 161 " --> pdb=" O VAL W 140 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY W 156 " --> pdb=" O LEU W 171 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 166 through 171 current: chain 'W' and resid 198 through 204 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 198 through 204 current: chain 'Z' and resid 315 through 318 Processing sheet with id=AD1, first strand: chain 'W' and resid 329 through 331 Processing sheet with id=AD2, first strand: chain 'X' and resid 44 through 45 Processing sheet with id=AD3, first strand: chain 'X' and resid 102 through 106 removed outlier: 6.351A pdb=" N CYS X 103 " --> pdb=" O PHE X 309 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ASP X 311 " --> pdb=" O CYS X 103 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU X 105 " --> pdb=" O ASP X 311 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N VAL X 370 " --> pdb=" O ALA X 74 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LEU X 76 " --> pdb=" O VAL X 370 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'X' and resid 344 through 346 Processing sheet with id=AD5, first strand: chain 'X' and resid 394 through 395 removed outlier: 7.529A pdb=" N GLN X 394 " --> pdb=" O ILE X 434 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'Y' and resid 40 through 41 Processing sheet with id=AD7, first strand: chain 'Y' and resid 98 through 102 removed outlier: 6.101A pdb=" N LEU Y 293 " --> pdb=" O MET Y 322 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ALA Y 324 " --> pdb=" O LEU Y 293 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE Y 295 " --> pdb=" O ALA Y 324 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ALA Y 70 " --> pdb=" O ILE Y 352 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ILE Y 354 " --> pdb=" O ALA Y 70 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LEU Y 72 " --> pdb=" O ILE Y 354 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Y' and resid 125 through 146 removed outlier: 6.769A pdb=" N THR Y 159 " --> pdb=" O VAL Y 141 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ILE Y 143 " --> pdb=" O LYS Y 157 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LYS Y 157 " --> pdb=" O ILE Y 143 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ILE Y 145 " --> pdb=" O GLN Y 155 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLN Y 155 " --> pdb=" O ILE Y 145 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLY Y 156 " --> pdb=" O LEU Y 171 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 166 through 171 current: chain 'Y' and resid 198 through 204 Processing sheet with id=AD9, first strand: chain 'Y' and resid 330 through 331 1117 hydrogen bonds defined for protein. 3258 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: 5.35 Time building geometry restraints manager: 3.32 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: 9094 1.34 - 1.46: 5439 1.46 - 1.58: 14344 1.58 - 1.70: 19 1.70 - 1.83: 166 Bond restraints: 29062 Sorted by residual: bond pdb=" C THR Q1427 " pdb=" O THR Q1427 " ideal model delta sigma weight residual 1.233 1.278 -0.044 1.17e-02 7.31e+03 1.43e+01 bond pdb=" N VAL Q 952 " pdb=" CA VAL Q 952 " ideal model delta sigma weight residual 1.458 1.495 -0.038 1.14e-02 7.69e+03 1.09e+01 bond pdb=" N LEU Q 953 " pdb=" CA LEU Q 953 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.18e-02 7.18e+03 1.03e+01 bond pdb=" N THR Y 394 " pdb=" CA THR Y 394 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.29e-02 6.01e+03 8.94e+00 bond pdb=" N VAL Q1419 " pdb=" CA VAL Q1419 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.17e-02 7.31e+03 8.83e+00 ... (remaining 29057 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.19: 39049 4.19 - 8.39: 235 8.39 - 12.58: 32 12.58 - 16.78: 7 16.78 - 20.97: 5 Bond angle restraints: 39328 Sorted by residual: angle pdb=" CA PRO R 126 " pdb=" N PRO R 126 " pdb=" CD PRO R 126 " ideal model delta sigma weight residual 112.00 95.99 16.01 1.40e+00 5.10e-01 1.31e+02 angle pdb=" CA LEU Q1372 " pdb=" CB LEU Q1372 " pdb=" CG LEU Q1372 " ideal model delta sigma weight residual 116.30 137.27 -20.97 3.50e+00 8.16e-02 3.59e+01 angle pdb=" CA LYS R 74 " pdb=" CB LYS R 74 " pdb=" CG LYS R 74 " ideal model delta sigma weight residual 114.10 125.72 -11.62 2.00e+00 2.50e-01 3.37e+01 angle pdb=" CB MET U 165 " pdb=" CG MET U 165 " pdb=" SD MET U 165 " ideal model delta sigma weight residual 112.70 129.94 -17.24 3.00e+00 1.11e-01 3.30e+01 angle pdb=" CB MET T 70 " pdb=" CG MET T 70 " pdb=" SD MET T 70 " ideal model delta sigma weight residual 112.70 129.69 -16.99 3.00e+00 1.11e-01 3.21e+01 ... (remaining 39323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.14: 16025 22.14 - 44.29: 1487 44.29 - 66.43: 300 66.43 - 88.57: 33 88.57 - 110.71: 3 Dihedral angle restraints: 17848 sinusoidal: 7268 harmonic: 10580 Sorted by residual: dihedral pdb=" CD ARG Z 311 " pdb=" NE ARG Z 311 " pdb=" CZ ARG Z 311 " pdb=" NH1 ARG Z 311 " ideal model delta sinusoidal sigma weight residual 0.00 -52.96 52.96 1 1.00e+01 1.00e-02 3.82e+01 dihedral pdb=" C5' ADP W 501 " pdb=" O5' ADP W 501 " pdb=" PA ADP W 501 " pdb=" O2A ADP W 501 " ideal model delta sinusoidal sigma weight residual -60.00 -170.71 110.71 1 2.00e+01 2.50e-03 3.25e+01 dihedral pdb=" C5' ADP X 501 " pdb=" O5' ADP X 501 " pdb=" PA ADP X 501 " pdb=" O2A ADP X 501 " ideal model delta sinusoidal sigma weight residual -60.00 -167.02 107.03 1 2.00e+01 2.50e-03 3.10e+01 ... (remaining 17845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 4414 0.116 - 0.232: 196 0.232 - 0.348: 6 0.348 - 0.464: 1 0.464 - 0.581: 1 Chirality restraints: 4618 Sorted by residual: chirality pdb=" CG LEU Q1308 " pdb=" CB LEU Q1308 " pdb=" CD1 LEU Q1308 " pdb=" CD2 LEU Q1308 " both_signs ideal model delta sigma weight residual False -2.59 -2.01 -0.58 2.00e-01 2.50e+01 8.43e+00 chirality pdb=" CG LEU R 122 " pdb=" CB LEU R 122 " pdb=" CD1 LEU R 122 " pdb=" CD2 LEU R 122 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" CA PHE R 104 " pdb=" N PHE R 104 " pdb=" C PHE R 104 " pdb=" CB PHE R 104 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 4615 not shown) Planarity restraints: 5041 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG Z 311 " -0.865 9.50e-02 1.11e+02 3.88e-01 9.12e+01 pdb=" NE ARG Z 311 " 0.053 2.00e-02 2.50e+03 pdb=" CZ ARG Z 311 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG Z 311 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG Z 311 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG Q1421 " -0.642 9.50e-02 1.11e+02 2.88e-01 5.06e+01 pdb=" NE ARG Q1421 " 0.037 2.00e-02 2.50e+03 pdb=" CZ ARG Q1421 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG Q1421 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG Q1421 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 104 " -0.031 2.00e-02 2.50e+03 5.27e-02 4.86e+01 pdb=" CG PHE R 104 " 0.114 2.00e-02 2.50e+03 pdb=" CD1 PHE R 104 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 PHE R 104 " -0.060 2.00e-02 2.50e+03 pdb=" CE1 PHE R 104 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE R 104 " 0.023 2.00e-02 2.50e+03 pdb=" CZ PHE R 104 " -0.011 2.00e-02 2.50e+03 ... (remaining 5038 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2253 2.74 - 3.28: 27595 3.28 - 3.82: 49915 3.82 - 4.36: 59085 4.36 - 4.90: 100308 Nonbonded interactions: 239156 Sorted by model distance: nonbonded pdb=" NE2 GLN W 47 " pdb=" O LYS W 357 " model vdw 2.205 3.120 nonbonded pdb=" OD1 ASP X 362 " pdb=" N LEU X 363 " model vdw 2.255 3.120 nonbonded pdb=" OH TYR S 125 " pdb=" O LEU Y 229 " model vdw 2.256 3.040 nonbonded pdb=" O PRO U 76 " pdb=" OG1 THR U 79 " model vdw 2.301 3.040 nonbonded pdb=" O ALA V 26 " pdb=" O3' ADP V 501 " model vdw 2.304 3.040 ... (remaining 239151 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 'T' and (resid 22 through 462 or (resid 463 and (name N or name CA or nam \ e C or name O or name CB )) or resid 501)) selection = (chain 'V' and (resid 22 through 43 or (resid 44 and (name N or name CA or name \ C or name O or name CB )) or resid 45 through 74 or (resid 75 and (name N or nam \ e CA or name C or name O or name CB )) or resid 76 through 154 or (resid 161 thr \ ough 163 and (name N or name CA or name C or name O or name CB )) or resid 164 t \ hrough 501)) selection = (chain 'X' and (resid 22 through 43 or (resid 44 and (name N or name CA or name \ C or name O or name CB )) or resid 45 through 74 or (resid 75 and (name N or nam \ e CA or name C or name O or name CB )) or resid 76 through 154 or (resid 161 thr \ ough 163 and (name N or name CA or name C or name O or name CB )) or resid 164 t \ hrough 462 or (resid 463 and (name N or name CA or name C or name O or name CB ) \ ) or resid 501)) } ncs_group { reference = (chain 'U' and (resid 18 through 167 or (resid 168 and (name N or name CA or nam \ e C or name O or name CB )) or resid 169 through 210 or resid 221 through 459 or \ resid 501)) selection = (chain 'W' and (resid 18 through 167 or (resid 168 and (name N or name CA or nam \ e C or name O or name CB )) or resid 169 through 210 or resid 221 through 501)) selection = (chain 'Y' and (resid 18 through 459 or resid 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 27.050 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 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 : 0.004 0.143 29062 Z= 0.222 Angle : 0.899 20.972 39328 Z= 0.467 Chirality : 0.053 0.581 4618 Planarity : 0.009 0.388 5041 Dihedral : 17.017 110.715 11016 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.03 % Allowed : 25.25 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -1.76 (0.12), residues: 3624 helix: -1.38 (0.11), residues: 1522 sheet: -0.12 (0.20), residues: 600 loop : -1.19 (0.15), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG T 191 TYR 0.046 0.002 TYR S 53 PHE 0.114 0.002 PHE R 104 TRP 0.017 0.002 TRP U 280 HIS 0.005 0.001 HIS R 121 Details of bonding type rmsd covalent geometry : bond 0.00436 (29062) covalent geometry : angle 0.89851 (39328) hydrogen bonds : bond 0.14859 ( 1117) hydrogen bonds : angle 6.47237 ( 3258) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 1.011 Fit side-chains revert: symmetry clash REVERT: Q 1361 TRP cc_start: 0.7480 (t-100) cc_final: 0.7084 (t-100) outliers start: 1 outliers final: 0 residues processed: 181 average time/residue: 0.7858 time to fit residues: 162.8964 Evaluate side-chains 160 residues out of total 3173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1323 GLN R 144 GLN S 75 ASN ** U 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 310 ASN X 27 HIS Y 415 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.073200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.053364 restraints weight = 76903.190| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 2.78 r_work: 0.2803 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.0842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 29062 Z= 0.121 Angle : 0.559 9.842 39328 Z= 0.278 Chirality : 0.043 0.230 4618 Planarity : 0.004 0.084 5041 Dihedral : 6.292 115.260 4006 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.13 % Allowed : 21.72 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.50 (0.13), residues: 3624 helix: 0.14 (0.12), residues: 1536 sheet: 0.07 (0.21), residues: 596 loop : -0.88 (0.15), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG S 39 TYR 0.017 0.001 TYR Q1321 PHE 0.019 0.001 PHE Q1391 TRP 0.011 0.001 TRP R 214 HIS 0.003 0.001 HIS R 121 Details of bonding type rmsd covalent geometry : bond 0.00273 (29062) covalent geometry : angle 0.55889 (39328) hydrogen bonds : bond 0.03657 ( 1117) hydrogen bonds : angle 4.52311 ( 3258) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 173 time to evaluate : 1.166 Fit side-chains revert: symmetry clash REVERT: Q 1323 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.7116 (tp40) REVERT: Q 1361 TRP cc_start: 0.7456 (t-100) cc_final: 0.7009 (t-100) REVERT: R 189 CYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8439 (p) REVERT: R 227 MET cc_start: 0.9006 (mmm) cc_final: 0.8546 (mmm) REVERT: S 69 ASP cc_start: 0.9154 (p0) cc_final: 0.8923 (p0) REVERT: V 312 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8141 (pt0) REVERT: X 154 ASN cc_start: 0.8666 (t0) cc_final: 0.8455 (t0) outliers start: 67 outliers final: 15 residues processed: 224 average time/residue: 0.6401 time to fit residues: 167.3307 Evaluate side-chains 181 residues out of total 3173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1186 VAL Chi-restraints excluded: chain Q residue 1323 GLN Chi-restraints excluded: chain R residue 189 CYS Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain R residue 609 GLN Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 273 LEU Chi-restraints excluded: chain U residue 302 ASP Chi-restraints excluded: chain U residue 352 ILE Chi-restraints excluded: chain V residue 220 THR Chi-restraints excluded: chain V residue 271 GLN Chi-restraints excluded: chain V residue 312 GLU Chi-restraints excluded: chain V residue 331 ASN Chi-restraints excluded: chain X residue 332 ILE Chi-restraints excluded: chain X residue 362 ASP Chi-restraints excluded: chain Z residue 294 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 350 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 327 optimal weight: 3.9990 chunk 358 optimal weight: 0.0770 chunk 245 optimal weight: 0.0970 chunk 163 optimal weight: 3.9990 chunk 293 optimal weight: 3.9990 chunk 36 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 150 optimal weight: 0.8980 chunk 225 optimal weight: 2.9990 overall best weight: 1.0138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1204 ASN R 121 HIS S 71 ASN S 131 ASN ** U 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 310 ASN ** Y 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.072584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.052611 restraints weight = 76892.552| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 2.78 r_work: 0.2786 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29062 Z= 0.122 Angle : 0.541 13.162 39328 Z= 0.266 Chirality : 0.043 0.276 4618 Planarity : 0.003 0.060 5041 Dihedral : 6.133 113.619 4006 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.26 % Allowed : 21.43 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.03 (0.14), residues: 3624 helix: 0.79 (0.13), residues: 1540 sheet: 0.12 (0.21), residues: 607 loop : -0.77 (0.16), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG S 39 TYR 0.017 0.001 TYR S 53 PHE 0.033 0.001 PHE R 104 TRP 0.009 0.001 TRP R 214 HIS 0.003 0.001 HIS R 121 Details of bonding type rmsd covalent geometry : bond 0.00282 (29062) covalent geometry : angle 0.54110 (39328) hydrogen bonds : bond 0.03272 ( 1117) hydrogen bonds : angle 4.19651 ( 3258) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 176 time to evaluate : 1.206 Fit side-chains revert: symmetry clash REVERT: Q 1291 MET cc_start: 0.9021 (tpt) cc_final: 0.8616 (tpt) REVERT: Q 1327 MET cc_start: 0.8749 (mmt) cc_final: 0.8408 (mpp) REVERT: Q 1361 TRP cc_start: 0.7402 (t-100) cc_final: 0.6922 (t-100) REVERT: R 104 PHE cc_start: 0.6733 (t80) cc_final: 0.6342 (t80) REVERT: R 189 CYS cc_start: 0.9133 (OUTLIER) cc_final: 0.8435 (p) REVERT: R 244 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7485 (mp0) REVERT: R 277 VAL cc_start: 0.8448 (OUTLIER) cc_final: 0.8241 (p) REVERT: S 69 ASP cc_start: 0.9150 (p0) cc_final: 0.8939 (p0) REVERT: S 104 GLU cc_start: 0.8349 (tp30) cc_final: 0.8115 (tp30) REVERT: U 157 LYS cc_start: 0.9367 (OUTLIER) cc_final: 0.8986 (mptt) REVERT: U 183 LYS cc_start: 0.8955 (mmmt) cc_final: 0.8643 (mmmt) REVERT: U 279 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7930 (pp20) REVERT: V 68 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8899 (mtpm) REVERT: V 312 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8062 (pt0) REVERT: X 154 ASN cc_start: 0.8705 (t0) cc_final: 0.8341 (t0) REVERT: X 298 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.7778 (mp10) REVERT: Y 252 GLN cc_start: 0.7202 (mp10) cc_final: 0.6665 (mp10) REVERT: Y 393 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8543 (mp0) outliers start: 71 outliers final: 15 residues processed: 234 average time/residue: 0.7225 time to fit residues: 195.9192 Evaluate side-chains 192 residues out of total 3173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 168 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1186 VAL Chi-restraints excluded: chain R residue 189 CYS Chi-restraints excluded: chain R residue 244 GLU Chi-restraints excluded: chain R residue 277 VAL Chi-restraints excluded: chain R residue 609 GLN Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 273 LEU Chi-restraints excluded: chain T residue 432 LYS Chi-restraints excluded: chain U residue 157 LYS Chi-restraints excluded: chain U residue 279 GLU Chi-restraints excluded: chain U residue 302 ASP Chi-restraints excluded: chain U residue 420 VAL Chi-restraints excluded: chain V residue 68 LYS Chi-restraints excluded: chain V residue 220 THR Chi-restraints excluded: chain V residue 312 GLU Chi-restraints excluded: chain V residue 331 ASN Chi-restraints excluded: chain W residue 302 ASP Chi-restraints excluded: chain X residue 298 GLN Chi-restraints excluded: chain X residue 362 ASP Chi-restraints excluded: chain Y residue 393 GLU Chi-restraints excluded: chain Z residue 294 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 344 optimal weight: 0.9990 chunk 52 optimal weight: 20.0000 chunk 278 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 181 optimal weight: 3.9990 chunk 240 optimal weight: 8.9990 chunk 226 optimal weight: 4.9990 chunk 179 optimal weight: 0.7980 chunk 224 optimal weight: 0.8980 chunk 310 optimal weight: 0.8980 chunk 198 optimal weight: 0.0570 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 ASN R 121 HIS S 131 ASN ** U 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 310 ASN ** Y 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.072895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.053148 restraints weight = 76507.811| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.75 r_work: 0.2798 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 29062 Z= 0.104 Angle : 0.529 12.259 39328 Z= 0.258 Chirality : 0.042 0.336 4618 Planarity : 0.003 0.050 5041 Dihedral : 5.981 112.239 4006 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.67 % Allowed : 21.34 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.36 (0.14), residues: 3624 helix: 1.12 (0.13), residues: 1540 sheet: 0.29 (0.21), residues: 596 loop : -0.65 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 64 TYR 0.014 0.001 TYR Q1334 PHE 0.022 0.001 PHE S 32 TRP 0.009 0.001 TRP R 214 HIS 0.003 0.000 HIS R 121 Details of bonding type rmsd covalent geometry : bond 0.00238 (29062) covalent geometry : angle 0.52945 (39328) hydrogen bonds : bond 0.02933 ( 1117) hydrogen bonds : angle 4.01589 ( 3258) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 183 time to evaluate : 0.827 Fit side-chains revert: symmetry clash REVERT: Q 1291 MET cc_start: 0.9068 (tpt) cc_final: 0.8844 (tpt) REVERT: Q 1361 TRP cc_start: 0.7407 (t-100) cc_final: 0.6955 (t-100) REVERT: Q 1391 PHE cc_start: 0.8402 (m-80) cc_final: 0.8176 (m-80) REVERT: Q 1432 MET cc_start: 0.7577 (ppp) cc_final: 0.7332 (ppp) REVERT: R 104 PHE cc_start: 0.6834 (t80) cc_final: 0.6310 (t80) REVERT: R 189 CYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8507 (p) REVERT: R 244 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7448 (mp0) REVERT: R 719 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7716 (mpp-170) REVERT: S 104 GLU cc_start: 0.8358 (tp30) cc_final: 0.8112 (tp30) REVERT: T 396 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.7878 (tm-30) REVERT: U 147 ARG cc_start: 0.8756 (mmm-85) cc_final: 0.8544 (mmm160) REVERT: U 157 LYS cc_start: 0.9381 (OUTLIER) cc_final: 0.8982 (mptt) REVERT: U 183 LYS cc_start: 0.8985 (mmmt) cc_final: 0.8730 (mmmt) REVERT: U 279 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7903 (pp20) REVERT: U 311 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.8663 (mmm160) REVERT: V 68 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8894 (mtpm) REVERT: V 312 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8085 (pt0) REVERT: V 447 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8917 (mp) REVERT: X 154 ASN cc_start: 0.8722 (t0) cc_final: 0.8277 (t0) REVERT: X 298 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.7785 (mp10) REVERT: Y 134 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8342 (mm-30) REVERT: Y 252 GLN cc_start: 0.7173 (mp10) cc_final: 0.6631 (mp10) REVERT: Y 393 GLU cc_start: 0.9043 (OUTLIER) cc_final: 0.8510 (mp0) outliers start: 84 outliers final: 20 residues processed: 249 average time/residue: 0.7278 time to fit residues: 209.3032 Evaluate side-chains 203 residues out of total 3173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 171 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1186 VAL Chi-restraints excluded: chain R residue 189 CYS Chi-restraints excluded: chain R residue 241 LEU Chi-restraints excluded: chain R residue 244 GLU Chi-restraints excluded: chain R residue 609 GLN Chi-restraints excluded: chain R residue 719 ARG Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 273 LEU Chi-restraints excluded: chain T residue 396 GLU Chi-restraints excluded: chain T residue 432 LYS Chi-restraints excluded: chain U residue 157 LYS Chi-restraints excluded: chain U residue 279 GLU Chi-restraints excluded: chain U residue 302 ASP Chi-restraints excluded: chain U residue 311 ARG Chi-restraints excluded: chain U residue 352 ILE Chi-restraints excluded: chain U residue 420 VAL Chi-restraints excluded: chain V residue 68 LYS Chi-restraints excluded: chain V residue 220 THR Chi-restraints excluded: chain V residue 271 GLN Chi-restraints excluded: chain V residue 312 GLU Chi-restraints excluded: chain V residue 331 ASN Chi-restraints excluded: chain V residue 447 LEU Chi-restraints excluded: chain W residue 285 LYS Chi-restraints excluded: chain W residue 302 ASP Chi-restraints excluded: chain W residue 428 LEU Chi-restraints excluded: chain X residue 298 GLN Chi-restraints excluded: chain X residue 362 ASP Chi-restraints excluded: chain Y residue 393 GLU Chi-restraints excluded: chain Z residue 294 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 176 optimal weight: 0.9990 chunk 274 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 258 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 197 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 316 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 121 HIS S 71 ASN S 131 ASN T 260 GLN U 242 HIS U 310 ASN X 190 GLN Y 119 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.071249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.051228 restraints weight = 76881.157| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 2.76 r_work: 0.2725 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 29062 Z= 0.157 Angle : 0.560 11.037 39328 Z= 0.274 Chirality : 0.043 0.356 4618 Planarity : 0.003 0.072 5041 Dihedral : 6.160 107.925 4006 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.42 % Allowed : 21.72 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.48 (0.14), residues: 3624 helix: 1.22 (0.13), residues: 1549 sheet: 0.26 (0.21), residues: 604 loop : -0.57 (0.16), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG S 39 TYR 0.016 0.001 TYR X 186 PHE 0.014 0.001 PHE Y 308 TRP 0.012 0.001 TRP R 214 HIS 0.003 0.001 HIS R 121 Details of bonding type rmsd covalent geometry : bond 0.00367 (29062) covalent geometry : angle 0.55979 (39328) hydrogen bonds : bond 0.03342 ( 1117) hydrogen bonds : angle 4.07153 ( 3258) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 181 time to evaluate : 1.294 Fit side-chains REVERT: Q 1361 TRP cc_start: 0.7393 (t-100) cc_final: 0.6916 (t-100) REVERT: Q 1432 MET cc_start: 0.7535 (ppp) cc_final: 0.7334 (ppp) REVERT: R 104 PHE cc_start: 0.6994 (t80) cc_final: 0.6375 (t80) REVERT: R 189 CYS cc_start: 0.9200 (OUTLIER) cc_final: 0.8582 (p) REVERT: R 244 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7534 (mp0) REVERT: R 719 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7840 (mpp-170) REVERT: S 104 GLU cc_start: 0.8403 (tp30) cc_final: 0.8170 (tp30) REVERT: T 396 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8084 (tm-30) REVERT: U 157 LYS cc_start: 0.9406 (OUTLIER) cc_final: 0.9017 (mptt) REVERT: U 183 LYS cc_start: 0.9097 (mmmt) cc_final: 0.8846 (mmmt) REVERT: U 279 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8120 (pp20) REVERT: V 258 ARG cc_start: 0.7939 (ptm160) cc_final: 0.7727 (ppp80) REVERT: V 312 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8316 (pt0) REVERT: V 447 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.8990 (mp) REVERT: X 154 ASN cc_start: 0.8769 (t0) cc_final: 0.8343 (t0) REVERT: X 298 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8011 (mp10) REVERT: Y 252 GLN cc_start: 0.7297 (mp10) cc_final: 0.6784 (mp10) REVERT: Y 379 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.9022 (pp) REVERT: Y 393 GLU cc_start: 0.9193 (OUTLIER) cc_final: 0.8685 (mp0) outliers start: 76 outliers final: 18 residues processed: 242 average time/residue: 0.7297 time to fit residues: 204.5026 Evaluate side-chains 194 residues out of total 3173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1186 VAL Chi-restraints excluded: chain R residue 188 SER Chi-restraints excluded: chain R residue 189 CYS Chi-restraints excluded: chain R residue 241 LEU Chi-restraints excluded: chain R residue 244 GLU Chi-restraints excluded: chain R residue 719 ARG Chi-restraints excluded: chain S residue 68 SER Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 273 LEU Chi-restraints excluded: chain T residue 396 GLU Chi-restraints excluded: chain U residue 157 LYS Chi-restraints excluded: chain U residue 279 GLU Chi-restraints excluded: chain U residue 302 ASP Chi-restraints excluded: chain U residue 418 VAL Chi-restraints excluded: chain U residue 420 VAL Chi-restraints excluded: chain V residue 220 THR Chi-restraints excluded: chain V residue 271 GLN Chi-restraints excluded: chain V residue 312 GLU Chi-restraints excluded: chain V residue 331 ASN Chi-restraints excluded: chain V residue 447 LEU Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 285 LYS Chi-restraints excluded: chain X residue 298 GLN Chi-restraints excluded: chain X residue 362 ASP Chi-restraints excluded: chain Y residue 379 LEU Chi-restraints excluded: chain Y residue 393 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 215 optimal weight: 2.9990 chunk 207 optimal weight: 0.9990 chunk 283 optimal weight: 4.9990 chunk 326 optimal weight: 0.8980 chunk 348 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 288 optimal weight: 0.7980 chunk 84 optimal weight: 9.9990 chunk 309 optimal weight: 0.0770 chunk 97 optimal weight: 4.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 121 HIS S 131 ASN ** T 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 310 ASN W 310 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.071575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.051641 restraints weight = 76463.376| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.76 r_work: 0.2750 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29062 Z= 0.130 Angle : 0.555 14.568 39328 Z= 0.271 Chirality : 0.043 0.336 4618 Planarity : 0.003 0.042 5041 Dihedral : 6.110 107.889 4006 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.03 % Allowed : 22.23 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.58 (0.14), residues: 3624 helix: 1.30 (0.13), residues: 1549 sheet: 0.36 (0.21), residues: 601 loop : -0.52 (0.16), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q1317 TYR 0.014 0.001 TYR X 186 PHE 0.012 0.001 PHE Y 308 TRP 0.011 0.001 TRP R 214 HIS 0.003 0.001 HIS R 121 Details of bonding type rmsd covalent geometry : bond 0.00304 (29062) covalent geometry : angle 0.55514 (39328) hydrogen bonds : bond 0.03089 ( 1117) hydrogen bonds : angle 3.98629 ( 3258) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 172 time to evaluate : 1.197 Fit side-chains REVERT: Q 1321 TYR cc_start: 0.5536 (OUTLIER) cc_final: 0.3647 (t80) REVERT: Q 1361 TRP cc_start: 0.7425 (t-100) cc_final: 0.6943 (t-100) REVERT: R 104 PHE cc_start: 0.7079 (t80) cc_final: 0.6338 (t80) REVERT: R 189 CYS cc_start: 0.9239 (OUTLIER) cc_final: 0.8624 (p) REVERT: R 244 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7614 (mp0) REVERT: R 719 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7819 (mpp-170) REVERT: S 104 GLU cc_start: 0.8434 (tp30) cc_final: 0.8209 (tp30) REVERT: T 187 GLU cc_start: 0.8619 (tp30) cc_final: 0.8302 (tm-30) REVERT: T 276 LYS cc_start: 0.8932 (ttpt) cc_final: 0.8708 (tttt) REVERT: T 396 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8164 (tm-30) REVERT: U 157 LYS cc_start: 0.9428 (OUTLIER) cc_final: 0.9018 (mptt) REVERT: U 183 LYS cc_start: 0.9111 (mmmt) cc_final: 0.8886 (mmmt) REVERT: U 279 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8132 (pp20) REVERT: V 312 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8349 (pt0) REVERT: X 154 ASN cc_start: 0.8752 (t0) cc_final: 0.8332 (t0) REVERT: X 298 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8018 (mp10) REVERT: Y 379 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.9040 (pp) REVERT: Y 393 GLU cc_start: 0.9190 (OUTLIER) cc_final: 0.8645 (mp0) outliers start: 64 outliers final: 19 residues processed: 224 average time/residue: 0.7388 time to fit residues: 191.4986 Evaluate side-chains 197 residues out of total 3173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 167 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1186 VAL Chi-restraints excluded: chain Q residue 1321 TYR Chi-restraints excluded: chain R residue 188 SER Chi-restraints excluded: chain R residue 189 CYS Chi-restraints excluded: chain R residue 241 LEU Chi-restraints excluded: chain R residue 244 GLU Chi-restraints excluded: chain R residue 719 ARG Chi-restraints excluded: chain S residue 68 SER Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 273 LEU Chi-restraints excluded: chain T residue 396 GLU Chi-restraints excluded: chain U residue 157 LYS Chi-restraints excluded: chain U residue 279 GLU Chi-restraints excluded: chain U residue 302 ASP Chi-restraints excluded: chain U residue 420 VAL Chi-restraints excluded: chain V residue 220 THR Chi-restraints excluded: chain V residue 271 GLN Chi-restraints excluded: chain V residue 312 GLU Chi-restraints excluded: chain V residue 331 ASN Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 285 LYS Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 298 GLN Chi-restraints excluded: chain X residue 362 ASP Chi-restraints excluded: chain Y residue 379 LEU Chi-restraints excluded: chain Y residue 393 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 130 optimal weight: 0.0170 chunk 107 optimal weight: 0.8980 chunk 289 optimal weight: 0.9980 chunk 131 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 200 optimal weight: 6.9990 chunk 291 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 259 optimal weight: 0.0870 chunk 274 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1106 ASN ** Q1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 121 HIS S 71 ASN S 75 ASN S 131 ASN ** T 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 190 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.072449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.052682 restraints weight = 76297.603| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 2.75 r_work: 0.2786 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 29062 Z= 0.102 Angle : 0.551 14.023 39328 Z= 0.267 Chirality : 0.042 0.382 4618 Planarity : 0.003 0.080 5041 Dihedral : 5.965 108.952 4006 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.78 % Allowed : 22.54 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.68 (0.14), residues: 3624 helix: 1.36 (0.13), residues: 1550 sheet: 0.44 (0.21), residues: 591 loop : -0.45 (0.16), residues: 1483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG S 39 TYR 0.013 0.001 TYR Q1321 PHE 0.013 0.001 PHE Q1391 TRP 0.011 0.001 TRP U 280 HIS 0.003 0.000 HIS R 121 Details of bonding type rmsd covalent geometry : bond 0.00235 (29062) covalent geometry : angle 0.55074 (39328) hydrogen bonds : bond 0.02796 ( 1117) hydrogen bonds : angle 3.90714 ( 3258) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 181 time to evaluate : 1.228 Fit side-chains revert: symmetry clash REVERT: Q 976 ASP cc_start: 0.9356 (m-30) cc_final: 0.9005 (p0) REVERT: Q 1321 TYR cc_start: 0.5309 (OUTLIER) cc_final: 0.4220 (t80) REVERT: Q 1361 TRP cc_start: 0.7444 (t-100) cc_final: 0.6977 (t-100) REVERT: Q 1391 PHE cc_start: 0.8014 (OUTLIER) cc_final: 0.7504 (t80) REVERT: Q 1432 MET cc_start: 0.7710 (ppp) cc_final: 0.7489 (ppp) REVERT: R 104 PHE cc_start: 0.7188 (t80) cc_final: 0.6468 (t80) REVERT: R 189 CYS cc_start: 0.9226 (OUTLIER) cc_final: 0.8623 (p) REVERT: R 244 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7622 (mp0) REVERT: T 187 GLU cc_start: 0.8632 (tp30) cc_final: 0.8295 (tm-30) REVERT: U 157 LYS cc_start: 0.9439 (OUTLIER) cc_final: 0.9022 (mptt) REVERT: U 279 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8132 (pp20) REVERT: U 311 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.8784 (mmm160) REVERT: V 271 GLN cc_start: 0.9124 (OUTLIER) cc_final: 0.8862 (mt0) REVERT: X 154 ASN cc_start: 0.8727 (t0) cc_final: 0.8297 (t0) REVERT: X 298 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8004 (mp10) REVERT: Y 379 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.9040 (pp) REVERT: Y 393 GLU cc_start: 0.9179 (OUTLIER) cc_final: 0.8631 (mp0) outliers start: 56 outliers final: 20 residues processed: 227 average time/residue: 0.8230 time to fit residues: 215.0131 Evaluate side-chains 196 residues out of total 3173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1186 VAL Chi-restraints excluded: chain Q residue 1321 TYR Chi-restraints excluded: chain Q residue 1391 PHE Chi-restraints excluded: chain R residue 188 SER Chi-restraints excluded: chain R residue 189 CYS Chi-restraints excluded: chain R residue 241 LEU Chi-restraints excluded: chain R residue 244 GLU Chi-restraints excluded: chain S residue 68 SER Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain S residue 125 TYR Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 273 LEU Chi-restraints excluded: chain T residue 396 GLU Chi-restraints excluded: chain U residue 157 LYS Chi-restraints excluded: chain U residue 279 GLU Chi-restraints excluded: chain U residue 302 ASP Chi-restraints excluded: chain U residue 311 ARG Chi-restraints excluded: chain U residue 418 VAL Chi-restraints excluded: chain U residue 420 VAL Chi-restraints excluded: chain V residue 220 THR Chi-restraints excluded: chain V residue 271 GLN Chi-restraints excluded: chain V residue 331 ASN Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain W residue 285 LYS Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 298 GLN Chi-restraints excluded: chain X residue 362 ASP Chi-restraints excluded: chain Y residue 379 LEU Chi-restraints excluded: chain Y residue 393 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 340 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 180 optimal weight: 5.9990 chunk 241 optimal weight: 6.9990 chunk 242 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 245 optimal weight: 5.9990 chunk 260 optimal weight: 0.5980 chunk 248 optimal weight: 4.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1106 ASN ** Q1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 269 ASN ** R 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 131 ASN U 23 HIS X 190 GLN ** X 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.069250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.049287 restraints weight = 77566.543| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 2.74 r_work: 0.2695 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2581 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 29062 Z= 0.246 Angle : 0.644 14.199 39328 Z= 0.315 Chirality : 0.046 0.400 4618 Planarity : 0.004 0.044 5041 Dihedral : 6.581 114.353 4006 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.13 % Allowed : 22.23 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.52 (0.14), residues: 3624 helix: 1.22 (0.13), residues: 1550 sheet: 0.34 (0.21), residues: 604 loop : -0.53 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG X 191 TYR 0.022 0.002 TYR V 295 PHE 0.018 0.002 PHE Q1167 TRP 0.015 0.002 TRP R 214 HIS 0.005 0.001 HIS R 121 Details of bonding type rmsd covalent geometry : bond 0.00578 (29062) covalent geometry : angle 0.64385 (39328) hydrogen bonds : bond 0.03973 ( 1117) hydrogen bonds : angle 4.23546 ( 3258) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 3173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 167 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1321 TYR cc_start: 0.6136 (OUTLIER) cc_final: 0.5216 (t80) REVERT: Q 1361 TRP cc_start: 0.7476 (t-100) cc_final: 0.7032 (t-100) REVERT: Q 1391 PHE cc_start: 0.8362 (OUTLIER) cc_final: 0.7878 (t80) REVERT: Q 1432 MET cc_start: 0.7572 (ppp) cc_final: 0.7352 (ppp) REVERT: R 104 PHE cc_start: 0.7410 (t80) cc_final: 0.6885 (t80) REVERT: R 189 CYS cc_start: 0.9303 (OUTLIER) cc_final: 0.8727 (p) REVERT: R 244 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7603 (mp0) REVERT: T 187 GLU cc_start: 0.8627 (tp30) cc_final: 0.8276 (tm-30) REVERT: T 276 LYS cc_start: 0.9025 (ttpt) cc_final: 0.8770 (tttt) REVERT: U 157 LYS cc_start: 0.9447 (OUTLIER) cc_final: 0.9043 (mptt) REVERT: U 243 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8561 (mt-10) REVERT: V 258 ARG cc_start: 0.7866 (ptm160) cc_final: 0.7563 (ppp80) REVERT: X 154 ASN cc_start: 0.8750 (t0) cc_final: 0.8323 (t0) REVERT: X 298 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8077 (mp10) REVERT: Y 379 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9066 (pp) REVERT: Y 393 GLU cc_start: 0.9198 (OUTLIER) cc_final: 0.8947 (mp0) REVERT: Z 313 GLU cc_start: 0.9083 (pm20) cc_final: 0.8837 (pm20) REVERT: Z 314 GLU cc_start: 0.8798 (pm20) cc_final: 0.8230 (pm20) outliers start: 67 outliers final: 21 residues processed: 218 average time/residue: 0.7032 time to fit residues: 177.5067 Evaluate side-chains 194 residues out of total 3173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 164 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1186 VAL Chi-restraints excluded: chain Q residue 1321 TYR Chi-restraints excluded: chain Q residue 1391 PHE Chi-restraints excluded: chain R residue 81 PHE Chi-restraints excluded: chain R residue 134 ILE Chi-restraints excluded: chain R residue 188 SER Chi-restraints excluded: chain R residue 189 CYS Chi-restraints excluded: chain R residue 241 LEU Chi-restraints excluded: chain R residue 244 GLU Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 273 LEU Chi-restraints excluded: chain T residue 396 GLU Chi-restraints excluded: chain U residue 157 LYS Chi-restraints excluded: chain U residue 243 GLU Chi-restraints excluded: chain U residue 302 ASP Chi-restraints excluded: chain U residue 418 VAL Chi-restraints excluded: chain U residue 420 VAL Chi-restraints excluded: chain V residue 40 VAL Chi-restraints excluded: chain V residue 220 THR Chi-restraints excluded: chain V residue 331 ASN Chi-restraints excluded: chain V residue 332 ILE Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain X residue 298 GLN Chi-restraints excluded: chain X residue 315 MET Chi-restraints excluded: chain X residue 362 ASP Chi-restraints excluded: chain Y residue 379 LEU Chi-restraints excluded: chain Y residue 393 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 166 optimal weight: 4.9990 chunk 218 optimal weight: 0.8980 chunk 344 optimal weight: 0.7980 chunk 145 optimal weight: 0.9990 chunk 156 optimal weight: 6.9990 chunk 303 optimal weight: 0.6980 chunk 312 optimal weight: 0.7980 chunk 340 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 244 optimal weight: 0.9980 chunk 40 optimal weight: 10.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q1207 GLN Q1323 GLN R 121 HIS R 269 ASN S 71 ASN S 131 ASN ** U 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 271 GLN X 190 GLN X 417 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.071160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.051268 restraints weight = 76519.433| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 2.76 r_work: 0.2741 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29062 Z= 0.119 Angle : 0.591 13.566 39328 Z= 0.286 Chirality : 0.043 0.376 4618 Planarity : 0.003 0.089 5041 Dihedral : 6.268 108.435 4006 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.37 % Allowed : 22.93 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.67 (0.14), residues: 3624 helix: 1.36 (0.13), residues: 1546 sheet: 0.39 (0.21), residues: 597 loop : -0.44 (0.16), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG S 39 TYR 0.025 0.001 TYR Q1321 PHE 0.011 0.001 PHE Q1294 TRP 0.013 0.001 TRP U 280 HIS 0.005 0.001 HIS R 745 Details of bonding type rmsd covalent geometry : bond 0.00278 (29062) covalent geometry : angle 0.59143 (39328) hydrogen bonds : bond 0.03067 ( 1117) hydrogen bonds : angle 4.01396 ( 3258) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 174 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 1323 GLN cc_start: 0.7516 (OUTLIER) cc_final: 0.7285 (tp40) REVERT: Q 1361 TRP cc_start: 0.7530 (t-100) cc_final: 0.7049 (t-100) REVERT: Q 1391 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.7825 (t80) REVERT: R 189 CYS cc_start: 0.9282 (OUTLIER) cc_final: 0.8714 (p) REVERT: T 187 GLU cc_start: 0.8644 (tp30) cc_final: 0.8315 (tm-30) REVERT: T 276 LYS cc_start: 0.9008 (ttpt) cc_final: 0.8805 (ttpp) REVERT: T 462 TYR cc_start: 0.6513 (OUTLIER) cc_final: 0.6060 (m-10) REVERT: U 157 LYS cc_start: 0.9453 (OUTLIER) cc_final: 0.9048 (mptt) REVERT: V 258 ARG cc_start: 0.7905 (ptm160) cc_final: 0.7525 (ptm-80) REVERT: X 154 ASN cc_start: 0.8717 (t0) cc_final: 0.8283 (t0) REVERT: X 298 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8047 (mp10) REVERT: Y 393 GLU cc_start: 0.9185 (OUTLIER) cc_final: 0.8953 (mp0) REVERT: Z 313 GLU cc_start: 0.9120 (pm20) cc_final: 0.8870 (pm20) REVERT: Z 314 GLU cc_start: 0.8844 (pm20) cc_final: 0.8251 (pm20) outliers start: 43 outliers final: 18 residues processed: 209 average time/residue: 0.7811 time to fit residues: 188.9261 Evaluate side-chains 186 residues out of total 3173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1186 VAL Chi-restraints excluded: chain Q residue 1323 GLN Chi-restraints excluded: chain Q residue 1391 PHE Chi-restraints excluded: chain R residue 81 PHE Chi-restraints excluded: chain R residue 134 ILE Chi-restraints excluded: chain R residue 188 SER Chi-restraints excluded: chain R residue 189 CYS Chi-restraints excluded: chain R residue 241 LEU Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 273 LEU Chi-restraints excluded: chain T residue 396 GLU Chi-restraints excluded: chain T residue 462 TYR Chi-restraints excluded: chain U residue 157 LYS Chi-restraints excluded: chain U residue 302 ASP Chi-restraints excluded: chain U residue 418 VAL Chi-restraints excluded: chain U residue 420 VAL Chi-restraints excluded: chain V residue 40 VAL Chi-restraints excluded: chain V residue 331 ASN Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 298 GLN Chi-restraints excluded: chain X residue 362 ASP Chi-restraints excluded: chain Y residue 393 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 293 optimal weight: 0.5980 chunk 281 optimal weight: 4.9990 chunk 210 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 278 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 245 optimal weight: 2.9990 chunk 348 optimal weight: 0.6980 chunk 187 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 333 optimal weight: 7.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 121 HIS S 75 ASN S 131 ASN ** U 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 271 GLN X 190 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.070576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.050667 restraints weight = 76970.844| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 2.75 r_work: 0.2731 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 29062 Z= 0.156 Angle : 0.608 13.357 39328 Z= 0.294 Chirality : 0.044 0.386 4618 Planarity : 0.003 0.052 5041 Dihedral : 6.292 109.955 4006 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.27 % Allowed : 23.02 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.67 (0.14), residues: 3624 helix: 1.37 (0.13), residues: 1547 sheet: 0.37 (0.21), residues: 607 loop : -0.44 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG U 147 TYR 0.049 0.001 TYR Q1321 PHE 0.051 0.001 PHE R 104 TRP 0.016 0.002 TRP U 280 HIS 0.004 0.001 HIS R 121 Details of bonding type rmsd covalent geometry : bond 0.00366 (29062) covalent geometry : angle 0.60769 (39328) hydrogen bonds : bond 0.03262 ( 1117) hydrogen bonds : angle 4.04019 ( 3258) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 1361 TRP cc_start: 0.7507 (t-100) cc_final: 0.7026 (t-100) REVERT: R 104 PHE cc_start: 0.7059 (t80) cc_final: 0.6670 (t80) REVERT: R 189 CYS cc_start: 0.9272 (OUTLIER) cc_final: 0.8704 (p) REVERT: R 227 MET cc_start: 0.8783 (mmm) cc_final: 0.8285 (mmm) REVERT: T 187 GLU cc_start: 0.8638 (tp30) cc_final: 0.8297 (tm-30) REVERT: T 462 TYR cc_start: 0.6577 (OUTLIER) cc_final: 0.6123 (m-10) REVERT: U 157 LYS cc_start: 0.9454 (OUTLIER) cc_final: 0.9044 (mptt) REVERT: V 258 ARG cc_start: 0.7925 (ptm160) cc_final: 0.7514 (ptm-80) REVERT: X 154 ASN cc_start: 0.8717 (t0) cc_final: 0.8287 (t0) REVERT: X 298 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8056 (mp10) REVERT: Y 379 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.9090 (pp) REVERT: Y 393 GLU cc_start: 0.9195 (OUTLIER) cc_final: 0.8963 (mp0) REVERT: Z 313 GLU cc_start: 0.9129 (pm20) cc_final: 0.8890 (pm20) REVERT: Z 314 GLU cc_start: 0.8879 (pm20) cc_final: 0.8264 (pm20) outliers start: 40 outliers final: 19 residues processed: 198 average time/residue: 0.8101 time to fit residues: 185.1532 Evaluate side-chains 186 residues out of total 3173 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 1186 VAL Chi-restraints excluded: chain R residue 81 PHE Chi-restraints excluded: chain R residue 134 ILE Chi-restraints excluded: chain R residue 188 SER Chi-restraints excluded: chain R residue 189 CYS Chi-restraints excluded: chain R residue 241 LEU Chi-restraints excluded: chain S residue 95 VAL Chi-restraints excluded: chain S residue 139 ILE Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 273 LEU Chi-restraints excluded: chain T residue 396 GLU Chi-restraints excluded: chain T residue 462 TYR Chi-restraints excluded: chain U residue 157 LYS Chi-restraints excluded: chain U residue 302 ASP Chi-restraints excluded: chain U residue 418 VAL Chi-restraints excluded: chain U residue 420 VAL Chi-restraints excluded: chain V residue 40 VAL Chi-restraints excluded: chain V residue 331 ASN Chi-restraints excluded: chain W residue 45 VAL Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 298 GLN Chi-restraints excluded: chain X residue 362 ASP Chi-restraints excluded: chain Y residue 45 VAL Chi-restraints excluded: chain Y residue 379 LEU Chi-restraints excluded: chain Y residue 393 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 208 optimal weight: 3.9990 chunk 219 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 236 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 152 optimal weight: 5.9990 chunk 215 optimal weight: 0.9980 chunk 214 optimal weight: 0.8980 chunk 289 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 121 HIS S 131 ASN ** U 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 271 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.071363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.051583 restraints weight = 77306.598| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.77 r_work: 0.2750 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29062 Z= 0.122 Angle : 0.594 13.157 39328 Z= 0.287 Chirality : 0.043 0.380 4618 Planarity : 0.004 0.092 5041 Dihedral : 6.165 106.690 4006 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.99 % Allowed : 23.37 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 0.71 (0.14), residues: 3624 helix: 1.40 (0.13), residues: 1546 sheet: 0.30 (0.21), residues: 617 loop : -0.39 (0.16), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG S 39 TYR 0.037 0.001 TYR Q1321 PHE 0.025 0.001 PHE S 32 TRP 0.016 0.001 TRP U 280 HIS 0.004 0.001 HIS R 121 Details of bonding type rmsd covalent geometry : bond 0.00284 (29062) covalent geometry : angle 0.59390 (39328) hydrogen bonds : bond 0.02998 ( 1117) hydrogen bonds : angle 3.97541 ( 3258) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10577.62 seconds wall clock time: 180 minutes 51.37 seconds (10851.37 seconds total)