Starting phenix.real_space_refine on Sat Aug 23 21:55:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hxx_35081/08_2025/8hxx_35081.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hxx_35081/08_2025/8hxx_35081.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hxx_35081/08_2025/8hxx_35081.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hxx_35081/08_2025/8hxx_35081.map" model { file = "/net/cci-nas-00/data/ceres_data/8hxx_35081/08_2025/8hxx_35081.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hxx_35081/08_2025/8hxx_35081.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 Zn 7 6.06 5 S 86 5.16 5 C 9509 2.51 5 N 2495 2.21 5 O 2776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s 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: 14873 Number of models: 1 Model: "" Number of chains: 10 Chain: "K" Number of atoms: 4597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4597 Classifications: {'peptide': 549} Link IDs: {'PTRANS': 12, 'TRANS': 536} Chain breaks: 2 Chain: "L" Number of atoms: 3048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3048 Classifications: {'peptide': 384} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 365} Chain: "M" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1483 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 175} Chain: "N" Number of atoms: 3073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 3073 Classifications: {'peptide': 375} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 354} Chain breaks: 4 Chain: "O" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1275 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 6, 'TRANS': 149} Chain: "P" Number of atoms: 1249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1249 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain breaks: 1 Chain: "E" Number of atoms: 141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 141 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 1, 'TRANS': 17} Chain breaks: 1 Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "P" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9819 SG CYS N 263 45.963 68.994 39.246 1.00123.38 S ATOM 9836 SG CYS N 266 48.958 69.515 41.538 1.00111.18 S ATOM 9989 SG CYS N 286 49.269 70.431 37.798 1.00106.05 S ATOM 11049 SG CYS N 417 77.849 73.690 75.575 1.00 96.77 S ATOM 11076 SG CYS N 420 79.211 75.302 78.750 1.00 97.97 S ATOM 11332 SG CYS N 451 79.007 77.343 75.487 1.00 98.53 S ATOM 9900 SG CYS N 275 36.695 65.748 31.700 1.00141.69 S ATOM 9921 SG CYS N 278 37.610 62.295 33.522 1.00141.96 S ATOM 10124 SG CYS N 303 39.677 63.649 30.741 1.00146.96 S ATOM 10147 SG CYS N 306 36.189 62.449 29.981 1.00147.99 S ATOM 11237 SG CYS N 440 73.876 67.215 66.045 1.00 96.86 S ATOM 11263 SG CYS N 443 76.742 64.878 67.738 1.00 82.67 S ATOM 11452 SG CYS N 466 77.409 68.411 66.364 1.00112.11 S ATOM 13527 SG CYS P 263 108.083 20.687 33.817 1.00188.32 S ATOM 13544 SG CYS P 266 111.335 21.756 32.197 1.00192.19 S ATOM 13697 SG CYS P 286 110.793 22.224 36.029 1.00184.29 S ATOM 13608 SG CYS P 275 98.333 17.940 40.836 1.00197.60 S ATOM 13629 SG CYS P 278 96.911 20.321 38.394 1.00204.77 S ATOM 13832 SG CYS P 303 98.410 21.767 41.533 1.00188.15 S ATOM 13855 SG CYS P 306 95.189 19.863 41.839 1.00201.77 S Time building chain proxies: 3.57, per 1000 atoms: 0.24 Number of scatterers: 14873 At special positions: 0 Unit cell: (140.7, 137.55, 133.35, 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) Zn 7 29.99 S 86 16.00 O 2776 8.00 N 2495 7.00 C 9509 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 643.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L 501 " pdb="ZN ZN L 501 " - pdb=" ND1 HIS L 188 " pdb=" ZN N 701 " pdb="ZN ZN N 701 " - pdb=" ND1 HIS N 283 " pdb="ZN ZN N 701 " - pdb=" SG CYS N 266 " pdb="ZN ZN N 701 " - pdb=" SG CYS N 263 " pdb="ZN ZN N 701 " - pdb=" SG CYS N 286 " pdb=" ZN N 702 " pdb="ZN ZN N 702 " - pdb=" ND1 HIS N 448 " pdb="ZN ZN N 702 " - pdb=" SG CYS N 417 " pdb="ZN ZN N 702 " - pdb=" SG CYS N 420 " pdb="ZN ZN N 702 " - pdb=" SG CYS N 451 " pdb=" ZN N 703 " pdb="ZN ZN N 703 " - pdb=" SG CYS N 303 " pdb="ZN ZN N 703 " - pdb=" SG CYS N 306 " pdb="ZN ZN N 703 " - pdb=" SG CYS N 275 " pdb="ZN ZN N 703 " - pdb=" SG CYS N 278 " pdb=" ZN N 704 " pdb="ZN ZN N 704 " - pdb=" NE2 HIS N 469 " pdb="ZN ZN N 704 " - pdb=" SG CYS N 440 " pdb="ZN ZN N 704 " - pdb=" SG CYS N 443 " pdb="ZN ZN N 704 " - pdb=" SG CYS N 466 " pdb=" ZN P 701 " pdb="ZN ZN P 701 " - pdb=" ND1 HIS P 283 " pdb="ZN ZN P 701 " - pdb=" SG CYS P 263 " pdb="ZN ZN P 701 " - pdb=" SG CYS P 266 " pdb="ZN ZN P 701 " - pdb=" SG CYS P 286 " pdb=" ZN P 702 " pdb="ZN ZN P 702 " - pdb=" SG CYS P 278 " pdb="ZN ZN P 702 " - pdb=" SG CYS P 303 " pdb="ZN ZN P 702 " - pdb=" SG CYS P 275 " pdb="ZN ZN P 702 " - pdb=" SG CYS P 306 " Number of angles added : 24 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3478 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 11 sheets defined 56.4% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'K' and resid 662 through 677 removed outlier: 5.321A pdb=" N PHE K 669 " --> pdb=" O GLU K 665 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N GLU K 670 " --> pdb=" O VAL K 666 " (cutoff:3.500A) Processing helix chain 'K' and resid 678 through 694 Processing helix chain 'K' and resid 698 through 710 Processing helix chain 'K' and resid 713 through 725 Processing helix chain 'K' and resid 759 through 764 removed outlier: 3.554A pdb=" N THR K 763 " --> pdb=" O PRO K 759 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE K 764 " --> pdb=" O LYS K 760 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 759 through 764' Processing helix chain 'K' and resid 771 through 778 Processing helix chain 'K' and resid 785 through 790 Processing helix chain 'K' and resid 801 through 840 removed outlier: 4.153A pdb=" N ASN K 840 " --> pdb=" O ASN K 836 " (cutoff:3.500A) Processing helix chain 'K' and resid 861 through 871 Processing helix chain 'K' and resid 872 through 886 removed outlier: 4.290A pdb=" N PHE K 877 " --> pdb=" O LYS K 873 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLU K 878 " --> pdb=" O GLU K 874 " (cutoff:3.500A) Processing helix chain 'K' and resid 886 through 929 removed outlier: 3.631A pdb=" N THR K 890 " --> pdb=" O HIS K 886 " (cutoff:3.500A) Proline residue: K 892 - end of helix removed outlier: 4.194A pdb=" N VAL K 915 " --> pdb=" O GLU K 911 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N PHE K 925 " --> pdb=" O GLN K 921 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N LYS K 926 " --> pdb=" O LYS K 922 " (cutoff:3.500A) Processing helix chain 'K' and resid 934 through 943 Processing helix chain 'K' and resid 944 through 964 removed outlier: 3.551A pdb=" N ILE K 952 " --> pdb=" O LEU K 948 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE K 964 " --> pdb=" O THR K 960 " (cutoff:3.500A) Processing helix chain 'K' and resid 982 through 999 removed outlier: 3.845A pdb=" N TYR K 986 " --> pdb=" O LYS K 982 " (cutoff:3.500A) Processing helix chain 'K' and resid 1003 through 1022 Processing helix chain 'K' and resid 1025 through 1032 Processing helix chain 'K' and resid 1141 through 1164 removed outlier: 3.641A pdb=" N ILE K1161 " --> pdb=" O ARG K1157 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET K1164 " --> pdb=" O GLU K1160 " (cutoff:3.500A) Processing helix chain 'K' and resid 1164 through 1174 Processing helix chain 'K' and resid 1178 through 1184 removed outlier: 3.538A pdb=" N LYS K1182 " --> pdb=" O VAL K1178 " (cutoff:3.500A) Processing helix chain 'K' and resid 1202 through 1216 Processing helix chain 'K' and resid 1220 through 1233 Processing helix chain 'K' and resid 1236 through 1240 Processing helix chain 'K' and resid 1241 through 1258 Processing helix chain 'K' and resid 1262 through 1275 Processing helix chain 'K' and resid 1280 through 1294 removed outlier: 3.673A pdb=" N HIS K1293 " --> pdb=" O GLN K1289 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET K1294 " --> pdb=" O VAL K1290 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 32 removed outlier: 4.070A pdb=" N GLY L 30 " --> pdb=" O ALA L 27 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N TYR L 32 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 55 removed outlier: 4.244A pdb=" N ARG L 46 " --> pdb=" O PRO L 42 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET L 47 " --> pdb=" O HIS L 43 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 61 Processing helix chain 'L' and resid 70 through 75 Processing helix chain 'L' and resid 79 through 89 Processing helix chain 'L' and resid 91 through 95 removed outlier: 4.021A pdb=" N LEU L 94 " --> pdb=" O PRO L 91 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLU L 95 " --> pdb=" O ASP L 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 91 through 95' Processing helix chain 'L' and resid 98 through 104 Processing helix chain 'L' and resid 115 through 136 Processing helix chain 'L' and resid 164 through 175 removed outlier: 3.578A pdb=" N LEU L 168 " --> pdb=" O ASN L 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 190 through 197 Processing helix chain 'L' and resid 226 through 230 removed outlier: 3.554A pdb=" N LYS L 230 " --> pdb=" O GLY L 227 " (cutoff:3.500A) Processing helix chain 'L' and resid 243 through 263 Proline residue: L 253 - end of helix Processing helix chain 'L' and resid 272 through 276 removed outlier: 3.694A pdb=" N SER L 275 " --> pdb=" O GLY L 272 " (cutoff:3.500A) Processing helix chain 'L' and resid 287 through 300 removed outlier: 4.138A pdb=" N CYS L 294 " --> pdb=" O GLY L 290 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL L 295 " --> pdb=" O HIS L 291 " (cutoff:3.500A) Processing helix chain 'L' and resid 314 through 329 Processing helix chain 'L' and resid 343 through 348 removed outlier: 3.564A pdb=" N TYR L 347 " --> pdb=" O TYR L 344 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLY L 348 " --> pdb=" O GLU L 345 " (cutoff:3.500A) Processing helix chain 'L' and resid 365 through 380 Processing helix chain 'L' and resid 381 through 383 No H-bonds generated for 'chain 'L' and resid 381 through 383' Processing helix chain 'M' and resid 225 through 241 Processing helix chain 'M' and resid 253 through 269 removed outlier: 3.631A pdb=" N GLN M 267 " --> pdb=" O HIS M 263 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU M 268 " --> pdb=" O GLU M 264 " (cutoff:3.500A) Processing helix chain 'M' and resid 271 through 297 removed outlier: 4.815A pdb=" N GLY M 294 " --> pdb=" O ASP M 290 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ASN M 295 " --> pdb=" O LYS M 291 " (cutoff:3.500A) Processing helix chain 'M' and resid 302 through 316 Processing helix chain 'M' and resid 321 through 326 Processing helix chain 'M' and resid 327 through 344 removed outlier: 3.663A pdb=" N LEU M 331 " --> pdb=" O GLY M 327 " (cutoff:3.500A) Proline residue: M 339 - end of helix Processing helix chain 'M' and resid 348 through 369 removed outlier: 3.847A pdb=" N MET M 368 " --> pdb=" O VAL M 364 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS M 369 " --> pdb=" O TRP M 365 " (cutoff:3.500A) Processing helix chain 'M' and resid 369 through 374 removed outlier: 3.572A pdb=" N TYR M 373 " --> pdb=" O HIS M 369 " (cutoff:3.500A) Processing helix chain 'M' and resid 391 through 399 Processing helix chain 'N' and resid 100 through 104 removed outlier: 3.532A pdb=" N GLU N 104 " --> pdb=" O THR N 101 " (cutoff:3.500A) Processing helix chain 'N' and resid 120 through 128 removed outlier: 4.964A pdb=" N GLU N 126 " --> pdb=" O LYS N 122 " (cutoff:3.500A) Processing helix chain 'N' and resid 171 through 176 removed outlier: 3.821A pdb=" N MET N 175 " --> pdb=" O LEU N 171 " (cutoff:3.500A) Processing helix chain 'N' and resid 303 through 315 Processing helix chain 'N' and resid 318 through 330 Processing helix chain 'N' and resid 336 through 343 removed outlier: 3.801A pdb=" N ILE N 343 " --> pdb=" O LEU N 339 " (cutoff:3.500A) Processing helix chain 'N' and resid 354 through 359 Processing helix chain 'N' and resid 382 through 388 removed outlier: 3.769A pdb=" N LEU N 386 " --> pdb=" O THR N 382 " (cutoff:3.500A) Processing helix chain 'N' and resid 430 through 434 Processing helix chain 'N' and resid 546 through 577 removed outlier: 3.527A pdb=" N PHE N 569 " --> pdb=" O LYS N 565 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N SER N 572 " --> pdb=" O GLN N 568 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU N 577 " --> pdb=" O LEU N 573 " (cutoff:3.500A) Processing helix chain 'O' and resid 225 through 241 removed outlier: 3.559A pdb=" N VAL O 231 " --> pdb=" O LYS O 227 " (cutoff:3.500A) Processing helix chain 'O' and resid 253 through 269 removed outlier: 3.933A pdb=" N VAL O 257 " --> pdb=" O THR O 253 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLN O 267 " --> pdb=" O HIS O 263 " (cutoff:3.500A) Processing helix chain 'O' and resid 271 through 293 removed outlier: 3.523A pdb=" N LEU O 293 " --> pdb=" O PHE O 289 " (cutoff:3.500A) Processing helix chain 'O' and resid 302 through 314 Processing helix chain 'O' and resid 328 through 343 Proline residue: O 339 - end of helix removed outlier: 3.514A pdb=" N SER O 343 " --> pdb=" O PRO O 339 " (cutoff:3.500A) Processing helix chain 'O' and resid 349 through 369 removed outlier: 3.756A pdb=" N GLN O 353 " --> pdb=" O LEU O 349 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N HIS O 369 " --> pdb=" O TRP O 365 " (cutoff:3.500A) Processing helix chain 'O' and resid 369 through 374 removed outlier: 4.469A pdb=" N TYR O 373 " --> pdb=" O HIS O 369 " (cutoff:3.500A) Processing helix chain 'P' and resid 303 through 313 Processing helix chain 'P' and resid 315 through 330 removed outlier: 4.037A pdb=" N LEU P 319 " --> pdb=" O SER P 315 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASN P 330 " --> pdb=" O PHE P 326 " (cutoff:3.500A) Processing helix chain 'P' and resid 331 through 335 removed outlier: 3.554A pdb=" N LYS P 334 " --> pdb=" O ASN P 331 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILE P 335 " --> pdb=" O ASN P 332 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 331 through 335' Processing helix chain 'P' and resid 336 through 345 removed outlier: 4.125A pdb=" N PHE P 341 " --> pdb=" O ALA P 337 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ASN P 342 " --> pdb=" O LYS P 338 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ILE P 343 " --> pdb=" O LEU P 339 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ASP P 344 " --> pdb=" O LEU P 340 " (cutoff:3.500A) Processing helix chain 'P' and resid 354 through 359 removed outlier: 3.854A pdb=" N GLU P 359 " --> pdb=" O ASN P 355 " (cutoff:3.500A) Processing helix chain 'P' and resid 533 through 538 removed outlier: 3.609A pdb=" N ASP P 536 " --> pdb=" O PHE P 533 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE P 537 " --> pdb=" O ASN P 534 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS P 538 " --> pdb=" O GLN P 535 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 533 through 538' Processing helix chain 'P' and resid 543 through 580 Processing helix chain 'E' and resid 18 through 22 Processing sheet with id=AA1, first strand: chain 'K' and resid 756 through 757 Processing sheet with id=AA2, first strand: chain 'K' and resid 975 through 978 removed outlier: 3.904A pdb=" N HIS K1311 " --> pdb=" O ASP K1306 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 1129 through 1130 removed outlier: 3.526A pdb=" N ILE K1130 " --> pdb=" O THR K1278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 233 through 238 removed outlier: 7.760A pdb=" N VAL L 234 " --> pdb=" O VAL L 203 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N THR L 205 " --> pdb=" O VAL L 234 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N VAL L 236 " --> pdb=" O THR L 205 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N SER L 207 " --> pdb=" O VAL L 236 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU L 238 " --> pdb=" O SER L 207 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N HIS L 209 " --> pdb=" O LEU L 238 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL L 180 " --> pdb=" O MET L 204 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N CYS L 206 " --> pdb=" O VAL L 180 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N TYR L 182 " --> pdb=" O CYS L 206 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N PHE L 208 " --> pdb=" O TYR L 182 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ASP L 184 " --> pdb=" O PHE L 208 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N LYS L 210 " --> pdb=" O ASP L 184 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL L 21 " --> pdb=" O GLU L 62 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N TYR L 64 " --> pdb=" O VAL L 21 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TYR L 23 " --> pdb=" O TYR L 64 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ALA L 66 " --> pdb=" O TYR L 23 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ILE L 63 " --> pdb=" O GLU N 177 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N SER N 179 " --> pdb=" O ILE L 63 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ARG L 65 " --> pdb=" O SER N 179 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 244 through 246 Processing sheet with id=AA6, first strand: chain 'N' and resid 85 through 87 removed outlier: 3.559A pdb=" N GLU N 86 " --> pdb=" O LYS N 95 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LYS N 95 " --> pdb=" O GLU N 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'N' and resid 281 through 283 Processing sheet with id=AA8, first strand: chain 'N' and resid 365 through 366 Processing sheet with id=AA9, first strand: chain 'N' and resid 437 through 439 Processing sheet with id=AB1, first strand: chain 'N' and resid 473 through 477 Processing sheet with id=AB2, first strand: chain 'N' and resid 505 through 506 removed outlier: 6.995A pdb=" N TYR N 506 " --> pdb=" O GLN P 541 " (cutoff:3.500A) 698 hydrogen bonds defined for protein. 2034 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: 2.62 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3964 1.33 - 1.46: 3086 1.46 - 1.58: 8015 1.58 - 1.70: 3 1.70 - 1.82: 127 Bond restraints: 15195 Sorted by residual: bond pdb=" CB PRO O 319 " pdb=" CG PRO O 319 " ideal model delta sigma weight residual 1.492 1.630 -0.138 5.00e-02 4.00e+02 7.64e+00 bond pdb=" CA GLN L 72 " pdb=" C GLN L 72 " ideal model delta sigma weight residual 1.524 1.492 0.032 1.26e-02 6.30e+03 6.43e+00 bond pdb=" N MET L 259 " pdb=" CA MET L 259 " ideal model delta sigma weight residual 1.459 1.433 0.026 1.19e-02 7.06e+03 4.70e+00 bond pdb=" CB ASP N 383 " pdb=" CG ASP N 383 " ideal model delta sigma weight residual 1.516 1.569 -0.053 2.50e-02 1.60e+03 4.56e+00 bond pdb=" CA PHE M 289 " pdb=" C PHE M 289 " ideal model delta sigma weight residual 1.524 1.498 0.026 1.24e-02 6.50e+03 4.46e+00 ... (remaining 15190 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.43: 20209 3.43 - 6.86: 237 6.86 - 10.29: 33 10.29 - 13.72: 11 13.72 - 17.15: 4 Bond angle restraints: 20494 Sorted by residual: angle pdb=" CA PRO O 319 " pdb=" N PRO O 319 " pdb=" CD PRO O 319 " ideal model delta sigma weight residual 112.00 100.72 11.28 1.40e+00 5.10e-01 6.49e+01 angle pdb=" CA GLU O 308 " pdb=" CB GLU O 308 " pdb=" CG GLU O 308 " ideal model delta sigma weight residual 114.10 126.93 -12.83 2.00e+00 2.50e-01 4.11e+01 angle pdb=" CB LYS N 298 " pdb=" CG LYS N 298 " pdb=" CD LYS N 298 " ideal model delta sigma weight residual 111.30 124.94 -13.64 2.30e+00 1.89e-01 3.52e+01 angle pdb=" CB MET O 296 " pdb=" CG MET O 296 " pdb=" SD MET O 296 " ideal model delta sigma weight residual 112.70 128.98 -16.28 3.00e+00 1.11e-01 2.94e+01 angle pdb=" CA MET N 560 " pdb=" CB MET N 560 " pdb=" CG MET N 560 " ideal model delta sigma weight residual 114.10 124.70 -10.60 2.00e+00 2.50e-01 2.81e+01 ... (remaining 20489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 7875 17.64 - 35.29: 1056 35.29 - 52.93: 230 52.93 - 70.58: 34 70.58 - 88.22: 16 Dihedral angle restraints: 9211 sinusoidal: 3846 harmonic: 5365 Sorted by residual: dihedral pdb=" CA ASP P 288 " pdb=" C ASP P 288 " pdb=" N PRO P 289 " pdb=" CA PRO P 289 " ideal model delta harmonic sigma weight residual 180.00 152.78 27.22 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA PRO P 354 " pdb=" C PRO P 354 " pdb=" N ASN P 355 " pdb=" CA ASN P 355 " ideal model delta harmonic sigma weight residual 180.00 -156.15 -23.85 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA LEU O 269 " pdb=" C LEU O 269 " pdb=" N GLU O 270 " pdb=" CA GLU O 270 " ideal model delta harmonic sigma weight residual 180.00 -156.41 -23.59 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 9208 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1828 0.061 - 0.122: 334 0.122 - 0.184: 48 0.184 - 0.245: 7 0.245 - 0.306: 4 Chirality restraints: 2221 Sorted by residual: chirality pdb=" CA PRO O 319 " pdb=" N PRO O 319 " pdb=" C PRO O 319 " pdb=" CB PRO O 319 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CB VAL O 337 " pdb=" CA VAL O 337 " pdb=" CG1 VAL O 337 " pdb=" CG2 VAL O 337 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CB ILE O 329 " pdb=" CA ILE O 329 " pdb=" CG1 ILE O 329 " pdb=" CG2 ILE O 329 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 2218 not shown) Planarity restraints: 2616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU N 507 " -0.088 5.00e-02 4.00e+02 1.31e-01 2.76e+01 pdb=" N PRO N 508 " 0.227 5.00e-02 4.00e+02 pdb=" CA PRO N 508 " -0.070 5.00e-02 4.00e+02 pdb=" CD PRO N 508 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS O 318 " -0.084 5.00e-02 4.00e+02 1.19e-01 2.26e+01 pdb=" N PRO O 319 " 0.205 5.00e-02 4.00e+02 pdb=" CA PRO O 319 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO O 319 " -0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP P 288 " 0.063 5.00e-02 4.00e+02 9.56e-02 1.46e+01 pdb=" N PRO P 289 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO P 289 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO P 289 " 0.052 5.00e-02 4.00e+02 ... (remaining 2613 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 129 2.57 - 3.15: 11887 3.15 - 3.73: 24940 3.73 - 4.32: 34106 4.32 - 4.90: 55229 Nonbonded interactions: 126291 Sorted by model distance: nonbonded pdb=" OD1 ASP L 186 " pdb="ZN ZN L 501 " model vdw 1.982 2.230 nonbonded pdb=" OD2 ASP L 274 " pdb="ZN ZN L 501 " model vdw 1.989 2.230 nonbonded pdb=" OD2 ASP L 186 " pdb="ZN ZN L 501 " model vdw 2.007 2.230 nonbonded pdb=" OD1 ASP L 186 " pdb=" OD2 ASP L 274 " model vdw 2.230 3.040 nonbonded pdb=" CG ASP L 186 " pdb="ZN ZN L 501 " model vdw 2.246 2.460 ... (remaining 126286 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 'M' and resid 221 through 376) selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.700 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:8.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 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 : 0.005 0.188 15220 Z= 0.279 Angle : 0.990 17.149 20518 Z= 0.546 Chirality : 0.050 0.306 2221 Planarity : 0.007 0.131 2616 Dihedral : 16.310 88.224 5733 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.18 % Allowed : 23.92 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.63 % 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: -1.25 (0.18), residues: 1787 helix: -0.60 (0.16), residues: 884 sheet: -0.05 (0.56), residues: 93 loop : -1.06 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG N 369 TYR 0.029 0.002 TYR O 373 PHE 0.045 0.002 PHE N 387 TRP 0.014 0.001 TRP K1151 HIS 0.018 0.001 HIS O 330 Details of bonding type rmsd covalent geometry : bond 0.00510 (15195) covalent geometry : angle 0.98315 (20494) hydrogen bonds : bond 0.14170 ( 698) hydrogen bonds : angle 6.72743 ( 2034) metal coordination : bond 0.03858 ( 25) metal coordination : angle 3.49374 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 240 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 698 ASP cc_start: 0.7897 (t70) cc_final: 0.7532 (m-30) REVERT: K 1294 MET cc_start: 0.8842 (ptm) cc_final: 0.8117 (ptm) REVERT: K 1300 MET cc_start: 0.8979 (tpp) cc_final: 0.7892 (tpp) REVERT: N 122 LYS cc_start: 0.9282 (pttt) cc_final: 0.9024 (ptpp) REVERT: N 369 ARG cc_start: 0.8903 (mtm110) cc_final: 0.8691 (mtm-85) REVERT: N 564 ARG cc_start: 0.8524 (tmm160) cc_final: 0.8137 (tmm-80) REVERT: O 289 PHE cc_start: 0.8508 (t80) cc_final: 0.8130 (t80) REVERT: O 295 ASN cc_start: 0.7310 (t0) cc_final: 0.6993 (t0) REVERT: O 333 ARG cc_start: 0.8267 (ttm110) cc_final: 0.8018 (mtp-110) REVERT: P 343 ILE cc_start: 0.8216 (mp) cc_final: 0.7624 (mt) outliers start: 3 outliers final: 5 residues processed: 242 average time/residue: 0.6302 time to fit residues: 168.3993 Evaluate side-chains 197 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 192 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 762 ASP Chi-restraints excluded: chain N residue 517 ASN Chi-restraints excluded: chain O residue 299 TYR Chi-restraints excluded: chain O residue 371 ASP Chi-restraints excluded: chain P residue 276 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.0980 chunk 149 optimal weight: 0.4980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 352 GLN N 385 GLN O 295 ASN ** P 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.092559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.063049 restraints weight = 35146.782| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 3.14 r_work: 0.2834 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15220 Z= 0.123 Angle : 0.592 11.023 20518 Z= 0.303 Chirality : 0.041 0.206 2221 Planarity : 0.005 0.077 2616 Dihedral : 4.972 88.407 1970 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.93 % Allowed : 22.49 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.63 % 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: 0.22 (0.19), residues: 1787 helix: 0.88 (0.17), residues: 893 sheet: 0.28 (0.58), residues: 91 loop : -0.66 (0.21), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 496 TYR 0.017 0.001 TYR O 238 PHE 0.014 0.001 PHE K 723 TRP 0.010 0.001 TRP K 912 HIS 0.003 0.001 HIS N 469 Details of bonding type rmsd covalent geometry : bond 0.00271 (15195) covalent geometry : angle 0.58513 (20494) hydrogen bonds : bond 0.04024 ( 698) hydrogen bonds : angle 4.64352 ( 2034) metal coordination : bond 0.01114 ( 25) metal coordination : angle 2.70721 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 209 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 698 ASP cc_start: 0.7898 (t70) cc_final: 0.7532 (m-30) REVERT: K 1026 PHE cc_start: 0.8195 (OUTLIER) cc_final: 0.7833 (t80) REVERT: L 53 MET cc_start: 0.9548 (mmm) cc_final: 0.9055 (mmm) REVERT: L 96 MET cc_start: 0.8880 (mpt) cc_final: 0.8673 (mpp) REVERT: M 267 GLN cc_start: 0.9133 (OUTLIER) cc_final: 0.8700 (mp10) REVERT: M 277 GLN cc_start: 0.9181 (mt0) cc_final: 0.8847 (mm-40) REVERT: M 308 GLU cc_start: 0.9098 (pt0) cc_final: 0.8743 (pp20) REVERT: M 347 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7898 (ttm) REVERT: O 289 PHE cc_start: 0.9034 (t80) cc_final: 0.8765 (t80) REVERT: O 303 ARG cc_start: 0.8759 (mtm-85) cc_final: 0.8524 (mtm-85) REVERT: O 333 ARG cc_start: 0.8514 (ttm110) cc_final: 0.8185 (mtp-110) outliers start: 49 outliers final: 13 residues processed: 238 average time/residue: 0.5633 time to fit residues: 149.7293 Evaluate side-chains 199 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 183 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 828 ILE Chi-restraints excluded: chain K residue 857 HIS Chi-restraints excluded: chain K residue 1026 PHE Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 316 ARG Chi-restraints excluded: chain M residue 267 GLN Chi-restraints excluded: chain M residue 336 SER Chi-restraints excluded: chain M residue 347 MET Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 123 ILE Chi-restraints excluded: chain N residue 312 ILE Chi-restraints excluded: chain N residue 383 ASP Chi-restraints excluded: chain N residue 566 LEU Chi-restraints excluded: chain O residue 282 CYS Chi-restraints excluded: chain O residue 291 LYS Chi-restraints excluded: chain O residue 299 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 146 optimal weight: 8.9990 chunk 118 optimal weight: 20.0000 chunk 95 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 10 optimal weight: 0.3980 chunk 161 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 84 optimal weight: 0.0030 chunk 80 optimal weight: 0.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 350 GLN O 223 GLN O 358 GLN ** P 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 350 GLN P 535 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.091610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.061574 restraints weight = 35511.493| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 3.22 r_work: 0.2824 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15220 Z= 0.118 Angle : 0.581 10.269 20518 Z= 0.291 Chirality : 0.041 0.206 2221 Planarity : 0.004 0.062 2616 Dihedral : 4.241 47.750 1962 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.75 % Allowed : 23.33 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.63 % 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 (0.20), residues: 1787 helix: 1.30 (0.17), residues: 895 sheet: 0.28 (0.58), residues: 91 loop : -0.46 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 496 TYR 0.022 0.001 TYR O 281 PHE 0.016 0.001 PHE N 387 TRP 0.009 0.001 TRP K 912 HIS 0.011 0.001 HIS O 330 Details of bonding type rmsd covalent geometry : bond 0.00263 (15195) covalent geometry : angle 0.57632 (20494) hydrogen bonds : bond 0.03645 ( 698) hydrogen bonds : angle 4.34849 ( 2034) metal coordination : bond 0.00841 ( 25) metal coordination : angle 2.30815 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 204 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 698 ASP cc_start: 0.8047 (t70) cc_final: 0.7569 (m-30) REVERT: K 701 ASP cc_start: 0.9380 (m-30) cc_final: 0.9140 (m-30) REVERT: K 816 GLU cc_start: 0.9235 (OUTLIER) cc_final: 0.8947 (tm-30) REVERT: K 1026 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.7905 (t80) REVERT: L 220 GLU cc_start: 0.8495 (tm-30) cc_final: 0.7956 (tm-30) REVERT: L 288 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8423 (ttm) REVERT: M 267 GLN cc_start: 0.9195 (OUTLIER) cc_final: 0.8876 (mp10) REVERT: M 277 GLN cc_start: 0.9176 (mt0) cc_final: 0.8858 (mm-40) REVERT: M 308 GLU cc_start: 0.9080 (pt0) cc_final: 0.8772 (pp20) REVERT: N 316 MET cc_start: 0.8365 (pmm) cc_final: 0.7799 (pmm) REVERT: N 383 ASP cc_start: 0.9082 (p0) cc_final: 0.8628 (t0) REVERT: N 387 PHE cc_start: 0.9256 (m-10) cc_final: 0.8982 (m-10) REVERT: N 560 MET cc_start: 0.8983 (mpp) cc_final: 0.8639 (mpp) REVERT: O 261 TYR cc_start: 0.8739 (t80) cc_final: 0.8420 (t80) REVERT: O 264 GLU cc_start: 0.9440 (mt-10) cc_final: 0.9223 (mt-10) REVERT: O 280 GLU cc_start: 0.8679 (tp30) cc_final: 0.8344 (tp30) REVERT: O 295 ASN cc_start: 0.7929 (t0) cc_final: 0.6528 (t0) REVERT: O 333 ARG cc_start: 0.8617 (ttm110) cc_final: 0.7884 (mtp-110) REVERT: O 353 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8365 (mp10) REVERT: P 353 LEU cc_start: 0.7073 (OUTLIER) cc_final: 0.6732 (tm) outliers start: 46 outliers final: 15 residues processed: 228 average time/residue: 0.5890 time to fit residues: 148.8853 Evaluate side-chains 206 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 816 GLU Chi-restraints excluded: chain K residue 857 HIS Chi-restraints excluded: chain K residue 886 HIS Chi-restraints excluded: chain K residue 1026 PHE Chi-restraints excluded: chain K residue 1191 LEU Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain L residue 316 ARG Chi-restraints excluded: chain M residue 267 GLN Chi-restraints excluded: chain M residue 336 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 312 ILE Chi-restraints excluded: chain N residue 382 THR Chi-restraints excluded: chain N residue 566 LEU Chi-restraints excluded: chain O residue 282 CYS Chi-restraints excluded: chain O residue 291 LYS Chi-restraints excluded: chain O residue 299 TYR Chi-restraints excluded: chain O residue 326 TYR Chi-restraints excluded: chain O residue 353 GLN Chi-restraints excluded: chain P residue 353 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 41 optimal weight: 8.9990 chunk 96 optimal weight: 7.9990 chunk 114 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 23 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 147 optimal weight: 10.0000 chunk 141 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 120 optimal weight: 0.0870 overall best weight: 2.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 305 GLN N 503 GLN O 277 GLN ** P 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 350 GLN ** P 535 GLN ** 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 = 0.3535 r_free = 0.3535 target = 0.087982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.057652 restraints weight = 35445.254| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 3.16 r_work: 0.2721 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15220 Z= 0.207 Angle : 0.608 9.223 20518 Z= 0.309 Chirality : 0.042 0.231 2221 Planarity : 0.004 0.054 2616 Dihedral : 4.268 49.138 1962 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.71 % Allowed : 22.85 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.63 % 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: 0.85 (0.20), residues: 1787 helix: 1.42 (0.17), residues: 912 sheet: 0.15 (0.55), residues: 92 loop : -0.35 (0.22), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG N 384 TYR 0.022 0.002 TYR O 281 PHE 0.013 0.001 PHE K 995 TRP 0.013 0.001 TRP K1151 HIS 0.009 0.001 HIS O 330 Details of bonding type rmsd covalent geometry : bond 0.00470 (15195) covalent geometry : angle 0.60310 (20494) hydrogen bonds : bond 0.03818 ( 698) hydrogen bonds : angle 4.22525 ( 2034) metal coordination : bond 0.01395 ( 25) metal coordination : angle 2.41917 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 196 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 698 ASP cc_start: 0.8078 (t70) cc_final: 0.7563 (m-30) REVERT: K 701 ASP cc_start: 0.9405 (m-30) cc_final: 0.9180 (m-30) REVERT: K 816 GLU cc_start: 0.9313 (OUTLIER) cc_final: 0.8957 (tm-30) REVERT: K 911 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.8659 (pp20) REVERT: L 220 GLU cc_start: 0.8556 (tm-30) cc_final: 0.7949 (tm-30) REVERT: M 267 GLN cc_start: 0.9165 (OUTLIER) cc_final: 0.8596 (mp10) REVERT: M 277 GLN cc_start: 0.9215 (mt0) cc_final: 0.8884 (mm-40) REVERT: M 308 GLU cc_start: 0.9121 (pt0) cc_final: 0.8751 (pp20) REVERT: N 122 LYS cc_start: 0.9284 (pttt) cc_final: 0.8980 (ptpp) REVERT: N 316 MET cc_start: 0.8362 (pmm) cc_final: 0.7866 (pmm) REVERT: O 261 TYR cc_start: 0.8617 (t80) cc_final: 0.8206 (t80) REVERT: O 264 GLU cc_start: 0.9461 (mt-10) cc_final: 0.9184 (mt-10) REVERT: O 280 GLU cc_start: 0.8683 (tp30) cc_final: 0.8302 (tp30) REVERT: O 289 PHE cc_start: 0.8923 (t80) cc_final: 0.8702 (t80) REVERT: O 308 GLU cc_start: 0.9333 (OUTLIER) cc_final: 0.9128 (pm20) REVERT: O 353 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.8457 (mp10) outliers start: 62 outliers final: 23 residues processed: 234 average time/residue: 0.6087 time to fit residues: 157.6020 Evaluate side-chains 204 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 801 ASN Chi-restraints excluded: chain K residue 816 GLU Chi-restraints excluded: chain K residue 828 ILE Chi-restraints excluded: chain K residue 911 GLU Chi-restraints excluded: chain K residue 915 VAL Chi-restraints excluded: chain K residue 957 VAL Chi-restraints excluded: chain K residue 1191 LEU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain M residue 267 GLN Chi-restraints excluded: chain M residue 287 LEU Chi-restraints excluded: chain M residue 323 ILE Chi-restraints excluded: chain M residue 336 SER Chi-restraints excluded: chain M residue 367 LEU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 123 ILE Chi-restraints excluded: chain N residue 312 ILE Chi-restraints excluded: chain N residue 382 THR Chi-restraints excluded: chain N residue 396 THR Chi-restraints excluded: chain N residue 566 LEU Chi-restraints excluded: chain O residue 267 GLN Chi-restraints excluded: chain O residue 282 CYS Chi-restraints excluded: chain O residue 291 LYS Chi-restraints excluded: chain O residue 299 TYR Chi-restraints excluded: chain O residue 308 GLU Chi-restraints excluded: chain O residue 326 TYR Chi-restraints excluded: chain O residue 353 GLN Chi-restraints excluded: chain O residue 369 HIS Chi-restraints excluded: chain P residue 276 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 30 optimal weight: 0.6980 chunk 122 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 170 optimal weight: 3.9990 chunk 140 optimal weight: 0.0770 chunk 150 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 139 optimal weight: 0.8980 chunk 132 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 295 ASN ** O 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 350 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.089697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.060100 restraints weight = 35104.975| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 3.11 r_work: 0.2766 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15220 Z= 0.120 Angle : 0.584 9.866 20518 Z= 0.293 Chirality : 0.041 0.275 2221 Planarity : 0.004 0.053 2616 Dihedral : 4.185 52.249 1962 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.17 % Allowed : 23.98 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.63 % 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: 0.99 (0.20), residues: 1787 helix: 1.56 (0.18), residues: 894 sheet: 0.04 (0.55), residues: 91 loop : -0.25 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG N 369 TYR 0.024 0.001 TYR O 281 PHE 0.010 0.001 PHE K 723 TRP 0.007 0.001 TRP K 912 HIS 0.015 0.001 HIS O 330 Details of bonding type rmsd covalent geometry : bond 0.00274 (15195) covalent geometry : angle 0.58020 (20494) hydrogen bonds : bond 0.03563 ( 698) hydrogen bonds : angle 4.11582 ( 2034) metal coordination : bond 0.00597 ( 25) metal coordination : angle 1.98272 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 205 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 698 ASP cc_start: 0.8142 (t70) cc_final: 0.7732 (t0) REVERT: K 816 GLU cc_start: 0.9266 (OUTLIER) cc_final: 0.8814 (tm-30) REVERT: K 911 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8631 (pp20) REVERT: M 267 GLN cc_start: 0.9210 (OUTLIER) cc_final: 0.8778 (mp10) REVERT: M 277 GLN cc_start: 0.9194 (mt0) cc_final: 0.8878 (mm-40) REVERT: M 308 GLU cc_start: 0.9071 (pt0) cc_final: 0.8750 (pp20) REVERT: M 361 ASP cc_start: 0.9196 (OUTLIER) cc_final: 0.8741 (m-30) REVERT: N 122 LYS cc_start: 0.9211 (pttt) cc_final: 0.8911 (ptpp) REVERT: N 501 LYS cc_start: 0.9090 (tptt) cc_final: 0.8806 (tptt) REVERT: N 515 GLN cc_start: 0.8587 (mp-120) cc_final: 0.8127 (tm-30) REVERT: O 233 VAL cc_start: 0.8067 (t) cc_final: 0.7832 (m) REVERT: O 300 ARG cc_start: 0.6671 (OUTLIER) cc_final: 0.6248 (mpt180) REVERT: O 333 ARG cc_start: 0.8728 (mtp-110) cc_final: 0.8132 (ptm160) REVERT: O 353 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8522 (mp10) REVERT: P 535 GLN cc_start: 0.8580 (pp30) cc_final: 0.7996 (pm20) outliers start: 53 outliers final: 19 residues processed: 239 average time/residue: 0.5622 time to fit residues: 150.4002 Evaluate side-chains 212 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 187 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 801 ASN Chi-restraints excluded: chain K residue 816 GLU Chi-restraints excluded: chain K residue 886 HIS Chi-restraints excluded: chain K residue 911 GLU Chi-restraints excluded: chain K residue 915 VAL Chi-restraints excluded: chain K residue 1191 LEU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain M residue 267 GLN Chi-restraints excluded: chain M residue 287 LEU Chi-restraints excluded: chain M residue 336 SER Chi-restraints excluded: chain M residue 341 LEU Chi-restraints excluded: chain M residue 361 ASP Chi-restraints excluded: chain M residue 367 LEU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 312 ILE Chi-restraints excluded: chain N residue 566 LEU Chi-restraints excluded: chain O residue 267 GLN Chi-restraints excluded: chain O residue 282 CYS Chi-restraints excluded: chain O residue 291 LYS Chi-restraints excluded: chain O residue 299 TYR Chi-restraints excluded: chain O residue 300 ARG Chi-restraints excluded: chain O residue 308 GLU Chi-restraints excluded: chain O residue 326 TYR Chi-restraints excluded: chain O residue 353 GLN Chi-restraints excluded: chain P residue 276 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 35 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 125 optimal weight: 9.9990 chunk 172 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 118 optimal weight: 9.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 330 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.087776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.057766 restraints weight = 35086.011| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 3.08 r_work: 0.2705 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15220 Z= 0.193 Angle : 0.624 12.547 20518 Z= 0.312 Chirality : 0.043 0.300 2221 Planarity : 0.004 0.054 2616 Dihedral : 4.256 51.338 1962 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.63 % Favored : 97.31 % Rotamer: Outliers : 2.99 % Allowed : 25.30 % Favored : 71.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.63 % 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: 1.03 (0.20), residues: 1787 helix: 1.51 (0.17), residues: 913 sheet: -0.07 (0.53), residues: 92 loop : -0.14 (0.23), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 369 TYR 0.029 0.002 TYR O 281 PHE 0.021 0.001 PHE N 387 TRP 0.012 0.001 TRP K1151 HIS 0.013 0.001 HIS O 330 Details of bonding type rmsd covalent geometry : bond 0.00445 (15195) covalent geometry : angle 0.61870 (20494) hydrogen bonds : bond 0.03792 ( 698) hydrogen bonds : angle 4.12414 ( 2034) metal coordination : bond 0.01307 ( 25) metal coordination : angle 2.50306 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 190 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 698 ASP cc_start: 0.8257 (t70) cc_final: 0.7879 (t0) REVERT: K 816 GLU cc_start: 0.9283 (OUTLIER) cc_final: 0.8839 (tm-30) REVERT: K 885 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8270 (mp0) REVERT: K 911 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8623 (pp20) REVERT: L 220 GLU cc_start: 0.8640 (tm-30) cc_final: 0.8150 (tm-30) REVERT: M 227 LYS cc_start: 0.9187 (tptt) cc_final: 0.8931 (tppp) REVERT: M 267 GLN cc_start: 0.9176 (OUTLIER) cc_final: 0.8636 (mp10) REVERT: M 277 GLN cc_start: 0.9197 (mt0) cc_final: 0.8866 (mm-40) REVERT: M 308 GLU cc_start: 0.9102 (pt0) cc_final: 0.8763 (pp20) REVERT: N 122 LYS cc_start: 0.9270 (pttt) cc_final: 0.8954 (ptpp) REVERT: N 383 ASP cc_start: 0.9120 (p0) cc_final: 0.8682 (t0) REVERT: N 387 PHE cc_start: 0.9293 (m-10) cc_final: 0.9047 (m-10) REVERT: N 501 LYS cc_start: 0.9080 (tptt) cc_final: 0.8772 (tptt) REVERT: N 515 GLN cc_start: 0.8691 (mp-120) cc_final: 0.8234 (tm-30) REVERT: O 353 GLN cc_start: 0.8954 (OUTLIER) cc_final: 0.8526 (mp10) REVERT: P 343 ILE cc_start: 0.8936 (mt) cc_final: 0.8722 (mt) REVERT: P 535 GLN cc_start: 0.8623 (pp30) cc_final: 0.8289 (tm-30) outliers start: 50 outliers final: 25 residues processed: 222 average time/residue: 0.5570 time to fit residues: 138.5394 Evaluate side-chains 209 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 179 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 704 GLU Chi-restraints excluded: chain K residue 801 ASN Chi-restraints excluded: chain K residue 816 GLU Chi-restraints excluded: chain K residue 828 ILE Chi-restraints excluded: chain K residue 885 GLU Chi-restraints excluded: chain K residue 886 HIS Chi-restraints excluded: chain K residue 911 GLU Chi-restraints excluded: chain K residue 915 VAL Chi-restraints excluded: chain K residue 1033 LEU Chi-restraints excluded: chain K residue 1191 LEU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain M residue 245 ILE Chi-restraints excluded: chain M residue 267 GLN Chi-restraints excluded: chain M residue 287 LEU Chi-restraints excluded: chain M residue 297 LEU Chi-restraints excluded: chain M residue 336 SER Chi-restraints excluded: chain M residue 367 LEU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 123 ILE Chi-restraints excluded: chain N residue 312 ILE Chi-restraints excluded: chain N residue 382 THR Chi-restraints excluded: chain N residue 429 SER Chi-restraints excluded: chain O residue 267 GLN Chi-restraints excluded: chain O residue 282 CYS Chi-restraints excluded: chain O residue 291 LYS Chi-restraints excluded: chain O residue 299 TYR Chi-restraints excluded: chain O residue 326 TYR Chi-restraints excluded: chain O residue 342 ILE Chi-restraints excluded: chain O residue 353 GLN Chi-restraints excluded: chain P residue 301 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 166 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 150 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 102 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 41 optimal weight: 8.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 275 GLN O 295 ASN ** P 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 350 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.088978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.059144 restraints weight = 34828.339| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 3.09 r_work: 0.2746 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15220 Z= 0.135 Angle : 0.632 11.422 20518 Z= 0.312 Chirality : 0.042 0.279 2221 Planarity : 0.004 0.059 2616 Dihedral : 4.260 52.169 1962 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.69 % Favored : 97.26 % Rotamer: Outliers : 2.57 % Allowed : 25.42 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.63 % 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: 1.14 (0.20), residues: 1787 helix: 1.61 (0.18), residues: 898 sheet: -0.06 (0.54), residues: 91 loop : -0.05 (0.23), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG N 384 TYR 0.030 0.001 TYR O 281 PHE 0.016 0.001 PHE N 387 TRP 0.009 0.001 TRP K1151 HIS 0.010 0.001 HIS O 330 Details of bonding type rmsd covalent geometry : bond 0.00311 (15195) covalent geometry : angle 0.62900 (20494) hydrogen bonds : bond 0.03615 ( 698) hydrogen bonds : angle 4.06744 ( 2034) metal coordination : bond 0.00777 ( 25) metal coordination : angle 2.01044 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 198 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 698 ASP cc_start: 0.8218 (t70) cc_final: 0.7818 (t0) REVERT: K 816 GLU cc_start: 0.9270 (OUTLIER) cc_final: 0.8810 (tm-30) REVERT: K 885 GLU cc_start: 0.9017 (OUTLIER) cc_final: 0.8550 (mp0) REVERT: K 911 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8596 (pp20) REVERT: L 260 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8678 (mp0) REVERT: M 277 GLN cc_start: 0.9142 (mt0) cc_final: 0.8786 (mm-40) REVERT: M 308 GLU cc_start: 0.9074 (pt0) cc_final: 0.8760 (pp20) REVERT: M 361 ASP cc_start: 0.9194 (OUTLIER) cc_final: 0.8749 (m-30) REVERT: N 122 LYS cc_start: 0.9261 (pttt) cc_final: 0.8940 (ptpp) REVERT: N 501 LYS cc_start: 0.9051 (tptt) cc_final: 0.8735 (tptt) REVERT: N 515 GLN cc_start: 0.8657 (mp-120) cc_final: 0.8132 (tm-30) REVERT: N 564 ARG cc_start: 0.8521 (ttm170) cc_final: 0.8152 (tmm-80) REVERT: O 264 GLU cc_start: 0.9444 (mt-10) cc_final: 0.9197 (mt-10) REVERT: O 295 ASN cc_start: 0.8241 (OUTLIER) cc_final: 0.6606 (t0) REVERT: O 296 MET cc_start: 0.9088 (tpp) cc_final: 0.8495 (mmm) REVERT: O 300 ARG cc_start: 0.6665 (OUTLIER) cc_final: 0.6259 (mpt180) REVERT: O 353 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8538 (mp10) REVERT: P 332 ASN cc_start: 0.8989 (m-40) cc_final: 0.8635 (p0) REVERT: P 343 ILE cc_start: 0.8897 (mt) cc_final: 0.8559 (mt) REVERT: P 535 GLN cc_start: 0.8620 (pp30) cc_final: 0.8306 (tm-30) REVERT: E 4 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7520 (ptpt) outliers start: 43 outliers final: 18 residues processed: 229 average time/residue: 0.6121 time to fit residues: 155.5532 Evaluate side-chains 208 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 801 ASN Chi-restraints excluded: chain K residue 816 GLU Chi-restraints excluded: chain K residue 828 ILE Chi-restraints excluded: chain K residue 885 GLU Chi-restraints excluded: chain K residue 886 HIS Chi-restraints excluded: chain K residue 911 GLU Chi-restraints excluded: chain K residue 915 VAL Chi-restraints excluded: chain K residue 1033 LEU Chi-restraints excluded: chain K residue 1191 LEU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain M residue 287 LEU Chi-restraints excluded: chain M residue 297 LEU Chi-restraints excluded: chain M residue 361 ASP Chi-restraints excluded: chain M residue 367 LEU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 312 ILE Chi-restraints excluded: chain N residue 396 THR Chi-restraints excluded: chain O residue 267 GLN Chi-restraints excluded: chain O residue 282 CYS Chi-restraints excluded: chain O residue 291 LYS Chi-restraints excluded: chain O residue 295 ASN Chi-restraints excluded: chain O residue 299 TYR Chi-restraints excluded: chain O residue 300 ARG Chi-restraints excluded: chain O residue 326 TYR Chi-restraints excluded: chain O residue 353 GLN Chi-restraints excluded: chain E residue 4 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 102 optimal weight: 0.0030 chunk 129 optimal weight: 0.9990 chunk 161 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 1 optimal weight: 0.0980 chunk 71 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 171 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 389 ASN ** P 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.090076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.060026 restraints weight = 35289.545| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 3.14 r_work: 0.2772 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15220 Z= 0.120 Angle : 0.619 11.023 20518 Z= 0.307 Chirality : 0.041 0.302 2221 Planarity : 0.004 0.065 2616 Dihedral : 4.192 51.757 1962 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.69 % Favored : 97.26 % Rotamer: Outliers : 2.33 % Allowed : 26.26 % Favored : 71.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.63 % 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: 1.24 (0.20), residues: 1787 helix: 1.71 (0.18), residues: 890 sheet: 0.01 (0.54), residues: 91 loop : -0.01 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG N 369 TYR 0.030 0.001 TYR O 281 PHE 0.022 0.001 PHE N 567 TRP 0.014 0.001 TRP O 236 HIS 0.009 0.001 HIS O 330 Details of bonding type rmsd covalent geometry : bond 0.00274 (15195) covalent geometry : angle 0.61534 (20494) hydrogen bonds : bond 0.03501 ( 698) hydrogen bonds : angle 4.04171 ( 2034) metal coordination : bond 0.00574 ( 25) metal coordination : angle 1.93738 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 194 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 698 ASP cc_start: 0.8155 (t70) cc_final: 0.7746 (t0) REVERT: K 704 GLU cc_start: 0.9111 (OUTLIER) cc_final: 0.8591 (pp20) REVERT: K 816 GLU cc_start: 0.9246 (OUTLIER) cc_final: 0.8797 (tm-30) REVERT: K 885 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.8539 (mp0) REVERT: K 911 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8589 (pp20) REVERT: M 308 GLU cc_start: 0.9087 (pt0) cc_final: 0.8767 (pp20) REVERT: M 361 ASP cc_start: 0.9209 (OUTLIER) cc_final: 0.8738 (m-30) REVERT: N 122 LYS cc_start: 0.9243 (pttt) cc_final: 0.8918 (ptpp) REVERT: N 501 LYS cc_start: 0.9058 (tptt) cc_final: 0.8737 (tptt) REVERT: N 515 GLN cc_start: 0.8635 (mp-120) cc_final: 0.8104 (tm-30) REVERT: O 264 GLU cc_start: 0.9445 (mt-10) cc_final: 0.9187 (mt-10) REVERT: O 295 ASN cc_start: 0.8137 (t0) cc_final: 0.6312 (t0) REVERT: O 296 MET cc_start: 0.9040 (tpp) cc_final: 0.8437 (mmm) REVERT: O 353 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8490 (mp10) REVERT: P 319 LEU cc_start: 0.8524 (pp) cc_final: 0.8300 (pp) REVERT: P 321 LYS cc_start: 0.9026 (ptpt) cc_final: 0.8747 (pttt) REVERT: P 332 ASN cc_start: 0.8980 (m-40) cc_final: 0.8641 (p0) REVERT: P 343 ILE cc_start: 0.8812 (mt) cc_final: 0.8501 (mt) REVERT: P 535 GLN cc_start: 0.8698 (pp30) cc_final: 0.8339 (tm-30) REVERT: E 4 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7514 (ptpt) outliers start: 39 outliers final: 19 residues processed: 222 average time/residue: 0.5699 time to fit residues: 141.2431 Evaluate side-chains 210 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 184 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 704 GLU Chi-restraints excluded: chain K residue 801 ASN Chi-restraints excluded: chain K residue 816 GLU Chi-restraints excluded: chain K residue 857 HIS Chi-restraints excluded: chain K residue 885 GLU Chi-restraints excluded: chain K residue 886 HIS Chi-restraints excluded: chain K residue 911 GLU Chi-restraints excluded: chain K residue 915 VAL Chi-restraints excluded: chain K residue 1033 LEU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain L residue 275 SER Chi-restraints excluded: chain M residue 287 LEU Chi-restraints excluded: chain M residue 297 LEU Chi-restraints excluded: chain M residue 361 ASP Chi-restraints excluded: chain M residue 367 LEU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 312 ILE Chi-restraints excluded: chain N residue 396 THR Chi-restraints excluded: chain O residue 267 GLN Chi-restraints excluded: chain O residue 282 CYS Chi-restraints excluded: chain O residue 291 LYS Chi-restraints excluded: chain O residue 299 TYR Chi-restraints excluded: chain O residue 326 TYR Chi-restraints excluded: chain O residue 353 GLN Chi-restraints excluded: chain O residue 371 ASP Chi-restraints excluded: chain E residue 4 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 47 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 161 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 155 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 133 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 295 ASN ** P 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 350 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.089309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.059505 restraints weight = 35230.149| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 3.10 r_work: 0.2754 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15220 Z= 0.142 Angle : 0.652 13.659 20518 Z= 0.319 Chirality : 0.042 0.326 2221 Planarity : 0.004 0.067 2616 Dihedral : 4.207 51.922 1962 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.57 % Favored : 97.37 % Rotamer: Outliers : 2.27 % Allowed : 26.67 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.63 % 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: 1.31 (0.20), residues: 1787 helix: 1.73 (0.18), residues: 890 sheet: 0.05 (0.54), residues: 91 loop : 0.08 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG N 369 TYR 0.033 0.001 TYR O 281 PHE 0.026 0.001 PHE N 387 TRP 0.022 0.001 TRP O 236 HIS 0.010 0.001 HIS O 330 Details of bonding type rmsd covalent geometry : bond 0.00330 (15195) covalent geometry : angle 0.64886 (20494) hydrogen bonds : bond 0.03567 ( 698) hydrogen bonds : angle 4.04058 ( 2034) metal coordination : bond 0.00839 ( 25) metal coordination : angle 2.04805 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 186 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 698 ASP cc_start: 0.8212 (t70) cc_final: 0.7809 (t0) REVERT: K 704 GLU cc_start: 0.9115 (OUTLIER) cc_final: 0.8610 (pp20) REVERT: K 816 GLU cc_start: 0.9245 (OUTLIER) cc_final: 0.8812 (tm-30) REVERT: K 885 GLU cc_start: 0.9014 (OUTLIER) cc_final: 0.8541 (mp0) REVERT: K 911 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8583 (pp20) REVERT: L 260 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8690 (mp0) REVERT: M 308 GLU cc_start: 0.9098 (pt0) cc_final: 0.8795 (pp20) REVERT: M 361 ASP cc_start: 0.9179 (OUTLIER) cc_final: 0.8724 (m-30) REVERT: N 122 LYS cc_start: 0.9251 (pttt) cc_final: 0.8927 (ptpp) REVERT: N 501 LYS cc_start: 0.9058 (tptt) cc_final: 0.8740 (tptt) REVERT: N 515 GLN cc_start: 0.8661 (mp-120) cc_final: 0.8204 (tm-30) REVERT: O 264 GLU cc_start: 0.9444 (mt-10) cc_final: 0.9191 (mt-10) REVERT: O 296 MET cc_start: 0.8956 (tpp) cc_final: 0.8526 (tpp) REVERT: O 353 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8519 (mp10) REVERT: P 321 LYS cc_start: 0.9025 (ptpt) cc_final: 0.8746 (pttt) REVERT: P 332 ASN cc_start: 0.8971 (m-40) cc_final: 0.8651 (p0) REVERT: P 535 GLN cc_start: 0.8708 (pp30) cc_final: 0.8361 (tm-30) REVERT: E 4 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.7504 (ptpt) outliers start: 38 outliers final: 21 residues processed: 212 average time/residue: 0.5987 time to fit residues: 141.1239 Evaluate side-chains 210 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 182 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 704 GLU Chi-restraints excluded: chain K residue 801 ASN Chi-restraints excluded: chain K residue 816 GLU Chi-restraints excluded: chain K residue 885 GLU Chi-restraints excluded: chain K residue 886 HIS Chi-restraints excluded: chain K residue 911 GLU Chi-restraints excluded: chain K residue 915 VAL Chi-restraints excluded: chain K residue 1033 LEU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain L residue 275 SER Chi-restraints excluded: chain M residue 287 LEU Chi-restraints excluded: chain M residue 297 LEU Chi-restraints excluded: chain M residue 336 SER Chi-restraints excluded: chain M residue 361 ASP Chi-restraints excluded: chain M residue 367 LEU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 312 ILE Chi-restraints excluded: chain N residue 396 THR Chi-restraints excluded: chain N residue 429 SER Chi-restraints excluded: chain O residue 235 ASP Chi-restraints excluded: chain O residue 267 GLN Chi-restraints excluded: chain O residue 282 CYS Chi-restraints excluded: chain O residue 291 LYS Chi-restraints excluded: chain O residue 299 TYR Chi-restraints excluded: chain O residue 326 TYR Chi-restraints excluded: chain O residue 353 GLN Chi-restraints excluded: chain O residue 371 ASP Chi-restraints excluded: chain E residue 4 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 51 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 156 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 162 optimal weight: 3.9990 chunk 175 optimal weight: 10.0000 chunk 27 optimal weight: 0.7980 chunk 165 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 295 ASN ** P 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.089913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.059878 restraints weight = 35121.959| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 3.13 r_work: 0.2766 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15220 Z= 0.132 Angle : 0.658 11.514 20518 Z= 0.324 Chirality : 0.042 0.324 2221 Planarity : 0.004 0.068 2616 Dihedral : 4.221 50.284 1962 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.57 % Favored : 97.37 % Rotamer: Outliers : 1.97 % Allowed : 27.03 % Favored : 70.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.63 % 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: 1.31 (0.20), residues: 1787 helix: 1.72 (0.18), residues: 892 sheet: 0.07 (0.54), residues: 91 loop : 0.09 (0.23), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG N 369 TYR 0.034 0.001 TYR O 281 PHE 0.035 0.001 PHE N 567 TRP 0.020 0.001 TRP O 236 HIS 0.010 0.001 HIS O 330 Details of bonding type rmsd covalent geometry : bond 0.00305 (15195) covalent geometry : angle 0.65513 (20494) hydrogen bonds : bond 0.03578 ( 698) hydrogen bonds : angle 4.05233 ( 2034) metal coordination : bond 0.00696 ( 25) metal coordination : angle 1.99289 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3574 Ramachandran restraints generated. 1787 Oldfield, 0 Emsley, 1787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 186 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 698 ASP cc_start: 0.8203 (t70) cc_final: 0.7799 (t0) REVERT: K 704 GLU cc_start: 0.9112 (OUTLIER) cc_final: 0.8621 (pp20) REVERT: K 816 GLU cc_start: 0.9240 (OUTLIER) cc_final: 0.8808 (tm-30) REVERT: K 885 GLU cc_start: 0.9007 (OUTLIER) cc_final: 0.8542 (mp0) REVERT: K 911 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8578 (pp20) REVERT: M 308 GLU cc_start: 0.9100 (pt0) cc_final: 0.8798 (pp20) REVERT: M 361 ASP cc_start: 0.9170 (OUTLIER) cc_final: 0.8712 (m-30) REVERT: N 122 LYS cc_start: 0.9247 (pttt) cc_final: 0.8925 (ptpp) REVERT: N 501 LYS cc_start: 0.9056 (tptt) cc_final: 0.8738 (tptt) REVERT: N 515 GLN cc_start: 0.8653 (mp-120) cc_final: 0.8199 (tm-30) REVERT: O 261 TYR cc_start: 0.8692 (t80) cc_final: 0.8456 (t80) REVERT: O 264 GLU cc_start: 0.9448 (mt-10) cc_final: 0.9194 (mt-10) REVERT: O 353 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8550 (mp10) REVERT: P 321 LYS cc_start: 0.8947 (ptpt) cc_final: 0.8671 (pttt) REVERT: P 332 ASN cc_start: 0.8955 (m-40) cc_final: 0.8645 (p0) REVERT: P 535 GLN cc_start: 0.8707 (pp30) cc_final: 0.8367 (tm-30) REVERT: E 4 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.7544 (ptpt) outliers start: 33 outliers final: 21 residues processed: 208 average time/residue: 0.4608 time to fit residues: 106.9299 Evaluate side-chains 204 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 704 GLU Chi-restraints excluded: chain K residue 801 ASN Chi-restraints excluded: chain K residue 816 GLU Chi-restraints excluded: chain K residue 885 GLU Chi-restraints excluded: chain K residue 886 HIS Chi-restraints excluded: chain K residue 911 GLU Chi-restraints excluded: chain K residue 915 VAL Chi-restraints excluded: chain K residue 1033 LEU Chi-restraints excluded: chain L residue 94 LEU Chi-restraints excluded: chain L residue 275 SER Chi-restraints excluded: chain M residue 287 LEU Chi-restraints excluded: chain M residue 297 LEU Chi-restraints excluded: chain M residue 336 SER Chi-restraints excluded: chain M residue 361 ASP Chi-restraints excluded: chain M residue 367 LEU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 312 ILE Chi-restraints excluded: chain N residue 396 THR Chi-restraints excluded: chain O residue 235 ASP Chi-restraints excluded: chain O residue 267 GLN Chi-restraints excluded: chain O residue 282 CYS Chi-restraints excluded: chain O residue 291 LYS Chi-restraints excluded: chain O residue 299 TYR Chi-restraints excluded: chain O residue 326 TYR Chi-restraints excluded: chain O residue 353 GLN Chi-restraints excluded: chain O residue 371 ASP Chi-restraints excluded: chain P residue 301 TRP Chi-restraints excluded: chain E residue 4 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 147 optimal weight: 9.9990 chunk 172 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 chunk 155 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 165 optimal weight: 8.9990 chunk 117 optimal weight: 0.9980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K1150 HIS ** M 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 295 ASN ** P 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 350 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.086648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.056240 restraints weight = 35051.786| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 3.08 r_work: 0.2681 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 15220 Z= 0.252 Angle : 0.721 12.120 20518 Z= 0.358 Chirality : 0.045 0.339 2221 Planarity : 0.004 0.069 2616 Dihedral : 4.442 50.940 1962 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.80 % Favored : 97.15 % Rotamer: Outliers : 2.21 % Allowed : 26.97 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.63 % 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: 1.19 (0.20), residues: 1787 helix: 1.57 (0.18), residues: 907 sheet: 0.07 (0.53), residues: 92 loop : 0.05 (0.23), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 132 TYR 0.035 0.002 TYR O 281 PHE 0.030 0.002 PHE N 387 TRP 0.019 0.001 TRP O 236 HIS 0.011 0.001 HIS O 369 Details of bonding type rmsd covalent geometry : bond 0.00579 (15195) covalent geometry : angle 0.71638 (20494) hydrogen bonds : bond 0.04015 ( 698) hydrogen bonds : angle 4.23912 ( 2034) metal coordination : bond 0.01903 ( 25) metal coordination : angle 2.46629 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5364.81 seconds wall clock time: 92 minutes 38.10 seconds (5558.10 seconds total)