Starting phenix.real_space_refine on Thu May 22 05:40:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8glk_40196/05_2025/8glk_40196.cif Found real_map, /net/cci-nas-00/data/ceres_data/8glk_40196/05_2025/8glk_40196.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8glk_40196/05_2025/8glk_40196.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8glk_40196/05_2025/8glk_40196.map" model { file = "/net/cci-nas-00/data/ceres_data/8glk_40196/05_2025/8glk_40196.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8glk_40196/05_2025/8glk_40196.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 13852 2.51 5 N 3661 2.21 5 O 4340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 21899 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 599 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 70} Chain: "A" Number of atoms: 17380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2191, 17380 Classifications: {'peptide': 2191} Link IDs: {'PCIS': 3, 'PTRANS': 99, 'TRANS': 2088} Chain breaks: 3 Chain: "B" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 990 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain breaks: 1 Chain: "F" Number of atoms: 2861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2861 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 17, 'TRANS': 349} Chain breaks: 1 Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'LMN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.03, per 1000 atoms: 0.55 Number of scatterers: 21899 At special positions: 0 Unit cell: (122.304, 128.96, 143.104, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 46 16.00 O 4340 8.00 N 3661 7.00 C 13852 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: 6.17 Conformation dependent library (CDL) restraints added in 2.5 seconds 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5118 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 21 sheets defined 14.6% alpha, 31.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.98 Creating SS restraints... Processing helix chain 'A' and resid 160 through 164 Processing helix chain 'A' and resid 284 through 286 No H-bonds generated for 'chain 'A' and resid 284 through 286' Processing helix chain 'A' and resid 295 through 306 removed outlier: 4.602A pdb=" N ASP A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N VAL A 304 " --> pdb=" O ASN A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 382 through 386 removed outlier: 4.199A pdb=" N ASN A 386 " --> pdb=" O ASN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.633A pdb=" N ILE A 393 " --> pdb=" O PRO A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 406 Processing helix chain 'A' and resid 410 through 414 removed outlier: 3.678A pdb=" N PHE A 414 " --> pdb=" O LYS A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 437 No H-bonds generated for 'chain 'A' and resid 435 through 437' Processing helix chain 'A' and resid 517 through 522 removed outlier: 3.902A pdb=" N ASN A 521 " --> pdb=" O ASN A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 573 removed outlier: 3.969A pdb=" N LYS A 573 " --> pdb=" O PRO A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 583 Processing helix chain 'A' and resid 626 through 633 Processing helix chain 'A' and resid 643 through 647 Processing helix chain 'A' and resid 650 through 655 Processing helix chain 'A' and resid 657 through 662 Processing helix chain 'A' and resid 663 through 668 Processing helix chain 'A' and resid 669 through 674 removed outlier: 6.089A pdb=" N ASP A 672 " --> pdb=" O GLN A 669 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS A 673 " --> pdb=" O ASP A 670 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN A 674 " --> pdb=" O SER A 671 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 669 through 674' Processing helix chain 'A' and resid 730 through 735 removed outlier: 3.599A pdb=" N ALA A 735 " --> pdb=" O PRO A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 819 removed outlier: 3.811A pdb=" N THR A 814 " --> pdb=" O VAL A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 847 No H-bonds generated for 'chain 'A' and resid 845 through 847' Processing helix chain 'A' and resid 872 through 876 Processing helix chain 'A' and resid 898 through 903 Processing helix chain 'A' and resid 926 through 931 removed outlier: 3.586A pdb=" N SER A 931 " --> pdb=" O ASP A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 944 Processing helix chain 'A' and resid 982 through 985 Processing helix chain 'A' and resid 998 through 1003 Processing helix chain 'A' and resid 1048 through 1052 removed outlier: 3.663A pdb=" N LEU A1052 " --> pdb=" O GLU A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1089 Processing helix chain 'A' and resid 1099 through 1103 removed outlier: 3.511A pdb=" N SER A1102 " --> pdb=" O ARG A1099 " (cutoff:3.500A) Processing helix chain 'A' and resid 1104 through 1108 removed outlier: 3.690A pdb=" N ALA A1108 " --> pdb=" O THR A1105 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1412 through 1417 Processing helix chain 'A' and resid 1418 through 1422 Processing helix chain 'A' and resid 1427 through 1438 Processing helix chain 'A' and resid 1454 through 1458 Processing helix chain 'A' and resid 1573 through 1576 Processing helix chain 'A' and resid 1577 through 1580 removed outlier: 3.628A pdb=" N TRP A1580 " --> pdb=" O PRO A1577 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1577 through 1580' Processing helix chain 'A' and resid 1607 through 1614 Processing helix chain 'A' and resid 1617 through 1629 removed outlier: 3.542A pdb=" N ILE A1629 " --> pdb=" O ARG A1625 " (cutoff:3.500A) Processing helix chain 'A' and resid 1656 through 1658 No H-bonds generated for 'chain 'A' and resid 1656 through 1658' Processing helix chain 'A' and resid 1830 through 1834 removed outlier: 3.603A pdb=" N LYS A1833 " --> pdb=" O PRO A1830 " (cutoff:3.500A) Processing helix chain 'A' and resid 1856 through 1861 Processing helix chain 'A' and resid 1976 through 1981 Processing helix chain 'A' and resid 1987 through 1995 Processing helix chain 'A' and resid 2071 through 2075 removed outlier: 3.512A pdb=" N THR A2074 " --> pdb=" O MET A2071 " (cutoff:3.500A) Processing helix chain 'A' and resid 2084 through 2106 removed outlier: 3.788A pdb=" N ARG A2094 " --> pdb=" O PHE A2090 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N LEU A2095 " --> pdb=" O ARG A2091 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ILE A2096 " --> pdb=" O SER A2092 " (cutoff:3.500A) Processing helix chain 'A' and resid 2129 through 2136 removed outlier: 3.804A pdb=" N ASN A2136 " --> pdb=" O VAL A2132 " (cutoff:3.500A) Processing helix chain 'A' and resid 2147 through 2161 Proline residue: A2153 - end of helix Processing helix chain 'A' and resid 2186 through 2190 Processing helix chain 'B' and resid 27 through 42 Processing helix chain 'B' and resid 126 through 133 Processing helix chain 'B' and resid 134 through 136 No H-bonds generated for 'chain 'B' and resid 134 through 136' Processing helix chain 'F' and resid 30 through 35 Processing helix chain 'F' and resid 38 through 44 Processing helix chain 'F' and resid 61 through 68 removed outlier: 3.551A pdb=" N LYS F 64 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA F 66 " --> pdb=" O ALA F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 297 removed outlier: 4.129A pdb=" N ASP F 288 " --> pdb=" O GLN F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 307 removed outlier: 3.811A pdb=" N PHE F 305 " --> pdb=" O VAL F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 319 Processing sheet with id=AA1, first strand: chain 'D' and resid 547 through 548 removed outlier: 8.941A pdb=" N SER D 548 " --> pdb=" O LYS D 610 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ILE D 612 " --> pdb=" O SER D 548 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N TYR D 563 " --> pdb=" O ASN D 580 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ASN D 580 " --> pdb=" O TYR D 563 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 551 through 553 Processing sheet with id=AA3, first strand: chain 'A' and resid 138 through 154 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 166 through 173 current: chain 'A' and resid 187 through 194 removed outlier: 6.555A pdb=" N PHE A 205 " --> pdb=" O ASN A 224 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ILE A 217 " --> pdb=" O GLN A 248 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLN A 248 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS A 219 " --> pdb=" O GLN A 246 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N MET A 227 " --> pdb=" O GLN A 238 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N GLN A 238 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR A 253 " --> pdb=" O GLU A 763 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ARG A 755 " --> pdb=" O GLN A 261 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N PHE A 770 " --> pdb=" O ILE A 766 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 770 through 773 current: chain 'A' and resid 796 through 809 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1559 through 1571 current: chain 'A' and resid 1630 through 1644 removed outlier: 5.433A pdb=" N THR A1632 " --> pdb=" O HIS A1672 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N HIS A1672 " --> pdb=" O THR A1632 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ARG A1634 " --> pdb=" O GLU A1670 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N GLU A1670 " --> pdb=" O ARG A1634 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N SER A1636 " --> pdb=" O GLN A1668 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLN A1668 " --> pdb=" O SER A1636 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ASN A1638 " --> pdb=" O TYR A1666 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N TYR A1666 " --> pdb=" O ASN A1638 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE A1640 " --> pdb=" O GLN A1664 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLN A1664 " --> pdb=" O ILE A1640 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LYS A1644 " --> pdb=" O PHE A1660 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N PHE A1660 " --> pdb=" O LYS A1644 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1757 through 1760 current: chain 'A' and resid 1779 through 1789 removed outlier: 5.588A pdb=" N ILE A1789 " --> pdb=" O PRO A1816 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N THR A1847 " --> pdb=" O SER A1881 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ASN A1874 " --> pdb=" O GLY A1962 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE A1945 " --> pdb=" O ASP A2022 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ASP A2022 " --> pdb=" O ILE A1945 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASN A1947 " --> pdb=" O ASN A2020 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN A1951 " --> pdb=" O LYS A2016 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU A2023 " --> pdb=" O LEU A2027 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LEU A2027 " --> pdb=" O LEU A2023 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ASP A2034 " --> pdb=" O SER A2068 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLN A2044 " --> pdb=" O SER A2058 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N SER A2058 " --> pdb=" O GLN A2044 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N SER A2046 " --> pdb=" O PRO A2056 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2054 through 2069 current: chain 'A' and resid 2197 through 2217 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 2238 through 2240 current: chain 'A' and resid 2264 through 2278 removed outlier: 4.018A pdb=" N VAL A2287 " --> pdb=" O ALA A2274 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ASP A2302 " --> pdb=" O SER A2319 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N SER A2319 " --> pdb=" O ASP A2302 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ASP A2320 " --> pdb=" O TYR A2361 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N TYR A2361 " --> pdb=" O ASP A2320 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ASN A2322 " --> pdb=" O ALA A2359 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA A2359 " --> pdb=" O ASN A2322 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LYS A2324 " --> pdb=" O LEU A2357 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LEU A2357 " --> pdb=" O LYS A2324 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASP A2326 " --> pdb=" O LEU A2355 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU A2355 " --> pdb=" O ASP A2326 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N SER A2328 " --> pdb=" O TRP A2353 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N TRP A2353 " --> pdb=" O SER A2328 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ARG A2330 " --> pdb=" O ASN A2351 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASN A2351 " --> pdb=" O ARG A2330 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ASN A2332 " --> pdb=" O GLY A2349 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLY A2349 " --> pdb=" O ASN A2332 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR A2334 " --> pdb=" O ALA A2347 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASN A2351 " --> pdb=" O LYS A2379 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 264 through 270 Processing sheet with id=AA5, first strand: chain 'A' and resid 275 through 282 Processing sheet with id=AA6, first strand: chain 'A' and resid 291 through 293 removed outlier: 3.909A pdb=" N TYR A 447 " --> pdb=" O ASN A 442 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 471 through 474 removed outlier: 6.387A pdb=" N LEU A 460 " --> pdb=" O LEU A 508 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N PHE A 464 " --> pdb=" O VAL A 504 " (cutoff:3.500A) removed outlier: 11.849A pdb=" N VAL A 504 " --> pdb=" O PHE A 464 " (cutoff:3.500A) removed outlier: 19.571A pdb=" N TYR A 466 " --> pdb=" O SER A 502 " (cutoff:3.500A) removed outlier: 23.900A pdb=" N SER A 502 " --> pdb=" O TYR A 466 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ARG A 342 " --> pdb=" O ASN A 430 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASN A 430 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N ILE A 318 " --> pdb=" O THR A 467 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N THR A 467 " --> pdb=" O ILE A 318 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 486 through 489 Processing sheet with id=AA9, first strand: chain 'A' and resid 527 through 529 Processing sheet with id=AB1, first strand: chain 'A' and resid 690 through 691 Processing sheet with id=AB2, first strand: chain 'A' and resid 849 through 850 Processing sheet with id=AB3, first strand: chain 'A' and resid 856 through 859 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 856 through 859 current: chain 'A' and resid 1326 through 1337 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1326 through 1337 current: chain 'A' and resid 1423 through 1426 No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 866 through 869 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 866 through 869 current: chain 'A' and resid 960 through 969 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 960 through 969 current: chain 'A' and resid 1208 through 1219 No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 877 through 878 Processing sheet with id=AB6, first strand: chain 'A' and resid 938 through 939 removed outlier: 4.536A pdb=" N ILE A 938 " --> pdb=" O VAL A 957 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1265 through 1266 removed outlier: 7.069A pdb=" N ARG A1343 " --> pdb=" O LYS A1491 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LYS A1491 " --> pdb=" O ARG A1343 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N VAL A1345 " --> pdb=" O GLY A1489 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N GLY A1489 " --> pdb=" O VAL A1345 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LYS A1347 " --> pdb=" O MET A1487 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N MET A1487 " --> pdb=" O LYS A1347 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL A1349 " --> pdb=" O ASN A1485 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ASN A1485 " --> pdb=" O VAL A1349 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1313 through 1315 Processing sheet with id=AB9, first strand: chain 'A' and resid 1862 through 1863 Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 48 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 54 through 59 current: chain 'B' and resid 110 through 113 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 110 through 113 current: chain 'B' and resid 166 through 174 Processing sheet with id=AC2, first strand: chain 'F' and resid 193 through 194 removed outlier: 3.590A pdb=" N ASN F 199 " --> pdb=" O ILE F 240 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE F 240 " --> pdb=" O ASN F 199 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ASP F 397 " --> pdb=" O ASP F 70 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ASP F 70 " --> pdb=" O ASP F 397 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N VAL F 182 " --> pdb=" O ASN F 210 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN F 210 " --> pdb=" O VAL F 182 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 118 through 120 removed outlier: 3.582A pdb=" N ARG F 131 " --> pdb=" O LEU F 120 " (cutoff:3.500A) 722 hydrogen bonds defined for protein. 1911 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: 11.19 Time building geometry restraints manager: 7.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7244 1.34 - 1.46: 4722 1.46 - 1.57: 10320 1.57 - 1.69: 8 1.69 - 1.81: 90 Bond restraints: 22384 Sorted by residual: bond pdb=" C1 LMN A2501 " pdb=" O5 LMN A2501 " ideal model delta sigma weight residual 1.403 1.564 -0.161 2.00e-02 2.50e+03 6.48e+01 bond pdb=" C4 LMN A2501 " pdb=" O4 LMN A2501 " ideal model delta sigma weight residual 1.409 1.507 -0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" CCF LMN A2501 " pdb=" OBX LMN A2501 " ideal model delta sigma weight residual 1.410 1.500 -0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" CCS LMN A2501 " pdb=" OBZ LMN A2501 " ideal model delta sigma weight residual 1.394 1.482 -0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" CCR LMN A2501 " pdb=" OBY LMN A2501 " ideal model delta sigma weight residual 1.393 1.474 -0.081 2.00e-02 2.50e+03 1.63e+01 ... (remaining 22379 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 29957 1.99 - 3.99: 389 3.99 - 5.98: 36 5.98 - 7.98: 6 7.98 - 9.97: 2 Bond angle restraints: 30390 Sorted by residual: angle pdb=" C4 LMN A2501 " pdb=" O4 LMN A2501 " pdb=" CCR LMN A2501 " ideal model delta sigma weight residual 120.22 110.25 9.97 3.00e+00 1.11e-01 1.11e+01 angle pdb=" CCQ LMN A2501 " pdb=" OCB LMN A2501 " pdb=" CCS LMN A2501 " ideal model delta sigma weight residual 119.65 110.02 9.63 3.00e+00 1.11e-01 1.03e+01 angle pdb=" C SER A2050 " pdb=" N THR A2051 " pdb=" CA THR A2051 " ideal model delta sigma weight residual 121.54 127.28 -5.74 1.91e+00 2.74e-01 9.03e+00 angle pdb=" N GLY D 550 " pdb=" CA GLY D 550 " pdb=" C GLY D 550 " ideal model delta sigma weight residual 114.48 111.01 3.47 1.19e+00 7.06e-01 8.52e+00 angle pdb=" N VAL D 575 " pdb=" CA VAL D 575 " pdb=" C VAL D 575 " ideal model delta sigma weight residual 113.53 110.74 2.79 9.80e-01 1.04e+00 8.08e+00 ... (remaining 30385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.51: 12865 24.51 - 49.01: 436 49.01 - 73.52: 55 73.52 - 98.03: 38 98.03 - 122.53: 15 Dihedral angle restraints: 13409 sinusoidal: 5388 harmonic: 8021 Sorted by residual: dihedral pdb=" CA PHE D 544 " pdb=" C PHE D 544 " pdb=" N PRO D 545 " pdb=" CA PRO D 545 " ideal model delta harmonic sigma weight residual -180.00 -141.33 -38.67 0 5.00e+00 4.00e-02 5.98e+01 dihedral pdb=" CA PRO A1063 " pdb=" C PRO A1063 " pdb=" N LEU A1064 " pdb=" CA LEU A1064 " ideal model delta harmonic sigma weight residual 180.00 158.60 21.40 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CCC LMN A2501 " pdb=" CCR LMN A2501 " pdb=" OBY LMN A2501 " pdb=" O4 LMN A2501 " ideal model delta sinusoidal sigma weight residual 60.74 -176.73 -122.53 1 3.00e+01 1.11e-03 1.64e+01 ... (remaining 13406 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2000 0.033 - 0.066: 863 0.066 - 0.099: 239 0.099 - 0.132: 189 0.132 - 0.165: 11 Chirality restraints: 3302 Sorted by residual: chirality pdb=" CCV LMN A2501 " pdb=" CCR LMN A2501 " pdb=" CCT LMN A2501 " pdb=" OAU LMN A2501 " both_signs ideal model delta sigma weight residual False 2.28 2.45 -0.16 2.00e-01 2.50e+01 6.78e-01 chirality pdb=" CB ILE B 100 " pdb=" CA ILE B 100 " pdb=" CG1 ILE B 100 " pdb=" CG2 ILE B 100 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.15 2.00e-01 2.50e+01 5.74e-01 chirality pdb=" CCW LMN A2501 " pdb=" CCS LMN A2501 " pdb=" CCU LMN A2501 " pdb=" OAV LMN A2501 " both_signs ideal model delta sigma weight residual False 2.30 2.45 -0.15 2.00e-01 2.50e+01 5.36e-01 ... (remaining 3299 not shown) Planarity restraints: 4025 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE D 544 " 0.061 5.00e-02 4.00e+02 9.36e-02 1.40e+01 pdb=" N PRO D 545 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO D 545 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO D 545 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A1639 " -0.012 2.00e-02 2.50e+03 2.49e-02 6.21e+00 pdb=" C PHE A1639 " 0.043 2.00e-02 2.50e+03 pdb=" O PHE A1639 " -0.016 2.00e-02 2.50e+03 pdb=" N ILE A1640 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 176 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.83e+00 pdb=" C SER A 176 " -0.038 2.00e-02 2.50e+03 pdb=" O SER A 176 " 0.014 2.00e-02 2.50e+03 pdb=" N MET A 177 " 0.013 2.00e-02 2.50e+03 ... (remaining 4022 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 560 2.70 - 3.25: 20837 3.25 - 3.80: 35517 3.80 - 4.35: 49146 4.35 - 4.90: 80838 Nonbonded interactions: 186898 Sorted by model distance: nonbonded pdb=" OE1 GLN A 865 " pdb=" OH TYR A1006 " model vdw 2.154 3.040 nonbonded pdb=" OG SER A 231 " pdb=" OE2 GLU A 836 " model vdw 2.161 3.040 nonbonded pdb=" OD2 ASP A 539 " pdb=" OH TYR A 590 " model vdw 2.181 3.040 nonbonded pdb=" O VAL A 810 " pdb=" OG SER A 829 " model vdw 2.184 3.040 nonbonded pdb=" O LEU A2156 " pdb=" OG1 THR A2160 " model vdw 2.184 3.040 ... (remaining 186893 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 2.990 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: 0.020 Extract box with map and model: 0.760 Check model and map are aligned: 0.160 Set scattering table: 0.180 Process input model: 51.530 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.161 22384 Z= 0.173 Angle : 0.557 9.973 30390 Z= 0.293 Chirality : 0.045 0.165 3302 Planarity : 0.004 0.094 4025 Dihedral : 14.056 122.534 8291 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.08 % Allowed : 0.25 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.16), residues: 2743 helix: -0.92 (0.30), residues: 297 sheet: 0.34 (0.16), residues: 1057 loop : -0.61 (0.16), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A1996 HIS 0.007 0.001 HIS B 90 PHE 0.031 0.001 PHE A 656 TYR 0.019 0.001 TYR A1679 ARG 0.007 0.000 ARG F 232 Details of bonding type rmsd hydrogen bonds : bond 0.11736 ( 722) hydrogen bonds : angle 5.96528 ( 1911) covalent geometry : bond 0.00349 (22384) covalent geometry : angle 0.55720 (30390) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 373 time to evaluate : 2.701 Fit side-chains REVERT: A 1724 TYR cc_start: 0.7491 (m-80) cc_final: 0.7210 (m-80) REVERT: B 47 GLN cc_start: 0.7953 (mt0) cc_final: 0.7745 (mt0) REVERT: F 304 ILE cc_start: 0.8723 (mt) cc_final: 0.8517 (mp) outliers start: 2 outliers final: 2 residues processed: 374 average time/residue: 1.4773 time to fit residues: 624.0592 Evaluate side-chains 234 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 232 time to evaluate : 2.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain B residue 39 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 231 optimal weight: 6.9990 chunk 207 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 140 optimal weight: 0.6980 chunk 110 optimal weight: 7.9990 chunk 214 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 159 optimal weight: 10.0000 chunk 248 optimal weight: 8.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 553 ASN D 579 GLN A 133 ASN A 196 GLN A 272 ASN A 613 GLN A 752 GLN A 792 GLN A1018 ASN A1062 GLN A1653 HIS A1767 GLN A1781 ASN A1955 ASN A2366 ASN ** F 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 385 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.096114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.070690 restraints weight = 35754.814| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 2.36 r_work: 0.2671 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2534 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 22384 Z= 0.298 Angle : 0.644 9.487 30390 Z= 0.333 Chirality : 0.049 0.245 3302 Planarity : 0.005 0.090 4025 Dihedral : 9.451 107.886 3148 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.67 % Allowed : 8.50 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.16), residues: 2743 helix: -0.91 (0.30), residues: 289 sheet: 0.17 (0.16), residues: 1060 loop : -0.63 (0.17), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A1996 HIS 0.009 0.002 HIS A2375 PHE 0.029 0.002 PHE A 656 TYR 0.019 0.002 TYR B 55 ARG 0.007 0.001 ARG F 232 Details of bonding type rmsd hydrogen bonds : bond 0.03669 ( 722) hydrogen bonds : angle 5.45485 ( 1911) covalent geometry : bond 0.00683 (22384) covalent geometry : angle 0.64407 (30390) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 254 time to evaluate : 2.582 Fit side-chains REVERT: D 560 ASN cc_start: 0.7528 (m-40) cc_final: 0.6898 (p0) REVERT: A 170 ASP cc_start: 0.8564 (m-30) cc_final: 0.8355 (m-30) REVERT: A 713 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8297 (tm-30) REVERT: A 1197 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8551 (mt-10) REVERT: A 1263 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8736 (mt-10) REVERT: B 30 GLU cc_start: 0.7741 (mp0) cc_final: 0.7527 (mp0) REVERT: B 47 GLN cc_start: 0.8162 (mt0) cc_final: 0.7856 (mt0) REVERT: B 104 TYR cc_start: 0.9158 (p90) cc_final: 0.8520 (p90) REVERT: B 116 GLU cc_start: 0.8863 (pm20) cc_final: 0.8654 (mp0) REVERT: B 169 GLU cc_start: 0.8543 (mt-10) cc_final: 0.7907 (mt-10) REVERT: F 304 ILE cc_start: 0.8364 (mt) cc_final: 0.8054 (mp) REVERT: F 365 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.7728 (ppp) outliers start: 40 outliers final: 14 residues processed: 274 average time/residue: 1.4430 time to fit residues: 449.4700 Evaluate side-chains 252 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 236 time to evaluate : 2.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 542 VAL Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 1197 GLU Chi-restraints excluded: chain A residue 1428 ASP Chi-restraints excluded: chain A residue 1555 GLU Chi-restraints excluded: chain A residue 2267 SER Chi-restraints excluded: chain A residue 2357 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 250 SER Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 365 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 114 optimal weight: 0.9980 chunk 212 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 chunk 49 optimal weight: 0.0050 chunk 141 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 chunk 189 optimal weight: 7.9990 chunk 230 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 overall best weight: 1.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 553 ASN A 511 ASN A 532 GLN A 613 GLN A 752 GLN A1200 ASN A1302 ASN A1653 HIS A1767 GLN ** A2136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2331 ASN B 94 ASN ** F 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 GLN ** F 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 353 GLN F 385 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.097951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.072743 restraints weight = 35668.419| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 2.38 r_work: 0.2711 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22384 Z= 0.151 Angle : 0.558 7.824 30390 Z= 0.287 Chirality : 0.046 0.324 3302 Planarity : 0.004 0.077 4025 Dihedral : 7.658 84.702 3144 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.79 % Allowed : 9.50 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.16), residues: 2743 helix: -0.91 (0.30), residues: 297 sheet: 0.18 (0.16), residues: 1058 loop : -0.59 (0.17), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1996 HIS 0.003 0.001 HIS A2375 PHE 0.016 0.001 PHE A1480 TYR 0.013 0.001 TYR B 54 ARG 0.006 0.000 ARG B 48 Details of bonding type rmsd hydrogen bonds : bond 0.02985 ( 722) hydrogen bonds : angle 5.25170 ( 1911) covalent geometry : bond 0.00341 (22384) covalent geometry : angle 0.55839 (30390) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 247 time to evaluate : 2.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 260 GLU cc_start: 0.9158 (mt-10) cc_final: 0.8928 (mm-30) REVERT: A 560 GLN cc_start: 0.8763 (tt0) cc_final: 0.8494 (tm-30) REVERT: A 713 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8301 (tm-30) REVERT: A 750 PHE cc_start: 0.7622 (m-80) cc_final: 0.7085 (m-10) REVERT: A 1263 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8706 (mt-10) REVERT: A 1580 TRP cc_start: 0.8137 (OUTLIER) cc_final: 0.6884 (p-90) REVERT: A 1970 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8874 (mm) REVERT: A 2016 LYS cc_start: 0.8704 (tppp) cc_final: 0.8428 (tppp) REVERT: A 2302 ASP cc_start: 0.7803 (m-30) cc_final: 0.7132 (p0) REVERT: B 30 GLU cc_start: 0.7758 (mp0) cc_final: 0.7510 (mp0) REVERT: B 59 LYS cc_start: 0.8663 (pttm) cc_final: 0.8071 (pptt) REVERT: B 104 TYR cc_start: 0.9280 (p90) cc_final: 0.8466 (p90) REVERT: B 116 GLU cc_start: 0.8886 (pm20) cc_final: 0.8640 (mp0) REVERT: F 84 ASP cc_start: 0.7618 (p0) cc_final: 0.7355 (p0) REVERT: F 304 ILE cc_start: 0.8265 (mt) cc_final: 0.7976 (mp) REVERT: F 365 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.7631 (ppp) outliers start: 43 outliers final: 15 residues processed: 267 average time/residue: 1.4835 time to fit residues: 448.6415 Evaluate side-chains 250 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 232 time to evaluate : 2.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 542 VAL Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 1428 ASP Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1970 LEU Chi-restraints excluded: chain A residue 2126 THR Chi-restraints excluded: chain A residue 2267 SER Chi-restraints excluded: chain A residue 2357 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain F residue 250 SER Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 365 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 232 optimal weight: 8.9990 chunk 139 optimal weight: 0.2980 chunk 256 optimal weight: 3.9990 chunk 229 optimal weight: 10.0000 chunk 227 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 170 optimal weight: 5.9990 chunk 219 optimal weight: 6.9990 chunk 30 optimal weight: 0.1980 chunk 257 optimal weight: 1.9990 chunk 100 optimal weight: 0.0270 overall best weight: 0.9042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 551 ASN D 553 ASN A 329 GLN A 511 ASN A 532 GLN A 613 GLN A 752 GLN A1653 HIS A1740 ASN A1767 GLN ** A1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2331 ASN F 47 GLN F 353 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.099011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.073692 restraints weight = 35923.290| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 2.40 r_work: 0.2731 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22384 Z= 0.119 Angle : 0.528 7.895 30390 Z= 0.272 Chirality : 0.045 0.360 3302 Planarity : 0.004 0.070 4025 Dihedral : 6.565 78.128 3144 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.87 % Allowed : 10.25 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.16), residues: 2743 helix: -0.79 (0.30), residues: 293 sheet: 0.22 (0.16), residues: 1064 loop : -0.55 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1996 HIS 0.003 0.001 HIS B 90 PHE 0.016 0.001 PHE A1242 TYR 0.012 0.001 TYR A1394 ARG 0.005 0.000 ARG A 164 Details of bonding type rmsd hydrogen bonds : bond 0.02663 ( 722) hydrogen bonds : angle 5.07573 ( 1911) covalent geometry : bond 0.00265 (22384) covalent geometry : angle 0.52822 (30390) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 254 time to evaluate : 2.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 578 LYS cc_start: 0.8928 (tptp) cc_final: 0.8494 (mmmt) REVERT: A 260 GLU cc_start: 0.9158 (mt-10) cc_final: 0.8891 (mm-30) REVERT: A 560 GLN cc_start: 0.8758 (tt0) cc_final: 0.8476 (tm-30) REVERT: A 573 LYS cc_start: 0.8901 (mttm) cc_final: 0.8589 (mtpp) REVERT: A 713 GLU cc_start: 0.8638 (tm-30) cc_final: 0.8345 (tm-30) REVERT: A 786 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8372 (pp30) REVERT: A 809 GLU cc_start: 0.8601 (tt0) cc_final: 0.7950 (tm-30) REVERT: A 870 MET cc_start: 0.9012 (mmp) cc_final: 0.8737 (mmp) REVERT: A 1263 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8713 (mt-10) REVERT: A 1949 GLN cc_start: 0.7497 (tt0) cc_final: 0.7247 (tp40) REVERT: A 1970 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8869 (mm) REVERT: A 2016 LYS cc_start: 0.8706 (tppp) cc_final: 0.8449 (tppp) REVERT: A 2333 GLU cc_start: 0.8741 (tt0) cc_final: 0.8446 (mp0) REVERT: B 30 GLU cc_start: 0.7813 (mp0) cc_final: 0.7558 (mp0) REVERT: B 48 ARG cc_start: 0.9112 (ttt-90) cc_final: 0.8877 (ttt-90) REVERT: B 59 LYS cc_start: 0.8692 (pttm) cc_final: 0.8220 (pptt) REVERT: B 104 TYR cc_start: 0.9275 (p90) cc_final: 0.8883 (p90) REVERT: B 116 GLU cc_start: 0.8842 (pm20) cc_final: 0.8550 (mp0) REVERT: B 169 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8135 (mt-10) REVERT: F 304 ILE cc_start: 0.8264 (mt) cc_final: 0.7972 (mp) outliers start: 45 outliers final: 15 residues processed: 278 average time/residue: 1.4974 time to fit residues: 474.5220 Evaluate side-chains 257 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 240 time to evaluate : 2.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 542 VAL Chi-restraints excluded: chain D residue 593 SER Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 786 GLN Chi-restraints excluded: chain A residue 1286 ASP Chi-restraints excluded: chain A residue 1428 ASP Chi-restraints excluded: chain A residue 1519 MET Chi-restraints excluded: chain A residue 1609 ASP Chi-restraints excluded: chain A residue 1970 LEU Chi-restraints excluded: chain A residue 2267 SER Chi-restraints excluded: chain A residue 2357 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain F residue 250 SER Chi-restraints excluded: chain F residue 323 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 94 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 186 optimal weight: 2.9990 chunk 139 optimal weight: 0.6980 chunk 113 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 170 optimal weight: 9.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 551 ASN D 553 ASN A 264 GLN A 329 GLN A 511 ASN A 613 GLN A 752 GLN A1348 ASN A1485 ASN A1740 ASN A1767 GLN ** A1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2331 ASN ** F 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 353 GLN F 385 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.096527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.071021 restraints weight = 35794.731| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 2.38 r_work: 0.2680 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2544 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 22384 Z= 0.233 Angle : 0.582 8.390 30390 Z= 0.301 Chirality : 0.047 0.379 3302 Planarity : 0.004 0.072 4025 Dihedral : 6.443 74.328 3144 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.96 % Allowed : 11.16 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.16), residues: 2743 helix: -0.80 (0.30), residues: 296 sheet: 0.16 (0.16), residues: 1062 loop : -0.58 (0.17), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1996 HIS 0.004 0.001 HIS A2375 PHE 0.022 0.002 PHE A1480 TYR 0.016 0.001 TYR A1104 ARG 0.009 0.001 ARG A2189 Details of bonding type rmsd hydrogen bonds : bond 0.03167 ( 722) hydrogen bonds : angle 5.20786 ( 1911) covalent geometry : bond 0.00535 (22384) covalent geometry : angle 0.58169 (30390) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 240 time to evaluate : 2.646 Fit side-chains revert: symmetry clash REVERT: D 578 LYS cc_start: 0.8914 (tptp) cc_final: 0.8678 (tppp) REVERT: A 560 GLN cc_start: 0.8755 (tt0) cc_final: 0.8494 (tm-30) REVERT: A 713 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8349 (tm-30) REVERT: A 722 GLN cc_start: 0.9012 (mp10) cc_final: 0.8685 (mp10) REVERT: A 723 LEU cc_start: 0.9007 (mt) cc_final: 0.8263 (tp) REVERT: A 786 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8398 (pp30) REVERT: A 809 GLU cc_start: 0.8595 (tt0) cc_final: 0.7945 (tm-30) REVERT: A 1263 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8703 (mt-10) REVERT: A 1580 TRP cc_start: 0.8245 (OUTLIER) cc_final: 0.6967 (p-90) REVERT: A 1949 GLN cc_start: 0.7497 (tt0) cc_final: 0.7233 (tp40) REVERT: A 1970 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8887 (mm) REVERT: A 2016 LYS cc_start: 0.8736 (tppp) cc_final: 0.8471 (tppp) REVERT: A 2207 ARG cc_start: 0.8605 (ptp90) cc_final: 0.8323 (ptp90) REVERT: A 2248 GLN cc_start: 0.8867 (tt0) cc_final: 0.8475 (tt0) REVERT: B 30 GLU cc_start: 0.7866 (mp0) cc_final: 0.7605 (mp0) REVERT: B 59 LYS cc_start: 0.8624 (pttm) cc_final: 0.8163 (pptt) REVERT: B 104 TYR cc_start: 0.9321 (p90) cc_final: 0.8912 (p90) REVERT: B 116 GLU cc_start: 0.8882 (pm20) cc_final: 0.8561 (mp0) REVERT: B 123 ARG cc_start: 0.8925 (ptp90) cc_final: 0.8720 (ptp-170) REVERT: F 304 ILE cc_start: 0.8279 (mt) cc_final: 0.7996 (mp) REVERT: F 365 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.7518 (ppp) outliers start: 47 outliers final: 19 residues processed: 270 average time/residue: 1.4472 time to fit residues: 444.5879 Evaluate side-chains 258 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 235 time to evaluate : 2.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 542 VAL Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 593 SER Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 786 GLN Chi-restraints excluded: chain A residue 1286 ASP Chi-restraints excluded: chain A residue 1428 ASP Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1740 ASN Chi-restraints excluded: chain A residue 1970 LEU Chi-restraints excluded: chain A residue 2267 SER Chi-restraints excluded: chain A residue 2357 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain F residue 250 SER Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 365 MET Chi-restraints excluded: chain F residue 392 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 219 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 195 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 221 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 137 optimal weight: 0.5980 chunk 134 optimal weight: 0.9990 chunk 116 optimal weight: 0.4980 chunk 14 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 551 ASN D 553 ASN A 511 ASN A 532 GLN A 613 GLN A 752 GLN A1740 ASN A1767 GLN ** A1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2136 ASN A2331 ASN ** F 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 GLN F 353 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.098569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.073248 restraints weight = 35606.851| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.39 r_work: 0.2724 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22384 Z= 0.114 Angle : 0.529 8.502 30390 Z= 0.273 Chirality : 0.046 0.348 3302 Planarity : 0.004 0.068 4025 Dihedral : 6.126 75.295 3144 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.71 % Allowed : 12.12 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.16), residues: 2743 helix: -0.74 (0.30), residues: 294 sheet: 0.19 (0.16), residues: 1062 loop : -0.53 (0.17), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A2353 HIS 0.002 0.001 HIS A1672 PHE 0.016 0.001 PHE A1804 TYR 0.012 0.001 TYR A1394 ARG 0.006 0.000 ARG A2199 Details of bonding type rmsd hydrogen bonds : bond 0.02667 ( 722) hydrogen bonds : angle 5.07180 ( 1911) covalent geometry : bond 0.00253 (22384) covalent geometry : angle 0.52908 (30390) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 250 time to evaluate : 2.614 Fit side-chains revert: symmetry clash REVERT: D 578 LYS cc_start: 0.8946 (tptp) cc_final: 0.8712 (tppp) REVERT: A 560 GLN cc_start: 0.8752 (tt0) cc_final: 0.8487 (tm-30) REVERT: A 573 LYS cc_start: 0.8930 (mttm) cc_final: 0.8618 (mtpp) REVERT: A 713 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8306 (tm-30) REVERT: A 722 GLN cc_start: 0.8978 (mp10) cc_final: 0.8640 (mp10) REVERT: A 723 LEU cc_start: 0.8954 (mt) cc_final: 0.8204 (tp) REVERT: A 786 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8371 (pp30) REVERT: A 809 GLU cc_start: 0.8586 (tt0) cc_final: 0.7931 (tm-30) REVERT: A 870 MET cc_start: 0.8987 (mmp) cc_final: 0.8656 (mmp) REVERT: A 1263 GLU cc_start: 0.9042 (mm-30) cc_final: 0.8702 (mt-10) REVERT: A 1580 TRP cc_start: 0.8177 (OUTLIER) cc_final: 0.6933 (p-90) REVERT: A 1851 MET cc_start: 0.9162 (OUTLIER) cc_final: 0.8777 (ttp) REVERT: A 1949 GLN cc_start: 0.7496 (tt0) cc_final: 0.7228 (tp40) REVERT: A 1970 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8889 (mm) REVERT: A 2016 LYS cc_start: 0.8715 (tppp) cc_final: 0.8449 (tppp) REVERT: A 2199 ARG cc_start: 0.7517 (ttp-110) cc_final: 0.6879 (ttp80) REVERT: A 2207 ARG cc_start: 0.8581 (ptp90) cc_final: 0.8237 (ptp90) REVERT: A 2248 GLN cc_start: 0.8855 (tt0) cc_final: 0.8454 (tt0) REVERT: A 2333 GLU cc_start: 0.8776 (tt0) cc_final: 0.8464 (mp0) REVERT: B 30 GLU cc_start: 0.7861 (mp0) cc_final: 0.7608 (mp0) REVERT: B 59 LYS cc_start: 0.8657 (pttm) cc_final: 0.8235 (pptt) REVERT: B 104 TYR cc_start: 0.9274 (p90) cc_final: 0.8959 (p90) REVERT: B 116 GLU cc_start: 0.8861 (pm20) cc_final: 0.8568 (mp0) REVERT: B 123 ARG cc_start: 0.8883 (ptp90) cc_final: 0.8655 (ptp90) REVERT: B 169 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8272 (mt-10) REVERT: F 304 ILE cc_start: 0.8202 (mt) cc_final: 0.7895 (mp) REVERT: F 365 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.7494 (ppp) outliers start: 41 outliers final: 19 residues processed: 273 average time/residue: 1.4463 time to fit residues: 452.6141 Evaluate side-chains 264 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 240 time to evaluate : 2.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 542 VAL Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 593 SER Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 786 GLN Chi-restraints excluded: chain A residue 1286 ASP Chi-restraints excluded: chain A residue 1428 ASP Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1609 ASP Chi-restraints excluded: chain A residue 1851 MET Chi-restraints excluded: chain A residue 1970 LEU Chi-restraints excluded: chain A residue 2357 LEU Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain F residue 250 SER Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 365 MET Chi-restraints excluded: chain F residue 392 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 31 optimal weight: 5.9990 chunk 119 optimal weight: 7.9990 chunk 213 optimal weight: 10.0000 chunk 191 optimal weight: 8.9990 chunk 225 optimal weight: 4.9990 chunk 234 optimal weight: 0.6980 chunk 185 optimal weight: 2.9990 chunk 238 optimal weight: 8.9990 chunk 150 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 551 ASN D 553 ASN A 511 ASN A 613 GLN A 752 GLN A1740 ASN A1767 GLN ** A1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2331 ASN ** F 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 GLN F 209 GLN F 291 ASN F 353 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.095693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.070302 restraints weight = 35956.490| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 2.36 r_work: 0.2667 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2530 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 22384 Z= 0.276 Angle : 0.605 8.819 30390 Z= 0.313 Chirality : 0.048 0.360 3302 Planarity : 0.004 0.070 4025 Dihedral : 6.305 72.454 3144 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.75 % Allowed : 12.62 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.16), residues: 2743 helix: -0.90 (0.30), residues: 302 sheet: 0.11 (0.16), residues: 1060 loop : -0.58 (0.17), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1996 HIS 0.004 0.001 HIS A1672 PHE 0.024 0.002 PHE A1480 TYR 0.017 0.002 TYR A1104 ARG 0.006 0.001 ARG A 164 Details of bonding type rmsd hydrogen bonds : bond 0.03279 ( 722) hydrogen bonds : angle 5.27132 ( 1911) covalent geometry : bond 0.00633 (22384) covalent geometry : angle 0.60465 (30390) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 238 time to evaluate : 2.481 Fit side-chains revert: symmetry clash REVERT: D 578 LYS cc_start: 0.8916 (tptp) cc_final: 0.8676 (tppp) REVERT: D 599 LYS cc_start: 0.9053 (ttmt) cc_final: 0.8762 (ttmt) REVERT: A 560 GLN cc_start: 0.8775 (tt0) cc_final: 0.8505 (tm-30) REVERT: A 713 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8337 (tm-30) REVERT: A 722 GLN cc_start: 0.9011 (mp10) cc_final: 0.8695 (mp10) REVERT: A 786 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8383 (pp30) REVERT: A 809 GLU cc_start: 0.8573 (tt0) cc_final: 0.7949 (tm-30) REVERT: A 1197 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8695 (mt-10) REVERT: A 1263 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8699 (mt-10) REVERT: A 1580 TRP cc_start: 0.8329 (OUTLIER) cc_final: 0.7032 (p-90) REVERT: A 1949 GLN cc_start: 0.7528 (tt0) cc_final: 0.7249 (tp40) REVERT: A 2016 LYS cc_start: 0.8713 (tppp) cc_final: 0.8449 (tppp) REVERT: A 2207 ARG cc_start: 0.8627 (ptp90) cc_final: 0.8347 (ptp90) REVERT: A 2248 GLN cc_start: 0.8886 (tt0) cc_final: 0.8484 (tt0) REVERT: B 30 GLU cc_start: 0.7897 (mp0) cc_final: 0.7627 (mp0) REVERT: B 104 TYR cc_start: 0.9318 (p90) cc_final: 0.8995 (p90) REVERT: B 169 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8250 (mt-10) REVERT: F 141 ASP cc_start: 0.8813 (p0) cc_final: 0.8604 (p0) REVERT: F 304 ILE cc_start: 0.8252 (mt) cc_final: 0.7954 (mp) REVERT: F 365 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.7481 (ppp) outliers start: 42 outliers final: 20 residues processed: 261 average time/residue: 1.4563 time to fit residues: 432.4565 Evaluate side-chains 257 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 233 time to evaluate : 2.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 542 VAL Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 786 GLN Chi-restraints excluded: chain A residue 1197 GLU Chi-restraints excluded: chain A residue 1286 ASP Chi-restraints excluded: chain A residue 1428 ASP Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1740 ASN Chi-restraints excluded: chain A residue 2267 SER Chi-restraints excluded: chain A residue 2290 MET Chi-restraints excluded: chain A residue 2357 LEU Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain F residue 250 SER Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 365 MET Chi-restraints excluded: chain F residue 392 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 36 optimal weight: 0.9990 chunk 142 optimal weight: 0.9980 chunk 267 optimal weight: 9.9990 chunk 258 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 222 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 195 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 265 optimal weight: 0.0970 chunk 116 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 551 ASN D 553 ASN A 511 ASN A 532 GLN A 613 GLN A 752 GLN A 818 ASN A1740 ASN A1767 GLN ** A1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2331 ASN B 94 ASN ** F 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 GLN F 291 ASN F 353 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.098427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.073255 restraints weight = 35649.043| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 2.37 r_work: 0.2724 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22384 Z= 0.115 Angle : 0.538 9.084 30390 Z= 0.278 Chirality : 0.046 0.317 3302 Planarity : 0.004 0.064 4025 Dihedral : 6.014 73.830 3144 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.46 % Allowed : 13.12 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.16), residues: 2743 helix: -0.73 (0.30), residues: 294 sheet: 0.17 (0.16), residues: 1061 loop : -0.54 (0.17), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2353 HIS 0.003 0.001 HIS A1672 PHE 0.020 0.001 PHE A1804 TYR 0.012 0.001 TYR A1394 ARG 0.014 0.001 ARG A1741 Details of bonding type rmsd hydrogen bonds : bond 0.02673 ( 722) hydrogen bonds : angle 5.09286 ( 1911) covalent geometry : bond 0.00257 (22384) covalent geometry : angle 0.53842 (30390) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 243 time to evaluate : 2.524 Fit side-chains revert: symmetry clash REVERT: A 560 GLN cc_start: 0.8755 (tt0) cc_final: 0.8491 (tm-30) REVERT: A 573 LYS cc_start: 0.8945 (mttm) cc_final: 0.8627 (mtpp) REVERT: A 713 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8275 (tm-30) REVERT: A 809 GLU cc_start: 0.8558 (tt0) cc_final: 0.7902 (tm-30) REVERT: A 870 MET cc_start: 0.8970 (mmp) cc_final: 0.8630 (mmp) REVERT: A 1197 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8653 (mt-10) REVERT: A 1263 GLU cc_start: 0.9024 (mm-30) cc_final: 0.8686 (mt-10) REVERT: A 1526 ASP cc_start: 0.8373 (m-30) cc_final: 0.8168 (m-30) REVERT: A 1580 TRP cc_start: 0.8278 (OUTLIER) cc_final: 0.6981 (p-90) REVERT: A 1949 GLN cc_start: 0.7511 (tt0) cc_final: 0.7234 (tp40) REVERT: A 2016 LYS cc_start: 0.8695 (tppp) cc_final: 0.8463 (tppp) REVERT: A 2190 TYR cc_start: 0.6929 (m-80) cc_final: 0.6555 (m-80) REVERT: A 2199 ARG cc_start: 0.7503 (ttp-110) cc_final: 0.6799 (ttp80) REVERT: A 2207 ARG cc_start: 0.8608 (ptp90) cc_final: 0.8306 (ptp90) REVERT: A 2248 GLN cc_start: 0.8854 (tt0) cc_final: 0.8450 (tt0) REVERT: A 2333 GLU cc_start: 0.8770 (tt0) cc_final: 0.8492 (mp0) REVERT: B 30 GLU cc_start: 0.7895 (mp0) cc_final: 0.7622 (mp0) REVERT: B 59 LYS cc_start: 0.8620 (pttm) cc_final: 0.8093 (pptt) REVERT: B 104 TYR cc_start: 0.9286 (p90) cc_final: 0.8947 (p90) REVERT: B 169 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8249 (mt-10) REVERT: F 84 ASP cc_start: 0.7562 (p0) cc_final: 0.7349 (p0) REVERT: F 141 ASP cc_start: 0.8735 (p0) cc_final: 0.8529 (p0) REVERT: F 304 ILE cc_start: 0.8204 (mt) cc_final: 0.7928 (mp) REVERT: F 365 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.7461 (ppp) outliers start: 35 outliers final: 16 residues processed: 261 average time/residue: 1.4249 time to fit residues: 422.6950 Evaluate side-chains 258 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 239 time to evaluate : 2.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 542 VAL Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 1197 GLU Chi-restraints excluded: chain A residue 1286 ASP Chi-restraints excluded: chain A residue 1428 ASP Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 2290 MET Chi-restraints excluded: chain A residue 2357 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain F residue 250 SER Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 365 MET Chi-restraints excluded: chain F residue 392 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 157 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 89 optimal weight: 0.4980 chunk 37 optimal weight: 5.9990 chunk 247 optimal weight: 0.9990 chunk 267 optimal weight: 10.0000 chunk 127 optimal weight: 7.9990 chunk 113 optimal weight: 0.6980 chunk 254 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 551 ASN D 553 ASN A 511 ASN A 613 GLN A 752 GLN A1767 GLN ** A1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2331 ASN F 47 GLN F 209 GLN F 291 ASN F 353 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.098399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.073170 restraints weight = 35611.975| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.37 r_work: 0.2724 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22384 Z= 0.125 Angle : 0.542 9.207 30390 Z= 0.280 Chirality : 0.046 0.304 3302 Planarity : 0.004 0.065 4025 Dihedral : 5.878 73.273 3144 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.46 % Allowed : 13.12 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.16), residues: 2743 helix: -0.68 (0.30), residues: 299 sheet: 0.19 (0.16), residues: 1060 loop : -0.50 (0.17), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1996 HIS 0.003 0.001 HIS A1672 PHE 0.016 0.001 PHE A1480 TYR 0.014 0.001 TYR D 563 ARG 0.008 0.000 ARG A2398 Details of bonding type rmsd hydrogen bonds : bond 0.02668 ( 722) hydrogen bonds : angle 4.99775 ( 1911) covalent geometry : bond 0.00284 (22384) covalent geometry : angle 0.54229 (30390) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 244 time to evaluate : 2.652 Fit side-chains revert: symmetry clash REVERT: D 599 LYS cc_start: 0.8885 (ttmt) cc_final: 0.8637 (mtmt) REVERT: A 560 GLN cc_start: 0.8750 (tt0) cc_final: 0.8485 (tm-30) REVERT: A 573 LYS cc_start: 0.8932 (mttm) cc_final: 0.8595 (mtpp) REVERT: A 713 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8270 (tm-30) REVERT: A 809 GLU cc_start: 0.8543 (tt0) cc_final: 0.7914 (tm-30) REVERT: A 870 MET cc_start: 0.8977 (mmp) cc_final: 0.8651 (mmp) REVERT: A 1197 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8668 (mt-10) REVERT: A 1263 GLU cc_start: 0.9026 (mm-30) cc_final: 0.8687 (mt-10) REVERT: A 1580 TRP cc_start: 0.8261 (OUTLIER) cc_final: 0.6980 (p-90) REVERT: A 1949 GLN cc_start: 0.7549 (tt0) cc_final: 0.7268 (tp40) REVERT: A 1970 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8872 (mm) REVERT: A 2016 LYS cc_start: 0.8695 (tppp) cc_final: 0.8492 (tppp) REVERT: A 2190 TYR cc_start: 0.6867 (m-80) cc_final: 0.6468 (m-80) REVERT: A 2207 ARG cc_start: 0.8606 (ptp90) cc_final: 0.8304 (ptp90) REVERT: A 2248 GLN cc_start: 0.8853 (tt0) cc_final: 0.8415 (tt0) REVERT: A 2333 GLU cc_start: 0.8737 (tt0) cc_final: 0.8484 (mp0) REVERT: B 30 GLU cc_start: 0.7887 (mp0) cc_final: 0.7608 (mp0) REVERT: B 59 LYS cc_start: 0.8639 (pttm) cc_final: 0.8130 (pptt) REVERT: B 104 TYR cc_start: 0.9309 (p90) cc_final: 0.8908 (p90) REVERT: F 84 ASP cc_start: 0.7420 (p0) cc_final: 0.7158 (p0) REVERT: F 304 ILE cc_start: 0.8215 (mt) cc_final: 0.7938 (mp) REVERT: F 365 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.7471 (ppp) outliers start: 35 outliers final: 18 residues processed: 262 average time/residue: 1.4616 time to fit residues: 434.5638 Evaluate side-chains 259 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 237 time to evaluate : 2.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 542 VAL Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain D residue 608 ILE Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 1197 GLU Chi-restraints excluded: chain A residue 1243 MET Chi-restraints excluded: chain A residue 1286 ASP Chi-restraints excluded: chain A residue 1428 ASP Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1970 LEU Chi-restraints excluded: chain A residue 2357 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain F residue 250 SER Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 365 MET Chi-restraints excluded: chain F residue 392 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 265 optimal weight: 6.9990 chunk 146 optimal weight: 4.9990 chunk 211 optimal weight: 5.9990 chunk 197 optimal weight: 7.9990 chunk 5 optimal weight: 0.7980 chunk 76 optimal weight: 9.9990 chunk 123 optimal weight: 0.3980 chunk 266 optimal weight: 0.0670 chunk 34 optimal weight: 2.9990 chunk 163 optimal weight: 8.9990 chunk 68 optimal weight: 7.9990 overall best weight: 1.8522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 551 ASN D 553 ASN A 511 ASN A 532 GLN A 613 GLN A 752 GLN A1767 GLN ** A1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2331 ASN F 47 GLN F 209 GLN F 291 ASN F 353 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.097181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.071847 restraints weight = 35866.944| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 2.37 r_work: 0.2697 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2561 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22384 Z= 0.180 Angle : 0.570 9.476 30390 Z= 0.295 Chirality : 0.046 0.301 3302 Planarity : 0.004 0.065 4025 Dihedral : 5.973 71.986 3144 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.04 % Allowed : 13.87 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.16), residues: 2743 helix: -0.68 (0.31), residues: 294 sheet: 0.14 (0.16), residues: 1061 loop : -0.53 (0.17), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1996 HIS 0.003 0.001 HIS A1672 PHE 0.019 0.001 PHE A1480 TYR 0.014 0.001 TYR A1104 ARG 0.010 0.000 ARG A2199 Details of bonding type rmsd hydrogen bonds : bond 0.02908 ( 722) hydrogen bonds : angle 5.08790 ( 1911) covalent geometry : bond 0.00413 (22384) covalent geometry : angle 0.57020 (30390) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5486 Ramachandran restraints generated. 2743 Oldfield, 0 Emsley, 2743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 237 time to evaluate : 2.599 Fit side-chains revert: symmetry clash REVERT: D 578 LYS cc_start: 0.8808 (tppp) cc_final: 0.7943 (tppt) REVERT: D 599 LYS cc_start: 0.8927 (ttmt) cc_final: 0.8680 (mtmt) REVERT: A 264 GLN cc_start: 0.8561 (pt0) cc_final: 0.8326 (pt0) REVERT: A 560 GLN cc_start: 0.8763 (tt0) cc_final: 0.8498 (tm-30) REVERT: A 573 LYS cc_start: 0.8946 (mttm) cc_final: 0.8593 (mtpp) REVERT: A 713 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8303 (tm-30) REVERT: A 809 GLU cc_start: 0.8573 (tt0) cc_final: 0.7908 (tm-30) REVERT: A 870 MET cc_start: 0.9023 (mmp) cc_final: 0.8648 (mmp) REVERT: A 1197 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8698 (mt-10) REVERT: A 1263 GLU cc_start: 0.9031 (mm-30) cc_final: 0.8691 (mt-10) REVERT: A 1580 TRP cc_start: 0.8330 (OUTLIER) cc_final: 0.7131 (p-90) REVERT: A 1949 GLN cc_start: 0.7584 (tt0) cc_final: 0.7296 (tp40) REVERT: A 1970 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8887 (mm) REVERT: A 2190 TYR cc_start: 0.6910 (m-80) cc_final: 0.6573 (m-80) REVERT: A 2207 ARG cc_start: 0.8624 (ptp90) cc_final: 0.8331 (ptp90) REVERT: A 2248 GLN cc_start: 0.8872 (tt0) cc_final: 0.8437 (tt0) REVERT: A 2264 ARG cc_start: 0.7994 (ptp90) cc_final: 0.7739 (ptp90) REVERT: A 2333 GLU cc_start: 0.8727 (tt0) cc_final: 0.8464 (mp0) REVERT: B 30 GLU cc_start: 0.7900 (mp0) cc_final: 0.7622 (mp0) REVERT: B 59 LYS cc_start: 0.8615 (pttm) cc_final: 0.8113 (pptt) REVERT: B 102 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8459 (tmmm) REVERT: B 104 TYR cc_start: 0.9292 (p90) cc_final: 0.8962 (p90) REVERT: F 84 ASP cc_start: 0.7493 (p0) cc_final: 0.7240 (p0) REVERT: F 304 ILE cc_start: 0.8238 (mt) cc_final: 0.7957 (mp) REVERT: F 365 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.7485 (ppp) outliers start: 25 outliers final: 15 residues processed: 254 average time/residue: 1.4969 time to fit residues: 432.4942 Evaluate side-chains 257 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 237 time to evaluate : 2.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 542 VAL Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 565 LEU Chi-restraints excluded: chain D residue 607 THR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 1197 GLU Chi-restraints excluded: chain A residue 1428 ASP Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1609 ASP Chi-restraints excluded: chain A residue 1970 LEU Chi-restraints excluded: chain A residue 2357 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain F residue 250 SER Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 365 MET Chi-restraints excluded: chain F residue 392 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 41 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 33 optimal weight: 0.0970 chunk 197 optimal weight: 7.9990 chunk 16 optimal weight: 0.4980 chunk 262 optimal weight: 7.9990 chunk 263 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 125 optimal weight: 3.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 551 ASN D 553 ASN A 511 ASN A 613 GLN A 752 GLN A1767 GLN A1795 ASN ** A1878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2331 ASN ** F 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 GLN F 291 ASN F 353 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.096819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.071439 restraints weight = 35709.018| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 2.37 r_work: 0.2690 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2554 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 22384 Z= 0.200 Angle : 0.582 9.403 30390 Z= 0.301 Chirality : 0.047 0.302 3302 Planarity : 0.004 0.066 4025 Dihedral : 5.982 71.570 3144 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.12 % Allowed : 13.99 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.16), residues: 2743 helix: -0.78 (0.30), residues: 300 sheet: 0.10 (0.16), residues: 1064 loop : -0.54 (0.17), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1580 HIS 0.003 0.001 HIS A1672 PHE 0.019 0.001 PHE A1480 TYR 0.015 0.001 TYR A1104 ARG 0.011 0.001 ARG A2199 Details of bonding type rmsd hydrogen bonds : bond 0.02975 ( 722) hydrogen bonds : angle 5.13105 ( 1911) covalent geometry : bond 0.00459 (22384) covalent geometry : angle 0.58191 (30390) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14468.17 seconds wall clock time: 250 minutes 0.97 seconds (15000.97 seconds total)