Starting phenix.real_space_refine on Thu Jun 19 12:11:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8glk_40196/06_2025/8glk_40196.cif Found real_map, /net/cci-nas-00/data/ceres_data/8glk_40196/06_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_40196/06_2025/8glk_40196.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8glk_40196/06_2025/8glk_40196.map" model { file = "/net/cci-nas-00/data/ceres_data/8glk_40196/06_2025/8glk_40196.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8glk_40196/06_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 13.61, per 1000 atoms: 0.62 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: 5.84 Conformation dependent library (CDL) restraints added in 3.0 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: 3.31 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: 14.09 Time building geometry restraints manager: 6.96 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: 0.000 Normalize map: mean=0, sd=1: 3.480 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: 0.050 Extract box with map and model: 1.000 Check model and map are aligned: 0.190 Set scattering table: 0.220 Process input model: 59.740 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.040 ------------------------------------------------------------------------------- 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 : 2.833 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: 1.4572 time to fit residues: 619.3893 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 : 2.679 ------------------------------------------------------------------------------- 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 = 0.096139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.070715 restraints weight = 35753.913| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 2.36 r_work: 0.2672 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2535 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 22384 Z= 0.296 Angle : 0.644 9.497 30390 Z= 0.333 Chirality : 0.049 0.230 3302 Planarity : 0.005 0.090 4025 Dihedral : 9.476 107.947 3148 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.60 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 A1104 ARG 0.008 0.001 ARG F 232 Details of bonding type rmsd hydrogen bonds : bond 0.03683 ( 722) hydrogen bonds : angle 5.45543 ( 1911) covalent geometry : bond 0.00679 (22384) covalent geometry : angle 0.64429 (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 : 2.429 Fit side-chains REVERT: D 560 ASN cc_start: 0.7518 (m-40) cc_final: 0.6904 (p0) REVERT: A 170 ASP cc_start: 0.8570 (m-30) cc_final: 0.8353 (m-30) REVERT: A 713 GLU cc_start: 0.8570 (tm-30) cc_final: 0.8311 (tm-30) REVERT: A 1197 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8545 (mt-10) REVERT: A 1263 GLU cc_start: 0.9059 (mm-30) cc_final: 0.8742 (mt-10) REVERT: B 30 GLU cc_start: 0.7756 (mp0) cc_final: 0.7546 (mp0) REVERT: B 47 GLN cc_start: 0.8175 (mt0) cc_final: 0.7869 (mt0) REVERT: B 104 TYR cc_start: 0.9173 (p90) cc_final: 0.8541 (p90) REVERT: B 116 GLU cc_start: 0.8869 (pm20) cc_final: 0.8658 (mp0) REVERT: B 166 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.9126 (mt) REVERT: F 304 ILE cc_start: 0.8376 (mt) cc_final: 0.8065 (mp) REVERT: F 365 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.7743 (ppp) outliers start: 40 outliers final: 14 residues processed: 274 average time/residue: 1.3836 time to fit residues: 431.1657 Evaluate side-chains 253 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 236 time to evaluate : 2.522 ------------------------------------------------------------------------------- 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 B residue 166 LEU 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: 1.9990 chunk 212 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 149 optimal weight: 4.9990 chunk 49 optimal weight: 0.0870 chunk 141 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 chunk 189 optimal weight: 7.9990 chunk 230 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 overall best weight: 1.7964 ------------------------------------------------------------------------------- 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 ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 353 GLN F 385 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.097355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.071983 restraints weight = 35690.341| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 2.39 r_work: 0.2697 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2561 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22384 Z= 0.178 Angle : 0.571 8.029 30390 Z= 0.294 Chirality : 0.047 0.318 3302 Planarity : 0.004 0.079 4025 Dihedral : 7.702 84.096 3144 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.96 % Allowed : 9.62 % Favored : 88.42 % 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: -0.57 (0.16), residues: 2743 helix: -0.90 (0.30), residues: 296 sheet: 0.16 (0.16), residues: 1058 loop : -0.60 (0.17), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1996 HIS 0.003 0.001 HIS A2375 PHE 0.017 0.001 PHE A1480 TYR 0.013 0.001 TYR B 54 ARG 0.006 0.001 ARG A2199 Details of bonding type rmsd hydrogen bonds : bond 0.03107 ( 722) hydrogen bonds : angle 5.28809 ( 1911) covalent geometry : bond 0.00402 (22384) covalent geometry : angle 0.57142 (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: 47 poor density : 243 time to evaluate : 2.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 260 GLU cc_start: 0.9160 (mt-10) cc_final: 0.8878 (mm-30) REVERT: A 560 GLN cc_start: 0.8768 (tt0) cc_final: 0.8498 (tm-30) REVERT: A 713 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8299 (tm-30) REVERT: A 737 ASN cc_start: 0.8368 (t0) cc_final: 0.8149 (t0) REVERT: A 750 PHE cc_start: 0.7653 (m-80) cc_final: 0.7162 (m-10) REVERT: A 1263 GLU cc_start: 0.9042 (mm-30) cc_final: 0.8709 (mt-10) REVERT: A 1580 TRP cc_start: 0.8189 (OUTLIER) cc_final: 0.6855 (p-90) REVERT: A 1970 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8865 (mm) REVERT: A 2016 LYS cc_start: 0.8710 (tppp) cc_final: 0.8433 (tppp) REVERT: A 2302 ASP cc_start: 0.7825 (m-30) cc_final: 0.7143 (p0) REVERT: B 30 GLU cc_start: 0.7756 (mp0) cc_final: 0.7505 (mp0) REVERT: B 59 LYS cc_start: 0.8647 (pttm) cc_final: 0.8046 (pptt) REVERT: B 104 TYR cc_start: 0.9182 (p90) cc_final: 0.8519 (p90) REVERT: B 116 GLU cc_start: 0.8890 (pm20) cc_final: 0.8644 (mp0) REVERT: B 166 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9092 (mt) REVERT: B 169 GLU cc_start: 0.8699 (mt-10) cc_final: 0.7943 (mt-10) REVERT: F 84 ASP cc_start: 0.7705 (p0) cc_final: 0.7448 (p0) REVERT: F 304 ILE cc_start: 0.8271 (mt) cc_final: 0.7970 (mp) REVERT: F 365 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.7659 (ppp) outliers start: 47 outliers final: 15 residues processed: 265 average time/residue: 1.4532 time to fit residues: 439.1453 Evaluate side-chains 251 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 232 time to evaluate : 2.587 ------------------------------------------------------------------------------- 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 235 ARG 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 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 166 LEU 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: 5.9990 chunk 139 optimal weight: 1.9990 chunk 256 optimal weight: 2.9990 chunk 229 optimal weight: 9.9990 chunk 227 optimal weight: 10.0000 chunk 72 optimal weight: 0.9990 chunk 170 optimal weight: 6.9990 chunk 219 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 257 optimal weight: 5.9990 chunk 100 optimal weight: 0.0010 overall best weight: 1.3392 ------------------------------------------------------------------------------- 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 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.097984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.072604 restraints weight = 36056.077| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 2.40 r_work: 0.2711 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2575 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.1642 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= 0.146 Angle : 0.542 7.928 30390 Z= 0.279 Chirality : 0.046 0.359 3302 Planarity : 0.004 0.074 4025 Dihedral : 6.660 77.172 3144 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.96 % Allowed : 10.62 % Favored : 87.42 % 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: -0.52 (0.16), residues: 2743 helix: -0.84 (0.30), residues: 294 sheet: 0.16 (0.16), residues: 1064 loop : -0.56 (0.17), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1996 HIS 0.002 0.001 HIS A2375 PHE 0.017 0.001 PHE A1480 TYR 0.012 0.001 TYR A1394 ARG 0.007 0.000 ARG B 48 Details of bonding type rmsd hydrogen bonds : bond 0.02811 ( 722) hydrogen bonds : angle 5.15356 ( 1911) covalent geometry : bond 0.00328 (22384) covalent geometry : angle 0.54195 (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 296 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 249 time to evaluate : 2.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 260 GLU cc_start: 0.9164 (mt-10) cc_final: 0.8849 (mm-30) REVERT: A 560 GLN cc_start: 0.8754 (tt0) cc_final: 0.8494 (tm-30) REVERT: A 713 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8338 (tm-30) REVERT: A 737 ASN cc_start: 0.8522 (t0) cc_final: 0.8301 (t0) REVERT: A 750 PHE cc_start: 0.7583 (m-80) cc_final: 0.7256 (m-10) REVERT: A 786 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8345 (pp30) REVERT: A 809 GLU cc_start: 0.8597 (tt0) cc_final: 0.7951 (tm-30) REVERT: A 870 MET cc_start: 0.9055 (mmp) cc_final: 0.8754 (mmp) REVERT: A 1263 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8697 (mt-10) REVERT: A 1580 TRP cc_start: 0.8207 (OUTLIER) cc_final: 0.6914 (p-90) REVERT: A 1949 GLN cc_start: 0.7497 (tt0) cc_final: 0.7245 (tp40) REVERT: A 1970 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8896 (mm) REVERT: A 2016 LYS cc_start: 0.8727 (tppp) cc_final: 0.8465 (tppp) REVERT: A 2333 GLU cc_start: 0.8731 (tt0) cc_final: 0.8439 (mp0) REVERT: B 30 GLU cc_start: 0.7815 (mp0) cc_final: 0.7561 (mp0) REVERT: B 59 LYS cc_start: 0.8667 (pttm) cc_final: 0.8183 (pptt) REVERT: B 104 TYR cc_start: 0.9252 (p90) cc_final: 0.8518 (p90) REVERT: B 116 GLU cc_start: 0.8858 (pm20) cc_final: 0.8557 (mp0) REVERT: B 143 GLN cc_start: 0.8967 (tt0) cc_final: 0.8711 (tt0) REVERT: B 166 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9095 (mt) REVERT: B 169 GLU cc_start: 0.8754 (mt-10) cc_final: 0.7798 (mt-10) REVERT: F 84 ASP cc_start: 0.7652 (p0) cc_final: 0.7381 (p0) REVERT: F 304 ILE cc_start: 0.8227 (mt) cc_final: 0.7926 (mp) REVERT: F 365 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.7636 (ppp) outliers start: 47 outliers final: 17 residues processed: 275 average time/residue: 1.5009 time to fit residues: 472.9110 Evaluate side-chains 254 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 232 time to evaluate : 2.565 ------------------------------------------------------------------------------- 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 465 GLU 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 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 B residue 166 LEU 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 Chi-restraints excluded: chain F residue 392 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: 0.0770 chunk 50 optimal weight: 0.0170 chunk 149 optimal weight: 6.9990 chunk 186 optimal weight: 2.9990 chunk 139 optimal weight: 0.3980 chunk 113 optimal weight: 0.6980 chunk 155 optimal weight: 0.5980 chunk 23 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 170 optimal weight: 8.9990 overall best weight: 0.3576 ------------------------------------------------------------------------------- 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 613 GLN A 752 GLN A1324 ASN A1653 HIS 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** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.100351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.075133 restraints weight = 35454.290| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.39 r_work: 0.2760 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 22384 Z= 0.092 Angle : 0.514 8.403 30390 Z= 0.264 Chirality : 0.045 0.347 3302 Planarity : 0.004 0.062 4025 Dihedral : 6.058 77.591 3144 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.79 % Allowed : 11.41 % Favored : 86.80 % 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: -0.40 (0.16), residues: 2743 helix: -0.73 (0.30), residues: 298 sheet: 0.26 (0.16), residues: 1060 loop : -0.49 (0.17), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A2353 HIS 0.002 0.001 HIS B 90 PHE 0.015 0.001 PHE A1242 TYR 0.012 0.001 TYR A1394 ARG 0.009 0.000 ARG A2189 Details of bonding type rmsd hydrogen bonds : bond 0.02463 ( 722) hydrogen bonds : angle 4.95686 ( 1911) covalent geometry : bond 0.00202 (22384) covalent geometry : angle 0.51423 (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 304 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 261 time to evaluate : 2.602 Fit side-chains revert: symmetry clash REVERT: D 576 PHE cc_start: 0.8580 (t80) cc_final: 0.8300 (t80) REVERT: D 578 LYS cc_start: 0.8826 (mmtt) cc_final: 0.8317 (mmmt) REVERT: A 260 GLU cc_start: 0.9130 (mt-10) cc_final: 0.8847 (mm-30) REVERT: A 264 GLN cc_start: 0.8631 (pt0) cc_final: 0.8413 (pt0) REVERT: A 560 GLN cc_start: 0.8756 (tt0) cc_final: 0.8455 (tm-30) REVERT: A 573 LYS cc_start: 0.8841 (mttm) cc_final: 0.8516 (mtpp) REVERT: A 713 GLU cc_start: 0.8606 (tm-30) cc_final: 0.8331 (tm-30) REVERT: A 722 GLN cc_start: 0.8989 (mp10) cc_final: 0.8654 (mp10) REVERT: A 723 LEU cc_start: 0.8988 (mt) cc_final: 0.8357 (tp) REVERT: A 737 ASN cc_start: 0.8492 (t0) cc_final: 0.8267 (t0) REVERT: A 750 PHE cc_start: 0.7411 (m-80) cc_final: 0.6895 (m-10) REVERT: A 786 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8331 (pp30) REVERT: A 809 GLU cc_start: 0.8547 (tt0) cc_final: 0.7918 (tm-30) REVERT: A 870 MET cc_start: 0.8972 (mmp) cc_final: 0.8693 (mmp) REVERT: A 1130 GLU cc_start: 0.8588 (mp0) cc_final: 0.8245 (mp0) REVERT: A 1263 GLU cc_start: 0.9032 (mm-30) cc_final: 0.8690 (mt-10) REVERT: A 1841 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7436 (ttmm) REVERT: A 1949 GLN cc_start: 0.7550 (tt0) cc_final: 0.7287 (tp40) REVERT: A 2016 LYS cc_start: 0.8719 (tppp) cc_final: 0.8478 (tppp) REVERT: A 2302 ASP cc_start: 0.7761 (m-30) cc_final: 0.7061 (p0) REVERT: A 2333 GLU cc_start: 0.8718 (tt0) cc_final: 0.8429 (mp0) REVERT: B 30 GLU cc_start: 0.7845 (mp0) cc_final: 0.7594 (mp0) REVERT: B 59 LYS cc_start: 0.8674 (pttm) cc_final: 0.8250 (pptt) REVERT: B 104 TYR cc_start: 0.9228 (p90) cc_final: 0.8799 (p90) REVERT: B 116 GLU cc_start: 0.8838 (pm20) cc_final: 0.8565 (mp0) REVERT: B 143 GLN cc_start: 0.9002 (tt0) cc_final: 0.8706 (tt0) REVERT: B 169 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8134 (mt-10) REVERT: F 304 ILE cc_start: 0.8210 (mt) cc_final: 0.7917 (mp) outliers start: 43 outliers final: 16 residues processed: 287 average time/residue: 1.3922 time to fit residues: 457.1604 Evaluate side-chains 261 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 243 time to evaluate : 2.514 ------------------------------------------------------------------------------- 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 607 THR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 277 GLN 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 1290 VAL Chi-restraints excluded: chain A residue 1428 ASP Chi-restraints excluded: chain A residue 1609 ASP Chi-restraints excluded: chain A residue 1841 LYS Chi-restraints excluded: chain A residue 2357 LEU Chi-restraints excluded: chain B residue 35 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 219 optimal weight: 6.9990 chunk 183 optimal weight: 0.6980 chunk 195 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 221 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 134 optimal weight: 8.9990 chunk 116 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 532 GLN 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 72 GLN F 209 GLN F 291 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.097527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.072081 restraints weight = 35758.957| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 2.38 r_work: 0.2701 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2565 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22384 Z= 0.188 Angle : 0.557 8.673 30390 Z= 0.286 Chirality : 0.047 0.351 3302 Planarity : 0.004 0.079 4025 Dihedral : 6.069 74.113 3144 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.75 % Allowed : 12.41 % Favored : 85.84 % 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: -0.42 (0.16), residues: 2743 helix: -0.70 (0.31), residues: 294 sheet: 0.22 (0.16), residues: 1062 loop : -0.49 (0.17), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1996 HIS 0.003 0.001 HIS A 291 PHE 0.024 0.001 PHE A 750 TYR 0.014 0.001 TYR A1104 ARG 0.006 0.000 ARG A 164 Details of bonding type rmsd hydrogen bonds : bond 0.02927 ( 722) hydrogen bonds : angle 5.06192 ( 1911) covalent geometry : bond 0.00432 (22384) covalent geometry : angle 0.55658 (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 288 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 246 time to evaluate : 2.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 576 PHE cc_start: 0.8718 (t80) cc_final: 0.8316 (t80) REVERT: A 560 GLN cc_start: 0.8755 (tt0) cc_final: 0.8488 (tm-30) REVERT: A 573 LYS cc_start: 0.8942 (mttm) cc_final: 0.8583 (mtpp) REVERT: A 713 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8330 (tm-30) REVERT: A 722 GLN cc_start: 0.9015 (mp10) cc_final: 0.8671 (mp10) REVERT: A 723 LEU cc_start: 0.8955 (mt) cc_final: 0.8204 (tp) REVERT: A 786 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8350 (pp30) REVERT: A 809 GLU cc_start: 0.8583 (tt0) cc_final: 0.7926 (tm-30) REVERT: A 870 MET cc_start: 0.9003 (mmp) cc_final: 0.8642 (mmp) REVERT: A 1263 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8695 (mt-10) REVERT: A 1580 TRP cc_start: 0.8190 (OUTLIER) cc_final: 0.6940 (p-90) REVERT: A 1949 GLN cc_start: 0.7510 (tt0) cc_final: 0.7247 (tp40) REVERT: A 2016 LYS cc_start: 0.8731 (tppp) cc_final: 0.8481 (tppp) REVERT: B 30 GLU cc_start: 0.7883 (mp0) cc_final: 0.7632 (mp0) REVERT: B 59 LYS cc_start: 0.8664 (pttm) cc_final: 0.8240 (pptt) REVERT: B 104 TYR cc_start: 0.9307 (p90) cc_final: 0.8856 (p90) REVERT: B 116 GLU cc_start: 0.8892 (pm20) cc_final: 0.8565 (mp0) REVERT: B 143 GLN cc_start: 0.9007 (tt0) cc_final: 0.8751 (tt0) REVERT: B 166 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9082 (mt) REVERT: B 169 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8078 (mt-10) REVERT: F 84 ASP cc_start: 0.7590 (p0) cc_final: 0.7336 (p0) REVERT: F 304 ILE cc_start: 0.8233 (mt) cc_final: 0.7953 (mp) REVERT: F 365 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.7514 (ppp) outliers start: 42 outliers final: 20 residues processed: 269 average time/residue: 1.4295 time to fit residues: 441.1472 Evaluate side-chains 263 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 239 time to evaluate : 2.617 ------------------------------------------------------------------------------- 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 235 ARG 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 1428 ASP Chi-restraints excluded: chain A residue 1580 TRP Chi-restraints excluded: chain A residue 1609 ASP Chi-restraints excluded: chain A residue 1740 ASN Chi-restraints excluded: chain A residue 2267 SER 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 106 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 166 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 31 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 213 optimal weight: 9.9990 chunk 191 optimal weight: 4.9990 chunk 225 optimal weight: 4.9990 chunk 234 optimal weight: 3.9990 chunk 185 optimal weight: 4.9990 chunk 238 optimal weight: 0.0010 chunk 150 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 overall best weight: 2.3592 ------------------------------------------------------------------------------- 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 532 GLN 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 209 GLN F 291 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.096845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.071420 restraints weight = 35796.202| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 2.38 r_work: 0.2685 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2550 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 22384 Z= 0.217 Angle : 0.569 8.829 30390 Z= 0.295 Chirality : 0.047 0.341 3302 Planarity : 0.004 0.075 4025 Dihedral : 6.115 73.294 3144 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.71 % Allowed : 12.87 % 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: -0.74 (0.30), residues: 296 sheet: 0.18 (0.16), residues: 1062 loop : -0.54 (0.17), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1996 HIS 0.004 0.001 HIS A1672 PHE 0.028 0.001 PHE A 750 TYR 0.015 0.001 TYR A1104 ARG 0.007 0.001 ARG A1741 Details of bonding type rmsd hydrogen bonds : bond 0.03025 ( 722) hydrogen bonds : angle 5.13552 ( 1911) covalent geometry : bond 0.00495 (22384) covalent geometry : angle 0.56907 (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 277 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 236 time to evaluate : 3.133 Fit side-chains revert: symmetry clash REVERT: A 560 GLN cc_start: 0.8768 (tt0) cc_final: 0.8502 (tm-30) REVERT: A 713 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8365 (tm-30) REVERT: A 786 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8366 (pp30) REVERT: A 809 GLU cc_start: 0.8592 (tt0) cc_final: 0.7931 (tm-30) REVERT: A 870 MET cc_start: 0.9018 (mmp) cc_final: 0.8653 (mmp) REVERT: A 1197 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8708 (mt-10) REVERT: A 1263 GLU cc_start: 0.9044 (mm-30) cc_final: 0.8690 (mt-10) REVERT: A 1580 TRP cc_start: 0.8259 (OUTLIER) cc_final: 0.7047 (p-90) REVERT: A 1949 GLN cc_start: 0.7527 (tt0) cc_final: 0.7256 (tp40) REVERT: A 1970 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8886 (mm) REVERT: A 2016 LYS cc_start: 0.8718 (tppp) cc_final: 0.8480 (tppp) REVERT: A 2199 ARG cc_start: 0.7563 (ttp-110) cc_final: 0.6909 (ttp80) REVERT: A 2248 GLN cc_start: 0.8872 (tt0) cc_final: 0.8439 (tt0) REVERT: B 30 GLU cc_start: 0.7900 (mp0) cc_final: 0.7637 (mp0) REVERT: B 48 ARG cc_start: 0.9137 (ttt-90) cc_final: 0.8837 (ttt-90) REVERT: B 104 TYR cc_start: 0.9304 (p90) cc_final: 0.8835 (p90) REVERT: B 116 GLU cc_start: 0.8895 (pm20) cc_final: 0.8561 (mp0) REVERT: B 143 GLN cc_start: 0.9017 (tt0) cc_final: 0.8716 (tt0) REVERT: B 166 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9079 (mt) REVERT: F 84 ASP cc_start: 0.7652 (p0) cc_final: 0.7394 (p0) REVERT: F 141 ASP cc_start: 0.8789 (p0) cc_final: 0.8564 (p0) REVERT: F 304 ILE cc_start: 0.8235 (mt) cc_final: 0.7955 (mp) REVERT: F 365 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.7497 (ppp) outliers start: 41 outliers final: 21 residues processed: 259 average time/residue: 1.7863 time to fit residues: 533.0935 Evaluate side-chains 257 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 230 time to evaluate : 4.036 ------------------------------------------------------------------------------- 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 607 THR Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 277 GLN 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 1609 ASP Chi-restraints excluded: chain A residue 1970 LEU 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 B residue 146 VAL Chi-restraints excluded: chain B residue 166 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 36 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 chunk 267 optimal weight: 9.9990 chunk 258 optimal weight: 5.9990 chunk 69 optimal weight: 0.9990 chunk 222 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 195 optimal weight: 0.0030 chunk 99 optimal weight: 0.9980 chunk 265 optimal weight: 0.6980 chunk 116 optimal weight: 0.6980 overall best weight: 0.6390 ------------------------------------------------------------------------------- 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 GLN F 291 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.099378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.074166 restraints weight = 35631.388| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.38 r_work: 0.2740 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2606 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 22384 Z= 0.103 Angle : 0.525 9.042 30390 Z= 0.271 Chirality : 0.045 0.301 3302 Planarity : 0.004 0.068 4025 Dihedral : 5.822 74.262 3144 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % 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: -0.41 (0.16), residues: 2743 helix: -0.67 (0.31), residues: 293 sheet: 0.24 (0.16), residues: 1060 loop : -0.51 (0.17), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A2353 HIS 0.002 0.001 HIS A1672 PHE 0.025 0.001 PHE A 750 TYR 0.011 0.001 TYR A1394 ARG 0.007 0.000 ARG A 164 Details of bonding type rmsd hydrogen bonds : bond 0.02549 ( 722) hydrogen bonds : angle 4.97498 ( 1911) covalent geometry : bond 0.00230 (22384) covalent geometry : angle 0.52509 (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 287 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 252 time to evaluate : 4.919 Fit side-chains revert: symmetry clash REVERT: D 578 LYS cc_start: 0.8877 (tptp) cc_final: 0.8438 (mmmt) REVERT: A 560 GLN cc_start: 0.8761 (tt0) cc_final: 0.8462 (tm-30) REVERT: A 573 LYS cc_start: 0.8880 (mttm) cc_final: 0.8540 (mtpp) REVERT: A 713 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8265 (tm-30) REVERT: A 786 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8375 (pp30) REVERT: A 809 GLU cc_start: 0.8565 (tt0) cc_final: 0.7926 (tm-30) REVERT: A 870 MET cc_start: 0.8947 (mmp) cc_final: 0.8605 (mmp) REVERT: A 1263 GLU cc_start: 0.9024 (mm-30) cc_final: 0.8674 (mt-10) REVERT: A 1580 TRP cc_start: 0.8181 (OUTLIER) cc_final: 0.6927 (p-90) REVERT: A 1949 GLN cc_start: 0.7556 (tt0) cc_final: 0.7284 (tp40) REVERT: A 1970 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8879 (mm) REVERT: A 2190 TYR cc_start: 0.6923 (m-80) cc_final: 0.6555 (m-80) REVERT: A 2248 GLN cc_start: 0.8867 (tt0) cc_final: 0.8429 (tt0) REVERT: A 2333 GLU cc_start: 0.8720 (tt0) cc_final: 0.8477 (mp0) REVERT: B 30 GLU cc_start: 0.7894 (mp0) cc_final: 0.7627 (mp0) REVERT: B 59 LYS cc_start: 0.8674 (pttm) cc_final: 0.8119 (pptt) REVERT: B 104 TYR cc_start: 0.9263 (p90) cc_final: 0.8947 (p90) REVERT: B 116 GLU cc_start: 0.8873 (pm20) cc_final: 0.8546 (mp0) REVERT: B 143 GLN cc_start: 0.9020 (tt0) cc_final: 0.8787 (tt0) REVERT: B 169 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8118 (mt-10) REVERT: F 141 ASP cc_start: 0.8680 (p0) cc_final: 0.8466 (p0) REVERT: F 304 ILE cc_start: 0.8245 (mt) cc_final: 0.7964 (mp) outliers start: 35 outliers final: 14 residues processed: 268 average time/residue: 1.6520 time to fit residues: 514.4463 Evaluate side-chains 259 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 242 time to evaluate : 2.536 ------------------------------------------------------------------------------- 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 235 ARG 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 1970 LEU Chi-restraints excluded: chain A residue 2290 MET 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 F residue 250 SER Chi-restraints excluded: chain F residue 323 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 157 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 247 optimal weight: 3.9990 chunk 267 optimal weight: 9.9990 chunk 127 optimal weight: 7.9990 chunk 113 optimal weight: 0.9990 chunk 254 optimal weight: 8.9990 chunk 132 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.096218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.070853 restraints weight = 35879.770| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 2.37 r_work: 0.2677 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2542 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 22384 Z= 0.249 Angle : 0.595 9.211 30390 Z= 0.308 Chirality : 0.048 0.317 3302 Planarity : 0.004 0.070 4025 Dihedral : 6.065 71.807 3144 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.42 % Allowed : 13.33 % Favored : 85.26 % 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: -0.52 (0.16), residues: 2743 helix: -0.82 (0.30), residues: 302 sheet: 0.15 (0.16), residues: 1062 loop : -0.53 (0.17), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1996 HIS 0.004 0.001 HIS A1672 PHE 0.031 0.002 PHE A 750 TYR 0.015 0.001 TYR A1104 ARG 0.008 0.001 ARG A2398 Details of bonding type rmsd hydrogen bonds : bond 0.03143 ( 722) hydrogen bonds : angle 5.16862 ( 1911) covalent geometry : bond 0.00569 (22384) covalent geometry : angle 0.59524 (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 272 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 238 time to evaluate : 2.612 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 578 LYS cc_start: 0.8872 (tptp) cc_final: 0.8435 (mmmt) REVERT: A 560 GLN cc_start: 0.8770 (tt0) cc_final: 0.8504 (tm-30) REVERT: A 713 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8288 (tm-30) REVERT: A 723 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8110 (pt) REVERT: A 786 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8342 (pp30) REVERT: A 809 GLU cc_start: 0.8566 (tt0) cc_final: 0.7922 (tm-30) REVERT: A 870 MET cc_start: 0.9030 (mmp) cc_final: 0.8653 (mmp) REVERT: A 1263 GLU cc_start: 0.9032 (mm-30) cc_final: 0.8693 (mt-10) REVERT: A 1580 TRP cc_start: 0.8363 (OUTLIER) cc_final: 0.7124 (p-90) REVERT: A 1949 GLN cc_start: 0.7525 (tt0) cc_final: 0.7239 (tp40) REVERT: A 2016 LYS cc_start: 0.8636 (tppp) cc_final: 0.8435 (tptm) REVERT: A 2190 TYR cc_start: 0.6908 (m-80) cc_final: 0.6477 (m-80) REVERT: A 2199 ARG cc_start: 0.7599 (ttp-110) cc_final: 0.6958 (ttp80) REVERT: B 30 GLU cc_start: 0.7909 (mp0) cc_final: 0.7645 (mp0) REVERT: B 59 LYS cc_start: 0.8635 (pttm) cc_final: 0.8071 (pptt) REVERT: B 104 TYR cc_start: 0.9313 (p90) cc_final: 0.8921 (p90) REVERT: B 143 GLN cc_start: 0.9017 (tt0) cc_final: 0.8754 (tt0) REVERT: B 166 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9096 (mt) REVERT: B 169 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8082 (mt-10) REVERT: F 141 ASP cc_start: 0.8772 (p0) cc_final: 0.8551 (p0) REVERT: F 304 ILE cc_start: 0.8257 (mt) cc_final: 0.7961 (mp) REVERT: F 365 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.7421 (ppp) outliers start: 34 outliers final: 18 residues processed: 261 average time/residue: 1.4605 time to fit residues: 434.5384 Evaluate side-chains 257 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 234 time to evaluate : 2.398 ------------------------------------------------------------------------------- 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 465 GLU Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 786 GLN 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 36 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 166 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 265 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 211 optimal weight: 0.9980 chunk 197 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 chunk 266 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 163 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 D 579 GLN A 264 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.097383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.072034 restraints weight = 35809.571| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 2.39 r_work: 0.2701 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2566 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22384 Z= 0.162 Angle : 0.565 9.536 30390 Z= 0.292 Chirality : 0.046 0.300 3302 Planarity : 0.004 0.068 4025 Dihedral : 5.993 72.188 3144 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.17 % Allowed : 13.79 % Favored : 85.05 % 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: -0.51 (0.16), residues: 2743 helix: -0.78 (0.30), residues: 300 sheet: 0.14 (0.16), residues: 1062 loop : -0.52 (0.17), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1996 HIS 0.004 0.001 HIS A1672 PHE 0.028 0.001 PHE A 750 TYR 0.013 0.001 TYR A1104 ARG 0.009 0.000 ARG A2398 Details of bonding type rmsd hydrogen bonds : bond 0.02869 ( 722) hydrogen bonds : angle 5.12266 ( 1911) covalent geometry : bond 0.00369 (22384) covalent geometry : angle 0.56532 (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 273 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 245 time to evaluate : 2.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 578 LYS cc_start: 0.8853 (tptp) cc_final: 0.8425 (mmmt) REVERT: A 560 GLN cc_start: 0.8789 (tt0) cc_final: 0.8508 (tm-30) REVERT: A 573 LYS cc_start: 0.8961 (mttm) cc_final: 0.8627 (mtpp) REVERT: A 713 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8305 (tm-30) REVERT: A 723 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8203 (pt) REVERT: A 786 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8343 (pp30) REVERT: A 809 GLU cc_start: 0.8577 (tt0) cc_final: 0.7919 (tm-30) REVERT: A 870 MET cc_start: 0.8995 (mmp) cc_final: 0.8635 (mmp) REVERT: A 1197 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8691 (mt-10) REVERT: A 1263 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8682 (mt-10) REVERT: A 1580 TRP cc_start: 0.8318 (OUTLIER) cc_final: 0.7064 (p-90) REVERT: A 1949 GLN cc_start: 0.7512 (tt0) cc_final: 0.7224 (tp40) REVERT: A 2016 LYS cc_start: 0.8639 (tppp) cc_final: 0.8438 (tptm) REVERT: A 2190 TYR cc_start: 0.6937 (m-80) cc_final: 0.6591 (m-80) REVERT: A 2199 ARG cc_start: 0.7558 (ttp-110) cc_final: 0.6906 (ttp80) REVERT: B 30 GLU cc_start: 0.7902 (mp0) cc_final: 0.7631 (mp0) REVERT: B 59 LYS cc_start: 0.8617 (pttm) cc_final: 0.8059 (pptt) REVERT: B 104 TYR cc_start: 0.9291 (p90) cc_final: 0.8909 (p90) REVERT: B 143 GLN cc_start: 0.9001 (tt0) cc_final: 0.8758 (tt0) REVERT: B 166 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9069 (mt) REVERT: B 169 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8092 (mt-10) REVERT: F 141 ASP cc_start: 0.8749 (p0) cc_final: 0.8537 (p0) REVERT: F 304 ILE cc_start: 0.8252 (mt) cc_final: 0.7970 (mp) REVERT: F 365 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.7388 (ppp) outliers start: 28 outliers final: 17 residues processed: 262 average time/residue: 1.3939 time to fit residues: 418.2002 Evaluate side-chains 266 residues out of total 2401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 243 time to evaluate : 2.397 ------------------------------------------------------------------------------- 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 235 ARG Chi-restraints excluded: chain A residue 554 ASN Chi-restraints excluded: chain A residue 697 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 786 GLN 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 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 36 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 102 LYS Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 166 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=1.00 ------------------------------------------------------------------------------- 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: 5.9990 chunk 43 optimal weight: 5.9990 chunk 33 optimal weight: 0.1980 chunk 197 optimal weight: 7.9990 chunk 16 optimal weight: 0.6980 chunk 262 optimal weight: 0.5980 chunk 263 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 D 579 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.097584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.072255 restraints weight = 35629.333| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 2.37 r_work: 0.2706 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2569 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22384 Z= 0.158 Angle : 0.563 9.585 30390 Z= 0.290 Chirality : 0.046 0.299 3302 Planarity : 0.004 0.067 4025 Dihedral : 5.955 72.190 3144 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.17 % Allowed : 13.99 % Favored : 84.84 % 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: -0.50 (0.16), residues: 2743 helix: -0.76 (0.30), residues: 300 sheet: 0.14 (0.16), residues: 1062 loop : -0.52 (0.17), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1996 HIS 0.004 0.001 HIS A1653 PHE 0.032 0.001 PHE A 750 TYR 0.015 0.001 TYR D 563 ARG 0.010 0.000 ARG A2398 Details of bonding type rmsd hydrogen bonds : bond 0.02848 ( 722) hydrogen bonds : angle 5.09468 ( 1911) covalent geometry : bond 0.00360 (22384) covalent geometry : angle 0.56257 (30390) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15771.44 seconds wall clock time: 274 minutes 49.73 seconds (16489.73 seconds total)