Starting phenix.real_space_refine on Fri Mar 6 05:09:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lht_23350/03_2026/7lht_23350.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lht_23350/03_2026/7lht_23350.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7lht_23350/03_2026/7lht_23350.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lht_23350/03_2026/7lht_23350.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7lht_23350/03_2026/7lht_23350.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lht_23350/03_2026/7lht_23350.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.077 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 178 5.16 5 C 18037 2.51 5 N 4873 2.21 5 O 5147 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 151 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28245 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 14057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1795, 14057 Classifications: {'peptide': 1795} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PCIS': 1, 'PTRANS': 75, 'TRANS': 1718} Chain breaks: 8 Unresolved non-hydrogen bonds: 209 Unresolved non-hydrogen angles: 259 Unresolved non-hydrogen dihedrals: 163 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 17, 'GLN:plan1': 6, 'GLU:plan': 18, 'HIS:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 165 Chain: "B" Number of atoms: 14070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1795, 14070 Classifications: {'peptide': 1795} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PCIS': 1, 'PTRANS': 75, 'TRANS': 1718} Chain breaks: 8 Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 241 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 17, 'GLN:plan1': 7, 'GLU:plan': 15, 'ARG:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 152 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.29, per 1000 atoms: 0.22 Number of scatterers: 28245 At special positions: 0 Unit cell: (175.938, 124.726, 147.028, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 178 16.00 P 10 15.00 O 5147 8.00 N 4873 7.00 C 18037 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.14 Conformation dependent library (CDL) restraints added in 1.3 seconds 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6836 Finding SS restraints... Secondary structure from input PDB file: 131 helices and 40 sheets defined 33.4% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 559 through 571 removed outlier: 3.779A pdb=" N SER A 569 " --> pdb=" O LYS A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 596 removed outlier: 4.189A pdb=" N LEU A 593 " --> pdb=" O VAL A 589 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN A 594 " --> pdb=" O LEU A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 605 Processing helix chain 'A' and resid 606 through 611 removed outlier: 3.819A pdb=" N ILE A 610 " --> pdb=" O GLY A 606 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY A 611 " --> pdb=" O LEU A 607 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 606 through 611' Processing helix chain 'A' and resid 625 through 638 removed outlier: 3.811A pdb=" N SER A 633 " --> pdb=" O LYS A 629 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER A 634 " --> pdb=" O ILE A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 657 Processing helix chain 'A' and resid 659 through 661 No H-bonds generated for 'chain 'A' and resid 659 through 661' Processing helix chain 'A' and resid 662 through 667 Processing helix chain 'A' and resid 670 through 679 removed outlier: 4.256A pdb=" N HIS A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 703 removed outlier: 3.782A pdb=" N LYS A 701 " --> pdb=" O LYS A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 715 removed outlier: 3.692A pdb=" N ASN A 710 " --> pdb=" O ASP A 706 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU A 714 " --> pdb=" O ASN A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 731 removed outlier: 3.691A pdb=" N LEU A 729 " --> pdb=" O VAL A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 751 removed outlier: 3.524A pdb=" N GLU A 750 " --> pdb=" O CYS A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 763 removed outlier: 3.873A pdb=" N LEU A 760 " --> pdb=" O LYS A 756 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 761 " --> pdb=" O LEU A 757 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN A 763 " --> pdb=" O GLU A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 781 removed outlier: 3.710A pdb=" N LYS A 773 " --> pdb=" O GLN A 769 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR A 776 " --> pdb=" O ARG A 772 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LYS A 781 " --> pdb=" O ILE A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 795 removed outlier: 3.646A pdb=" N ARG A 792 " --> pdb=" O SER A 788 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG A 793 " --> pdb=" O LEU A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 819 removed outlier: 3.720A pdb=" N LEU A 818 " --> pdb=" O GLU A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 822 No H-bonds generated for 'chain 'A' and resid 820 through 822' Processing helix chain 'A' and resid 833 through 853 removed outlier: 3.695A pdb=" N GLU A 853 " --> pdb=" O LYS A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1001 Processing helix chain 'A' and resid 1009 through 1013 Processing helix chain 'A' and resid 1029 through 1033 Processing helix chain 'A' and resid 1053 through 1057 Processing helix chain 'A' and resid 1101 through 1106 Processing helix chain 'A' and resid 1189 through 1194 removed outlier: 3.728A pdb=" N ASN A1194 " --> pdb=" O GLU A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1213 through 1217 removed outlier: 4.066A pdb=" N TRP A1217 " --> pdb=" O PRO A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1245 Processing helix chain 'A' and resid 1261 through 1267 removed outlier: 3.548A pdb=" N GLY A1265 " --> pdb=" O PRO A1262 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A1267 " --> pdb=" O ILE A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1285 through 1291 removed outlier: 3.653A pdb=" N GLY A1289 " --> pdb=" O ASN A1286 " (cutoff:3.500A) Processing helix chain 'A' and resid 1316 through 1328 removed outlier: 3.852A pdb=" N LEU A1326 " --> pdb=" O LEU A1322 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS A1327 " --> pdb=" O GLN A1323 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS A1328 " --> pdb=" O GLN A1324 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1355 Processing helix chain 'A' and resid 1404 through 1408 Processing helix chain 'A' and resid 1420 through 1424 Processing helix chain 'A' and resid 1428 through 1430 No H-bonds generated for 'chain 'A' and resid 1428 through 1430' Processing helix chain 'A' and resid 1431 through 1442 Processing helix chain 'A' and resid 1463 through 1465 No H-bonds generated for 'chain 'A' and resid 1463 through 1465' Processing helix chain 'A' and resid 1466 through 1473 Processing helix chain 'A' and resid 1494 through 1509 removed outlier: 3.921A pdb=" N LEU A1500 " --> pdb=" O ALA A1496 " (cutoff:3.500A) Processing helix chain 'A' and resid 1517 through 1520 Processing helix chain 'A' and resid 1525 through 1539 removed outlier: 4.042A pdb=" N LYS A1539 " --> pdb=" O LEU A1535 " (cutoff:3.500A) Processing helix chain 'A' and resid 1550 through 1560 removed outlier: 3.545A pdb=" N VAL A1557 " --> pdb=" O LEU A1553 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG A1558 " --> pdb=" O LEU A1554 " (cutoff:3.500A) Processing helix chain 'A' and resid 1568 through 1579 removed outlier: 3.920A pdb=" N HIS A1574 " --> pdb=" O PRO A1570 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER A1579 " --> pdb=" O PHE A1575 " (cutoff:3.500A) Processing helix chain 'A' and resid 1599 through 1607 removed outlier: 4.144A pdb=" N LEU A1603 " --> pdb=" O GLU A1599 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS A1605 " --> pdb=" O LYS A1601 " (cutoff:3.500A) Processing helix chain 'A' and resid 1644 through 1654 removed outlier: 3.783A pdb=" N PHE A1650 " --> pdb=" O MET A1646 " (cutoff:3.500A) Processing helix chain 'A' and resid 1704 through 1709 Processing helix chain 'A' and resid 1770 through 1792 removed outlier: 3.575A pdb=" N ILE A1775 " --> pdb=" O ARG A1771 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU A1776 " --> pdb=" O LYS A1772 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASP A1782 " --> pdb=" O GLY A1778 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS A1783 " --> pdb=" O GLN A1779 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET A1788 " --> pdb=" O ILE A1784 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU A1790 " --> pdb=" O SER A1786 " (cutoff:3.500A) Processing helix chain 'A' and resid 1829 through 1834 Processing helix chain 'A' and resid 1852 through 1856 Processing helix chain 'A' and resid 1865 through 1869 removed outlier: 3.640A pdb=" N MET A1869 " --> pdb=" O ARG A1866 " (cutoff:3.500A) Processing helix chain 'A' and resid 1913 through 1925 removed outlier: 3.834A pdb=" N VAL A1922 " --> pdb=" O ARG A1918 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL A1923 " --> pdb=" O GLN A1919 " (cutoff:3.500A) Processing helix chain 'A' and resid 1954 through 1962 removed outlier: 3.763A pdb=" N LEU A1958 " --> pdb=" O SER A1954 " (cutoff:3.500A) Processing helix chain 'A' and resid 1969 through 1986 removed outlier: 3.640A pdb=" N ARG A1973 " --> pdb=" O THR A1969 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA A1975 " --> pdb=" O GLN A1971 " (cutoff:3.500A) Processing helix chain 'A' and resid 2017 through 2026 removed outlier: 3.887A pdb=" N ALA A2021 " --> pdb=" O ASP A2017 " (cutoff:3.500A) Processing helix chain 'A' and resid 2040 through 2045 Processing helix chain 'A' and resid 2051 through 2068 removed outlier: 4.249A pdb=" N ASP A2055 " --> pdb=" O ASN A2051 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A2056 " --> pdb=" O GLN A2052 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR A2057 " --> pdb=" O GLN A2053 " (cutoff:3.500A) Processing helix chain 'A' and resid 2070 through 2077 removed outlier: 3.866A pdb=" N VAL A2074 " --> pdb=" O GLY A2070 " (cutoff:3.500A) Processing helix chain 'A' and resid 2079 through 2089 removed outlier: 3.540A pdb=" N GLU A2085 " --> pdb=" O ASN A2081 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A2086 " --> pdb=" O GLU A2082 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLU A2087 " --> pdb=" O PHE A2083 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN A2089 " --> pdb=" O GLU A2085 " (cutoff:3.500A) Processing helix chain 'A' and resid 2107 through 2115 Processing helix chain 'A' and resid 2118 through 2122 Processing helix chain 'A' and resid 2124 through 2131 Processing helix chain 'A' and resid 2278 through 2282 removed outlier: 4.142A pdb=" N LYS A2281 " --> pdb=" O LYS A2278 " (cutoff:3.500A) Processing helix chain 'A' and resid 2389 through 2397 removed outlier: 4.910A pdb=" N GLU A2395 " --> pdb=" O HIS A2391 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL A2396 " --> pdb=" O PHE A2392 " (cutoff:3.500A) Processing helix chain 'A' and resid 2402 through 2407 removed outlier: 3.551A pdb=" N LYS A2405 " --> pdb=" O LYS A2402 " (cutoff:3.500A) Processing helix chain 'A' and resid 2481 through 2485 Processing helix chain 'A' and resid 2499 through 2527 removed outlier: 3.745A pdb=" N GLN A2505 " --> pdb=" O PRO A2501 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU A2508 " --> pdb=" O VAL A2504 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU A2512 " --> pdb=" O GLU A2508 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG A2514 " --> pdb=" O HIS A2510 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG A2522 " --> pdb=" O ALA A2518 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR A2524 " --> pdb=" O LYS A2520 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER A2525 " --> pdb=" O MET A2521 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL A2526 " --> pdb=" O ARG A2522 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 571 removed outlier: 3.779A pdb=" N SER B 569 " --> pdb=" O LYS B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 596 removed outlier: 4.190A pdb=" N LEU B 593 " --> pdb=" O VAL B 589 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN B 594 " --> pdb=" O LEU B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 605 Processing helix chain 'B' and resid 606 through 611 removed outlier: 3.820A pdb=" N ILE B 610 " --> pdb=" O GLY B 606 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY B 611 " --> pdb=" O LEU B 607 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 606 through 611' Processing helix chain 'B' and resid 625 through 638 removed outlier: 3.812A pdb=" N SER B 633 " --> pdb=" O LYS B 629 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER B 634 " --> pdb=" O ILE B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 657 Processing helix chain 'B' and resid 659 through 661 No H-bonds generated for 'chain 'B' and resid 659 through 661' Processing helix chain 'B' and resid 662 through 667 Processing helix chain 'B' and resid 670 through 679 removed outlier: 4.256A pdb=" N HIS B 677 " --> pdb=" O LEU B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 703 removed outlier: 3.782A pdb=" N LYS B 701 " --> pdb=" O LYS B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 715 removed outlier: 3.692A pdb=" N ASN B 710 " --> pdb=" O ASP B 706 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU B 714 " --> pdb=" O ASN B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 731 removed outlier: 3.690A pdb=" N LEU B 729 " --> pdb=" O VAL B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 751 removed outlier: 3.524A pdb=" N GLU B 750 " --> pdb=" O CYS B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 763 removed outlier: 3.873A pdb=" N LEU B 760 " --> pdb=" O LYS B 756 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU B 761 " --> pdb=" O LEU B 757 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN B 763 " --> pdb=" O GLU B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 767 through 781 removed outlier: 3.710A pdb=" N LYS B 773 " --> pdb=" O GLN B 769 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR B 776 " --> pdb=" O ARG B 772 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LYS B 781 " --> pdb=" O ILE B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 795 removed outlier: 3.646A pdb=" N ARG B 792 " --> pdb=" O SER B 788 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG B 793 " --> pdb=" O LEU B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 819 removed outlier: 3.720A pdb=" N LEU B 818 " --> pdb=" O GLU B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 820 through 822 No H-bonds generated for 'chain 'B' and resid 820 through 822' Processing helix chain 'B' and resid 833 through 853 removed outlier: 3.695A pdb=" N GLU B 853 " --> pdb=" O LYS B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1001 Processing helix chain 'B' and resid 1009 through 1013 Processing helix chain 'B' and resid 1029 through 1033 Processing helix chain 'B' and resid 1053 through 1057 Processing helix chain 'B' and resid 1101 through 1106 Processing helix chain 'B' and resid 1189 through 1194 removed outlier: 3.728A pdb=" N ASN B1194 " --> pdb=" O GLU B1190 " (cutoff:3.500A) Processing helix chain 'B' and resid 1213 through 1217 removed outlier: 4.066A pdb=" N TRP B1217 " --> pdb=" O PRO B1214 " (cutoff:3.500A) Processing helix chain 'B' and resid 1241 through 1245 Processing helix chain 'B' and resid 1261 through 1267 removed outlier: 3.548A pdb=" N GLY B1265 " --> pdb=" O PRO B1262 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU B1267 " --> pdb=" O ILE B1264 " (cutoff:3.500A) Processing helix chain 'B' and resid 1285 through 1291 removed outlier: 3.653A pdb=" N GLY B1289 " --> pdb=" O ASN B1286 " (cutoff:3.500A) Processing helix chain 'B' and resid 1316 through 1328 removed outlier: 3.852A pdb=" N LEU B1326 " --> pdb=" O LEU B1322 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS B1327 " --> pdb=" O GLN B1323 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS B1328 " --> pdb=" O GLN B1324 " (cutoff:3.500A) Processing helix chain 'B' and resid 1350 through 1355 Processing helix chain 'B' and resid 1404 through 1408 Processing helix chain 'B' and resid 1420 through 1424 Processing helix chain 'B' and resid 1428 through 1430 No H-bonds generated for 'chain 'B' and resid 1428 through 1430' Processing helix chain 'B' and resid 1431 through 1442 Processing helix chain 'B' and resid 1463 through 1465 No H-bonds generated for 'chain 'B' and resid 1463 through 1465' Processing helix chain 'B' and resid 1466 through 1473 Processing helix chain 'B' and resid 1494 through 1509 removed outlier: 3.921A pdb=" N LEU B1500 " --> pdb=" O ALA B1496 " (cutoff:3.500A) Processing helix chain 'B' and resid 1517 through 1520 Processing helix chain 'B' and resid 1525 through 1539 removed outlier: 4.042A pdb=" N LYS B1539 " --> pdb=" O LEU B1535 " (cutoff:3.500A) Processing helix chain 'B' and resid 1550 through 1560 removed outlier: 3.545A pdb=" N VAL B1557 " --> pdb=" O LEU B1553 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG B1558 " --> pdb=" O LEU B1554 " (cutoff:3.500A) Processing helix chain 'B' and resid 1568 through 1579 removed outlier: 3.920A pdb=" N HIS B1574 " --> pdb=" O PRO B1570 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER B1579 " --> pdb=" O PHE B1575 " (cutoff:3.500A) Processing helix chain 'B' and resid 1599 through 1607 removed outlier: 4.145A pdb=" N LEU B1603 " --> pdb=" O GLU B1599 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS B1605 " --> pdb=" O LYS B1601 " (cutoff:3.500A) Processing helix chain 'B' and resid 1644 through 1654 removed outlier: 3.784A pdb=" N PHE B1650 " --> pdb=" O MET B1646 " (cutoff:3.500A) Processing helix chain 'B' and resid 1704 through 1709 Processing helix chain 'B' and resid 1770 through 1792 removed outlier: 3.575A pdb=" N ILE B1775 " --> pdb=" O ARG B1771 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU B1776 " --> pdb=" O LYS B1772 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASP B1782 " --> pdb=" O GLY B1778 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N HIS B1783 " --> pdb=" O GLN B1779 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET B1788 " --> pdb=" O ILE B1784 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU B1790 " --> pdb=" O SER B1786 " (cutoff:3.500A) Processing helix chain 'B' and resid 1829 through 1834 Processing helix chain 'B' and resid 1852 through 1856 Processing helix chain 'B' and resid 1865 through 1869 removed outlier: 3.641A pdb=" N MET B1869 " --> pdb=" O ARG B1866 " (cutoff:3.500A) Processing helix chain 'B' and resid 1913 through 1925 removed outlier: 3.834A pdb=" N VAL B1922 " --> pdb=" O ARG B1918 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL B1923 " --> pdb=" O GLN B1919 " (cutoff:3.500A) Processing helix chain 'B' and resid 1954 through 1962 removed outlier: 3.763A pdb=" N LEU B1958 " --> pdb=" O SER B1954 " (cutoff:3.500A) Processing helix chain 'B' and resid 1969 through 1986 removed outlier: 3.640A pdb=" N ARG B1973 " --> pdb=" O THR B1969 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA B1975 " --> pdb=" O GLN B1971 " (cutoff:3.500A) Processing helix chain 'B' and resid 2017 through 2026 removed outlier: 3.887A pdb=" N ALA B2021 " --> pdb=" O ASP B2017 " (cutoff:3.500A) Processing helix chain 'B' and resid 2040 through 2045 Processing helix chain 'B' and resid 2051 through 2068 removed outlier: 4.249A pdb=" N ASP B2055 " --> pdb=" O ASN B2051 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL B2056 " --> pdb=" O GLN B2052 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR B2057 " --> pdb=" O GLN B2053 " (cutoff:3.500A) Processing helix chain 'B' and resid 2070 through 2077 removed outlier: 3.866A pdb=" N VAL B2074 " --> pdb=" O GLY B2070 " (cutoff:3.500A) Processing helix chain 'B' and resid 2079 through 2089 removed outlier: 3.541A pdb=" N GLU B2085 " --> pdb=" O ASN B2081 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU B2086 " --> pdb=" O GLU B2082 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLU B2087 " --> pdb=" O PHE B2083 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN B2089 " --> pdb=" O GLU B2085 " (cutoff:3.500A) Processing helix chain 'B' and resid 2094 through 2099 removed outlier: 3.659A pdb=" N TYR B2099 " --> pdb=" O PRO B2095 " (cutoff:3.500A) Processing helix chain 'B' and resid 2107 through 2115 Processing helix chain 'B' and resid 2118 through 2122 Processing helix chain 'B' and resid 2124 through 2131 Processing helix chain 'B' and resid 2278 through 2282 removed outlier: 4.141A pdb=" N LYS B2281 " --> pdb=" O LYS B2278 " (cutoff:3.500A) Processing helix chain 'B' and resid 2389 through 2397 removed outlier: 4.910A pdb=" N GLU B2395 " --> pdb=" O HIS B2391 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL B2396 " --> pdb=" O PHE B2392 " (cutoff:3.500A) Processing helix chain 'B' and resid 2402 through 2407 removed outlier: 3.552A pdb=" N LYS B2405 " --> pdb=" O LYS B2402 " (cutoff:3.500A) Processing helix chain 'B' and resid 2481 through 2485 Processing helix chain 'B' and resid 2499 through 2527 removed outlier: 3.746A pdb=" N GLN B2505 " --> pdb=" O PRO B2501 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU B2508 " --> pdb=" O VAL B2504 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU B2512 " --> pdb=" O GLU B2508 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG B2514 " --> pdb=" O HIS B2510 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG B2522 " --> pdb=" O ALA B2518 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR B2524 " --> pdb=" O LYS B2520 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER B2525 " --> pdb=" O MET B2521 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL B2526 " --> pdb=" O ARG B2522 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 802 through 804 removed outlier: 6.481A pdb=" N ILE A 803 " --> pdb=" O ASP A 988 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LEU A 987 " --> pdb=" O GLU A1017 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU A1016 " --> pdb=" O ASP A1041 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 1063 through 1064 removed outlier: 6.972A pdb=" N LEU A1063 " --> pdb=" O ASN A1089 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A1113 " --> pdb=" O PHE A1088 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1177 through 1179 removed outlier: 7.017A pdb=" N LEU A1178 " --> pdb=" O ASP A1202 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU A1201 " --> pdb=" O LEU A1226 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU A1250 " --> pdb=" O ASP A1274 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1329 through 1332 removed outlier: 4.286A pdb=" N GLN A1521 " --> pdb=" O TYR A1332 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1336 through 1339 removed outlier: 3.665A pdb=" N LEU A1388 " --> pdb=" O ILE A1378 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A1390 " --> pdb=" O TRP A1376 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP A1376 " --> pdb=" O LEU A1390 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1415 through 1418 removed outlier: 7.340A pdb=" N TYR A1415 " --> pdb=" O ILE A1448 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N VAL A1450 " --> pdb=" O TYR A1415 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ALA A1417 " --> pdb=" O VAL A1450 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N VAL A1447 " --> pdb=" O ARG A1483 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TYR A1485 " --> pdb=" O VAL A1447 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU A1449 " --> pdb=" O TYR A1485 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 1547 through 1549 Processing sheet with id=AA8, first strand: chain 'A' and resid 1680 through 1681 removed outlier: 3.590A pdb=" N ARG B1731 " --> pdb=" O GLU A1681 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1690 through 1692 removed outlier: 6.456A pdb=" N TYR A1747 " --> pdb=" O PRO A1768 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N CYS A1748 " --> pdb=" O ASN A1741 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ASN A1741 " --> pdb=" O CYS A1748 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1731 through 1732 removed outlier: 3.586A pdb=" N ARG A1731 " --> pdb=" O GLU B1681 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1811 through 1814 Processing sheet with id=AB3, first strand: chain 'A' and resid 1840 through 1841 Processing sheet with id=AB4, first strand: chain 'A' and resid 1896 through 1898 removed outlier: 3.554A pdb=" N GLY A1939 " --> pdb=" O MET A1944 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA A1937 " --> pdb=" O VAL A1946 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLU A1948 " --> pdb=" O LEU A1935 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N LEU A1935 " --> pdb=" O GLU A1948 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2144 through 2145 removed outlier: 3.501A pdb=" N LEU A2493 " --> pdb=" O ILE A2144 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS A2467 " --> pdb=" O LEU A2463 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N LEU A2463 " --> pdb=" O LYS A2467 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 2155 through 2157 Processing sheet with id=AB7, first strand: chain 'A' and resid 2178 through 2179 Processing sheet with id=AB8, first strand: chain 'A' and resid 2199 through 2207 removed outlier: 6.870A pdb=" N GLY A2218 " --> pdb=" O LEU A2200 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N LEU A2202 " --> pdb=" O VAL A2216 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL A2216 " --> pdb=" O LEU A2202 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N LEU A2204 " --> pdb=" O TRP A2214 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N TRP A2214 " --> pdb=" O LEU A2204 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N HIS A2206 " --> pdb=" O GLU A2212 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N GLU A2212 " --> pdb=" O HIS A2206 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL A2226 " --> pdb=" O HIS A2236 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS A2236 " --> pdb=" O VAL A2226 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 2264 through 2265 removed outlier: 3.574A pdb=" N ALA A2273 " --> pdb=" O VAL A2265 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A2272 " --> pdb=" O LEU A2291 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 2354 through 2359 removed outlier: 6.636A pdb=" N ALA A2366 " --> pdb=" O ILE A2355 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N VAL A2357 " --> pdb=" O TYR A2364 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TYR A2364 " --> pdb=" O VAL A2357 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N LYS A2367 " --> pdb=" O VAL A2372 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL A2372 " --> pdb=" O LYS A2367 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 2414 through 2419 removed outlier: 3.581A pdb=" N THR A2416 " --> pdb=" O GLY A2428 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE A2434 " --> pdb=" O VAL A2447 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL A2447 " --> pdb=" O ILE A2434 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LEU A2436 " --> pdb=" O ILE A2445 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 2477 through 2478 removed outlier: 3.677A pdb=" N GLU A2488 " --> pdb=" O LYS A2478 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 802 through 804 removed outlier: 6.482A pdb=" N ILE B 803 " --> pdb=" O ASP B 988 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU B 987 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU B1016 " --> pdb=" O ASP B1041 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 1063 through 1064 removed outlier: 6.972A pdb=" N LEU B1063 " --> pdb=" O ASN B1089 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE B1113 " --> pdb=" O PHE B1088 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1177 through 1179 removed outlier: 7.017A pdb=" N LEU B1178 " --> pdb=" O ASP B1202 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU B1201 " --> pdb=" O LEU B1226 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU B1250 " --> pdb=" O ASP B1274 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1329 through 1332 removed outlier: 4.286A pdb=" N GLN B1521 " --> pdb=" O TYR B1332 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1336 through 1339 removed outlier: 3.666A pdb=" N LEU B1388 " --> pdb=" O ILE B1378 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU B1390 " --> pdb=" O TRP B1376 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP B1376 " --> pdb=" O LEU B1390 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1415 through 1418 removed outlier: 7.340A pdb=" N TYR B1415 " --> pdb=" O ILE B1448 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N VAL B1450 " --> pdb=" O TYR B1415 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ALA B1417 " --> pdb=" O VAL B1450 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N VAL B1447 " --> pdb=" O ARG B1483 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N TYR B1485 " --> pdb=" O VAL B1447 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU B1449 " --> pdb=" O TYR B1485 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 1547 through 1549 Processing sheet with id=AD2, first strand: chain 'B' and resid 1690 through 1692 removed outlier: 6.456A pdb=" N TYR B1747 " --> pdb=" O PRO B1768 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N CYS B1748 " --> pdb=" O ASN B1741 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ASN B1741 " --> pdb=" O CYS B1748 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1811 through 1814 Processing sheet with id=AD4, first strand: chain 'B' and resid 1840 through 1841 Processing sheet with id=AD5, first strand: chain 'B' and resid 1896 through 1898 removed outlier: 3.555A pdb=" N GLY B1939 " --> pdb=" O MET B1944 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA B1937 " --> pdb=" O VAL B1946 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLU B1948 " --> pdb=" O LEU B1935 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N LEU B1935 " --> pdb=" O GLU B1948 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 2144 through 2145 removed outlier: 3.502A pdb=" N LEU B2493 " --> pdb=" O ILE B2144 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS B2467 " --> pdb=" O LEU B2463 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N LEU B2463 " --> pdb=" O LYS B2467 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 2155 through 2157 Processing sheet with id=AD8, first strand: chain 'B' and resid 2178 through 2179 Processing sheet with id=AD9, first strand: chain 'B' and resid 2199 through 2207 removed outlier: 6.870A pdb=" N GLY B2218 " --> pdb=" O LEU B2200 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LEU B2202 " --> pdb=" O VAL B2216 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL B2216 " --> pdb=" O LEU B2202 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N LEU B2204 " --> pdb=" O TRP B2214 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N TRP B2214 " --> pdb=" O LEU B2204 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N HIS B2206 " --> pdb=" O GLU B2212 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N GLU B2212 " --> pdb=" O HIS B2206 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL B2226 " --> pdb=" O HIS B2236 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS B2236 " --> pdb=" O VAL B2226 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 2264 through 2265 removed outlier: 3.574A pdb=" N ALA B2273 " --> pdb=" O VAL B2265 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU B2272 " --> pdb=" O LEU B2291 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 2354 through 2359 removed outlier: 6.636A pdb=" N ALA B2366 " --> pdb=" O ILE B2355 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL B2357 " --> pdb=" O TYR B2364 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TYR B2364 " --> pdb=" O VAL B2357 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N LYS B2367 " --> pdb=" O VAL B2372 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL B2372 " --> pdb=" O LYS B2367 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 2414 through 2419 removed outlier: 3.582A pdb=" N THR B2416 " --> pdb=" O GLY B2428 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE B2434 " --> pdb=" O VAL B2447 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL B2447 " --> pdb=" O ILE B2434 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LEU B2436 " --> pdb=" O ILE B2445 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 2477 through 2478 removed outlier: 3.676A pdb=" N GLU B2488 " --> pdb=" O LYS B2478 " (cutoff:3.500A) 727 hydrogen bonds defined for protein. 1905 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: 6.38 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5441 1.33 - 1.45: 6315 1.45 - 1.57: 16750 1.57 - 1.69: 16 1.69 - 1.81: 260 Bond restraints: 28782 Sorted by residual: bond pdb=" C4 ATP B2602 " pdb=" C5 ATP B2602 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.91e+01 bond pdb=" C5 ATP B2602 " pdb=" C6 ATP B2602 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.41e+01 bond pdb=" C4 ATP A2602 " pdb=" N9 ATP A2602 " ideal model delta sigma weight residual 1.374 1.309 0.065 1.00e-02 1.00e+04 4.19e+01 bond pdb=" C5 ATP A2602 " pdb=" N7 ATP A2602 " ideal model delta sigma weight residual 1.387 1.323 0.064 1.00e-02 1.00e+04 4.15e+01 bond pdb=" C4 ATP A2602 " pdb=" C5 ATP A2602 " ideal model delta sigma weight residual 1.388 1.443 -0.055 1.00e-02 1.00e+04 3.07e+01 ... (remaining 28777 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.72: 38725 3.72 - 7.44: 209 7.44 - 11.16: 27 11.16 - 14.88: 4 14.88 - 18.60: 3 Bond angle restraints: 38968 Sorted by residual: angle pdb=" PB ATP B2602 " pdb=" O3B ATP B2602 " pdb=" PG ATP B2602 " ideal model delta sigma weight residual 139.87 121.27 18.60 1.00e+00 1.00e+00 3.46e+02 angle pdb=" PA ATP B2602 " pdb=" O3A ATP B2602 " pdb=" PB ATP B2602 " ideal model delta sigma weight residual 136.83 120.34 16.49 1.00e+00 1.00e+00 2.72e+02 angle pdb=" PA ATP A2602 " pdb=" O3A ATP A2602 " pdb=" PB ATP A2602 " ideal model delta sigma weight residual 136.83 121.34 15.49 1.00e+00 1.00e+00 2.40e+02 angle pdb=" PB ATP A2602 " pdb=" O3B ATP A2602 " pdb=" PG ATP A2602 " ideal model delta sigma weight residual 139.87 127.62 12.25 1.00e+00 1.00e+00 1.50e+02 angle pdb=" C5 ATP B2602 " pdb=" C4 ATP B2602 " pdb=" N3 ATP B2602 " ideal model delta sigma weight residual 126.80 118.93 7.87 1.00e+00 1.00e+00 6.19e+01 ... (remaining 38963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.62: 16160 20.62 - 41.25: 1304 41.25 - 61.87: 130 61.87 - 82.49: 33 82.49 - 103.11: 9 Dihedral angle restraints: 17636 sinusoidal: 7138 harmonic: 10498 Sorted by residual: dihedral pdb=" CA ARG A1941 " pdb=" C ARG A1941 " pdb=" N PRO A1942 " pdb=" CA PRO A1942 " ideal model delta harmonic sigma weight residual 0.00 -34.90 34.90 0 5.00e+00 4.00e-02 4.87e+01 dihedral pdb=" C LEU A2137 " pdb=" N LEU A2137 " pdb=" CA LEU A2137 " pdb=" CB LEU A2137 " ideal model delta harmonic sigma weight residual -122.60 -107.90 -14.70 0 2.50e+00 1.60e-01 3.46e+01 dihedral pdb=" C LEU B2137 " pdb=" N LEU B2137 " pdb=" CA LEU B2137 " pdb=" CB LEU B2137 " ideal model delta harmonic sigma weight residual -122.60 -108.35 -14.25 0 2.50e+00 1.60e-01 3.25e+01 ... (remaining 17633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 3972 0.070 - 0.139: 513 0.139 - 0.209: 46 0.209 - 0.278: 9 0.278 - 0.348: 4 Chirality restraints: 4544 Sorted by residual: chirality pdb=" CA LEU A2137 " pdb=" N LEU A2137 " pdb=" C LEU A2137 " pdb=" CB LEU A2137 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CA LEU B2137 " pdb=" N LEU B2137 " pdb=" C LEU B2137 " pdb=" CB LEU B2137 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CA VAL B1598 " pdb=" N VAL B1598 " pdb=" C VAL B1598 " pdb=" CB VAL B1598 " both_signs ideal model delta sigma weight residual False 2.44 2.76 -0.32 2.00e-01 2.50e+01 2.49e+00 ... (remaining 4541 not shown) Planarity restraints: 4891 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP B2496 " 0.020 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C TRP B2496 " -0.070 2.00e-02 2.50e+03 pdb=" O TRP B2496 " 0.027 2.00e-02 2.50e+03 pdb=" N ASP B2497 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A2496 " -0.020 2.00e-02 2.50e+03 4.04e-02 1.63e+01 pdb=" C TRP A2496 " 0.070 2.00e-02 2.50e+03 pdb=" O TRP A2496 " -0.027 2.00e-02 2.50e+03 pdb=" N ASP A2497 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B1057 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.65e+00 pdb=" C MET B1057 " -0.037 2.00e-02 2.50e+03 pdb=" O MET B1057 " 0.014 2.00e-02 2.50e+03 pdb=" N SER B1058 " 0.012 2.00e-02 2.50e+03 ... (remaining 4888 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 651 2.68 - 3.23: 28565 3.23 - 3.79: 39794 3.79 - 4.34: 57836 4.34 - 4.90: 92969 Nonbonded interactions: 219815 Sorted by model distance: nonbonded pdb=" OH TYR A1992 " pdb=" O ALA A2016 " model vdw 2.121 3.040 nonbonded pdb=" OH TYR B1992 " pdb=" O ALA B2016 " model vdw 2.121 3.040 nonbonded pdb=" O SER A2213 " pdb=" OG1 THR A2229 " model vdw 2.161 3.040 nonbonded pdb=" O SER B2213 " pdb=" OG1 THR B2229 " model vdw 2.161 3.040 nonbonded pdb=" NH1 ARG A1731 " pdb=" OE2 GLU B1681 " model vdw 2.181 3.120 ... (remaining 219810 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 558 through 1424 or (resid 1425 through 1426 and (name N o \ r name CA or name C or name O or name CB )) or resid 1427 through 2602)) selection = (chain 'B' and (resid 558 through 1680 or (resid 1681 and (name N or name CA or \ name C or name O or name CB )) or resid 1682 through 1683 or (resid 1684 and (na \ me N or name CA or name C or name O or name CB )) or resid 1685 through 1688 or \ (resid 1689 and (name N or name CA or name C or name O or name CB )) or resid 16 \ 90 through 1744 or (resid 1745 through 1746 and (name N or name CA or name C or \ name O or name CB )) or resid 1747 through 2602)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 25.240 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6128 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 28782 Z= 0.254 Angle : 0.808 18.595 38968 Z= 0.485 Chirality : 0.049 0.348 4544 Planarity : 0.004 0.043 4891 Dihedral : 14.564 103.113 10800 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.16 % Favored : 87.84 % Rotamer: Outliers : 0.06 % Allowed : 8.38 % Favored : 91.55 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.40 (0.11), residues: 3554 helix: -4.02 (0.10), residues: 982 sheet: -3.78 (0.20), residues: 464 loop : -3.45 (0.12), residues: 2108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1067 TYR 0.014 0.002 TYR A2364 PHE 0.014 0.001 PHE A1585 TRP 0.012 0.001 TRP B1705 HIS 0.011 0.001 HIS A1310 Details of bonding type rmsd covalent geometry : bond 0.00466 (28782) covalent geometry : angle 0.80816 (38968) hydrogen bonds : bond 0.29956 ( 727) hydrogen bonds : angle 10.16570 ( 1905) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 461 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 586 MET cc_start: 0.3474 (ttt) cc_final: 0.3143 (ttp) REVERT: A 800 ASN cc_start: 0.6675 (t0) cc_final: 0.6467 (t0) REVERT: A 1431 MET cc_start: 0.7897 (tmm) cc_final: 0.7694 (ttm) REVERT: A 1516 GLN cc_start: 0.7306 (mm110) cc_final: 0.6963 (tm-30) REVERT: A 1754 VAL cc_start: 0.8313 (p) cc_final: 0.7885 (m) REVERT: B 586 MET cc_start: 0.3320 (ttt) cc_final: 0.2980 (ttp) REVERT: B 800 ASN cc_start: 0.6673 (t0) cc_final: 0.6449 (t0) REVERT: B 1516 GLN cc_start: 0.7300 (mm110) cc_final: 0.6981 (tt0) REVERT: B 1788 MET cc_start: 0.8768 (tpp) cc_final: 0.8263 (tpp) outliers start: 2 outliers final: 0 residues processed: 463 average time/residue: 0.1935 time to fit residues: 138.5060 Evaluate side-chains 213 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 682 ASN A 992 ASN A1021 ASN ** A1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 ASN A1140 HIS A1163 ASN A1516 GLN A1871 ASN A1998 HIS ** A2433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2453 ASN ** A2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 682 ASN B 992 ASN B1020 GLN B1021 ASN ** B1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 ASN B1163 ASN B1305 ASN B1516 GLN B1758 HIS B1871 ASN ** B2433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2453 ASN ** B2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.141153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.107829 restraints weight = 55164.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.106906 restraints weight = 41400.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.107754 restraints weight = 46483.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.108666 restraints weight = 31374.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.110292 restraints weight = 27669.612| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 28782 Z= 0.158 Angle : 0.692 10.802 38968 Z= 0.350 Chirality : 0.045 0.169 4544 Planarity : 0.005 0.045 4891 Dihedral : 6.738 85.219 3910 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 1.70 % Allowed : 15.46 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.32 (0.12), residues: 3554 helix: -2.53 (0.13), residues: 1090 sheet: -3.38 (0.21), residues: 468 loop : -3.00 (0.13), residues: 1996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A2523 TYR 0.016 0.001 TYR B1739 PHE 0.013 0.002 PHE A1883 TRP 0.012 0.002 TRP B1705 HIS 0.007 0.001 HIS B 669 Details of bonding type rmsd covalent geometry : bond 0.00360 (28782) covalent geometry : angle 0.69176 (38968) hydrogen bonds : bond 0.05125 ( 727) hydrogen bonds : angle 5.97485 ( 1905) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 228 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1364 MET cc_start: 0.3152 (tpt) cc_final: 0.2730 (tpt) REVERT: A 1516 GLN cc_start: 0.7697 (mm-40) cc_final: 0.7143 (tt0) REVERT: A 1646 MET cc_start: 0.6465 (mmt) cc_final: 0.6230 (mmt) REVERT: A 1702 MET cc_start: 0.8723 (tpp) cc_final: 0.8460 (tpp) REVERT: A 2459 MET cc_start: 0.5818 (ptp) cc_final: 0.5162 (ptp) REVERT: B 672 ASP cc_start: 0.6604 (m-30) cc_final: 0.6332 (m-30) REVERT: B 1364 MET cc_start: 0.3160 (tpt) cc_final: 0.2731 (tpt) REVERT: B 1646 MET cc_start: 0.6440 (mmt) cc_final: 0.6185 (mmt) REVERT: B 1702 MET cc_start: 0.8771 (tpp) cc_final: 0.8495 (tpp) outliers start: 53 outliers final: 31 residues processed: 269 average time/residue: 0.1594 time to fit residues: 72.3074 Evaluate side-chains 208 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 177 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 612 TYR Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 1049 SER Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1615 VAL Chi-restraints excluded: chain A residue 1650 PHE Chi-restraints excluded: chain A residue 1679 VAL Chi-restraints excluded: chain A residue 2086 LEU Chi-restraints excluded: chain A residue 2088 ILE Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2323 ILE Chi-restraints excluded: chain A residue 2418 CYS Chi-restraints excluded: chain A residue 2426 TRP Chi-restraints excluded: chain A residue 2448 ILE Chi-restraints excluded: chain A residue 2455 VAL Chi-restraints excluded: chain B residue 612 TYR Chi-restraints excluded: chain B residue 670 SER Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 1049 SER Chi-restraints excluded: chain B residue 1268 GLU Chi-restraints excluded: chain B residue 1650 PHE Chi-restraints excluded: chain B residue 1679 VAL Chi-restraints excluded: chain B residue 2086 LEU Chi-restraints excluded: chain B residue 2088 ILE Chi-restraints excluded: chain B residue 2137 LEU Chi-restraints excluded: chain B residue 2323 ILE Chi-restraints excluded: chain B residue 2418 CYS Chi-restraints excluded: chain B residue 2426 TRP Chi-restraints excluded: chain B residue 2448 ILE Chi-restraints excluded: chain B residue 2455 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 61 optimal weight: 0.0670 chunk 73 optimal weight: 0.9980 chunk 261 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 307 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 271 optimal weight: 7.9990 chunk 205 optimal weight: 9.9990 chunk 197 optimal weight: 0.9980 chunk 185 optimal weight: 1.9990 overall best weight: 0.8118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 682 ASN ** A1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1353 GLN A1586 GLN ** A2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 682 ASN B1062 ASN B1353 GLN B1586 GLN ** B2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.140795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.106547 restraints weight = 54751.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.104824 restraints weight = 40887.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.106074 restraints weight = 44629.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.106899 restraints weight = 30903.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.108000 restraints weight = 27725.851| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28782 Z= 0.129 Angle : 0.615 10.144 38968 Z= 0.309 Chirality : 0.043 0.149 4544 Planarity : 0.004 0.046 4891 Dihedral : 6.333 72.296 3910 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 2.62 % Allowed : 16.90 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.68 (0.13), residues: 3554 helix: -1.80 (0.14), residues: 1112 sheet: -3.16 (0.21), residues: 532 loop : -2.65 (0.13), residues: 1910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1127 TYR 0.016 0.001 TYR A 707 PHE 0.014 0.001 PHE A1650 TRP 0.012 0.001 TRP B1217 HIS 0.006 0.001 HIS A2510 Details of bonding type rmsd covalent geometry : bond 0.00296 (28782) covalent geometry : angle 0.61501 (38968) hydrogen bonds : bond 0.03956 ( 727) hydrogen bonds : angle 5.23158 ( 1905) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 208 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 665 LEU cc_start: 0.9123 (mt) cc_final: 0.8753 (mp) REVERT: A 787 ILE cc_start: 0.7755 (mt) cc_final: 0.7353 (tp) REVERT: A 842 MET cc_start: 0.7293 (mmm) cc_final: 0.7043 (mtt) REVERT: A 1702 MET cc_start: 0.8558 (tpp) cc_final: 0.8304 (tpp) REVERT: A 1830 LEU cc_start: 0.7612 (tp) cc_final: 0.7237 (mp) REVERT: A 2155 MET cc_start: 0.7191 (ppp) cc_final: 0.6626 (ppp) REVERT: A 2301 MET cc_start: 0.6068 (ttm) cc_final: 0.5461 (ttm) REVERT: A 2323 ILE cc_start: 0.5454 (OUTLIER) cc_final: 0.5228 (pt) REVERT: B 665 LEU cc_start: 0.9116 (mt) cc_final: 0.8748 (mp) REVERT: B 672 ASP cc_start: 0.6618 (m-30) cc_final: 0.6386 (m-30) REVERT: B 787 ILE cc_start: 0.7647 (mt) cc_final: 0.7304 (tp) REVERT: B 1702 MET cc_start: 0.8641 (tpp) cc_final: 0.8335 (tpp) REVERT: B 1830 LEU cc_start: 0.7702 (tp) cc_final: 0.7301 (mp) REVERT: B 2204 LEU cc_start: 0.8158 (tp) cc_final: 0.7912 (mt) REVERT: B 2301 MET cc_start: 0.6105 (ttm) cc_final: 0.5520 (ttm) REVERT: B 2323 ILE cc_start: 0.5450 (OUTLIER) cc_final: 0.5212 (pt) outliers start: 82 outliers final: 48 residues processed: 277 average time/residue: 0.1567 time to fit residues: 73.2580 Evaluate side-chains 234 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 184 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 612 TYR Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain A residue 809 CYS Chi-restraints excluded: chain A residue 1049 SER Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1541 VAL Chi-restraints excluded: chain A residue 1650 PHE Chi-restraints excluded: chain A residue 1679 VAL Chi-restraints excluded: chain A residue 1765 ILE Chi-restraints excluded: chain A residue 1850 ILE Chi-restraints excluded: chain A residue 1893 VAL Chi-restraints excluded: chain A residue 1990 ILE Chi-restraints excluded: chain A residue 2086 LEU Chi-restraints excluded: chain A residue 2088 ILE Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2323 ILE Chi-restraints excluded: chain A residue 2418 CYS Chi-restraints excluded: chain A residue 2426 TRP Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2448 ILE Chi-restraints excluded: chain A residue 2455 VAL Chi-restraints excluded: chain B residue 612 TYR Chi-restraints excluded: chain B residue 670 SER Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 1049 SER Chi-restraints excluded: chain B residue 1389 VAL Chi-restraints excluded: chain B residue 1541 VAL Chi-restraints excluded: chain B residue 1650 PHE Chi-restraints excluded: chain B residue 1679 VAL Chi-restraints excluded: chain B residue 1765 ILE Chi-restraints excluded: chain B residue 1850 ILE Chi-restraints excluded: chain B residue 1893 VAL Chi-restraints excluded: chain B residue 1990 ILE Chi-restraints excluded: chain B residue 2004 THR Chi-restraints excluded: chain B residue 2027 MET Chi-restraints excluded: chain B residue 2035 THR Chi-restraints excluded: chain B residue 2086 LEU Chi-restraints excluded: chain B residue 2088 ILE Chi-restraints excluded: chain B residue 2137 LEU Chi-restraints excluded: chain B residue 2205 VAL Chi-restraints excluded: chain B residue 2323 ILE Chi-restraints excluded: chain B residue 2418 CYS Chi-restraints excluded: chain B residue 2426 TRP Chi-restraints excluded: chain B residue 2448 ILE Chi-restraints excluded: chain B residue 2455 VAL Chi-restraints excluded: chain B residue 2469 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 273 optimal weight: 3.9990 chunk 205 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 chunk 340 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 77 optimal weight: 0.6980 chunk 189 optimal weight: 9.9990 chunk 287 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 277 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1062 ASN A1926 HIS ** A2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1303 HIS B1926 HIS ** B2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.138247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.098479 restraints weight = 54870.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.098918 restraints weight = 35929.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.099267 restraints weight = 30180.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.099945 restraints weight = 29732.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.099993 restraints weight = 25947.795| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 28782 Z= 0.160 Angle : 0.630 10.116 38968 Z= 0.315 Chirality : 0.044 0.173 4544 Planarity : 0.004 0.046 4891 Dihedral : 6.284 80.004 3910 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Rotamer: Outliers : 3.58 % Allowed : 16.32 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.31 (0.13), residues: 3554 helix: -1.36 (0.15), residues: 1112 sheet: -2.91 (0.22), residues: 500 loop : -2.55 (0.13), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1127 TYR 0.021 0.001 TYR B 707 PHE 0.014 0.001 PHE B1148 TRP 0.027 0.002 TRP A2376 HIS 0.004 0.001 HIS B2510 Details of bonding type rmsd covalent geometry : bond 0.00379 (28782) covalent geometry : angle 0.63022 (38968) hydrogen bonds : bond 0.03552 ( 727) hydrogen bonds : angle 5.03302 ( 1905) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 206 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 672 ASP cc_start: 0.6321 (m-30) cc_final: 0.5998 (m-30) REVERT: A 787 ILE cc_start: 0.7800 (mt) cc_final: 0.7467 (tp) REVERT: A 842 MET cc_start: 0.7458 (mmm) cc_final: 0.7080 (mtt) REVERT: A 1390 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8464 (pp) REVERT: A 1830 LEU cc_start: 0.7703 (tp) cc_final: 0.7311 (mp) REVERT: A 2155 MET cc_start: 0.6987 (ppp) cc_final: 0.6422 (ppp) REVERT: A 2204 LEU cc_start: 0.7821 (tp) cc_final: 0.7616 (mp) REVERT: A 2301 MET cc_start: 0.6122 (ttm) cc_final: 0.5471 (ttm) REVERT: A 2323 ILE cc_start: 0.4892 (OUTLIER) cc_final: 0.4558 (pt) REVERT: A 2339 ARG cc_start: 0.5541 (tpt170) cc_final: 0.5058 (tpt90) REVERT: B 672 ASP cc_start: 0.6403 (m-30) cc_final: 0.5972 (m-30) REVERT: B 712 MET cc_start: 0.8145 (mmt) cc_final: 0.7842 (mtt) REVERT: B 787 ILE cc_start: 0.7600 (mt) cc_final: 0.7319 (tp) REVERT: B 842 MET cc_start: 0.7476 (mmm) cc_final: 0.7163 (mtt) REVERT: B 1390 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8325 (pp) REVERT: B 1830 LEU cc_start: 0.7743 (tp) cc_final: 0.7292 (mp) REVERT: B 2215 ILE cc_start: 0.7568 (OUTLIER) cc_final: 0.7037 (tp) REVERT: B 2301 MET cc_start: 0.6062 (ttm) cc_final: 0.5407 (ttm) REVERT: B 2323 ILE cc_start: 0.4857 (OUTLIER) cc_final: 0.4553 (pt) REVERT: B 2339 ARG cc_start: 0.5561 (tpt170) cc_final: 0.5071 (tpt90) outliers start: 112 outliers final: 60 residues processed: 303 average time/residue: 0.1536 time to fit residues: 78.8819 Evaluate side-chains 249 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 184 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 612 TYR Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain A residue 1049 SER Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1350 LEU Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain A residue 1491 THR Chi-restraints excluded: chain A residue 1541 VAL Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain A residue 1650 PHE Chi-restraints excluded: chain A residue 1679 VAL Chi-restraints excluded: chain A residue 1765 ILE Chi-restraints excluded: chain A residue 1850 ILE Chi-restraints excluded: chain A residue 1893 VAL Chi-restraints excluded: chain A residue 1960 GLN Chi-restraints excluded: chain A residue 1990 ILE Chi-restraints excluded: chain A residue 2004 THR Chi-restraints excluded: chain A residue 2035 THR Chi-restraints excluded: chain A residue 2086 LEU Chi-restraints excluded: chain A residue 2088 ILE Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2323 ILE Chi-restraints excluded: chain A residue 2387 ILE Chi-restraints excluded: chain A residue 2418 CYS Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2448 ILE Chi-restraints excluded: chain A residue 2455 VAL Chi-restraints excluded: chain A residue 2469 VAL Chi-restraints excluded: chain B residue 612 TYR Chi-restraints excluded: chain B residue 670 SER Chi-restraints excluded: chain B residue 725 VAL Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 1049 SER Chi-restraints excluded: chain B residue 1268 GLU Chi-restraints excluded: chain B residue 1389 VAL Chi-restraints excluded: chain B residue 1390 LEU Chi-restraints excluded: chain B residue 1491 THR Chi-restraints excluded: chain B residue 1541 VAL Chi-restraints excluded: chain B residue 1548 ILE Chi-restraints excluded: chain B residue 1650 PHE Chi-restraints excluded: chain B residue 1679 VAL Chi-restraints excluded: chain B residue 1765 ILE Chi-restraints excluded: chain B residue 1850 ILE Chi-restraints excluded: chain B residue 1893 VAL Chi-restraints excluded: chain B residue 1935 LEU Chi-restraints excluded: chain B residue 1944 MET Chi-restraints excluded: chain B residue 1960 GLN Chi-restraints excluded: chain B residue 1990 ILE Chi-restraints excluded: chain B residue 2004 THR Chi-restraints excluded: chain B residue 2027 MET Chi-restraints excluded: chain B residue 2035 THR Chi-restraints excluded: chain B residue 2086 LEU Chi-restraints excluded: chain B residue 2088 ILE Chi-restraints excluded: chain B residue 2137 LEU Chi-restraints excluded: chain B residue 2215 ILE Chi-restraints excluded: chain B residue 2315 MET Chi-restraints excluded: chain B residue 2323 ILE Chi-restraints excluded: chain B residue 2387 ILE Chi-restraints excluded: chain B residue 2418 CYS Chi-restraints excluded: chain B residue 2427 ILE Chi-restraints excluded: chain B residue 2448 ILE Chi-restraints excluded: chain B residue 2455 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 357 optimal weight: 0.9990 chunk 157 optimal weight: 20.0000 chunk 206 optimal weight: 7.9990 chunk 146 optimal weight: 7.9990 chunk 116 optimal weight: 0.7980 chunk 168 optimal weight: 6.9990 chunk 83 optimal weight: 8.9990 chunk 174 optimal weight: 5.9990 chunk 262 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 217 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1183 ASN A1254 HIS A1407 HIS ** A1567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2462 GLN ** A2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 682 ASN B1183 ASN B1254 HIS B1407 HIS ** B1567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.133425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.093154 restraints weight = 55168.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.093186 restraints weight = 39873.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.093566 restraints weight = 31875.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.094032 restraints weight = 31800.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.094430 restraints weight = 28199.282| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 28782 Z= 0.290 Angle : 0.765 11.269 38968 Z= 0.384 Chirality : 0.049 0.173 4544 Planarity : 0.005 0.048 4891 Dihedral : 6.790 88.553 3910 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.68 % Favored : 88.32 % Rotamer: Outliers : 3.97 % Allowed : 17.89 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.38 (0.13), residues: 3554 helix: -1.43 (0.15), residues: 1126 sheet: -2.87 (0.22), residues: 500 loop : -2.62 (0.13), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1320 TYR 0.023 0.002 TYR B1739 PHE 0.019 0.002 PHE A1511 TRP 0.023 0.003 TRP A2376 HIS 0.008 0.001 HIS B1039 Details of bonding type rmsd covalent geometry : bond 0.00702 (28782) covalent geometry : angle 0.76491 (38968) hydrogen bonds : bond 0.03980 ( 727) hydrogen bonds : angle 5.29444 ( 1905) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 190 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 787 ILE cc_start: 0.7832 (mt) cc_final: 0.7600 (tp) REVERT: A 1128 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.6893 (mt) REVERT: A 1364 MET cc_start: 0.3778 (tpt) cc_final: 0.2990 (tmm) REVERT: A 1731 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.8209 (ptt-90) REVERT: A 2155 MET cc_start: 0.7117 (ppp) cc_final: 0.6783 (ppp) REVERT: A 2204 LEU cc_start: 0.7803 (tp) cc_final: 0.7594 (mp) REVERT: A 2315 MET cc_start: 0.4520 (tmm) cc_final: 0.3750 (tmm) REVERT: A 2339 ARG cc_start: 0.5626 (tpt170) cc_final: 0.5270 (tpt170) REVERT: B 672 ASP cc_start: 0.6246 (m-30) cc_final: 0.5827 (m-30) REVERT: B 682 ASN cc_start: 0.8115 (OUTLIER) cc_final: 0.7879 (t0) REVERT: B 787 ILE cc_start: 0.7760 (mt) cc_final: 0.7555 (tp) REVERT: B 842 MET cc_start: 0.7488 (mmm) cc_final: 0.7153 (mtt) REVERT: B 1128 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.6879 (mt) REVERT: B 1390 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8482 (pp) REVERT: B 1788 MET cc_start: 0.8979 (tpp) cc_final: 0.8558 (tpp) REVERT: B 2215 ILE cc_start: 0.7468 (OUTLIER) cc_final: 0.7095 (tp) REVERT: B 2326 PHE cc_start: 0.4525 (p90) cc_final: 0.3975 (p90) REVERT: B 2339 ARG cc_start: 0.5631 (tpt170) cc_final: 0.5256 (tpt170) outliers start: 124 outliers final: 79 residues processed: 294 average time/residue: 0.1600 time to fit residues: 78.7622 Evaluate side-chains 262 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 177 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 612 TYR Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1128 LEU Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1350 LEU Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1431 MET Chi-restraints excluded: chain A residue 1482 ILE Chi-restraints excluded: chain A residue 1491 THR Chi-restraints excluded: chain A residue 1541 VAL Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain A residue 1650 PHE Chi-restraints excluded: chain A residue 1679 VAL Chi-restraints excluded: chain A residue 1702 MET Chi-restraints excluded: chain A residue 1731 ARG Chi-restraints excluded: chain A residue 1765 ILE Chi-restraints excluded: chain A residue 1810 LYS Chi-restraints excluded: chain A residue 1850 ILE Chi-restraints excluded: chain A residue 1893 VAL Chi-restraints excluded: chain A residue 1916 LEU Chi-restraints excluded: chain A residue 1944 MET Chi-restraints excluded: chain A residue 1990 ILE Chi-restraints excluded: chain A residue 2004 THR Chi-restraints excluded: chain A residue 2020 ILE Chi-restraints excluded: chain A residue 2027 MET Chi-restraints excluded: chain A residue 2035 THR Chi-restraints excluded: chain A residue 2047 ASN Chi-restraints excluded: chain A residue 2086 LEU Chi-restraints excluded: chain A residue 2088 ILE Chi-restraints excluded: chain A residue 2137 LEU Chi-restraints excluded: chain A residue 2267 THR Chi-restraints excluded: chain A residue 2323 ILE Chi-restraints excluded: chain A residue 2331 THR Chi-restraints excluded: chain A residue 2387 ILE Chi-restraints excluded: chain A residue 2418 CYS Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2448 ILE Chi-restraints excluded: chain A residue 2455 VAL Chi-restraints excluded: chain B residue 612 TYR Chi-restraints excluded: chain B residue 670 SER Chi-restraints excluded: chain B residue 682 ASN Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 1042 LEU Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain B residue 1268 GLU Chi-restraints excluded: chain B residue 1350 LEU Chi-restraints excluded: chain B residue 1389 VAL Chi-restraints excluded: chain B residue 1390 LEU Chi-restraints excluded: chain B residue 1431 MET Chi-restraints excluded: chain B residue 1482 ILE Chi-restraints excluded: chain B residue 1541 VAL Chi-restraints excluded: chain B residue 1548 ILE Chi-restraints excluded: chain B residue 1650 PHE Chi-restraints excluded: chain B residue 1679 VAL Chi-restraints excluded: chain B residue 1702 MET Chi-restraints excluded: chain B residue 1765 ILE Chi-restraints excluded: chain B residue 1810 LYS Chi-restraints excluded: chain B residue 1850 ILE Chi-restraints excluded: chain B residue 1893 VAL Chi-restraints excluded: chain B residue 1944 MET Chi-restraints excluded: chain B residue 1990 ILE Chi-restraints excluded: chain B residue 2004 THR Chi-restraints excluded: chain B residue 2020 ILE Chi-restraints excluded: chain B residue 2027 MET Chi-restraints excluded: chain B residue 2035 THR Chi-restraints excluded: chain B residue 2047 ASN Chi-restraints excluded: chain B residue 2086 LEU Chi-restraints excluded: chain B residue 2088 ILE Chi-restraints excluded: chain B residue 2137 LEU Chi-restraints excluded: chain B residue 2205 VAL Chi-restraints excluded: chain B residue 2215 ILE Chi-restraints excluded: chain B residue 2267 THR Chi-restraints excluded: chain B residue 2323 ILE Chi-restraints excluded: chain B residue 2331 THR Chi-restraints excluded: chain B residue 2387 ILE Chi-restraints excluded: chain B residue 2418 CYS Chi-restraints excluded: chain B residue 2427 ILE Chi-restraints excluded: chain B residue 2448 ILE Chi-restraints excluded: chain B residue 2455 VAL Chi-restraints excluded: chain B residue 2459 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 207 optimal weight: 1.9990 chunk 308 optimal weight: 0.9980 chunk 160 optimal weight: 20.0000 chunk 172 optimal weight: 8.9990 chunk 171 optimal weight: 5.9990 chunk 289 optimal weight: 0.0070 chunk 338 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 175 optimal weight: 9.9990 chunk 249 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 682 ASN ** A1567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1758 HIS ** A2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 682 ASN ** B1567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.137313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.098679 restraints weight = 54446.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.098425 restraints weight = 34640.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.099268 restraints weight = 30041.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.099803 restraints weight = 26816.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.099821 restraints weight = 25206.069| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28782 Z= 0.120 Angle : 0.610 9.795 38968 Z= 0.304 Chirality : 0.043 0.161 4544 Planarity : 0.004 0.047 4891 Dihedral : 6.275 78.033 3910 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 2.88 % Allowed : 19.52 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.03 (0.14), residues: 3554 helix: -1.00 (0.15), residues: 1142 sheet: -2.77 (0.22), residues: 526 loop : -2.46 (0.14), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1866 TYR 0.015 0.001 TYR B1739 PHE 0.014 0.001 PHE A2326 TRP 0.026 0.002 TRP A2316 HIS 0.003 0.001 HIS A1758 Details of bonding type rmsd covalent geometry : bond 0.00281 (28782) covalent geometry : angle 0.60979 (38968) hydrogen bonds : bond 0.03130 ( 727) hydrogen bonds : angle 4.94830 ( 1905) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 200 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 673 LEU cc_start: 0.8622 (mm) cc_final: 0.8092 (tp) REVERT: A 682 ASN cc_start: 0.8068 (OUTLIER) cc_final: 0.7833 (t0) REVERT: A 787 ILE cc_start: 0.7725 (mt) cc_final: 0.7494 (tp) REVERT: A 842 MET cc_start: 0.7372 (mmm) cc_final: 0.7139 (mtt) REVERT: A 1390 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8508 (pp) REVERT: A 1788 MET cc_start: 0.8919 (tpp) cc_final: 0.8538 (tpp) REVERT: A 2155 MET cc_start: 0.7288 (ppp) cc_final: 0.6927 (ppp) REVERT: A 2303 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.6533 (mp) REVERT: A 2315 MET cc_start: 0.5100 (tmm) cc_final: 0.3568 (tmm) REVERT: A 2339 ARG cc_start: 0.5662 (tpt170) cc_final: 0.5371 (tpt170) REVERT: B 672 ASP cc_start: 0.6132 (m-30) cc_final: 0.5664 (m-30) REVERT: B 673 LEU cc_start: 0.8623 (mm) cc_final: 0.8086 (tp) REVERT: B 712 MET cc_start: 0.7981 (mmt) cc_final: 0.7708 (mtt) REVERT: B 842 MET cc_start: 0.7396 (mmm) cc_final: 0.7115 (mtt) REVERT: B 1390 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8353 (pp) REVERT: B 1788 MET cc_start: 0.8897 (tpp) cc_final: 0.8417 (tpp) REVERT: B 2215 ILE cc_start: 0.7399 (OUTLIER) cc_final: 0.7019 (tp) REVERT: B 2339 ARG cc_start: 0.5665 (tpt170) cc_final: 0.5366 (tpt170) outliers start: 90 outliers final: 63 residues processed: 273 average time/residue: 0.1560 time to fit residues: 71.9572 Evaluate side-chains 252 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 184 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 612 TYR Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 682 ASN Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain A residue 983 TYR Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1216 HIS Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1299 LEU Chi-restraints excluded: chain A residue 1350 LEU Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain A residue 1541 VAL Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain A residue 1650 PHE Chi-restraints excluded: chain A residue 1679 VAL Chi-restraints excluded: chain A residue 1697 MET Chi-restraints excluded: chain A residue 1702 MET Chi-restraints excluded: chain A residue 1765 ILE Chi-restraints excluded: chain A residue 1893 VAL Chi-restraints excluded: chain A residue 2020 ILE Chi-restraints excluded: chain A residue 2035 THR Chi-restraints excluded: chain A residue 2047 ASN Chi-restraints excluded: chain A residue 2086 LEU Chi-restraints excluded: chain A residue 2088 ILE Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2303 LEU Chi-restraints excluded: chain A residue 2323 ILE Chi-restraints excluded: chain A residue 2387 ILE Chi-restraints excluded: chain A residue 2418 CYS Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2448 ILE Chi-restraints excluded: chain A residue 2455 VAL Chi-restraints excluded: chain A residue 2469 VAL Chi-restraints excluded: chain B residue 612 TYR Chi-restraints excluded: chain B residue 670 SER Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1042 LEU Chi-restraints excluded: chain B residue 1106 VAL Chi-restraints excluded: chain B residue 1268 GLU Chi-restraints excluded: chain B residue 1350 LEU Chi-restraints excluded: chain B residue 1389 VAL Chi-restraints excluded: chain B residue 1390 LEU Chi-restraints excluded: chain B residue 1541 VAL Chi-restraints excluded: chain B residue 1548 ILE Chi-restraints excluded: chain B residue 1650 PHE Chi-restraints excluded: chain B residue 1679 VAL Chi-restraints excluded: chain B residue 1697 MET Chi-restraints excluded: chain B residue 1702 MET Chi-restraints excluded: chain B residue 1765 ILE Chi-restraints excluded: chain B residue 1893 VAL Chi-restraints excluded: chain B residue 2020 ILE Chi-restraints excluded: chain B residue 2027 MET Chi-restraints excluded: chain B residue 2035 THR Chi-restraints excluded: chain B residue 2047 ASN Chi-restraints excluded: chain B residue 2086 LEU Chi-restraints excluded: chain B residue 2088 ILE Chi-restraints excluded: chain B residue 2205 VAL Chi-restraints excluded: chain B residue 2215 ILE Chi-restraints excluded: chain B residue 2323 ILE Chi-restraints excluded: chain B residue 2387 ILE Chi-restraints excluded: chain B residue 2418 CYS Chi-restraints excluded: chain B residue 2427 ILE Chi-restraints excluded: chain B residue 2448 ILE Chi-restraints excluded: chain B residue 2455 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 165 optimal weight: 0.4980 chunk 21 optimal weight: 0.5980 chunk 222 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 229 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 127 optimal weight: 0.1980 chunk 48 optimal weight: 0.6980 chunk 237 optimal weight: 0.0980 chunk 52 optimal weight: 3.9990 chunk 157 optimal weight: 9.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 669 HIS ** A1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 669 HIS B 682 ASN ** B1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.138754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.105702 restraints weight = 54480.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.104587 restraints weight = 39145.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.105661 restraints weight = 42453.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.106438 restraints weight = 28636.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.107659 restraints weight = 25541.212| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 28782 Z= 0.104 Angle : 0.586 9.056 38968 Z= 0.290 Chirality : 0.043 0.220 4544 Planarity : 0.004 0.047 4891 Dihedral : 5.951 69.389 3910 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 3.01 % Allowed : 20.13 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.75 (0.14), residues: 3554 helix: -0.69 (0.16), residues: 1144 sheet: -2.78 (0.21), residues: 528 loop : -2.29 (0.14), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1707 TYR 0.019 0.001 TYR A1527 PHE 0.016 0.001 PHE B2326 TRP 0.025 0.002 TRP A2316 HIS 0.003 0.001 HIS B1584 Details of bonding type rmsd covalent geometry : bond 0.00237 (28782) covalent geometry : angle 0.58609 (38968) hydrogen bonds : bond 0.02880 ( 727) hydrogen bonds : angle 4.75525 ( 1905) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 201 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 673 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.7604 (tp) REVERT: A 679 MET cc_start: 0.8497 (mmm) cc_final: 0.8161 (mmp) REVERT: A 787 ILE cc_start: 0.7773 (mt) cc_final: 0.7516 (tp) REVERT: A 1128 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.6953 (mt) REVERT: A 1364 MET cc_start: 0.3280 (tpt) cc_final: 0.2598 (tmm) REVERT: A 1390 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8245 (pp) REVERT: A 2155 MET cc_start: 0.7338 (ppp) cc_final: 0.7030 (ppp) REVERT: A 2303 LEU cc_start: 0.6962 (OUTLIER) cc_final: 0.6358 (mt) REVERT: A 2315 MET cc_start: 0.5338 (tmm) cc_final: 0.3759 (tmm) REVERT: A 2339 ARG cc_start: 0.5708 (tpt170) cc_final: 0.5404 (tpt90) REVERT: B 673 LEU cc_start: 0.8517 (mm) cc_final: 0.8031 (tp) REVERT: B 1128 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.6980 (mt) REVERT: B 1390 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8016 (pp) REVERT: B 1832 LYS cc_start: 0.8555 (ttpp) cc_final: 0.8165 (tmmt) REVERT: B 2339 ARG cc_start: 0.5750 (tpt170) cc_final: 0.5534 (tpt170) REVERT: B 2483 THR cc_start: 0.5157 (OUTLIER) cc_final: 0.4512 (t) outliers start: 94 outliers final: 59 residues processed: 275 average time/residue: 0.1579 time to fit residues: 73.5785 Evaluate side-chains 248 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 182 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 612 TYR Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain A residue 983 TYR Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1128 LEU Chi-restraints excluded: chain A residue 1268 GLU Chi-restraints excluded: chain A residue 1350 LEU Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain A residue 1541 VAL Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain A residue 1569 LEU Chi-restraints excluded: chain A residue 1679 VAL Chi-restraints excluded: chain A residue 1697 MET Chi-restraints excluded: chain A residue 1702 MET Chi-restraints excluded: chain A residue 1765 ILE Chi-restraints excluded: chain A residue 1830 LEU Chi-restraints excluded: chain A residue 1893 VAL Chi-restraints excluded: chain A residue 1990 ILE Chi-restraints excluded: chain A residue 2020 ILE Chi-restraints excluded: chain A residue 2035 THR Chi-restraints excluded: chain A residue 2047 ASN Chi-restraints excluded: chain A residue 2088 ILE Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2303 LEU Chi-restraints excluded: chain A residue 2323 ILE Chi-restraints excluded: chain A residue 2387 ILE Chi-restraints excluded: chain A residue 2418 CYS Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2448 ILE Chi-restraints excluded: chain A residue 2455 VAL Chi-restraints excluded: chain B residue 612 TYR Chi-restraints excluded: chain B residue 670 SER Chi-restraints excluded: chain B residue 682 ASN Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 1042 LEU Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain B residue 1106 VAL Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain B residue 1268 GLU Chi-restraints excluded: chain B residue 1350 LEU Chi-restraints excluded: chain B residue 1389 VAL Chi-restraints excluded: chain B residue 1390 LEU Chi-restraints excluded: chain B residue 1491 THR Chi-restraints excluded: chain B residue 1541 VAL Chi-restraints excluded: chain B residue 1548 ILE Chi-restraints excluded: chain B residue 1679 VAL Chi-restraints excluded: chain B residue 1697 MET Chi-restraints excluded: chain B residue 1702 MET Chi-restraints excluded: chain B residue 1765 ILE Chi-restraints excluded: chain B residue 1830 LEU Chi-restraints excluded: chain B residue 1893 VAL Chi-restraints excluded: chain B residue 2020 ILE Chi-restraints excluded: chain B residue 2047 ASN Chi-restraints excluded: chain B residue 2088 ILE Chi-restraints excluded: chain B residue 2205 VAL Chi-restraints excluded: chain B residue 2323 ILE Chi-restraints excluded: chain B residue 2387 ILE Chi-restraints excluded: chain B residue 2418 CYS Chi-restraints excluded: chain B residue 2427 ILE Chi-restraints excluded: chain B residue 2448 ILE Chi-restraints excluded: chain B residue 2455 VAL Chi-restraints excluded: chain B residue 2469 VAL Chi-restraints excluded: chain B residue 2483 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 340 optimal weight: 7.9990 chunk 352 optimal weight: 1.9990 chunk 186 optimal weight: 0.9980 chunk 277 optimal weight: 2.9990 chunk 85 optimal weight: 0.1980 chunk 51 optimal weight: 0.2980 chunk 111 optimal weight: 0.3980 chunk 147 optimal weight: 9.9990 chunk 270 optimal weight: 0.0010 chunk 333 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 overall best weight: 0.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 992 ASN ** A1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1183 ASN ** A1567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 682 ASN B 992 ASN ** B1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1183 ASN ** B1567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1919 GLN ** B2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.139237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.106191 restraints weight = 54646.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.105052 restraints weight = 40340.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.106295 restraints weight = 42466.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.106982 restraints weight = 28862.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.108267 restraints weight = 25992.280| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.4331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 28782 Z= 0.103 Angle : 0.580 9.108 38968 Z= 0.287 Chirality : 0.042 0.188 4544 Planarity : 0.004 0.049 4891 Dihedral : 5.799 63.184 3910 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 2.56 % Allowed : 20.61 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.14), residues: 3554 helix: -0.49 (0.16), residues: 1144 sheet: -2.80 (0.21), residues: 560 loop : -2.15 (0.14), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1707 TYR 0.014 0.001 TYR B1527 PHE 0.015 0.001 PHE A1585 TRP 0.018 0.001 TRP A2316 HIS 0.003 0.001 HIS B 669 Details of bonding type rmsd covalent geometry : bond 0.00231 (28782) covalent geometry : angle 0.57985 (38968) hydrogen bonds : bond 0.02805 ( 727) hydrogen bonds : angle 4.65559 ( 1905) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 199 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 679 MET cc_start: 0.8546 (mmm) cc_final: 0.8212 (mmp) REVERT: A 787 ILE cc_start: 0.7823 (mt) cc_final: 0.7560 (tp) REVERT: A 1128 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.6919 (mt) REVERT: A 1364 MET cc_start: 0.3375 (tpt) cc_final: 0.2634 (tmm) REVERT: A 1390 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8195 (pp) REVERT: A 2155 MET cc_start: 0.7353 (ppp) cc_final: 0.7054 (ppp) REVERT: A 2303 LEU cc_start: 0.6813 (OUTLIER) cc_final: 0.6272 (mt) REVERT: A 2315 MET cc_start: 0.5309 (tmm) cc_final: 0.3713 (tmm) REVERT: B 673 LEU cc_start: 0.8469 (mm) cc_final: 0.7632 (tp) REVERT: B 682 ASN cc_start: 0.7930 (OUTLIER) cc_final: 0.7672 (t0) REVERT: B 1128 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.7001 (mp) REVERT: B 1390 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8022 (pp) REVERT: B 1832 LYS cc_start: 0.8506 (ttpp) cc_final: 0.8298 (ttpt) REVERT: B 2303 LEU cc_start: 0.7089 (mt) cc_final: 0.6853 (mm) outliers start: 80 outliers final: 59 residues processed: 264 average time/residue: 0.1549 time to fit residues: 69.5919 Evaluate side-chains 247 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 182 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 612 TYR Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain A residue 1037 LEU Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1128 LEU Chi-restraints excluded: chain A residue 1350 LEU Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain A residue 1541 VAL Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain A residue 1679 VAL Chi-restraints excluded: chain A residue 1697 MET Chi-restraints excluded: chain A residue 1702 MET Chi-restraints excluded: chain A residue 1765 ILE Chi-restraints excluded: chain A residue 1893 VAL Chi-restraints excluded: chain A residue 2035 THR Chi-restraints excluded: chain A residue 2047 ASN Chi-restraints excluded: chain A residue 2086 LEU Chi-restraints excluded: chain A residue 2088 ILE Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2303 LEU Chi-restraints excluded: chain A residue 2323 ILE Chi-restraints excluded: chain A residue 2331 THR Chi-restraints excluded: chain A residue 2387 ILE Chi-restraints excluded: chain A residue 2418 CYS Chi-restraints excluded: chain A residue 2427 ILE Chi-restraints excluded: chain A residue 2455 VAL Chi-restraints excluded: chain B residue 612 TYR Chi-restraints excluded: chain B residue 670 SER Chi-restraints excluded: chain B residue 682 ASN Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1042 LEU Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain B residue 1103 THR Chi-restraints excluded: chain B residue 1106 VAL Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain B residue 1268 GLU Chi-restraints excluded: chain B residue 1350 LEU Chi-restraints excluded: chain B residue 1389 VAL Chi-restraints excluded: chain B residue 1390 LEU Chi-restraints excluded: chain B residue 1491 THR Chi-restraints excluded: chain B residue 1541 VAL Chi-restraints excluded: chain B residue 1548 ILE Chi-restraints excluded: chain B residue 1679 VAL Chi-restraints excluded: chain B residue 1697 MET Chi-restraints excluded: chain B residue 1702 MET Chi-restraints excluded: chain B residue 1765 ILE Chi-restraints excluded: chain B residue 1893 VAL Chi-restraints excluded: chain B residue 1916 LEU Chi-restraints excluded: chain B residue 1990 ILE Chi-restraints excluded: chain B residue 2047 ASN Chi-restraints excluded: chain B residue 2086 LEU Chi-restraints excluded: chain B residue 2088 ILE Chi-restraints excluded: chain B residue 2205 VAL Chi-restraints excluded: chain B residue 2323 ILE Chi-restraints excluded: chain B residue 2331 THR Chi-restraints excluded: chain B residue 2387 ILE Chi-restraints excluded: chain B residue 2418 CYS Chi-restraints excluded: chain B residue 2427 ILE Chi-restraints excluded: chain B residue 2448 ILE Chi-restraints excluded: chain B residue 2455 VAL Chi-restraints excluded: chain B residue 2463 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 356 optimal weight: 1.9990 chunk 255 optimal weight: 0.0770 chunk 308 optimal weight: 8.9990 chunk 282 optimal weight: 0.0470 chunk 272 optimal weight: 0.0010 chunk 77 optimal weight: 0.9980 chunk 164 optimal weight: 9.9990 chunk 256 optimal weight: 1.9990 chunk 262 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.3642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1567 ASN A2313 ASN ** A2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 682 ASN ** B1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.139560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.106259 restraints weight = 54375.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.104339 restraints weight = 39106.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.105926 restraints weight = 40818.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.106421 restraints weight = 28486.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.107761 restraints weight = 26078.442| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 28782 Z= 0.103 Angle : 0.582 10.345 38968 Z= 0.285 Chirality : 0.042 0.180 4544 Planarity : 0.004 0.049 4891 Dihedral : 5.691 59.448 3910 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 2.46 % Allowed : 21.12 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.48 (0.14), residues: 3554 helix: -0.42 (0.16), residues: 1148 sheet: -2.74 (0.20), residues: 580 loop : -2.08 (0.14), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1707 TYR 0.017 0.001 TYR B1527 PHE 0.021 0.001 PHE B2326 TRP 0.010 0.001 TRP B1734 HIS 0.003 0.001 HIS B1407 Details of bonding type rmsd covalent geometry : bond 0.00230 (28782) covalent geometry : angle 0.58166 (38968) hydrogen bonds : bond 0.02745 ( 727) hydrogen bonds : angle 4.57722 ( 1905) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 195 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 668 HIS cc_start: 0.8119 (t-90) cc_final: 0.7903 (m90) REVERT: A 679 MET cc_start: 0.8508 (mmm) cc_final: 0.8227 (mmp) REVERT: A 787 ILE cc_start: 0.7672 (mt) cc_final: 0.7406 (tp) REVERT: A 1128 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.6860 (mt) REVERT: A 1364 MET cc_start: 0.3427 (tpt) cc_final: 0.2650 (tmm) REVERT: A 1390 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8194 (pp) REVERT: A 2155 MET cc_start: 0.7337 (ppp) cc_final: 0.7028 (ppp) REVERT: A 2303 LEU cc_start: 0.6772 (OUTLIER) cc_final: 0.6400 (mt) REVERT: A 2315 MET cc_start: 0.5233 (tmm) cc_final: 0.3552 (tmm) REVERT: B 668 HIS cc_start: 0.8152 (t-90) cc_final: 0.7890 (m90) REVERT: B 1128 LEU cc_start: 0.7370 (OUTLIER) cc_final: 0.6741 (mp) REVERT: B 1390 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.7963 (pp) REVERT: B 1832 LYS cc_start: 0.8440 (ttpp) cc_final: 0.8236 (ttpt) REVERT: B 2303 LEU cc_start: 0.7117 (mt) cc_final: 0.6838 (mm) REVERT: B 2323 ILE cc_start: 0.5727 (OUTLIER) cc_final: 0.5474 (pt) outliers start: 77 outliers final: 57 residues processed: 259 average time/residue: 0.1578 time to fit residues: 69.4310 Evaluate side-chains 249 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 186 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 612 TYR Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1128 LEU Chi-restraints excluded: chain A residue 1299 LEU Chi-restraints excluded: chain A residue 1350 LEU Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain A residue 1541 VAL Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain A residue 1679 VAL Chi-restraints excluded: chain A residue 1697 MET Chi-restraints excluded: chain A residue 1702 MET Chi-restraints excluded: chain A residue 1765 ILE Chi-restraints excluded: chain A residue 1893 VAL Chi-restraints excluded: chain A residue 1990 ILE Chi-restraints excluded: chain A residue 2020 ILE Chi-restraints excluded: chain A residue 2035 THR Chi-restraints excluded: chain A residue 2086 LEU Chi-restraints excluded: chain A residue 2088 ILE Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2303 LEU Chi-restraints excluded: chain A residue 2323 ILE Chi-restraints excluded: chain A residue 2331 THR Chi-restraints excluded: chain A residue 2387 ILE Chi-restraints excluded: chain A residue 2418 CYS Chi-restraints excluded: chain A residue 2455 VAL Chi-restraints excluded: chain B residue 612 TYR Chi-restraints excluded: chain B residue 670 SER Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 1042 LEU Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain B residue 1103 THR Chi-restraints excluded: chain B residue 1106 VAL Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain B residue 1299 LEU Chi-restraints excluded: chain B residue 1350 LEU Chi-restraints excluded: chain B residue 1389 VAL Chi-restraints excluded: chain B residue 1390 LEU Chi-restraints excluded: chain B residue 1491 THR Chi-restraints excluded: chain B residue 1541 VAL Chi-restraints excluded: chain B residue 1548 ILE Chi-restraints excluded: chain B residue 1679 VAL Chi-restraints excluded: chain B residue 1697 MET Chi-restraints excluded: chain B residue 1702 MET Chi-restraints excluded: chain B residue 1765 ILE Chi-restraints excluded: chain B residue 1893 VAL Chi-restraints excluded: chain B residue 1916 LEU Chi-restraints excluded: chain B residue 1990 ILE Chi-restraints excluded: chain B residue 2020 ILE Chi-restraints excluded: chain B residue 2035 THR Chi-restraints excluded: chain B residue 2086 LEU Chi-restraints excluded: chain B residue 2088 ILE Chi-restraints excluded: chain B residue 2205 VAL Chi-restraints excluded: chain B residue 2323 ILE Chi-restraints excluded: chain B residue 2387 ILE Chi-restraints excluded: chain B residue 2418 CYS Chi-restraints excluded: chain B residue 2427 ILE Chi-restraints excluded: chain B residue 2455 VAL Chi-restraints excluded: chain B residue 2463 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 208 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 312 optimal weight: 2.9990 chunk 285 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 221 optimal weight: 2.9990 chunk 35 optimal weight: 0.0770 chunk 170 optimal weight: 9.9990 chunk 261 optimal weight: 0.9990 chunk 326 optimal weight: 2.9990 chunk 348 optimal weight: 10.0000 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1567 ASN ** A2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.138548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.105009 restraints weight = 54279.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.103154 restraints weight = 39221.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.104562 restraints weight = 42349.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.105118 restraints weight = 29382.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.106490 restraints weight = 26852.596| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28782 Z= 0.114 Angle : 0.589 9.007 38968 Z= 0.288 Chirality : 0.043 0.169 4544 Planarity : 0.004 0.048 4891 Dihedral : 5.675 59.340 3910 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 2.24 % Allowed : 21.28 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.14), residues: 3554 helix: -0.39 (0.16), residues: 1152 sheet: -2.71 (0.20), residues: 580 loop : -2.06 (0.14), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A2339 TYR 0.013 0.001 TYR A1527 PHE 0.019 0.001 PHE B2326 TRP 0.011 0.001 TRP A1434 HIS 0.003 0.001 HIS B2510 Details of bonding type rmsd covalent geometry : bond 0.00265 (28782) covalent geometry : angle 0.58905 (38968) hydrogen bonds : bond 0.02778 ( 727) hydrogen bonds : angle 4.54341 ( 1905) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 194 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 712 MET cc_start: 0.7777 (mtt) cc_final: 0.7513 (mmt) REVERT: A 787 ILE cc_start: 0.7630 (mt) cc_final: 0.7403 (tp) REVERT: A 1128 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.6848 (mt) REVERT: A 1364 MET cc_start: 0.3678 (tpt) cc_final: 0.2809 (tmm) REVERT: A 1390 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8238 (pp) REVERT: A 2155 MET cc_start: 0.7351 (ppp) cc_final: 0.7029 (ppp) REVERT: A 2303 LEU cc_start: 0.6857 (OUTLIER) cc_final: 0.6488 (mt) REVERT: A 2315 MET cc_start: 0.5170 (tmm) cc_final: 0.3520 (tmm) REVERT: B 1128 LEU cc_start: 0.7352 (OUTLIER) cc_final: 0.6815 (mt) REVERT: B 1390 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8048 (pp) REVERT: B 1832 LYS cc_start: 0.8521 (ttpp) cc_final: 0.8305 (tmmt) REVERT: B 2303 LEU cc_start: 0.7116 (mt) cc_final: 0.6859 (mm) outliers start: 70 outliers final: 60 residues processed: 252 average time/residue: 0.1633 time to fit residues: 69.3529 Evaluate side-chains 251 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 186 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 612 TYR Chi-restraints excluded: chain A residue 745 ILE Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 983 TYR Chi-restraints excluded: chain A residue 1042 LEU Chi-restraints excluded: chain A residue 1128 LEU Chi-restraints excluded: chain A residue 1350 LEU Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain A residue 1491 THR Chi-restraints excluded: chain A residue 1541 VAL Chi-restraints excluded: chain A residue 1548 ILE Chi-restraints excluded: chain A residue 1567 ASN Chi-restraints excluded: chain A residue 1679 VAL Chi-restraints excluded: chain A residue 1697 MET Chi-restraints excluded: chain A residue 1702 MET Chi-restraints excluded: chain A residue 1757 ASN Chi-restraints excluded: chain A residue 1765 ILE Chi-restraints excluded: chain A residue 1893 VAL Chi-restraints excluded: chain A residue 1990 ILE Chi-restraints excluded: chain A residue 2020 ILE Chi-restraints excluded: chain A residue 2035 THR Chi-restraints excluded: chain A residue 2086 LEU Chi-restraints excluded: chain A residue 2088 ILE Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2303 LEU Chi-restraints excluded: chain A residue 2323 ILE Chi-restraints excluded: chain A residue 2331 THR Chi-restraints excluded: chain A residue 2387 ILE Chi-restraints excluded: chain A residue 2418 CYS Chi-restraints excluded: chain A residue 2455 VAL Chi-restraints excluded: chain B residue 612 TYR Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 757 LEU Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 1042 LEU Chi-restraints excluded: chain B residue 1102 LEU Chi-restraints excluded: chain B residue 1103 THR Chi-restraints excluded: chain B residue 1106 VAL Chi-restraints excluded: chain B residue 1128 LEU Chi-restraints excluded: chain B residue 1350 LEU Chi-restraints excluded: chain B residue 1389 VAL Chi-restraints excluded: chain B residue 1390 LEU Chi-restraints excluded: chain B residue 1491 THR Chi-restraints excluded: chain B residue 1541 VAL Chi-restraints excluded: chain B residue 1548 ILE Chi-restraints excluded: chain B residue 1679 VAL Chi-restraints excluded: chain B residue 1697 MET Chi-restraints excluded: chain B residue 1702 MET Chi-restraints excluded: chain B residue 1765 ILE Chi-restraints excluded: chain B residue 1830 LEU Chi-restraints excluded: chain B residue 1893 VAL Chi-restraints excluded: chain B residue 1916 LEU Chi-restraints excluded: chain B residue 1990 ILE Chi-restraints excluded: chain B residue 2020 ILE Chi-restraints excluded: chain B residue 2035 THR Chi-restraints excluded: chain B residue 2086 LEU Chi-restraints excluded: chain B residue 2088 ILE Chi-restraints excluded: chain B residue 2205 VAL Chi-restraints excluded: chain B residue 2323 ILE Chi-restraints excluded: chain B residue 2387 ILE Chi-restraints excluded: chain B residue 2418 CYS Chi-restraints excluded: chain B residue 2427 ILE Chi-restraints excluded: chain B residue 2455 VAL Chi-restraints excluded: chain B residue 2458 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 124 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 271 optimal weight: 20.0000 chunk 356 optimal weight: 1.9990 chunk 3 optimal weight: 0.0030 chunk 33 optimal weight: 0.0070 chunk 8 optimal weight: 5.9990 chunk 68 optimal weight: 0.0000 chunk 144 optimal weight: 20.0000 chunk 95 optimal weight: 5.9990 chunk 212 optimal weight: 5.9990 overall best weight: 1.0016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1303 HIS ** A2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.138317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.105152 restraints weight = 54802.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.103494 restraints weight = 44630.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.104835 restraints weight = 41266.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.105806 restraints weight = 30143.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.106059 restraints weight = 28130.465| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.4612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28782 Z= 0.128 Angle : 0.605 12.326 38968 Z= 0.295 Chirality : 0.043 0.164 4544 Planarity : 0.004 0.061 4891 Dihedral : 5.690 59.232 3910 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 2.30 % Allowed : 21.47 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.14), residues: 3554 helix: -0.40 (0.16), residues: 1162 sheet: -2.56 (0.21), residues: 540 loop : -2.14 (0.14), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B2339 TYR 0.017 0.001 TYR A1527 PHE 0.018 0.001 PHE B2326 TRP 0.012 0.001 TRP B1434 HIS 0.007 0.001 HIS B 668 Details of bonding type rmsd covalent geometry : bond 0.00302 (28782) covalent geometry : angle 0.60513 (38968) hydrogen bonds : bond 0.02804 ( 727) hydrogen bonds : angle 4.54031 ( 1905) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4240.69 seconds wall clock time: 74 minutes 28.16 seconds (4468.16 seconds total)