Starting phenix.real_space_refine on Tue Jun 10 04:16:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gkm_51429/06_2025/9gkm_51429.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gkm_51429/06_2025/9gkm_51429.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gkm_51429/06_2025/9gkm_51429.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gkm_51429/06_2025/9gkm_51429.map" model { file = "/net/cci-nas-00/data/ceres_data/9gkm_51429/06_2025/9gkm_51429.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gkm_51429/06_2025/9gkm_51429.cif" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 7197 2.51 5 N 1911 2.21 5 O 2057 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 11231 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 573 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 579 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "D" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 591 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 9481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1222, 9481 Classifications: {'peptide': 1222} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PCIS': 1, 'PTRANS': 58, 'TRANS': 1162} Chain breaks: 11 Unresolved non-hydrogen bonds: 291 Unresolved non-hydrogen angles: 347 Unresolved non-hydrogen dihedrals: 241 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 22, 'ARG:plan': 9, 'ASP:plan': 9, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 195 Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'SY8': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.64, per 1000 atoms: 0.59 Number of scatterers: 11231 At special positions: 0 Unit cell: (105.549, 142.15, 130.234, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 2057 8.00 N 1911 7.00 C 7197 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 additional links: simple=1, symmetry=0 Simple link: pdb=" C GLY B 75 " - pdb=" N SY8 B2101 " Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.57 Conformation dependent library (CDL) restraints added in 1.4 seconds 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2754 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 8 sheets defined 51.7% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'B' and resid 23 through 34 Processing helix chain 'C' and resid 23 through 34 Processing helix chain 'C' and resid 56 through 59 Processing helix chain 'D' and resid 23 through 34 Processing helix chain 'A' and resid 484 through 495 removed outlier: 3.645A pdb=" N GLN A 489 " --> pdb=" O SER A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 514 Processing helix chain 'A' and resid 526 through 538 Proline residue: A 531 - end of helix Processing helix chain 'A' and resid 543 through 559 removed outlier: 4.436A pdb=" N ASN A 547 " --> pdb=" O PHE A 543 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N HIS A 548 " --> pdb=" O ASP A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 568 removed outlier: 5.305A pdb=" N VAL A 568 " --> pdb=" O SER A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 579 Processing helix chain 'A' and resid 584 through 599 removed outlier: 3.993A pdb=" N ARG A 599 " --> pdb=" O GLU A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 608 Processing helix chain 'A' and resid 610 through 615 removed outlier: 4.964A pdb=" N LEU A 615 " --> pdb=" O LEU A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 638 removed outlier: 4.065A pdb=" N ARG A 627 " --> pdb=" O ILE A 623 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ASN A 628 " --> pdb=" O ASN A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 649 Processing helix chain 'A' and resid 651 through 659 Processing helix chain 'A' and resid 664 through 681 Processing helix chain 'A' and resid 685 through 692 Processing helix chain 'A' and resid 694 through 705 removed outlier: 4.160A pdb=" N THR A 698 " --> pdb=" O LYS A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 729 Processing helix chain 'A' and resid 731 through 739 Processing helix chain 'A' and resid 742 through 751 Processing helix chain 'A' and resid 769 through 782 Processing helix chain 'A' and resid 793 through 798 removed outlier: 4.270A pdb=" N MET A 797 " --> pdb=" O ALA A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 874 Processing helix chain 'A' and resid 876 through 895 removed outlier: 5.151A pdb=" N GLY A 888 " --> pdb=" O LYS A 884 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N VAL A 889 " --> pdb=" O THR A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 916 removed outlier: 3.717A pdb=" N HIS A 904 " --> pdb=" O PRO A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 926 Processing helix chain 'A' and resid 931 through 939 Processing helix chain 'A' and resid 944 through 960 removed outlier: 5.179A pdb=" N VAL A 948 " --> pdb=" O LEU A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 966 removed outlier: 3.778A pdb=" N SER A 966 " --> pdb=" O ASP A 963 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 963 through 966' Processing helix chain 'A' and resid 967 through 972 Processing helix chain 'A' and resid 974 through 983 Processing helix chain 'A' and resid 1132 through 1152 Processing helix chain 'A' and resid 1167 through 1178 removed outlier: 3.654A pdb=" N GLN A1177 " --> pdb=" O ALA A1173 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A1178 " --> pdb=" O ALA A1174 " (cutoff:3.500A) Processing helix chain 'A' and resid 1187 through 1198 Processing helix chain 'A' and resid 1204 through 1209 Processing helix chain 'A' and resid 1211 through 1220 Processing helix chain 'A' and resid 1230 through 1241 Processing helix chain 'A' and resid 1261 through 1277 Processing helix chain 'A' and resid 1306 through 1312 Processing helix chain 'A' and resid 1343 through 1351 Processing helix chain 'A' and resid 1406 through 1414 Processing helix chain 'A' and resid 1435 through 1440 Processing helix chain 'A' and resid 1484 through 1488 Processing helix chain 'A' and resid 1498 through 1502 Processing helix chain 'A' and resid 1517 through 1532 Processing helix chain 'A' and resid 1555 through 1564 Processing helix chain 'A' and resid 1567 through 1572 Processing helix chain 'A' and resid 1577 through 1586 Processing helix chain 'A' and resid 1592 through 1603 Processing helix chain 'A' and resid 1606 through 1616 Processing helix chain 'A' and resid 1646 through 1657 Processing helix chain 'A' and resid 1676 through 1691 removed outlier: 4.307A pdb=" N GLN A1691 " --> pdb=" O SER A1687 " (cutoff:3.500A) Processing helix chain 'A' and resid 1735 through 1757 removed outlier: 3.524A pdb=" N MET A1757 " --> pdb=" O ALA A1753 " (cutoff:3.500A) Processing helix chain 'A' and resid 1768 through 1775 Processing helix chain 'A' and resid 1783 through 1789 removed outlier: 3.832A pdb=" N PHE A1787 " --> pdb=" O HIS A1784 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP A1788 " --> pdb=" O ASP A1785 " (cutoff:3.500A) Processing helix chain 'A' and resid 1792 through 1812 removed outlier: 3.925A pdb=" N SER A1796 " --> pdb=" O VAL A1792 " (cutoff:3.500A) Processing helix chain 'A' and resid 1818 through 1827 Processing helix chain 'A' and resid 1834 through 1838 Processing helix chain 'A' and resid 1866 through 1879 Processing helix chain 'A' and resid 1883 through 1893 Processing helix chain 'A' and resid 1907 through 1915 removed outlier: 5.117A pdb=" N ASP A1911 " --> pdb=" O PRO A1907 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N GLN A1912 " --> pdb=" O GLU A1908 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A1913 " --> pdb=" O GLU A1909 " (cutoff:3.500A) Processing helix chain 'A' and resid 1924 through 1930 removed outlier: 4.694A pdb=" N GLU A1929 " --> pdb=" O LYS A1925 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N CYS A1930 " --> pdb=" O THR A1926 " (cutoff:3.500A) Processing helix chain 'A' and resid 1942 through 1953 removed outlier: 3.888A pdb=" N SER A1952 " --> pdb=" O PHE A1948 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N SER A1953 " --> pdb=" O GLU A1949 " (cutoff:3.500A) Processing helix chain 'A' and resid 1956 through 1967 Processing helix chain 'A' and resid 1976 through 1979 Processing helix chain 'A' and resid 2019 through 2032 removed outlier: 3.975A pdb=" N ILE A2028 " --> pdb=" O GLU A2024 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 11 through 17 removed outlier: 5.107A pdb=" N LYS B 11 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N VAL B 17 " --> pdb=" O MET B 1 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N MET B 1 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N SER B 65 " --> pdb=" O GLN B 2 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N HIS B 68 " --> pdb=" O PHE B 45 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N PHE B 45 " --> pdb=" O HIS B 68 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL B 70 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N LEU B 43 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ARG B 72 " --> pdb=" O GLN B 41 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N GLN B 41 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N LEU B 43 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 17 removed outlier: 4.631A pdb=" N LYS C 11 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR C 7 " --> pdb=" O LYS C 11 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU C 64 " --> pdb=" O GLN C 2 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N PHE C 4 " --> pdb=" O GLU C 64 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N THR C 66 " --> pdb=" O PHE C 4 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N LYS C 6 " --> pdb=" O THR C 66 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N HIS C 68 " --> pdb=" O LYS C 6 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N HIS C 68 " --> pdb=" O PHE C 45 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N PHE C 45 " --> pdb=" O HIS C 68 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N VAL C 70 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N LEU C 43 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ARG C 72 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLN C 41 " --> pdb=" O ARG C 72 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LEU C 43 " --> pdb=" O LEU C 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 10 through 17 removed outlier: 5.656A pdb=" N LYS D 11 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N THR D 7 " --> pdb=" O LYS D 11 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N MET D 1 " --> pdb=" O VAL D 17 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N PHE D 4 " --> pdb=" O GLU D 64 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR D 66 " --> pdb=" O PHE D 4 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LYS D 6 " --> pdb=" O THR D 66 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N HIS D 68 " --> pdb=" O LYS D 6 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N HIS D 68 " --> pdb=" O PHE D 45 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N PHE D 45 " --> pdb=" O HIS D 68 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL D 70 " --> pdb=" O LEU D 43 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU D 43 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ARG D 72 " --> pdb=" O GLN D 41 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N GLN D 41 " --> pdb=" O ARG D 72 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N LEU D 43 " --> pdb=" O LEU D 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1334 through 1337 removed outlier: 4.706A pdb=" N HIS A1442 " --> pdb=" O LYS A1315 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE A1444 " --> pdb=" O GLN A1317 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN A1319 " --> pdb=" O ILE A1444 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR A1446 " --> pdb=" O GLN A1319 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE A1396 " --> pdb=" O HIS A1399 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1636 through 1641 removed outlier: 6.062A pdb=" N LYS A1637 " --> pdb=" O GLU A1665 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N GLN A1667 " --> pdb=" O LYS A1637 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ARG A1639 " --> pdb=" O GLN A1667 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 1701 through 1704 Processing sheet with id=AA7, first strand: chain 'A' and resid 1842 through 1844 removed outlier: 8.839A pdb=" N PHE A1842 " --> pdb=" O LEU A1852 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ILE A1850 " --> pdb=" O LEU A1844 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1933 through 1935 removed outlier: 4.373A pdb=" N ARG A1988 " --> pdb=" O ASP A1934 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR A1985 " --> pdb=" O ASN A2009 " (cutoff:3.500A) 500 hydrogen bonds defined for protein. 1461 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: 3.48 Time building geometry restraints manager: 3.08 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: 2376 1.33 - 1.45: 2381 1.45 - 1.57: 6580 1.57 - 1.69: 0 1.69 - 1.81: 105 Bond restraints: 11442 Sorted by residual: bond pdb=" N SY8 B2101 " pdb=" C4 SY8 B2101 " ideal model delta sigma weight residual 1.456 1.486 -0.030 2.00e-02 2.50e+03 2.28e+00 bond pdb=" C PRO B 37 " pdb=" N PRO B 38 " ideal model delta sigma weight residual 1.334 1.367 -0.033 2.34e-02 1.83e+03 1.95e+00 bond pdb=" N ASN C 60 " pdb=" CA ASN C 60 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.46e+00 bond pdb=" CB ASN C 60 " pdb=" CG ASN C 60 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.98e-01 bond pdb=" CB CYS A1273 " pdb=" SG CYS A1273 " ideal model delta sigma weight residual 1.808 1.781 0.027 3.30e-02 9.18e+02 6.57e-01 ... (remaining 11437 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 15067 1.23 - 2.46: 333 2.46 - 3.69: 86 3.69 - 4.92: 16 4.92 - 6.15: 11 Bond angle restraints: 15513 Sorted by residual: angle pdb=" N LYS A 945 " pdb=" CA LYS A 945 " pdb=" C LYS A 945 " ideal model delta sigma weight residual 114.04 107.89 6.15 1.24e+00 6.50e-01 2.46e+01 angle pdb=" N VAL A1672 " pdb=" CA VAL A1672 " pdb=" C VAL A1672 " ideal model delta sigma weight residual 113.42 108.76 4.66 1.17e+00 7.31e-01 1.59e+01 angle pdb=" C ILE A 571 " pdb=" CA ILE A 571 " pdb=" CB ILE A 571 " ideal model delta sigma weight residual 113.70 110.77 2.93 9.50e-01 1.11e+00 9.53e+00 angle pdb=" C ALA A 570 " pdb=" N ILE A 571 " pdb=" CA ILE A 571 " ideal model delta sigma weight residual 120.43 123.27 -2.84 9.60e-01 1.09e+00 8.75e+00 angle pdb=" CA VAL A1672 " pdb=" C VAL A1672 " pdb=" N GLY A1673 " ideal model delta sigma weight residual 118.90 116.48 2.42 9.40e-01 1.13e+00 6.60e+00 ... (remaining 15508 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.18: 6684 27.18 - 54.36: 235 54.36 - 81.54: 25 81.54 - 108.72: 5 108.72 - 135.91: 3 Dihedral angle restraints: 6952 sinusoidal: 2731 harmonic: 4221 Sorted by residual: dihedral pdb=" C SY8 B2101 " pdb=" C1 SY8 B2101 " pdb=" C2 SY8 B2101 " pdb=" C3 SY8 B2101 " ideal model delta sinusoidal sigma weight residual 62.79 -161.30 -135.91 1 3.00e+01 1.11e-03 1.83e+01 dihedral pdb=" O SY8 B2101 " pdb=" C1 SY8 B2101 " pdb=" C2 SY8 B2101 " pdb=" C3 SY8 B2101 " ideal model delta sinusoidal sigma weight residual -116.28 18.85 -135.13 1 3.00e+01 1.11e-03 1.82e+01 dihedral pdb=" N SY8 B2101 " pdb=" C3 SY8 B2101 " pdb=" C4 SY8 B2101 " pdb=" C2 SY8 B2101 " ideal model delta sinusoidal sigma weight residual -59.10 63.17 -122.27 1 3.00e+01 1.11e-03 1.64e+01 ... (remaining 6949 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1188 0.030 - 0.061: 432 0.061 - 0.091: 128 0.091 - 0.121: 60 0.121 - 0.151: 10 Chirality restraints: 1818 Sorted by residual: chirality pdb=" CA ASN A 741 " pdb=" N ASN A 741 " pdb=" C ASN A 741 " pdb=" CB ASN A 741 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.72e-01 chirality pdb=" CA ASN C 60 " pdb=" N ASN C 60 " pdb=" C ASN C 60 " pdb=" CB ASN C 60 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.50e-01 chirality pdb=" CA LEU A 886 " pdb=" N LEU A 886 " pdb=" C LEU A 886 " pdb=" CB LEU A 886 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.78e-01 ... (remaining 1815 not shown) Planarity restraints: 1985 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A1847 " -0.032 5.00e-02 4.00e+02 4.92e-02 3.87e+00 pdb=" N PRO A1848 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO A1848 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A1848 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A1956 " -0.009 2.00e-02 2.50e+03 1.86e-02 3.48e+00 pdb=" C ASN A1956 " 0.032 2.00e-02 2.50e+03 pdb=" O ASN A1956 " -0.012 2.00e-02 2.50e+03 pdb=" N GLU A1957 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A1677 " 0.027 5.00e-02 4.00e+02 4.15e-02 2.75e+00 pdb=" N PRO A1678 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A1678 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A1678 " 0.023 5.00e-02 4.00e+02 ... (remaining 1982 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1319 2.75 - 3.29: 10606 3.29 - 3.83: 17551 3.83 - 4.36: 18860 4.36 - 4.90: 34058 Nonbonded interactions: 82394 Sorted by model distance: nonbonded pdb=" O THR A1938 " pdb=" OG SER A1941 " model vdw 2.216 3.040 nonbonded pdb=" OG1 THR A1862 " pdb=" OD1 ASN A1865 " model vdw 2.258 3.040 nonbonded pdb=" OG1 THR B 22 " pdb=" OE1 GLU B 24 " model vdw 2.270 3.040 nonbonded pdb=" O GLN D 62 " pdb=" OG SER D 65 " model vdw 2.285 3.040 nonbonded pdb=" O ARG A1795 " pdb=" ND1 HIS A1799 " model vdw 2.317 3.120 ... (remaining 82389 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 'B' and (resid 1 through 28 or resid 30 through 47 or resid 49 through 71 \ or (resid 72 and (name N or name CA or name C or name O or name CB )) or resid \ 73)) selection = (chain 'C' and (resid 1 or (resid 2 and (name N or name CA or name C or name O o \ r name CB )) or resid 3 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 28 or resid 30 through 32 or (resid \ 33 through 34 and (name N or name CA or name C or name O or name CB )) or resid \ 35 through 47 or resid 49 through 62 or (resid 63 through 64 and (name N or nam \ e CA or name C or name O or name CB )) or resid 65 through 71 or (resid 72 and ( \ name N or name CA or name C or name O or name CB )) or resid 73)) selection = (chain 'D' and (resid 1 or (resid 2 and (name N or name CA or name C or name O o \ r name CB )) or resid 3 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 28 or resid 30 through 32 or (resid \ 33 through 34 and (name N or name CA or name C or name O or name CB )) or resid \ 35 through 47 or resid 49 through 62 or (resid 63 through 64 and (name N or nam \ e CA or name C or name O or name CB )) or resid 65 through 73)) } 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: 2.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.550 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 11446 Z= 0.165 Angle : 0.499 6.154 15515 Z= 0.266 Chirality : 0.038 0.151 1818 Planarity : 0.004 0.049 1984 Dihedral : 13.897 135.905 4197 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.24), residues: 1416 helix: 1.79 (0.20), residues: 746 sheet: 0.42 (0.55), residues: 108 loop : -1.02 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1773 HIS 0.002 0.000 HIS A 747 PHE 0.015 0.001 PHE A 723 TYR 0.009 0.001 TYR A1668 ARG 0.005 0.000 ARG A1760 Details of bonding type rmsd link_TRANS : bond 0.00614 ( 1) link_TRANS : angle 3.86433 ( 2) hydrogen bonds : bond 0.07510 ( 500) hydrogen bonds : angle 3.92732 ( 1461) covalent geometry : bond 0.00220 (11442) covalent geometry : angle 0.49731 (15513) Misc. bond : bond 0.07921 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.4404 (ttt) cc_final: 0.3520 (ppp) REVERT: C 6 LYS cc_start: 0.7820 (pttp) cc_final: 0.7501 (ttpp) REVERT: C 24 GLU cc_start: 0.7779 (tt0) cc_final: 0.7525 (tm-30) REVERT: A 492 GLN cc_start: 0.7969 (mp10) cc_final: 0.7715 (mp10) REVERT: A 504 GLN cc_start: 0.8260 (mm-40) cc_final: 0.7912 (mm-40) REVERT: A 521 LEU cc_start: 0.7986 (mt) cc_final: 0.7712 (mt) REVERT: A 556 MET cc_start: 0.7812 (tpp) cc_final: 0.7589 (ttm) REVERT: A 597 LEU cc_start: 0.8491 (mt) cc_final: 0.8256 (mt) REVERT: A 622 SER cc_start: 0.8455 (t) cc_final: 0.8066 (p) REVERT: A 678 VAL cc_start: 0.7977 (t) cc_final: 0.7772 (p) REVERT: A 679 ASP cc_start: 0.7544 (t70) cc_final: 0.7070 (t0) REVERT: A 872 MET cc_start: 0.2686 (ttm) cc_final: 0.1819 (ttm) REVERT: A 889 VAL cc_start: 0.8213 (t) cc_final: 0.8008 (p) REVERT: A 1153 PHE cc_start: 0.6433 (m-80) cc_final: 0.6076 (m-80) REVERT: A 1200 ASP cc_start: 0.6433 (p0) cc_final: 0.6214 (p0) REVERT: A 1254 ARG cc_start: 0.6914 (ttp-170) cc_final: 0.6389 (ttp-170) REVERT: A 1539 ASN cc_start: 0.7927 (t0) cc_final: 0.7476 (t0) REVERT: A 1543 LYS cc_start: 0.7760 (ttpp) cc_final: 0.7341 (ttpp) REVERT: A 1571 MET cc_start: 0.7001 (mmm) cc_final: 0.6555 (mmm) REVERT: A 1639 ARG cc_start: 0.7479 (mmt90) cc_final: 0.7210 (mmm-85) REVERT: A 1698 TRP cc_start: 0.8142 (m100) cc_final: 0.7092 (m100) REVERT: A 1746 ARG cc_start: 0.7929 (mtp85) cc_final: 0.7588 (mtp85) REVERT: A 1760 ARG cc_start: 0.8108 (mmt90) cc_final: 0.7878 (mpt-90) REVERT: A 1789 ILE cc_start: 0.7935 (mm) cc_final: 0.7621 (mt) REVERT: A 1812 GLN cc_start: 0.8225 (mm110) cc_final: 0.7768 (mm-40) REVERT: A 1836 GLU cc_start: 0.7793 (tp30) cc_final: 0.7518 (tp30) REVERT: A 1851 GLU cc_start: 0.6790 (mm-30) cc_final: 0.6461 (mm-30) REVERT: A 1854 LYS cc_start: 0.7723 (tptm) cc_final: 0.7431 (ttmm) REVERT: A 1997 PRO cc_start: 0.7213 (Cg_endo) cc_final: 0.6916 (Cg_exo) REVERT: A 2018 SER cc_start: 0.8713 (t) cc_final: 0.8312 (p) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.2375 time to fit residues: 75.0762 Evaluate side-chains 209 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 57 optimal weight: 0.0570 chunk 112 optimal weight: 0.0980 chunk 43 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 83 optimal weight: 40.0000 chunk 129 optimal weight: 0.0070 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 538 GLN A 980 HIS A1146 HIS A1272 ASN A2038 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.161383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.126166 restraints weight = 18405.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.128353 restraints weight = 10411.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.129969 restraints weight = 7692.740| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.0638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11446 Z= 0.100 Angle : 0.478 6.526 15515 Z= 0.242 Chirality : 0.038 0.152 1818 Planarity : 0.004 0.053 1984 Dihedral : 5.511 99.028 1537 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.91 % Allowed : 6.61 % Favored : 92.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.24), residues: 1416 helix: 1.79 (0.20), residues: 741 sheet: 0.66 (0.52), residues: 123 loop : -1.03 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1773 HIS 0.006 0.000 HIS A 980 PHE 0.021 0.001 PHE A1242 TYR 0.010 0.001 TYR A1668 ARG 0.004 0.000 ARG A1760 Details of bonding type rmsd link_TRANS : bond 0.00212 ( 1) link_TRANS : angle 0.56589 ( 2) hydrogen bonds : bond 0.03218 ( 500) hydrogen bonds : angle 3.85306 ( 1461) covalent geometry : bond 0.00226 (11442) covalent geometry : angle 0.47828 (15513) Misc. bond : bond 0.00198 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 214 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.4569 (ttt) cc_final: 0.3609 (ppp) REVERT: C 6 LYS cc_start: 0.7875 (pttp) cc_final: 0.7509 (ttpp) REVERT: C 24 GLU cc_start: 0.7829 (tt0) cc_final: 0.7589 (tm-30) REVERT: A 504 GLN cc_start: 0.8330 (mm-40) cc_final: 0.7941 (mm-40) REVERT: A 521 LEU cc_start: 0.7993 (mt) cc_final: 0.7738 (mt) REVERT: A 615 LEU cc_start: 0.7638 (mp) cc_final: 0.7298 (mp) REVERT: A 622 SER cc_start: 0.8394 (t) cc_final: 0.8009 (p) REVERT: A 679 ASP cc_start: 0.7542 (t70) cc_final: 0.7074 (t0) REVERT: A 872 MET cc_start: 0.2710 (ttm) cc_final: 0.1793 (ttm) REVERT: A 889 VAL cc_start: 0.8277 (t) cc_final: 0.8041 (p) REVERT: A 1153 PHE cc_start: 0.6398 (m-80) cc_final: 0.6060 (m-80) REVERT: A 1254 ARG cc_start: 0.7001 (ttp-170) cc_final: 0.6445 (ttp-170) REVERT: A 1539 ASN cc_start: 0.7877 (t0) cc_final: 0.7485 (t0) REVERT: A 1543 LYS cc_start: 0.7843 (ttpp) cc_final: 0.7408 (ttpp) REVERT: A 1639 ARG cc_start: 0.7488 (mmt90) cc_final: 0.7241 (mmm-85) REVERT: A 1642 ASN cc_start: 0.7723 (t0) cc_final: 0.7469 (t0) REVERT: A 1668 TYR cc_start: 0.7408 (m-80) cc_final: 0.6883 (m-10) REVERT: A 1698 TRP cc_start: 0.8157 (m100) cc_final: 0.7088 (m100) REVERT: A 1746 ARG cc_start: 0.7864 (mtp85) cc_final: 0.7585 (mtp85) REVERT: A 1760 ARG cc_start: 0.8109 (mmt90) cc_final: 0.7888 (mpt-90) REVERT: A 1789 ILE cc_start: 0.7895 (mm) cc_final: 0.7540 (mt) REVERT: A 1812 GLN cc_start: 0.8245 (mm110) cc_final: 0.7787 (mm-40) REVERT: A 1836 GLU cc_start: 0.7865 (tp30) cc_final: 0.7594 (tp30) REVERT: A 1851 GLU cc_start: 0.6278 (mm-30) cc_final: 0.6054 (mm-30) REVERT: A 1854 LYS cc_start: 0.7761 (tptm) cc_final: 0.7429 (ttmm) REVERT: A 1957 GLU cc_start: 0.6549 (tm-30) cc_final: 0.6315 (tm-30) REVERT: A 1997 PRO cc_start: 0.7304 (Cg_endo) cc_final: 0.6990 (Cg_exo) REVERT: A 2018 SER cc_start: 0.8737 (t) cc_final: 0.8261 (p) outliers start: 11 outliers final: 7 residues processed: 217 average time/residue: 0.2475 time to fit residues: 76.2079 Evaluate side-chains 214 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 207 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 683 HIS Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 1172 CYS Chi-restraints excluded: chain A residue 1538 ASP Chi-restraints excluded: chain A residue 1928 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 26 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 120 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 118 optimal weight: 0.4980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1272 ASN A2038 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.155780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.121488 restraints weight = 18565.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.122168 restraints weight = 10029.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.123969 restraints weight = 7240.693| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 11446 Z= 0.258 Angle : 0.610 6.801 15515 Z= 0.312 Chirality : 0.043 0.168 1818 Planarity : 0.005 0.058 1984 Dihedral : 5.240 83.644 1537 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 1.57 % Allowed : 8.51 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.23), residues: 1416 helix: 1.26 (0.20), residues: 730 sheet: 0.54 (0.51), residues: 124 loop : -0.94 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1773 HIS 0.006 0.001 HIS C 68 PHE 0.035 0.003 PHE A1148 TYR 0.016 0.002 TYR A1717 ARG 0.004 0.000 ARG A1639 Details of bonding type rmsd link_TRANS : bond 0.00026 ( 1) link_TRANS : angle 0.63244 ( 2) hydrogen bonds : bond 0.05696 ( 500) hydrogen bonds : angle 4.36777 ( 1461) covalent geometry : bond 0.00622 (11442) covalent geometry : angle 0.61041 (15513) Misc. bond : bond 0.00086 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 213 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.4624 (ttt) cc_final: 0.3450 (ptt) REVERT: C 6 LYS cc_start: 0.7928 (pttp) cc_final: 0.7590 (ttpp) REVERT: C 24 GLU cc_start: 0.7851 (tt0) cc_final: 0.7598 (tm-30) REVERT: D 1 MET cc_start: 0.0418 (ptm) cc_final: -0.0598 (ptm) REVERT: A 504 GLN cc_start: 0.8288 (mm-40) cc_final: 0.7928 (mm-40) REVERT: A 615 LEU cc_start: 0.7760 (mp) cc_final: 0.7408 (mp) REVERT: A 622 SER cc_start: 0.8542 (t) cc_final: 0.8189 (p) REVERT: A 723 PHE cc_start: 0.8242 (OUTLIER) cc_final: 0.7864 (m-10) REVERT: A 872 MET cc_start: 0.2728 (ttm) cc_final: 0.1733 (ttm) REVERT: A 889 VAL cc_start: 0.8270 (t) cc_final: 0.8033 (p) REVERT: A 958 MET cc_start: 0.7259 (tmm) cc_final: 0.6857 (tmm) REVERT: A 1153 PHE cc_start: 0.6617 (m-80) cc_final: 0.6331 (m-80) REVERT: A 1254 ARG cc_start: 0.7007 (ttp-170) cc_final: 0.6494 (ttp-170) REVERT: A 1539 ASN cc_start: 0.7949 (t0) cc_final: 0.7593 (t0) REVERT: A 1543 LYS cc_start: 0.7842 (ttpp) cc_final: 0.7451 (ttpp) REVERT: A 1668 TYR cc_start: 0.7542 (m-80) cc_final: 0.7076 (m-80) REVERT: A 1698 TRP cc_start: 0.8090 (m100) cc_final: 0.7101 (m100) REVERT: A 1746 ARG cc_start: 0.7884 (mtp85) cc_final: 0.7619 (mtp85) REVERT: A 1752 MET cc_start: 0.8069 (mtp) cc_final: 0.7819 (mtp) REVERT: A 1854 LYS cc_start: 0.7789 (tptm) cc_final: 0.7498 (ttmt) REVERT: A 1957 GLU cc_start: 0.6665 (tm-30) cc_final: 0.6346 (tm-30) REVERT: A 1997 PRO cc_start: 0.7483 (Cg_endo) cc_final: 0.7200 (Cg_exo) REVERT: A 2018 SER cc_start: 0.8704 (t) cc_final: 0.8181 (p) outliers start: 19 outliers final: 13 residues processed: 220 average time/residue: 0.2252 time to fit residues: 71.1214 Evaluate side-chains 223 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 209 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 583 CYS Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 723 PHE Chi-restraints excluded: chain A residue 726 MET Chi-restraints excluded: chain A residue 1172 CYS Chi-restraints excluded: chain A residue 1491 CYS Chi-restraints excluded: chain A residue 1538 ASP Chi-restraints excluded: chain A residue 1928 MET Chi-restraints excluded: chain A residue 1939 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 106 optimal weight: 0.0770 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 55 optimal weight: 0.2980 chunk 134 optimal weight: 4.9990 chunk 25 optimal weight: 0.0980 chunk 53 optimal weight: 0.6980 chunk 104 optimal weight: 0.9980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1272 ASN A1691 GLN A1939 HIS A2038 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.158949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.123200 restraints weight = 18395.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.126399 restraints weight = 10184.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.128419 restraints weight = 6928.371| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11446 Z= 0.107 Angle : 0.486 6.898 15515 Z= 0.249 Chirality : 0.038 0.152 1818 Planarity : 0.004 0.060 1984 Dihedral : 4.783 84.531 1537 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.73 % Allowed : 10.32 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.24), residues: 1416 helix: 1.59 (0.20), residues: 730 sheet: 0.58 (0.52), residues: 123 loop : -0.90 (0.28), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1486 HIS 0.002 0.000 HIS A1487 PHE 0.021 0.001 PHE A1242 TYR 0.011 0.001 TYR A1668 ARG 0.002 0.000 ARG A1760 Details of bonding type rmsd link_TRANS : bond 0.00058 ( 1) link_TRANS : angle 0.34483 ( 2) hydrogen bonds : bond 0.03614 ( 500) hydrogen bonds : angle 4.01060 ( 1461) covalent geometry : bond 0.00242 (11442) covalent geometry : angle 0.48557 (15513) Misc. bond : bond 0.00070 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 206 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.4107 (ttt) cc_final: 0.3197 (ptm) REVERT: C 6 LYS cc_start: 0.7886 (pttp) cc_final: 0.7527 (ttpp) REVERT: C 24 GLU cc_start: 0.7742 (tt0) cc_final: 0.7511 (tm-30) REVERT: A 495 GLN cc_start: 0.7598 (pm20) cc_final: 0.7300 (pm20) REVERT: A 504 GLN cc_start: 0.8221 (mm-40) cc_final: 0.7868 (mm-40) REVERT: A 515 MET cc_start: 0.8703 (mmt) cc_final: 0.8268 (mmt) REVERT: A 615 LEU cc_start: 0.7723 (mp) cc_final: 0.7435 (mp) REVERT: A 622 SER cc_start: 0.8465 (t) cc_final: 0.8086 (p) REVERT: A 679 ASP cc_start: 0.7446 (t70) cc_final: 0.7031 (t0) REVERT: A 783 MET cc_start: 0.7346 (tpp) cc_final: 0.7117 (mmm) REVERT: A 872 MET cc_start: 0.2731 (ttm) cc_final: 0.1704 (ttm) REVERT: A 889 VAL cc_start: 0.8232 (t) cc_final: 0.7980 (p) REVERT: A 958 MET cc_start: 0.7229 (tmm) cc_final: 0.6810 (tmm) REVERT: A 1153 PHE cc_start: 0.6487 (m-80) cc_final: 0.6243 (m-80) REVERT: A 1254 ARG cc_start: 0.6949 (ttp-170) cc_final: 0.6504 (ttp-170) REVERT: A 1539 ASN cc_start: 0.7931 (t0) cc_final: 0.7579 (t0) REVERT: A 1668 TYR cc_start: 0.7513 (m-80) cc_final: 0.7201 (m-80) REVERT: A 1698 TRP cc_start: 0.8093 (m100) cc_final: 0.7053 (m100) REVERT: A 1746 ARG cc_start: 0.7858 (mtp85) cc_final: 0.7625 (mtp85) REVERT: A 1752 MET cc_start: 0.7980 (mtp) cc_final: 0.7778 (mtm) REVERT: A 1854 LYS cc_start: 0.7734 (tptm) cc_final: 0.7434 (tppt) REVERT: A 1865 ASN cc_start: 0.7436 (p0) cc_final: 0.6611 (p0) REVERT: A 1957 GLU cc_start: 0.6386 (tm-30) cc_final: 0.6039 (tm-30) REVERT: A 1997 PRO cc_start: 0.7389 (Cg_endo) cc_final: 0.7101 (Cg_exo) REVERT: A 2018 SER cc_start: 0.8683 (t) cc_final: 0.8222 (p) outliers start: 21 outliers final: 14 residues processed: 213 average time/residue: 0.2399 time to fit residues: 73.1005 Evaluate side-chains 215 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 201 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 683 HIS Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 1172 CYS Chi-restraints excluded: chain A residue 1491 CYS Chi-restraints excluded: chain A residue 1538 ASP Chi-restraints excluded: chain A residue 1541 MET Chi-restraints excluded: chain A residue 1704 THR Chi-restraints excluded: chain A residue 1743 MET Chi-restraints excluded: chain A residue 1928 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 131 optimal weight: 0.9980 chunk 79 optimal weight: 20.0000 chunk 132 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 19 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1272 ASN A2038 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.156488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.121149 restraints weight = 18340.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.123808 restraints weight = 10176.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.124147 restraints weight = 7602.941| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 11446 Z= 0.201 Angle : 0.552 6.506 15515 Z= 0.283 Chirality : 0.041 0.164 1818 Planarity : 0.005 0.061 1984 Dihedral : 4.875 93.360 1537 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.39 % Allowed : 10.73 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.24), residues: 1416 helix: 1.38 (0.20), residues: 730 sheet: 0.48 (0.52), residues: 124 loop : -0.94 (0.28), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A1773 HIS 0.004 0.001 HIS C 68 PHE 0.028 0.002 PHE A1148 TYR 0.016 0.001 TYR A1937 ARG 0.002 0.000 ARG A1606 Details of bonding type rmsd link_TRANS : bond 0.00087 ( 1) link_TRANS : angle 0.47694 ( 2) hydrogen bonds : bond 0.04992 ( 500) hydrogen bonds : angle 4.21089 ( 1461) covalent geometry : bond 0.00482 (11442) covalent geometry : angle 0.55237 (15513) Misc. bond : bond 0.00065 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 206 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.4803 (ttt) cc_final: 0.3739 (ptm) REVERT: C 24 GLU cc_start: 0.7811 (tt0) cc_final: 0.7561 (tm-30) REVERT: A 504 GLN cc_start: 0.8336 (mm-40) cc_final: 0.7965 (mm-40) REVERT: A 515 MET cc_start: 0.8699 (mmt) cc_final: 0.8295 (mmt) REVERT: A 615 LEU cc_start: 0.7852 (mp) cc_final: 0.7504 (mp) REVERT: A 622 SER cc_start: 0.8527 (t) cc_final: 0.8142 (p) REVERT: A 783 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.6226 (mpp) REVERT: A 872 MET cc_start: 0.2855 (ttm) cc_final: 0.1758 (ttm) REVERT: A 889 VAL cc_start: 0.8236 (t) cc_final: 0.7982 (p) REVERT: A 958 MET cc_start: 0.7417 (tmm) cc_final: 0.6632 (tmm) REVERT: A 1153 PHE cc_start: 0.6607 (m-80) cc_final: 0.6369 (m-80) REVERT: A 1200 ASP cc_start: 0.6845 (p0) cc_final: 0.6605 (p0) REVERT: A 1254 ARG cc_start: 0.7037 (ttp-170) cc_final: 0.6593 (ttp-170) REVERT: A 1539 ASN cc_start: 0.7957 (t0) cc_final: 0.7587 (t0) REVERT: A 1698 TRP cc_start: 0.8081 (m100) cc_final: 0.7077 (m100) REVERT: A 1746 ARG cc_start: 0.7850 (mtp85) cc_final: 0.7605 (mtp85) REVERT: A 1752 MET cc_start: 0.8067 (mtp) cc_final: 0.7812 (mtp) REVERT: A 1854 LYS cc_start: 0.7762 (tptm) cc_final: 0.7476 (tppt) REVERT: A 1957 GLU cc_start: 0.6644 (tm-30) cc_final: 0.6274 (tm-30) REVERT: A 1997 PRO cc_start: 0.7481 (Cg_endo) cc_final: 0.7193 (Cg_exo) REVERT: A 2018 SER cc_start: 0.8704 (t) cc_final: 0.8203 (p) outliers start: 29 outliers final: 21 residues processed: 215 average time/residue: 0.2704 time to fit residues: 84.5778 Evaluate side-chains 227 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 205 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain A residue 583 CYS Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 783 MET Chi-restraints excluded: chain A residue 1172 CYS Chi-restraints excluded: chain A residue 1491 CYS Chi-restraints excluded: chain A residue 1534 TYR Chi-restraints excluded: chain A residue 1538 ASP Chi-restraints excluded: chain A residue 1541 MET Chi-restraints excluded: chain A residue 1704 THR Chi-restraints excluded: chain A residue 1803 ILE Chi-restraints excluded: chain A residue 1817 THR Chi-restraints excluded: chain A residue 1928 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 121 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 80 optimal weight: 0.0670 chunk 101 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1272 ASN A2038 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.157325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.122298 restraints weight = 18604.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.124271 restraints weight = 10238.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.125889 restraints weight = 7442.427| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11446 Z= 0.147 Angle : 0.514 6.918 15515 Z= 0.263 Chirality : 0.039 0.165 1818 Planarity : 0.004 0.063 1984 Dihedral : 4.758 95.138 1537 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.06 % Allowed : 12.30 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.24), residues: 1416 helix: 1.48 (0.20), residues: 730 sheet: 0.41 (0.51), residues: 124 loop : -0.93 (0.28), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1773 HIS 0.003 0.000 HIS C 68 PHE 0.022 0.002 PHE A1148 TYR 0.010 0.001 TYR A1668 ARG 0.002 0.000 ARG A 551 Details of bonding type rmsd link_TRANS : bond 0.00074 ( 1) link_TRANS : angle 0.37208 ( 2) hydrogen bonds : bond 0.04257 ( 500) hydrogen bonds : angle 4.10411 ( 1461) covalent geometry : bond 0.00349 (11442) covalent geometry : angle 0.51441 (15513) Misc. bond : bond 0.00054 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 204 time to evaluate : 1.158 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.4684 (ttt) cc_final: 0.3570 (ptp) REVERT: C 24 GLU cc_start: 0.7809 (tt0) cc_final: 0.7568 (tm-30) REVERT: A 495 GLN cc_start: 0.7797 (pm20) cc_final: 0.7372 (pm20) REVERT: A 504 GLN cc_start: 0.8298 (mm-40) cc_final: 0.7923 (mm-40) REVERT: A 515 MET cc_start: 0.8701 (mmt) cc_final: 0.8218 (mmt) REVERT: A 615 LEU cc_start: 0.7828 (mp) cc_final: 0.7511 (mp) REVERT: A 622 SER cc_start: 0.8511 (t) cc_final: 0.8134 (p) REVERT: A 872 MET cc_start: 0.2812 (ttm) cc_final: 0.1783 (ttm) REVERT: A 889 VAL cc_start: 0.8237 (t) cc_final: 0.7967 (p) REVERT: A 1153 PHE cc_start: 0.6604 (m-80) cc_final: 0.6387 (m-80) REVERT: A 1254 ARG cc_start: 0.7016 (ttp-170) cc_final: 0.6704 (ttp-170) REVERT: A 1405 MET cc_start: 0.5417 (ttp) cc_final: 0.5157 (ttp) REVERT: A 1668 TYR cc_start: 0.7645 (m-80) cc_final: 0.7376 (m-80) REVERT: A 1698 TRP cc_start: 0.8092 (m100) cc_final: 0.7034 (m100) REVERT: A 1746 ARG cc_start: 0.7839 (mtp85) cc_final: 0.7619 (mtp85) REVERT: A 1752 MET cc_start: 0.8034 (mtp) cc_final: 0.7830 (mtm) REVERT: A 1854 LYS cc_start: 0.7797 (tptm) cc_final: 0.7485 (tppt) REVERT: A 1957 GLU cc_start: 0.6670 (tm-30) cc_final: 0.6297 (tm-30) REVERT: A 1997 PRO cc_start: 0.7433 (Cg_endo) cc_final: 0.7122 (Cg_exo) REVERT: A 2018 SER cc_start: 0.8682 (t) cc_final: 0.8183 (p) outliers start: 25 outliers final: 18 residues processed: 213 average time/residue: 0.2312 time to fit residues: 70.7845 Evaluate side-chains 218 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 200 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 1172 CYS Chi-restraints excluded: chain A residue 1217 LEU Chi-restraints excluded: chain A residue 1491 CYS Chi-restraints excluded: chain A residue 1534 TYR Chi-restraints excluded: chain A residue 1541 MET Chi-restraints excluded: chain A residue 1672 VAL Chi-restraints excluded: chain A residue 1704 THR Chi-restraints excluded: chain A residue 1803 ILE Chi-restraints excluded: chain A residue 1817 THR Chi-restraints excluded: chain A residue 1928 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 121 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 24 optimal weight: 0.0030 chunk 94 optimal weight: 0.0470 chunk 65 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 48 optimal weight: 0.0770 chunk 116 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 overall best weight: 0.3646 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1272 ASN A1553 ASN A2038 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.159351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.122927 restraints weight = 18594.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.126430 restraints weight = 9926.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.128498 restraints weight = 6539.118| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11446 Z= 0.104 Angle : 0.491 9.981 15515 Z= 0.248 Chirality : 0.038 0.160 1818 Planarity : 0.004 0.063 1984 Dihedral : 4.554 98.338 1537 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.73 % Allowed : 12.72 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.24), residues: 1416 helix: 1.69 (0.20), residues: 729 sheet: 0.43 (0.51), residues: 124 loop : -0.87 (0.28), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1773 HIS 0.002 0.000 HIS A 661 PHE 0.035 0.001 PHE A1242 TYR 0.009 0.001 TYR A1668 ARG 0.004 0.000 ARG A1988 Details of bonding type rmsd link_TRANS : bond 0.00086 ( 1) link_TRANS : angle 0.24940 ( 2) hydrogen bonds : bond 0.03426 ( 500) hydrogen bonds : angle 3.93059 ( 1461) covalent geometry : bond 0.00238 (11442) covalent geometry : angle 0.49116 (15513) Misc. bond : bond 0.00083 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 208 time to evaluate : 1.148 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.4329 (ttt) cc_final: 0.3459 (ptp) REVERT: C 6 LYS cc_start: 0.7893 (pttp) cc_final: 0.7527 (ttpp) REVERT: C 24 GLU cc_start: 0.7760 (tt0) cc_final: 0.7518 (tm-30) REVERT: A 495 GLN cc_start: 0.7682 (pm20) cc_final: 0.7383 (pm20) REVERT: A 504 GLN cc_start: 0.8204 (mm-40) cc_final: 0.7839 (mm-40) REVERT: A 551 ARG cc_start: 0.7668 (ttm170) cc_final: 0.7355 (ttm170) REVERT: A 615 LEU cc_start: 0.7784 (mp) cc_final: 0.7483 (mp) REVERT: A 622 SER cc_start: 0.8485 (t) cc_final: 0.8103 (p) REVERT: A 679 ASP cc_start: 0.7432 (t70) cc_final: 0.7020 (t0) REVERT: A 872 MET cc_start: 0.2786 (ttm) cc_final: 0.1713 (ttm) REVERT: A 889 VAL cc_start: 0.8198 (t) cc_final: 0.7923 (p) REVERT: A 958 MET cc_start: 0.7035 (tmm) cc_final: 0.6728 (tmm) REVERT: A 1153 PHE cc_start: 0.6518 (m-80) cc_final: 0.6250 (m-80) REVERT: A 1254 ARG cc_start: 0.6984 (ttp-170) cc_final: 0.6688 (ttp-170) REVERT: A 1260 ASN cc_start: 0.7825 (p0) cc_final: 0.7561 (p0) REVERT: A 1272 ASN cc_start: 0.7490 (m-40) cc_final: 0.7274 (t0) REVERT: A 1405 MET cc_start: 0.5447 (ttp) cc_final: 0.5200 (ttp) REVERT: A 1602 THR cc_start: 0.8267 (t) cc_final: 0.8009 (t) REVERT: A 1698 TRP cc_start: 0.8097 (m100) cc_final: 0.7019 (m100) REVERT: A 1746 ARG cc_start: 0.7848 (mtp85) cc_final: 0.7606 (mtp85) REVERT: A 1854 LYS cc_start: 0.7742 (tptm) cc_final: 0.7439 (tppt) REVERT: A 1957 GLU cc_start: 0.6557 (tm-30) cc_final: 0.6307 (tm-30) REVERT: A 1997 PRO cc_start: 0.7424 (Cg_endo) cc_final: 0.7138 (Cg_exo) REVERT: A 2018 SER cc_start: 0.8686 (t) cc_final: 0.8231 (p) outliers start: 21 outliers final: 15 residues processed: 217 average time/residue: 0.2338 time to fit residues: 72.9165 Evaluate side-chains 216 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 201 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 683 HIS Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 1172 CYS Chi-restraints excluded: chain A residue 1491 CYS Chi-restraints excluded: chain A residue 1541 MET Chi-restraints excluded: chain A residue 1672 VAL Chi-restraints excluded: chain A residue 1704 THR Chi-restraints excluded: chain A residue 1803 ILE Chi-restraints excluded: chain A residue 1817 THR Chi-restraints excluded: chain A residue 1928 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 99 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 86 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 13 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 117 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2038 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.157599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.121598 restraints weight = 18507.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.124759 restraints weight = 10286.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.126522 restraints weight = 6998.316| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11446 Z= 0.152 Angle : 0.536 10.950 15515 Z= 0.269 Chirality : 0.039 0.165 1818 Planarity : 0.004 0.067 1984 Dihedral : 4.642 100.590 1537 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 1.65 % Allowed : 12.72 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.24), residues: 1416 helix: 1.55 (0.20), residues: 731 sheet: 0.31 (0.50), residues: 126 loop : -0.87 (0.28), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1773 HIS 0.003 0.001 HIS C 68 PHE 0.030 0.002 PHE A1242 TYR 0.011 0.001 TYR A1668 ARG 0.004 0.000 ARG A 551 Details of bonding type rmsd link_TRANS : bond 0.00084 ( 1) link_TRANS : angle 0.35307 ( 2) hydrogen bonds : bond 0.04206 ( 500) hydrogen bonds : angle 4.04976 ( 1461) covalent geometry : bond 0.00363 (11442) covalent geometry : angle 0.53565 (15513) Misc. bond : bond 0.00061 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 202 time to evaluate : 1.465 Fit side-chains revert: symmetry clash REVERT: B 1 MET cc_start: 0.4555 (ttt) cc_final: 0.3657 (ptp) REVERT: C 24 GLU cc_start: 0.7727 (tt0) cc_final: 0.7496 (tm-30) REVERT: D 1 MET cc_start: -0.0090 (ptm) cc_final: -0.0658 (ptm) REVERT: A 495 GLN cc_start: 0.7692 (pm20) cc_final: 0.7383 (pm20) REVERT: A 504 GLN cc_start: 0.8155 (mm-40) cc_final: 0.7831 (mm-40) REVERT: A 515 MET cc_start: 0.8694 (mmt) cc_final: 0.8223 (mmt) REVERT: A 615 LEU cc_start: 0.7863 (mp) cc_final: 0.7536 (mp) REVERT: A 622 SER cc_start: 0.8502 (t) cc_final: 0.8131 (p) REVERT: A 679 ASP cc_start: 0.7458 (t70) cc_final: 0.7058 (t0) REVERT: A 872 MET cc_start: 0.2739 (ttm) cc_final: 0.1666 (ttm) REVERT: A 889 VAL cc_start: 0.8219 (t) cc_final: 0.7935 (p) REVERT: A 958 MET cc_start: 0.7179 (tmm) cc_final: 0.6969 (tmm) REVERT: A 1153 PHE cc_start: 0.6565 (m-80) cc_final: 0.6324 (m-80) REVERT: A 1254 ARG cc_start: 0.6995 (ttp-170) cc_final: 0.6696 (ttp-170) REVERT: A 1602 THR cc_start: 0.8297 (t) cc_final: 0.8046 (t) REVERT: A 1668 TYR cc_start: 0.7659 (m-80) cc_final: 0.7441 (m-80) REVERT: A 1698 TRP cc_start: 0.8073 (m100) cc_final: 0.7035 (m100) REVERT: A 1746 ARG cc_start: 0.7835 (mtp85) cc_final: 0.7613 (mtp85) REVERT: A 1830 MET cc_start: 0.6928 (ttp) cc_final: 0.6597 (ttm) REVERT: A 1854 LYS cc_start: 0.7737 (tptm) cc_final: 0.7432 (tppt) REVERT: A 1997 PRO cc_start: 0.7395 (Cg_endo) cc_final: 0.7081 (Cg_exo) REVERT: A 2018 SER cc_start: 0.8707 (t) cc_final: 0.8238 (p) outliers start: 20 outliers final: 16 residues processed: 209 average time/residue: 0.2576 time to fit residues: 78.8745 Evaluate side-chains 217 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 201 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 1172 CYS Chi-restraints excluded: chain A residue 1491 CYS Chi-restraints excluded: chain A residue 1534 TYR Chi-restraints excluded: chain A residue 1541 MET Chi-restraints excluded: chain A residue 1672 VAL Chi-restraints excluded: chain A residue 1704 THR Chi-restraints excluded: chain A residue 1803 ILE Chi-restraints excluded: chain A residue 1817 THR Chi-restraints excluded: chain A residue 1928 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 12 optimal weight: 0.0270 chunk 76 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 17 optimal weight: 0.0070 chunk 107 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 15 optimal weight: 20.0000 chunk 55 optimal weight: 0.6980 chunk 129 optimal weight: 0.0770 chunk 80 optimal weight: 0.0370 chunk 114 optimal weight: 0.2980 overall best weight: 0.0892 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1272 ASN A2038 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.161379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.125741 restraints weight = 18647.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.129057 restraints weight = 10363.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.131035 restraints weight = 6997.384| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11446 Z= 0.092 Angle : 0.494 11.517 15515 Z= 0.245 Chirality : 0.037 0.164 1818 Planarity : 0.004 0.066 1984 Dihedral : 4.396 97.109 1537 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.74 % Allowed : 14.20 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.24), residues: 1416 helix: 1.80 (0.20), residues: 729 sheet: 0.42 (0.50), residues: 125 loop : -0.81 (0.28), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1533 HIS 0.002 0.000 HIS A 661 PHE 0.027 0.001 PHE A1242 TYR 0.006 0.001 TYR A2010 ARG 0.002 0.000 ARG A 551 Details of bonding type rmsd link_TRANS : bond 0.00054 ( 1) link_TRANS : angle 0.16307 ( 2) hydrogen bonds : bond 0.02698 ( 500) hydrogen bonds : angle 3.80916 ( 1461) covalent geometry : bond 0.00204 (11442) covalent geometry : angle 0.49438 (15513) Misc. bond : bond 0.00048 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 209 time to evaluate : 1.720 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.4431 (ttt) cc_final: 0.3690 (ptp) REVERT: C 24 GLU cc_start: 0.7699 (tt0) cc_final: 0.7461 (tm-30) REVERT: D 1 MET cc_start: -0.0275 (ptm) cc_final: -0.0862 (ptm) REVERT: A 495 GLN cc_start: 0.7673 (pm20) cc_final: 0.7384 (pm20) REVERT: A 504 GLN cc_start: 0.8117 (mm-40) cc_final: 0.7772 (mm-40) REVERT: A 615 LEU cc_start: 0.7713 (mp) cc_final: 0.7437 (mp) REVERT: A 622 SER cc_start: 0.8425 (t) cc_final: 0.8024 (p) REVERT: A 679 ASP cc_start: 0.7381 (t70) cc_final: 0.6960 (t0) REVERT: A 872 MET cc_start: 0.2800 (ttm) cc_final: 0.1773 (ttm) REVERT: A 889 VAL cc_start: 0.8182 (t) cc_final: 0.7891 (p) REVERT: A 1153 PHE cc_start: 0.6428 (m-80) cc_final: 0.6157 (m-80) REVERT: A 1254 ARG cc_start: 0.6969 (ttp-170) cc_final: 0.6539 (ttp-170) REVERT: A 1272 ASN cc_start: 0.7528 (m-40) cc_final: 0.7323 (t0) REVERT: A 1539 ASN cc_start: 0.7699 (t0) cc_final: 0.7368 (t0) REVERT: A 1602 THR cc_start: 0.8163 (t) cc_final: 0.7920 (t) REVERT: A 1746 ARG cc_start: 0.7815 (mtp85) cc_final: 0.7559 (mtp85) REVERT: A 1752 MET cc_start: 0.7907 (mtm) cc_final: 0.7672 (mtt) REVERT: A 1997 PRO cc_start: 0.7443 (Cg_endo) cc_final: 0.7159 (Cg_exo) REVERT: A 2018 SER cc_start: 0.8628 (t) cc_final: 0.8170 (p) outliers start: 9 outliers final: 8 residues processed: 211 average time/residue: 0.2898 time to fit residues: 88.4499 Evaluate side-chains 214 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 206 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 1491 CYS Chi-restraints excluded: chain A residue 1541 MET Chi-restraints excluded: chain A residue 1672 VAL Chi-restraints excluded: chain A residue 1817 THR Chi-restraints excluded: chain A residue 1928 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 56 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 112 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2038 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.157875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.121091 restraints weight = 18412.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.124446 restraints weight = 9903.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.126510 restraints weight = 6593.024| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 11446 Z= 0.156 Angle : 0.560 11.261 15515 Z= 0.277 Chirality : 0.040 0.166 1818 Planarity : 0.004 0.070 1984 Dihedral : 4.590 100.816 1537 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.99 % Allowed : 14.29 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.24), residues: 1416 helix: 1.59 (0.20), residues: 732 sheet: 0.32 (0.50), residues: 126 loop : -0.80 (0.28), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1773 HIS 0.002 0.000 HIS A 661 PHE 0.030 0.002 PHE A1242 TYR 0.013 0.001 TYR A1668 ARG 0.003 0.000 ARG A 721 Details of bonding type rmsd link_TRANS : bond 0.00136 ( 1) link_TRANS : angle 0.39638 ( 2) hydrogen bonds : bond 0.04327 ( 500) hydrogen bonds : angle 4.02399 ( 1461) covalent geometry : bond 0.00373 (11442) covalent geometry : angle 0.55973 (15513) Misc. bond : bond 0.00061 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2832 Ramachandran restraints generated. 1416 Oldfield, 0 Emsley, 1416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 206 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 24 GLU cc_start: 0.7739 (tt0) cc_final: 0.7496 (tm-30) REVERT: D 1 MET cc_start: -0.0185 (ptm) cc_final: -0.0774 (ptm) REVERT: A 495 GLN cc_start: 0.7699 (pm20) cc_final: 0.7407 (pm20) REVERT: A 504 GLN cc_start: 0.8151 (mm-40) cc_final: 0.7793 (mm-40) REVERT: A 515 MET cc_start: 0.8710 (mmt) cc_final: 0.8257 (mmt) REVERT: A 615 LEU cc_start: 0.7846 (mp) cc_final: 0.7525 (mp) REVERT: A 622 SER cc_start: 0.8467 (t) cc_final: 0.8083 (m) REVERT: A 679 ASP cc_start: 0.7465 (t70) cc_final: 0.7067 (t0) REVERT: A 872 MET cc_start: 0.2827 (ttm) cc_final: 0.1767 (ttm) REVERT: A 889 VAL cc_start: 0.8212 (t) cc_final: 0.7933 (p) REVERT: A 1153 PHE cc_start: 0.6515 (m-80) cc_final: 0.6286 (m-80) REVERT: A 1254 ARG cc_start: 0.7015 (ttp-170) cc_final: 0.6707 (ttp-170) REVERT: A 1602 THR cc_start: 0.8288 (t) cc_final: 0.8022 (t) REVERT: A 1698 TRP cc_start: 0.8099 (m100) cc_final: 0.7076 (m100) REVERT: A 1746 ARG cc_start: 0.7835 (mtp85) cc_final: 0.7602 (mtp85) REVERT: A 1752 MET cc_start: 0.8015 (mtm) cc_final: 0.7797 (mtt) REVERT: A 1997 PRO cc_start: 0.7408 (Cg_endo) cc_final: 0.7091 (Cg_exo) REVERT: A 2018 SER cc_start: 0.8686 (t) cc_final: 0.8227 (p) outliers start: 12 outliers final: 9 residues processed: 208 average time/residue: 0.2359 time to fit residues: 69.7163 Evaluate side-chains 215 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 206 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 571 ILE Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 1491 CYS Chi-restraints excluded: chain A residue 1534 TYR Chi-restraints excluded: chain A residue 1541 MET Chi-restraints excluded: chain A residue 1672 VAL Chi-restraints excluded: chain A residue 1817 THR Chi-restraints excluded: chain A residue 1928 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 26 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 56 optimal weight: 0.4980 chunk 55 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1272 ASN A2038 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.157998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.122140 restraints weight = 18380.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.125303 restraints weight = 10260.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.127157 restraints weight = 6957.059| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11446 Z= 0.140 Angle : 0.544 11.581 15515 Z= 0.269 Chirality : 0.039 0.168 1818 Planarity : 0.004 0.069 1984 Dihedral : 4.627 101.712 1537 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.99 % Allowed : 14.62 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.24), residues: 1416 helix: 1.57 (0.20), residues: 731 sheet: 0.30 (0.49), residues: 126 loop : -0.84 (0.28), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1773 HIS 0.002 0.000 HIS A 747 PHE 0.029 0.002 PHE A1242 TYR 0.012 0.001 TYR A1152 ARG 0.004 0.000 ARG A 551 Details of bonding type rmsd link_TRANS : bond 0.00086 ( 1) link_TRANS : angle 0.32565 ( 2) hydrogen bonds : bond 0.03968 ( 500) hydrogen bonds : angle 3.99316 ( 1461) covalent geometry : bond 0.00334 (11442) covalent geometry : angle 0.54407 (15513) Misc. bond : bond 0.00048 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3949.06 seconds wall clock time: 70 minutes 5.11 seconds (4205.11 seconds total)