Starting phenix.real_space_refine on Mon Apr 8 22:45:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gkc_40182/04_2024/8gkc_40182_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gkc_40182/04_2024/8gkc_40182.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gkc_40182/04_2024/8gkc_40182_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gkc_40182/04_2024/8gkc_40182_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gkc_40182/04_2024/8gkc_40182_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gkc_40182/04_2024/8gkc_40182.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gkc_40182/04_2024/8gkc_40182.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gkc_40182/04_2024/8gkc_40182_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gkc_40182/04_2024/8gkc_40182_neut_updated.pdb" } resolution = 2.45 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= 0.520 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 52 5.16 5 C 9280 2.51 5 N 2574 2.21 5 O 2698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 915": "OE1" <-> "OE2" Residue "A GLU 934": "OE1" <-> "OE2" Residue "A GLU 948": "OE1" <-> "OE2" Residue "A GLU 1010": "OE1" <-> "OE2" Residue "A GLU 1014": "OE1" <-> "OE2" Residue "A GLU 1525": "OE1" <-> "OE2" Residue "A GLU 1643": "OE1" <-> "OE2" Residue "A GLU 1703": "OE1" <-> "OE2" Residue "A GLU 1729": "OE1" <-> "OE2" Residue "A GLU 1750": "OE1" <-> "OE2" Residue "A GLU 1768": "OE1" <-> "OE2" Residue "A GLU 2051": "OE1" <-> "OE2" Residue "D GLU 915": "OE1" <-> "OE2" Residue "D GLU 934": "OE1" <-> "OE2" Residue "D GLU 948": "OE1" <-> "OE2" Residue "D GLU 1010": "OE1" <-> "OE2" Residue "D GLU 1014": "OE1" <-> "OE2" Residue "D GLU 1525": "OE1" <-> "OE2" Residue "D GLU 1643": "OE1" <-> "OE2" Residue "D GLU 1703": "OE1" <-> "OE2" Residue "D GLU 1729": "OE1" <-> "OE2" Residue "D GLU 1750": "OE1" <-> "OE2" Residue "D GLU 1768": "OE1" <-> "OE2" Residue "D GLU 2051": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 14616 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 966, 7179 Classifications: {'peptide': 966} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 47, 'TRANS': 918} Chain breaks: 2 Unresolved non-hydrogen bonds: 279 Unresolved non-hydrogen angles: 343 Unresolved non-hydrogen dihedrals: 219 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 10, 'ASN:plan1': 3, 'HIS:plan': 2, 'GLU:plan': 12, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 151 Chain: "D" Number of atoms: 7179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 966, 7179 Classifications: {'peptide': 966} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 47, 'TRANS': 918} Chain breaks: 2 Unresolved non-hydrogen bonds: 279 Unresolved non-hydrogen angles: 343 Unresolved non-hydrogen dihedrals: 219 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 10, 'ASN:plan1': 3, 'HIS:plan': 2, 'GLU:plan': 12, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 151 Chain: "A" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'NDP': 2, 'X5O': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 129 Unusual residues: {'NDP': 2, 'X5O': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 8.20, per 1000 atoms: 0.56 Number of scatterers: 14616 At special positions: 0 Unit cell: (120.51, 169.95, 87.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 P 12 15.00 O 2698 8.00 N 2574 7.00 C 9280 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.89 Conformation dependent library (CDL) restraints added in 3.1 seconds 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3536 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 74 helices and 18 sheets defined 33.1% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.31 Creating SS restraints... Processing helix chain 'A' and resid 873 through 877 Processing helix chain 'A' and resid 888 through 902 Processing helix chain 'A' and resid 907 through 909 No H-bonds generated for 'chain 'A' and resid 907 through 909' Processing helix chain 'A' and resid 966 through 969 Processing helix chain 'A' and resid 987 through 997 Processing helix chain 'A' and resid 1003 through 1005 No H-bonds generated for 'chain 'A' and resid 1003 through 1005' Processing helix chain 'A' and resid 1026 through 1039 Processing helix chain 'A' and resid 1059 through 1065 removed outlier: 3.513A pdb=" N GLN A1064 " --> pdb=" O ALA A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1424 through 1433 Processing helix chain 'A' and resid 1453 through 1461 Processing helix chain 'A' and resid 1466 through 1469 No H-bonds generated for 'chain 'A' and resid 1466 through 1469' Processing helix chain 'A' and resid 1491 through 1499 Processing helix chain 'A' and resid 1541 through 1543 No H-bonds generated for 'chain 'A' and resid 1541 through 1543' Processing helix chain 'A' and resid 1550 through 1553 No H-bonds generated for 'chain 'A' and resid 1550 through 1553' Processing helix chain 'A' and resid 1573 through 1579 Processing helix chain 'A' and resid 1585 through 1587 No H-bonds generated for 'chain 'A' and resid 1585 through 1587' Processing helix chain 'A' and resid 1630 through 1632 No H-bonds generated for 'chain 'A' and resid 1630 through 1632' Processing helix chain 'A' and resid 1642 through 1647 removed outlier: 4.473A pdb=" N SER A1647 " --> pdb=" O GLU A1643 " (cutoff:3.500A) Processing helix chain 'A' and resid 1649 through 1659 Processing helix chain 'A' and resid 1679 through 1691 Processing helix chain 'A' and resid 1702 through 1711 Processing helix chain 'A' and resid 1717 through 1719 No H-bonds generated for 'chain 'A' and resid 1717 through 1719' Processing helix chain 'A' and resid 1728 through 1735 Processing helix chain 'A' and resid 1750 through 1759 removed outlier: 3.899A pdb=" N ALA A1755 " --> pdb=" O LYS A1752 " (cutoff:3.500A) Processing helix chain 'A' and resid 1772 through 1775 No H-bonds generated for 'chain 'A' and resid 1772 through 1775' Processing helix chain 'A' and resid 1782 through 1787 Processing helix chain 'A' and resid 1796 through 1800 removed outlier: 3.542A pdb=" N PHE A1800 " --> pdb=" O ASP A1797 " (cutoff:3.500A) Processing helix chain 'A' and resid 1805 through 1819 removed outlier: 3.665A pdb=" N VAL A1810 " --> pdb=" O ASP A1806 " (cutoff:3.500A) Processing helix chain 'A' and resid 1836 through 1845 removed outlier: 3.573A pdb=" N GLN A1845 " --> pdb=" O ARG A1841 " (cutoff:3.500A) Processing helix chain 'A' and resid 1895 through 1907 Processing helix chain 'A' and resid 1923 through 1935 Processing helix chain 'A' and resid 1949 through 1962 removed outlier: 3.632A pdb=" N LEU A1962 " --> pdb=" O GLU A1958 " (cutoff:3.500A) Processing helix chain 'A' and resid 1985 through 2009 Proline residue: A1994 - end of helix removed outlier: 3.643A pdb=" N SER A1997 " --> pdb=" O LYS A1993 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY A1998 " --> pdb=" O PRO A1994 " (cutoff:3.500A) Processing helix chain 'A' and resid 2022 through 2025 No H-bonds generated for 'chain 'A' and resid 2022 through 2025' Processing helix chain 'A' and resid 2032 through 2050 Processing helix chain 'A' and resid 2068 through 2071 No H-bonds generated for 'chain 'A' and resid 2068 through 2071' Processing helix chain 'A' and resid 2088 through 2100 removed outlier: 3.762A pdb=" N ASN A2100 " --> pdb=" O ASP A2096 " (cutoff:3.500A) Processing helix chain 'D' and resid 873 through 877 Processing helix chain 'D' and resid 888 through 902 Processing helix chain 'D' and resid 907 through 909 No H-bonds generated for 'chain 'D' and resid 907 through 909' Processing helix chain 'D' and resid 966 through 969 Processing helix chain 'D' and resid 987 through 997 Processing helix chain 'D' and resid 1003 through 1005 No H-bonds generated for 'chain 'D' and resid 1003 through 1005' Processing helix chain 'D' and resid 1026 through 1039 Processing helix chain 'D' and resid 1059 through 1065 removed outlier: 3.513A pdb=" N GLN D1064 " --> pdb=" O ALA D1060 " (cutoff:3.500A) Processing helix chain 'D' and resid 1424 through 1433 Processing helix chain 'D' and resid 1453 through 1461 Processing helix chain 'D' and resid 1466 through 1469 No H-bonds generated for 'chain 'D' and resid 1466 through 1469' Processing helix chain 'D' and resid 1491 through 1499 Processing helix chain 'D' and resid 1541 through 1543 No H-bonds generated for 'chain 'D' and resid 1541 through 1543' Processing helix chain 'D' and resid 1550 through 1553 No H-bonds generated for 'chain 'D' and resid 1550 through 1553' Processing helix chain 'D' and resid 1573 through 1579 Processing helix chain 'D' and resid 1585 through 1587 No H-bonds generated for 'chain 'D' and resid 1585 through 1587' Processing helix chain 'D' and resid 1630 through 1632 No H-bonds generated for 'chain 'D' and resid 1630 through 1632' Processing helix chain 'D' and resid 1642 through 1647 removed outlier: 4.473A pdb=" N SER D1647 " --> pdb=" O GLU D1643 " (cutoff:3.500A) Processing helix chain 'D' and resid 1649 through 1659 Processing helix chain 'D' and resid 1679 through 1691 Processing helix chain 'D' and resid 1702 through 1711 Processing helix chain 'D' and resid 1717 through 1719 No H-bonds generated for 'chain 'D' and resid 1717 through 1719' Processing helix chain 'D' and resid 1728 through 1735 Processing helix chain 'D' and resid 1750 through 1759 removed outlier: 3.899A pdb=" N ALA D1755 " --> pdb=" O LYS D1752 " (cutoff:3.500A) Processing helix chain 'D' and resid 1772 through 1775 No H-bonds generated for 'chain 'D' and resid 1772 through 1775' Processing helix chain 'D' and resid 1782 through 1787 Processing helix chain 'D' and resid 1796 through 1800 removed outlier: 3.542A pdb=" N PHE D1800 " --> pdb=" O ASP D1797 " (cutoff:3.500A) Processing helix chain 'D' and resid 1805 through 1819 removed outlier: 3.666A pdb=" N VAL D1810 " --> pdb=" O ASP D1806 " (cutoff:3.500A) Processing helix chain 'D' and resid 1836 through 1845 removed outlier: 3.573A pdb=" N GLN D1845 " --> pdb=" O ARG D1841 " (cutoff:3.500A) Processing helix chain 'D' and resid 1895 through 1907 Processing helix chain 'D' and resid 1923 through 1935 Processing helix chain 'D' and resid 1949 through 1962 removed outlier: 3.632A pdb=" N LEU D1962 " --> pdb=" O GLU D1958 " (cutoff:3.500A) Processing helix chain 'D' and resid 1985 through 2009 Proline residue: D1994 - end of helix removed outlier: 3.643A pdb=" N SER D1997 " --> pdb=" O LYS D1993 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY D1998 " --> pdb=" O PRO D1994 " (cutoff:3.500A) Processing helix chain 'D' and resid 2022 through 2025 No H-bonds generated for 'chain 'D' and resid 2022 through 2025' Processing helix chain 'D' and resid 2032 through 2050 Processing helix chain 'D' and resid 2068 through 2071 No H-bonds generated for 'chain 'D' and resid 2068 through 2071' Processing helix chain 'D' and resid 2088 through 2100 removed outlier: 3.762A pdb=" N ASN D2100 " --> pdb=" O ASP D2096 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 860 through 864 removed outlier: 3.636A pdb=" N GLY A 956 " --> pdb=" O PHE A 944 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLU A 948 " --> pdb=" O LEU A 952 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N LEU A 952 " --> pdb=" O GLU A 948 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N SER A1017 " --> pdb=" O SER A1012 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU A1010 " --> pdb=" O ARG A1019 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU A1021 " --> pdb=" O ILE A1008 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE A1008 " --> pdb=" O LEU A1021 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 878 through 880 removed outlier: 3.808A pdb=" N THR A 879 " --> pdb=" O ASP A1000 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 1413 through 1416 removed outlier: 5.971A pdb=" N VAL A1472 " --> pdb=" O LEU A1443 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N ALA A1445 " --> pdb=" O VAL A1472 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU A1474 " --> pdb=" O ALA A1445 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N MET A1503 " --> pdb=" O PHE A1514 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N PHE A1514 " --> pdb=" O MET A1503 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG A1515 " --> pdb=" O CYS A1118 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N CYS A1118 " --> pdb=" O ARG A1515 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL A2105 " --> pdb=" O PHE A1117 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ALA A2057 " --> pdb=" O LEU A2106 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N SER A2108 " --> pdb=" O ALA A2057 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLN A2059 " --> pdb=" O SER A2108 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N ILE A1888 " --> pdb=" O GLY A1966 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL A1968 " --> pdb=" O ILE A1888 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ALA A1890 " --> pdb=" O VAL A1968 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ASN A1970 " --> pdb=" O ALA A1890 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LYS A1911 " --> pdb=" O TYR A1887 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ILE A1889 " --> pdb=" O LYS A1911 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL A1913 " --> pdb=" O ILE A1889 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N GLN A1938 " --> pdb=" O LEU A1912 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LEU A1914 " --> pdb=" O GLN A1938 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N GLN A1940 " --> pdb=" O LEU A1914 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 1525 through 1528 Processing sheet with id= E, first strand: chain 'A' and resid 1531 through 1535 Processing sheet with id= F, first strand: chain 'A' and resid 1625 through 1628 removed outlier: 6.791A pdb=" N SER A1604 " --> pdb=" O TYR A1567 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ALA A1569 " --> pdb=" O GLU A1602 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N GLU A1602 " --> pdb=" O ALA A1569 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1568 through 1570 Processing sheet with id= H, first strand: chain 'A' and resid 1790 through 1793 Processing sheet with id= I, first strand: chain 'A' and resid 1047 through 1052 removed outlier: 6.876A pdb=" N HIS A1098 " --> pdb=" O THR A1050 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 860 through 864 removed outlier: 3.637A pdb=" N GLY D 956 " --> pdb=" O PHE D 944 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLU D 948 " --> pdb=" O LEU D 952 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N LEU D 952 " --> pdb=" O GLU D 948 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N SER D1017 " --> pdb=" O SER D1012 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU D1010 " --> pdb=" O ARG D1019 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU D1021 " --> pdb=" O ILE D1008 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE D1008 " --> pdb=" O LEU D1021 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 878 through 880 removed outlier: 3.807A pdb=" N THR D 879 " --> pdb=" O ASP D1000 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 1413 through 1416 removed outlier: 5.970A pdb=" N VAL D1472 " --> pdb=" O LEU D1443 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N ALA D1445 " --> pdb=" O VAL D1472 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU D1474 " --> pdb=" O ALA D1445 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N MET D1503 " --> pdb=" O PHE D1514 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N PHE D1514 " --> pdb=" O MET D1503 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG D1515 " --> pdb=" O CYS D1118 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N CYS D1118 " --> pdb=" O ARG D1515 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL D2105 " --> pdb=" O PHE D1117 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ALA D2057 " --> pdb=" O LEU D2106 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N SER D2108 " --> pdb=" O ALA D2057 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLN D2059 " --> pdb=" O SER D2108 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N ILE D1888 " --> pdb=" O GLY D1966 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VAL D1968 " --> pdb=" O ILE D1888 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ALA D1890 " --> pdb=" O VAL D1968 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ASN D1970 " --> pdb=" O ALA D1890 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LYS D1911 " --> pdb=" O TYR D1887 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ILE D1889 " --> pdb=" O LYS D1911 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL D1913 " --> pdb=" O ILE D1889 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N GLN D1938 " --> pdb=" O LEU D1912 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LEU D1914 " --> pdb=" O GLN D1938 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N GLN D1940 " --> pdb=" O LEU D1914 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 1525 through 1528 Processing sheet with id= N, first strand: chain 'D' and resid 1531 through 1535 Processing sheet with id= O, first strand: chain 'D' and resid 1625 through 1628 removed outlier: 6.792A pdb=" N SER D1604 " --> pdb=" O TYR D1567 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ALA D1569 " --> pdb=" O GLU D1602 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N GLU D1602 " --> pdb=" O ALA D1569 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 1568 through 1570 Processing sheet with id= Q, first strand: chain 'D' and resid 1790 through 1793 Processing sheet with id= R, first strand: chain 'D' and resid 1047 through 1052 removed outlier: 6.876A pdb=" N HIS D1098 " --> pdb=" O THR D1050 " (cutoff:3.500A) 578 hydrogen bonds defined for protein. 1578 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.64 Time building geometry restraints manager: 6.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 2370 1.27 - 1.41: 3817 1.41 - 1.55: 8649 1.55 - 1.68: 58 1.68 - 1.82: 76 Bond restraints: 14970 Sorted by residual: bond pdb=" C1B NDP A2603 " pdb=" C2B NDP A2603 " ideal model delta sigma weight residual 1.575 1.286 0.289 3.70e-02 7.30e+02 6.10e+01 bond pdb=" C1B NDP D2603 " pdb=" C2B NDP D2603 " ideal model delta sigma weight residual 1.575 1.287 0.288 3.70e-02 7.30e+02 6.06e+01 bond pdb=" C2D NDP A2603 " pdb=" C3D NDP A2603 " ideal model delta sigma weight residual 1.545 1.265 0.280 3.60e-02 7.72e+02 6.05e+01 bond pdb=" C2D NDP D2603 " pdb=" C3D NDP D2603 " ideal model delta sigma weight residual 1.545 1.265 0.280 3.60e-02 7.72e+02 6.05e+01 bond pdb=" C2D NDP A2602 " pdb=" C3D NDP A2602 " ideal model delta sigma weight residual 1.545 1.268 0.277 3.60e-02 7.72e+02 5.92e+01 ... (remaining 14965 not shown) Histogram of bond angle deviations from ideal: 82.20 - 101.64: 36 101.64 - 121.09: 16058 121.09 - 140.53: 4360 140.53 - 159.97: 0 159.97 - 179.41: 2 Bond angle restraints: 20456 Sorted by residual: angle pdb=" C12 X5O D2601 " pdb=" C13 X5O D2601 " pdb=" C16 X5O D2601 " ideal model delta sigma weight residual 108.96 82.20 26.76 3.00e+00 1.11e-01 7.96e+01 angle pdb=" C12 X5O A2601 " pdb=" C13 X5O A2601 " pdb=" C16 X5O A2601 " ideal model delta sigma weight residual 108.96 82.22 26.74 3.00e+00 1.11e-01 7.95e+01 angle pdb=" PA NDP A2602 " pdb=" O3 NDP A2602 " pdb=" PN NDP A2602 " ideal model delta sigma weight residual 107.74 124.36 -16.62 1.95e+00 2.62e-01 7.23e+01 angle pdb=" PA NDP D2602 " pdb=" O3 NDP D2602 " pdb=" PN NDP D2602 " ideal model delta sigma weight residual 107.74 124.34 -16.60 1.95e+00 2.62e-01 7.22e+01 angle pdb=" C14 X5O A2601 " pdb=" C13 X5O A2601 " pdb=" C16 X5O A2601 " ideal model delta sigma weight residual 109.03 133.18 -24.15 3.00e+00 1.11e-01 6.48e+01 ... (remaining 20451 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 8414 35.94 - 71.88: 250 71.88 - 107.82: 20 107.82 - 143.76: 8 143.76 - 179.70: 2 Dihedral angle restraints: 8694 sinusoidal: 3188 harmonic: 5506 Sorted by residual: dihedral pdb=" C5B NDP D2602 " pdb=" O5B NDP D2602 " pdb=" PA NDP D2602 " pdb=" O3 NDP D2602 " ideal model delta sinusoidal sigma weight residual 175.04 -5.26 -179.70 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C5B NDP A2602 " pdb=" O5B NDP A2602 " pdb=" PA NDP A2602 " pdb=" O3 NDP A2602 " ideal model delta sinusoidal sigma weight residual 175.04 -2.05 177.09 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C15 X5O A2601 " pdb=" C13 X5O A2601 " pdb=" C14 X5O A2601 " pdb=" C16 X5O A2601 " ideal model delta sinusoidal sigma weight residual 67.66 -165.32 -127.02 1 3.00e+01 1.11e-03 1.71e+01 ... (remaining 8691 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.091: 2328 1.091 - 2.182: 0 2.182 - 3.273: 0 3.273 - 4.364: 0 4.364 - 5.455: 4 Chirality restraints: 2332 Sorted by residual: chirality pdb=" C30 X5O D2601 " pdb=" C04 X5O D2601 " pdb=" C31 X5O D2601 " pdb=" C33 X5O D2601 " both_signs ideal model delta sigma weight residual False -2.81 2.64 -5.46 2.00e-01 2.50e+01 7.44e+02 chirality pdb=" C30 X5O A2601 " pdb=" C04 X5O A2601 " pdb=" C31 X5O A2601 " pdb=" C33 X5O A2601 " both_signs ideal model delta sigma weight residual False -2.81 2.64 -5.45 2.00e-01 2.50e+01 7.43e+02 chirality pdb=" C13 X5O D2601 " pdb=" C12 X5O D2601 " pdb=" C14 X5O D2601 " pdb=" C16 X5O D2601 " both_signs ideal model delta sigma weight residual False -2.67 2.33 -5.00 2.00e-01 2.50e+01 6.26e+02 ... (remaining 2329 not shown) Planarity restraints: 2628 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D1120 " -0.065 5.00e-02 4.00e+02 9.72e-02 1.51e+01 pdb=" N PRO D1121 " 0.168 5.00e-02 4.00e+02 pdb=" CA PRO D1121 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO D1121 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A1120 " 0.065 5.00e-02 4.00e+02 9.72e-02 1.51e+01 pdb=" N PRO A1121 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO A1121 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A1121 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 991 " -0.020 2.00e-02 2.50e+03 1.23e-02 3.02e+00 pdb=" CG TYR A 991 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR A 991 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR A 991 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 991 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 991 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 991 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR A 991 " -0.002 2.00e-02 2.50e+03 ... (remaining 2625 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 547 2.71 - 3.26: 14697 3.26 - 3.80: 26714 3.80 - 4.35: 34212 4.35 - 4.90: 55471 Nonbonded interactions: 131641 Sorted by model distance: nonbonded pdb=" OE2 GLU D2042 " pdb=" NE2 GLN D2059 " model vdw 2.160 2.520 nonbonded pdb=" OE2 GLU A2042 " pdb=" NE2 GLN A2059 " model vdw 2.161 2.520 nonbonded pdb=" OH TYR A 891 " pdb=" OG1 THR A 923 " model vdw 2.163 2.440 nonbonded pdb=" OH TYR D 891 " pdb=" OG1 THR D 923 " model vdw 2.163 2.440 nonbonded pdb=" OD2 ASP A1716 " pdb=" OG1 THR A1718 " model vdw 2.228 2.440 ... (remaining 131636 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.040 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 45.160 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 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 : 0.012 0.289 14970 Z= 0.810 Angle : 1.061 26.760 20456 Z= 0.487 Chirality : 0.223 5.455 2332 Planarity : 0.005 0.097 2628 Dihedral : 17.507 179.697 5158 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.00 % Allowed : 22.53 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.15 (0.18), residues: 1920 helix: -0.54 (0.19), residues: 666 sheet: -1.20 (0.27), residues: 342 loop : -0.59 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D1807 HIS 0.006 0.001 HIS D1735 PHE 0.011 0.002 PHE D1005 TYR 0.027 0.002 TYR A 991 ARG 0.004 0.001 ARG A1538 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 1.660 Fit side-chains REVERT: A 1644 GLU cc_start: 0.7488 (mt-10) cc_final: 0.7249 (mt-10) REVERT: A 1819 ARG cc_start: 0.7199 (ptt-90) cc_final: 0.6735 (ptt-90) REVERT: A 2051 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7671 (mt-10) REVERT: D 1644 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7277 (mt-10) REVERT: D 1819 ARG cc_start: 0.7187 (ptt-90) cc_final: 0.6731 (ptt-90) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 1.5894 time to fit residues: 285.8562 Evaluate side-chains 145 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 1.9990 chunk 145 optimal weight: 0.0470 chunk 80 optimal weight: 0.9980 chunk 49 optimal weight: 0.0070 chunk 98 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1835 GLN A2059 GLN ** A2101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1835 GLN D2059 GLN ** D2101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.0790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14970 Z= 0.173 Angle : 0.550 8.244 20456 Z= 0.261 Chirality : 0.041 0.156 2332 Planarity : 0.004 0.074 2628 Dihedral : 11.318 176.761 2134 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.50 % Allowed : 20.24 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.54 (0.19), residues: 1920 helix: 0.18 (0.20), residues: 664 sheet: -1.06 (0.28), residues: 336 loop : -0.32 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1807 HIS 0.003 0.001 HIS A1735 PHE 0.007 0.001 PHE D 914 TYR 0.023 0.001 TYR A 991 ARG 0.003 0.000 ARG D1931 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 150 time to evaluate : 1.712 Fit side-chains REVERT: A 1082 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7638 (mtt-85) REVERT: A 1644 GLU cc_start: 0.7306 (mt-10) cc_final: 0.7042 (mt-10) REVERT: A 1819 ARG cc_start: 0.7276 (ptt-90) cc_final: 0.6808 (ptt-90) REVERT: D 1082 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7659 (mtt-85) REVERT: D 1644 GLU cc_start: 0.7316 (mt-10) cc_final: 0.7050 (mt-10) REVERT: D 1819 ARG cc_start: 0.7248 (ptt-90) cc_final: 0.6778 (ptt-90) outliers start: 36 outliers final: 10 residues processed: 178 average time/residue: 1.4505 time to fit residues: 282.5636 Evaluate side-chains 150 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 138 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1082 ARG Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1537 THR Chi-restraints excluded: chain A residue 1915 THR Chi-restraints excluded: chain A residue 1974 VAL Chi-restraints excluded: chain D residue 1082 ARG Chi-restraints excluded: chain D residue 1095 SER Chi-restraints excluded: chain D residue 1537 THR Chi-restraints excluded: chain D residue 1651 VAL Chi-restraints excluded: chain D residue 1915 THR Chi-restraints excluded: chain D residue 1974 VAL Chi-restraints excluded: chain D residue 2070 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 174 optimal weight: 4.9990 chunk 188 optimal weight: 7.9990 chunk 155 optimal weight: 0.9990 chunk 173 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 140 optimal weight: 0.3980 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2059 GLN ** A2101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2059 GLN ** D2101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.0875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14970 Z= 0.248 Angle : 0.564 8.509 20456 Z= 0.277 Chirality : 0.043 0.157 2332 Planarity : 0.004 0.062 2628 Dihedral : 11.777 178.069 2134 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.78 % Allowed : 20.10 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.41 (0.19), residues: 1920 helix: 0.32 (0.20), residues: 664 sheet: -1.02 (0.27), residues: 336 loop : -0.26 (0.21), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1807 HIS 0.004 0.001 HIS A1093 PHE 0.011 0.001 PHE D1005 TYR 0.027 0.002 TYR A 991 ARG 0.004 0.000 ARG A1051 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 149 time to evaluate : 1.693 Fit side-chains REVERT: A 1082 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7910 (mtt-85) REVERT: A 1085 ARG cc_start: 0.7985 (mpt-90) cc_final: 0.7672 (mpp80) REVERT: A 1819 ARG cc_start: 0.7349 (ptt-90) cc_final: 0.6859 (ptt-90) REVERT: A 1865 LEU cc_start: 0.6697 (OUTLIER) cc_final: 0.6340 (tt) REVERT: A 2104 MET cc_start: 0.7928 (mpp) cc_final: 0.7591 (mpt) REVERT: D 1082 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7998 (mtt-85) REVERT: D 1085 ARG cc_start: 0.7977 (mpt-90) cc_final: 0.7672 (mpp80) REVERT: D 1644 GLU cc_start: 0.7358 (mt-10) cc_final: 0.7068 (mt-10) REVERT: D 1819 ARG cc_start: 0.7257 (ptt-90) cc_final: 0.6772 (ptt-90) REVERT: D 1865 LEU cc_start: 0.6777 (OUTLIER) cc_final: 0.6445 (tt) outliers start: 40 outliers final: 17 residues processed: 179 average time/residue: 1.4540 time to fit residues: 284.3129 Evaluate side-chains 157 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 136 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1000 ASP Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1082 ARG Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1537 THR Chi-restraints excluded: chain A residue 1602 GLU Chi-restraints excluded: chain A residue 1609 SER Chi-restraints excluded: chain A residue 1726 THR Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 1974 VAL Chi-restraints excluded: chain D residue 1000 ASP Chi-restraints excluded: chain D residue 1082 ARG Chi-restraints excluded: chain D residue 1095 SER Chi-restraints excluded: chain D residue 1537 THR Chi-restraints excluded: chain D residue 1602 GLU Chi-restraints excluded: chain D residue 1609 SER Chi-restraints excluded: chain D residue 1651 VAL Chi-restraints excluded: chain D residue 1726 THR Chi-restraints excluded: chain D residue 1865 LEU Chi-restraints excluded: chain D residue 1974 VAL Chi-restraints excluded: chain D residue 2070 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 4.9990 chunk 131 optimal weight: 50.0000 chunk 90 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 83 optimal weight: 9.9990 chunk 117 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 185 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2059 GLN ** A2101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1902 GLN D2059 GLN ** D2101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14970 Z= 0.341 Angle : 0.617 8.684 20456 Z= 0.307 Chirality : 0.045 0.191 2332 Planarity : 0.004 0.055 2628 Dihedral : 11.958 175.315 2134 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.82 % Allowed : 18.29 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.39 (0.19), residues: 1920 helix: 0.36 (0.20), residues: 640 sheet: -1.12 (0.27), residues: 338 loop : -0.20 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D1807 HIS 0.004 0.001 HIS A1735 PHE 0.013 0.002 PHE D1005 TYR 0.032 0.002 TYR D 991 ARG 0.004 0.001 ARG D1104 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 158 time to evaluate : 1.701 Fit side-chains REVERT: A 1614 MET cc_start: 0.9122 (OUTLIER) cc_final: 0.8602 (ptt) REVERT: A 1767 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8560 (mt) REVERT: A 1835 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7617 (pm20) REVERT: A 1865 LEU cc_start: 0.6937 (OUTLIER) cc_final: 0.6626 (tt) REVERT: A 1980 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.7137 (tp) REVERT: D 1614 MET cc_start: 0.9127 (OUTLIER) cc_final: 0.8889 (ptt) REVERT: D 1767 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8561 (mt) REVERT: D 1835 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7624 (pm20) REVERT: D 1980 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.7212 (tp) outliers start: 55 outliers final: 21 residues processed: 197 average time/residue: 1.4558 time to fit residues: 313.9828 Evaluate side-chains 182 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 152 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1000 ASP Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1118 CYS Chi-restraints excluded: chain A residue 1523 LYS Chi-restraints excluded: chain A residue 1537 THR Chi-restraints excluded: chain A residue 1602 GLU Chi-restraints excluded: chain A residue 1614 MET Chi-restraints excluded: chain A residue 1651 VAL Chi-restraints excluded: chain A residue 1726 THR Chi-restraints excluded: chain A residue 1767 LEU Chi-restraints excluded: chain A residue 1835 GLN Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 1974 VAL Chi-restraints excluded: chain A residue 1980 LEU Chi-restraints excluded: chain D residue 1000 ASP Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1095 SER Chi-restraints excluded: chain D residue 1118 CYS Chi-restraints excluded: chain D residue 1537 THR Chi-restraints excluded: chain D residue 1602 GLU Chi-restraints excluded: chain D residue 1614 MET Chi-restraints excluded: chain D residue 1651 VAL Chi-restraints excluded: chain D residue 1726 THR Chi-restraints excluded: chain D residue 1767 LEU Chi-restraints excluded: chain D residue 1835 GLN Chi-restraints excluded: chain D residue 1865 LEU Chi-restraints excluded: chain D residue 1974 VAL Chi-restraints excluded: chain D residue 1980 LEU Chi-restraints excluded: chain D residue 2070 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 128 optimal weight: 20.0000 chunk 0 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1902 GLN ** A2101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1902 GLN ** D2101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 14970 Z= 0.362 Angle : 0.629 9.400 20456 Z= 0.314 Chirality : 0.045 0.200 2332 Planarity : 0.004 0.049 2628 Dihedral : 11.997 173.262 2134 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.96 % Allowed : 18.01 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.43 (0.19), residues: 1920 helix: 0.31 (0.20), residues: 640 sheet: -1.13 (0.27), residues: 346 loop : -0.21 (0.21), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D1807 HIS 0.005 0.001 HIS D1516 PHE 0.013 0.002 PHE A1005 TYR 0.033 0.002 TYR A 991 ARG 0.004 0.001 ARG D1104 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 154 time to evaluate : 1.760 Fit side-chains REVERT: A 1601 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8253 (mtm) REVERT: A 1614 MET cc_start: 0.9137 (OUTLIER) cc_final: 0.8626 (ptt) REVERT: A 1711 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.6268 (tpt170) REVERT: A 1767 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8554 (mt) REVERT: A 1835 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7601 (pm20) REVERT: A 1980 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7203 (tp) REVERT: D 1601 MET cc_start: 0.8665 (ttm) cc_final: 0.8282 (mtm) REVERT: D 1614 MET cc_start: 0.9133 (OUTLIER) cc_final: 0.8621 (ptt) REVERT: D 1711 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.6268 (tpt170) REVERT: D 1767 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8553 (mt) REVERT: D 1980 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7260 (tp) outliers start: 57 outliers final: 29 residues processed: 196 average time/residue: 1.4644 time to fit residues: 313.4091 Evaluate side-chains 184 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 145 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1000 ASP Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1118 CYS Chi-restraints excluded: chain A residue 1537 THR Chi-restraints excluded: chain A residue 1538 ARG Chi-restraints excluded: chain A residue 1601 MET Chi-restraints excluded: chain A residue 1602 GLU Chi-restraints excluded: chain A residue 1614 MET Chi-restraints excluded: chain A residue 1651 VAL Chi-restraints excluded: chain A residue 1699 VAL Chi-restraints excluded: chain A residue 1711 ARG Chi-restraints excluded: chain A residue 1726 THR Chi-restraints excluded: chain A residue 1767 LEU Chi-restraints excluded: chain A residue 1835 GLN Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 1974 VAL Chi-restraints excluded: chain A residue 1980 LEU Chi-restraints excluded: chain A residue 2068 ILE Chi-restraints excluded: chain D residue 1000 ASP Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1095 SER Chi-restraints excluded: chain D residue 1537 THR Chi-restraints excluded: chain D residue 1538 ARG Chi-restraints excluded: chain D residue 1602 GLU Chi-restraints excluded: chain D residue 1614 MET Chi-restraints excluded: chain D residue 1651 VAL Chi-restraints excluded: chain D residue 1699 VAL Chi-restraints excluded: chain D residue 1711 ARG Chi-restraints excluded: chain D residue 1726 THR Chi-restraints excluded: chain D residue 1767 LEU Chi-restraints excluded: chain D residue 1865 LEU Chi-restraints excluded: chain D residue 1974 VAL Chi-restraints excluded: chain D residue 1980 LEU Chi-restraints excluded: chain D residue 2068 ILE Chi-restraints excluded: chain D residue 2070 VAL Chi-restraints excluded: chain D residue 2104 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 3.9990 chunk 167 optimal weight: 0.7980 chunk 36 optimal weight: 20.0000 chunk 108 optimal weight: 6.9990 chunk 45 optimal weight: 0.2980 chunk 185 optimal weight: 0.9980 chunk 154 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2101 GLN A2103 HIS D1835 GLN D2101 GLN D2103 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14970 Z= 0.222 Angle : 0.556 8.844 20456 Z= 0.275 Chirality : 0.042 0.153 2332 Planarity : 0.004 0.046 2628 Dihedral : 11.815 175.190 2134 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.78 % Allowed : 19.68 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.27 (0.19), residues: 1920 helix: 0.42 (0.20), residues: 640 sheet: -0.98 (0.28), residues: 330 loop : -0.14 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1807 HIS 0.005 0.001 HIS D1516 PHE 0.008 0.001 PHE D1005 TYR 0.029 0.002 TYR D 991 ARG 0.002 0.000 ARG A1664 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 146 time to evaluate : 1.730 Fit side-chains REVERT: A 1085 ARG cc_start: 0.7917 (mpt-90) cc_final: 0.7608 (mpp80) REVERT: A 1767 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8430 (mt) REVERT: A 1819 ARG cc_start: 0.7269 (ptt-90) cc_final: 0.7020 (ptt-90) REVERT: A 1835 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7498 (pm20) REVERT: A 1865 LEU cc_start: 0.6615 (OUTLIER) cc_final: 0.6268 (tt) REVERT: A 1980 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.7250 (tp) REVERT: D 1085 ARG cc_start: 0.7930 (mpt-90) cc_final: 0.7630 (mpp80) REVERT: D 1767 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8439 (mt) REVERT: D 1819 ARG cc_start: 0.7063 (ptt-90) cc_final: 0.6802 (ptt-90) REVERT: D 1835 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7367 (pm20) REVERT: D 1865 LEU cc_start: 0.6686 (OUTLIER) cc_final: 0.6374 (tt) REVERT: D 1980 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7251 (tp) outliers start: 40 outliers final: 22 residues processed: 176 average time/residue: 1.4784 time to fit residues: 285.0858 Evaluate side-chains 169 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 139 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1000 ASP Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1537 THR Chi-restraints excluded: chain A residue 1602 GLU Chi-restraints excluded: chain A residue 1651 VAL Chi-restraints excluded: chain A residue 1726 THR Chi-restraints excluded: chain A residue 1767 LEU Chi-restraints excluded: chain A residue 1835 GLN Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 1974 VAL Chi-restraints excluded: chain A residue 1980 LEU Chi-restraints excluded: chain A residue 2068 ILE Chi-restraints excluded: chain D residue 1000 ASP Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1095 SER Chi-restraints excluded: chain D residue 1474 LEU Chi-restraints excluded: chain D residue 1537 THR Chi-restraints excluded: chain D residue 1602 GLU Chi-restraints excluded: chain D residue 1651 VAL Chi-restraints excluded: chain D residue 1726 THR Chi-restraints excluded: chain D residue 1767 LEU Chi-restraints excluded: chain D residue 1835 GLN Chi-restraints excluded: chain D residue 1865 LEU Chi-restraints excluded: chain D residue 1974 VAL Chi-restraints excluded: chain D residue 1980 LEU Chi-restraints excluded: chain D residue 2068 ILE Chi-restraints excluded: chain D residue 2104 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 135 optimal weight: 7.9990 chunk 156 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 185 optimal weight: 6.9990 chunk 115 optimal weight: 0.5980 chunk 112 optimal weight: 0.1980 chunk 85 optimal weight: 0.6980 chunk 114 optimal weight: 0.0010 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14970 Z= 0.189 Angle : 0.537 8.555 20456 Z= 0.264 Chirality : 0.042 0.148 2332 Planarity : 0.003 0.044 2628 Dihedral : 11.760 176.070 2134 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.85 % Allowed : 19.54 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.21 (0.19), residues: 1920 helix: 0.45 (0.20), residues: 652 sheet: -0.82 (0.29), residues: 334 loop : -0.15 (0.21), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1807 HIS 0.004 0.001 HIS A1516 PHE 0.025 0.001 PHE D2109 TYR 0.028 0.002 TYR D 991 ARG 0.002 0.000 ARG A1664 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 141 time to evaluate : 1.543 Fit side-chains REVERT: A 1085 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7589 (mpp80) REVERT: A 1767 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8435 (mt) REVERT: A 1819 ARG cc_start: 0.7312 (ptt-90) cc_final: 0.7047 (ptt-90) REVERT: A 1865 LEU cc_start: 0.6563 (OUTLIER) cc_final: 0.6231 (tt) REVERT: A 2104 MET cc_start: 0.8010 (mpp) cc_final: 0.7801 (mpt) REVERT: D 1085 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7607 (mpp80) REVERT: D 1767 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8433 (mt) REVERT: D 1819 ARG cc_start: 0.7308 (ptt-90) cc_final: 0.7032 (ptt-90) REVERT: D 1865 LEU cc_start: 0.6570 (OUTLIER) cc_final: 0.6234 (tt) REVERT: D 2109 PHE cc_start: 0.8288 (p90) cc_final: 0.8068 (p90) outliers start: 41 outliers final: 24 residues processed: 172 average time/residue: 1.4481 time to fit residues: 273.2390 Evaluate side-chains 164 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 134 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1000 ASP Chi-restraints excluded: chain A residue 1010 GLU Chi-restraints excluded: chain A residue 1085 ARG Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1537 THR Chi-restraints excluded: chain A residue 1538 ARG Chi-restraints excluded: chain A residue 1602 GLU Chi-restraints excluded: chain A residue 1651 VAL Chi-restraints excluded: chain A residue 1699 VAL Chi-restraints excluded: chain A residue 1767 LEU Chi-restraints excluded: chain A residue 1830 VAL Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 1915 THR Chi-restraints excluded: chain A residue 1974 VAL Chi-restraints excluded: chain A residue 2068 ILE Chi-restraints excluded: chain D residue 1000 ASP Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1085 ARG Chi-restraints excluded: chain D residue 1095 SER Chi-restraints excluded: chain D residue 1474 LEU Chi-restraints excluded: chain D residue 1537 THR Chi-restraints excluded: chain D residue 1538 ARG Chi-restraints excluded: chain D residue 1602 GLU Chi-restraints excluded: chain D residue 1651 VAL Chi-restraints excluded: chain D residue 1699 VAL Chi-restraints excluded: chain D residue 1767 LEU Chi-restraints excluded: chain D residue 1865 LEU Chi-restraints excluded: chain D residue 1915 THR Chi-restraints excluded: chain D residue 1974 VAL Chi-restraints excluded: chain D residue 2068 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 0.9990 chunk 110 optimal weight: 0.3980 chunk 55 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 35 optimal weight: 30.0000 chunk 117 optimal weight: 5.9990 chunk 126 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2101 GLN ** D1835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14970 Z= 0.254 Angle : 0.572 8.999 20456 Z= 0.282 Chirality : 0.043 0.157 2332 Planarity : 0.004 0.042 2628 Dihedral : 11.843 175.274 2134 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.64 % Allowed : 20.03 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.20 (0.19), residues: 1920 helix: 0.45 (0.20), residues: 640 sheet: -0.82 (0.29), residues: 326 loop : -0.13 (0.21), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1807 HIS 0.005 0.001 HIS D1516 PHE 0.022 0.001 PHE D2109 TYR 0.029 0.002 TYR D 991 ARG 0.002 0.000 ARG D1664 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 141 time to evaluate : 1.550 Fit side-chains REVERT: A 1085 ARG cc_start: 0.7927 (mpt-90) cc_final: 0.7596 (mpp80) REVERT: A 1767 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8443 (mt) REVERT: A 1819 ARG cc_start: 0.7331 (ptt-90) cc_final: 0.7053 (ptt-90) REVERT: A 1865 LEU cc_start: 0.6580 (OUTLIER) cc_final: 0.6225 (tt) REVERT: D 1085 ARG cc_start: 0.7929 (mpt-90) cc_final: 0.7606 (mpp80) REVERT: D 1767 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8443 (mt) REVERT: D 1819 ARG cc_start: 0.7331 (ptt-90) cc_final: 0.7042 (ptt-90) REVERT: D 1865 LEU cc_start: 0.6583 (OUTLIER) cc_final: 0.6251 (tt) REVERT: D 2109 PHE cc_start: 0.8262 (p90) cc_final: 0.8037 (p90) outliers start: 38 outliers final: 24 residues processed: 171 average time/residue: 1.4745 time to fit residues: 276.5234 Evaluate side-chains 167 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 139 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1000 ASP Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1537 THR Chi-restraints excluded: chain A residue 1538 ARG Chi-restraints excluded: chain A residue 1602 GLU Chi-restraints excluded: chain A residue 1651 VAL Chi-restraints excluded: chain A residue 1699 VAL Chi-restraints excluded: chain A residue 1767 LEU Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 1974 VAL Chi-restraints excluded: chain A residue 2000 LEU Chi-restraints excluded: chain A residue 2068 ILE Chi-restraints excluded: chain D residue 1000 ASP Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1095 SER Chi-restraints excluded: chain D residue 1474 LEU Chi-restraints excluded: chain D residue 1537 THR Chi-restraints excluded: chain D residue 1538 ARG Chi-restraints excluded: chain D residue 1602 GLU Chi-restraints excluded: chain D residue 1651 VAL Chi-restraints excluded: chain D residue 1699 VAL Chi-restraints excluded: chain D residue 1767 LEU Chi-restraints excluded: chain D residue 1865 LEU Chi-restraints excluded: chain D residue 1974 VAL Chi-restraints excluded: chain D residue 2068 ILE Chi-restraints excluded: chain D residue 2104 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 5.9990 chunk 161 optimal weight: 0.8980 chunk 172 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 chunk 135 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 163 optimal weight: 2.9990 chunk 171 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2101 GLN ** D1835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 14970 Z= 0.300 Angle : 0.602 9.446 20456 Z= 0.298 Chirality : 0.044 0.173 2332 Planarity : 0.004 0.041 2628 Dihedral : 11.831 174.667 2134 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.64 % Allowed : 19.96 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.30 (0.19), residues: 1920 helix: 0.37 (0.20), residues: 640 sheet: -0.82 (0.27), residues: 354 loop : -0.19 (0.21), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1807 HIS 0.006 0.001 HIS A1516 PHE 0.020 0.002 PHE D2109 TYR 0.030 0.002 TYR A 991 ARG 0.003 0.000 ARG D1104 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 146 time to evaluate : 1.705 Fit side-chains REVERT: A 1767 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8497 (mt) REVERT: A 1873 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.7934 (ptt) REVERT: D 1767 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8493 (mt) REVERT: D 2109 PHE cc_start: 0.8246 (p90) cc_final: 0.7989 (p90) outliers start: 38 outliers final: 32 residues processed: 172 average time/residue: 1.4728 time to fit residues: 276.2811 Evaluate side-chains 181 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 146 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1000 ASP Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1085 ARG Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1537 THR Chi-restraints excluded: chain A residue 1538 ARG Chi-restraints excluded: chain A residue 1602 GLU Chi-restraints excluded: chain A residue 1651 VAL Chi-restraints excluded: chain A residue 1699 VAL Chi-restraints excluded: chain A residue 1726 THR Chi-restraints excluded: chain A residue 1767 LEU Chi-restraints excluded: chain A residue 1830 VAL Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 1873 MET Chi-restraints excluded: chain A residue 1974 VAL Chi-restraints excluded: chain A residue 2000 LEU Chi-restraints excluded: chain A residue 2068 ILE Chi-restraints excluded: chain D residue 1000 ASP Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1085 ARG Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1095 SER Chi-restraints excluded: chain D residue 1474 LEU Chi-restraints excluded: chain D residue 1537 THR Chi-restraints excluded: chain D residue 1538 ARG Chi-restraints excluded: chain D residue 1602 GLU Chi-restraints excluded: chain D residue 1651 VAL Chi-restraints excluded: chain D residue 1699 VAL Chi-restraints excluded: chain D residue 1726 THR Chi-restraints excluded: chain D residue 1767 LEU Chi-restraints excluded: chain D residue 1865 LEU Chi-restraints excluded: chain D residue 1974 VAL Chi-restraints excluded: chain D residue 2068 ILE Chi-restraints excluded: chain D residue 2104 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 9.9990 chunk 111 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 126 optimal weight: 20.0000 chunk 191 optimal weight: 5.9990 chunk 176 optimal weight: 9.9990 chunk 152 optimal weight: 0.3980 chunk 15 optimal weight: 0.4980 chunk 117 optimal weight: 5.9990 chunk 93 optimal weight: 0.0970 chunk 120 optimal weight: 2.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2101 GLN ** D1835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14970 Z= 0.223 Angle : 0.565 8.902 20456 Z= 0.279 Chirality : 0.042 0.153 2332 Planarity : 0.004 0.042 2628 Dihedral : 11.729 175.613 2134 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.57 % Allowed : 20.10 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.25 (0.19), residues: 1920 helix: 0.43 (0.20), residues: 640 sheet: -0.80 (0.27), residues: 358 loop : -0.17 (0.21), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1807 HIS 0.005 0.001 HIS A1516 PHE 0.020 0.001 PHE D2109 TYR 0.028 0.002 TYR D 991 ARG 0.002 0.000 ARG A1664 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3840 Ramachandran restraints generated. 1920 Oldfield, 0 Emsley, 1920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 138 time to evaluate : 1.674 Fit side-chains REVERT: A 1085 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7619 (mpp80) REVERT: A 1767 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8431 (mt) REVERT: A 1819 ARG cc_start: 0.7311 (ptt-90) cc_final: 0.7078 (ptt-90) REVERT: A 1865 LEU cc_start: 0.6570 (OUTLIER) cc_final: 0.6234 (tt) REVERT: A 1873 MET cc_start: 0.8106 (OUTLIER) cc_final: 0.7849 (ppp) REVERT: D 1085 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7612 (mpp80) REVERT: D 1767 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8429 (mt) REVERT: D 1819 ARG cc_start: 0.7323 (ptt-90) cc_final: 0.7082 (ptt-90) REVERT: D 1865 LEU cc_start: 0.6571 (OUTLIER) cc_final: 0.6234 (tt) REVERT: D 2109 PHE cc_start: 0.8250 (p90) cc_final: 0.8011 (p90) outliers start: 37 outliers final: 27 residues processed: 166 average time/residue: 1.4886 time to fit residues: 270.5745 Evaluate side-chains 170 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 136 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1000 ASP Chi-restraints excluded: chain A residue 1075 VAL Chi-restraints excluded: chain A residue 1085 ARG Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1537 THR Chi-restraints excluded: chain A residue 1538 ARG Chi-restraints excluded: chain A residue 1602 GLU Chi-restraints excluded: chain A residue 1651 VAL Chi-restraints excluded: chain A residue 1699 VAL Chi-restraints excluded: chain A residue 1767 LEU Chi-restraints excluded: chain A residue 1830 VAL Chi-restraints excluded: chain A residue 1865 LEU Chi-restraints excluded: chain A residue 1873 MET Chi-restraints excluded: chain A residue 1915 THR Chi-restraints excluded: chain A residue 1974 VAL Chi-restraints excluded: chain A residue 2068 ILE Chi-restraints excluded: chain D residue 1000 ASP Chi-restraints excluded: chain D residue 1075 VAL Chi-restraints excluded: chain D residue 1085 ARG Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1095 SER Chi-restraints excluded: chain D residue 1474 LEU Chi-restraints excluded: chain D residue 1537 THR Chi-restraints excluded: chain D residue 1538 ARG Chi-restraints excluded: chain D residue 1602 GLU Chi-restraints excluded: chain D residue 1651 VAL Chi-restraints excluded: chain D residue 1699 VAL Chi-restraints excluded: chain D residue 1767 LEU Chi-restraints excluded: chain D residue 1865 LEU Chi-restraints excluded: chain D residue 1915 THR Chi-restraints excluded: chain D residue 1974 VAL Chi-restraints excluded: chain D residue 2068 ILE Chi-restraints excluded: chain D residue 2104 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 140 optimal weight: 0.0470 chunk 22 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 152 optimal weight: 0.0980 chunk 63 optimal weight: 2.9990 chunk 156 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 133 optimal weight: 7.9990 overall best weight: 0.7882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2101 GLN ** D1835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.174077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.136537 restraints weight = 14745.384| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.77 r_work: 0.3382 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14970 Z= 0.199 Angle : 0.549 8.830 20456 Z= 0.270 Chirality : 0.042 0.150 2332 Planarity : 0.003 0.041 2628 Dihedral : 11.697 176.445 2134 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.57 % Allowed : 20.10 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.21 (0.19), residues: 1920 helix: 0.44 (0.20), residues: 652 sheet: -0.73 (0.28), residues: 358 loop : -0.16 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1807 HIS 0.005 0.001 HIS D1516 PHE 0.024 0.001 PHE A2109 TYR 0.028 0.002 TYR D 991 ARG 0.002 0.000 ARG A1664 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5415.41 seconds wall clock time: 98 minutes 13.58 seconds (5893.58 seconds total)