Starting phenix.real_space_refine on Sun Aug 9 07:47:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l06_62690/08_2026/9l06_62690_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l06_62690/08_2026/9l06_62690.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9l06_62690/08_2026/9l06_62690_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l06_62690/08_2026/9l06_62690_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9l06_62690/08_2026/9l06_62690.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l06_62690/08_2026/9l06_62690.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 28 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians P 296 5.49 5 Mg 1 5.21 5 S 40 5.16 5 C 10209 2.51 5 N 3255 2.21 5 O 3892 1.98 5 H 14796 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32489 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1622 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1464 Classifications: {'peptide': 87} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "C" Number of atoms: 1660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1660 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 1439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1439 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 1584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 1584 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1373 Classifications: {'peptide': 86} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG%NH3:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 1675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 1675 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 1469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1469 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 4648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 4648 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 4678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 4678 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 6481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 6481 Classifications: {'peptide': 393} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 380} Chain breaks: 2 Chain: "K" Number of atoms: 4368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 4368 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 89} Link IDs: {'PTRANS': 8, 'TRANS': 322} Chain breaks: 2 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 267 Unresolved non-hydrogen dihedrals: 89 Planarities with less than four sites: {'UNK:plan-1': 89} Unresolved non-hydrogen planarities: 89 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.00, per 1000 atoms: 0.15 Number of scatterers: 32489 At special positions: 0 Unit cell: (108.95, 164.38, 139.532, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 40 16.00 P 296 15.00 Mg 1 11.99 O 3892 8.00 N 3255 7.00 C 10209 6.00 H 14796 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied TRANS " UNK K1901 " - " GLY K1900 " Time building additional restraints: 2.54 Conformation dependent library (CDL) restraints added in 753.9 milliseconds 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2814 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 14 sheets defined 65.0% alpha, 5.4% beta 147 base pairs and 253 stacking pairs defined. Time for finding SS restraints: 5.30 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.699A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.573A pdb=" N GLN A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.782A pdb=" N ILE A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.926A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.552A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.619A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 121 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.529A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.558A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.503A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.936A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.542A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.526A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.624A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.652A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 1490 through 1511 Processing helix chain 'K' and resid 1553 through 1560 removed outlier: 4.272A pdb=" N LYS K1559 " --> pdb=" O ASN K1555 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU K1560 " --> pdb=" O MET K1556 " (cutoff:3.500A) Processing helix chain 'K' and resid 1561 through 1576 removed outlier: 4.058A pdb=" N ASP K1566 " --> pdb=" O PRO K1562 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY K1567 " --> pdb=" O HIS K1563 " (cutoff:3.500A) Processing helix chain 'K' and resid 1578 through 1583 removed outlier: 3.923A pdb=" N LYS K1583 " --> pdb=" O VAL K1579 " (cutoff:3.500A) Processing helix chain 'K' and resid 1601 through 1613 removed outlier: 3.705A pdb=" N THR K1610 " --> pdb=" O SER K1606 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU K1613 " --> pdb=" O HIS K1609 " (cutoff:3.500A) Processing helix chain 'K' and resid 1630 through 1642 removed outlier: 3.910A pdb=" N MET K1635 " --> pdb=" O ALA K1631 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN K1636 " --> pdb=" O LEU K1632 " (cutoff:3.500A) Processing helix chain 'K' and resid 1646 through 1650 removed outlier: 3.970A pdb=" N LYS K1650 " --> pdb=" O ASP K1647 " (cutoff:3.500A) Processing helix chain 'K' and resid 1661 through 1676 removed outlier: 4.034A pdb=" N TYR K1667 " --> pdb=" O GLN K1663 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N MET K1668 " --> pdb=" O GLU K1664 " (cutoff:3.500A) Processing helix chain 'K' and resid 1683 through 1692 removed outlier: 3.576A pdb=" N ASN K1688 " --> pdb=" O GLU K1684 " (cutoff:3.500A) Processing helix chain 'K' and resid 1697 through 1709 removed outlier: 3.507A pdb=" N GLU K1702 " --> pdb=" O ARG K1698 " (cutoff:3.500A) Processing helix chain 'K' and resid 1721 through 1724 Processing helix chain 'K' and resid 1729 through 1737 Processing helix chain 'K' and resid 1755 through 1766 removed outlier: 4.285A pdb=" N MET K1761 " --> pdb=" O GLU K1757 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N PHE K1764 " --> pdb=" O CYS K1760 " (cutoff:3.500A) Processing helix chain 'K' and resid 1772 through 1780 Processing helix chain 'K' and resid 1780 through 1789 removed outlier: 4.061A pdb=" N GLY K1787 " --> pdb=" O PRO K1783 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLN K1788 " --> pdb=" O ILE K1784 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N CYS K1789 " --> pdb=" O GLN K1785 " (cutoff:3.500A) Processing helix chain 'K' and resid 1793 through 1810 removed outlier: 3.898A pdb=" N LYS K1802 " --> pdb=" O ARG K1798 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA K1804 " --> pdb=" O MET K1800 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N HIS K1805 " --> pdb=" O LYS K1801 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR K1808 " --> pdb=" O ALA K1804 " (cutoff:3.500A) Processing helix chain 'K' and resid 1820 through 1825 removed outlier: 3.704A pdb=" N LYS K1825 " --> pdb=" O THR K1821 " (cutoff:3.500A) Processing helix chain 'K' and resid 1840 through 1854 Processing helix chain 'K' and resid 1871 through 1883 Processing helix chain 'K' and resid 1887 through 1898 Processing helix chain 'K' and resid 1966 through 1970 Processing helix chain 'K' and resid 1972 through 1976 removed outlier: 3.948A pdb=" N UNK K1975 " --> pdb=" O UNK K1972 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N UNK K1976 " --> pdb=" O UNK K1973 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 1972 through 1976' Processing helix chain 'K' and resid 2000 through 2005 removed outlier: 3.595A pdb=" N ASP K2004 " --> pdb=" O TRP K2001 " (cutoff:3.500A) Processing helix chain 'K' and resid 2007 through 2013 removed outlier: 3.572A pdb=" N ALA K2011 " --> pdb=" O ASP K2008 " (cutoff:3.500A) Processing helix chain 'K' and resid 2017 through 2034 Processing helix chain 'K' and resid 2044 through 2063 removed outlier: 3.774A pdb=" N LYS K2061 " --> pdb=" O ALA K2057 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR K2062 " --> pdb=" O SER K2058 " (cutoff:3.500A) Processing helix chain 'K' and resid 2091 through 2104 Processing helix chain 'K' and resid 2117 through 2121 Processing helix chain 'K' and resid 2140 through 2149 removed outlier: 4.306A pdb=" N ASP K2144 " --> pdb=" O ASN K2140 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE K2149 " --> pdb=" O ILE K2145 " (cutoff:3.500A) Processing helix chain 'K' and resid 2170 through 2190 removed outlier: 4.110A pdb=" N LYS K2174 " --> pdb=" O THR K2170 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG K2188 " --> pdb=" O SER K2184 " (cutoff:3.500A) Processing helix chain 'K' and resid 2234 through 2244 removed outlier: 4.051A pdb=" N GLN K2242 " --> pdb=" O ALA K2238 " (cutoff:3.500A) Processing helix chain 'K' and resid 2245 through 2248 removed outlier: 3.599A pdb=" N ILE K2248 " --> pdb=" O LYS K2245 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 2245 through 2248' Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.034A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.509A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.819A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.031A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.480A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 1538 through 1541 removed outlier: 7.162A pdb=" N VAL K1538 " --> pdb=" O GLN K1551 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLN K1551 " --> pdb=" O VAL K1538 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ASP K1540 " --> pdb=" O LEU K1549 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 1716 through 1719 removed outlier: 4.116A pdb=" N LYS K1818 " --> pdb=" O ALA K1593 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 1623 through 1626 removed outlier: 6.100A pdb=" N VAL K1624 " --> pdb=" O ILE K1681 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N SER K1654 " --> pdb=" O ILE K1680 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N GLY K1682 " --> pdb=" O SER K1654 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'K' and resid 1833 through 1837 removed outlier: 7.566A pdb=" N VAL K2037 " --> pdb=" O PHE K2113 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ILE K2115 " --> pdb=" O VAL K2037 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL K2039 " --> pdb=" O ILE K2115 " (cutoff:3.500A) 622 hydrogen bonds defined for protein. 1803 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 376 hydrogen bonds 752 hydrogen bond angles 0 basepair planarities 147 basepair parallelities 253 stacking parallelities Total time for adding SS restraints: 8.88 Time building geometry restraints manager: 3.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 14781 1.03 - 1.23: 146 1.23 - 1.42: 8046 1.42 - 1.62: 10358 1.62 - 1.81: 67 Bond restraints: 33398 Sorted by residual: bond pdb=" C4 ADP K2601 " pdb=" C5 ADP K2601 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.10e+01 bond pdb=" C5 ADP K2601 " pdb=" C6 ADP K2601 " ideal model delta sigma weight residual 1.490 1.406 0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" C1' DC I 56 " pdb=" N1 DC I 56 " ideal model delta sigma weight residual 1.468 1.516 -0.048 1.40e-02 5.10e+03 1.18e+01 bond pdb=" C1' DT I 57 " pdb=" N1 DT I 57 " ideal model delta sigma weight residual 1.468 1.516 -0.048 1.40e-02 5.10e+03 1.16e+01 bond pdb=" O3' DC J 127 " pdb=" P DT J 128 " ideal model delta sigma weight residual 1.607 1.648 -0.041 1.20e-02 6.94e+03 1.15e+01 ... (remaining 33393 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 59553 2.34 - 4.68: 688 4.68 - 7.02: 11 7.02 - 9.37: 17 9.37 - 11.71: 32 Bond angle restraints: 60301 Sorted by residual: angle pdb=" N3 DT J 128 " pdb=" C4 DT J 128 " pdb=" O4 DT J 128 " ideal model delta sigma weight residual 119.90 122.63 -2.73 6.00e-01 2.78e+00 2.06e+01 angle pdb=" N3 DT J 51 " pdb=" C4 DT J 51 " pdb=" O4 DT J 51 " ideal model delta sigma weight residual 119.90 122.62 -2.72 6.00e-01 2.78e+00 2.05e+01 angle pdb=" N3 DT I 32 " pdb=" C4 DT I 32 " pdb=" O4 DT I 32 " ideal model delta sigma weight residual 119.90 122.61 -2.71 6.00e-01 2.78e+00 2.03e+01 angle pdb=" N3 DT I 115 " pdb=" C4 DT I 115 " pdb=" O4 DT I 115 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" N3 DT I 142 " pdb=" C4 DT I 142 " pdb=" O4 DT I 142 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 ... (remaining 60296 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.62: 12664 33.62 - 67.23: 1746 67.23 - 100.85: 47 100.85 - 134.46: 1 134.46 - 168.08: 4 Dihedral angle restraints: 14462 sinusoidal: 9545 harmonic: 4917 Sorted by residual: dihedral pdb=" C5' ADP K2601 " pdb=" O5' ADP K2601 " pdb=" PA ADP K2601 " pdb=" O2A ADP K2601 " ideal model delta sinusoidal sigma weight residual -60.00 38.44 -98.43 1 2.00e+01 2.50e-03 2.75e+01 dihedral pdb=" C4' DC J 142 " pdb=" C3' DC J 142 " pdb=" O3' DC J 142 " pdb=" P DT J 143 " ideal model delta sinusoidal sigma weight residual 220.00 51.92 168.08 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DA J 2 " pdb=" C3' DA J 2 " pdb=" O3' DA J 2 " pdb=" P DT J 3 " ideal model delta sinusoidal sigma weight residual 220.00 55.75 164.25 1 3.50e+01 8.16e-04 1.54e+01 ... (remaining 14459 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 2737 0.122 - 0.243: 239 0.243 - 0.365: 4 0.365 - 0.486: 18 0.486 - 0.608: 1 Chirality restraints: 2999 Sorted by residual: chirality pdb=" P DC J 127 " pdb=" OP1 DC J 127 " pdb=" OP2 DC J 127 " pdb=" O5' DC J 127 " both_signs ideal model delta sigma weight residual True 2.34 -2.94 -0.61 2.00e-01 2.50e+01 9.25e+00 chirality pdb=" P DC J 145 " pdb=" OP1 DC J 145 " pdb=" OP2 DC J 145 " pdb=" O5' DC J 145 " both_signs ideal model delta sigma weight residual True 2.34 -2.78 -0.44 2.00e-01 2.50e+01 4.94e+00 chirality pdb=" P DT I 146 " pdb=" OP1 DT I 146 " pdb=" OP2 DT I 146 " pdb=" O5' DT I 146 " both_signs ideal model delta sigma weight residual True 2.34 -2.77 -0.43 2.00e-01 2.50e+01 4.72e+00 ... (remaining 2996 not shown) Planarity restraints: 3915 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS K1899 " -0.017 2.00e-02 2.50e+03 3.10e-02 9.63e+00 pdb=" N GLY K1900 " 0.053 2.00e-02 2.50e+03 pdb=" CA GLY K1900 " -0.014 2.00e-02 2.50e+03 pdb=" H GLY K1900 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS K1899 " -0.014 2.00e-02 2.50e+03 2.82e-02 7.95e+00 pdb=" C LYS K1899 " 0.049 2.00e-02 2.50e+03 pdb=" O LYS K1899 " -0.019 2.00e-02 2.50e+03 pdb=" N GLY K1900 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 127 " 0.001 2.00e-02 2.50e+03 1.62e-02 7.19e+00 pdb=" N1 DC J 127 " -0.036 2.00e-02 2.50e+03 pdb=" C2 DC J 127 " -0.017 2.00e-02 2.50e+03 pdb=" O2 DC J 127 " 0.021 2.00e-02 2.50e+03 pdb=" N3 DC J 127 " 0.015 2.00e-02 2.50e+03 pdb=" C4 DC J 127 " -0.001 2.00e-02 2.50e+03 pdb=" N4 DC J 127 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DC J 127 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DC J 127 " -0.001 2.00e-02 2.50e+03 pdb=" H5 DC J 127 " -0.002 2.00e-02 2.50e+03 pdb=" H6 DC J 127 " 0.025 2.00e-02 2.50e+03 ... (remaining 3912 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.38: 10304 2.38 - 2.93: 66103 2.93 - 3.49: 75430 3.49 - 4.04: 110958 4.04 - 4.60: 161599 Nonbonded interactions: 424394 Sorted by model distance: nonbonded pdb=" HE2 HIS K1594 " pdb="HE21 GLN K1816 " model vdw 1.824 2.100 nonbonded pdb=" HB3 GLN H 44 " pdb="HE21 GLN H 44 " model vdw 1.907 2.270 nonbonded pdb=" HD3 ARG K1779 " pdb="HH11 ARG K1779 " model vdw 1.912 2.270 nonbonded pdb=" HD3 ARG B 39 " pdb="HH11 ARG B 39 " model vdw 1.914 2.270 nonbonded pdb=" H2' DC I 26 " pdb=" H6 DC I 26 " model vdw 1.918 2.270 ... (remaining 424389 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and ((resid 17 and (name N or name CA or name C or name O or name CB \ or name HA )) or resid 18 or (resid 19 through 20 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 21 through 22 or (resid \ 23 and (name N or name CA or name C or name O or name CB or name H or name HA ) \ ) or resid 24 through 100 or (resid 101 and (name N or name CA or name C or name \ O or name H or name HA2 or name HA3)))) selection = (chain 'F' and ((resid 17 and (name N or name CA or name C or name O or name CB \ or name HA )) or resid 18 through 101)) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 75 through 118)) selection = (chain 'G' and (resid 12 or (resid 13 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 14 through 35 or (resid 36 and (nam \ e N or name CA or name C or name O or name CB or name H or name HA )) or resid 3 \ 7 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 32 through 53 or (resid \ 54 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 55 through 121)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.200 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 33.690 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 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 : 0.006 0.111 18603 Z= 0.450 Angle : 0.831 11.707 26400 Z= 0.606 Chirality : 0.064 0.608 2999 Planarity : 0.004 0.077 2339 Dihedral : 24.217 168.077 7653 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.67 % Allowed : 6.95 % Favored : 92.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.23), residues: 1373 helix: 1.57 (0.19), residues: 818 sheet: -1.21 (0.64), residues: 61 loop : -0.78 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K1661 TYR 0.009 0.001 TYR K1847 PHE 0.010 0.001 PHE A 84 TRP 0.008 0.001 TRP K1883 HIS 0.003 0.001 HIS K1805 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.45 (18602) covalent geometry : angle 0.83047 / 0.61 (26397) hydrogen bonds : bond 0.16670 / 11.30 ( 998) hydrogen bonds : angle 5.00156 / 3.61 ( 2555) link_TRANS : bond 0.01622 / 0.85 ( 1) link_TRANS : angle 2.41387 / 1.23 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7921 (mt-10) REVERT: F 91 LYS cc_start: 0.8788 (ttmt) cc_final: 0.8363 (ttpt) REVERT: K 1481 ARG cc_start: 0.7689 (OUTLIER) cc_final: 0.6932 (mpt180) outliers start: 8 outliers final: 6 residues processed: 112 average time/residue: 0.3354 time to fit residues: 53.6073 Evaluate side-chains 106 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 99 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain K residue 1481 ARG Chi-restraints excluded: chain K residue 1588 SER Chi-restraints excluded: chain K residue 1630 THR Chi-restraints excluded: chain K residue 1694 ASN Chi-restraints excluded: chain K residue 1765 ILE Chi-restraints excluded: chain K residue 1814 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.135404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.100932 restraints weight = 71869.892| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.87 r_work: 0.3092 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.0580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18603 Z= 0.179 Angle : 0.599 7.520 26400 Z= 0.375 Chirality : 0.042 0.293 2999 Planarity : 0.004 0.073 2339 Dihedral : 27.177 166.806 4870 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.92 % Allowed : 7.28 % Favored : 91.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.23), residues: 1373 helix: 1.81 (0.18), residues: 837 sheet: -1.27 (0.64), residues: 56 loop : -0.85 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K1661 TYR 0.013 0.001 TYR K1847 PHE 0.008 0.001 PHE K2135 TRP 0.006 0.001 TRP K1883 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.18 (18602) covalent geometry : angle 0.59883 / 0.38 (26397) hydrogen bonds : bond 0.07068 / 4.77 ( 998) hydrogen bonds : angle 3.87704 / 2.80 ( 2555) link_TRANS : bond 0.00288 / 0.15 ( 1) link_TRANS : angle 0.47368 / 0.19 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Evaluate side-chains 108 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.785 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8180 (mt-10) REVERT: F 91 LYS cc_start: 0.8870 (ttmt) cc_final: 0.8452 (ttpt) REVERT: K 1481 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7006 (mpt180) outliers start: 11 outliers final: 9 residues processed: 104 average time/residue: 0.2925 time to fit residues: 45.1153 Evaluate side-chains 106 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain K residue 1481 ARG Chi-restraints excluded: chain K residue 1588 SER Chi-restraints excluded: chain K residue 1630 THR Chi-restraints excluded: chain K residue 1668 MET Chi-restraints excluded: chain K residue 1694 ASN Chi-restraints excluded: chain K residue 1696 LYS Chi-restraints excluded: chain K residue 1765 ILE Chi-restraints excluded: chain K residue 2180 VAL Chi-restraints excluded: chain K residue 2205 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 82 optimal weight: 7.9990 chunk 133 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 78 optimal weight: 7.9990 chunk 100 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 136 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 85 optimal weight: 20.0000 chunk 29 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K1569 GLN ** K1694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.135677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.101236 restraints weight = 71343.781| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.88 r_work: 0.3094 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.0930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18603 Z= 0.169 Angle : 0.566 6.512 26400 Z= 0.356 Chirality : 0.040 0.274 2999 Planarity : 0.004 0.050 2339 Dihedral : 27.278 167.420 4867 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.34 % Allowed : 7.03 % Favored : 91.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.23), residues: 1373 helix: 1.91 (0.19), residues: 845 sheet: -1.56 (0.61), residues: 58 loop : -1.08 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K1803 TYR 0.014 0.001 TYR K1847 PHE 0.009 0.001 PHE K2024 TRP 0.013 0.001 TRP K1883 HIS 0.003 0.001 HIS K1609 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.17 (18602) covalent geometry : angle 0.56649 / 0.36 (26397) hydrogen bonds : bond 0.06015 / 4.03 ( 998) hydrogen bonds : angle 3.54415 / 2.55 ( 2555) link_TRANS : bond 0.00191 / 0.10 ( 1) link_TRANS : angle 0.38989 / 0.16 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.650 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8175 (mt-10) REVERT: C 90 ASP cc_start: 0.8935 (t0) cc_final: 0.8616 (t70) REVERT: F 91 LYS cc_start: 0.8874 (ttmt) cc_final: 0.8474 (ttpt) REVERT: H 65 ASP cc_start: 0.8937 (t0) cc_final: 0.8674 (t0) REVERT: K 1481 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7587 (mmt-90) outliers start: 16 outliers final: 11 residues processed: 112 average time/residue: 0.3031 time to fit residues: 50.6830 Evaluate side-chains 110 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain K residue 1481 ARG Chi-restraints excluded: chain K residue 1557 VAL Chi-restraints excluded: chain K residue 1588 SER Chi-restraints excluded: chain K residue 1630 THR Chi-restraints excluded: chain K residue 1694 ASN Chi-restraints excluded: chain K residue 1765 ILE Chi-restraints excluded: chain K residue 1814 CYS Chi-restraints excluded: chain K residue 2135 PHE Chi-restraints excluded: chain K residue 2180 VAL Chi-restraints excluded: chain K residue 2205 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 97 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 68 optimal weight: 0.4980 chunk 69 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K1694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.135879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.101775 restraints weight = 71540.804| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.83 r_work: 0.3103 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18603 Z= 0.157 Angle : 0.556 6.253 26400 Z= 0.348 Chirality : 0.040 0.287 2999 Planarity : 0.004 0.044 2339 Dihedral : 27.369 167.881 4867 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.09 % Allowed : 8.12 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.23), residues: 1373 helix: 2.07 (0.19), residues: 843 sheet: -1.57 (0.62), residues: 58 loop : -1.06 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K1803 TYR 0.013 0.001 TYR K1847 PHE 0.008 0.001 PHE K2135 TRP 0.012 0.001 TRP K1883 HIS 0.003 0.001 HIS K2244 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.16 (18602) covalent geometry : angle 0.55639 / 0.35 (26397) hydrogen bonds : bond 0.05415 / 3.63 ( 998) hydrogen bonds : angle 3.36293 / 2.42 ( 2555) link_TRANS : bond 0.00089 / 0.05 ( 1) link_TRANS : angle 0.16164 / 0.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Evaluate side-chains 112 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8162 (mt-10) REVERT: C 90 ASP cc_start: 0.8943 (t0) cc_final: 0.8639 (t70) REVERT: F 91 LYS cc_start: 0.8839 (ttmt) cc_final: 0.8449 (ttpt) REVERT: H 65 ASP cc_start: 0.8952 (t0) cc_final: 0.8735 (t0) REVERT: K 1481 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7289 (mpt180) outliers start: 13 outliers final: 11 residues processed: 109 average time/residue: 0.2768 time to fit residues: 45.0044 Evaluate side-chains 110 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain K residue 1481 ARG Chi-restraints excluded: chain K residue 1588 SER Chi-restraints excluded: chain K residue 1625 VAL Chi-restraints excluded: chain K residue 1630 THR Chi-restraints excluded: chain K residue 1694 ASN Chi-restraints excluded: chain K residue 1696 LYS Chi-restraints excluded: chain K residue 1765 ILE Chi-restraints excluded: chain K residue 1814 CYS Chi-restraints excluded: chain K residue 2135 PHE Chi-restraints excluded: chain K residue 2180 VAL Chi-restraints excluded: chain K residue 2205 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K1694 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.134855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.100886 restraints weight = 71765.541| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.82 r_work: 0.3085 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 18603 Z= 0.191 Angle : 0.570 6.572 26400 Z= 0.354 Chirality : 0.040 0.282 2999 Planarity : 0.004 0.044 2339 Dihedral : 27.437 167.846 4867 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.26 % Allowed : 8.20 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.23), residues: 1373 helix: 2.06 (0.19), residues: 843 sheet: -1.68 (0.61), residues: 58 loop : -1.18 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K2178 TYR 0.014 0.001 TYR D 39 PHE 0.008 0.001 PHE K1776 TRP 0.012 0.001 TRP K1883 HIS 0.004 0.001 HIS K1609 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.19 (18602) covalent geometry : angle 0.57004 / 0.35 (26397) hydrogen bonds : bond 0.05722 / 3.82 ( 998) hydrogen bonds : angle 3.41126 / 2.45 ( 2555) link_TRANS : bond 0.00079 / 0.04 ( 1) link_TRANS : angle 0.37102 / 0.17 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8149 (mt-10) REVERT: C 90 ASP cc_start: 0.8931 (t0) cc_final: 0.8599 (t70) REVERT: F 91 LYS cc_start: 0.8857 (ttmt) cc_final: 0.8463 (ttpt) REVERT: H 65 ASP cc_start: 0.8983 (t0) cc_final: 0.8765 (t0) REVERT: K 1481 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7320 (mpt180) outliers start: 15 outliers final: 13 residues processed: 111 average time/residue: 0.3172 time to fit residues: 52.4362 Evaluate side-chains 113 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain K residue 1481 ARG Chi-restraints excluded: chain K residue 1557 VAL Chi-restraints excluded: chain K residue 1588 SER Chi-restraints excluded: chain K residue 1625 VAL Chi-restraints excluded: chain K residue 1630 THR Chi-restraints excluded: chain K residue 1694 ASN Chi-restraints excluded: chain K residue 1696 LYS Chi-restraints excluded: chain K residue 1765 ILE Chi-restraints excluded: chain K residue 1814 CYS Chi-restraints excluded: chain K residue 2135 PHE Chi-restraints excluded: chain K residue 2180 VAL Chi-restraints excluded: chain K residue 2205 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 47 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 76 optimal weight: 10.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.135486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.101421 restraints weight = 71320.305| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.82 r_work: 0.3098 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 18603 Z= 0.153 Angle : 0.550 6.342 26400 Z= 0.344 Chirality : 0.039 0.286 2999 Planarity : 0.004 0.043 2339 Dihedral : 27.472 167.919 4867 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.17 % Allowed : 8.37 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.23), residues: 1373 helix: 2.12 (0.19), residues: 843 sheet: -1.66 (0.62), residues: 58 loop : -1.13 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K1803 TYR 0.012 0.001 TYR K1847 PHE 0.007 0.001 PHE K2135 TRP 0.012 0.001 TRP K1883 HIS 0.002 0.001 HIS K1609 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.15 (18602) covalent geometry : angle 0.55000 / 0.34 (26397) hydrogen bonds : bond 0.05270 / 3.53 ( 998) hydrogen bonds : angle 3.31893 / 2.38 ( 2555) link_TRANS : bond 0.00065 / 0.03 ( 1) link_TRANS : angle 0.12674 / 0.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.756 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8139 (mt-10) REVERT: C 90 ASP cc_start: 0.8913 (t0) cc_final: 0.8606 (t70) REVERT: D 90 GLU cc_start: 0.9281 (OUTLIER) cc_final: 0.8356 (mp0) REVERT: E 42 ARG cc_start: 0.8315 (mtp85) cc_final: 0.7936 (mtp85) REVERT: F 91 LYS cc_start: 0.8869 (ttmt) cc_final: 0.8484 (ttpt) REVERT: H 65 ASP cc_start: 0.8977 (t0) cc_final: 0.8740 (t0) REVERT: K 1481 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7144 (mpt180) outliers start: 14 outliers final: 11 residues processed: 109 average time/residue: 0.3286 time to fit residues: 53.0117 Evaluate side-chains 112 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain K residue 1481 ARG Chi-restraints excluded: chain K residue 1588 SER Chi-restraints excluded: chain K residue 1625 VAL Chi-restraints excluded: chain K residue 1630 THR Chi-restraints excluded: chain K residue 1696 LYS Chi-restraints excluded: chain K residue 1765 ILE Chi-restraints excluded: chain K residue 1814 CYS Chi-restraints excluded: chain K residue 2135 PHE Chi-restraints excluded: chain K residue 2180 VAL Chi-restraints excluded: chain K residue 2205 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 34 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 116 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K1694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.134536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.100539 restraints weight = 71693.658| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.82 r_work: 0.3080 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 18603 Z= 0.187 Angle : 0.571 6.845 26400 Z= 0.352 Chirality : 0.040 0.285 2999 Planarity : 0.004 0.045 2339 Dihedral : 27.520 167.925 4865 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.26 % Allowed : 8.37 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.23), residues: 1373 helix: 2.09 (0.19), residues: 842 sheet: -1.74 (0.61), residues: 58 loop : -1.23 (0.26), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K1803 TYR 0.014 0.001 TYR K1847 PHE 0.008 0.001 PHE A 84 TRP 0.011 0.001 TRP K1883 HIS 0.004 0.001 HIS K1609 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.19 (18602) covalent geometry : angle 0.57138 / 0.35 (26397) hydrogen bonds : bond 0.05641 / 3.77 ( 998) hydrogen bonds : angle 3.36202 / 2.41 ( 2555) link_TRANS : bond 0.00066 / 0.03 ( 1) link_TRANS : angle 0.17250 / 0.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.751 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8152 (mt-10) REVERT: C 90 ASP cc_start: 0.8922 (t0) cc_final: 0.8600 (t70) REVERT: D 90 GLU cc_start: 0.9300 (OUTLIER) cc_final: 0.8253 (mp0) REVERT: E 42 ARG cc_start: 0.8330 (mtp85) cc_final: 0.7966 (mtp85) REVERT: F 91 LYS cc_start: 0.8873 (ttmt) cc_final: 0.8485 (ttpt) REVERT: H 65 ASP cc_start: 0.8993 (t0) cc_final: 0.8764 (t0) REVERT: K 1481 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7338 (mpt180) outliers start: 15 outliers final: 12 residues processed: 110 average time/residue: 0.3120 time to fit residues: 50.8841 Evaluate side-chains 113 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain K residue 1481 ARG Chi-restraints excluded: chain K residue 1557 VAL Chi-restraints excluded: chain K residue 1588 SER Chi-restraints excluded: chain K residue 1625 VAL Chi-restraints excluded: chain K residue 1630 THR Chi-restraints excluded: chain K residue 1696 LYS Chi-restraints excluded: chain K residue 1765 ILE Chi-restraints excluded: chain K residue 1814 CYS Chi-restraints excluded: chain K residue 2135 PHE Chi-restraints excluded: chain K residue 2180 VAL Chi-restraints excluded: chain K residue 2205 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 118 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 chunk 115 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 74 optimal weight: 20.0000 chunk 61 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 85 optimal weight: 20.0000 chunk 84 optimal weight: 10.0000 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K1694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.134701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.100572 restraints weight = 71316.016| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.83 r_work: 0.3081 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18603 Z= 0.175 Angle : 0.562 6.811 26400 Z= 0.348 Chirality : 0.040 0.285 2999 Planarity : 0.004 0.047 2339 Dihedral : 27.534 167.800 4865 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.17 % Allowed : 8.79 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.23), residues: 1373 helix: 2.17 (0.19), residues: 836 sheet: -1.78 (0.61), residues: 58 loop : -1.15 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K1803 TYR 0.013 0.001 TYR K1847 PHE 0.007 0.001 PHE K2024 TRP 0.011 0.001 TRP K1883 HIS 0.003 0.001 HIS K1609 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.17 (18602) covalent geometry : angle 0.56239 / 0.35 (26397) hydrogen bonds : bond 0.05496 / 3.67 ( 998) hydrogen bonds : angle 3.33573 / 2.39 ( 2555) link_TRANS : bond 0.00054 / 0.03 ( 1) link_TRANS : angle 0.13290 / 0.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.785 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8149 (mt-10) REVERT: C 90 ASP cc_start: 0.8921 (t0) cc_final: 0.8595 (t70) REVERT: D 90 GLU cc_start: 0.9294 (OUTLIER) cc_final: 0.8245 (mp0) REVERT: E 42 ARG cc_start: 0.8333 (mtp85) cc_final: 0.7964 (mtp85) REVERT: F 91 LYS cc_start: 0.8868 (ttmt) cc_final: 0.8458 (ttpt) REVERT: H 65 ASP cc_start: 0.8989 (t0) cc_final: 0.8746 (t0) REVERT: K 1481 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7302 (mpt180) outliers start: 14 outliers final: 11 residues processed: 109 average time/residue: 0.3386 time to fit residues: 53.5692 Evaluate side-chains 113 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain K residue 1481 ARG Chi-restraints excluded: chain K residue 1588 SER Chi-restraints excluded: chain K residue 1625 VAL Chi-restraints excluded: chain K residue 1630 THR Chi-restraints excluded: chain K residue 1696 LYS Chi-restraints excluded: chain K residue 1765 ILE Chi-restraints excluded: chain K residue 1814 CYS Chi-restraints excluded: chain K residue 2135 PHE Chi-restraints excluded: chain K residue 2180 VAL Chi-restraints excluded: chain K residue 2205 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 60 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K1694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.134622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.100043 restraints weight = 71296.227| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.86 r_work: 0.3078 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18603 Z= 0.173 Angle : 0.560 6.816 26400 Z= 0.347 Chirality : 0.039 0.286 2999 Planarity : 0.004 0.044 2339 Dihedral : 27.546 167.760 4865 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.42 % Allowed : 8.62 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.23), residues: 1373 helix: 2.18 (0.19), residues: 836 sheet: -1.83 (0.61), residues: 58 loop : -1.16 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K2153 TYR 0.012 0.001 TYR K1847 PHE 0.007 0.001 PHE K2024 TRP 0.011 0.001 TRP K1883 HIS 0.003 0.001 HIS K1609 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.17 (18602) covalent geometry : angle 0.56047 / 0.35 (26397) hydrogen bonds : bond 0.05446 / 3.64 ( 998) hydrogen bonds : angle 3.32477 / 2.38 ( 2555) link_TRANS : bond 0.00052 / 0.03 ( 1) link_TRANS : angle 0.12629 / 0.05 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Evaluate side-chains 117 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.754 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8134 (mt-10) REVERT: C 90 ASP cc_start: 0.8924 (t0) cc_final: 0.8607 (t70) REVERT: D 90 GLU cc_start: 0.9277 (OUTLIER) cc_final: 0.8253 (mp0) REVERT: F 91 LYS cc_start: 0.8864 (ttmt) cc_final: 0.8451 (ttpt) REVERT: H 65 ASP cc_start: 0.8989 (t0) cc_final: 0.8748 (t0) REVERT: K 1481 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7293 (mpt180) outliers start: 17 outliers final: 13 residues processed: 111 average time/residue: 0.3319 time to fit residues: 53.6852 Evaluate side-chains 114 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain K residue 1481 ARG Chi-restraints excluded: chain K residue 1557 VAL Chi-restraints excluded: chain K residue 1588 SER Chi-restraints excluded: chain K residue 1625 VAL Chi-restraints excluded: chain K residue 1630 THR Chi-restraints excluded: chain K residue 1696 LYS Chi-restraints excluded: chain K residue 1765 ILE Chi-restraints excluded: chain K residue 1814 CYS Chi-restraints excluded: chain K residue 2135 PHE Chi-restraints excluded: chain K residue 2180 VAL Chi-restraints excluded: chain K residue 2205 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 114 optimal weight: 0.5980 chunk 95 optimal weight: 10.0000 chunk 105 optimal weight: 0.4980 chunk 63 optimal weight: 0.0270 chunk 45 optimal weight: 7.9990 chunk 23 optimal weight: 0.3980 chunk 48 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K1694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.136779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.102607 restraints weight = 71562.953| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.87 r_work: 0.3120 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 18603 Z= 0.124 Angle : 0.526 6.099 26400 Z= 0.332 Chirality : 0.038 0.286 2999 Planarity : 0.004 0.046 2339 Dihedral : 27.560 167.682 4865 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.00 % Allowed : 9.04 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.24), residues: 1373 helix: 2.36 (0.19), residues: 836 sheet: -1.65 (0.62), residues: 58 loop : -0.98 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K1803 TYR 0.009 0.001 TYR D 39 PHE 0.011 0.001 PHE K1873 TRP 0.015 0.001 TRP K1883 HIS 0.002 0.001 HIS K1831 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.12 (18602) covalent geometry : angle 0.52643 / 0.33 (26397) hydrogen bonds : bond 0.04601 / 3.10 ( 998) hydrogen bonds : angle 3.16360 / 2.27 ( 2555) link_TRANS : bond 0.00057 / 0.03 ( 1) link_TRANS : angle 0.09696 / 0.03 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2746 Ramachandran restraints generated. 1373 Oldfield, 0 Emsley, 1373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 54 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8114 (mt-10) REVERT: C 90 ASP cc_start: 0.8888 (t0) cc_final: 0.8562 (t70) REVERT: C 99 ARG cc_start: 0.8986 (mmm-85) cc_final: 0.8589 (mtp85) REVERT: D 90 GLU cc_start: 0.9222 (OUTLIER) cc_final: 0.8380 (mp0) REVERT: E 42 ARG cc_start: 0.8340 (mtp85) cc_final: 0.7979 (mtp85) REVERT: F 91 LYS cc_start: 0.8865 (ttmt) cc_final: 0.8432 (ttpt) REVERT: G 35 ARG cc_start: 0.8360 (mtm180) cc_final: 0.8158 (mtm180) REVERT: H 65 ASP cc_start: 0.8937 (t0) cc_final: 0.8623 (t0) REVERT: K 1481 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7196 (mpt180) outliers start: 12 outliers final: 8 residues processed: 111 average time/residue: 0.3567 time to fit residues: 56.9621 Evaluate side-chains 111 residues out of total 1209 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain K residue 1481 ARG Chi-restraints excluded: chain K residue 1588 SER Chi-restraints excluded: chain K residue 1625 VAL Chi-restraints excluded: chain K residue 1630 THR Chi-restraints excluded: chain K residue 1696 LYS Chi-restraints excluded: chain K residue 1765 ILE Chi-restraints excluded: chain K residue 2135 PHE Chi-restraints excluded: chain K residue 2205 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 108 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.135234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.100593 restraints weight = 71833.208| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.91 r_work: 0.3089 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 18603 Z= 0.172 Angle : 0.553 6.890 26400 Z= 0.342 Chirality : 0.039 0.286 2999 Planarity : 0.004 0.046 2339 Dihedral : 27.553 167.492 4865 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.75 % Allowed : 9.29 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.24), residues: 1373 helix: 2.32 (0.19), residues: 836 sheet: -1.76 (0.61), residues: 58 loop : -1.06 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K1803 TYR 0.012 0.001 TYR K1847 PHE 0.008 0.001 PHE K1873 TRP 0.012 0.001 TRP K1883 HIS 0.003 0.001 HIS K1609 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.17 (18602) covalent geometry : angle 0.55299 / 0.34 (26397) hydrogen bonds : bond 0.05203 / 3.48 ( 998) hydrogen bonds : angle 3.23034 / 2.31 ( 2555) link_TRANS : bond 0.00051 / 0.03 ( 1) link_TRANS : angle 0.10406 / 0.04 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7567.99 seconds wall clock time: 128 minutes 53.58 seconds (7733.58 seconds total)