Starting phenix.real_space_refine on Thu Sep 18 09:33:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vgl_43204/09_2025/8vgl_43204.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vgl_43204/09_2025/8vgl_43204.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vgl_43204/09_2025/8vgl_43204.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vgl_43204/09_2025/8vgl_43204.map" model { file = "/net/cci-nas-00/data/ceres_data/8vgl_43204/09_2025/8vgl_43204.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vgl_43204/09_2025/8vgl_43204.cif" } resolution = 2.6 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= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 10188 2.51 5 N 2496 2.21 5 O 2846 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15622 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2239 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 8, 'TRANS': 262} Chain: "B" Number of atoms: 2239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2239 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 8, 'TRANS': 262} Chain: "C" Number of atoms: 2239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2239 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 8, 'TRANS': 262} Chain: "D" Number of atoms: 2239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2239 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 8, 'TRANS': 262} Chain: "H" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1685 Classifications: {'peptide': 223} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 210} Chain: "L" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1648 Classifications: {'peptide': 215} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 204} Chain: "F" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1648 Classifications: {'peptide': 215} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 204} Chain: "E" Number of atoms: 1685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1685 Classifications: {'peptide': 223} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 210} Time building chain proxies: 4.18, per 1000 atoms: 0.27 Number of scatterers: 15622 At special positions: 0 Unit cell: (105.734, 107.605, 185.269, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 92 16.00 O 2846 8.00 N 2496 7.00 C 10188 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 132 " - pdb=" SG CYS L 214 " distance=2.03 Simple disulfide: pdb=" SG CYS H 144 " - pdb=" SG CYS H 199 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 134 " - pdb=" SG CYS F 194 " distance=2.03 Simple disulfide: pdb=" SG CYS F 214 " - pdb=" SG CYS E 132 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 144 " - pdb=" SG CYS E 199 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 762.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3716 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 22 sheets defined 56.3% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 1490 through 1502 removed outlier: 3.792A pdb=" N TYR A1494 " --> pdb=" O GLY A1490 " (cutoff:3.500A) Processing helix chain 'A' and resid 1503 through 1524 removed outlier: 3.566A pdb=" N VAL A1523 " --> pdb=" O VAL A1519 " (cutoff:3.500A) Processing helix chain 'A' and resid 1529 through 1559 removed outlier: 3.548A pdb=" N GLU A1550 " --> pdb=" O LEU A1546 " (cutoff:3.500A) Processing helix chain 'A' and resid 1560 through 1564 removed outlier: 3.859A pdb=" N PHE A1563 " --> pdb=" O ILE A1560 " (cutoff:3.500A) Processing helix chain 'A' and resid 1565 through 1584 removed outlier: 3.626A pdb=" N MET A1582 " --> pdb=" O SER A1578 " (cutoff:3.500A) Processing helix chain 'A' and resid 1584 through 1590 Processing helix chain 'A' and resid 1596 through 1601 Processing helix chain 'A' and resid 1602 through 1616 removed outlier: 3.596A pdb=" N ARG A1608 " --> pdb=" O ALA A1604 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LEU A1612 " --> pdb=" O ARG A1608 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL A1613 " --> pdb=" O ILE A1609 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL A1616 " --> pdb=" O LEU A1612 " (cutoff:3.500A) Processing helix chain 'A' and resid 1616 through 1656 removed outlier: 3.791A pdb=" N ILE A1630 " --> pdb=" O LEU A1626 " (cutoff:3.500A) Proline residue: A1631 - end of helix removed outlier: 4.984A pdb=" N SER A1635 " --> pdb=" O PRO A1631 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N VAL A1636 " --> pdb=" O GLY A1632 " (cutoff:3.500A) Processing helix chain 'A' and resid 1659 through 1664 Processing helix chain 'A' and resid 1665 through 1678 Processing helix chain 'A' and resid 1686 through 1692 Processing helix chain 'A' and resid 1693 through 1696 removed outlier: 6.607A pdb=" N TYR A1696 " --> pdb=" O VAL A1693 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1693 through 1696' Processing helix chain 'A' and resid 1697 through 1751 Proline residue: A1703 - end of helix removed outlier: 3.959A pdb=" N LYS A1730 " --> pdb=" O ILE A1726 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU A1749 " --> pdb=" O ASN A1745 " (cutoff:3.500A) Processing helix chain 'A' and resid 1751 through 1756 removed outlier: 4.054A pdb=" N GLU A1755 " --> pdb=" O ILE A1751 " (cutoff:3.500A) Processing helix chain 'A' and resid 1757 through 1759 No H-bonds generated for 'chain 'A' and resid 1757 through 1759' Processing helix chain 'B' and resid 1489 through 1489 No H-bonds generated for 'chain 'B' and resid 1489 through 1489' Processing helix chain 'B' and resid 1490 through 1502 removed outlier: 3.627A pdb=" N TYR B1494 " --> pdb=" O GLY B1490 " (cutoff:3.500A) Processing helix chain 'B' and resid 1503 through 1524 removed outlier: 3.602A pdb=" N VAL B1523 " --> pdb=" O VAL B1519 " (cutoff:3.500A) Processing helix chain 'B' and resid 1529 through 1559 removed outlier: 3.544A pdb=" N GLU B1550 " --> pdb=" O LEU B1546 " (cutoff:3.500A) Processing helix chain 'B' and resid 1560 through 1562 No H-bonds generated for 'chain 'B' and resid 1560 through 1562' Processing helix chain 'B' and resid 1565 through 1584 removed outlier: 3.919A pdb=" N MET B1582 " --> pdb=" O SER B1578 " (cutoff:3.500A) Processing helix chain 'B' and resid 1584 through 1590 Processing helix chain 'B' and resid 1594 through 1601 removed outlier: 3.921A pdb=" N PHE B1598 " --> pdb=" O SER B1594 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG B1599 " --> pdb=" O PRO B1595 " (cutoff:3.500A) Processing helix chain 'B' and resid 1602 through 1616 removed outlier: 3.514A pdb=" N ARG B1608 " --> pdb=" O ALA B1604 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU B1612 " --> pdb=" O ARG B1608 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL B1613 " --> pdb=" O ILE B1609 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL B1616 " --> pdb=" O LEU B1612 " (cutoff:3.500A) Processing helix chain 'B' and resid 1616 through 1656 removed outlier: 3.766A pdb=" N ILE B1630 " --> pdb=" O LEU B1626 " (cutoff:3.500A) Proline residue: B1631 - end of helix removed outlier: 4.984A pdb=" N SER B1635 " --> pdb=" O PRO B1631 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N VAL B1636 " --> pdb=" O GLY B1632 " (cutoff:3.500A) Processing helix chain 'B' and resid 1659 through 1664 Processing helix chain 'B' and resid 1665 through 1678 Processing helix chain 'B' and resid 1686 through 1692 Processing helix chain 'B' and resid 1693 through 1696 removed outlier: 6.641A pdb=" N TYR B1696 " --> pdb=" O VAL B1693 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1693 through 1696' Processing helix chain 'B' and resid 1697 through 1757 Proline residue: B1703 - end of helix removed outlier: 3.863A pdb=" N LYS B1730 " --> pdb=" O ILE B1726 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLU B1749 " --> pdb=" O ASN B1745 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARG B1754 " --> pdb=" O ILE B1750 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU B1755 " --> pdb=" O ILE B1751 " (cutoff:3.500A) Processing helix chain 'B' and resid 1758 through 1759 No H-bonds generated for 'chain 'B' and resid 1758 through 1759' Processing helix chain 'C' and resid 1489 through 1489 No H-bonds generated for 'chain 'C' and resid 1489 through 1489' Processing helix chain 'C' and resid 1490 through 1502 removed outlier: 3.734A pdb=" N TYR C1494 " --> pdb=" O GLY C1490 " (cutoff:3.500A) Processing helix chain 'C' and resid 1503 through 1524 removed outlier: 3.551A pdb=" N VAL C1523 " --> pdb=" O VAL C1519 " (cutoff:3.500A) Processing helix chain 'C' and resid 1529 through 1559 removed outlier: 3.544A pdb=" N GLU C1550 " --> pdb=" O LEU C1546 " (cutoff:3.500A) Processing helix chain 'C' and resid 1560 through 1564 removed outlier: 3.865A pdb=" N PHE C1563 " --> pdb=" O ILE C1560 " (cutoff:3.500A) Processing helix chain 'C' and resid 1565 through 1584 removed outlier: 3.617A pdb=" N MET C1582 " --> pdb=" O SER C1578 " (cutoff:3.500A) Processing helix chain 'C' and resid 1584 through 1590 Processing helix chain 'C' and resid 1596 through 1601 Processing helix chain 'C' and resid 1602 through 1616 removed outlier: 3.593A pdb=" N ARG C1608 " --> pdb=" O ALA C1604 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEU C1612 " --> pdb=" O ARG C1608 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL C1613 " --> pdb=" O ILE C1609 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL C1616 " --> pdb=" O LEU C1612 " (cutoff:3.500A) Processing helix chain 'C' and resid 1616 through 1656 removed outlier: 3.791A pdb=" N ILE C1630 " --> pdb=" O LEU C1626 " (cutoff:3.500A) Proline residue: C1631 - end of helix removed outlier: 4.982A pdb=" N SER C1635 " --> pdb=" O PRO C1631 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N VAL C1636 " --> pdb=" O GLY C1632 " (cutoff:3.500A) Processing helix chain 'C' and resid 1659 through 1664 Processing helix chain 'C' and resid 1665 through 1678 Processing helix chain 'C' and resid 1686 through 1692 Processing helix chain 'C' and resid 1693 through 1696 removed outlier: 6.642A pdb=" N TYR C1696 " --> pdb=" O VAL C1693 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1693 through 1696' Processing helix chain 'C' and resid 1697 through 1751 Proline residue: C1703 - end of helix removed outlier: 3.881A pdb=" N LYS C1730 " --> pdb=" O ILE C1726 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU C1749 " --> pdb=" O ASN C1745 " (cutoff:3.500A) Processing helix chain 'C' and resid 1751 through 1756 removed outlier: 4.090A pdb=" N GLU C1755 " --> pdb=" O ILE C1751 " (cutoff:3.500A) Processing helix chain 'C' and resid 1757 through 1759 No H-bonds generated for 'chain 'C' and resid 1757 through 1759' Processing helix chain 'D' and resid 1489 through 1489 No H-bonds generated for 'chain 'D' and resid 1489 through 1489' Processing helix chain 'D' and resid 1490 through 1502 removed outlier: 3.626A pdb=" N TYR D1494 " --> pdb=" O GLY D1490 " (cutoff:3.500A) Processing helix chain 'D' and resid 1503 through 1524 removed outlier: 3.596A pdb=" N VAL D1523 " --> pdb=" O VAL D1519 " (cutoff:3.500A) Processing helix chain 'D' and resid 1529 through 1559 removed outlier: 3.536A pdb=" N GLU D1550 " --> pdb=" O LEU D1546 " (cutoff:3.500A) Processing helix chain 'D' and resid 1560 through 1562 No H-bonds generated for 'chain 'D' and resid 1560 through 1562' Processing helix chain 'D' and resid 1565 through 1584 removed outlier: 3.944A pdb=" N MET D1582 " --> pdb=" O SER D1578 " (cutoff:3.500A) Processing helix chain 'D' and resid 1584 through 1590 Processing helix chain 'D' and resid 1596 through 1601 Processing helix chain 'D' and resid 1602 through 1616 removed outlier: 3.513A pdb=" N ARG D1608 " --> pdb=" O ALA D1604 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU D1612 " --> pdb=" O ARG D1608 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL D1613 " --> pdb=" O ILE D1609 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL D1616 " --> pdb=" O LEU D1612 " (cutoff:3.500A) Processing helix chain 'D' and resid 1616 through 1656 removed outlier: 3.765A pdb=" N ILE D1630 " --> pdb=" O LEU D1626 " (cutoff:3.500A) Proline residue: D1631 - end of helix removed outlier: 4.988A pdb=" N SER D1635 " --> pdb=" O PRO D1631 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N VAL D1636 " --> pdb=" O GLY D1632 " (cutoff:3.500A) Processing helix chain 'D' and resid 1659 through 1664 Processing helix chain 'D' and resid 1665 through 1678 Processing helix chain 'D' and resid 1686 through 1692 Processing helix chain 'D' and resid 1693 through 1696 removed outlier: 6.648A pdb=" N TYR D1696 " --> pdb=" O VAL D1693 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1693 through 1696' Processing helix chain 'D' and resid 1697 through 1757 Proline residue: D1703 - end of helix removed outlier: 3.900A pdb=" N LYS D1730 " --> pdb=" O ILE D1726 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLU D1749 " --> pdb=" O ASN D1745 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG D1754 " --> pdb=" O ILE D1750 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU D1755 " --> pdb=" O ILE D1751 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 160 through 162 No H-bonds generated for 'chain 'H' and resid 160 through 162' Processing helix chain 'H' and resid 188 through 192 Processing helix chain 'H' and resid 204 through 207 Processing helix chain 'L' and resid 29 through 31 No H-bonds generated for 'chain 'L' and resid 29 through 31' Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'L' and resid 121 through 127 Processing helix chain 'L' and resid 183 through 188 Processing helix chain 'F' and resid 29 through 31 No H-bonds generated for 'chain 'F' and resid 29 through 31' Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'F' and resid 121 through 127 Processing helix chain 'F' and resid 183 through 188 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'E' and resid 160 through 162 No H-bonds generated for 'chain 'E' and resid 160 through 162' Processing helix chain 'E' and resid 188 through 192 Processing helix chain 'E' and resid 204 through 207 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.021A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N MET H 34 " --> pdb=" O THR H 50 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N THR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.021A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 124 through 128 removed outlier: 3.843A pdb=" N GLY H 143 " --> pdb=" O LEU H 128 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N TYR H 179 " --> pdb=" O GLY H 148 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N THR H 180 " --> pdb=" O ALA H 172 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ALA H 172 " --> pdb=" O THR H 180 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER H 182 " --> pdb=" O PHE H 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 155 through 158 Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7 removed outlier: 5.263A pdb=" N THR L 69 " --> pdb=" O VAL L 25 " (cutoff:3.500A) removed outlier: 9.442A pdb=" N LEU L 27 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 9.346A pdb=" N SER L 67 " --> pdb=" O LEU L 27 " (cutoff:3.500A) removed outlier: 12.001A pdb=" N ILE L 28 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 12.148A pdb=" N SER L 65 " --> pdb=" O ILE L 28 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.104A pdb=" N MET L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TRP L 35 " --> pdb=" O TRP L 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.104A pdb=" N MET L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 114 through 118 removed outlier: 5.653A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 144 through 145 Processing sheet with id=AB2, first strand: chain 'L' and resid 153 through 154 removed outlier: 3.624A pdb=" N SER L 153 " --> pdb=" O ILE L 150 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 4 through 7 removed outlier: 5.255A pdb=" N THR F 69 " --> pdb=" O VAL F 25 " (cutoff:3.500A) removed outlier: 9.440A pdb=" N LEU F 27 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 9.344A pdb=" N SER F 67 " --> pdb=" O LEU F 27 " (cutoff:3.500A) removed outlier: 12.001A pdb=" N ILE F 28 " --> pdb=" O SER F 65 " (cutoff:3.500A) removed outlier: 12.145A pdb=" N SER F 65 " --> pdb=" O ILE F 28 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.207A pdb=" N MET F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TRP F 35 " --> pdb=" O TRP F 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.207A pdb=" N MET F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 114 through 118 removed outlier: 5.662A pdb=" N TYR F 173 " --> pdb=" O ASN F 138 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 144 through 145 Processing sheet with id=AB8, first strand: chain 'F' and resid 153 through 154 removed outlier: 3.631A pdb=" N SER F 153 " --> pdb=" O ILE F 150 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AC1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.049A pdb=" N GLY E 10 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N MET E 34 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N THR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.049A pdb=" N GLY E 10 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR E 102 " --> pdb=" O ARG E 94 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 124 through 128 removed outlier: 3.840A pdb=" N GLY E 143 " --> pdb=" O LEU E 128 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N TYR E 179 " --> pdb=" O GLY E 148 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N THR E 180 " --> pdb=" O ALA E 172 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ALA E 172 " --> pdb=" O THR E 180 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N SER E 182 " --> pdb=" O PHE E 170 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 155 through 158 962 hydrogen bonds defined for protein. 2706 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: 2.76 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4796 1.34 - 1.46: 4029 1.46 - 1.58: 7019 1.58 - 1.70: 0 1.70 - 1.82: 164 Bond restraints: 16008 Sorted by residual: bond pdb=" CG PRO H 171 " pdb=" CD PRO H 171 " ideal model delta sigma weight residual 1.503 1.536 -0.033 3.40e-02 8.65e+02 9.44e-01 bond pdb=" CG PRO E 171 " pdb=" CD PRO E 171 " ideal model delta sigma weight residual 1.503 1.536 -0.033 3.40e-02 8.65e+02 9.32e-01 bond pdb=" CA ILE D1630 " pdb=" CB ILE D1630 " ideal model delta sigma weight residual 1.539 1.534 0.005 5.40e-03 3.43e+04 9.13e-01 bond pdb=" CB ARG E 38 " pdb=" CG ARG E 38 " ideal model delta sigma weight residual 1.520 1.498 0.022 3.00e-02 1.11e+03 5.40e-01 bond pdb=" CB ARG H 38 " pdb=" CG ARG H 38 " ideal model delta sigma weight residual 1.520 1.498 0.022 3.00e-02 1.11e+03 5.14e-01 ... (remaining 16003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 20945 1.21 - 2.41: 629 2.41 - 3.62: 150 3.62 - 4.83: 26 4.83 - 6.03: 12 Bond angle restraints: 21762 Sorted by residual: angle pdb=" C ILE L 205 " pdb=" N VAL L 206 " pdb=" CA VAL L 206 " ideal model delta sigma weight residual 121.97 125.96 -3.99 1.80e+00 3.09e-01 4.92e+00 angle pdb=" C ILE F 205 " pdb=" N VAL F 206 " pdb=" CA VAL F 206 " ideal model delta sigma weight residual 121.97 125.94 -3.97 1.80e+00 3.09e-01 4.86e+00 angle pdb=" N VAL H 48 " pdb=" CA VAL H 48 " pdb=" C VAL H 48 " ideal model delta sigma weight residual 109.34 113.76 -4.42 2.08e+00 2.31e-01 4.51e+00 angle pdb=" N VAL E 48 " pdb=" CA VAL E 48 " pdb=" C VAL E 48 " ideal model delta sigma weight residual 109.34 113.75 -4.41 2.08e+00 2.31e-01 4.49e+00 angle pdb=" CA CYS E 92 " pdb=" CB CYS E 92 " pdb=" SG CYS E 92 " ideal model delta sigma weight residual 114.40 118.79 -4.39 2.30e+00 1.89e-01 3.65e+00 ... (remaining 21757 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 8695 17.17 - 34.34: 578 34.34 - 51.51: 121 51.51 - 68.69: 25 68.69 - 85.86: 35 Dihedral angle restraints: 9454 sinusoidal: 3706 harmonic: 5748 Sorted by residual: dihedral pdb=" CA PRO E 123 " pdb=" C PRO E 123 " pdb=" N SER E 124 " pdb=" CA SER E 124 " ideal model delta harmonic sigma weight residual 180.00 156.06 23.94 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA PRO H 123 " pdb=" C PRO H 123 " pdb=" N SER H 124 " pdb=" CA SER H 124 " ideal model delta harmonic sigma weight residual 180.00 156.07 23.93 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA PRO H 153 " pdb=" C PRO H 153 " pdb=" N VAL H 154 " pdb=" CA VAL H 154 " ideal model delta harmonic sigma weight residual 180.00 156.19 23.81 0 5.00e+00 4.00e-02 2.27e+01 ... (remaining 9451 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1458 0.030 - 0.060: 737 0.060 - 0.090: 226 0.090 - 0.120: 104 0.120 - 0.151: 5 Chirality restraints: 2530 Sorted by residual: chirality pdb=" CA VAL E 173 " pdb=" N VAL E 173 " pdb=" C VAL E 173 " pdb=" CB VAL E 173 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.66e-01 chirality pdb=" CA VAL H 173 " pdb=" N VAL H 173 " pdb=" C VAL H 173 " pdb=" CB VAL H 173 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.60e-01 chirality pdb=" CA ILE L 150 " pdb=" N ILE L 150 " pdb=" C ILE L 150 " pdb=" CB ILE L 150 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 ... (remaining 2527 not shown) Planarity restraints: 2678 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG L 108 " -0.366 9.50e-02 1.11e+02 1.65e-01 2.11e+01 pdb=" NE ARG L 108 " 0.034 2.00e-02 2.50e+03 pdb=" CZ ARG L 108 " -0.033 2.00e-02 2.50e+03 pdb=" NH1 ARG L 108 " 0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG L 108 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 108 " 0.364 9.50e-02 1.11e+02 1.64e-01 2.10e+01 pdb=" NE ARG F 108 " -0.034 2.00e-02 2.50e+03 pdb=" CZ ARG F 108 " 0.033 2.00e-02 2.50e+03 pdb=" NH1 ARG F 108 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG F 108 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 38 " -0.217 9.50e-02 1.11e+02 9.80e-02 7.18e+00 pdb=" NE ARG H 38 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG H 38 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG H 38 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG H 38 " -0.001 2.00e-02 2.50e+03 ... (remaining 2675 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3041 2.77 - 3.30: 16228 3.30 - 3.84: 27016 3.84 - 4.37: 32802 4.37 - 4.90: 54123 Nonbonded interactions: 133210 Sorted by model distance: nonbonded pdb=" OD1 ASP F 170 " pdb=" OG1 THR F 172 " model vdw 2.239 3.040 nonbonded pdb=" OE1 GLU F 105 " pdb=" OH TYR F 173 " model vdw 2.243 3.040 nonbonded pdb=" OD1 ASP L 151 " pdb=" OG SER L 191 " model vdw 2.245 3.040 nonbonded pdb=" OD1 ASP L 170 " pdb=" OG1 THR L 172 " model vdw 2.245 3.040 nonbonded pdb=" OE1 GLU L 105 " pdb=" OH TYR L 173 " model vdw 2.271 3.040 ... (remaining 133205 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'L' } 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: 6.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.540 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16018 Z= 0.121 Angle : 0.545 6.034 21782 Z= 0.285 Chirality : 0.040 0.151 2530 Planarity : 0.009 0.165 2678 Dihedral : 13.652 85.857 5708 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.20 % Favored : 94.60 % Rotamer: Outliers : 0.62 % Allowed : 4.37 % Favored : 95.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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 aren not related in a simple way. whole: -1.44 (0.18), residues: 1944 helix: -0.88 (0.15), residues: 908 sheet: -0.54 (0.26), residues: 388 loop : -1.00 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.037 0.004 ARG F 108 TYR 0.011 0.002 TYR E 102 PHE 0.018 0.001 PHE D1701 TRP 0.017 0.002 TRP F 163 HIS 0.004 0.001 HIS C1742 Details of bonding type rmsd covalent geometry : bond 0.00293 (16008) covalent geometry : angle 0.54466 (21762) SS BOND : bond 0.00217 ( 10) SS BOND : angle 0.90747 ( 20) hydrogen bonds : bond 0.20753 ( 950) hydrogen bonds : angle 7.87751 ( 2706) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 312 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1494 TYR cc_start: 0.7318 (t80) cc_final: 0.7062 (t80) REVERT: A 1508 LYS cc_start: 0.8149 (mttm) cc_final: 0.7904 (mttm) REVERT: A 1565 ASP cc_start: 0.8030 (t0) cc_final: 0.7701 (t0) REVERT: A 1653 GLN cc_start: 0.8817 (tt0) cc_final: 0.8583 (mt0) REVERT: A 1722 ASP cc_start: 0.8689 (t0) cc_final: 0.8468 (t0) REVERT: A 1724 MET cc_start: 0.8577 (mmm) cc_final: 0.8215 (tpp) REVERT: B 1571 ASP cc_start: 0.8723 (m-30) cc_final: 0.8312 (m-30) REVERT: B 1614 THR cc_start: 0.9110 (m) cc_final: 0.8793 (p) REVERT: B 1722 ASP cc_start: 0.8604 (t0) cc_final: 0.8256 (t0) REVERT: B 1724 MET cc_start: 0.8399 (mmm) cc_final: 0.8101 (mmm) REVERT: C 1508 LYS cc_start: 0.8109 (mttm) cc_final: 0.7872 (mttm) REVERT: C 1565 ASP cc_start: 0.8029 (t0) cc_final: 0.7700 (t0) REVERT: C 1653 GLN cc_start: 0.8867 (tt0) cc_final: 0.8620 (mt0) REVERT: C 1722 ASP cc_start: 0.8754 (t0) cc_final: 0.8493 (t0) REVERT: C 1724 MET cc_start: 0.8567 (mmm) cc_final: 0.8167 (tpp) REVERT: D 1571 ASP cc_start: 0.8734 (m-30) cc_final: 0.8292 (m-30) REVERT: D 1614 THR cc_start: 0.9120 (m) cc_final: 0.8800 (p) REVERT: D 1722 ASP cc_start: 0.8582 (t0) cc_final: 0.8259 (t0) REVERT: D 1724 MET cc_start: 0.8401 (mmm) cc_final: 0.8132 (mmm) REVERT: H 3 GLN cc_start: 0.9159 (tt0) cc_final: 0.8872 (tp40) REVERT: H 72 ASP cc_start: 0.8606 (t0) cc_final: 0.8033 (t0) REVERT: H 75 LYS cc_start: 0.9225 (mttp) cc_final: 0.9000 (mtmt) REVERT: L 53 LYS cc_start: 0.8640 (tttt) cc_final: 0.8388 (tttm) REVERT: L 77 SER cc_start: 0.8398 (t) cc_final: 0.7967 (p) REVERT: L 81 GLU cc_start: 0.8601 (pt0) cc_final: 0.8371 (pm20) REVERT: L 185 GLU cc_start: 0.6736 (mm-30) cc_final: 0.6192 (mm-30) REVERT: F 17 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7493 (mt-10) REVERT: F 53 LYS cc_start: 0.8648 (tttt) cc_final: 0.8411 (tttm) REVERT: E 3 GLN cc_start: 0.9142 (tt0) cc_final: 0.8847 (tp40) REVERT: E 72 ASP cc_start: 0.8580 (t0) cc_final: 0.8120 (t0) REVERT: E 75 LYS cc_start: 0.9229 (mttp) cc_final: 0.9022 (mtmt) outliers start: 11 outliers final: 2 residues processed: 322 average time/residue: 0.7164 time to fit residues: 250.8068 Evaluate side-chains 230 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 228 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain E residue 135 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 8.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN H 175 GLN L 166 GLN F 166 GLN E 76 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.144262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.078482 restraints weight = 26504.487| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.60 r_work: 0.2825 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16018 Z= 0.169 Angle : 0.625 8.158 21782 Z= 0.332 Chirality : 0.043 0.165 2530 Planarity : 0.004 0.035 2678 Dihedral : 5.385 52.239 2116 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.65 % Allowed : 10.95 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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 aren not related in a simple way. whole: 0.36 (0.19), residues: 1944 helix: 1.03 (0.17), residues: 882 sheet: -0.37 (0.25), residues: 388 loop : -0.26 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1496 TYR 0.020 0.001 TYR B1591 PHE 0.019 0.002 PHE E 150 TRP 0.012 0.001 TRP H 103 HIS 0.006 0.001 HIS C1742 Details of bonding type rmsd covalent geometry : bond 0.00378 (16008) covalent geometry : angle 0.62489 (21762) SS BOND : bond 0.00290 ( 10) SS BOND : angle 0.62647 ( 20) hydrogen bonds : bond 0.05430 ( 950) hydrogen bonds : angle 5.71239 ( 2706) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 264 time to evaluate : 0.623 Fit side-chains revert: symmetry clash REVERT: A 1524 GLU cc_start: 0.7482 (pp20) cc_final: 0.7272 (pp20) REVERT: A 1582 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.7949 (tmm) REVERT: A 1621 LYS cc_start: 0.8695 (ttpp) cc_final: 0.8399 (ttmm) REVERT: A 1653 GLN cc_start: 0.8823 (tt0) cc_final: 0.8455 (mt0) REVERT: A 1722 ASP cc_start: 0.8497 (t0) cc_final: 0.8274 (t0) REVERT: A 1724 MET cc_start: 0.8573 (mmm) cc_final: 0.8043 (tpp) REVERT: A 1738 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8154 (mm-30) REVERT: B 1493 MET cc_start: 0.8256 (ptt) cc_final: 0.8002 (pp-130) REVERT: B 1505 PHE cc_start: 0.8068 (t80) cc_final: 0.7808 (t80) REVERT: B 1507 THR cc_start: 0.8433 (m) cc_final: 0.8134 (p) REVERT: B 1724 MET cc_start: 0.8494 (mmm) cc_final: 0.8185 (mmm) REVERT: C 1493 MET cc_start: 0.8132 (mmp) cc_final: 0.7662 (ttt) REVERT: C 1524 GLU cc_start: 0.7458 (pp20) cc_final: 0.7236 (pp20) REVERT: C 1582 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.8050 (tmm) REVERT: C 1621 LYS cc_start: 0.8701 (ttpp) cc_final: 0.8399 (ttmm) REVERT: C 1653 GLN cc_start: 0.8850 (tt0) cc_final: 0.8478 (mt0) REVERT: C 1722 ASP cc_start: 0.8486 (t0) cc_final: 0.8260 (t0) REVERT: C 1724 MET cc_start: 0.8501 (mmm) cc_final: 0.7987 (tpp) REVERT: D 1493 MET cc_start: 0.8258 (ptt) cc_final: 0.8007 (pp-130) REVERT: D 1494 TYR cc_start: 0.7199 (t80) cc_final: 0.6995 (t80) REVERT: D 1505 PHE cc_start: 0.8098 (t80) cc_final: 0.7834 (t80) REVERT: D 1507 THR cc_start: 0.8427 (m) cc_final: 0.8130 (p) REVERT: D 1724 MET cc_start: 0.8456 (mmm) cc_final: 0.8184 (mmm) REVERT: H 3 GLN cc_start: 0.9161 (tt0) cc_final: 0.8869 (tp40) REVERT: H 72 ASP cc_start: 0.8517 (t0) cc_final: 0.8039 (t70) REVERT: H 75 LYS cc_start: 0.9329 (mttp) cc_final: 0.9067 (mtmt) REVERT: H 178 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.8645 (mp) REVERT: L 17 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7868 (mt-10) REVERT: L 53 LYS cc_start: 0.8736 (tttt) cc_final: 0.8456 (tttm) REVERT: L 81 GLU cc_start: 0.8930 (pt0) cc_final: 0.8704 (pm20) REVERT: L 142 LYS cc_start: 0.8080 (tttp) cc_final: 0.7752 (mttt) REVERT: L 169 LYS cc_start: 0.8598 (pttt) cc_final: 0.8183 (pptt) REVERT: F 17 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7764 (mt-10) REVERT: F 53 LYS cc_start: 0.8752 (tttt) cc_final: 0.8478 (tttm) REVERT: F 169 LYS cc_start: 0.8524 (pttt) cc_final: 0.8040 (pptt) REVERT: F 185 GLU cc_start: 0.6006 (mm-30) cc_final: 0.5676 (mm-30) REVERT: E 3 GLN cc_start: 0.9154 (tt0) cc_final: 0.8846 (tp40) REVERT: E 72 ASP cc_start: 0.8510 (t0) cc_final: 0.8015 (t70) REVERT: E 75 LYS cc_start: 0.9340 (mttp) cc_final: 0.9069 (mtmt) outliers start: 29 outliers final: 8 residues processed: 281 average time/residue: 0.6902 time to fit residues: 211.9831 Evaluate side-chains 242 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 231 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1541 VAL Chi-restraints excluded: chain A residue 1548 THR Chi-restraints excluded: chain A residue 1580 VAL Chi-restraints excluded: chain A residue 1582 MET Chi-restraints excluded: chain C residue 1541 VAL Chi-restraints excluded: chain C residue 1548 THR Chi-restraints excluded: chain C residue 1580 VAL Chi-restraints excluded: chain C residue 1582 MET Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain L residue 41 GLU Chi-restraints excluded: chain E residue 201 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 179 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 118 optimal weight: 0.0980 chunk 85 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1734 HIS ** A1742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1540 ASN B1653 GLN B1748 ASN ** C1729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1734 HIS ** C1742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1540 ASN D1653 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.145239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.080799 restraints weight = 27229.219| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.63 r_work: 0.2890 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16018 Z= 0.142 Angle : 0.573 8.140 21782 Z= 0.300 Chirality : 0.042 0.151 2530 Planarity : 0.004 0.043 2678 Dihedral : 4.806 23.273 2112 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.36 % Allowed : 13.17 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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 aren not related in a simple way. whole: 0.81 (0.19), residues: 1944 helix: 1.56 (0.17), residues: 882 sheet: -0.21 (0.25), residues: 392 loop : -0.23 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1496 TYR 0.014 0.001 TYR L 140 PHE 0.014 0.001 PHE E 150 TRP 0.019 0.001 TRP L 163 HIS 0.006 0.001 HIS B1742 Details of bonding type rmsd covalent geometry : bond 0.00308 (16008) covalent geometry : angle 0.57294 (21762) SS BOND : bond 0.00260 ( 10) SS BOND : angle 0.54036 ( 20) hydrogen bonds : bond 0.04732 ( 950) hydrogen bonds : angle 5.30853 ( 2706) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 267 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1524 GLU cc_start: 0.7553 (pp20) cc_final: 0.7346 (pp20) REVERT: A 1559 ARG cc_start: 0.7935 (mtt180) cc_final: 0.7721 (mtp-110) REVERT: A 1569 LEU cc_start: 0.8762 (tp) cc_final: 0.8552 (mt) REVERT: A 1621 LYS cc_start: 0.8747 (ttpp) cc_final: 0.8490 (ttmm) REVERT: A 1653 GLN cc_start: 0.8840 (tt0) cc_final: 0.8518 (mt0) REVERT: A 1724 MET cc_start: 0.8707 (mmm) cc_final: 0.8495 (mmm) REVERT: A 1737 ASP cc_start: 0.8723 (OUTLIER) cc_final: 0.8522 (p0) REVERT: B 1494 TYR cc_start: 0.7111 (t80) cc_final: 0.6602 (t80) REVERT: B 1505 PHE cc_start: 0.8051 (t80) cc_final: 0.7825 (t80) REVERT: B 1507 THR cc_start: 0.8438 (m) cc_final: 0.8161 (p) REVERT: B 1530 GLN cc_start: 0.8824 (tp40) cc_final: 0.8510 (tm-30) REVERT: B 1565 ASP cc_start: 0.8662 (t0) cc_final: 0.8455 (t0) REVERT: B 1571 ASP cc_start: 0.8444 (m-30) cc_final: 0.8171 (t0) REVERT: B 1582 MET cc_start: 0.8282 (ttm) cc_final: 0.8046 (ttp) REVERT: B 1724 MET cc_start: 0.8638 (mmm) cc_final: 0.8355 (mmm) REVERT: C 1500 ILE cc_start: 0.9081 (mm) cc_final: 0.8862 (mp) REVERT: C 1524 GLU cc_start: 0.7514 (pp20) cc_final: 0.7312 (pp20) REVERT: C 1559 ARG cc_start: 0.8130 (mtt180) cc_final: 0.7636 (mtt-85) REVERT: C 1569 LEU cc_start: 0.8740 (tp) cc_final: 0.8536 (mt) REVERT: C 1621 LYS cc_start: 0.8748 (ttpp) cc_final: 0.8493 (ttmm) REVERT: C 1653 GLN cc_start: 0.8814 (tt0) cc_final: 0.8501 (mt0) REVERT: C 1724 MET cc_start: 0.8671 (mmm) cc_final: 0.8386 (mmm) REVERT: D 1494 TYR cc_start: 0.7344 (t80) cc_final: 0.6896 (t80) REVERT: D 1505 PHE cc_start: 0.8074 (t80) cc_final: 0.7839 (t80) REVERT: D 1507 THR cc_start: 0.8442 (m) cc_final: 0.8165 (p) REVERT: D 1530 GLN cc_start: 0.8857 (tp40) cc_final: 0.8558 (tm-30) REVERT: D 1571 ASP cc_start: 0.8453 (m-30) cc_final: 0.8174 (t0) REVERT: D 1582 MET cc_start: 0.8281 (ttm) cc_final: 0.8052 (ttp) REVERT: D 1724 MET cc_start: 0.8595 (mmm) cc_final: 0.8334 (mmm) REVERT: H 3 GLN cc_start: 0.9212 (tt0) cc_final: 0.8964 (tp40) REVERT: H 72 ASP cc_start: 0.8652 (t0) cc_final: 0.7947 (t70) REVERT: H 75 LYS cc_start: 0.9339 (mttp) cc_final: 0.9053 (mtmt) REVERT: H 178 LEU cc_start: 0.9295 (mp) cc_final: 0.9063 (mt) REVERT: L 53 LYS cc_start: 0.8790 (tttt) cc_final: 0.8536 (tttm) REVERT: L 169 LYS cc_start: 0.8575 (pttt) cc_final: 0.8194 (pptt) REVERT: F 53 LYS cc_start: 0.8811 (tttt) cc_final: 0.8561 (tttm) REVERT: F 169 LYS cc_start: 0.8588 (pttt) cc_final: 0.8079 (pptt) REVERT: F 175 MET cc_start: 0.6112 (ttt) cc_final: 0.5869 (ttt) REVERT: F 189 HIS cc_start: 0.6447 (m-70) cc_final: 0.6225 (m-70) REVERT: E 3 GLN cc_start: 0.9199 (tt0) cc_final: 0.8952 (tp40) REVERT: E 72 ASP cc_start: 0.8636 (t0) cc_final: 0.7901 (t70) REVERT: E 75 LYS cc_start: 0.9335 (mttp) cc_final: 0.9045 (mtmt) outliers start: 24 outliers final: 4 residues processed: 281 average time/residue: 0.6576 time to fit residues: 202.7284 Evaluate side-chains 246 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 241 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1737 ASP Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain L residue 147 LYS Chi-restraints excluded: chain E residue 201 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 146 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 chunk 92 optimal weight: 0.0870 chunk 154 optimal weight: 0.9980 chunk 122 optimal weight: 9.9990 chunk 155 optimal weight: 3.9990 chunk 64 optimal weight: 20.0000 chunk 100 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1729 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1531 HIS B1653 GLN ** C1742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1531 HIS D1653 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.143968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.078917 restraints weight = 26022.670| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.47 r_work: 0.2798 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16018 Z= 0.142 Angle : 0.568 7.817 21782 Z= 0.294 Chirality : 0.042 0.145 2530 Planarity : 0.004 0.051 2678 Dihedral : 4.609 23.176 2112 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.82 % Allowed : 13.90 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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 aren not related in a simple way. whole: 0.82 (0.19), residues: 1944 helix: 1.60 (0.17), residues: 906 sheet: -0.14 (0.26), residues: 396 loop : -0.43 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 108 TYR 0.022 0.001 TYR F 140 PHE 0.013 0.001 PHE H 150 TRP 0.014 0.001 TRP L 163 HIS 0.004 0.001 HIS B1742 Details of bonding type rmsd covalent geometry : bond 0.00318 (16008) covalent geometry : angle 0.56848 (21762) SS BOND : bond 0.00238 ( 10) SS BOND : angle 0.52642 ( 20) hydrogen bonds : bond 0.04473 ( 950) hydrogen bonds : angle 5.14869 ( 2706) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 252 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1493 MET cc_start: 0.8358 (tpp) cc_final: 0.7922 (ttt) REVERT: A 1524 GLU cc_start: 0.7545 (pp20) cc_final: 0.7334 (pp20) REVERT: A 1537 TYR cc_start: 0.7621 (t80) cc_final: 0.7377 (t80) REVERT: A 1582 MET cc_start: 0.8302 (tmm) cc_final: 0.7975 (tmm) REVERT: A 1621 LYS cc_start: 0.8788 (ttpp) cc_final: 0.8534 (ttmm) REVERT: A 1653 GLN cc_start: 0.8843 (tt0) cc_final: 0.8522 (mt0) REVERT: B 1494 TYR cc_start: 0.7133 (t80) cc_final: 0.6572 (t80) REVERT: B 1505 PHE cc_start: 0.8022 (t80) cc_final: 0.7815 (t80) REVERT: B 1507 THR cc_start: 0.8464 (m) cc_final: 0.8191 (p) REVERT: B 1530 GLN cc_start: 0.8851 (tp40) cc_final: 0.8514 (tm-30) REVERT: B 1724 MET cc_start: 0.8655 (mmm) cc_final: 0.8403 (mmm) REVERT: C 1493 MET cc_start: 0.8334 (tpp) cc_final: 0.7881 (ttt) REVERT: C 1524 GLU cc_start: 0.7492 (pp20) cc_final: 0.7280 (pp20) REVERT: C 1537 TYR cc_start: 0.7604 (t80) cc_final: 0.7369 (t80) REVERT: C 1559 ARG cc_start: 0.8124 (mtt180) cc_final: 0.7646 (mtt-85) REVERT: C 1582 MET cc_start: 0.8288 (tmm) cc_final: 0.7883 (tmm) REVERT: C 1621 LYS cc_start: 0.8788 (ttpp) cc_final: 0.8536 (ttmm) REVERT: C 1653 GLN cc_start: 0.8854 (tt0) cc_final: 0.8558 (mt0) REVERT: C 1724 MET cc_start: 0.8729 (mmm) cc_final: 0.8467 (mmm) REVERT: D 1494 TYR cc_start: 0.7375 (t80) cc_final: 0.6961 (t80) REVERT: D 1505 PHE cc_start: 0.8002 (t80) cc_final: 0.7775 (t80) REVERT: D 1507 THR cc_start: 0.8477 (m) cc_final: 0.8203 (p) REVERT: D 1530 GLN cc_start: 0.8863 (tp40) cc_final: 0.8535 (tm-30) REVERT: D 1724 MET cc_start: 0.8626 (mmm) cc_final: 0.8396 (mmm) REVERT: H 3 GLN cc_start: 0.9190 (tt0) cc_final: 0.8975 (tp40) REVERT: H 72 ASP cc_start: 0.8758 (t0) cc_final: 0.7936 (t70) REVERT: H 75 LYS cc_start: 0.9357 (mttp) cc_final: 0.9077 (mtmt) REVERT: H 147 LYS cc_start: 0.6633 (mtpp) cc_final: 0.6127 (tttt) REVERT: H 178 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.9001 (mt) REVERT: L 169 LYS cc_start: 0.8605 (pttt) cc_final: 0.8289 (pttm) REVERT: F 53 LYS cc_start: 0.8844 (tttt) cc_final: 0.8624 (tttm) REVERT: F 78 MET cc_start: 0.8501 (ttt) cc_final: 0.8247 (ttm) REVERT: F 169 LYS cc_start: 0.8692 (pttt) cc_final: 0.8491 (pttt) REVERT: F 175 MET cc_start: 0.6098 (ttt) cc_final: 0.5382 (ttt) REVERT: F 211 ARG cc_start: 0.5973 (ttp80) cc_final: 0.5743 (ttp80) REVERT: E 3 GLN cc_start: 0.9145 (tt0) cc_final: 0.8930 (tp40) REVERT: E 72 ASP cc_start: 0.8741 (t0) cc_final: 0.7879 (t70) REVERT: E 75 LYS cc_start: 0.9352 (mttp) cc_final: 0.9071 (mtmt) REVERT: E 159 ASN cc_start: 0.7862 (m-40) cc_final: 0.7581 (m110) outliers start: 32 outliers final: 11 residues processed: 267 average time/residue: 0.6543 time to fit residues: 190.8749 Evaluate side-chains 244 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 232 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1548 THR Chi-restraints excluded: chain A residue 1557 VAL Chi-restraints excluded: chain B residue 1603 LEU Chi-restraints excluded: chain B residue 1691 MET Chi-restraints excluded: chain C residue 1548 THR Chi-restraints excluded: chain C residue 1691 MET Chi-restraints excluded: chain D residue 1603 LEU Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain F residue 140 TYR Chi-restraints excluded: chain E residue 201 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 85 optimal weight: 3.9990 chunk 163 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 143 optimal weight: 0.6980 chunk 191 optimal weight: 10.0000 chunk 146 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 chunk 109 optimal weight: 8.9990 chunk 125 optimal weight: 7.9990 chunk 137 optimal weight: 3.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1517 ASN A1540 ASN ** A1742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1653 GLN C1517 ASN C1540 ASN ** C1742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1558 HIS D1653 GLN ** E 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.140121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.073427 restraints weight = 26361.680| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 2.63 r_work: 0.2703 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2579 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.071 16018 Z= 0.360 Angle : 0.678 9.765 21782 Z= 0.352 Chirality : 0.047 0.165 2530 Planarity : 0.005 0.053 2678 Dihedral : 4.882 21.438 2112 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.61 % Allowed : 14.98 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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 aren not related in a simple way. whole: 0.58 (0.19), residues: 1944 helix: 1.38 (0.17), residues: 906 sheet: -0.26 (0.26), residues: 398 loop : -0.48 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 108 TYR 0.031 0.002 TYR F 140 PHE 0.028 0.002 PHE H 150 TRP 0.015 0.002 TRP E 103 HIS 0.005 0.001 HIS B1558 Details of bonding type rmsd covalent geometry : bond 0.00861 (16008) covalent geometry : angle 0.67822 (21762) SS BOND : bond 0.00357 ( 10) SS BOND : angle 0.84308 ( 20) hydrogen bonds : bond 0.05305 ( 950) hydrogen bonds : angle 5.43020 ( 2706) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 241 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1493 MET cc_start: 0.8434 (tpp) cc_final: 0.8002 (ttt) REVERT: A 1524 GLU cc_start: 0.7752 (pp20) cc_final: 0.7533 (pp20) REVERT: A 1582 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.7831 (tmm) REVERT: A 1621 LYS cc_start: 0.8947 (ttpp) cc_final: 0.8656 (ttmm) REVERT: A 1653 GLN cc_start: 0.8904 (tt0) cc_final: 0.8566 (mt0) REVERT: A 1724 MET cc_start: 0.8698 (mmm) cc_final: 0.8104 (tpp) REVERT: B 1494 TYR cc_start: 0.7123 (t80) cc_final: 0.6629 (t80) REVERT: B 1505 PHE cc_start: 0.8101 (t80) cc_final: 0.7881 (t80) REVERT: B 1507 THR cc_start: 0.8603 (m) cc_final: 0.8280 (p) REVERT: B 1530 GLN cc_start: 0.8890 (tp40) cc_final: 0.8479 (tm-30) REVERT: B 1540 ASN cc_start: 0.7870 (OUTLIER) cc_final: 0.7460 (t0) REVERT: B 1565 ASP cc_start: 0.8715 (t0) cc_final: 0.8512 (t0) REVERT: B 1722 ASP cc_start: 0.8588 (t0) cc_final: 0.8377 (t70) REVERT: B 1724 MET cc_start: 0.8700 (mmm) cc_final: 0.8387 (mmm) REVERT: C 1493 MET cc_start: 0.8382 (tpp) cc_final: 0.7934 (ttt) REVERT: C 1524 GLU cc_start: 0.7717 (pp20) cc_final: 0.7491 (pp20) REVERT: C 1582 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.8096 (tmm) REVERT: C 1621 LYS cc_start: 0.8957 (ttpp) cc_final: 0.8668 (ttmm) REVERT: C 1653 GLN cc_start: 0.8902 (tt0) cc_final: 0.8563 (mt0) REVERT: C 1724 MET cc_start: 0.8763 (mmm) cc_final: 0.8278 (tpp) REVERT: D 1505 PHE cc_start: 0.8121 (t80) cc_final: 0.7894 (t80) REVERT: D 1507 THR cc_start: 0.8604 (m) cc_final: 0.8288 (p) REVERT: D 1530 GLN cc_start: 0.8890 (tp40) cc_final: 0.8485 (tm-30) REVERT: D 1722 ASP cc_start: 0.8591 (t0) cc_final: 0.8379 (t70) REVERT: D 1724 MET cc_start: 0.8685 (mmm) cc_final: 0.8424 (mmm) REVERT: H 3 GLN cc_start: 0.9254 (tt0) cc_final: 0.9024 (tp40) REVERT: H 72 ASP cc_start: 0.8838 (t0) cc_final: 0.7933 (t70) REVERT: H 75 LYS cc_start: 0.9348 (mttp) cc_final: 0.9068 (mtmt) REVERT: H 147 LYS cc_start: 0.6803 (mtpp) cc_final: 0.6348 (tttt) REVERT: L 169 LYS cc_start: 0.8672 (pttt) cc_final: 0.8350 (pptt) REVERT: L 170 ASP cc_start: 0.8629 (p0) cc_final: 0.8367 (p0) REVERT: F 175 MET cc_start: 0.6143 (ttt) cc_final: 0.5458 (ttt) REVERT: F 211 ARG cc_start: 0.6214 (ttp80) cc_final: 0.5955 (ttp80) REVERT: E 3 GLN cc_start: 0.9259 (tt0) cc_final: 0.9033 (tp40) REVERT: E 72 ASP cc_start: 0.8833 (t0) cc_final: 0.7898 (t70) REVERT: E 75 LYS cc_start: 0.9342 (mttp) cc_final: 0.9062 (mtmt) REVERT: E 177 ASP cc_start: 0.8838 (m-30) cc_final: 0.8483 (m-30) outliers start: 46 outliers final: 20 residues processed: 268 average time/residue: 0.6786 time to fit residues: 199.0875 Evaluate side-chains 252 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 229 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1548 THR Chi-restraints excluded: chain A residue 1557 VAL Chi-restraints excluded: chain A residue 1577 ILE Chi-restraints excluded: chain A residue 1582 MET Chi-restraints excluded: chain B residue 1540 ASN Chi-restraints excluded: chain B residue 1603 LEU Chi-restraints excluded: chain B residue 1691 MET Chi-restraints excluded: chain C residue 1548 THR Chi-restraints excluded: chain C residue 1557 VAL Chi-restraints excluded: chain C residue 1577 ILE Chi-restraints excluded: chain C residue 1582 MET Chi-restraints excluded: chain D residue 1603 LEU Chi-restraints excluded: chain D residue 1691 MET Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 200 ASN Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 140 TYR Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain E residue 13 LYS Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain E residue 201 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 128 optimal weight: 6.9990 chunk 168 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 142 optimal weight: 0.6980 chunk 167 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 chunk 36 optimal weight: 3.9990 chunk 177 optimal weight: 0.6980 chunk 131 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 37 optimal weight: 20.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1540 ASN B1653 GLN B1748 ASN ** C1742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1540 ASN D1653 GLN F 138 ASN E 159 ASN E 200 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.144365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.080045 restraints weight = 26794.786| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.54 r_work: 0.2878 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16018 Z= 0.143 Angle : 0.580 9.138 21782 Z= 0.298 Chirality : 0.042 0.166 2530 Planarity : 0.004 0.054 2678 Dihedral : 4.609 22.659 2112 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.93 % Allowed : 16.80 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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 aren not related in a simple way. whole: 0.78 (0.19), residues: 1944 helix: 1.53 (0.17), residues: 936 sheet: -0.13 (0.26), residues: 396 loop : -0.51 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 108 TYR 0.026 0.001 TYR F 140 PHE 0.014 0.001 PHE E 150 TRP 0.019 0.001 TRP L 163 HIS 0.004 0.001 HIS L 94 Details of bonding type rmsd covalent geometry : bond 0.00322 (16008) covalent geometry : angle 0.58039 (21762) SS BOND : bond 0.00253 ( 10) SS BOND : angle 0.45322 ( 20) hydrogen bonds : bond 0.04398 ( 950) hydrogen bonds : angle 5.13871 ( 2706) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 241 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1493 MET cc_start: 0.8490 (tpp) cc_final: 0.8043 (ttt) REVERT: A 1621 LYS cc_start: 0.8736 (ttpp) cc_final: 0.8476 (ttmm) REVERT: A 1653 GLN cc_start: 0.8753 (tt0) cc_final: 0.8409 (mt0) REVERT: A 1724 MET cc_start: 0.8664 (mmm) cc_final: 0.8065 (tpp) REVERT: B 1505 PHE cc_start: 0.7963 (t80) cc_final: 0.7761 (t80) REVERT: B 1507 THR cc_start: 0.8438 (m) cc_final: 0.8159 (p) REVERT: B 1565 ASP cc_start: 0.8579 (t0) cc_final: 0.8364 (t0) REVERT: B 1722 ASP cc_start: 0.8526 (t0) cc_final: 0.8314 (t70) REVERT: B 1724 MET cc_start: 0.8621 (mmm) cc_final: 0.8368 (mmm) REVERT: C 1493 MET cc_start: 0.8444 (tpp) cc_final: 0.8002 (ttt) REVERT: C 1559 ARG cc_start: 0.8047 (mtt180) cc_final: 0.7575 (mtt-85) REVERT: C 1621 LYS cc_start: 0.8733 (ttpp) cc_final: 0.8474 (ttmm) REVERT: C 1653 GLN cc_start: 0.8720 (tt0) cc_final: 0.8400 (mt0) REVERT: D 1494 TYR cc_start: 0.7011 (t80) cc_final: 0.6590 (t80) REVERT: D 1505 PHE cc_start: 0.7943 (t80) cc_final: 0.7738 (t80) REVERT: D 1507 THR cc_start: 0.8443 (m) cc_final: 0.8193 (p) REVERT: D 1530 GLN cc_start: 0.8904 (tp40) cc_final: 0.8537 (tm-30) REVERT: D 1722 ASP cc_start: 0.8530 (t0) cc_final: 0.8303 (t70) REVERT: D 1724 MET cc_start: 0.8638 (mmm) cc_final: 0.8289 (mmm) REVERT: H 3 GLN cc_start: 0.9282 (tt0) cc_final: 0.9029 (tp40) REVERT: H 72 ASP cc_start: 0.8705 (t0) cc_final: 0.7888 (t70) REVERT: H 75 LYS cc_start: 0.9349 (mttp) cc_final: 0.9037 (mtmt) REVERT: H 147 LYS cc_start: 0.6659 (mtpp) cc_final: 0.6182 (tttt) REVERT: L 169 LYS cc_start: 0.8616 (pttt) cc_final: 0.8374 (pptt) REVERT: L 175 MET cc_start: 0.5719 (ttt) cc_final: 0.5104 (ttt) REVERT: F 53 LYS cc_start: 0.8764 (tttt) cc_final: 0.8519 (tttm) REVERT: F 78 MET cc_start: 0.8558 (ttt) cc_final: 0.8279 (ttm) REVERT: F 81 GLU cc_start: 0.8949 (pt0) cc_final: 0.8706 (pm20) REVERT: F 169 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8425 (pptt) REVERT: F 175 MET cc_start: 0.5991 (ttt) cc_final: 0.5382 (ttt) REVERT: F 195 GLU cc_start: 0.5828 (mt-10) cc_final: 0.5449 (mm-30) REVERT: E 3 GLN cc_start: 0.9269 (tt0) cc_final: 0.9018 (tp40) REVERT: E 72 ASP cc_start: 0.8684 (t0) cc_final: 0.7814 (t70) REVERT: E 75 LYS cc_start: 0.9341 (mttp) cc_final: 0.9034 (mtmt) outliers start: 34 outliers final: 14 residues processed: 259 average time/residue: 0.6809 time to fit residues: 192.5505 Evaluate side-chains 244 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 229 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1557 VAL Chi-restraints excluded: chain A residue 1691 MET Chi-restraints excluded: chain B residue 1603 LEU Chi-restraints excluded: chain B residue 1691 MET Chi-restraints excluded: chain D residue 1691 MET Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 200 ASN Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 140 TYR Chi-restraints excluded: chain F residue 169 LYS Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 201 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 154 optimal weight: 0.9990 chunk 176 optimal weight: 0.0370 chunk 4 optimal weight: 10.0000 chunk 180 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 113 optimal weight: 0.0870 chunk 88 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1653 GLN ** C1742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1653 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.144375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.078901 restraints weight = 26001.133| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 2.54 r_work: 0.2803 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16018 Z= 0.129 Angle : 0.572 9.615 21782 Z= 0.294 Chirality : 0.041 0.153 2530 Planarity : 0.004 0.056 2678 Dihedral : 4.459 23.128 2112 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.82 % Allowed : 17.48 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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 aren not related in a simple way. whole: 0.93 (0.19), residues: 1944 helix: 1.65 (0.17), residues: 936 sheet: -0.06 (0.26), residues: 400 loop : -0.43 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 108 TYR 0.020 0.001 TYR F 140 PHE 0.011 0.001 PHE E 150 TRP 0.018 0.001 TRP L 163 HIS 0.003 0.001 HIS L 189 Details of bonding type rmsd covalent geometry : bond 0.00283 (16008) covalent geometry : angle 0.57178 (21762) SS BOND : bond 0.00230 ( 10) SS BOND : angle 0.45086 ( 20) hydrogen bonds : bond 0.04162 ( 950) hydrogen bonds : angle 4.98687 ( 2706) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 240 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1493 MET cc_start: 0.8498 (tpp) cc_final: 0.8043 (ttt) REVERT: A 1559 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7504 (mmm-85) REVERT: A 1621 LYS cc_start: 0.8675 (ttpp) cc_final: 0.8434 (ttmm) REVERT: A 1653 GLN cc_start: 0.8735 (tt0) cc_final: 0.8372 (mt0) REVERT: B 1507 THR cc_start: 0.8463 (m) cc_final: 0.8216 (p) REVERT: B 1722 ASP cc_start: 0.8495 (t0) cc_final: 0.8289 (t70) REVERT: B 1724 MET cc_start: 0.8585 (mmm) cc_final: 0.8309 (mmm) REVERT: C 1493 MET cc_start: 0.8442 (tpp) cc_final: 0.7997 (ttt) REVERT: C 1559 ARG cc_start: 0.8044 (mtt180) cc_final: 0.7603 (mtt-85) REVERT: C 1621 LYS cc_start: 0.8673 (ttpp) cc_final: 0.8436 (ttmm) REVERT: C 1653 GLN cc_start: 0.8701 (tt0) cc_final: 0.8372 (mt0) REVERT: C 1724 MET cc_start: 0.8603 (mmm) cc_final: 0.7982 (tpp) REVERT: D 1494 TYR cc_start: 0.6990 (t80) cc_final: 0.6528 (t80) REVERT: D 1507 THR cc_start: 0.8440 (m) cc_final: 0.8212 (p) REVERT: D 1722 ASP cc_start: 0.8522 (t0) cc_final: 0.8316 (t70) REVERT: D 1724 MET cc_start: 0.8602 (mmm) cc_final: 0.8387 (mmm) REVERT: H 3 GLN cc_start: 0.9233 (tt0) cc_final: 0.9013 (tp40) REVERT: H 55 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.8273 (ttp-110) REVERT: H 72 ASP cc_start: 0.8729 (t0) cc_final: 0.7836 (t70) REVERT: H 75 LYS cc_start: 0.9349 (mttp) cc_final: 0.9037 (mtmt) REVERT: H 147 LYS cc_start: 0.6604 (mtpp) cc_final: 0.6137 (tttt) REVERT: L 17 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8099 (mt-10) REVERT: L 169 LYS cc_start: 0.8619 (pttt) cc_final: 0.8297 (pptt) REVERT: L 175 MET cc_start: 0.5601 (ttt) cc_final: 0.5022 (ttt) REVERT: F 53 LYS cc_start: 0.8765 (tttt) cc_final: 0.8531 (tttm) REVERT: F 78 MET cc_start: 0.8566 (ttt) cc_final: 0.8322 (ttm) REVERT: F 175 MET cc_start: 0.5931 (ttt) cc_final: 0.5348 (ttt) REVERT: E 3 GLN cc_start: 0.9234 (tt0) cc_final: 0.9018 (tp40) REVERT: E 72 ASP cc_start: 0.8718 (t0) cc_final: 0.7792 (t70) REVERT: E 75 LYS cc_start: 0.9346 (mttp) cc_final: 0.9034 (mtmt) REVERT: E 83 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.8011 (mtt-85) outliers start: 32 outliers final: 14 residues processed: 256 average time/residue: 0.6554 time to fit residues: 183.3356 Evaluate side-chains 250 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 233 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1559 ARG Chi-restraints excluded: chain B residue 1582 MET Chi-restraints excluded: chain B residue 1603 LEU Chi-restraints excluded: chain B residue 1691 MET Chi-restraints excluded: chain D residue 1603 LEU Chi-restraints excluded: chain D residue 1691 MET Chi-restraints excluded: chain H residue 55 ARG Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 200 ASN Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain F residue 140 TYR Chi-restraints excluded: chain F residue 169 LYS Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 201 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 61 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 150 optimal weight: 8.9990 chunk 182 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 39 optimal weight: 0.4980 chunk 188 optimal weight: 10.0000 chunk 173 optimal weight: 0.3980 chunk 193 optimal weight: 0.4980 chunk 169 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1653 GLN ** C1742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1653 GLN E 159 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.144523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.079248 restraints weight = 26187.933| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.58 r_work: 0.2809 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16018 Z= 0.132 Angle : 0.596 8.922 21782 Z= 0.302 Chirality : 0.041 0.159 2530 Planarity : 0.004 0.057 2678 Dihedral : 4.381 24.014 2112 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.48 % Allowed : 18.50 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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 aren not related in a simple way. whole: 1.01 (0.19), residues: 1944 helix: 1.69 (0.17), residues: 936 sheet: 0.07 (0.27), residues: 396 loop : -0.40 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 108 TYR 0.020 0.001 TYR B1591 PHE 0.025 0.001 PHE B1505 TRP 0.017 0.001 TRP L 163 HIS 0.003 0.001 HIS L 189 Details of bonding type rmsd covalent geometry : bond 0.00295 (16008) covalent geometry : angle 0.59638 (21762) SS BOND : bond 0.00233 ( 10) SS BOND : angle 0.42222 ( 20) hydrogen bonds : bond 0.04070 ( 950) hydrogen bonds : angle 4.93845 ( 2706) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 232 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1493 MET cc_start: 0.8499 (tpp) cc_final: 0.8047 (ttt) REVERT: A 1559 ARG cc_start: 0.8196 (OUTLIER) cc_final: 0.7479 (mmm-85) REVERT: A 1621 LYS cc_start: 0.8675 (ttpp) cc_final: 0.8463 (ttmm) REVERT: A 1653 GLN cc_start: 0.8724 (tt0) cc_final: 0.8370 (mt0) REVERT: A 1724 MET cc_start: 0.8623 (mmm) cc_final: 0.8060 (tpp) REVERT: B 1507 THR cc_start: 0.8450 (m) cc_final: 0.8237 (p) REVERT: B 1569 LEU cc_start: 0.8582 (tp) cc_final: 0.8347 (mt) REVERT: B 1722 ASP cc_start: 0.8530 (t0) cc_final: 0.8329 (t70) REVERT: B 1724 MET cc_start: 0.8587 (mmm) cc_final: 0.8337 (mmm) REVERT: C 1493 MET cc_start: 0.8449 (tpp) cc_final: 0.8011 (ttt) REVERT: C 1559 ARG cc_start: 0.8025 (mtt180) cc_final: 0.7584 (mtt-85) REVERT: C 1621 LYS cc_start: 0.8686 (ttpp) cc_final: 0.8459 (ttmm) REVERT: C 1653 GLN cc_start: 0.8704 (tt0) cc_final: 0.8373 (mt0) REVERT: C 1724 MET cc_start: 0.8637 (mmm) cc_final: 0.8012 (tpp) REVERT: D 1507 THR cc_start: 0.8434 (m) cc_final: 0.8219 (p) REVERT: D 1569 LEU cc_start: 0.8572 (tp) cc_final: 0.8330 (mt) REVERT: D 1722 ASP cc_start: 0.8528 (t0) cc_final: 0.8319 (t70) REVERT: D 1724 MET cc_start: 0.8560 (mmm) cc_final: 0.8322 (mmm) REVERT: H 3 GLN cc_start: 0.9224 (tt0) cc_final: 0.9009 (tp40) REVERT: H 72 ASP cc_start: 0.8729 (t0) cc_final: 0.7894 (t70) REVERT: H 75 LYS cc_start: 0.9352 (mttp) cc_final: 0.9056 (mtmt) REVERT: H 147 LYS cc_start: 0.6683 (mtpp) cc_final: 0.6219 (tttt) REVERT: L 175 MET cc_start: 0.5633 (ttt) cc_final: 0.5097 (ttt) REVERT: F 53 LYS cc_start: 0.8761 (tttt) cc_final: 0.8538 (tttm) REVERT: F 169 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8372 (pptt) REVERT: F 195 GLU cc_start: 0.5666 (mt-10) cc_final: 0.5340 (mm-30) REVERT: E 3 GLN cc_start: 0.9231 (tt0) cc_final: 0.9024 (tp40) REVERT: E 72 ASP cc_start: 0.8727 (t0) cc_final: 0.7871 (t70) REVERT: E 75 LYS cc_start: 0.9348 (mttp) cc_final: 0.9053 (mtmt) REVERT: E 83 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.8069 (mtt-85) outliers start: 26 outliers final: 17 residues processed: 244 average time/residue: 0.6903 time to fit residues: 184.1175 Evaluate side-chains 249 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 229 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1559 ARG Chi-restraints excluded: chain A residue 1644 PHE Chi-restraints excluded: chain A residue 1691 MET Chi-restraints excluded: chain B residue 1603 LEU Chi-restraints excluded: chain B residue 1691 MET Chi-restraints excluded: chain C residue 1541 VAL Chi-restraints excluded: chain C residue 1644 PHE Chi-restraints excluded: chain D residue 1582 MET Chi-restraints excluded: chain D residue 1691 MET Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 200 ASN Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain F residue 140 TYR Chi-restraints excluded: chain F residue 169 LYS Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 201 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 62 optimal weight: 0.9980 chunk 129 optimal weight: 0.4980 chunk 182 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 111 optimal weight: 0.9980 chunk 188 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 97 optimal weight: 0.8980 chunk 106 optimal weight: 10.0000 chunk 155 optimal weight: 0.0020 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1653 GLN ** C1742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1653 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.145286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.081451 restraints weight = 26935.121| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.53 r_work: 0.2890 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16018 Z= 0.141 Angle : 0.605 8.811 21782 Z= 0.306 Chirality : 0.041 0.160 2530 Planarity : 0.004 0.056 2678 Dihedral : 4.361 25.025 2112 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.70 % Allowed : 18.56 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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 aren not related in a simple way. whole: 1.02 (0.19), residues: 1944 helix: 1.67 (0.17), residues: 936 sheet: 0.09 (0.27), residues: 410 loop : -0.37 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 108 TYR 0.023 0.001 TYR C1537 PHE 0.012 0.001 PHE E 150 TRP 0.017 0.001 TRP L 163 HIS 0.003 0.001 HIS L 189 Details of bonding type rmsd covalent geometry : bond 0.00321 (16008) covalent geometry : angle 0.60506 (21762) SS BOND : bond 0.00248 ( 10) SS BOND : angle 0.43811 ( 20) hydrogen bonds : bond 0.04092 ( 950) hydrogen bonds : angle 4.92764 ( 2706) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 238 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1493 MET cc_start: 0.8488 (tpp) cc_final: 0.8037 (ttt) REVERT: A 1559 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7626 (mmm-85) REVERT: A 1621 LYS cc_start: 0.8695 (ttpp) cc_final: 0.8475 (ttmm) REVERT: A 1653 GLN cc_start: 0.8724 (tt0) cc_final: 0.8356 (mt0) REVERT: A 1724 MET cc_start: 0.8667 (mmm) cc_final: 0.8076 (tpp) REVERT: B 1507 THR cc_start: 0.8461 (m) cc_final: 0.8246 (p) REVERT: B 1722 ASP cc_start: 0.8517 (t0) cc_final: 0.8302 (t70) REVERT: B 1724 MET cc_start: 0.8618 (mmm) cc_final: 0.8365 (mmm) REVERT: C 1493 MET cc_start: 0.8440 (tpp) cc_final: 0.8004 (ttt) REVERT: C 1559 ARG cc_start: 0.8032 (mtt180) cc_final: 0.7602 (mtt-85) REVERT: C 1621 LYS cc_start: 0.8679 (ttpp) cc_final: 0.8457 (ttmm) REVERT: C 1653 GLN cc_start: 0.8701 (tt0) cc_final: 0.8363 (mt0) REVERT: C 1724 MET cc_start: 0.8676 (mmm) cc_final: 0.8044 (tpp) REVERT: D 1507 THR cc_start: 0.8430 (m) cc_final: 0.8193 (p) REVERT: D 1569 LEU cc_start: 0.8586 (tp) cc_final: 0.8330 (mt) REVERT: D 1722 ASP cc_start: 0.8519 (t0) cc_final: 0.8298 (t70) REVERT: D 1724 MET cc_start: 0.8582 (mmm) cc_final: 0.8346 (mmm) REVERT: H 3 GLN cc_start: 0.9263 (tt0) cc_final: 0.9029 (tp40) REVERT: H 72 ASP cc_start: 0.8732 (t0) cc_final: 0.7908 (t70) REVERT: H 75 LYS cc_start: 0.9356 (mttp) cc_final: 0.9049 (mtmt) REVERT: L 17 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8096 (mt-10) REVERT: F 41 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8165 (tm-30) REVERT: F 53 LYS cc_start: 0.8777 (tttt) cc_final: 0.8567 (tttm) REVERT: E 3 GLN cc_start: 0.9253 (tt0) cc_final: 0.9036 (tp40) REVERT: E 72 ASP cc_start: 0.8715 (t0) cc_final: 0.7862 (t70) REVERT: E 75 LYS cc_start: 0.9353 (mttp) cc_final: 0.9045 (mtmt) REVERT: E 83 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.8093 (mtt-85) outliers start: 30 outliers final: 18 residues processed: 253 average time/residue: 0.7249 time to fit residues: 200.0446 Evaluate side-chains 251 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 230 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1499 ASN Chi-restraints excluded: chain A residue 1541 VAL Chi-restraints excluded: chain A residue 1559 ARG Chi-restraints excluded: chain A residue 1644 PHE Chi-restraints excluded: chain A residue 1691 MET Chi-restraints excluded: chain B residue 1603 LEU Chi-restraints excluded: chain B residue 1691 MET Chi-restraints excluded: chain C residue 1541 VAL Chi-restraints excluded: chain D residue 1582 MET Chi-restraints excluded: chain D residue 1691 MET Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain F residue 140 TYR Chi-restraints excluded: chain F residue 169 LYS Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain E residue 201 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 41 optimal weight: 0.0570 chunk 171 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 chunk 76 optimal weight: 0.6980 chunk 73 optimal weight: 0.0770 chunk 167 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 175 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 121 optimal weight: 5.9990 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1653 GLN ** C1742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1653 GLN E 159 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.144923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.079802 restraints weight = 26090.788| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.55 r_work: 0.2824 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16018 Z= 0.129 Angle : 0.604 9.512 21782 Z= 0.304 Chirality : 0.041 0.165 2530 Planarity : 0.004 0.058 2678 Dihedral : 4.291 24.773 2112 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.08 % Allowed : 19.35 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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 aren not related in a simple way. whole: 1.08 (0.19), residues: 1944 helix: 1.72 (0.17), residues: 936 sheet: 0.14 (0.27), residues: 412 loop : -0.35 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 108 TYR 0.021 0.001 TYR B1591 PHE 0.010 0.001 PHE E 150 TRP 0.017 0.001 TRP L 163 HIS 0.003 0.001 HIS L 189 Details of bonding type rmsd covalent geometry : bond 0.00290 (16008) covalent geometry : angle 0.60418 (21762) SS BOND : bond 0.00240 ( 10) SS BOND : angle 0.42669 ( 20) hydrogen bonds : bond 0.03962 ( 950) hydrogen bonds : angle 4.85699 ( 2706) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 232 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1493 MET cc_start: 0.8467 (tpp) cc_final: 0.8047 (ttt) REVERT: A 1559 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7612 (mmm-85) REVERT: A 1621 LYS cc_start: 0.8688 (ttpp) cc_final: 0.8462 (ttmm) REVERT: A 1653 GLN cc_start: 0.8699 (tt0) cc_final: 0.8340 (mt0) REVERT: A 1724 MET cc_start: 0.8667 (mmm) cc_final: 0.8081 (tpp) REVERT: B 1507 THR cc_start: 0.8433 (m) cc_final: 0.8208 (p) REVERT: B 1572 PHE cc_start: 0.8263 (t80) cc_final: 0.7928 (t80) REVERT: B 1722 ASP cc_start: 0.8498 (t0) cc_final: 0.8296 (t70) REVERT: B 1724 MET cc_start: 0.8587 (mmm) cc_final: 0.8360 (mmm) REVERT: C 1493 MET cc_start: 0.8448 (tpp) cc_final: 0.8011 (ttt) REVERT: C 1559 ARG cc_start: 0.8013 (mtt180) cc_final: 0.7535 (mtt-85) REVERT: C 1621 LYS cc_start: 0.8676 (ttpp) cc_final: 0.8452 (ttmm) REVERT: C 1653 GLN cc_start: 0.8676 (tt0) cc_final: 0.8344 (mt0) REVERT: D 1507 THR cc_start: 0.8435 (m) cc_final: 0.8214 (p) REVERT: D 1569 LEU cc_start: 0.8596 (tp) cc_final: 0.8362 (mt) REVERT: D 1722 ASP cc_start: 0.8491 (t0) cc_final: 0.8276 (t70) REVERT: D 1724 MET cc_start: 0.8556 (mmm) cc_final: 0.8309 (mmm) REVERT: H 3 GLN cc_start: 0.9212 (tt0) cc_final: 0.9007 (tp40) REVERT: H 72 ASP cc_start: 0.8751 (t0) cc_final: 0.7939 (t70) REVERT: H 75 LYS cc_start: 0.9349 (mttp) cc_final: 0.9038 (mtmt) REVERT: H 147 LYS cc_start: 0.6768 (mtpp) cc_final: 0.6312 (tttt) REVERT: L 169 LYS cc_start: 0.8661 (pttt) cc_final: 0.8323 (pptt) REVERT: F 169 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8336 (pptt) REVERT: F 195 GLU cc_start: 0.5738 (mt-10) cc_final: 0.5363 (mm-30) REVERT: E 72 ASP cc_start: 0.8737 (t0) cc_final: 0.7914 (t70) REVERT: E 75 LYS cc_start: 0.9346 (mttp) cc_final: 0.9041 (mtmt) REVERT: E 83 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.8080 (mtt-85) outliers start: 19 outliers final: 15 residues processed: 242 average time/residue: 0.6266 time to fit residues: 165.7124 Evaluate side-chains 244 residues out of total 1762 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 226 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1541 VAL Chi-restraints excluded: chain A residue 1559 ARG Chi-restraints excluded: chain A residue 1644 PHE Chi-restraints excluded: chain A residue 1691 MET Chi-restraints excluded: chain B residue 1603 LEU Chi-restraints excluded: chain B residue 1691 MET Chi-restraints excluded: chain C residue 1644 PHE Chi-restraints excluded: chain D residue 1691 MET Chi-restraints excluded: chain H residue 135 THR Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain F residue 140 TYR Chi-restraints excluded: chain F residue 169 LYS Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain E residue 201 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 96 optimal weight: 0.5980 chunk 141 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 chunk 176 optimal weight: 0.6980 chunk 190 optimal weight: 6.9990 chunk 115 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 chunk 79 optimal weight: 30.0000 chunk 181 optimal weight: 1.9990 chunk 88 optimal weight: 0.0870 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1653 GLN C1734 HIS ** C1742 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1653 GLN L 156 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.145555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.081793 restraints weight = 26692.055| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.53 r_work: 0.2893 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16018 Z= 0.141 Angle : 0.612 9.384 21782 Z= 0.308 Chirality : 0.041 0.165 2530 Planarity : 0.004 0.058 2678 Dihedral : 4.294 26.043 2112 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.31 % Allowed : 19.07 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.89 % 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 aren not related in a simple way. whole: 1.10 (0.19), residues: 1944 helix: 1.70 (0.17), residues: 936 sheet: 0.20 (0.27), residues: 410 loop : -0.35 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 55 TYR 0.018 0.001 TYR F 140 PHE 0.022 0.001 PHE D1505 TRP 0.016 0.001 TRP L 163 HIS 0.002 0.001 HIS D1742 Details of bonding type rmsd covalent geometry : bond 0.00325 (16008) covalent geometry : angle 0.61186 (21762) SS BOND : bond 0.00244 ( 10) SS BOND : angle 0.41232 ( 20) hydrogen bonds : bond 0.04015 ( 950) hydrogen bonds : angle 4.85837 ( 2706) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8804.11 seconds wall clock time: 150 minutes 7.87 seconds (9007.87 seconds total)