Starting phenix.real_space_refine on Mon Jan 20 21:04:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vgm_43208/01_2025/8vgm_43208.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vgm_43208/01_2025/8vgm_43208.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/8vgm_43208/01_2025/8vgm_43208.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vgm_43208/01_2025/8vgm_43208.map" model { file = "/net/cci-nas-00/data/ceres_data/8vgm_43208/01_2025/8vgm_43208.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vgm_43208/01_2025/8vgm_43208.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 1.014 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 108 5.16 5 C 10182 2.51 5 N 2498 2.21 5 O 2838 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 15626 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: "H" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1688 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 212} Chain: "L" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1647 Classifications: {'peptide': 215} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 204} 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: "E" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1688 Classifications: {'peptide': 224} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 212} Chain: "F" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1647 Classifications: {'peptide': 215} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 204} Time building chain proxies: 9.68, per 1000 atoms: 0.62 Number of scatterers: 15626 At special positions: 0 Unit cell: (109.477, 109.477, 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 108 16.00 O 2838 8.00 N 2498 7.00 C 10182 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS H 11 " - pdb=" SG CYS H 151 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 108 " - pdb=" SG CYS H 153 " 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 200 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 40 " - pdb=" SG CYS L 165 " distance=2.03 Simple disulfide: pdb=" SG CYS L 80 " - pdb=" SG CYS L 171 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 Simple disulfide: pdb=" SG CYS E 11 " - pdb=" SG CYS E 151 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 108 " - pdb=" SG CYS E 153 " distance=2.03 Simple disulfide: pdb=" SG CYS E 132 " - pdb=" SG CYS F 214 " distance=2.03 Simple disulfide: pdb=" SG CYS E 144 " - pdb=" SG CYS E 200 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 165 " distance=2.03 Simple disulfide: pdb=" SG CYS F 80 " - pdb=" SG CYS F 171 " distance=2.03 Simple disulfide: pdb=" SG CYS F 134 " - pdb=" SG CYS F 194 " distance=2.04 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: 3.69 Conformation dependent library (CDL) restraints added in 1.9 seconds 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3720 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 22 sheets defined 55.1% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 1490 through 1502 Processing helix chain 'A' and resid 1503 through 1524 removed outlier: 3.571A pdb=" N GLU A1524 " --> pdb=" O THR A1520 " (cutoff:3.500A) Processing helix chain 'A' and resid 1529 through 1559 Processing helix chain 'A' and resid 1560 through 1562 No H-bonds generated for 'chain 'A' and resid 1560 through 1562' Processing helix chain 'A' and resid 1565 through 1584 removed outlier: 3.648A 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: 3.633A pdb=" N ARG A1608 " --> pdb=" O ALA A1604 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU A1612 " --> pdb=" O ARG A1608 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N VAL A1613 " --> pdb=" O ILE A1609 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL A1616 " --> pdb=" O LEU A1612 " (cutoff:3.500A) Processing helix chain 'A' and resid 1616 through 1656 removed outlier: 3.763A pdb=" N ILE A1630 " --> pdb=" O LEU A1626 " (cutoff:3.500A) Proline residue: A1631 - end of helix removed outlier: 4.969A pdb=" N SER A1635 " --> pdb=" O PRO A1631 " (cutoff:3.500A) removed outlier: 5.217A 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: 6.610A 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 1756 Proline residue: A1703 - end of helix removed outlier: 3.850A pdb=" N LYS A1730 " --> pdb=" O ILE A1726 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU A1749 " --> pdb=" O ASN A1745 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS A1752 " --> pdb=" O ASN A1748 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG A1754 " --> pdb=" O ILE A1750 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU A1755 " --> pdb=" O ILE A1751 " (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 161 through 163 No H-bonds generated for 'chain 'H' and resid 161 through 163' Processing helix chain 'H' and resid 189 through 193 Processing helix chain 'H' and resid 205 through 208 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 removed outlier: 3.695A pdb=" N LEU L 125 " --> pdb=" O SER L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 188 Processing helix chain 'B' and resid 1490 through 1502 Processing helix chain 'B' and resid 1503 through 1524 removed outlier: 3.512A pdb=" N GLU B1524 " --> pdb=" O THR B1520 " (cutoff:3.500A) Processing helix chain 'B' and resid 1529 through 1559 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: 3.694A 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 1596 through 1601 Processing helix chain 'B' and resid 1602 through 1616 removed outlier: 3.587A pdb=" N ARG B1608 " --> pdb=" O ALA B1604 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU B1612 " --> pdb=" O ARG B1608 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL B1613 " --> pdb=" O ILE B1609 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL B1616 " --> pdb=" O LEU B1612 " (cutoff:3.500A) Processing helix chain 'B' and resid 1616 through 1656 removed outlier: 3.741A pdb=" N ILE B1630 " --> pdb=" O LEU B1626 " (cutoff:3.500A) Proline residue: B1631 - end of helix removed outlier: 3.500A pdb=" N LEU B1634 " --> pdb=" O ILE B1630 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N SER B1635 " --> pdb=" O PRO B1631 " (cutoff:3.500A) removed outlier: 5.173A 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: 6.637A 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 1756 Proline residue: B1703 - end of helix removed outlier: 3.866A pdb=" N LYS B1730 " --> pdb=" O ILE B1726 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLU B1749 " --> pdb=" O ASN B1745 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS B1752 " --> pdb=" O ASN B1748 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG B1754 " --> pdb=" O ILE B1750 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU B1755 " --> pdb=" O ILE B1751 " (cutoff:3.500A) Processing helix chain 'C' and resid 1490 through 1502 Processing helix chain 'C' and resid 1503 through 1524 removed outlier: 3.566A pdb=" N GLU C1524 " --> pdb=" O THR C1520 " (cutoff:3.500A) Processing helix chain 'C' and resid 1529 through 1559 Processing helix chain 'C' and resid 1560 through 1562 No H-bonds generated for 'chain 'C' and resid 1560 through 1562' Processing helix chain 'C' and resid 1565 through 1584 removed outlier: 3.646A 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: 3.629A pdb=" N ARG C1608 " --> pdb=" O ALA C1604 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU C1612 " --> pdb=" O ARG C1608 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL C1613 " --> pdb=" O ILE C1609 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL C1616 " --> pdb=" O LEU C1612 " (cutoff:3.500A) Processing helix chain 'C' and resid 1616 through 1656 removed outlier: 3.764A pdb=" N ILE C1630 " --> pdb=" O LEU C1626 " (cutoff:3.500A) Proline residue: C1631 - end of helix removed outlier: 4.967A pdb=" N SER C1635 " --> pdb=" O PRO C1631 " (cutoff:3.500A) removed outlier: 5.210A 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: 6.616A 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 1756 Proline residue: C1703 - end of helix removed outlier: 3.856A pdb=" N LYS C1730 " --> pdb=" O ILE C1726 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLU C1749 " --> pdb=" O ASN C1745 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS C1752 " --> pdb=" O ASN C1748 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG C1754 " --> pdb=" O ILE C1750 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU C1755 " --> pdb=" O ILE C1751 " (cutoff:3.500A) Processing helix chain 'D' and resid 1490 through 1502 Processing helix chain 'D' and resid 1503 through 1524 removed outlier: 3.514A pdb=" N GLU D1524 " --> pdb=" O THR D1520 " (cutoff:3.500A) Processing helix chain 'D' and resid 1529 through 1559 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: 3.690A 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: 3.590A pdb=" N ARG D1608 " --> pdb=" O ALA D1604 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU D1612 " --> pdb=" O ARG D1608 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N VAL D1613 " --> pdb=" O ILE D1609 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL D1616 " --> pdb=" O LEU D1612 " (cutoff:3.500A) Processing helix chain 'D' and resid 1616 through 1656 removed outlier: 3.740A pdb=" N ILE D1630 " --> pdb=" O LEU D1626 " (cutoff:3.500A) Proline residue: D1631 - end of helix removed outlier: 3.502A pdb=" N LEU D1634 " --> pdb=" O ILE D1630 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N SER D1635 " --> pdb=" O PRO D1631 " (cutoff:3.500A) removed outlier: 5.176A 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: 6.638A 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 1756 Proline residue: D1703 - end of helix removed outlier: 3.865A pdb=" N LYS D1730 " --> pdb=" O ILE D1726 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU D1749 " --> pdb=" O ASN D1745 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS D1752 " --> pdb=" O ASN D1748 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG D1754 " --> pdb=" O ILE D1750 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU D1755 " --> pdb=" O ILE D1751 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'E' and resid 161 through 163 No H-bonds generated for 'chain 'E' and resid 161 through 163' Processing helix chain 'E' and resid 189 through 193 Processing helix chain 'E' and resid 205 through 208 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 removed outlier: 3.689A pdb=" N LEU F 125 " --> pdb=" O SER F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 188 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: 6.739A pdb=" N MET H 34 " --> pdb=" O THR H 50 " (cutoff:3.500A) removed outlier: 4.451A 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: 3.734A 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: 3.659A pdb=" N GLY H 143 " --> pdb=" O LEU H 128 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N TYR H 180 " --> pdb=" O GLY H 148 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N SER H 183 " --> pdb=" O PRO H 172 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N SER H 185 " --> pdb=" O THR H 170 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N THR H 170 " --> pdb=" O SER H 185 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N THR H 187 " --> pdb=" O VAL H 168 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL H 168 " --> pdb=" O THR H 187 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 156 through 159 Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7 removed outlier: 5.256A pdb=" N THR L 69 " --> pdb=" O VAL L 25 " (cutoff:3.500A) removed outlier: 9.576A pdb=" N LEU L 27 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 9.568A pdb=" N SER L 67 " --> pdb=" O LEU L 27 " (cutoff:3.500A) removed outlier: 12.154A pdb=" N ILE L 28 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 12.291A 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: 5.784A pdb=" N MET L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.486A 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: 5.784A 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: 5.621A 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: 3.821A pdb=" N SER L 153 " --> pdb=" O ILE L 150 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS L 207 " --> pdb=" O CYS L 194 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.742A pdb=" N MET E 34 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N THR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.727A pdb=" N TYR E 102 " --> pdb=" O ARG E 94 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 124 through 128 removed outlier: 3.652A pdb=" N GLY E 143 " --> pdb=" O LEU E 128 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N TYR E 180 " --> pdb=" O GLY E 148 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N SER E 183 " --> pdb=" O PRO E 172 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N SER E 185 " --> pdb=" O THR E 170 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N THR E 170 " --> pdb=" O SER E 185 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N THR E 187 " --> pdb=" O VAL E 168 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL E 168 " --> pdb=" O THR E 187 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 156 through 159 Processing sheet with id=AB8, first strand: chain 'F' and resid 4 through 7 removed outlier: 5.250A pdb=" N THR F 69 " --> pdb=" O VAL F 25 " (cutoff:3.500A) removed outlier: 9.584A pdb=" N LEU F 27 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 9.581A pdb=" N SER F 67 " --> pdb=" O LEU F 27 " (cutoff:3.500A) removed outlier: 12.159A pdb=" N ILE F 28 " --> pdb=" O SER F 65 " (cutoff:3.500A) removed outlier: 12.286A pdb=" N SER F 65 " --> pdb=" O ILE F 28 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 10 through 13 removed outlier: 5.798A pdb=" N MET F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TRP F 35 " --> pdb=" O TRP F 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 10 through 13 removed outlier: 5.798A pdb=" N MET F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 114 through 118 removed outlier: 5.640A pdb=" N TYR F 173 " --> pdb=" O ASN F 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 144 through 145 Processing sheet with id=AC4, first strand: chain 'F' and resid 153 through 154 removed outlier: 3.828A pdb=" N SER F 153 " --> pdb=" O ILE F 150 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS F 207 " --> pdb=" O CYS F 194 " (cutoff:3.500A) 974 hydrogen bonds defined for protein. 2736 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: 5.68 Time building geometry restraints manager: 4.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4796 1.34 - 1.46: 4098 1.46 - 1.58: 6936 1.58 - 1.70: 0 1.70 - 1.82: 180 Bond restraints: 16010 Sorted by residual: bond pdb=" CG LEU D1690 " pdb=" CD2 LEU D1690 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.44e-01 bond pdb=" CG LEU B1690 " pdb=" CD2 LEU B1690 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.91e-01 bond pdb=" CG LEU D1690 " pdb=" CD1 LEU D1690 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.43e-01 bond pdb=" CG LEU B1690 " pdb=" CD1 LEU B1690 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.04e-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 5.34e-01 ... (remaining 16005 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 20859 1.29 - 2.59: 742 2.59 - 3.88: 119 3.88 - 5.18: 34 5.18 - 6.47: 6 Bond angle restraints: 21760 Sorted by residual: angle pdb=" C PHE E 150 " pdb=" N CYS E 151 " pdb=" CA CYS E 151 " ideal model delta sigma weight residual 121.54 128.01 -6.47 1.91e+00 2.74e-01 1.15e+01 angle pdb=" C PHE H 150 " pdb=" N CYS H 151 " pdb=" CA CYS H 151 " ideal model delta sigma weight residual 121.54 127.95 -6.41 1.91e+00 2.74e-01 1.12e+01 angle pdb=" C ILE F 205 " pdb=" N VAL F 206 " pdb=" CA VAL F 206 " ideal model delta sigma weight residual 121.97 126.09 -4.12 1.80e+00 3.09e-01 5.24e+00 angle pdb=" C ILE L 205 " pdb=" N VAL L 206 " pdb=" CA VAL L 206 " ideal model delta sigma weight residual 121.97 126.03 -4.06 1.80e+00 3.09e-01 5.09e+00 angle pdb=" CA CYS E 92 " pdb=" CB CYS E 92 " pdb=" SG CYS E 92 " ideal model delta sigma weight residual 114.40 119.56 -5.16 2.30e+00 1.89e-01 5.04e+00 ... (remaining 21755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 8707 17.25 - 34.50: 591 34.50 - 51.76: 128 51.76 - 69.01: 26 69.01 - 86.26: 28 Dihedral angle restraints: 9480 sinusoidal: 3726 harmonic: 5754 Sorted by residual: dihedral pdb=" CA ARG H 38 " pdb=" C ARG H 38 " pdb=" N GLN H 39 " pdb=" CA GLN H 39 " ideal model delta harmonic sigma weight residual 180.00 152.87 27.13 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA ARG E 38 " pdb=" C ARG E 38 " pdb=" N GLN E 39 " pdb=" CA GLN E 39 " ideal model delta harmonic sigma weight residual 180.00 152.97 27.03 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA LEU H 175 " pdb=" C LEU H 175 " pdb=" N GLN H 176 " pdb=" CA GLN H 176 " ideal model delta harmonic sigma weight residual 180.00 153.23 26.77 0 5.00e+00 4.00e-02 2.87e+01 ... (remaining 9477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1503 0.035 - 0.070: 784 0.070 - 0.105: 190 0.105 - 0.140: 47 0.140 - 0.174: 6 Chirality restraints: 2530 Sorted by residual: chirality pdb=" CB ILE L 106 " pdb=" CA ILE L 106 " pdb=" CG1 ILE L 106 " pdb=" CG2 ILE L 106 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.61e-01 chirality pdb=" CB ILE F 106 " pdb=" CA ILE F 106 " pdb=" CG1 ILE F 106 " pdb=" CG2 ILE F 106 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.27e-01 chirality pdb=" CA CYS L 171 " pdb=" N CYS L 171 " pdb=" C CYS L 171 " pdb=" CB CYS L 171 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.52e-01 ... (remaining 2527 not shown) Planarity restraints: 2676 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D1599 " -0.406 9.50e-02 1.11e+02 1.83e-01 2.55e+01 pdb=" NE ARG D1599 " 0.038 2.00e-02 2.50e+03 pdb=" CZ ARG D1599 " -0.035 2.00e-02 2.50e+03 pdb=" NH1 ARG D1599 " 0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG D1599 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B1599 " 0.405 9.50e-02 1.11e+02 1.83e-01 2.55e+01 pdb=" NE ARG B1599 " -0.038 2.00e-02 2.50e+03 pdb=" CZ ARG B1599 " 0.035 2.00e-02 2.50e+03 pdb=" NH1 ARG B1599 " -0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG B1599 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C1599 " 0.401 9.50e-02 1.11e+02 1.81e-01 2.53e+01 pdb=" NE ARG C1599 " -0.038 2.00e-02 2.50e+03 pdb=" CZ ARG C1599 " 0.036 2.00e-02 2.50e+03 pdb=" NH1 ARG C1599 " -0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG C1599 " 0.001 2.00e-02 2.50e+03 ... (remaining 2673 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 918 2.74 - 3.28: 17204 3.28 - 3.82: 27103 3.82 - 4.36: 33373 4.36 - 4.90: 55347 Nonbonded interactions: 133945 Sorted by model distance: nonbonded pdb=" OE2 GLU H 152 " pdb=" OH TYR H 180 " model vdw 2.195 3.040 nonbonded pdb=" OE2 GLU E 152 " pdb=" OH TYR E 180 " model vdw 2.198 3.040 nonbonded pdb=" NZ LYS F 183 " pdb=" OE2 GLU F 187 " model vdw 2.269 3.120 nonbonded pdb=" OE1 GLU L 105 " pdb=" OH TYR L 173 " model vdw 2.279 3.040 nonbonded pdb=" NZ LYS L 183 " pdb=" OE2 GLU L 187 " model vdw 2.285 3.120 ... (remaining 133940 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: 0.09 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'L' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.000 Set scattering table: 0.120 Process input model: 36.540 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 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 0.028 16010 Z= 0.203 Angle : 0.591 6.474 21760 Z= 0.328 Chirality : 0.043 0.174 2530 Planarity : 0.011 0.183 2676 Dihedral : 13.749 86.262 5706 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.62 % Favored : 95.27 % Rotamer: Outliers : 0.11 % Allowed : 4.25 % Favored : 95.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.18), residues: 1946 helix: -0.93 (0.15), residues: 938 sheet: -0.21 (0.26), residues: 386 loop : -0.76 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 163 HIS 0.006 0.001 HIS H 95 PHE 0.024 0.002 PHE D1701 TYR 0.024 0.003 TYR L 140 ARG 0.040 0.005 ARG C1599 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 382 time to evaluate : 1.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1565 ASP cc_start: 0.8238 (t0) cc_final: 0.7972 (t0) REVERT: A 1605 ARG cc_start: 0.7621 (ttm-80) cc_final: 0.7133 (ttt180) REVERT: A 1653 GLN cc_start: 0.8945 (tt0) cc_final: 0.8636 (mp-120) REVERT: H 115 LYS cc_start: 0.9280 (tttt) cc_final: 0.9060 (tptt) REVERT: L 11 MET cc_start: 0.8595 (ttt) cc_final: 0.8388 (ttm) REVERT: L 143 ASP cc_start: 0.9063 (t0) cc_final: 0.8854 (t0) REVERT: L 195 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8173 (mp0) REVERT: B 1495 LEU cc_start: 0.9121 (tp) cc_final: 0.8848 (pp) REVERT: B 1657 GLU cc_start: 0.8854 (tt0) cc_final: 0.8345 (pm20) REVERT: B 1722 ASP cc_start: 0.8287 (t0) cc_final: 0.8075 (t0) REVERT: B 1729 GLN cc_start: 0.8595 (tm-30) cc_final: 0.8274 (tm-30) REVERT: B 1734 HIS cc_start: 0.8186 (m170) cc_final: 0.7697 (m170) REVERT: B 1747 ASN cc_start: 0.8988 (t0) cc_final: 0.8025 (t0) REVERT: C 1493 MET cc_start: 0.8565 (mmm) cc_final: 0.8349 (ptm) REVERT: C 1565 ASP cc_start: 0.8207 (t0) cc_final: 0.7945 (t0) REVERT: C 1605 ARG cc_start: 0.7636 (ttm-80) cc_final: 0.7138 (ttt180) REVERT: C 1653 GLN cc_start: 0.8971 (tt0) cc_final: 0.8655 (mp-120) REVERT: D 1495 LEU cc_start: 0.9132 (tp) cc_final: 0.8871 (pp) REVERT: D 1657 GLU cc_start: 0.8845 (tt0) cc_final: 0.8343 (pm20) REVERT: D 1722 ASP cc_start: 0.8283 (t0) cc_final: 0.8067 (t0) REVERT: D 1729 GLN cc_start: 0.8605 (tm-30) cc_final: 0.8277 (tm-30) REVERT: D 1734 HIS cc_start: 0.8168 (m170) cc_final: 0.7654 (m170) REVERT: D 1740 GLN cc_start: 0.9250 (mt0) cc_final: 0.9045 (mm110) REVERT: F 11 MET cc_start: 0.8607 (ttt) cc_final: 0.8358 (ttm) outliers start: 2 outliers final: 0 residues processed: 384 average time/residue: 1.3448 time to fit residues: 568.1871 Evaluate side-chains 254 residues out of total 1766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 1.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 0.9980 chunk 147 optimal weight: 0.6980 chunk 81 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 152 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 113 optimal weight: 0.9980 chunk 176 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1540 ASN A1728 ASN A1745 ASN H 76 ASN H 176 GLN L 161 ASN B1540 ASN B1728 ASN B1745 ASN B1747 ASN C1540 ASN C1728 ASN D1492 HIS D1540 ASN D1728 ASN D1745 ASN D1747 ASN E 76 ASN E 81 GLN ** E 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.133215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.072933 restraints weight = 25163.124| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 2.28 r_work: 0.2759 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16010 Z= 0.230 Angle : 0.619 6.393 21760 Z= 0.330 Chirality : 0.044 0.185 2530 Planarity : 0.004 0.034 2676 Dihedral : 5.351 28.555 2114 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.80 % Favored : 98.10 % Rotamer: Outliers : 3.06 % Allowed : 11.27 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.19), residues: 1946 helix: 1.07 (0.17), residues: 898 sheet: 0.06 (0.26), residues: 384 loop : -0.08 (0.26), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP L 163 HIS 0.005 0.001 HIS C1492 PHE 0.021 0.002 PHE B1701 TYR 0.029 0.002 TYR F 140 ARG 0.006 0.001 ARG C1496 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 304 time to evaluate : 2.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1532 MET cc_start: 0.5890 (tpp) cc_final: 0.5490 (tpp) REVERT: A 1564 LYS cc_start: 0.7872 (tptm) cc_final: 0.7607 (mtmt) REVERT: A 1565 ASP cc_start: 0.8424 (t0) cc_final: 0.8089 (t0) REVERT: A 1653 GLN cc_start: 0.8942 (tt0) cc_final: 0.8634 (mp-120) REVERT: H 213 LYS cc_start: 0.7906 (mmtm) cc_final: 0.7596 (tmmm) REVERT: L 11 MET cc_start: 0.8695 (ttt) cc_final: 0.8441 (ttm) REVERT: L 108 ARG cc_start: 0.8104 (ttt90) cc_final: 0.7741 (ppp-140) REVERT: B 1564 LYS cc_start: 0.8810 (ttpt) cc_final: 0.8568 (mttp) REVERT: B 1657 GLU cc_start: 0.8895 (tt0) cc_final: 0.8447 (pm20) REVERT: B 1722 ASP cc_start: 0.8270 (t0) cc_final: 0.7981 (t0) REVERT: B 1729 GLN cc_start: 0.8492 (tm-30) cc_final: 0.7879 (tm-30) REVERT: B 1733 GLN cc_start: 0.8438 (pp30) cc_final: 0.8138 (pp30) REVERT: C 1493 MET cc_start: 0.8765 (tmm) cc_final: 0.8243 (ptm) REVERT: C 1564 LYS cc_start: 0.7796 (tptt) cc_final: 0.7509 (mtmt) REVERT: C 1565 ASP cc_start: 0.8371 (t0) cc_final: 0.8031 (t0) REVERT: C 1653 GLN cc_start: 0.8949 (tt0) cc_final: 0.8637 (mp-120) REVERT: C 1738 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8228 (mm-30) REVERT: C 1744 ASP cc_start: 0.9244 (m-30) cc_final: 0.9042 (m-30) REVERT: D 1564 LYS cc_start: 0.8794 (ttpt) cc_final: 0.8543 (mttp) REVERT: D 1657 GLU cc_start: 0.8890 (tt0) cc_final: 0.8460 (pm20) REVERT: D 1722 ASP cc_start: 0.8262 (t0) cc_final: 0.7971 (t0) REVERT: D 1729 GLN cc_start: 0.8511 (tm-30) cc_final: 0.7897 (tm-30) REVERT: D 1730 LYS cc_start: 0.8810 (mtpm) cc_final: 0.8542 (mtpm) REVERT: D 1733 GLN cc_start: 0.8408 (pp30) cc_final: 0.8087 (pp30) REVERT: E 3 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.8611 (tt0) REVERT: E 115 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8670 (ptmm) REVERT: F 11 MET cc_start: 0.8684 (ttt) cc_final: 0.8418 (ttm) REVERT: F 108 ARG cc_start: 0.8205 (ttt90) cc_final: 0.7914 (ptm-80) REVERT: F 110 ASP cc_start: 0.8638 (m-30) cc_final: 0.8373 (m-30) REVERT: F 150 ILE cc_start: 0.7869 (mm) cc_final: 0.7413 (tt) REVERT: F 213 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.6869 (pm20) outliers start: 54 outliers final: 14 residues processed: 335 average time/residue: 1.3069 time to fit residues: 484.9519 Evaluate side-chains 281 residues out of total 1766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 263 time to evaluate : 2.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1520 THR Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 153 CYS Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain C residue 1520 THR Chi-restraints excluded: chain C residue 1535 VAL Chi-restraints excluded: chain C residue 1738 GLU Chi-restraints excluded: chain D residue 1492 HIS Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 153 CYS Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain F residue 213 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 129 optimal weight: 0.9980 chunk 155 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 141 optimal weight: 0.8980 chunk 174 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 182 optimal weight: 0.9990 chunk 185 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1733 GLN ** H 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1733 GLN D1492 HIS E 160 ASN ** E 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.135920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.080036 restraints weight = 27113.340| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.23 r_work: 0.3002 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16010 Z= 0.214 Angle : 0.595 7.568 21760 Z= 0.313 Chirality : 0.043 0.155 2530 Planarity : 0.004 0.033 2676 Dihedral : 5.088 32.857 2114 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.95 % Favored : 97.94 % Rotamer: Outliers : 2.72 % Allowed : 13.53 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.19), residues: 1946 helix: 1.45 (0.17), residues: 898 sheet: 0.15 (0.26), residues: 392 loop : 0.11 (0.26), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 163 HIS 0.007 0.001 HIS D1492 PHE 0.025 0.001 PHE H 150 TYR 0.026 0.001 TYR D1494 ARG 0.003 0.000 ARG F 155 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 282 time to evaluate : 1.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1532 MET cc_start: 0.6024 (tpp) cc_final: 0.5656 (tpp) REVERT: A 1564 LYS cc_start: 0.7879 (tptm) cc_final: 0.7604 (mtmt) REVERT: A 1565 ASP cc_start: 0.8397 (t0) cc_final: 0.8030 (t0) REVERT: A 1653 GLN cc_start: 0.8850 (tt0) cc_final: 0.8552 (mp-120) REVERT: A 1733 GLN cc_start: 0.9021 (tp-100) cc_final: 0.8358 (tp40) REVERT: A 1737 ASP cc_start: 0.9145 (m-30) cc_final: 0.8725 (m-30) REVERT: A 1740 GLN cc_start: 0.9194 (mm-40) cc_final: 0.8942 (mm-40) REVERT: H 213 LYS cc_start: 0.7874 (mmtm) cc_final: 0.7605 (tmmm) REVERT: L 11 MET cc_start: 0.8762 (ttt) cc_final: 0.8452 (ttm) REVERT: L 108 ARG cc_start: 0.8060 (ttt90) cc_final: 0.7827 (ppp-140) REVERT: L 150 ILE cc_start: 0.7879 (mm) cc_final: 0.7473 (tt) REVERT: B 1564 LYS cc_start: 0.8816 (ttpt) cc_final: 0.8578 (mttp) REVERT: B 1591 TYR cc_start: 0.7678 (m-80) cc_final: 0.6903 (t80) REVERT: B 1657 GLU cc_start: 0.8845 (tt0) cc_final: 0.8412 (pm20) REVERT: B 1722 ASP cc_start: 0.8288 (t0) cc_final: 0.8005 (t0) REVERT: B 1729 GLN cc_start: 0.8645 (tm-30) cc_final: 0.8120 (tm-30) REVERT: B 1733 GLN cc_start: 0.8441 (pp30) cc_final: 0.8063 (pp30) REVERT: C 1493 MET cc_start: 0.8664 (tmm) cc_final: 0.8302 (ptm) REVERT: C 1564 LYS cc_start: 0.7806 (tptt) cc_final: 0.7501 (mtmt) REVERT: C 1565 ASP cc_start: 0.8401 (t0) cc_final: 0.8013 (t0) REVERT: C 1653 GLN cc_start: 0.8856 (tt0) cc_final: 0.8547 (mp-120) REVERT: C 1733 GLN cc_start: 0.9015 (tp-100) cc_final: 0.8509 (tp40) REVERT: C 1737 ASP cc_start: 0.9140 (m-30) cc_final: 0.8877 (m-30) REVERT: C 1738 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8183 (mm-30) REVERT: C 1740 GLN cc_start: 0.9183 (mm-40) cc_final: 0.8931 (mm-40) REVERT: C 1744 ASP cc_start: 0.9253 (m-30) cc_final: 0.8998 (m-30) REVERT: C 1753 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8026 (mm) REVERT: D 1564 LYS cc_start: 0.8827 (ttpt) cc_final: 0.8602 (mttp) REVERT: D 1591 TYR cc_start: 0.7744 (m-80) cc_final: 0.7061 (t80) REVERT: D 1657 GLU cc_start: 0.8823 (tt0) cc_final: 0.8421 (pm20) REVERT: D 1722 ASP cc_start: 0.8283 (t0) cc_final: 0.7999 (t0) REVERT: D 1729 GLN cc_start: 0.8645 (tm-30) cc_final: 0.8256 (tm-30) REVERT: E 3 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.8576 (tt0) REVERT: E 115 LYS cc_start: 0.8863 (tttp) cc_final: 0.8636 (ptmm) REVERT: F 11 MET cc_start: 0.8729 (ttt) cc_final: 0.8461 (ttm) REVERT: F 110 ASP cc_start: 0.8758 (m-30) cc_final: 0.8499 (m-30) REVERT: F 150 ILE cc_start: 0.8018 (mm) cc_final: 0.7644 (tt) outliers start: 48 outliers final: 19 residues processed: 313 average time/residue: 1.2636 time to fit residues: 437.5352 Evaluate side-chains 281 residues out of total 1766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 259 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1513 LEU Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain L residue 40 CYS Chi-restraints excluded: chain L residue 160 LEU Chi-restraints excluded: chain B residue 1531 HIS Chi-restraints excluded: chain B residue 1541 VAL Chi-restraints excluded: chain C residue 1513 LEU Chi-restraints excluded: chain C residue 1535 VAL Chi-restraints excluded: chain C residue 1691 MET Chi-restraints excluded: chain C residue 1738 GLU Chi-restraints excluded: chain C residue 1753 LEU Chi-restraints excluded: chain D residue 1531 HIS Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain F residue 160 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 153 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 181 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 191 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 19 optimal weight: 0.0030 chunk 46 optimal weight: 0.0670 overall best weight: 0.9332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 GLN ** F 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.135539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.079546 restraints weight = 27008.002| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.22 r_work: 0.2989 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16010 Z= 0.235 Angle : 0.578 8.161 21760 Z= 0.302 Chirality : 0.042 0.144 2530 Planarity : 0.004 0.049 2676 Dihedral : 4.856 29.912 2114 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.80 % Favored : 98.10 % Rotamer: Outliers : 2.83 % Allowed : 14.21 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.19), residues: 1946 helix: 1.64 (0.17), residues: 898 sheet: 0.06 (0.25), residues: 404 loop : 0.08 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 163 HIS 0.004 0.001 HIS F 189 PHE 0.021 0.001 PHE H 150 TYR 0.030 0.001 TYR L 140 ARG 0.003 0.000 ARG F 155 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 272 time to evaluate : 1.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1532 MET cc_start: 0.6096 (tpp) cc_final: 0.5665 (tpp) REVERT: A 1564 LYS cc_start: 0.7889 (tptm) cc_final: 0.7578 (mtmt) REVERT: A 1565 ASP cc_start: 0.8352 (t0) cc_final: 0.7964 (t0) REVERT: A 1653 GLN cc_start: 0.8905 (tt0) cc_final: 0.8563 (mp-120) REVERT: A 1733 GLN cc_start: 0.8978 (tp-100) cc_final: 0.8440 (tp40) REVERT: A 1737 ASP cc_start: 0.9019 (m-30) cc_final: 0.8589 (m-30) REVERT: H 25 SER cc_start: 0.8790 (OUTLIER) cc_final: 0.8498 (p) REVERT: H 75 LYS cc_start: 0.9257 (mttp) cc_final: 0.9056 (mttm) REVERT: H 85 GLU cc_start: 0.8781 (mp0) cc_final: 0.8577 (mp0) REVERT: H 150 PHE cc_start: 0.7300 (t80) cc_final: 0.7056 (t80) REVERT: H 176 GLN cc_start: 0.8186 (mt0) cc_final: 0.7985 (mt0) REVERT: H 213 LYS cc_start: 0.7805 (mmtm) cc_final: 0.7589 (tmmm) REVERT: L 11 MET cc_start: 0.8794 (ttt) cc_final: 0.8456 (ttm) REVERT: L 150 ILE cc_start: 0.8007 (mm) cc_final: 0.7655 (tt) REVERT: B 1564 LYS cc_start: 0.8927 (ttpt) cc_final: 0.8706 (mttp) REVERT: B 1657 GLU cc_start: 0.8887 (tt0) cc_final: 0.8468 (mp0) REVERT: B 1722 ASP cc_start: 0.8312 (t0) cc_final: 0.8036 (t0) REVERT: B 1729 GLN cc_start: 0.8673 (tm-30) cc_final: 0.8120 (tm-30) REVERT: B 1730 LYS cc_start: 0.8851 (mtpm) cc_final: 0.8527 (mtpp) REVERT: B 1733 GLN cc_start: 0.8445 (pp30) cc_final: 0.8065 (pp30) REVERT: C 1493 MET cc_start: 0.8685 (tmm) cc_final: 0.8355 (ptm) REVERT: C 1564 LYS cc_start: 0.7818 (tptt) cc_final: 0.7458 (mtmt) REVERT: C 1565 ASP cc_start: 0.8358 (t0) cc_final: 0.7952 (t0) REVERT: C 1653 GLN cc_start: 0.8902 (tt0) cc_final: 0.8569 (mp-120) REVERT: C 1733 GLN cc_start: 0.8950 (tp-100) cc_final: 0.8430 (tp40) REVERT: C 1737 ASP cc_start: 0.9072 (m-30) cc_final: 0.8757 (m-30) REVERT: C 1738 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8123 (mm-30) REVERT: C 1740 GLN cc_start: 0.9203 (mm-40) cc_final: 0.8885 (mm-40) REVERT: C 1744 ASP cc_start: 0.9317 (m-30) cc_final: 0.9035 (m-30) REVERT: D 1564 LYS cc_start: 0.8945 (ttpt) cc_final: 0.8732 (mttp) REVERT: D 1657 GLU cc_start: 0.8851 (tt0) cc_final: 0.8472 (mp0) REVERT: D 1722 ASP cc_start: 0.8322 (t0) cc_final: 0.8043 (t0) REVERT: D 1729 GLN cc_start: 0.8717 (tm-30) cc_final: 0.8302 (tm-30) REVERT: E 3 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8585 (tt0) REVERT: E 25 SER cc_start: 0.8820 (OUTLIER) cc_final: 0.8501 (p) REVERT: E 150 PHE cc_start: 0.7282 (t80) cc_final: 0.7024 (t80) REVERT: F 11 MET cc_start: 0.8780 (ttt) cc_final: 0.8519 (ttm) REVERT: F 150 ILE cc_start: 0.8051 (mm) cc_final: 0.7585 (tt) REVERT: F 185 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8322 (mp0) REVERT: F 190 ASN cc_start: 0.7922 (OUTLIER) cc_final: 0.7647 (t0) outliers start: 50 outliers final: 24 residues processed: 304 average time/residue: 1.2762 time to fit residues: 429.6018 Evaluate side-chains 283 residues out of total 1766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 253 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1520 THR Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1549 ILE Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain L residue 40 CYS Chi-restraints excluded: chain L residue 160 LEU Chi-restraints excluded: chain B residue 1531 HIS Chi-restraints excluded: chain C residue 1520 THR Chi-restraints excluded: chain C residue 1535 VAL Chi-restraints excluded: chain C residue 1549 ILE Chi-restraints excluded: chain C residue 1691 MET Chi-restraints excluded: chain C residue 1738 GLU Chi-restraints excluded: chain D residue 1531 HIS Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 11 CYS Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 201 ASN Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain F residue 190 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 63 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 162 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 181 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 176 GLN B1492 HIS ** F 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 190 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.135421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.079660 restraints weight = 27450.139| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.22 r_work: 0.2982 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16010 Z= 0.229 Angle : 0.579 8.979 21760 Z= 0.300 Chirality : 0.042 0.165 2530 Planarity : 0.004 0.041 2676 Dihedral : 4.715 28.936 2114 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.00 % Favored : 97.89 % Rotamer: Outliers : 3.28 % Allowed : 14.21 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.19), residues: 1946 helix: 1.71 (0.17), residues: 898 sheet: 0.04 (0.25), residues: 404 loop : 0.05 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 163 HIS 0.009 0.001 HIS B1492 PHE 0.021 0.001 PHE E 150 TYR 0.023 0.001 TYR L 140 ARG 0.005 0.000 ARG F 108 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 261 time to evaluate : 1.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1493 MET cc_start: 0.7769 (ptt) cc_final: 0.7229 (ppp) REVERT: A 1532 MET cc_start: 0.6126 (tpp) cc_final: 0.5709 (tpp) REVERT: A 1564 LYS cc_start: 0.7899 (tptm) cc_final: 0.7563 (mtmt) REVERT: A 1565 ASP cc_start: 0.8367 (t0) cc_final: 0.7950 (t0) REVERT: A 1653 GLN cc_start: 0.8888 (tt0) cc_final: 0.8552 (mp-120) REVERT: A 1733 GLN cc_start: 0.9031 (tp-100) cc_final: 0.8484 (tp40) REVERT: A 1737 ASP cc_start: 0.9052 (m-30) cc_final: 0.8597 (m-30) REVERT: A 1747 ASN cc_start: 0.9181 (t0) cc_final: 0.8294 (p0) REVERT: H 25 SER cc_start: 0.8805 (OUTLIER) cc_final: 0.8532 (p) REVERT: H 85 GLU cc_start: 0.8810 (mp0) cc_final: 0.8538 (mp0) REVERT: H 150 PHE cc_start: 0.7098 (t80) cc_final: 0.6860 (t80) REVERT: H 176 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7877 (mt0) REVERT: H 213 LYS cc_start: 0.7762 (mmtm) cc_final: 0.7552 (ttpp) REVERT: L 11 MET cc_start: 0.8831 (ttt) cc_final: 0.8554 (ttm) REVERT: L 150 ILE cc_start: 0.8157 (mm) cc_final: 0.7763 (tt) REVERT: B 1564 LYS cc_start: 0.8929 (ttpt) cc_final: 0.8723 (mttp) REVERT: B 1582 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7924 (ttp) REVERT: B 1657 GLU cc_start: 0.8890 (tt0) cc_final: 0.8405 (mp0) REVERT: B 1722 ASP cc_start: 0.8337 (t0) cc_final: 0.8073 (t0) REVERT: B 1729 GLN cc_start: 0.8687 (tm-30) cc_final: 0.8139 (tm-30) REVERT: B 1730 LYS cc_start: 0.8828 (mtpm) cc_final: 0.8518 (mtpp) REVERT: B 1733 GLN cc_start: 0.8506 (pp30) cc_final: 0.8114 (pp30) REVERT: C 1493 MET cc_start: 0.8648 (tmm) cc_final: 0.8205 (ptm) REVERT: C 1564 LYS cc_start: 0.7839 (tptt) cc_final: 0.7391 (mtmt) REVERT: C 1565 ASP cc_start: 0.8364 (t0) cc_final: 0.7963 (t0) REVERT: C 1653 GLN cc_start: 0.8882 (tt0) cc_final: 0.8543 (mp-120) REVERT: C 1733 GLN cc_start: 0.8948 (tp-100) cc_final: 0.8394 (tp40) REVERT: C 1737 ASP cc_start: 0.9139 (m-30) cc_final: 0.8826 (m-30) REVERT: C 1738 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8085 (mm-30) REVERT: C 1740 GLN cc_start: 0.9193 (mm-40) cc_final: 0.8948 (mm-40) REVERT: C 1747 ASN cc_start: 0.9210 (t0) cc_final: 0.8379 (p0) REVERT: D 1564 LYS cc_start: 0.8932 (ttpt) cc_final: 0.8729 (mttp) REVERT: D 1657 GLU cc_start: 0.8848 (tt0) cc_final: 0.8454 (mp0) REVERT: D 1722 ASP cc_start: 0.8338 (t0) cc_final: 0.8094 (t0) REVERT: D 1729 GLN cc_start: 0.8751 (tm-30) cc_final: 0.8323 (tm-30) REVERT: E 3 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8601 (tt0) REVERT: E 25 SER cc_start: 0.8818 (OUTLIER) cc_final: 0.8531 (p) REVERT: E 150 PHE cc_start: 0.7238 (t80) cc_final: 0.6982 (t80) REVERT: E 179 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8721 (mm) REVERT: E 213 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7442 (ttpp) REVERT: F 11 MET cc_start: 0.8786 (ttt) cc_final: 0.8553 (ttm) REVERT: F 150 ILE cc_start: 0.8194 (mm) cc_final: 0.7738 (tt) REVERT: F 185 GLU cc_start: 0.8712 (OUTLIER) cc_final: 0.8266 (mp0) REVERT: F 190 ASN cc_start: 0.8055 (t0) cc_final: 0.7847 (t0) REVERT: F 213 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7350 (pm20) outliers start: 58 outliers final: 25 residues processed: 301 average time/residue: 1.2742 time to fit residues: 424.0344 Evaluate side-chains 286 residues out of total 1766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 251 time to evaluate : 1.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1513 LEU Chi-restraints excluded: chain A residue 1520 THR Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 176 GLN Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 160 LEU Chi-restraints excluded: chain B residue 1513 LEU Chi-restraints excluded: chain B residue 1531 HIS Chi-restraints excluded: chain B residue 1582 MET Chi-restraints excluded: chain C residue 1520 THR Chi-restraints excluded: chain C residue 1535 VAL Chi-restraints excluded: chain C residue 1691 MET Chi-restraints excluded: chain C residue 1738 GLU Chi-restraints excluded: chain C residue 1752 LYS Chi-restraints excluded: chain D residue 1513 LEU Chi-restraints excluded: chain D residue 1531 HIS Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 11 CYS Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 201 ASN Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 213 LYS Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 160 LEU Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain F residue 213 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 35 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 193 optimal weight: 0.3980 chunk 85 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1492 HIS B1528 GLN D1492 HIS E 176 GLN ** F 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.132965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.077081 restraints weight = 27530.946| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.18 r_work: 0.2928 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 16010 Z= 0.395 Angle : 0.635 13.076 21760 Z= 0.329 Chirality : 0.045 0.190 2530 Planarity : 0.005 0.047 2676 Dihedral : 4.837 28.733 2114 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.95 % Favored : 97.94 % Rotamer: Outliers : 3.62 % Allowed : 14.72 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.19), residues: 1946 helix: 1.61 (0.17), residues: 898 sheet: 0.02 (0.26), residues: 392 loop : 0.05 (0.26), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 163 HIS 0.009 0.001 HIS B1492 PHE 0.025 0.002 PHE H 150 TYR 0.030 0.002 TYR F 140 ARG 0.008 0.001 ARG H 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 255 time to evaluate : 1.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1493 MET cc_start: 0.7811 (ptt) cc_final: 0.7272 (ppp) REVERT: A 1532 MET cc_start: 0.6218 (tpp) cc_final: 0.5863 (tpp) REVERT: A 1564 LYS cc_start: 0.7908 (tptm) cc_final: 0.7575 (mtmt) REVERT: A 1565 ASP cc_start: 0.8421 (t0) cc_final: 0.7988 (t0) REVERT: A 1653 GLN cc_start: 0.8986 (tt0) cc_final: 0.8659 (mp-120) REVERT: A 1733 GLN cc_start: 0.9047 (tp-100) cc_final: 0.8588 (tp40) REVERT: H 25 SER cc_start: 0.8845 (OUTLIER) cc_final: 0.8548 (p) REVERT: H 85 GLU cc_start: 0.8789 (mp0) cc_final: 0.8517 (mp0) REVERT: H 213 LYS cc_start: 0.7789 (mmtm) cc_final: 0.7551 (tmmm) REVERT: L 150 ILE cc_start: 0.8114 (mm) cc_final: 0.7725 (tt) REVERT: L 175 MET cc_start: 0.8369 (OUTLIER) cc_final: 0.7735 (tpt) REVERT: B 1657 GLU cc_start: 0.8950 (tt0) cc_final: 0.8538 (mp0) REVERT: B 1722 ASP cc_start: 0.8278 (t0) cc_final: 0.8040 (t0) REVERT: B 1729 GLN cc_start: 0.8719 (tm-30) cc_final: 0.8355 (tm-30) REVERT: C 1564 LYS cc_start: 0.7858 (tptt) cc_final: 0.7464 (mtmt) REVERT: C 1565 ASP cc_start: 0.8426 (t0) cc_final: 0.8016 (t0) REVERT: C 1653 GLN cc_start: 0.8978 (tt0) cc_final: 0.8595 (mp-120) REVERT: C 1733 GLN cc_start: 0.9018 (tp-100) cc_final: 0.8569 (tp40) REVERT: C 1737 ASP cc_start: 0.9070 (m-30) cc_final: 0.8781 (m-30) REVERT: C 1738 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8126 (mm-30) REVERT: C 1747 ASN cc_start: 0.9236 (t0) cc_final: 0.8387 (p0) REVERT: D 1657 GLU cc_start: 0.8904 (tt0) cc_final: 0.8556 (mp0) REVERT: D 1722 ASP cc_start: 0.8303 (t0) cc_final: 0.8054 (t0) REVERT: D 1729 GLN cc_start: 0.8792 (tm-30) cc_final: 0.8354 (tm-30) REVERT: E 3 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8605 (tt0) REVERT: E 25 SER cc_start: 0.8836 (OUTLIER) cc_final: 0.8523 (p) REVERT: E 75 LYS cc_start: 0.9321 (mttp) cc_final: 0.9101 (mttp) REVERT: F 150 ILE cc_start: 0.8263 (mm) cc_final: 0.7745 (tt) REVERT: F 185 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8270 (mp0) REVERT: F 190 ASN cc_start: 0.8075 (t0) cc_final: 0.7851 (t0) REVERT: F 210 ASN cc_start: 0.8418 (t0) cc_final: 0.7435 (t0) REVERT: F 213 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7574 (pm20) outliers start: 64 outliers final: 33 residues processed: 294 average time/residue: 1.3570 time to fit residues: 439.6683 Evaluate side-chains 289 residues out of total 1766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 249 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1520 THR Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1541 VAL Chi-restraints excluded: chain A residue 1549 ILE Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 175 MET Chi-restraints excluded: chain B residue 1513 LEU Chi-restraints excluded: chain B residue 1531 HIS Chi-restraints excluded: chain B residue 1603 LEU Chi-restraints excluded: chain C residue 1495 LEU Chi-restraints excluded: chain C residue 1497 ILE Chi-restraints excluded: chain C residue 1513 LEU Chi-restraints excluded: chain C residue 1520 THR Chi-restraints excluded: chain C residue 1535 VAL Chi-restraints excluded: chain C residue 1541 VAL Chi-restraints excluded: chain C residue 1549 ILE Chi-restraints excluded: chain C residue 1577 ILE Chi-restraints excluded: chain C residue 1691 MET Chi-restraints excluded: chain C residue 1738 GLU Chi-restraints excluded: chain C residue 1752 LYS Chi-restraints excluded: chain D residue 1513 LEU Chi-restraints excluded: chain D residue 1531 HIS Chi-restraints excluded: chain D residue 1553 LEU Chi-restraints excluded: chain D residue 1603 LEU Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 11 CYS Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 201 ASN Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain F residue 213 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 140 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 185 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 150 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 138 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 176 GLN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 145 ASN ** L 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1492 HIS B1653 GLN D1492 HIS D1653 GLN E 176 GLN ** F 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 161 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.134793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.079216 restraints weight = 27331.295| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.22 r_work: 0.2971 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16010 Z= 0.215 Angle : 0.593 16.037 21760 Z= 0.305 Chirality : 0.042 0.167 2530 Planarity : 0.004 0.040 2676 Dihedral : 4.621 27.340 2114 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.26 % Favored : 97.64 % Rotamer: Outliers : 2.72 % Allowed : 15.97 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.19), residues: 1946 helix: 1.79 (0.17), residues: 900 sheet: 0.03 (0.26), residues: 392 loop : 0.06 (0.26), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 163 HIS 0.013 0.001 HIS B1492 PHE 0.020 0.001 PHE H 150 TYR 0.023 0.001 TYR F 140 ARG 0.007 0.000 ARG H 55 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 258 time to evaluate : 1.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1493 MET cc_start: 0.7807 (ptt) cc_final: 0.7217 (ppp) REVERT: A 1532 MET cc_start: 0.6180 (tpp) cc_final: 0.5823 (tpp) REVERT: A 1559 ARG cc_start: 0.8272 (mtt180) cc_final: 0.7880 (mmm-85) REVERT: A 1564 LYS cc_start: 0.7871 (tptm) cc_final: 0.7547 (mtmt) REVERT: A 1565 ASP cc_start: 0.8400 (t0) cc_final: 0.7960 (t0) REVERT: A 1653 GLN cc_start: 0.8869 (tt0) cc_final: 0.8572 (mp-120) REVERT: A 1733 GLN cc_start: 0.9036 (tp-100) cc_final: 0.8512 (tp40) REVERT: H 85 GLU cc_start: 0.8803 (mp0) cc_final: 0.8533 (mp0) REVERT: H 92 CYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8677 (p) REVERT: H 213 LYS cc_start: 0.7763 (mmtm) cc_final: 0.7555 (ttpp) REVERT: B 1528 GLN cc_start: 0.5613 (OUTLIER) cc_final: 0.5394 (pp30) REVERT: B 1657 GLU cc_start: 0.8885 (tt0) cc_final: 0.8502 (mp0) REVERT: B 1722 ASP cc_start: 0.8289 (t0) cc_final: 0.8072 (t0) REVERT: B 1729 GLN cc_start: 0.8753 (tm-30) cc_final: 0.8304 (tm-30) REVERT: C 1493 MET cc_start: 0.7857 (ptt) cc_final: 0.7314 (ppp) REVERT: C 1532 MET cc_start: 0.6004 (tpp) cc_final: 0.5605 (tpp) REVERT: C 1564 LYS cc_start: 0.7872 (tptt) cc_final: 0.7393 (mtmt) REVERT: C 1565 ASP cc_start: 0.8385 (t0) cc_final: 0.7969 (t0) REVERT: C 1653 GLN cc_start: 0.8869 (tt0) cc_final: 0.8572 (mp-120) REVERT: C 1733 GLN cc_start: 0.8959 (tp-100) cc_final: 0.8513 (tp40) REVERT: C 1737 ASP cc_start: 0.9080 (m-30) cc_final: 0.8779 (m-30) REVERT: C 1738 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8161 (mm-30) REVERT: C 1753 LEU cc_start: 0.8766 (tm) cc_final: 0.8529 (mm) REVERT: D 1657 GLU cc_start: 0.8836 (tt0) cc_final: 0.8523 (mp0) REVERT: D 1722 ASP cc_start: 0.8327 (t0) cc_final: 0.8085 (t0) REVERT: D 1729 GLN cc_start: 0.8762 (tm-30) cc_final: 0.8304 (tm-30) REVERT: E 3 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8595 (tt0) REVERT: E 75 LYS cc_start: 0.9280 (mttp) cc_final: 0.9078 (mttp) REVERT: E 92 CYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8674 (p) REVERT: F 185 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8252 (mp0) REVERT: F 213 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7337 (pm20) outliers start: 48 outliers final: 20 residues processed: 292 average time/residue: 1.3552 time to fit residues: 435.6435 Evaluate side-chains 271 residues out of total 1766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 244 time to evaluate : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain L residue 40 CYS Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain B residue 1528 GLN Chi-restraints excluded: chain B residue 1531 HIS Chi-restraints excluded: chain C residue 1495 LEU Chi-restraints excluded: chain C residue 1513 LEU Chi-restraints excluded: chain C residue 1520 THR Chi-restraints excluded: chain C residue 1535 VAL Chi-restraints excluded: chain C residue 1691 MET Chi-restraints excluded: chain C residue 1738 GLU Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 11 CYS Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 201 ASN Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain F residue 213 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 73 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 133 optimal weight: 10.0000 chunk 144 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 137 optimal weight: 0.5980 chunk 67 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 84 optimal weight: 0.0670 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1499 ASN A1733 GLN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 145 ASN ** L 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1492 HIS B1733 GLN D1492 HIS E 176 GLN ** F 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 190 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.135418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.080317 restraints weight = 27279.206| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.22 r_work: 0.3015 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16010 Z= 0.183 Angle : 0.586 16.055 21760 Z= 0.301 Chirality : 0.042 0.169 2530 Planarity : 0.004 0.041 2676 Dihedral : 4.495 30.783 2114 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.31 % Favored : 97.58 % Rotamer: Outliers : 2.49 % Allowed : 16.99 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.19), residues: 1946 helix: 1.92 (0.17), residues: 900 sheet: 0.01 (0.26), residues: 404 loop : 0.06 (0.26), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP F 163 HIS 0.013 0.001 HIS B1492 PHE 0.026 0.001 PHE H 150 TYR 0.019 0.001 TYR F 140 ARG 0.010 0.000 ARG H 55 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 257 time to evaluate : 1.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1493 MET cc_start: 0.7681 (ptt) cc_final: 0.7150 (ppp) REVERT: A 1532 MET cc_start: 0.6105 (tpp) cc_final: 0.5732 (tpp) REVERT: A 1559 ARG cc_start: 0.8235 (mtt180) cc_final: 0.7825 (mmm-85) REVERT: A 1564 LYS cc_start: 0.7953 (tptm) cc_final: 0.7576 (mtmt) REVERT: A 1565 ASP cc_start: 0.8392 (t0) cc_final: 0.7914 (t0) REVERT: A 1653 GLN cc_start: 0.8844 (tt0) cc_final: 0.8539 (mp-120) REVERT: A 1733 GLN cc_start: 0.8998 (tp40) cc_final: 0.8539 (tp40) REVERT: H 3 GLN cc_start: 0.8915 (tt0) cc_final: 0.8637 (tt0) REVERT: H 25 SER cc_start: 0.8812 (OUTLIER) cc_final: 0.8528 (p) REVERT: H 85 GLU cc_start: 0.8800 (mp0) cc_final: 0.8496 (mp0) REVERT: H 213 LYS cc_start: 0.7783 (mmtm) cc_final: 0.7570 (ttpp) REVERT: L 210 ASN cc_start: 0.7918 (t0) cc_final: 0.7576 (p0) REVERT: B 1528 GLN cc_start: 0.5502 (OUTLIER) cc_final: 0.5292 (pp30) REVERT: B 1657 GLU cc_start: 0.8865 (tt0) cc_final: 0.8506 (mp0) REVERT: B 1729 GLN cc_start: 0.8747 (tm-30) cc_final: 0.8318 (tm-30) REVERT: B 1745 ASN cc_start: 0.9328 (m-40) cc_final: 0.8961 (t0) REVERT: C 1493 MET cc_start: 0.7832 (ptt) cc_final: 0.7327 (ppp) REVERT: C 1532 MET cc_start: 0.6029 (tpp) cc_final: 0.5621 (tpp) REVERT: C 1559 ARG cc_start: 0.8257 (mtt180) cc_final: 0.7724 (mmm-85) REVERT: C 1564 LYS cc_start: 0.7878 (tptt) cc_final: 0.7399 (mtmt) REVERT: C 1565 ASP cc_start: 0.8391 (t0) cc_final: 0.7952 (t0) REVERT: C 1653 GLN cc_start: 0.8846 (tt0) cc_final: 0.8551 (mp-120) REVERT: C 1733 GLN cc_start: 0.8956 (tp-100) cc_final: 0.8493 (tp40) REVERT: C 1737 ASP cc_start: 0.9065 (m-30) cc_final: 0.8758 (m-30) REVERT: C 1738 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8099 (mm-30) REVERT: D 1657 GLU cc_start: 0.8835 (tt0) cc_final: 0.8528 (mp0) REVERT: D 1722 ASP cc_start: 0.8330 (t0) cc_final: 0.8097 (t0) REVERT: D 1729 GLN cc_start: 0.8747 (tm-30) cc_final: 0.8313 (tm-30) REVERT: D 1745 ASN cc_start: 0.9080 (m-40) cc_final: 0.8812 (t0) REVERT: D 1747 ASN cc_start: 0.8901 (p0) cc_final: 0.8674 (t0) REVERT: E 3 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.8627 (tt0) REVERT: F 185 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8229 (mp0) REVERT: F 210 ASN cc_start: 0.8740 (m-40) cc_final: 0.8116 (p0) outliers start: 44 outliers final: 21 residues processed: 288 average time/residue: 1.3042 time to fit residues: 414.4624 Evaluate side-chains 275 residues out of total 1766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 249 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1495 LEU Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain L residue 40 CYS Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 160 LEU Chi-restraints excluded: chain B residue 1528 GLN Chi-restraints excluded: chain B residue 1531 HIS Chi-restraints excluded: chain C residue 1495 LEU Chi-restraints excluded: chain C residue 1535 VAL Chi-restraints excluded: chain C residue 1691 MET Chi-restraints excluded: chain C residue 1738 GLU Chi-restraints excluded: chain D residue 1492 HIS Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 11 CYS Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 201 ASN Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 185 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 190 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 110 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 136 optimal weight: 0.4980 chunk 128 optimal weight: 0.0570 chunk 31 optimal weight: 1.9990 chunk 149 optimal weight: 8.9990 chunk 45 optimal weight: 0.4980 chunk 64 optimal weight: 0.0370 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1499 ASN L 124 GLN L 145 ASN ** L 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1492 HIS D1492 HIS ** F 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 190 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.135981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.080874 restraints weight = 27327.781| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.21 r_work: 0.3033 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16010 Z= 0.176 Angle : 0.596 15.689 21760 Z= 0.306 Chirality : 0.041 0.204 2530 Planarity : 0.004 0.039 2676 Dihedral : 4.442 30.625 2114 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.42 % Favored : 97.48 % Rotamer: Outliers : 1.93 % Allowed : 18.23 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.19), residues: 1946 helix: 1.85 (0.16), residues: 924 sheet: 0.07 (0.26), residues: 402 loop : 0.05 (0.27), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 163 HIS 0.017 0.001 HIS D1492 PHE 0.022 0.001 PHE H 150 TYR 0.030 0.001 TYR L 140 ARG 0.009 0.000 ARG E 55 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 264 time to evaluate : 1.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1493 MET cc_start: 0.7617 (ptt) cc_final: 0.7150 (ppp) REVERT: A 1532 MET cc_start: 0.6120 (tpp) cc_final: 0.5747 (tpp) REVERT: A 1559 ARG cc_start: 0.8263 (mtt180) cc_final: 0.7830 (mmm-85) REVERT: A 1564 LYS cc_start: 0.7928 (tptm) cc_final: 0.7556 (mtmt) REVERT: A 1565 ASP cc_start: 0.8364 (t0) cc_final: 0.7968 (t0) REVERT: A 1653 GLN cc_start: 0.8828 (tt0) cc_final: 0.8487 (mp-120) REVERT: A 1733 GLN cc_start: 0.9048 (tp40) cc_final: 0.8550 (tp40) REVERT: A 1737 ASP cc_start: 0.8965 (m-30) cc_final: 0.8532 (m-30) REVERT: H 3 GLN cc_start: 0.8932 (tt0) cc_final: 0.8641 (tt0) REVERT: H 25 SER cc_start: 0.8823 (OUTLIER) cc_final: 0.8535 (p) REVERT: H 55 ARG cc_start: 0.8921 (mtm-85) cc_final: 0.8418 (mtm110) REVERT: H 85 GLU cc_start: 0.8793 (mp0) cc_final: 0.8584 (mp0) REVERT: H 213 LYS cc_start: 0.7751 (mmtm) cc_final: 0.7516 (ttpp) REVERT: L 210 ASN cc_start: 0.7962 (t0) cc_final: 0.7550 (p0) REVERT: B 1528 GLN cc_start: 0.5318 (OUTLIER) cc_final: 0.5111 (pp30) REVERT: B 1657 GLU cc_start: 0.8822 (tt0) cc_final: 0.8518 (mp0) REVERT: B 1729 GLN cc_start: 0.8785 (tm-30) cc_final: 0.8350 (tm-30) REVERT: B 1745 ASN cc_start: 0.9308 (m-40) cc_final: 0.8936 (t0) REVERT: C 1493 MET cc_start: 0.7855 (ptt) cc_final: 0.7335 (ppp) REVERT: C 1532 MET cc_start: 0.5996 (tpp) cc_final: 0.5634 (tpp) REVERT: C 1559 ARG cc_start: 0.8235 (mtt180) cc_final: 0.7722 (mmm-85) REVERT: C 1564 LYS cc_start: 0.7953 (tptt) cc_final: 0.7483 (mtmt) REVERT: C 1565 ASP cc_start: 0.8368 (t0) cc_final: 0.7929 (t0) REVERT: C 1653 GLN cc_start: 0.8846 (tt0) cc_final: 0.8534 (mp-120) REVERT: C 1733 GLN cc_start: 0.8902 (tp-100) cc_final: 0.8321 (tp40) REVERT: C 1737 ASP cc_start: 0.9064 (m-30) cc_final: 0.8700 (m-30) REVERT: C 1738 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8057 (mm-30) REVERT: D 1657 GLU cc_start: 0.8813 (tt0) cc_final: 0.8541 (mp0) REVERT: D 1729 GLN cc_start: 0.8728 (tm-30) cc_final: 0.8295 (tm-30) REVERT: D 1745 ASN cc_start: 0.9145 (m-40) cc_final: 0.8914 (t0) REVERT: E 3 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8639 (tt0) REVERT: E 72 ASP cc_start: 0.8628 (t70) cc_final: 0.8399 (t70) REVERT: E 85 GLU cc_start: 0.8658 (mp0) cc_final: 0.8341 (mp0) REVERT: F 124 GLN cc_start: 0.8642 (pt0) cc_final: 0.8409 (pp30) REVERT: F 185 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8247 (mp0) REVERT: F 213 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7409 (pm20) outliers start: 34 outliers final: 19 residues processed: 289 average time/residue: 1.3260 time to fit residues: 422.1076 Evaluate side-chains 274 residues out of total 1766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 249 time to evaluate : 1.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1495 LEU Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain L residue 40 CYS Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 160 LEU Chi-restraints excluded: chain B residue 1492 HIS Chi-restraints excluded: chain B residue 1528 GLN Chi-restraints excluded: chain C residue 1535 VAL Chi-restraints excluded: chain C residue 1691 MET Chi-restraints excluded: chain C residue 1738 GLU Chi-restraints excluded: chain D residue 1492 HIS Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 11 CYS Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 193 TRP Chi-restraints excluded: chain E residue 201 ASN Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain F residue 213 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 14 optimal weight: 0.2980 chunk 84 optimal weight: 0.0370 chunk 120 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 107 optimal weight: 0.0570 chunk 164 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 28 optimal weight: 0.2980 chunk 12 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 overall best weight: 0.2776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1499 ASN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 145 ASN ** L 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1492 HIS D1492 HIS ** F 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.136990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.081907 restraints weight = 27615.397| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.24 r_work: 0.3039 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16010 Z= 0.174 Angle : 0.621 16.252 21760 Z= 0.317 Chirality : 0.042 0.214 2530 Planarity : 0.004 0.042 2676 Dihedral : 4.400 31.189 2114 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.52 % Favored : 97.38 % Rotamer: Outliers : 1.70 % Allowed : 18.86 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.19), residues: 1946 helix: 1.94 (0.16), residues: 924 sheet: 0.07 (0.26), residues: 402 loop : 0.03 (0.27), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP F 163 HIS 0.018 0.001 HIS D1492 PHE 0.020 0.001 PHE H 150 TYR 0.038 0.001 TYR F 192 ARG 0.009 0.000 ARG E 55 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3892 Ramachandran restraints generated. 1946 Oldfield, 0 Emsley, 1946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 258 time to evaluate : 1.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1493 MET cc_start: 0.7623 (ptt) cc_final: 0.7168 (ppp) REVERT: A 1532 MET cc_start: 0.6148 (tpp) cc_final: 0.5835 (tpp) REVERT: A 1548 THR cc_start: 0.8532 (m) cc_final: 0.8274 (m) REVERT: A 1559 ARG cc_start: 0.8291 (mtt180) cc_final: 0.7875 (mmm-85) REVERT: A 1564 LYS cc_start: 0.7920 (tptm) cc_final: 0.7543 (mtmt) REVERT: A 1565 ASP cc_start: 0.8325 (t0) cc_final: 0.7921 (t0) REVERT: A 1653 GLN cc_start: 0.8805 (tt0) cc_final: 0.8468 (mp-120) REVERT: A 1733 GLN cc_start: 0.9047 (tp40) cc_final: 0.8572 (tp40) REVERT: H 3 GLN cc_start: 0.8955 (tt0) cc_final: 0.8676 (tt0) REVERT: H 25 SER cc_start: 0.8826 (OUTLIER) cc_final: 0.8537 (p) REVERT: H 55 ARG cc_start: 0.8912 (mtm-85) cc_final: 0.8420 (mtm110) REVERT: H 85 GLU cc_start: 0.8797 (mp0) cc_final: 0.8590 (mp0) REVERT: H 213 LYS cc_start: 0.7719 (mmtm) cc_final: 0.7496 (tmmm) REVERT: L 175 MET cc_start: 0.8149 (tpt) cc_final: 0.7819 (tpp) REVERT: L 210 ASN cc_start: 0.7943 (t0) cc_final: 0.7509 (p0) REVERT: B 1657 GLU cc_start: 0.8830 (tt0) cc_final: 0.8505 (mp0) REVERT: B 1729 GLN cc_start: 0.8776 (tm-30) cc_final: 0.8292 (tp-100) REVERT: B 1745 ASN cc_start: 0.9259 (m-40) cc_final: 0.8870 (t0) REVERT: C 1493 MET cc_start: 0.7833 (ptt) cc_final: 0.7314 (ppp) REVERT: C 1532 MET cc_start: 0.6051 (tpp) cc_final: 0.5669 (tpp) REVERT: C 1559 ARG cc_start: 0.8246 (mtt180) cc_final: 0.7685 (mmm-85) REVERT: C 1564 LYS cc_start: 0.7945 (tptt) cc_final: 0.7475 (mtmt) REVERT: C 1565 ASP cc_start: 0.8356 (t0) cc_final: 0.7933 (t0) REVERT: C 1653 GLN cc_start: 0.8816 (tt0) cc_final: 0.8494 (mp-120) REVERT: C 1733 GLN cc_start: 0.8877 (tp-100) cc_final: 0.8394 (tp40) REVERT: C 1737 ASP cc_start: 0.9064 (m-30) cc_final: 0.8755 (m-30) REVERT: C 1738 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8023 (mm-30) REVERT: C 1747 ASN cc_start: 0.9166 (m-40) cc_final: 0.8352 (p0) REVERT: D 1657 GLU cc_start: 0.8807 (tt0) cc_final: 0.8530 (mp0) REVERT: D 1729 GLN cc_start: 0.8722 (tm-30) cc_final: 0.8251 (tp-100) REVERT: D 1733 GLN cc_start: 0.9014 (tp-100) cc_final: 0.8801 (tp40) REVERT: D 1744 ASP cc_start: 0.9194 (p0) cc_final: 0.8837 (p0) REVERT: D 1745 ASN cc_start: 0.9139 (m-40) cc_final: 0.8874 (t0) REVERT: D 1747 ASN cc_start: 0.8878 (p0) cc_final: 0.8611 (m-40) REVERT: E 3 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8650 (tt0) REVERT: E 85 GLU cc_start: 0.8672 (mp0) cc_final: 0.8383 (mp0) REVERT: F 124 GLN cc_start: 0.8641 (pt0) cc_final: 0.8396 (pp30) REVERT: F 185 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8272 (mp0) REVERT: F 213 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7455 (pm20) outliers start: 30 outliers final: 16 residues processed: 277 average time/residue: 1.3311 time to fit residues: 407.5356 Evaluate side-chains 273 residues out of total 1766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 252 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1495 LEU Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain H residue 11 CYS Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain L residue 40 CYS Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 160 LEU Chi-restraints excluded: chain C residue 1535 VAL Chi-restraints excluded: chain C residue 1738 GLU Chi-restraints excluded: chain D residue 1492 HIS Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 11 CYS Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 193 TRP Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain F residue 40 CYS Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain F residue 213 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 97 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 135 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 177 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 193 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 79 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1499 ASN H 81 GLN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 145 ASN ** L 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1492 HIS D1492 HIS ** F 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.134558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.079198 restraints weight = 27581.014| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.18 r_work: 0.2992 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16010 Z= 0.240 Angle : 0.639 15.856 21760 Z= 0.328 Chirality : 0.044 0.574 2530 Planarity : 0.004 0.046 2676 Dihedral : 4.522 31.303 2114 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.62 % Favored : 97.28 % Rotamer: Outliers : 1.59 % Allowed : 19.25 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.19), residues: 1946 helix: 1.85 (0.16), residues: 924 sheet: 0.11 (0.27), residues: 390 loop : 0.05 (0.27), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP F 163 HIS 0.019 0.001 HIS D1492 PHE 0.023 0.001 PHE H 150 TYR 0.034 0.001 TYR L 140 ARG 0.008 0.000 ARG H 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15049.78 seconds wall clock time: 269 minutes 33.65 seconds (16173.65 seconds total)