Starting phenix.real_space_refine on Mon Jul 6 04:42:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9orp_70780/07_2026/9orp_70780.cif Found real_map, /net/cci-nas-00/data/ceres_data/9orp_70780/07_2026/9orp_70780.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9orp_70780/07_2026/9orp_70780.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9orp_70780/07_2026/9orp_70780.map" model { file = "/net/cci-nas-00/data/ceres_data/9orp_70780/07_2026/9orp_70780.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9orp_70780/07_2026/9orp_70780.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 48 5.16 5 C 10400 2.51 5 N 2912 2.21 5 O 2992 1.98 5 H 15888 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32240 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2015 Classifications: {'peptide': 134} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 127} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2015 Classifications: {'peptide': 134} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 127} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2015 Classifications: {'peptide': 134} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 127} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "D" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2015 Classifications: {'peptide': 134} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 127} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "E" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2015 Classifications: {'peptide': 134} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 127} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "F" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2015 Classifications: {'peptide': 134} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 127} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "G" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2015 Classifications: {'peptide': 134} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 127} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "H" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2015 Classifications: {'peptide': 134} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 127} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "I" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2015 Classifications: {'peptide': 134} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 127} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "J" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2015 Classifications: {'peptide': 134} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 127} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "K" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2015 Classifications: {'peptide': 134} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 127} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "L" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2015 Classifications: {'peptide': 134} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 127} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "M" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2015 Classifications: {'peptide': 134} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 127} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "N" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2015 Classifications: {'peptide': 134} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 127} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "O" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2015 Classifications: {'peptide': 134} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 127} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "P" Number of atoms: 2015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2015 Classifications: {'peptide': 134} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 127} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 29 Time building chain proxies: 4.87, per 1000 atoms: 0.15 Number of scatterers: 32240 At special positions: 0 Unit cell: (105.41, 105.41, 110.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 O 2992 8.00 N 2912 7.00 C 10400 6.00 H 15888 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.93 Conformation dependent library (CDL) restraints added in 874.8 milliseconds 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3872 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 7 sheets defined 56.7% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid -11 through 23 removed outlier: 3.685A pdb=" N GLU A 18 " --> pdb=" O ARG A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 49 Processing helix chain 'A' and resid 50 through 69 removed outlier: 3.529A pdb=" N LYS A 67 " --> pdb=" O GLN A 63 " (cutoff:3.500A) Processing helix chain 'B' and resid -11 through 23 removed outlier: 3.678A pdb=" N GLU B 18 " --> pdb=" O ARG B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 49 Processing helix chain 'B' and resid 50 through 69 removed outlier: 3.579A pdb=" N GLU B 64 " --> pdb=" O LYS B 60 " (cutoff:3.500A) Processing helix chain 'C' and resid -11 through 23 removed outlier: 3.652A pdb=" N GLU C 18 " --> pdb=" O ARG C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 49 Processing helix chain 'C' and resid 50 through 69 removed outlier: 3.500A pdb=" N GLU C 64 " --> pdb=" O LYS C 60 " (cutoff:3.500A) Processing helix chain 'D' and resid -11 through 23 removed outlier: 3.587A pdb=" N GLU D 18 " --> pdb=" O ARG D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 49 Processing helix chain 'D' and resid 50 through 69 removed outlier: 3.673A pdb=" N GLU D 64 " --> pdb=" O LYS D 60 " (cutoff:3.500A) Processing helix chain 'E' and resid -11 through 23 removed outlier: 3.610A pdb=" N GLU E 18 " --> pdb=" O ARG E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 49 Processing helix chain 'E' and resid 50 through 69 removed outlier: 3.518A pdb=" N LYS E 67 " --> pdb=" O GLN E 63 " (cutoff:3.500A) Processing helix chain 'F' and resid -11 through 23 removed outlier: 3.632A pdb=" N GLU F 18 " --> pdb=" O ARG F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 49 Processing helix chain 'F' and resid 50 through 69 removed outlier: 3.511A pdb=" N GLU F 64 " --> pdb=" O LYS F 60 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS F 67 " --> pdb=" O GLN F 63 " (cutoff:3.500A) Processing helix chain 'G' and resid -11 through 23 removed outlier: 3.694A pdb=" N GLU G 18 " --> pdb=" O ARG G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 49 Processing helix chain 'G' and resid 50 through 69 removed outlier: 3.529A pdb=" N GLU G 64 " --> pdb=" O LYS G 60 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS G 67 " --> pdb=" O GLN G 63 " (cutoff:3.500A) Processing helix chain 'H' and resid -11 through 23 removed outlier: 3.668A pdb=" N GLU H 18 " --> pdb=" O ARG H 14 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 49 Processing helix chain 'H' and resid 50 through 69 removed outlier: 3.608A pdb=" N GLU H 64 " --> pdb=" O LYS H 60 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS H 67 " --> pdb=" O GLN H 63 " (cutoff:3.500A) Processing helix chain 'I' and resid -11 through 23 removed outlier: 3.695A pdb=" N GLU I 18 " --> pdb=" O ARG I 14 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 49 Processing helix chain 'I' and resid 50 through 69 Processing helix chain 'J' and resid -11 through 23 removed outlier: 3.604A pdb=" N GLU J 18 " --> pdb=" O ARG J 14 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 49 Processing helix chain 'J' and resid 50 through 69 removed outlier: 3.590A pdb=" N GLU J 64 " --> pdb=" O LYS J 60 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS J 67 " --> pdb=" O GLN J 63 " (cutoff:3.500A) Processing helix chain 'K' and resid -11 through 23 removed outlier: 3.665A pdb=" N GLU K 18 " --> pdb=" O ARG K 14 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 49 Processing helix chain 'K' and resid 50 through 69 removed outlier: 3.672A pdb=" N GLU K 64 " --> pdb=" O LYS K 60 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS K 67 " --> pdb=" O GLN K 63 " (cutoff:3.500A) Processing helix chain 'L' and resid -11 through 23 removed outlier: 3.683A pdb=" N GLU L 18 " --> pdb=" O ARG L 14 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 49 Processing helix chain 'L' and resid 50 through 69 removed outlier: 3.507A pdb=" N GLU L 64 " --> pdb=" O LYS L 60 " (cutoff:3.500A) Processing helix chain 'M' and resid -11 through 23 removed outlier: 3.701A pdb=" N GLU M 18 " --> pdb=" O ARG M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 49 Processing helix chain 'M' and resid 50 through 69 removed outlier: 3.555A pdb=" N GLU M 64 " --> pdb=" O LYS M 60 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS M 67 " --> pdb=" O GLN M 63 " (cutoff:3.500A) Processing helix chain 'N' and resid -11 through 23 removed outlier: 3.623A pdb=" N GLU N 18 " --> pdb=" O ARG N 14 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 49 Processing helix chain 'N' and resid 50 through 69 removed outlier: 3.559A pdb=" N GLU N 64 " --> pdb=" O LYS N 60 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS N 67 " --> pdb=" O GLN N 63 " (cutoff:3.500A) Processing helix chain 'O' and resid -11 through 23 removed outlier: 3.725A pdb=" N GLU O 18 " --> pdb=" O ARG O 14 " (cutoff:3.500A) Processing helix chain 'O' and resid 29 through 49 Processing helix chain 'O' and resid 50 through 69 removed outlier: 3.612A pdb=" N GLU O 64 " --> pdb=" O LYS O 60 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS O 67 " --> pdb=" O GLN O 63 " (cutoff:3.500A) Processing helix chain 'P' and resid -11 through 23 removed outlier: 3.593A pdb=" N GLU P 18 " --> pdb=" O ARG P 14 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 49 Processing helix chain 'P' and resid 50 through 69 removed outlier: 3.661A pdb=" N GLU P 64 " --> pdb=" O LYS P 60 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS P 67 " --> pdb=" O GLN P 63 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 83 Processing sheet with id=AA2, first strand: chain 'A' and resid 88 through 89 Processing sheet with id=AA3, first strand: chain 'B' and resid 88 through 89 Processing sheet with id=AA4, first strand: chain 'C' and resid 88 through 89 Processing sheet with id=AA5, first strand: chain 'D' and resid 104 through 105 Processing sheet with id=AA6, first strand: chain 'I' and resid 73 through 83 Processing sheet with id=AA7, first strand: chain 'K' and resid 88 through 89 1294 hydrogen bonds defined for protein. 3705 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: 7.10 Time building geometry restraints manager: 4.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 15888 1.03 - 1.22: 1 1.22 - 1.42: 6895 1.42 - 1.62: 9648 1.62 - 1.81: 96 Bond restraints: 32528 Sorted by residual: bond pdb=" CG1 ILE E 115 " pdb=" CD1 ILE E 115 " ideal model delta sigma weight residual 1.513 1.479 0.034 3.90e-02 6.57e+02 7.61e-01 bond pdb=" CG1 ILE I 115 " pdb=" CD1 ILE I 115 " ideal model delta sigma weight residual 1.513 1.480 0.033 3.90e-02 6.57e+02 7.37e-01 bond pdb=" CG1 ILE O 115 " pdb=" CD1 ILE O 115 " ideal model delta sigma weight residual 1.513 1.480 0.033 3.90e-02 6.57e+02 7.03e-01 bond pdb=" CG1 ILE C 115 " pdb=" CD1 ILE C 115 " ideal model delta sigma weight residual 1.513 1.482 0.031 3.90e-02 6.57e+02 6.39e-01 bond pdb=" CA PRO F 97 " pdb=" C PRO F 97 " ideal model delta sigma weight residual 1.517 1.512 0.005 6.70e-03 2.23e+04 6.11e-01 ... (remaining 32523 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 55140 1.29 - 2.58: 3223 2.58 - 3.87: 221 3.87 - 5.16: 34 5.16 - 6.44: 22 Bond angle restraints: 58640 Sorted by residual: angle pdb=" N GLY O 120 " pdb=" CA GLY O 120 " pdb=" C GLY O 120 " ideal model delta sigma weight residual 110.91 116.06 -5.15 1.49e+00 4.50e-01 1.20e+01 angle pdb=" CG ARG C 14 " pdb=" CD ARG C 14 " pdb=" NE ARG C 14 " ideal model delta sigma weight residual 112.00 118.08 -6.08 2.20e+00 2.07e-01 7.65e+00 angle pdb=" CG ARG E 14 " pdb=" CD ARG E 14 " pdb=" NE ARG E 14 " ideal model delta sigma weight residual 112.00 117.90 -5.90 2.20e+00 2.07e-01 7.20e+00 angle pdb=" CG ARG K 14 " pdb=" CD ARG K 14 " pdb=" NE ARG K 14 " ideal model delta sigma weight residual 112.00 117.88 -5.88 2.20e+00 2.07e-01 7.15e+00 angle pdb=" CD ARG E 14 " pdb=" NE ARG E 14 " pdb=" CZ ARG E 14 " ideal model delta sigma weight residual 124.40 127.90 -3.50 1.40e+00 5.10e-01 6.26e+00 ... (remaining 58635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.56: 13416 16.56 - 33.12: 1085 33.12 - 49.68: 458 49.68 - 66.24: 226 66.24 - 82.80: 63 Dihedral angle restraints: 15248 sinusoidal: 8304 harmonic: 6944 Sorted by residual: dihedral pdb=" CA THR I 106 " pdb=" C THR I 106 " pdb=" N PRO I 107 " pdb=" CA PRO I 107 " ideal model delta harmonic sigma weight residual 180.00 160.98 19.02 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA THR C 106 " pdb=" C THR C 106 " pdb=" N PRO C 107 " pdb=" CA PRO C 107 " ideal model delta harmonic sigma weight residual 180.00 161.22 18.78 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA THR A 106 " pdb=" C THR A 106 " pdb=" N PRO A 107 " pdb=" CA PRO A 107 " ideal model delta harmonic sigma weight residual 180.00 161.41 18.59 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 15245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1738 0.035 - 0.070: 555 0.070 - 0.104: 147 0.104 - 0.139: 63 0.139 - 0.174: 41 Chirality restraints: 2544 Sorted by residual: chirality pdb=" CA ILE I 78 " pdb=" N ILE I 78 " pdb=" C ILE I 78 " pdb=" CB ILE I 78 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.56e-01 chirality pdb=" CG LEU H 59 " pdb=" CB LEU H 59 " pdb=" CD1 LEU H 59 " pdb=" CD2 LEU H 59 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.55e-01 chirality pdb=" CA ILE O 78 " pdb=" N ILE O 78 " pdb=" C ILE O 78 " pdb=" CB ILE O 78 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.55e-01 ... (remaining 2541 not shown) Planarity restraints: 5008 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG J 10 " -0.205 9.50e-02 1.11e+02 6.83e-02 5.12e+00 pdb=" NE ARG J 10 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG J 10 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG J 10 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG J 10 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG J 10 " 0.001 2.00e-02 2.50e+03 pdb="HH12 ARG J 10 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG J 10 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG J 10 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 10 " -0.193 9.50e-02 1.11e+02 6.45e-02 4.86e+00 pdb=" NE ARG F 10 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG F 10 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG F 10 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG F 10 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG F 10 " 0.003 2.00e-02 2.50e+03 pdb="HH12 ARG F 10 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG F 10 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG F 10 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG N 10 " -0.191 9.50e-02 1.11e+02 6.41e-02 4.82e+00 pdb=" NE ARG N 10 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG N 10 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG N 10 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG N 10 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG N 10 " 0.003 2.00e-02 2.50e+03 pdb="HH12 ARG N 10 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG N 10 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG N 10 " -0.001 2.00e-02 2.50e+03 ... (remaining 5005 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.29: 5704 2.29 - 2.87: 73185 2.87 - 3.45: 85874 3.45 - 4.02: 119525 4.02 - 4.60: 183856 Nonbonded interactions: 468144 Sorted by model distance: nonbonded pdb=" HG2 ARG E 14 " pdb="HH11 ARG E 14 " model vdw 1.714 2.270 nonbonded pdb=" HG2 ARG K 14 " pdb="HH11 ARG K 14 " model vdw 1.747 2.270 nonbonded pdb=" HG2 ARG C 14 " pdb="HH11 ARG C 14 " model vdw 1.751 2.270 nonbonded pdb=" HH TYR G 57 " pdb="HH22 ARG H 25 " model vdw 1.808 2.100 nonbonded pdb=" HH TYR C 57 " pdb="HH22 ARG D 25 " model vdw 1.834 2.100 ... (remaining 468139 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.080 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: 0.240 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 28.560 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 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 0.034 16640 Z= 0.142 Angle : 0.677 6.444 22560 Z= 0.356 Chirality : 0.044 0.174 2544 Planarity : 0.007 0.089 2976 Dihedral : 15.808 82.797 6096 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.38 % Allowed : 10.44 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.16), residues: 2112 helix: -0.97 (0.13), residues: 1200 sheet: 0.36 (0.26), residues: 320 loop : -0.77 (0.22), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 10 TYR 0.008 0.001 TYR D 44 PHE 0.014 0.001 PHE H 99 TRP 0.009 0.001 TRP H 72 HIS 0.005 0.003 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (16640) covalent geometry : angle 0.67667 / 0.36 (22560) hydrogen bonds : bond 0.20661 / 14.01 ( 1294) hydrogen bonds : angle 7.52962 / 5.43 ( 3705) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Evaluate side-chains 459 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 453 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A -9 GLU cc_start: 0.7777 (tp30) cc_final: 0.7525 (mm-30) REVERT: A 13 GLU cc_start: 0.7452 (mm-30) cc_final: 0.7229 (mm-30) REVERT: G -9 GLU cc_start: 0.7737 (tp30) cc_final: 0.7472 (mm-30) REVERT: G 59 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8230 (mp) REVERT: G 64 GLU cc_start: 0.7375 (tp30) cc_final: 0.7131 (tp30) REVERT: J 14 ARG cc_start: 0.7404 (mtp85) cc_final: 0.6995 (mtp85) REVERT: J 22 LEU cc_start: 0.8449 (tp) cc_final: 0.8210 (tt) REVERT: K -9 GLU cc_start: 0.8018 (tp30) cc_final: 0.7793 (tp30) REVERT: K -1 ASP cc_start: 0.7387 (m-30) cc_final: 0.7181 (m-30) REVERT: M -9 GLU cc_start: 0.7973 (tp30) cc_final: 0.7772 (mm-30) REVERT: P 14 ARG cc_start: 0.7280 (mtp85) cc_final: 0.6827 (mtp85) REVERT: P 64 GLU cc_start: 0.7391 (tp30) cc_final: 0.7154 (tp30) outliers start: 6 outliers final: 0 residues processed: 454 average time/residue: 1.5998 time to fit residues: 786.5119 Evaluate side-chains 417 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 416 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 59 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K -10 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.139170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.123144 restraints weight = 58858.824| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.02 r_work: 0.3466 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 16640 Z= 0.258 Angle : 0.670 5.603 22560 Z= 0.353 Chirality : 0.043 0.161 2544 Planarity : 0.007 0.068 2976 Dihedral : 5.156 24.768 2386 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 1.50 % Allowed : 15.25 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.16), residues: 2112 helix: 0.90 (0.14), residues: 1168 sheet: 0.63 (0.24), residues: 320 loop : -0.47 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 14 TYR 0.018 0.002 TYR L 44 PHE 0.009 0.002 PHE I 99 TRP 0.004 0.001 TRP H 72 HIS 0.002 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00579 / 0.26 (16640) covalent geometry : angle 0.66997 / 0.35 (22560) hydrogen bonds : bond 0.07275 / 4.94 ( 1294) hydrogen bonds : angle 4.75555 / 3.44 ( 3705) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Evaluate side-chains 436 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 412 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A -9 GLU cc_start: 0.8030 (tp30) cc_final: 0.7775 (mm-30) REVERT: A 13 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7515 (mm-30) REVERT: A 16 ARG cc_start: 0.7524 (ttp80) cc_final: 0.7314 (tpm170) REVERT: B 13 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7452 (mm-30) REVERT: C 16 ARG cc_start: 0.7270 (ttm-80) cc_final: 0.6992 (ttm170) REVERT: C 64 GLU cc_start: 0.7223 (mm-30) cc_final: 0.6943 (mm-30) REVERT: D 25 ARG cc_start: 0.5770 (OUTLIER) cc_final: 0.5476 (ptt-90) REVERT: E 14 ARG cc_start: 0.7751 (mtp85) cc_final: 0.7521 (mmm-85) REVERT: G -9 GLU cc_start: 0.8022 (tp30) cc_final: 0.7727 (mm-30) REVERT: G 53 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7422 (mt-10) REVERT: G 59 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8115 (mp) REVERT: I 59 LEU cc_start: 0.8293 (mm) cc_final: 0.7941 (mp) REVERT: J 13 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7515 (mm-30) REVERT: K -9 GLU cc_start: 0.8267 (tp30) cc_final: 0.7992 (mm-30) REVERT: K 110 PHE cc_start: 0.8604 (m-80) cc_final: 0.8328 (m-80) REVERT: M 14 ARG cc_start: 0.7874 (tpp80) cc_final: 0.7590 (mtp-110) REVERT: O -9 GLU cc_start: 0.7983 (tp30) cc_final: 0.7604 (mm-30) REVERT: O 6 GLU cc_start: 0.7713 (tp30) cc_final: 0.7387 (tp30) REVERT: O 64 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7068 (mm-30) REVERT: O 102 ASN cc_start: 0.8639 (p0) cc_final: 0.8435 (p0) REVERT: P 6 GLU cc_start: 0.7557 (tp30) cc_final: 0.7330 (tp30) REVERT: P 10 ARG cc_start: 0.8235 (mmt90) cc_final: 0.7825 (mtt180) REVERT: P 14 ARG cc_start: 0.7612 (mtp85) cc_final: 0.7079 (mtp85) REVERT: P 64 GLU cc_start: 0.7700 (tp30) cc_final: 0.7466 (tp30) outliers start: 24 outliers final: 4 residues processed: 428 average time/residue: 1.8785 time to fit residues: 865.3375 Evaluate side-chains 416 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 410 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain J residue 115 ILE Chi-restraints excluded: chain L residue 115 ILE Chi-restraints excluded: chain N residue 114 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 166 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 25 optimal weight: 0.0970 chunk 54 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 10 optimal weight: 0.1980 chunk 157 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.141106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.124852 restraints weight = 57875.754| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.06 r_work: 0.3492 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16640 Z= 0.147 Angle : 0.548 5.518 22560 Z= 0.285 Chirality : 0.040 0.147 2544 Planarity : 0.005 0.065 2976 Dihedral : 4.599 24.573 2386 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 1.62 % Allowed : 17.38 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.16), residues: 2112 helix: 1.61 (0.14), residues: 1184 sheet: 0.94 (0.24), residues: 320 loop : -0.25 (0.22), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 14 TYR 0.010 0.001 TYR L 44 PHE 0.007 0.001 PHE G 1 TRP 0.004 0.001 TRP I 72 HIS 0.001 0.000 HIS K 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (16640) covalent geometry : angle 0.54827 / 0.29 (22560) hydrogen bonds : bond 0.05993 / 4.06 ( 1294) hydrogen bonds : angle 4.12492 / 2.99 ( 3705) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Evaluate side-chains 432 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 406 time to evaluate : 0.947 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: A -9 GLU cc_start: 0.7954 (tp30) cc_final: 0.7685 (mm-30) REVERT: A 13 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7468 (mm-30) REVERT: A 16 ARG cc_start: 0.7491 (ttp80) cc_final: 0.7214 (tpm170) REVERT: C 16 ARG cc_start: 0.7190 (ttm-80) cc_final: 0.6923 (ttm170) REVERT: C 55 LEU cc_start: 0.8332 (mm) cc_final: 0.8096 (mt) REVERT: C 64 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6874 (mm-30) REVERT: C 72 TRP cc_start: 0.6025 (m100) cc_final: 0.5058 (m100) REVERT: D -9 GLU cc_start: 0.7957 (tp30) cc_final: 0.7728 (mm-30) REVERT: D 25 ARG cc_start: 0.5772 (OUTLIER) cc_final: 0.5445 (ptt-90) REVERT: F 55 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.8007 (mp) REVERT: G -9 GLU cc_start: 0.7939 (tp30) cc_final: 0.7654 (mm-30) REVERT: G 19 ILE cc_start: 0.7535 (mm) cc_final: 0.7333 (mm) REVERT: G 53 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7329 (mt-10) REVERT: G 59 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8032 (mp) REVERT: H 59 LEU cc_start: 0.8251 (mm) cc_final: 0.7950 (mp) REVERT: J -9 GLU cc_start: 0.8029 (tp30) cc_final: 0.7765 (tp30) REVERT: J 13 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7462 (mm-30) REVERT: K 110 PHE cc_start: 0.8569 (m-80) cc_final: 0.8333 (m-80) REVERT: M 14 ARG cc_start: 0.7869 (tpp80) cc_final: 0.7586 (mmm-85) REVERT: O -9 GLU cc_start: 0.7927 (tp30) cc_final: 0.7574 (mm-30) REVERT: O 6 GLU cc_start: 0.7627 (tp30) cc_final: 0.7328 (tp30) REVERT: P 10 ARG cc_start: 0.8176 (mmt90) cc_final: 0.7853 (mtt180) REVERT: P 64 GLU cc_start: 0.7650 (tp30) cc_final: 0.7431 (tp30) outliers start: 26 outliers final: 7 residues processed: 423 average time/residue: 1.8158 time to fit residues: 829.2687 Evaluate side-chains 410 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 400 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain J residue 115 ILE Chi-restraints excluded: chain L residue 115 ILE Chi-restraints excluded: chain N residue 60 LYS Chi-restraints excluded: chain P residue 19 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 52 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 179 optimal weight: 0.0010 chunk 192 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 190 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.138736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.122605 restraints weight = 57380.350| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.04 r_work: 0.3463 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 16640 Z= 0.296 Angle : 0.601 7.080 22560 Z= 0.317 Chirality : 0.043 0.157 2544 Planarity : 0.006 0.092 2976 Dihedral : 4.700 26.318 2386 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.75 % Allowed : 18.88 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.16), residues: 2112 helix: 1.51 (0.14), residues: 1200 sheet: 1.63 (0.24), residues: 320 loop : -0.16 (0.21), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 14 TYR 0.013 0.002 TYR K 56 PHE 0.013 0.002 PHE M 1 TRP 0.004 0.001 TRP I 72 HIS 0.003 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00710 / 0.30 (16640) covalent geometry : angle 0.60087 / 0.32 (22560) hydrogen bonds : bond 0.06462 / 4.40 ( 1294) hydrogen bonds : angle 4.14782 / 3.01 ( 3705) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Evaluate side-chains 402 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 374 time to evaluate : 0.917 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A -9 GLU cc_start: 0.7928 (tp30) cc_final: 0.7666 (mm-30) REVERT: A 16 ARG cc_start: 0.7584 (ttp80) cc_final: 0.7338 (tpm170) REVERT: C 16 ARG cc_start: 0.7239 (ttm-80) cc_final: 0.6964 (ttm170) REVERT: C 59 LEU cc_start: 0.8285 (mm) cc_final: 0.7996 (mp) REVERT: C 64 GLU cc_start: 0.7276 (mm-30) cc_final: 0.7003 (mm-30) REVERT: D -9 GLU cc_start: 0.7960 (tp30) cc_final: 0.7724 (mm-30) REVERT: D 25 ARG cc_start: 0.5945 (OUTLIER) cc_final: 0.5594 (ptt-90) REVERT: G -9 GLU cc_start: 0.7898 (tp30) cc_final: 0.7638 (mm-30) REVERT: G 53 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7341 (mt-10) REVERT: G 59 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8024 (mp) REVERT: G 96 ARG cc_start: 0.8212 (ptt-90) cc_final: 0.7996 (ptt-90) REVERT: I 59 LEU cc_start: 0.8215 (mm) cc_final: 0.7859 (mp) REVERT: J 13 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7553 (mm-30) REVERT: K 59 LEU cc_start: 0.8283 (mm) cc_final: 0.7975 (mp) REVERT: M 14 ARG cc_start: 0.7906 (tpp80) cc_final: 0.7623 (mmm-85) REVERT: M 102 ASN cc_start: 0.8509 (p0) cc_final: 0.8274 (p0) REVERT: N 60 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7815 (tptm) REVERT: O 6 GLU cc_start: 0.7655 (tp30) cc_final: 0.7382 (tp30) REVERT: O 64 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7171 (mm-30) REVERT: O 102 ASN cc_start: 0.8649 (p0) cc_final: 0.8417 (p0) REVERT: P 64 GLU cc_start: 0.7653 (tp30) cc_final: 0.7436 (tp30) REVERT: P 110 PHE cc_start: 0.8455 (m-80) cc_final: 0.8083 (m-80) outliers start: 28 outliers final: 13 residues processed: 386 average time/residue: 1.8325 time to fit residues: 764.9567 Evaluate side-chains 388 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 372 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain B residue -12 MET Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain D residue -12 MET Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain F residue -12 MET Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain H residue -12 MET Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain J residue 115 ILE Chi-restraints excluded: chain N residue 60 LYS Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain O residue 19 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 163 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 chunk 158 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 169 optimal weight: 0.9990 chunk 181 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.140517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.124325 restraints weight = 57337.411| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.05 r_work: 0.3493 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 16640 Z= 0.164 Angle : 0.525 5.022 22560 Z= 0.275 Chirality : 0.039 0.145 2544 Planarity : 0.005 0.056 2976 Dihedral : 4.417 25.610 2386 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 1.19 % Allowed : 19.69 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.16), residues: 2112 helix: 1.98 (0.14), residues: 1200 sheet: 1.77 (0.23), residues: 320 loop : -0.04 (0.21), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 21 TYR 0.008 0.001 TYR L 44 PHE 0.009 0.001 PHE C 1 TRP 0.004 0.001 TRP I 72 HIS 0.001 0.000 HIS I 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (16640) covalent geometry : angle 0.52458 / 0.27 (22560) hydrogen bonds : bond 0.05606 / 3.81 ( 1294) hydrogen bonds : angle 3.92766 / 2.84 ( 3705) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Evaluate side-chains 385 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 366 time to evaluate : 0.888 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: symmetry clash revert: symmetry clash REVERT: A -9 GLU cc_start: 0.7897 (tp30) cc_final: 0.7647 (mm-30) REVERT: B 119 LEU cc_start: 0.7513 (tp) cc_final: 0.7303 (mp) REVERT: C 16 ARG cc_start: 0.7175 (ttm-80) cc_final: 0.6908 (ttm170) REVERT: C 59 LEU cc_start: 0.8233 (mm) cc_final: 0.7938 (mp) REVERT: C 64 GLU cc_start: 0.7219 (mm-30) cc_final: 0.6902 (mm-30) REVERT: D -9 GLU cc_start: 0.7846 (tp30) cc_final: 0.7600 (mm-30) REVERT: D 25 ARG cc_start: 0.5825 (OUTLIER) cc_final: 0.5490 (ptt-90) REVERT: E 14 ARG cc_start: 0.7928 (mmm-85) cc_final: 0.7565 (mmm-85) REVERT: G -9 GLU cc_start: 0.7875 (tp30) cc_final: 0.7593 (mm-30) REVERT: G 53 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7321 (mt-10) REVERT: G 59 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7989 (mp) REVERT: G 96 ARG cc_start: 0.8159 (ptt-90) cc_final: 0.7929 (ptt-90) REVERT: K 59 LEU cc_start: 0.8248 (mm) cc_final: 0.7921 (mp) REVERT: M 14 ARG cc_start: 0.7872 (tpp80) cc_final: 0.7530 (mmm-85) REVERT: M 96 ARG cc_start: 0.8285 (ptt-90) cc_final: 0.8058 (ptt-90) REVERT: N 60 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7814 (tptm) REVERT: O 6 GLU cc_start: 0.7577 (tp30) cc_final: 0.7325 (tp30) REVERT: O 64 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7127 (mm-30) REVERT: O 102 ASN cc_start: 0.8605 (p0) cc_final: 0.8381 (p0) REVERT: P 64 GLU cc_start: 0.7631 (tp30) cc_final: 0.7418 (tp30) REVERT: P 110 PHE cc_start: 0.8436 (m-80) cc_final: 0.8046 (m-80) outliers start: 19 outliers final: 9 residues processed: 377 average time/residue: 1.9354 time to fit residues: 786.5527 Evaluate side-chains 375 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 363 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain J residue 115 ILE Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 115 ILE Chi-restraints excluded: chain N residue 60 LYS Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain P residue 19 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 141 optimal weight: 0.5980 chunk 125 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 201 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.139217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.123085 restraints weight = 57131.144| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.04 r_work: 0.3469 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 16640 Z= 0.267 Angle : 0.557 5.896 22560 Z= 0.295 Chirality : 0.041 0.153 2544 Planarity : 0.005 0.052 2976 Dihedral : 4.503 26.499 2386 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.38 % Allowed : 20.56 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.17), residues: 2112 helix: 1.84 (0.14), residues: 1200 sheet: 2.37 (0.23), residues: 336 loop : -0.07 (0.22), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 21 TYR 0.017 0.002 TYR A 56 PHE 0.012 0.002 PHE M 1 TRP 0.003 0.001 TRP I 72 HIS 0.002 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00641 / 0.27 (16640) covalent geometry : angle 0.55731 / 0.29 (22560) hydrogen bonds : bond 0.06140 / 4.18 ( 1294) hydrogen bonds : angle 4.02962 / 2.91 ( 3705) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Evaluate side-chains 392 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 370 time to evaluate : 0.909 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 -9 GLU cc_start: 0.7896 (tp30) cc_final: 0.7648 (mm-30) REVERT: C 16 ARG cc_start: 0.7305 (ttm-80) cc_final: 0.7062 (ttm170) REVERT: C 59 LEU cc_start: 0.8249 (mm) cc_final: 0.7948 (mp) REVERT: C 60 LYS cc_start: 0.8328 (tppp) cc_final: 0.8067 (tttm) REVERT: C 64 GLU cc_start: 0.7305 (mm-30) cc_final: 0.7056 (mm-30) REVERT: D -9 GLU cc_start: 0.7928 (tp30) cc_final: 0.7691 (mm-30) REVERT: D 25 ARG cc_start: 0.5953 (OUTLIER) cc_final: 0.5608 (ptt-90) REVERT: F 14 ARG cc_start: 0.8098 (mtp85) cc_final: 0.7868 (mmm-85) REVERT: G -9 GLU cc_start: 0.7901 (tp30) cc_final: 0.7610 (mm-30) REVERT: G 53 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7360 (mt-10) REVERT: G 59 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8004 (mp) REVERT: G 96 ARG cc_start: 0.8174 (ptt-90) cc_final: 0.7930 (ptt-90) REVERT: G 102 ASN cc_start: 0.8305 (p0) cc_final: 0.8024 (p0) REVERT: K 59 LEU cc_start: 0.8242 (mm) cc_final: 0.7906 (mp) REVERT: M 14 ARG cc_start: 0.7879 (tpp80) cc_final: 0.7668 (mmm-85) REVERT: M 102 ASN cc_start: 0.8483 (p0) cc_final: 0.8233 (p0) REVERT: N 60 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7855 (tptm) REVERT: O 6 GLU cc_start: 0.7636 (tp30) cc_final: 0.7375 (tp30) REVERT: O 64 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7157 (mm-30) REVERT: O 102 ASN cc_start: 0.8627 (p0) cc_final: 0.8379 (p0) REVERT: P 64 GLU cc_start: 0.7660 (tp30) cc_final: 0.7452 (tp30) REVERT: P 110 PHE cc_start: 0.8437 (m-80) cc_final: 0.8105 (m-80) outliers start: 22 outliers final: 15 residues processed: 380 average time/residue: 1.9062 time to fit residues: 783.1912 Evaluate side-chains 379 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 361 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain B residue -12 MET Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain F residue -12 MET Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain J residue -12 MET Chi-restraints excluded: chain J residue 115 ILE Chi-restraints excluded: chain N residue 60 LYS Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain P residue -12 MET Chi-restraints excluded: chain P residue 19 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 0 optimal weight: 1.9990 chunk 201 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 204 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 171 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.139791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.123670 restraints weight = 56999.484| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.05 r_work: 0.3479 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 16640 Z= 0.220 Angle : 0.539 5.732 22560 Z= 0.284 Chirality : 0.040 0.149 2544 Planarity : 0.005 0.054 2976 Dihedral : 4.429 26.412 2386 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.31 % Allowed : 21.12 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.17), residues: 2112 helix: 1.98 (0.14), residues: 1200 sheet: 2.51 (0.23), residues: 336 loop : -0.04 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 14 TYR 0.012 0.002 TYR L 44 PHE 0.011 0.001 PHE M 1 TRP 0.004 0.001 TRP D 72 HIS 0.001 0.000 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.22 (16640) covalent geometry : angle 0.53896 / 0.28 (22560) hydrogen bonds : bond 0.05861 / 3.99 ( 1294) hydrogen bonds : angle 3.96626 / 2.86 ( 3705) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Evaluate side-chains 381 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 360 time to evaluate : 0.913 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: symmetry clash REVERT: A -9 GLU cc_start: 0.7915 (tp30) cc_final: 0.7675 (mm-30) REVERT: A 60 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7936 (ttmm) REVERT: C 16 ARG cc_start: 0.7322 (ttm-80) cc_final: 0.7072 (ttm170) REVERT: C 59 LEU cc_start: 0.8211 (mm) cc_final: 0.7889 (mp) REVERT: C 60 LYS cc_start: 0.8298 (tppp) cc_final: 0.8048 (tttm) REVERT: C 64 GLU cc_start: 0.7319 (mm-30) cc_final: 0.7064 (mm-30) REVERT: D -9 GLU cc_start: 0.7856 (tp30) cc_final: 0.7601 (mm-30) REVERT: D 25 ARG cc_start: 0.5908 (OUTLIER) cc_final: 0.5575 (ptt-90) REVERT: F 14 ARG cc_start: 0.8078 (mtp85) cc_final: 0.7867 (mmm-85) REVERT: F 110 PHE cc_start: 0.8505 (m-80) cc_final: 0.8233 (m-80) REVERT: G -9 GLU cc_start: 0.7881 (tp30) cc_final: 0.7604 (mm-30) REVERT: G 53 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7345 (mt-10) REVERT: G 59 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7972 (mp) REVERT: G 96 ARG cc_start: 0.8165 (ptt-90) cc_final: 0.7919 (ptt-90) REVERT: K 72 TRP cc_start: 0.6020 (m100) cc_final: 0.5336 (m100) REVERT: M 102 ASN cc_start: 0.8473 (p0) cc_final: 0.8230 (p0) REVERT: N 60 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7851 (tptm) REVERT: O 6 GLU cc_start: 0.7622 (tp30) cc_final: 0.7385 (tp30) REVERT: O 64 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7175 (mm-30) REVERT: O 102 ASN cc_start: 0.8621 (p0) cc_final: 0.8367 (p0) REVERT: P 110 PHE cc_start: 0.8436 (m-80) cc_final: 0.8040 (m-80) outliers start: 21 outliers final: 18 residues processed: 369 average time/residue: 1.9030 time to fit residues: 757.6422 Evaluate side-chains 378 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 356 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain B residue -12 MET Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain D residue -12 MET Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain F residue -12 MET Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain H residue -12 MET Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain J residue -12 MET Chi-restraints excluded: chain J residue 115 ILE Chi-restraints excluded: chain L residue 115 ILE Chi-restraints excluded: chain N residue 60 LYS Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain P residue -12 MET Chi-restraints excluded: chain P residue 60 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 15 optimal weight: 0.6980 chunk 189 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 120 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.140746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.124666 restraints weight = 56948.537| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.04 r_work: 0.3492 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 16640 Z= 0.171 Angle : 0.511 4.698 22560 Z= 0.269 Chirality : 0.039 0.145 2544 Planarity : 0.005 0.108 2976 Dihedral : 4.305 26.579 2386 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.00 % Allowed : 21.69 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.55 (0.17), residues: 2112 helix: 2.41 (0.14), residues: 1168 sheet: 2.62 (0.23), residues: 336 loop : -0.36 (0.23), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG M 14 TYR 0.014 0.001 TYR M 44 PHE 0.008 0.001 PHE G 1 TRP 0.004 0.001 TRP D 72 HIS 0.001 0.000 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 (16640) covalent geometry : angle 0.51110 / 0.27 (22560) hydrogen bonds : bond 0.05452 / 3.71 ( 1294) hydrogen bonds : angle 3.84927 / 2.77 ( 3705) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Evaluate side-chains 372 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 356 time to evaluate : 0.865 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: symmetry clash revert: symmetry clash REVERT: A -9 GLU cc_start: 0.7855 (tp30) cc_final: 0.7617 (mm-30) REVERT: C 16 ARG cc_start: 0.7308 (ttm-80) cc_final: 0.7058 (ttm170) REVERT: C 59 LEU cc_start: 0.8199 (mm) cc_final: 0.7871 (mp) REVERT: C 60 LYS cc_start: 0.8271 (tppp) cc_final: 0.8018 (tttm) REVERT: C 64 GLU cc_start: 0.7314 (mm-30) cc_final: 0.7036 (mm-30) REVERT: D -9 GLU cc_start: 0.7814 (tp30) cc_final: 0.7574 (mm-30) REVERT: D 25 ARG cc_start: 0.5883 (OUTLIER) cc_final: 0.5558 (ptt-90) REVERT: G -9 GLU cc_start: 0.7839 (tp30) cc_final: 0.7569 (mm-30) REVERT: G 53 GLU cc_start: 0.7541 (mt-10) cc_final: 0.7336 (mt-10) REVERT: G 59 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7886 (mp) REVERT: G 96 ARG cc_start: 0.8187 (ptt-90) cc_final: 0.7933 (ptt-90) REVERT: K 72 TRP cc_start: 0.6010 (m100) cc_final: 0.5333 (m100) REVERT: L 18 GLU cc_start: 0.7379 (tt0) cc_final: 0.7123 (tt0) REVERT: M 96 ARG cc_start: 0.8292 (ptt-90) cc_final: 0.8063 (ptt-90) REVERT: M 102 ASN cc_start: 0.8437 (p0) cc_final: 0.8191 (p0) REVERT: N 60 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7854 (tptm) REVERT: O 6 GLU cc_start: 0.7576 (tp30) cc_final: 0.7376 (tp30) REVERT: O 64 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7162 (mm-30) REVERT: O 102 ASN cc_start: 0.8595 (p0) cc_final: 0.8356 (p0) REVERT: P 110 PHE cc_start: 0.8428 (m-80) cc_final: 0.8038 (m-80) outliers start: 16 outliers final: 14 residues processed: 364 average time/residue: 1.7693 time to fit residues: 696.0526 Evaluate side-chains 369 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 352 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain D residue -12 MET Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain J residue -12 MET Chi-restraints excluded: chain J residue 19 ILE Chi-restraints excluded: chain J residue 115 ILE Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 115 ILE Chi-restraints excluded: chain N residue 60 LYS Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain P residue -12 MET Chi-restraints excluded: chain P residue 19 ILE Chi-restraints excluded: chain P residue 60 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 28 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 159 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 181 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.139215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.123206 restraints weight = 56830.561| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.02 r_work: 0.3471 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 16640 Z= 0.276 Angle : 0.551 4.530 22560 Z= 0.292 Chirality : 0.042 0.154 2544 Planarity : 0.005 0.079 2976 Dihedral : 4.434 26.985 2386 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.06 % Allowed : 21.75 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.36 (0.17), residues: 2112 helix: 2.04 (0.14), residues: 1184 sheet: 2.75 (0.23), residues: 336 loop : -0.12 (0.22), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG M 14 TYR 0.015 0.002 TYR A 56 PHE 0.012 0.002 PHE G 1 TRP 0.004 0.001 TRP D 72 HIS 0.002 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00667 / 0.28 (16640) covalent geometry : angle 0.55109 / 0.29 (22560) hydrogen bonds : bond 0.06063 / 4.13 ( 1294) hydrogen bonds : angle 3.98338 / 2.87 ( 3705) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Evaluate side-chains 378 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 361 time to evaluate : 0.903 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: symmetry clash revert: symmetry clash REVERT: A -9 GLU cc_start: 0.7876 (tp30) cc_final: 0.7633 (mm-30) REVERT: C 16 ARG cc_start: 0.7378 (ttm-80) cc_final: 0.7136 (ttm170) REVERT: C 59 LEU cc_start: 0.8216 (mm) cc_final: 0.7879 (mp) REVERT: C 60 LYS cc_start: 0.8290 (tppp) cc_final: 0.8040 (tttm) REVERT: C 64 GLU cc_start: 0.7345 (mm-30) cc_final: 0.7089 (mm-30) REVERT: D -9 GLU cc_start: 0.7876 (tp30) cc_final: 0.7620 (mm-30) REVERT: D 25 ARG cc_start: 0.5933 (OUTLIER) cc_final: 0.5608 (ptt-90) REVERT: E 14 ARG cc_start: 0.8050 (mmm-85) cc_final: 0.7706 (mmm-85) REVERT: F 110 PHE cc_start: 0.8532 (m-80) cc_final: 0.8285 (m-80) REVERT: G -9 GLU cc_start: 0.7893 (tp30) cc_final: 0.7618 (mm-30) REVERT: G 53 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7348 (mt-10) REVERT: G 59 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7966 (mp) REVERT: J 17 GLU cc_start: 0.7406 (mm-30) cc_final: 0.7145 (mm-30) REVERT: L 18 GLU cc_start: 0.7381 (tt0) cc_final: 0.7111 (tt0) REVERT: M 102 ASN cc_start: 0.8454 (p0) cc_final: 0.8230 (p0) REVERT: N 60 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7917 (tptm) REVERT: O 64 GLU cc_start: 0.7488 (mm-30) cc_final: 0.7176 (mm-30) REVERT: P 110 PHE cc_start: 0.8427 (m-80) cc_final: 0.8070 (m-80) outliers start: 17 outliers final: 13 residues processed: 370 average time/residue: 1.7876 time to fit residues: 714.2479 Evaluate side-chains 370 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 354 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain D residue -12 MET Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 102 ASN Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain J residue 115 ILE Chi-restraints excluded: chain L residue 115 ILE Chi-restraints excluded: chain N residue 60 LYS Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain P residue -12 MET Chi-restraints excluded: chain P residue 19 ILE Chi-restraints excluded: chain P residue 60 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 4 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 202 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 142 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.141454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.125172 restraints weight = 56484.976| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.04 r_work: 0.3495 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16640 Z= 0.180 Angle : 0.519 4.821 22560 Z= 0.274 Chirality : 0.040 0.144 2544 Planarity : 0.005 0.058 2976 Dihedral : 4.304 27.017 2386 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 0.94 % Allowed : 22.31 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.58 (0.17), residues: 2112 helix: 2.37 (0.14), residues: 1168 sheet: 2.77 (0.23), residues: 336 loop : -0.30 (0.23), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 21 TYR 0.013 0.001 TYR A 56 PHE 0.009 0.001 PHE G 1 TRP 0.004 0.001 TRP D 72 HIS 0.001 0.000 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (16640) covalent geometry : angle 0.51868 / 0.27 (22560) hydrogen bonds : bond 0.05550 / 3.77 ( 1294) hydrogen bonds : angle 3.87092 / 2.79 ( 3705) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Residue LYS 27 is missing expected H atoms. Skipping. Residue LYS 67 is missing expected H atoms. Skipping. Residue VAL 68 is missing expected H atoms. Skipping. Residue THR 70 is missing expected H atoms. Skipping. Residue SER 73 is missing expected H atoms. Skipping. Residue SER 81 is missing expected H atoms. Skipping. Evaluate side-chains 375 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 360 time to evaluate : 0.931 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: symmetry clash REVERT: A -9 GLU cc_start: 0.7894 (tp30) cc_final: 0.7665 (mm-30) REVERT: A 64 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7224 (mm-30) REVERT: C 16 ARG cc_start: 0.7345 (ttm-80) cc_final: 0.7099 (ttm170) REVERT: C 59 LEU cc_start: 0.8184 (mm) cc_final: 0.7852 (mp) REVERT: C 60 LYS cc_start: 0.8283 (tppp) cc_final: 0.8044 (tttm) REVERT: C 64 GLU cc_start: 0.7346 (mm-30) cc_final: 0.7072 (mm-30) REVERT: D -9 GLU cc_start: 0.7883 (tp30) cc_final: 0.7637 (mm-30) REVERT: D 25 ARG cc_start: 0.5909 (OUTLIER) cc_final: 0.5585 (ptt-90) REVERT: E 102 ASN cc_start: 0.8304 (p0) cc_final: 0.8026 (p0) REVERT: F 110 PHE cc_start: 0.8510 (m-80) cc_final: 0.8268 (m-80) REVERT: G -9 GLU cc_start: 0.7884 (tp30) cc_final: 0.7622 (mm-30) REVERT: G 53 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7357 (mt-10) REVERT: G 59 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7873 (mp) REVERT: G 96 ARG cc_start: 0.8182 (ptt-90) cc_final: 0.7922 (ptt-90) REVERT: J 17 GLU cc_start: 0.7374 (mm-30) cc_final: 0.7153 (mm-30) REVERT: L 18 GLU cc_start: 0.7386 (tt0) cc_final: 0.7123 (tt0) REVERT: M 102 ASN cc_start: 0.8441 (p0) cc_final: 0.8208 (p0) REVERT: N 60 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7756 (tttp) REVERT: O 64 GLU cc_start: 0.7618 (mm-30) cc_final: 0.7304 (mm-30) REVERT: O 102 ASN cc_start: 0.8609 (p0) cc_final: 0.8358 (p0) REVERT: P 110 PHE cc_start: 0.8420 (m-80) cc_final: 0.8062 (m-80) outliers start: 15 outliers final: 18 residues processed: 369 average time/residue: 1.8588 time to fit residues: 741.0048 Evaluate side-chains 379 residues out of total 1824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 358 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 102 ASN Chi-restraints excluded: chain D residue -12 MET Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 25 ARG Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 102 ASN Chi-restraints excluded: chain H residue -12 MET Chi-restraints excluded: chain H residue 19 ILE Chi-restraints excluded: chain H residue 114 SER Chi-restraints excluded: chain J residue 115 ILE Chi-restraints excluded: chain L residue 115 ILE Chi-restraints excluded: chain N residue 60 LYS Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 115 ILE Chi-restraints excluded: chain P residue -12 MET Chi-restraints excluded: chain P residue 19 ILE Chi-restraints excluded: chain P residue 102 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 191 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 188 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 90 optimal weight: 0.3980 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.141190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.124953 restraints weight = 56662.411| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.03 r_work: 0.3492 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 16640 Z= 0.200 Angle : 0.524 5.604 22560 Z= 0.276 Chirality : 0.040 0.144 2544 Planarity : 0.005 0.066 2976 Dihedral : 4.297 27.466 2386 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.00 % Allowed : 22.38 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.58 (0.17), residues: 2112 helix: 2.23 (0.14), residues: 1184 sheet: 2.80 (0.23), residues: 336 loop : -0.05 (0.23), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 21 TYR 0.011 0.001 TYR A 56 PHE 0.010 0.001 PHE G 1 TRP 0.004 0.001 TRP D 72 HIS 0.001 0.000 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.20 (16640) covalent geometry : angle 0.52352 / 0.28 (22560) hydrogen bonds : bond 0.05614 / 3.82 ( 1294) hydrogen bonds : angle 3.86753 / 2.79 ( 3705) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13256.92 seconds wall clock time: 224 minutes 9.53 seconds (13449.53 seconds total)