Starting phenix.real_space_refine on Wed Feb 4 16:06:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l5w_62847/02_2026/9l5w_62847.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l5w_62847/02_2026/9l5w_62847.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9l5w_62847/02_2026/9l5w_62847.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l5w_62847/02_2026/9l5w_62847.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9l5w_62847/02_2026/9l5w_62847.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l5w_62847/02_2026/9l5w_62847.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 7326 2.51 5 N 2106 2.21 5 O 2196 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11682 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 649 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "B" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 649 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "C" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 649 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "D" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 649 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "E" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 649 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "F" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 649 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "G" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 649 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "H" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 649 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "I" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 649 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "J" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 649 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "K" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 649 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "L" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 649 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "M" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 649 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "N" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 649 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "O" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 649 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "P" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 649 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "Q" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 649 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "R" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 649 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Time building chain proxies: 2.05, per 1000 atoms: 0.18 Number of scatterers: 11682 At special positions: 0 Unit cell: (92.354, 92.354, 114.307, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 2196 8.00 N 2106 7.00 C 7326 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 0.55 Conformation dependent library (CDL) restraints added in 352.1 milliseconds 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2772 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 0 sheets defined 75.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 removed outlier: 3.539A pdb=" N SER A 14 " --> pdb=" O SER A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 27 Processing helix chain 'A' and resid 32 through 37 Processing helix chain 'A' and resid 41 through 52 removed outlier: 3.692A pdb=" N LEU A 45 " --> pdb=" O SER A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 70 Processing helix chain 'A' and resid 72 through 79 removed outlier: 3.657A pdb=" N ARG A 78 " --> pdb=" O ASP A 74 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 13 Processing helix chain 'B' and resid 16 through 27 Processing helix chain 'B' and resid 32 through 37 Processing helix chain 'B' and resid 41 through 52 removed outlier: 3.578A pdb=" N LEU B 45 " --> pdb=" O SER B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 70 Processing helix chain 'B' and resid 72 through 79 removed outlier: 3.726A pdb=" N ARG B 78 " --> pdb=" O ASP B 74 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 14 removed outlier: 3.600A pdb=" N SER C 14 " --> pdb=" O SER C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 27 Processing helix chain 'C' and resid 32 through 37 Processing helix chain 'C' and resid 41 through 52 removed outlier: 3.630A pdb=" N LEU C 45 " --> pdb=" O SER C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 72 through 79 removed outlier: 3.729A pdb=" N ARG C 78 " --> pdb=" O ASP C 74 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL C 79 " --> pdb=" O LEU C 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 13 Processing helix chain 'D' and resid 16 through 27 Processing helix chain 'D' and resid 32 through 37 Processing helix chain 'D' and resid 41 through 52 removed outlier: 3.614A pdb=" N LEU D 45 " --> pdb=" O SER D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 70 Processing helix chain 'D' and resid 72 through 79 removed outlier: 3.732A pdb=" N ARG D 78 " --> pdb=" O ASP D 74 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL D 79 " --> pdb=" O LEU D 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 14 removed outlier: 3.608A pdb=" N SER E 14 " --> pdb=" O SER E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 27 Processing helix chain 'E' and resid 32 through 37 Processing helix chain 'E' and resid 41 through 52 removed outlier: 3.634A pdb=" N LEU E 45 " --> pdb=" O SER E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 70 Processing helix chain 'E' and resid 72 through 79 removed outlier: 3.748A pdb=" N ARG E 78 " --> pdb=" O ASP E 74 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL E 79 " --> pdb=" O LEU E 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 13 Processing helix chain 'F' and resid 16 through 27 Processing helix chain 'F' and resid 32 through 37 Processing helix chain 'F' and resid 41 through 52 removed outlier: 3.668A pdb=" N LEU F 45 " --> pdb=" O SER F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 70 Processing helix chain 'F' and resid 72 through 79 removed outlier: 3.742A pdb=" N ARG F 78 " --> pdb=" O ASP F 74 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL F 79 " --> pdb=" O LEU F 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 13 Processing helix chain 'G' and resid 16 through 27 Processing helix chain 'G' and resid 32 through 37 Processing helix chain 'G' and resid 41 through 52 removed outlier: 3.641A pdb=" N LEU G 45 " --> pdb=" O SER G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 70 Processing helix chain 'G' and resid 72 through 79 removed outlier: 3.664A pdb=" N ARG G 78 " --> pdb=" O ASP G 74 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL G 79 " --> pdb=" O LEU G 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 14 removed outlier: 3.592A pdb=" N SER H 14 " --> pdb=" O SER H 10 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 27 Processing helix chain 'H' and resid 32 through 37 Processing helix chain 'H' and resid 41 through 52 removed outlier: 3.661A pdb=" N LEU H 45 " --> pdb=" O SER H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 70 Processing helix chain 'H' and resid 72 through 79 removed outlier: 3.744A pdb=" N ARG H 78 " --> pdb=" O ASP H 74 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL H 79 " --> pdb=" O LEU H 75 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 14 removed outlier: 3.569A pdb=" N SER I 14 " --> pdb=" O SER I 10 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 27 Processing helix chain 'I' and resid 32 through 37 Processing helix chain 'I' and resid 41 through 52 removed outlier: 3.688A pdb=" N LEU I 45 " --> pdb=" O SER I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 70 Processing helix chain 'I' and resid 72 through 79 removed outlier: 3.697A pdb=" N ARG I 78 " --> pdb=" O ASP I 74 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL I 79 " --> pdb=" O LEU I 75 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 14 removed outlier: 3.533A pdb=" N SER J 14 " --> pdb=" O SER J 10 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 27 Processing helix chain 'J' and resid 32 through 37 Processing helix chain 'J' and resid 41 through 52 removed outlier: 3.709A pdb=" N LEU J 45 " --> pdb=" O SER J 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 70 Processing helix chain 'J' and resid 72 through 79 removed outlier: 3.663A pdb=" N ARG J 78 " --> pdb=" O ASP J 74 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL J 79 " --> pdb=" O LEU J 75 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 13 Processing helix chain 'K' and resid 16 through 27 Processing helix chain 'K' and resid 32 through 37 Processing helix chain 'K' and resid 41 through 52 removed outlier: 3.587A pdb=" N LEU K 45 " --> pdb=" O SER K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 70 Processing helix chain 'K' and resid 72 through 79 removed outlier: 3.703A pdb=" N ARG K 78 " --> pdb=" O ASP K 74 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL K 79 " --> pdb=" O LEU K 75 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 14 removed outlier: 3.640A pdb=" N SER L 14 " --> pdb=" O SER L 10 " (cutoff:3.500A) Processing helix chain 'L' and resid 16 through 27 Processing helix chain 'L' and resid 32 through 37 Processing helix chain 'L' and resid 41 through 52 removed outlier: 3.770A pdb=" N LEU L 45 " --> pdb=" O SER L 41 " (cutoff:3.500A) Processing helix chain 'L' and resid 60 through 70 Processing helix chain 'L' and resid 72 through 79 removed outlier: 3.755A pdb=" N ARG L 78 " --> pdb=" O ASP L 74 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL L 79 " --> pdb=" O LEU L 75 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 14 removed outlier: 3.602A pdb=" N SER M 14 " --> pdb=" O SER M 10 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 27 Processing helix chain 'M' and resid 32 through 37 Processing helix chain 'M' and resid 41 through 52 removed outlier: 3.680A pdb=" N LEU M 45 " --> pdb=" O SER M 41 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 70 Processing helix chain 'M' and resid 72 through 79 removed outlier: 3.723A pdb=" N ARG M 78 " --> pdb=" O ASP M 74 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL M 79 " --> pdb=" O LEU M 75 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 14 removed outlier: 3.511A pdb=" N SER N 14 " --> pdb=" O SER N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 27 Processing helix chain 'N' and resid 32 through 37 Processing helix chain 'N' and resid 41 through 52 removed outlier: 3.712A pdb=" N LEU N 45 " --> pdb=" O SER N 41 " (cutoff:3.500A) Processing helix chain 'N' and resid 60 through 70 Processing helix chain 'N' and resid 72 through 79 removed outlier: 3.721A pdb=" N ARG N 78 " --> pdb=" O ASP N 74 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL N 79 " --> pdb=" O LEU N 75 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 13 Processing helix chain 'O' and resid 16 through 27 Processing helix chain 'O' and resid 32 through 37 Processing helix chain 'O' and resid 41 through 52 removed outlier: 3.619A pdb=" N LEU O 45 " --> pdb=" O SER O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 60 through 70 Processing helix chain 'O' and resid 72 through 77 Processing helix chain 'P' and resid 2 through 14 removed outlier: 3.612A pdb=" N SER P 14 " --> pdb=" O SER P 10 " (cutoff:3.500A) Processing helix chain 'P' and resid 16 through 27 Processing helix chain 'P' and resid 32 through 37 Processing helix chain 'P' and resid 41 through 52 removed outlier: 3.624A pdb=" N LEU P 45 " --> pdb=" O SER P 41 " (cutoff:3.500A) Processing helix chain 'P' and resid 60 through 70 Processing helix chain 'P' and resid 72 through 79 removed outlier: 3.712A pdb=" N ARG P 78 " --> pdb=" O ASP P 74 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL P 79 " --> pdb=" O LEU P 75 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 14 removed outlier: 3.529A pdb=" N SER Q 14 " --> pdb=" O SER Q 10 " (cutoff:3.500A) Processing helix chain 'Q' and resid 16 through 27 Processing helix chain 'Q' and resid 32 through 37 Processing helix chain 'Q' and resid 41 through 52 removed outlier: 3.709A pdb=" N LEU Q 45 " --> pdb=" O SER Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 60 through 70 Processing helix chain 'Q' and resid 72 through 79 removed outlier: 3.705A pdb=" N ARG Q 78 " --> pdb=" O ASP Q 74 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL Q 79 " --> pdb=" O LEU Q 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 13 Processing helix chain 'R' and resid 16 through 27 Processing helix chain 'R' and resid 32 through 37 Processing helix chain 'R' and resid 41 through 52 removed outlier: 3.590A pdb=" N LEU R 45 " --> pdb=" O SER R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 70 Processing helix chain 'R' and resid 72 through 77 612 hydrogen bonds defined for protein. 1836 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: 1.25 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4014 1.34 - 1.46: 1207 1.46 - 1.57: 6497 1.57 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 11808 Sorted by residual: bond pdb=" CG PRO A 57 " pdb=" CD PRO A 57 " ideal model delta sigma weight residual 1.503 1.438 0.065 3.40e-02 8.65e+02 3.70e+00 bond pdb=" CG PRO M 3 " pdb=" CD PRO M 3 " ideal model delta sigma weight residual 1.503 1.537 -0.034 3.40e-02 8.65e+02 9.88e-01 bond pdb=" CB GLU I 65 " pdb=" CG GLU I 65 " ideal model delta sigma weight residual 1.520 1.493 0.027 3.00e-02 1.11e+03 8.18e-01 bond pdb=" CB GLU A 65 " pdb=" CG GLU A 65 " ideal model delta sigma weight residual 1.520 1.493 0.027 3.00e-02 1.11e+03 7.88e-01 bond pdb=" CG GLU I 65 " pdb=" CD GLU I 65 " ideal model delta sigma weight residual 1.516 1.495 0.021 2.50e-02 1.60e+03 6.94e-01 ... (remaining 11803 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 15718 2.71 - 5.42: 117 5.42 - 8.12: 2 8.12 - 10.83: 2 10.83 - 13.54: 1 Bond angle restraints: 15840 Sorted by residual: angle pdb=" N PRO A 57 " pdb=" CD PRO A 57 " pdb=" CG PRO A 57 " ideal model delta sigma weight residual 103.20 93.85 9.35 1.50e+00 4.44e-01 3.89e+01 angle pdb=" CA PRO A 57 " pdb=" N PRO A 57 " pdb=" CD PRO A 57 " ideal model delta sigma weight residual 112.00 105.08 6.92 1.40e+00 5.10e-01 2.44e+01 angle pdb=" CA PRO A 57 " pdb=" CB PRO A 57 " pdb=" CG PRO A 57 " ideal model delta sigma weight residual 104.50 96.43 8.07 1.90e+00 2.77e-01 1.80e+01 angle pdb=" CB PRO A 57 " pdb=" CG PRO A 57 " pdb=" CD PRO A 57 " ideal model delta sigma weight residual 106.10 92.56 13.54 3.20e+00 9.77e-02 1.79e+01 angle pdb=" N VAL E 79 " pdb=" CA VAL E 79 " pdb=" C VAL E 79 " ideal model delta sigma weight residual 111.91 108.19 3.72 8.90e-01 1.26e+00 1.75e+01 ... (remaining 15835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 5980 17.80 - 35.61: 1035 35.61 - 53.41: 298 53.41 - 71.21: 70 71.21 - 89.01: 15 Dihedral angle restraints: 7398 sinusoidal: 3186 harmonic: 4212 Sorted by residual: dihedral pdb=" CB GLU C 65 " pdb=" CG GLU C 65 " pdb=" CD GLU C 65 " pdb=" OE1 GLU C 65 " ideal model delta sinusoidal sigma weight residual 0.00 89.01 -89.01 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU E 61 " pdb=" CG GLU E 61 " pdb=" CD GLU E 61 " pdb=" OE1 GLU E 61 " ideal model delta sinusoidal sigma weight residual 0.00 88.76 -88.76 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB GLU N 22 " pdb=" CG GLU N 22 " pdb=" CD GLU N 22 " pdb=" OE1 GLU N 22 " ideal model delta sinusoidal sigma weight residual 0.00 87.93 -87.93 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 7395 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1054 0.028 - 0.055: 543 0.055 - 0.083: 197 0.083 - 0.111: 84 0.111 - 0.138: 12 Chirality restraints: 1890 Sorted by residual: chirality pdb=" CA GLU N 22 " pdb=" N GLU N 22 " pdb=" C GLU N 22 " pdb=" CB GLU N 22 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA PRO M 3 " pdb=" N PRO M 3 " pdb=" C PRO M 3 " pdb=" CB PRO M 3 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.05e-01 chirality pdb=" CA VAL L 79 " pdb=" N VAL L 79 " pdb=" C VAL L 79 " pdb=" CB VAL L 79 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.42e-01 ... (remaining 1887 not shown) Planarity restraints: 2016 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP M 2 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO M 3 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO M 3 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO M 3 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 2 " -0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO C 3 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO C 3 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 3 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU G 56 " -0.027 5.00e-02 4.00e+02 4.01e-02 2.57e+00 pdb=" N PRO G 57 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO G 57 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO G 57 " -0.022 5.00e-02 4.00e+02 ... (remaining 2013 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1286 2.75 - 3.29: 10918 3.29 - 3.83: 18455 3.83 - 4.36: 23332 4.36 - 4.90: 39389 Nonbonded interactions: 93380 Sorted by model distance: nonbonded pdb=" OE2 GLU B 51 " pdb=" NZ LYS D 33 " model vdw 2.213 3.120 nonbonded pdb=" NZ LYS A 33 " pdb=" OE2 GLU J 51 " model vdw 2.228 3.120 nonbonded pdb=" OE2 GLU F 51 " pdb=" NZ LYS I 33 " model vdw 2.228 3.120 nonbonded pdb=" OE2 GLU D 51 " pdb=" NZ LYS G 33 " model vdw 2.229 3.120 nonbonded pdb=" OE2 GLU N 51 " pdb=" NZ LYS Q 33 " model vdw 2.233 3.120 ... (remaining 93375 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' 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' selection = chain 'Q' selection = chain 'R' } 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: 2.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.910 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:6.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 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 0.065 11808 Z= 0.126 Angle : 0.592 13.538 15840 Z= 0.306 Chirality : 0.040 0.138 1890 Planarity : 0.004 0.051 2016 Dihedral : 19.382 89.013 4626 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.27 % Allowed : 32.89 % Favored : 64.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.27 (0.22), residues: 1422 helix: 1.42 (0.16), residues: 1116 sheet: None (None), residues: 0 loop : -1.20 (0.28), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 30 PHE 0.006 0.001 PHE K 4 HIS 0.005 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00286 (11808) covalent geometry : angle 0.59160 (15840) hydrogen bonds : bond 0.13454 ( 612) hydrogen bonds : angle 4.11503 ( 1836) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 415 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.6018 (tpp-160) cc_final: 0.4500 (ptp-170) REVERT: I 71 ARG cc_start: 0.7731 (mtm180) cc_final: 0.7469 (ttt90) outliers start: 31 outliers final: 20 residues processed: 440 average time/residue: 0.9663 time to fit residues: 443.1481 Evaluate side-chains 398 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 378 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain E residue 13 SER Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain M residue 13 SER Chi-restraints excluded: chain M residue 18 SER Chi-restraints excluded: chain N residue 48 MET Chi-restraints excluded: chain O residue 41 SER Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 18 SER Chi-restraints excluded: chain Q residue 22 GLU Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain R residue 79 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN B 9 HIS B 52 GLN C 9 HIS D 9 HIS D 53 ASN E 9 HIS F 9 HIS ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 9 HIS H 52 GLN I 9 HIS I 52 GLN J 9 HIS J 40 GLN K 53 ASN L 9 HIS M 9 HIS N 9 HIS O 9 HIS P 59 HIS Q 9 HIS Q 40 GLN Q 53 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.091697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.078918 restraints weight = 22343.263| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 3.00 r_work: 0.2984 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11808 Z= 0.101 Angle : 0.512 7.341 15840 Z= 0.255 Chirality : 0.037 0.110 1890 Planarity : 0.003 0.036 2016 Dihedral : 4.457 64.680 1608 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 6.43 % Allowed : 27.78 % Favored : 65.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.04 (0.23), residues: 1422 helix: 1.98 (0.16), residues: 1116 sheet: None (None), residues: 0 loop : -0.99 (0.29), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 30 PHE 0.004 0.001 PHE D 4 HIS 0.002 0.000 HIS Q 73 Details of bonding type rmsd covalent geometry : bond 0.00242 (11808) covalent geometry : angle 0.51184 (15840) hydrogen bonds : bond 0.02824 ( 612) hydrogen bonds : angle 3.16676 ( 1836) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 395 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.5155 (tpp-160) cc_final: 0.3435 (ptp-170) REVERT: B 1 MET cc_start: 0.6265 (ttm) cc_final: 0.6004 (mtt) REVERT: C 64 ARG cc_start: 0.8825 (mtt-85) cc_final: 0.8589 (mtt-85) REVERT: D 65 GLU cc_start: 0.8477 (tt0) cc_final: 0.8195 (tt0) REVERT: E 19 GLU cc_start: 0.8531 (mp0) cc_final: 0.8044 (mp0) REVERT: E 64 ARG cc_start: 0.8922 (mtt-85) cc_final: 0.8546 (mtp180) REVERT: E 77 ARG cc_start: 0.8451 (tpp80) cc_final: 0.7789 (ttp80) REVERT: F 22 GLU cc_start: 0.6758 (OUTLIER) cc_final: 0.5850 (mm-30) REVERT: G 56 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7635 (mt-10) REVERT: G 77 ARG cc_start: 0.7481 (tmm-80) cc_final: 0.7268 (tmm-80) REVERT: H 19 GLU cc_start: 0.8428 (mp0) cc_final: 0.8120 (mp0) REVERT: H 21 THR cc_start: 0.9011 (m) cc_final: 0.8796 (p) REVERT: H 38 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7943 (mtt180) REVERT: I 71 ARG cc_start: 0.8799 (mtm180) cc_final: 0.7714 (ttp-170) REVERT: L 19 GLU cc_start: 0.8384 (mp0) cc_final: 0.7887 (mt-10) REVERT: L 48 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8411 (mtm) REVERT: L 71 ARG cc_start: 0.6092 (OUTLIER) cc_final: 0.4523 (mtp180) REVERT: M 77 ARG cc_start: 0.8283 (tpp80) cc_final: 0.7703 (ttp80) REVERT: P 64 ARG cc_start: 0.8741 (mtt-85) cc_final: 0.8500 (mtt-85) REVERT: P 77 ARG cc_start: 0.8355 (tpp80) cc_final: 0.7659 (ttp80) REVERT: R 74 ASP cc_start: 0.9226 (p0) cc_final: 0.8994 (p0) outliers start: 88 outliers final: 27 residues processed: 448 average time/residue: 0.9112 time to fit residues: 425.9871 Evaluate side-chains 400 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 368 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 53 ASN Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain F residue 22 GLU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain K residue 53 ASN Chi-restraints excluded: chain L residue 48 MET Chi-restraints excluded: chain L residue 71 ARG Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 65 GLU Chi-restraints excluded: chain O residue 7 LEU Chi-restraints excluded: chain O residue 18 SER Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain Q residue 7 LEU Chi-restraints excluded: chain Q residue 22 GLU Chi-restraints excluded: chain Q residue 37 GLU Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain R residue 18 SER Chi-restraints excluded: chain R residue 79 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 4 optimal weight: 0.9980 chunk 83 optimal weight: 6.9990 chunk 135 optimal weight: 0.7980 chunk 16 optimal weight: 7.9990 chunk 136 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 138 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 GLN K 9 HIS N 40 GLN N 52 GLN P 59 HIS Q 40 GLN Q 53 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.090432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.077557 restraints weight = 22610.329| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 3.00 r_work: 0.3017 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11808 Z= 0.100 Angle : 0.494 7.516 15840 Z= 0.248 Chirality : 0.036 0.111 1890 Planarity : 0.003 0.034 2016 Dihedral : 4.182 63.134 1594 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 6.07 % Allowed : 29.09 % Favored : 64.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.33 (0.23), residues: 1422 helix: 2.18 (0.17), residues: 1116 sheet: None (None), residues: 0 loop : -0.88 (0.29), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 30 PHE 0.004 0.001 PHE D 4 HIS 0.004 0.001 HIS F 59 Details of bonding type rmsd covalent geometry : bond 0.00243 (11808) covalent geometry : angle 0.49446 (15840) hydrogen bonds : bond 0.02571 ( 612) hydrogen bonds : angle 3.00865 ( 1836) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 386 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.5043 (tpp-160) cc_final: 0.3338 (ptp-170) REVERT: B 1 MET cc_start: 0.6307 (OUTLIER) cc_final: 0.6031 (mtt) REVERT: C 64 ARG cc_start: 0.8814 (mtt-85) cc_final: 0.8517 (mtt-85) REVERT: C 71 ARG cc_start: 0.6331 (OUTLIER) cc_final: 0.6028 (ttt-90) REVERT: E 19 GLU cc_start: 0.8568 (mp0) cc_final: 0.8187 (mp0) REVERT: E 64 ARG cc_start: 0.8918 (mtt-85) cc_final: 0.8612 (mtp180) REVERT: F 22 GLU cc_start: 0.6746 (OUTLIER) cc_final: 0.5813 (mm-30) REVERT: G 1 MET cc_start: 0.2318 (OUTLIER) cc_final: 0.1906 (mtt) REVERT: G 34 ARG cc_start: 0.6975 (mmt-90) cc_final: 0.6562 (mmt180) REVERT: G 56 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7605 (mt-10) REVERT: H 19 GLU cc_start: 0.8471 (mp0) cc_final: 0.8051 (mp0) REVERT: H 38 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.8081 (mtt180) REVERT: H 64 ARG cc_start: 0.8846 (mtp85) cc_final: 0.8572 (mtp180) REVERT: I 71 ARG cc_start: 0.8773 (mtm180) cc_final: 0.7713 (ttp-170) REVERT: L 19 GLU cc_start: 0.8401 (mp0) cc_final: 0.7940 (mp0) REVERT: L 22 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.6817 (mt-10) REVERT: L 48 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8415 (mtm) REVERT: M 71 ARG cc_start: 0.8129 (mtp180) cc_final: 0.7921 (mtp180) REVERT: M 77 ARG cc_start: 0.8336 (tpp80) cc_final: 0.7777 (ttp80) REVERT: O 70 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8262 (mp) REVERT: P 21 THR cc_start: 0.8895 (m) cc_final: 0.8665 (p) REVERT: P 64 ARG cc_start: 0.8720 (mtt-85) cc_final: 0.8413 (mtt-85) REVERT: P 71 ARG cc_start: 0.8083 (mtp180) cc_final: 0.7868 (mtt-85) REVERT: P 77 ARG cc_start: 0.8359 (tpp80) cc_final: 0.7692 (ttp80) REVERT: Q 71 ARG cc_start: 0.8771 (mtp180) cc_final: 0.8469 (mtp85) REVERT: R 65 GLU cc_start: 0.8379 (tt0) cc_final: 0.8174 (tt0) outliers start: 83 outliers final: 33 residues processed: 436 average time/residue: 0.8865 time to fit residues: 403.5279 Evaluate side-chains 408 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 366 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain F residue 22 GLU Chi-restraints excluded: chain F residue 41 SER Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain J residue 41 SER Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain L residue 22 GLU Chi-restraints excluded: chain L residue 48 MET Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 22 GLU Chi-restraints excluded: chain O residue 7 LEU Chi-restraints excluded: chain O residue 17 SER Chi-restraints excluded: chain O residue 18 SER Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 7 LEU Chi-restraints excluded: chain Q residue 22 GLU Chi-restraints excluded: chain Q residue 37 GLU Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain R residue 18 SER Chi-restraints excluded: chain R residue 41 SER Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 79 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 14 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 128 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN I 40 GLN P 59 HIS Q 40 GLN ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.089448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.076607 restraints weight = 22585.829| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.00 r_work: 0.2961 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11808 Z= 0.114 Angle : 0.512 6.031 15840 Z= 0.256 Chirality : 0.037 0.122 1890 Planarity : 0.004 0.042 2016 Dihedral : 4.120 64.949 1592 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 6.29 % Allowed : 30.34 % Favored : 63.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.44 (0.23), residues: 1422 helix: 2.25 (0.17), residues: 1116 sheet: None (None), residues: 0 loop : -0.80 (0.30), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 34 PHE 0.005 0.001 PHE B 4 HIS 0.003 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00284 (11808) covalent geometry : angle 0.51235 (15840) hydrogen bonds : bond 0.02819 ( 612) hydrogen bonds : angle 2.99727 ( 1836) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 370 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.5059 (tpp-160) cc_final: 0.3318 (ptp-170) REVERT: B 1 MET cc_start: 0.6451 (OUTLIER) cc_final: 0.6179 (mtt) REVERT: C 38 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.8184 (mtt180) REVERT: C 64 ARG cc_start: 0.8863 (mtt-85) cc_final: 0.8395 (mtt-85) REVERT: D 65 GLU cc_start: 0.8645 (tt0) cc_final: 0.8321 (tt0) REVERT: E 19 GLU cc_start: 0.8586 (mp0) cc_final: 0.8189 (mp0) REVERT: E 64 ARG cc_start: 0.8935 (mtt-85) cc_final: 0.8590 (mtp180) REVERT: E 77 ARG cc_start: 0.8474 (tpp80) cc_final: 0.7833 (ttp80) REVERT: F 22 GLU cc_start: 0.6671 (OUTLIER) cc_final: 0.5725 (mm-30) REVERT: F 71 ARG cc_start: 0.5973 (OUTLIER) cc_final: 0.4257 (mtp180) REVERT: G 34 ARG cc_start: 0.6861 (mmt-90) cc_final: 0.6548 (mmt180) REVERT: G 56 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7794 (tm-30) REVERT: H 19 GLU cc_start: 0.8522 (mp0) cc_final: 0.8155 (mp0) REVERT: H 38 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.8102 (mtt180) REVERT: H 64 ARG cc_start: 0.8869 (mtp85) cc_final: 0.8569 (mtp180) REVERT: I 71 ARG cc_start: 0.8773 (mtm180) cc_final: 0.7726 (ttp-170) REVERT: L 19 GLU cc_start: 0.8432 (mp0) cc_final: 0.7839 (mp0) REVERT: L 22 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.6869 (mt-10) REVERT: L 48 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8440 (mtm) REVERT: M 40 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8237 (mp10) REVERT: M 77 ARG cc_start: 0.8324 (tpp80) cc_final: 0.7767 (ttp80) REVERT: O 70 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8452 (mp) REVERT: O 74 ASP cc_start: 0.9248 (p0) cc_final: 0.8947 (p0) REVERT: P 48 MET cc_start: 0.8976 (tpp) cc_final: 0.8728 (mmm) REVERT: P 64 ARG cc_start: 0.8775 (mtt-85) cc_final: 0.8518 (mtt-85) REVERT: P 77 ARG cc_start: 0.8366 (tpp80) cc_final: 0.7705 (ttp80) REVERT: Q 71 ARG cc_start: 0.8816 (mtp180) cc_final: 0.8609 (mtp85) outliers start: 86 outliers final: 35 residues processed: 420 average time/residue: 0.8994 time to fit residues: 393.9482 Evaluate side-chains 400 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 355 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 22 GLU Chi-restraints excluded: chain F residue 41 SER Chi-restraints excluded: chain F residue 71 ARG Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 41 SER Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 22 GLU Chi-restraints excluded: chain L residue 48 MET Chi-restraints excluded: chain M residue 40 GLN Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain O residue 7 LEU Chi-restraints excluded: chain O residue 18 SER Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 7 LEU Chi-restraints excluded: chain Q residue 22 GLU Chi-restraints excluded: chain Q residue 37 GLU Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain R residue 18 SER Chi-restraints excluded: chain R residue 41 SER Chi-restraints excluded: chain R residue 70 LEU Chi-restraints excluded: chain R residue 79 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 64 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 43 optimal weight: 0.0000 chunk 132 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN I 40 GLN L 59 HIS P 59 HIS Q 40 GLN ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.092638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.080032 restraints weight = 22245.445| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.93 r_work: 0.3028 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11808 Z= 0.101 Angle : 0.506 6.522 15840 Z= 0.255 Chirality : 0.036 0.114 1890 Planarity : 0.004 0.041 2016 Dihedral : 4.147 64.257 1592 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 5.34 % Allowed : 32.02 % Favored : 62.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.52 (0.23), residues: 1422 helix: 2.30 (0.16), residues: 1116 sheet: None (None), residues: 0 loop : -0.73 (0.31), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 77 PHE 0.004 0.001 PHE Q 4 HIS 0.004 0.001 HIS F 59 Details of bonding type rmsd covalent geometry : bond 0.00252 (11808) covalent geometry : angle 0.50567 (15840) hydrogen bonds : bond 0.02342 ( 612) hydrogen bonds : angle 2.93065 ( 1836) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 376 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.5300 (tpp-160) cc_final: 0.3483 (ptp-170) REVERT: B 56 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7906 (tm-30) REVERT: C 38 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.8093 (mtt180) REVERT: C 64 ARG cc_start: 0.8918 (mtt-85) cc_final: 0.8451 (mtt-85) REVERT: C 71 ARG cc_start: 0.6418 (OUTLIER) cc_final: 0.4671 (mtp180) REVERT: E 19 GLU cc_start: 0.8595 (mp0) cc_final: 0.8286 (mp0) REVERT: E 64 ARG cc_start: 0.8941 (mtt-85) cc_final: 0.8672 (mtp85) REVERT: E 77 ARG cc_start: 0.8397 (tpp80) cc_final: 0.7885 (ttp80) REVERT: F 22 GLU cc_start: 0.6742 (OUTLIER) cc_final: 0.5764 (mm-30) REVERT: F 71 ARG cc_start: 0.6024 (OUTLIER) cc_final: 0.4384 (mtp180) REVERT: G 56 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7877 (tm-30) REVERT: H 19 GLU cc_start: 0.8527 (mp0) cc_final: 0.8251 (mp0) REVERT: H 38 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.8069 (mtt180) REVERT: H 56 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7804 (mp0) REVERT: H 64 ARG cc_start: 0.8915 (mtp85) cc_final: 0.8613 (mtp180) REVERT: H 71 ARG cc_start: 0.8261 (mtp180) cc_final: 0.8057 (mtp180) REVERT: I 52 GLN cc_start: 0.8373 (mt0) cc_final: 0.7773 (mt0) REVERT: I 65 GLU cc_start: 0.8530 (tt0) cc_final: 0.8008 (tt0) REVERT: I 71 ARG cc_start: 0.8825 (mtm180) cc_final: 0.7818 (ttp-170) REVERT: J 19 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8210 (mt-10) REVERT: J 65 GLU cc_start: 0.8667 (tt0) cc_final: 0.8348 (tt0) REVERT: K 65 GLU cc_start: 0.8746 (tt0) cc_final: 0.8544 (tt0) REVERT: L 22 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.6971 (mt-10) REVERT: L 71 ARG cc_start: 0.6282 (OUTLIER) cc_final: 0.4723 (mtp180) REVERT: M 64 ARG cc_start: 0.8905 (mtt-85) cc_final: 0.8582 (mtp180) REVERT: M 77 ARG cc_start: 0.8262 (tpp80) cc_final: 0.7803 (ttp80) REVERT: N 65 GLU cc_start: 0.8565 (tt0) cc_final: 0.8321 (tt0) REVERT: O 1 MET cc_start: 0.6451 (OUTLIER) cc_final: 0.5990 (mtt) REVERT: O 70 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8533 (mp) REVERT: P 1 MET cc_start: 0.7331 (mmm) cc_final: 0.5972 (mpt) REVERT: P 48 MET cc_start: 0.8993 (tpp) cc_final: 0.8753 (mmm) REVERT: P 56 GLU cc_start: 0.8478 (mt-10) cc_final: 0.7686 (mp0) REVERT: P 64 ARG cc_start: 0.8817 (mtt-85) cc_final: 0.8550 (mtt-85) REVERT: P 77 ARG cc_start: 0.8304 (tpp80) cc_final: 0.7734 (ttp80) REVERT: R 65 GLU cc_start: 0.8554 (tt0) cc_final: 0.8308 (tt0) outliers start: 73 outliers final: 30 residues processed: 417 average time/residue: 0.8881 time to fit residues: 385.8743 Evaluate side-chains 402 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 360 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain F residue 22 GLU Chi-restraints excluded: chain F residue 41 SER Chi-restraints excluded: chain F residue 71 ARG Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 33 LYS Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain H residue 38 ARG Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 41 SER Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain L residue 22 GLU Chi-restraints excluded: chain L residue 71 ARG Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 7 LEU Chi-restraints excluded: chain O residue 18 SER Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain Q residue 22 GLU Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 65 GLU Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain R residue 18 SER Chi-restraints excluded: chain R residue 41 SER Chi-restraints excluded: chain R residue 70 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 117 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 52 GLN F 40 GLN F 59 HIS I 40 GLN L 59 HIS P 59 HIS Q 40 GLN ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 HIS R 52 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.092078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.079698 restraints weight = 22141.272| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.90 r_work: 0.3036 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11808 Z= 0.110 Angle : 0.522 7.016 15840 Z= 0.263 Chirality : 0.037 0.116 1890 Planarity : 0.004 0.047 2016 Dihedral : 4.022 65.423 1591 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 5.70 % Allowed : 31.94 % Favored : 62.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.57 (0.23), residues: 1422 helix: 2.33 (0.16), residues: 1116 sheet: None (None), residues: 0 loop : -0.73 (0.31), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 30 PHE 0.004 0.001 PHE Q 4 HIS 0.004 0.001 HIS Q 59 Details of bonding type rmsd covalent geometry : bond 0.00275 (11808) covalent geometry : angle 0.52206 (15840) hydrogen bonds : bond 0.02527 ( 612) hydrogen bonds : angle 2.93781 ( 1836) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 372 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6832 (tpp) cc_final: 0.6314 (mtt) REVERT: A 34 ARG cc_start: 0.5286 (tpp-160) cc_final: 0.3482 (ptp-170) REVERT: C 38 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.8179 (mtt90) REVERT: C 64 ARG cc_start: 0.8901 (mtt-85) cc_final: 0.8397 (mtt-85) REVERT: C 71 ARG cc_start: 0.6448 (OUTLIER) cc_final: 0.4529 (mtp180) REVERT: E 19 GLU cc_start: 0.8590 (mp0) cc_final: 0.8229 (mp0) REVERT: E 64 ARG cc_start: 0.8894 (mtt-85) cc_final: 0.8669 (mtp180) REVERT: E 77 ARG cc_start: 0.8379 (tpp80) cc_final: 0.7922 (ttp80) REVERT: F 22 GLU cc_start: 0.6774 (OUTLIER) cc_final: 0.5799 (mm-30) REVERT: F 71 ARG cc_start: 0.6036 (OUTLIER) cc_final: 0.4353 (mtp180) REVERT: F 77 ARG cc_start: 0.8587 (tpp-160) cc_final: 0.8332 (tmm-80) REVERT: G 34 ARG cc_start: 0.7037 (mmt-90) cc_final: 0.6632 (mmt180) REVERT: G 56 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7681 (mt-10) REVERT: H 19 GLU cc_start: 0.8517 (mp0) cc_final: 0.8213 (mp0) REVERT: H 56 GLU cc_start: 0.8350 (mt-10) cc_final: 0.7791 (mp0) REVERT: I 52 GLN cc_start: 0.8459 (mt0) cc_final: 0.7885 (mt0) REVERT: I 71 ARG cc_start: 0.8845 (mtm180) cc_final: 0.7841 (ttp-170) REVERT: J 65 GLU cc_start: 0.8702 (tt0) cc_final: 0.8458 (tt0) REVERT: L 19 GLU cc_start: 0.8551 (mm-30) cc_final: 0.7689 (mp0) REVERT: L 22 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.6988 (mt-10) REVERT: L 71 ARG cc_start: 0.6226 (OUTLIER) cc_final: 0.4604 (mtp180) REVERT: M 40 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8198 (mp10) REVERT: M 77 ARG cc_start: 0.8284 (tpp80) cc_final: 0.7808 (ttp80) REVERT: N 34 ARG cc_start: 0.8963 (ptm-80) cc_final: 0.8763 (ptm160) REVERT: O 1 MET cc_start: 0.6386 (ttm) cc_final: 0.6017 (mtt) REVERT: O 70 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8624 (mp) REVERT: P 1 MET cc_start: 0.7232 (mmm) cc_final: 0.5891 (mpt) REVERT: P 48 MET cc_start: 0.8983 (tpp) cc_final: 0.8747 (mmm) REVERT: P 56 GLU cc_start: 0.8494 (mt-10) cc_final: 0.7726 (mp0) REVERT: P 64 ARG cc_start: 0.8791 (mtt-85) cc_final: 0.8502 (mtt-85) REVERT: P 71 ARG cc_start: 0.8108 (mtp180) cc_final: 0.7792 (mtt-85) REVERT: P 77 ARG cc_start: 0.8293 (tpp80) cc_final: 0.7755 (ttp80) REVERT: Q 65 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8332 (tt0) REVERT: R 65 GLU cc_start: 0.8576 (tt0) cc_final: 0.8359 (tt0) outliers start: 78 outliers final: 35 residues processed: 419 average time/residue: 0.9364 time to fit residues: 408.7995 Evaluate side-chains 400 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 355 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 22 GLU Chi-restraints excluded: chain F residue 41 SER Chi-restraints excluded: chain F residue 71 ARG Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 41 SER Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 70 LEU Chi-restraints excluded: chain K residue 78 ARG Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 22 GLU Chi-restraints excluded: chain L residue 71 ARG Chi-restraints excluded: chain M residue 40 GLN Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 35 LYS Chi-restraints excluded: chain O residue 7 LEU Chi-restraints excluded: chain O residue 18 SER Chi-restraints excluded: chain O residue 70 LEU Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain Q residue 22 GLU Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 65 GLU Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain R residue 18 SER Chi-restraints excluded: chain R residue 41 SER Chi-restraints excluded: chain R residue 70 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 41 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 80 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 93 optimal weight: 0.3980 chunk 104 optimal weight: 7.9990 chunk 4 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 52 GLN A 59 HIS F 59 HIS I 40 GLN L 59 HIS ** N 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 59 HIS Q 40 GLN ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.092232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.079834 restraints weight = 22180.890| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.88 r_work: 0.3045 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11808 Z= 0.115 Angle : 0.544 7.155 15840 Z= 0.274 Chirality : 0.037 0.118 1890 Planarity : 0.004 0.047 2016 Dihedral : 3.952 66.671 1591 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.68 % Allowed : 33.19 % Favored : 62.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.56 (0.23), residues: 1422 helix: 2.32 (0.16), residues: 1116 sheet: None (None), residues: 0 loop : -0.73 (0.31), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 77 PHE 0.004 0.001 PHE N 4 HIS 0.002 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00288 (11808) covalent geometry : angle 0.54386 (15840) hydrogen bonds : bond 0.02581 ( 612) hydrogen bonds : angle 2.98776 ( 1836) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 366 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.5352 (tpp-160) cc_final: 0.3518 (ptp-170) REVERT: B 56 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7915 (tm-30) REVERT: C 38 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.8130 (mtt180) REVERT: C 64 ARG cc_start: 0.8900 (mtt-85) cc_final: 0.8543 (mtt-85) REVERT: E 19 GLU cc_start: 0.8591 (mp0) cc_final: 0.8219 (mp0) REVERT: E 64 ARG cc_start: 0.8887 (mtt-85) cc_final: 0.8657 (mtp180) REVERT: E 77 ARG cc_start: 0.8355 (tpp80) cc_final: 0.7929 (ttp80) REVERT: F 22 GLU cc_start: 0.6781 (OUTLIER) cc_final: 0.5778 (mm-30) REVERT: F 71 ARG cc_start: 0.6080 (OUTLIER) cc_final: 0.4343 (mtp180) REVERT: F 77 ARG cc_start: 0.8653 (tpp-160) cc_final: 0.8380 (tmm-80) REVERT: G 56 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7894 (tm-30) REVERT: H 19 GLU cc_start: 0.8519 (mp0) cc_final: 0.8197 (mp0) REVERT: H 56 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7826 (mp0) REVERT: H 64 ARG cc_start: 0.8895 (mtp180) cc_final: 0.8603 (mtp180) REVERT: I 52 GLN cc_start: 0.8403 (mt0) cc_final: 0.7902 (mt0) REVERT: I 61 GLU cc_start: 0.8335 (pm20) cc_final: 0.8091 (pm20) REVERT: I 71 ARG cc_start: 0.8830 (mtm180) cc_final: 0.7854 (ttp-170) REVERT: J 19 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8229 (mt-10) REVERT: J 65 GLU cc_start: 0.8705 (tt0) cc_final: 0.8413 (tt0) REVERT: L 22 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.6987 (mt-10) REVERT: L 71 ARG cc_start: 0.6261 (OUTLIER) cc_final: 0.4626 (mtp180) REVERT: M 40 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8152 (mp10) REVERT: M 77 ARG cc_start: 0.8272 (tpp80) cc_final: 0.7820 (ttp80) REVERT: O 1 MET cc_start: 0.6332 (ttm) cc_final: 0.5963 (mtt) REVERT: P 1 MET cc_start: 0.7232 (mmm) cc_final: 0.5874 (mpt) REVERT: P 48 MET cc_start: 0.8996 (tpp) cc_final: 0.8764 (mmm) REVERT: P 56 GLU cc_start: 0.8508 (mt-10) cc_final: 0.7731 (mp0) REVERT: P 64 ARG cc_start: 0.8795 (mtt-85) cc_final: 0.8521 (mtt-85) REVERT: P 77 ARG cc_start: 0.8293 (tpp80) cc_final: 0.7796 (ttp80) REVERT: Q 65 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8408 (pt0) REVERT: R 65 GLU cc_start: 0.8582 (tt0) cc_final: 0.8309 (tt0) outliers start: 64 outliers final: 33 residues processed: 406 average time/residue: 1.0425 time to fit residues: 440.3686 Evaluate side-chains 399 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 356 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 22 GLU Chi-restraints excluded: chain F residue 41 SER Chi-restraints excluded: chain F residue 71 ARG Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain J residue 19 GLU Chi-restraints excluded: chain J residue 41 SER Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain K residue 78 ARG Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 22 GLU Chi-restraints excluded: chain L residue 71 ARG Chi-restraints excluded: chain M residue 40 GLN Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain O residue 7 LEU Chi-restraints excluded: chain O residue 18 SER Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain Q residue 7 LEU Chi-restraints excluded: chain Q residue 22 GLU Chi-restraints excluded: chain Q residue 37 GLU Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 48 MET Chi-restraints excluded: chain Q residue 65 GLU Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain R residue 41 SER Chi-restraints excluded: chain R residue 70 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 66 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 120 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 52 GLN A 59 HIS ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 GLN ** J 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 59 HIS N 52 GLN N 59 HIS P 59 HIS Q 40 GLN ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 9 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.091709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.079318 restraints weight = 22157.946| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.91 r_work: 0.3031 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11808 Z= 0.126 Angle : 0.570 7.716 15840 Z= 0.287 Chirality : 0.037 0.135 1890 Planarity : 0.004 0.046 2016 Dihedral : 3.952 67.991 1591 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.31 % Allowed : 33.19 % Favored : 62.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.54 (0.23), residues: 1422 helix: 2.32 (0.16), residues: 1116 sheet: None (None), residues: 0 loop : -0.76 (0.32), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 77 PHE 0.005 0.001 PHE Q 4 HIS 0.003 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00314 (11808) covalent geometry : angle 0.56986 (15840) hydrogen bonds : bond 0.02705 ( 612) hydrogen bonds : angle 3.02706 ( 1836) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 362 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5113 (mtm) cc_final: 0.4900 (mpt) REVERT: A 34 ARG cc_start: 0.5303 (tpp-160) cc_final: 0.3484 (ptp-170) REVERT: B 56 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7899 (tm-30) REVERT: B 59 HIS cc_start: 0.7434 (t-90) cc_final: 0.6865 (t-90) REVERT: C 38 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.8153 (mtt180) REVERT: C 64 ARG cc_start: 0.8880 (mtt-85) cc_final: 0.8510 (mtt-85) REVERT: D 56 GLU cc_start: 0.8138 (tp30) cc_final: 0.7819 (tm-30) REVERT: E 77 ARG cc_start: 0.8376 (tpp80) cc_final: 0.7934 (ttp80) REVERT: F 22 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.5796 (mm-30) REVERT: F 61 GLU cc_start: 0.8539 (pm20) cc_final: 0.8330 (pm20) REVERT: F 71 ARG cc_start: 0.6105 (OUTLIER) cc_final: 0.4336 (mtp180) REVERT: G 33 LYS cc_start: 0.4982 (OUTLIER) cc_final: 0.4111 (pttp) REVERT: G 56 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7900 (tm-30) REVERT: H 19 GLU cc_start: 0.8524 (mp0) cc_final: 0.8160 (mp0) REVERT: H 64 ARG cc_start: 0.8926 (mtp180) cc_final: 0.8604 (mtp180) REVERT: H 71 ARG cc_start: 0.8161 (mtp180) cc_final: 0.7790 (mtp180) REVERT: I 52 GLN cc_start: 0.8369 (mt0) cc_final: 0.7750 (mt0) REVERT: I 61 GLU cc_start: 0.8378 (pm20) cc_final: 0.8114 (pm20) REVERT: I 65 GLU cc_start: 0.8367 (tt0) cc_final: 0.8135 (tt0) REVERT: I 71 ARG cc_start: 0.8831 (mtm180) cc_final: 0.7836 (ttp-170) REVERT: J 34 ARG cc_start: 0.9195 (ptm-80) cc_final: 0.8931 (ptm-80) REVERT: J 65 GLU cc_start: 0.8675 (tt0) cc_final: 0.8281 (pp20) REVERT: L 22 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.6962 (mt-10) REVERT: L 71 ARG cc_start: 0.6246 (OUTLIER) cc_final: 0.4604 (mtp180) REVERT: M 40 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8157 (mp10) REVERT: M 48 MET cc_start: 0.9028 (mpp) cc_final: 0.8774 (mmm) REVERT: M 77 ARG cc_start: 0.8316 (tpp80) cc_final: 0.7780 (ttp80) REVERT: O 1 MET cc_start: 0.6281 (ttm) cc_final: 0.5896 (mtt) REVERT: O 74 ASP cc_start: 0.9311 (p0) cc_final: 0.8995 (p0) REVERT: P 1 MET cc_start: 0.7225 (mmm) cc_final: 0.5883 (mpt) REVERT: P 48 MET cc_start: 0.8992 (tpp) cc_final: 0.8750 (mmm) REVERT: P 56 GLU cc_start: 0.8528 (mt-10) cc_final: 0.7826 (mp0) REVERT: P 64 ARG cc_start: 0.8776 (mtt-85) cc_final: 0.8481 (mtt-85) REVERT: P 77 ARG cc_start: 0.8321 (tpp80) cc_final: 0.7803 (ttp80) REVERT: R 65 GLU cc_start: 0.8611 (tt0) cc_final: 0.8394 (tt0) outliers start: 59 outliers final: 33 residues processed: 398 average time/residue: 1.0056 time to fit residues: 416.4130 Evaluate side-chains 394 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 352 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 22 GLU Chi-restraints excluded: chain F residue 41 SER Chi-restraints excluded: chain F residue 71 ARG Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 33 LYS Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain J residue 41 SER Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 22 GLU Chi-restraints excluded: chain L residue 71 ARG Chi-restraints excluded: chain M residue 40 GLN Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 35 LYS Chi-restraints excluded: chain O residue 18 SER Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain Q residue 7 LEU Chi-restraints excluded: chain Q residue 22 GLU Chi-restraints excluded: chain Q residue 37 GLU Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 48 MET Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain R residue 41 SER Chi-restraints excluded: chain R residue 70 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 43 optimal weight: 6.9990 chunk 109 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 52 GLN A 59 HIS F 59 HIS G 53 ASN I 40 GLN ** J 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 59 HIS ** N 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 59 HIS Q 40 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.091878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.079538 restraints weight = 22125.275| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.92 r_work: 0.3035 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11808 Z= 0.118 Angle : 0.580 8.604 15840 Z= 0.294 Chirality : 0.037 0.165 1890 Planarity : 0.005 0.054 2016 Dihedral : 3.960 67.792 1590 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.73 % Allowed : 34.14 % Favored : 62.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.53 (0.23), residues: 1422 helix: 2.30 (0.16), residues: 1116 sheet: None (None), residues: 0 loop : -0.74 (0.32), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG J 77 PHE 0.005 0.001 PHE Q 4 HIS 0.004 0.001 HIS N 59 Details of bonding type rmsd covalent geometry : bond 0.00295 (11808) covalent geometry : angle 0.58033 (15840) hydrogen bonds : bond 0.02539 ( 612) hydrogen bonds : angle 3.01232 ( 1836) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 364 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.5278 (tpp-160) cc_final: 0.3465 (ptp-170) REVERT: B 59 HIS cc_start: 0.7471 (t-90) cc_final: 0.6850 (t-90) REVERT: C 38 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8129 (mtt180) REVERT: C 64 ARG cc_start: 0.8833 (mtt-85) cc_final: 0.8462 (mtt-85) REVERT: C 71 ARG cc_start: 0.6419 (OUTLIER) cc_final: 0.4527 (mtp180) REVERT: D 56 GLU cc_start: 0.8143 (tp30) cc_final: 0.7801 (tm-30) REVERT: D 78 ARG cc_start: 0.8900 (ttp-170) cc_final: 0.8646 (ttm-80) REVERT: E 19 GLU cc_start: 0.8578 (mp0) cc_final: 0.8020 (mp0) REVERT: E 77 ARG cc_start: 0.8371 (tpp80) cc_final: 0.7944 (ttp80) REVERT: F 1 MET cc_start: 0.7954 (pmm) cc_final: 0.7715 (pmm) REVERT: F 22 GLU cc_start: 0.6767 (OUTLIER) cc_final: 0.5769 (mm-30) REVERT: F 71 ARG cc_start: 0.6072 (OUTLIER) cc_final: 0.4339 (mtp180) REVERT: G 56 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7904 (tm-30) REVERT: H 19 GLU cc_start: 0.8552 (mp0) cc_final: 0.8176 (mp0) REVERT: H 64 ARG cc_start: 0.8931 (mtp180) cc_final: 0.8606 (mtp180) REVERT: H 71 ARG cc_start: 0.8138 (mtp180) cc_final: 0.7778 (mtp180) REVERT: I 52 GLN cc_start: 0.8352 (mt0) cc_final: 0.7693 (mt0) REVERT: I 61 GLU cc_start: 0.8397 (pm20) cc_final: 0.8115 (pm20) REVERT: I 71 ARG cc_start: 0.8814 (mtm180) cc_final: 0.7837 (ttp-170) REVERT: J 34 ARG cc_start: 0.9168 (ptm-80) cc_final: 0.8940 (ptm-80) REVERT: J 65 GLU cc_start: 0.8693 (tt0) cc_final: 0.8182 (pp20) REVERT: L 19 GLU cc_start: 0.8575 (mm-30) cc_final: 0.7725 (mp0) REVERT: L 22 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.6980 (mt-10) REVERT: M 77 ARG cc_start: 0.8307 (tpp80) cc_final: 0.7782 (ttp80) REVERT: O 1 MET cc_start: 0.6293 (ttm) cc_final: 0.5848 (mtt) REVERT: P 1 MET cc_start: 0.7152 (mmm) cc_final: 0.5794 (mpt) REVERT: P 48 MET cc_start: 0.8999 (tpp) cc_final: 0.8761 (mmm) REVERT: P 56 GLU cc_start: 0.8519 (mt-10) cc_final: 0.7817 (mp0) REVERT: P 64 ARG cc_start: 0.8765 (mtt-85) cc_final: 0.8461 (mtt-85) REVERT: P 77 ARG cc_start: 0.8350 (tpp80) cc_final: 0.7812 (ttp80) REVERT: Q 74 ASP cc_start: 0.9462 (p0) cc_final: 0.9179 (p0) REVERT: R 65 GLU cc_start: 0.8603 (tt0) cc_final: 0.8384 (tt0) outliers start: 51 outliers final: 31 residues processed: 392 average time/residue: 0.9986 time to fit residues: 407.1159 Evaluate side-chains 392 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 355 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 22 GLU Chi-restraints excluded: chain F residue 41 SER Chi-restraints excluded: chain F residue 71 ARG Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 53 ASN Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain J residue 41 SER Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 22 GLU Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 35 LYS Chi-restraints excluded: chain O residue 18 SER Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain Q residue 7 LEU Chi-restraints excluded: chain Q residue 22 GLU Chi-restraints excluded: chain Q residue 37 GLU Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 48 MET Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain R residue 41 SER Chi-restraints excluded: chain R residue 70 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 70 optimal weight: 0.8980 chunk 7 optimal weight: 0.4980 chunk 104 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 141 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 125 optimal weight: 7.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 52 GLN ** F 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN H 9 HIS I 40 GLN ** J 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 59 HIS P 59 HIS Q 40 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.092707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.080405 restraints weight = 22252.621| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.89 r_work: 0.3053 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11808 Z= 0.115 Angle : 0.597 9.253 15840 Z= 0.302 Chirality : 0.037 0.196 1890 Planarity : 0.004 0.049 2016 Dihedral : 3.875 67.284 1589 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.07 % Allowed : 35.01 % Favored : 61.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.53 (0.23), residues: 1422 helix: 2.30 (0.16), residues: 1116 sheet: None (None), residues: 0 loop : -0.73 (0.32), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 77 PHE 0.004 0.001 PHE Q 4 HIS 0.003 0.001 HIS F 59 Details of bonding type rmsd covalent geometry : bond 0.00287 (11808) covalent geometry : angle 0.59681 (15840) hydrogen bonds : bond 0.02384 ( 612) hydrogen bonds : angle 3.02976 ( 1836) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 366 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.5267 (tpp-160) cc_final: 0.3502 (ptp-170) REVERT: B 59 HIS cc_start: 0.7441 (t-90) cc_final: 0.6889 (t-90) REVERT: C 38 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.8101 (mtt180) REVERT: C 64 ARG cc_start: 0.8832 (mtt-85) cc_final: 0.8464 (mtt-85) REVERT: C 71 ARG cc_start: 0.6457 (OUTLIER) cc_final: 0.4518 (mtp180) REVERT: D 56 GLU cc_start: 0.8122 (tp30) cc_final: 0.7799 (tm-30) REVERT: D 78 ARG cc_start: 0.8875 (ttp-170) cc_final: 0.8623 (ttm-80) REVERT: E 19 GLU cc_start: 0.8605 (mp0) cc_final: 0.8044 (mp0) REVERT: E 77 ARG cc_start: 0.8338 (tpp80) cc_final: 0.7942 (ttp80) REVERT: F 22 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.5780 (mm-30) REVERT: F 71 ARG cc_start: 0.6105 (OUTLIER) cc_final: 0.4353 (mtp180) REVERT: G 33 LYS cc_start: 0.4966 (OUTLIER) cc_final: 0.4194 (pttp) REVERT: G 56 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7942 (tm-30) REVERT: H 19 GLU cc_start: 0.8523 (mp0) cc_final: 0.8166 (mp0) REVERT: H 38 ARG cc_start: 0.8648 (mpp80) cc_final: 0.8403 (pmm-80) REVERT: H 64 ARG cc_start: 0.8932 (mtp180) cc_final: 0.8588 (mtp180) REVERT: H 71 ARG cc_start: 0.8109 (mtp180) cc_final: 0.7769 (mtp180) REVERT: I 52 GLN cc_start: 0.8363 (mt0) cc_final: 0.7715 (mt0) REVERT: I 61 GLU cc_start: 0.8422 (pm20) cc_final: 0.8143 (pm20) REVERT: I 71 ARG cc_start: 0.8815 (mtm180) cc_final: 0.7853 (ttp-170) REVERT: J 34 ARG cc_start: 0.9150 (ptm-80) cc_final: 0.8940 (ptm-80) REVERT: J 59 HIS cc_start: 0.7562 (t-90) cc_final: 0.7284 (t70) REVERT: J 65 GLU cc_start: 0.8607 (tt0) cc_final: 0.8131 (pp20) REVERT: L 19 GLU cc_start: 0.8582 (mm-30) cc_final: 0.7727 (mp0) REVERT: L 22 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.6997 (mt-10) REVERT: M 48 MET cc_start: 0.9012 (mpp) cc_final: 0.8727 (mmm) REVERT: M 77 ARG cc_start: 0.8274 (tpp80) cc_final: 0.7784 (ttp80) REVERT: N 1 MET cc_start: 0.7294 (mpp) cc_final: 0.7047 (pmm) REVERT: N 65 GLU cc_start: 0.8494 (tt0) cc_final: 0.8114 (tt0) REVERT: O 1 MET cc_start: 0.6205 (ttm) cc_final: 0.5761 (mtt) REVERT: P 1 MET cc_start: 0.7141 (mmm) cc_final: 0.5786 (mpt) REVERT: P 48 MET cc_start: 0.8969 (tpp) cc_final: 0.8737 (mmm) REVERT: P 56 GLU cc_start: 0.8487 (mt-10) cc_final: 0.7815 (mp0) REVERT: P 64 ARG cc_start: 0.8735 (mtt-85) cc_final: 0.8423 (mtt-85) REVERT: P 77 ARG cc_start: 0.8294 (tpp80) cc_final: 0.7813 (ttp80) REVERT: Q 65 GLU cc_start: 0.8613 (pt0) cc_final: 0.8203 (pp20) REVERT: R 65 GLU cc_start: 0.8599 (tt0) cc_final: 0.8389 (tt0) outliers start: 42 outliers final: 26 residues processed: 390 average time/residue: 1.0519 time to fit residues: 426.3247 Evaluate side-chains 388 residues out of total 1368 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 355 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 SER Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain B residue 56 GLU Chi-restraints excluded: chain C residue 38 ARG Chi-restraints excluded: chain C residue 48 MET Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain D residue 41 SER Chi-restraints excluded: chain F residue 22 GLU Chi-restraints excluded: chain F residue 41 SER Chi-restraints excluded: chain F residue 71 ARG Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 33 LYS Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain I residue 22 GLU Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain J residue 41 SER Chi-restraints excluded: chain K residue 7 LEU Chi-restraints excluded: chain L residue 13 SER Chi-restraints excluded: chain L residue 22 GLU Chi-restraints excluded: chain M residue 70 LEU Chi-restraints excluded: chain N residue 7 LEU Chi-restraints excluded: chain N residue 12 SER Chi-restraints excluded: chain N residue 35 LYS Chi-restraints excluded: chain P residue 7 LEU Chi-restraints excluded: chain Q residue 7 LEU Chi-restraints excluded: chain Q residue 22 GLU Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain R residue 41 SER Chi-restraints excluded: chain R residue 70 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 135 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN A 52 GLN I 40 GLN ** J 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 59 HIS P 59 HIS ** Q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.090882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.078625 restraints weight = 22430.143| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.89 r_work: 0.3030 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11808 Z= 0.147 Angle : 0.641 12.409 15840 Z= 0.323 Chirality : 0.039 0.217 1890 Planarity : 0.005 0.055 2016 Dihedral : 4.048 70.571 1589 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.29 % Allowed : 34.80 % Favored : 61.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.46 (0.23), residues: 1422 helix: 2.27 (0.17), residues: 1116 sheet: None (None), residues: 0 loop : -0.84 (0.31), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG Q 77 PHE 0.005 0.001 PHE Q 4 HIS 0.004 0.001 HIS A 73 Details of bonding type rmsd covalent geometry : bond 0.00366 (11808) covalent geometry : angle 0.64053 (15840) hydrogen bonds : bond 0.03121 ( 612) hydrogen bonds : angle 3.13018 ( 1836) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5906.63 seconds wall clock time: 100 minutes 37.61 seconds (6037.61 seconds total)