Starting phenix.real_space_refine on Mon Jul 6 13:50:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jqe_61729/07_2026/9jqe_61729.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jqe_61729/07_2026/9jqe_61729.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jqe_61729/07_2026/9jqe_61729.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jqe_61729/07_2026/9jqe_61729.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jqe_61729/07_2026/9jqe_61729.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jqe_61729/07_2026/9jqe_61729.map" } resolution = 1.83 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.084 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Cu 48 5.60 5 S 168 5.16 5 C 21336 2.51 5 N 5976 2.21 5 O 9360 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 36888 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1415 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'MHS:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CU': 2} Chain breaks: 2 Chain: "A" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 120 Classifications: {'water': 120} Link IDs: {None: 119} Chain: "B" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 120 Classifications: {'water': 120} Link IDs: {None: 119} Chain: "C" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 120 Classifications: {'water': 120} Link IDs: {None: 119} Chain: "D" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 120 Classifications: {'water': 120} Link IDs: {None: 119} Chain: "E" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 120 Classifications: {'water': 120} Link IDs: {None: 119} Chain: "F" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 120 Classifications: {'water': 120} Link IDs: {None: 119} Chain: "G" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 120 Classifications: {'water': 120} Link IDs: {None: 119} Chain: "H" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 120 Classifications: {'water': 120} Link IDs: {None: 119} Chain: "I" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 120 Classifications: {'water': 120} Link IDs: {None: 119} Chain: "J" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 120 Classifications: {'water': 120} Link IDs: {None: 119} Chain: "K" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 120 Classifications: {'water': 120} Link IDs: {None: 119} Chain: "L" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 120 Classifications: {'water': 120} Link IDs: {None: 119} Chain: "M" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 120 Classifications: {'water': 120} Link IDs: {None: 119} Chain: "N" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 120 Classifications: {'water': 120} Link IDs: {None: 119} Chain: "O" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 120 Classifications: {'water': 120} Link IDs: {None: 119} Chain: "P" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 120 Classifications: {'water': 120} Link IDs: {None: 119} Chain: "Q" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 120 Classifications: {'water': 120} Link IDs: {None: 119} Chain: "R" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 120 Classifications: {'water': 120} Link IDs: {None: 119} Chain: "S" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 120 Classifications: {'water': 120} Link IDs: {None: 119} Chain: "T" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 120 Classifications: {'water': 120} Link IDs: {None: 119} Chain: "U" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 120 Classifications: {'water': 120} Link IDs: {None: 119} Chain: "V" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 120 Classifications: {'water': 120} Link IDs: {None: 119} Chain: "W" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 120 Classifications: {'water': 120} Link IDs: {None: 119} Chain: "X" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 120 Classifications: {'water': 120} Link IDs: {None: 119} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X Time building chain proxies: 4.22, per 1000 atoms: 0.11 Number of scatterers: 36888 At special positions: 0 Unit cell: (132.932, 132.932, 132.932, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cu 48 28.99 S 168 16.00 O 9360 8.00 N 5976 7.00 C 21336 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: 3.76 Conformation dependent library (CDL) restraints added in 1.6 seconds 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7920 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 79.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 13 through 42 Processing helix chain 'A' and resid 48 through 76 Processing helix chain 'A' and resid 95 through 124 Processing helix chain 'A' and resid 126 through 137 Processing helix chain 'A' and resid 137 through 159 Processing helix chain 'A' and resid 163 through 174 removed outlier: 3.506A pdb=" N GLU A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 42 Processing helix chain 'B' and resid 48 through 76 Processing helix chain 'B' and resid 95 through 124 Processing helix chain 'B' and resid 126 through 137 Processing helix chain 'B' and resid 137 through 159 Processing helix chain 'B' and resid 163 through 174 removed outlier: 3.506A pdb=" N GLU B 167 " --> pdb=" O SER B 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 42 Processing helix chain 'C' and resid 48 through 76 Processing helix chain 'C' and resid 95 through 124 Processing helix chain 'C' and resid 126 through 137 Processing helix chain 'C' and resid 137 through 159 Processing helix chain 'C' and resid 163 through 174 removed outlier: 3.506A pdb=" N GLU C 167 " --> pdb=" O SER C 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 42 Processing helix chain 'D' and resid 48 through 76 Processing helix chain 'D' and resid 95 through 124 Processing helix chain 'D' and resid 126 through 137 Processing helix chain 'D' and resid 137 through 159 Processing helix chain 'D' and resid 163 through 174 removed outlier: 3.506A pdb=" N GLU D 167 " --> pdb=" O SER D 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 42 Processing helix chain 'E' and resid 48 through 76 Processing helix chain 'E' and resid 95 through 124 Processing helix chain 'E' and resid 126 through 137 Processing helix chain 'E' and resid 137 through 159 Processing helix chain 'E' and resid 163 through 174 removed outlier: 3.506A pdb=" N GLU E 167 " --> pdb=" O SER E 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 42 Processing helix chain 'F' and resid 48 through 76 Processing helix chain 'F' and resid 95 through 124 Processing helix chain 'F' and resid 126 through 137 Processing helix chain 'F' and resid 137 through 159 Processing helix chain 'F' and resid 163 through 174 removed outlier: 3.506A pdb=" N GLU F 167 " --> pdb=" O SER F 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 42 Processing helix chain 'G' and resid 48 through 76 Processing helix chain 'G' and resid 95 through 124 Processing helix chain 'G' and resid 126 through 137 Processing helix chain 'G' and resid 137 through 159 Processing helix chain 'G' and resid 163 through 174 removed outlier: 3.506A pdb=" N GLU G 167 " --> pdb=" O SER G 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 42 Processing helix chain 'H' and resid 48 through 76 Processing helix chain 'H' and resid 95 through 124 Processing helix chain 'H' and resid 126 through 137 Processing helix chain 'H' and resid 137 through 159 Processing helix chain 'H' and resid 163 through 174 removed outlier: 3.506A pdb=" N GLU H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 42 Processing helix chain 'I' and resid 48 through 76 Processing helix chain 'I' and resid 95 through 124 Processing helix chain 'I' and resid 126 through 137 Processing helix chain 'I' and resid 137 through 159 Processing helix chain 'I' and resid 163 through 174 removed outlier: 3.506A pdb=" N GLU I 167 " --> pdb=" O SER I 163 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 42 Processing helix chain 'J' and resid 48 through 76 Processing helix chain 'J' and resid 95 through 124 Processing helix chain 'J' and resid 126 through 137 Processing helix chain 'J' and resid 137 through 159 Processing helix chain 'J' and resid 163 through 174 removed outlier: 3.506A pdb=" N GLU J 167 " --> pdb=" O SER J 163 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 42 Processing helix chain 'K' and resid 48 through 76 Processing helix chain 'K' and resid 95 through 124 Processing helix chain 'K' and resid 126 through 137 Processing helix chain 'K' and resid 137 through 159 Processing helix chain 'K' and resid 163 through 174 removed outlier: 3.506A pdb=" N GLU K 167 " --> pdb=" O SER K 163 " (cutoff:3.500A) Processing helix chain 'L' and resid 13 through 42 Processing helix chain 'L' and resid 48 through 76 Processing helix chain 'L' and resid 95 through 124 Processing helix chain 'L' and resid 126 through 137 Processing helix chain 'L' and resid 137 through 159 Processing helix chain 'L' and resid 163 through 174 removed outlier: 3.506A pdb=" N GLU L 167 " --> pdb=" O SER L 163 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 42 Processing helix chain 'M' and resid 48 through 76 Processing helix chain 'M' and resid 95 through 124 Processing helix chain 'M' and resid 126 through 137 Processing helix chain 'M' and resid 137 through 159 Processing helix chain 'M' and resid 163 through 174 removed outlier: 3.506A pdb=" N GLU M 167 " --> pdb=" O SER M 163 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 42 Processing helix chain 'N' and resid 48 through 76 Processing helix chain 'N' and resid 95 through 124 Processing helix chain 'N' and resid 126 through 137 Processing helix chain 'N' and resid 137 through 159 Processing helix chain 'N' and resid 163 through 174 removed outlier: 3.506A pdb=" N GLU N 167 " --> pdb=" O SER N 163 " (cutoff:3.500A) Processing helix chain 'O' and resid 13 through 42 Processing helix chain 'O' and resid 48 through 76 Processing helix chain 'O' and resid 95 through 124 Processing helix chain 'O' and resid 126 through 137 Processing helix chain 'O' and resid 137 through 159 Processing helix chain 'O' and resid 163 through 174 removed outlier: 3.506A pdb=" N GLU O 167 " --> pdb=" O SER O 163 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 42 Processing helix chain 'P' and resid 48 through 76 Processing helix chain 'P' and resid 95 through 124 Processing helix chain 'P' and resid 126 through 137 Processing helix chain 'P' and resid 137 through 159 Processing helix chain 'P' and resid 163 through 174 removed outlier: 3.506A pdb=" N GLU P 167 " --> pdb=" O SER P 163 " (cutoff:3.500A) Processing helix chain 'Q' and resid 13 through 42 Processing helix chain 'Q' and resid 48 through 76 Processing helix chain 'Q' and resid 95 through 124 Processing helix chain 'Q' and resid 126 through 137 Processing helix chain 'Q' and resid 137 through 159 Processing helix chain 'Q' and resid 163 through 174 removed outlier: 3.506A pdb=" N GLU Q 167 " --> pdb=" O SER Q 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 13 through 42 Processing helix chain 'R' and resid 48 through 76 Processing helix chain 'R' and resid 95 through 124 Processing helix chain 'R' and resid 126 through 137 Processing helix chain 'R' and resid 137 through 159 Processing helix chain 'R' and resid 163 through 174 removed outlier: 3.506A pdb=" N GLU R 167 " --> pdb=" O SER R 163 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 42 Processing helix chain 'S' and resid 48 through 76 Processing helix chain 'S' and resid 95 through 124 Processing helix chain 'S' and resid 126 through 137 Processing helix chain 'S' and resid 137 through 159 Processing helix chain 'S' and resid 163 through 174 removed outlier: 3.506A pdb=" N GLU S 167 " --> pdb=" O SER S 163 " (cutoff:3.500A) Processing helix chain 'T' and resid 13 through 42 Processing helix chain 'T' and resid 48 through 76 Processing helix chain 'T' and resid 95 through 124 Processing helix chain 'T' and resid 126 through 137 Processing helix chain 'T' and resid 137 through 159 Processing helix chain 'T' and resid 163 through 174 removed outlier: 3.506A pdb=" N GLU T 167 " --> pdb=" O SER T 163 " (cutoff:3.500A) Processing helix chain 'U' and resid 13 through 42 Processing helix chain 'U' and resid 48 through 76 Processing helix chain 'U' and resid 95 through 124 Processing helix chain 'U' and resid 126 through 137 Processing helix chain 'U' and resid 137 through 159 Processing helix chain 'U' and resid 163 through 174 removed outlier: 3.506A pdb=" N GLU U 167 " --> pdb=" O SER U 163 " (cutoff:3.500A) Processing helix chain 'V' and resid 13 through 42 Processing helix chain 'V' and resid 48 through 76 Processing helix chain 'V' and resid 95 through 124 Processing helix chain 'V' and resid 126 through 137 Processing helix chain 'V' and resid 137 through 159 Processing helix chain 'V' and resid 163 through 174 removed outlier: 3.506A pdb=" N GLU V 167 " --> pdb=" O SER V 163 " (cutoff:3.500A) Processing helix chain 'W' and resid 13 through 42 Processing helix chain 'W' and resid 48 through 76 Processing helix chain 'W' and resid 95 through 124 Processing helix chain 'W' and resid 126 through 137 Processing helix chain 'W' and resid 137 through 159 Processing helix chain 'W' and resid 163 through 174 removed outlier: 3.506A pdb=" N GLU W 167 " --> pdb=" O SER W 163 " (cutoff:3.500A) Processing helix chain 'X' and resid 13 through 42 Processing helix chain 'X' and resid 48 through 76 Processing helix chain 'X' and resid 95 through 124 Processing helix chain 'X' and resid 126 through 137 Processing helix chain 'X' and resid 137 through 159 Processing helix chain 'X' and resid 163 through 174 removed outlier: 3.506A pdb=" N GLU X 167 " --> pdb=" O SER X 163 " (cutoff:3.500A) 2664 hydrogen bonds defined for protein. 7992 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: 6.98 Time building geometry restraints manager: 4.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 6000 1.31 - 1.44: 9360 1.44 - 1.56: 19080 1.56 - 1.69: 0 1.69 - 1.81: 264 Bond restraints: 34704 Sorted by residual: bond pdb=" CG MHS G 67 " pdb=" ND1 MHS G 67 " ideal model delta sigma weight residual 1.373 1.312 0.061 2.00e-02 2.50e+03 9.20e+00 bond pdb=" CG MHS L 67 " pdb=" ND1 MHS L 67 " ideal model delta sigma weight residual 1.373 1.313 0.060 2.00e-02 2.50e+03 9.03e+00 bond pdb=" CG MHS M 67 " pdb=" ND1 MHS M 67 " ideal model delta sigma weight residual 1.373 1.313 0.060 2.00e-02 2.50e+03 9.03e+00 bond pdb=" CG MHS N 67 " pdb=" ND1 MHS N 67 " ideal model delta sigma weight residual 1.373 1.313 0.060 2.00e-02 2.50e+03 9.03e+00 bond pdb=" CG MHS O 67 " pdb=" ND1 MHS O 67 " ideal model delta sigma weight residual 1.373 1.313 0.060 2.00e-02 2.50e+03 9.03e+00 ... (remaining 34699 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 45169 1.13 - 2.26: 1032 2.26 - 3.40: 311 3.40 - 4.53: 192 4.53 - 5.66: 96 Bond angle restraints: 46800 Sorted by residual: angle pdb=" C TRP Q 93 " pdb=" N GLU Q 94 " pdb=" CA GLU Q 94 " ideal model delta sigma weight residual 121.54 126.20 -4.66 1.91e+00 2.74e-01 5.95e+00 angle pdb=" C TRP L 93 " pdb=" N GLU L 94 " pdb=" CA GLU L 94 " ideal model delta sigma weight residual 121.54 126.20 -4.66 1.91e+00 2.74e-01 5.94e+00 angle pdb=" C TRP R 93 " pdb=" N GLU R 94 " pdb=" CA GLU R 94 " ideal model delta sigma weight residual 121.54 126.20 -4.66 1.91e+00 2.74e-01 5.94e+00 angle pdb=" C TRP J 93 " pdb=" N GLU J 94 " pdb=" CA GLU J 94 " ideal model delta sigma weight residual 121.54 126.20 -4.66 1.91e+00 2.74e-01 5.94e+00 angle pdb=" C TRP M 93 " pdb=" N GLU M 94 " pdb=" CA GLU M 94 " ideal model delta sigma weight residual 121.54 126.20 -4.66 1.91e+00 2.74e-01 5.94e+00 ... (remaining 46795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.58: 19224 16.58 - 33.16: 1102 33.16 - 49.74: 146 49.74 - 66.32: 216 66.32 - 82.90: 96 Dihedral angle restraints: 20784 sinusoidal: 8544 harmonic: 12240 Sorted by residual: dihedral pdb=" CA TRP V 93 " pdb=" C TRP V 93 " pdb=" N GLU V 94 " pdb=" CA GLU V 94 " ideal model delta harmonic sigma weight residual 180.00 162.76 17.24 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA TRP K 93 " pdb=" C TRP K 93 " pdb=" N GLU K 94 " pdb=" CA GLU K 94 " ideal model delta harmonic sigma weight residual 180.00 162.76 17.24 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA TRP F 93 " pdb=" C TRP F 93 " pdb=" N GLU F 94 " pdb=" CA GLU F 94 " ideal model delta harmonic sigma weight residual 180.00 162.77 17.23 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 20781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 3260 0.026 - 0.053: 986 0.053 - 0.079: 408 0.079 - 0.105: 146 0.105 - 0.131: 96 Chirality restraints: 4896 Sorted by residual: chirality pdb=" CA TYR E 39 " pdb=" N TYR E 39 " pdb=" C TYR E 39 " pdb=" CB TYR E 39 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.31e-01 chirality pdb=" CA TYR K 39 " pdb=" N TYR K 39 " pdb=" C TYR K 39 " pdb=" CB TYR K 39 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.28e-01 chirality pdb=" CA TYR B 39 " pdb=" N TYR B 39 " pdb=" C TYR B 39 " pdb=" CB TYR B 39 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 4893 not shown) Planarity restraints: 6144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR N 32 " -0.012 2.00e-02 2.50e+03 9.20e-03 1.69e+00 pdb=" CG TYR N 32 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR N 32 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR N 32 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR N 32 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR N 32 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR N 32 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR N 32 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 32 " -0.012 2.00e-02 2.50e+03 9.17e-03 1.68e+00 pdb=" CG TYR R 32 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR R 32 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR R 32 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR R 32 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR R 32 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR R 32 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR R 32 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 32 " 0.012 2.00e-02 2.50e+03 9.16e-03 1.68e+00 pdb=" CG TYR H 32 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR H 32 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR H 32 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR H 32 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR H 32 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR H 32 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR H 32 " 0.001 2.00e-02 2.50e+03 ... (remaining 6141 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 2108 2.68 - 3.24: 38559 3.24 - 3.79: 74453 3.79 - 4.35: 95544 4.35 - 4.90: 150380 Nonbonded interactions: 361044 Sorted by model distance: nonbonded pdb=" OE2 GLU G 62 " pdb="CU CU G 202 " model vdw 2.126 2.980 nonbonded pdb=" OE2 GLU U 62 " pdb="CU CU U 202 " model vdw 2.126 2.980 nonbonded pdb=" OE2 GLU J 62 " pdb="CU CU J 202 " model vdw 2.126 2.980 nonbonded pdb=" OE2 GLU V 62 " pdb="CU CU V 202 " model vdw 2.127 2.980 nonbonded pdb=" OE2 GLU M 62 " pdb="CU CU M 202 " model vdw 2.127 2.980 ... (remaining 361039 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: 0.13 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' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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: 7.230 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: 0.040 Extract box with map and model: 0.730 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 29.190 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.100 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:7.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 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 : 0.004 0.061 34704 Z= 0.226 Angle : 0.558 5.662 46800 Z= 0.283 Chirality : 0.035 0.131 4896 Planarity : 0.002 0.015 6144 Dihedral : 14.328 82.903 12864 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.06 (0.13), residues: 3936 helix: 3.93 (0.09), residues: 3120 sheet: None (None), residues: 0 loop : 0.73 (0.24), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 76 TYR 0.022 0.002 TYR N 32 PHE 0.013 0.002 PHE A 41 TRP 0.010 0.002 TRP D 93 HIS 0.003 0.001 HIS M 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.23 (34704) covalent geometry : angle 0.55849 / 0.28 (46800) hydrogen bonds : bond 0.08103 / 5.31 ( 2664) hydrogen bonds : angle 3.96394 / 2.91 ( 7992) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1080 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1080 time to evaluate : 1.573 Fit side-chains REVERT: A 70 MET cc_start: 0.9022 (mtp) cc_final: 0.8776 (mtp) REVERT: A 86 LYS cc_start: 0.8425 (mmmt) cc_final: 0.8067 (mppt) REVERT: A 157 LYS cc_start: 0.8321 (mttt) cc_final: 0.8065 (mtpt) REVERT: B 70 MET cc_start: 0.9027 (mtp) cc_final: 0.8804 (mtp) REVERT: B 86 LYS cc_start: 0.8433 (mmmt) cc_final: 0.8077 (mppt) REVERT: B 157 LYS cc_start: 0.8318 (mttt) cc_final: 0.8055 (mtpt) REVERT: C 70 MET cc_start: 0.9031 (mtp) cc_final: 0.8783 (mtp) REVERT: C 86 LYS cc_start: 0.8443 (mmmt) cc_final: 0.8085 (mppt) REVERT: C 157 LYS cc_start: 0.8317 (mttt) cc_final: 0.8056 (mtpt) REVERT: D 70 MET cc_start: 0.9031 (mtp) cc_final: 0.8783 (mtp) REVERT: D 86 LYS cc_start: 0.8444 (mmmt) cc_final: 0.8085 (mppt) REVERT: D 157 LYS cc_start: 0.8318 (mttt) cc_final: 0.8058 (mtpt) REVERT: E 70 MET cc_start: 0.9029 (mtp) cc_final: 0.8786 (mtp) REVERT: E 86 LYS cc_start: 0.8449 (mmmt) cc_final: 0.8092 (mppt) REVERT: E 157 LYS cc_start: 0.8318 (mttt) cc_final: 0.8056 (mtpt) REVERT: F 70 MET cc_start: 0.9029 (mtp) cc_final: 0.8807 (mtp) REVERT: F 86 LYS cc_start: 0.8433 (mmmt) cc_final: 0.8078 (mppt) REVERT: F 157 LYS cc_start: 0.8316 (mttt) cc_final: 0.8053 (mtpt) REVERT: G 70 MET cc_start: 0.9027 (mtp) cc_final: 0.8805 (mtp) REVERT: G 86 LYS cc_start: 0.8432 (mmmt) cc_final: 0.8076 (mppt) REVERT: G 157 LYS cc_start: 0.8315 (mttt) cc_final: 0.8051 (mtpt) REVERT: H 70 MET cc_start: 0.9039 (mtp) cc_final: 0.8799 (mtp) REVERT: H 86 LYS cc_start: 0.8447 (mmmt) cc_final: 0.8093 (mppt) REVERT: H 157 LYS cc_start: 0.8310 (mttt) cc_final: 0.8043 (mtpt) REVERT: I 70 MET cc_start: 0.9022 (mtp) cc_final: 0.8777 (mtp) REVERT: I 86 LYS cc_start: 0.8425 (mmmt) cc_final: 0.8067 (mppt) REVERT: I 157 LYS cc_start: 0.8321 (mttt) cc_final: 0.8063 (mtpt) REVERT: J 70 MET cc_start: 0.9030 (mtp) cc_final: 0.8782 (mtp) REVERT: J 86 LYS cc_start: 0.8440 (mmmt) cc_final: 0.8084 (mppt) REVERT: J 157 LYS cc_start: 0.8317 (mttt) cc_final: 0.8055 (mtpt) REVERT: K 70 MET cc_start: 0.9035 (mtp) cc_final: 0.8796 (mtp) REVERT: K 86 LYS cc_start: 0.8445 (mmmt) cc_final: 0.8091 (mppt) REVERT: K 157 LYS cc_start: 0.8314 (mttt) cc_final: 0.8048 (mtpt) REVERT: L 70 MET cc_start: 0.9033 (mtp) cc_final: 0.8791 (mtp) REVERT: L 86 LYS cc_start: 0.8423 (mmmt) cc_final: 0.8066 (mppt) REVERT: L 157 LYS cc_start: 0.8317 (mttt) cc_final: 0.8055 (mtpt) REVERT: M 70 MET cc_start: 0.9036 (mtp) cc_final: 0.8793 (mtp) REVERT: M 86 LYS cc_start: 0.8422 (mmmt) cc_final: 0.8063 (mppt) REVERT: M 157 LYS cc_start: 0.8313 (mttt) cc_final: 0.8051 (mtpt) REVERT: N 70 MET cc_start: 0.9032 (mtp) cc_final: 0.8791 (mtp) REVERT: N 86 LYS cc_start: 0.8422 (mmmt) cc_final: 0.8064 (mppt) REVERT: N 157 LYS cc_start: 0.8317 (mttt) cc_final: 0.8055 (mtpt) REVERT: O 70 MET cc_start: 0.9036 (mtp) cc_final: 0.8794 (mtp) REVERT: O 86 LYS cc_start: 0.8422 (mmmt) cc_final: 0.8065 (mppt) REVERT: O 157 LYS cc_start: 0.8315 (mttt) cc_final: 0.8051 (mtpt) REVERT: P 70 MET cc_start: 0.9028 (mtp) cc_final: 0.8807 (mtp) REVERT: P 86 LYS cc_start: 0.8433 (mmmt) cc_final: 0.8077 (mppt) REVERT: P 157 LYS cc_start: 0.8316 (mttt) cc_final: 0.8054 (mtpt) REVERT: Q 70 MET cc_start: 0.9018 (mtp) cc_final: 0.8772 (mtp) REVERT: Q 86 LYS cc_start: 0.8424 (mmmt) cc_final: 0.8068 (mppt) REVERT: Q 157 LYS cc_start: 0.8323 (mttt) cc_final: 0.8067 (mtpt) REVERT: R 70 MET cc_start: 0.9037 (mtp) cc_final: 0.8798 (mtp) REVERT: R 86 LYS cc_start: 0.8446 (mmmt) cc_final: 0.8094 (mppt) REVERT: R 157 LYS cc_start: 0.8311 (mttt) cc_final: 0.8045 (mtpt) REVERT: S 70 MET cc_start: 0.9031 (mtp) cc_final: 0.8782 (mtp) REVERT: S 86 LYS cc_start: 0.8443 (mmmt) cc_final: 0.8085 (mppt) REVERT: S 157 LYS cc_start: 0.8318 (mttt) cc_final: 0.8058 (mtpt) REVERT: T 70 MET cc_start: 0.9028 (mtp) cc_final: 0.8785 (mtp) REVERT: T 86 LYS cc_start: 0.8450 (mmmt) cc_final: 0.8095 (mppt) REVERT: T 157 LYS cc_start: 0.8320 (mttt) cc_final: 0.8058 (mtpt) REVERT: U 70 MET cc_start: 0.9022 (mtp) cc_final: 0.8776 (mtp) REVERT: U 86 LYS cc_start: 0.8426 (mmmt) cc_final: 0.8069 (mppt) REVERT: U 157 LYS cc_start: 0.8321 (mttt) cc_final: 0.8065 (mtpt) REVERT: V 70 MET cc_start: 0.9037 (mtp) cc_final: 0.8797 (mtp) REVERT: V 86 LYS cc_start: 0.8445 (mmmt) cc_final: 0.8092 (mppt) REVERT: V 157 LYS cc_start: 0.8312 (mttt) cc_final: 0.8048 (mtpt) REVERT: W 70 MET cc_start: 0.9025 (mtp) cc_final: 0.8782 (mtp) REVERT: W 86 LYS cc_start: 0.8450 (mmmt) cc_final: 0.8096 (mppt) REVERT: W 157 LYS cc_start: 0.8331 (mttt) cc_final: 0.8070 (mtpt) REVERT: X 70 MET cc_start: 0.9027 (mtp) cc_final: 0.8784 (mtp) REVERT: X 86 LYS cc_start: 0.8450 (mmmt) cc_final: 0.8095 (mppt) REVERT: X 157 LYS cc_start: 0.8317 (mttt) cc_final: 0.8053 (mtpt) outliers start: 0 outliers final: 0 residues processed: 1080 average time/residue: 1.0638 time to fit residues: 1308.0328 Evaluate side-chains 900 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 900 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 9.9990 chunk 401 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 7.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 HIS A 83 GLN A 112 GLN B 60 HIS B 83 GLN B 112 GLN C 60 HIS C 83 GLN C 112 GLN D 60 HIS D 83 GLN D 112 GLN E 60 HIS E 83 GLN E 112 GLN F 60 HIS F 83 GLN F 112 GLN G 60 HIS G 83 GLN G 112 GLN H 60 HIS H 83 GLN H 112 GLN I 60 HIS I 83 GLN I 112 GLN J 60 HIS J 83 GLN J 112 GLN K 60 HIS K 83 GLN K 112 GLN L 60 HIS L 83 GLN L 112 GLN M 60 HIS M 83 GLN M 112 GLN N 60 HIS N 83 GLN N 112 GLN O 60 HIS O 83 GLN O 112 GLN P 60 HIS P 83 GLN P 112 GLN Q 60 HIS Q 83 GLN Q 112 GLN R 60 HIS R 83 GLN R 112 GLN S 60 HIS S 83 GLN S 112 GLN T 60 HIS T 83 GLN T 112 GLN U 60 HIS U 83 GLN U 112 GLN V 60 HIS V 83 GLN V 112 GLN W 60 HIS W 83 GLN W 112 GLN X 60 HIS X 83 GLN X 112 GLN Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.148658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.134889 restraints weight = 11662.514| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 0.27 r_work: 0.3336 rms_B_bonded: 0.54 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 1.01 restraints_weight: 0.2500 r_work: 0.2852 rms_B_bonded: 2.83 restraints_weight: 0.1250 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 34704 Z= 0.182 Angle : 0.614 6.370 46800 Z= 0.338 Chirality : 0.038 0.152 4896 Planarity : 0.004 0.024 6144 Dihedral : 7.583 83.302 4512 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.81 (0.13), residues: 3936 helix: 3.73 (0.09), residues: 3120 sheet: None (None), residues: 0 loop : 0.78 (0.25), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 156 TYR 0.023 0.003 TYR G 32 PHE 0.020 0.003 PHE X 41 TRP 0.003 0.001 TRP O 93 HIS 0.008 0.001 HIS P 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.18 (34704) covalent geometry : angle 0.61364 / 0.34 (46800) hydrogen bonds : bond 0.05871 / 3.92 ( 2664) hydrogen bonds : angle 3.72865 / 2.76 ( 7992) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 665 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.9090 (mtp) cc_final: 0.8862 (mtp) REVERT: B 70 MET cc_start: 0.9089 (mtp) cc_final: 0.8860 (mtp) REVERT: C 70 MET cc_start: 0.9088 (mtp) cc_final: 0.8840 (mtp) REVERT: C 81 PHE cc_start: 0.8282 (t80) cc_final: 0.7984 (m-80) REVERT: D 70 MET cc_start: 0.9091 (mtp) cc_final: 0.8845 (mtp) REVERT: D 81 PHE cc_start: 0.8282 (t80) cc_final: 0.7976 (m-80) REVERT: E 70 MET cc_start: 0.9087 (mtp) cc_final: 0.8854 (mtp) REVERT: F 70 MET cc_start: 0.9091 (mtp) cc_final: 0.8861 (mtp) REVERT: G 70 MET cc_start: 0.9088 (mtp) cc_final: 0.8859 (mtp) REVERT: H 70 MET cc_start: 0.9085 (mtp) cc_final: 0.8855 (mtp) REVERT: I 70 MET cc_start: 0.9091 (mtp) cc_final: 0.8862 (mtp) REVERT: J 70 MET cc_start: 0.9089 (mtp) cc_final: 0.8845 (mtp) REVERT: J 81 PHE cc_start: 0.8265 (t80) cc_final: 0.7972 (m-80) REVERT: K 70 MET cc_start: 0.9085 (mtp) cc_final: 0.8835 (mtp) REVERT: K 81 PHE cc_start: 0.8267 (t80) cc_final: 0.7978 (m-80) REVERT: L 70 MET cc_start: 0.9090 (mtp) cc_final: 0.8861 (mtp) REVERT: M 70 MET cc_start: 0.9089 (mtp) cc_final: 0.8840 (mtp) REVERT: M 81 PHE cc_start: 0.8284 (t80) cc_final: 0.7966 (m-80) REVERT: N 70 MET cc_start: 0.9087 (mtp) cc_final: 0.8840 (mtp) REVERT: N 81 PHE cc_start: 0.8285 (t80) cc_final: 0.7979 (m-80) REVERT: O 70 MET cc_start: 0.9088 (mtp) cc_final: 0.8859 (mtp) REVERT: P 70 MET cc_start: 0.9090 (mtp) cc_final: 0.8862 (mtp) REVERT: Q 70 MET cc_start: 0.9089 (mtp) cc_final: 0.8859 (mtp) REVERT: R 70 MET cc_start: 0.9089 (mtp) cc_final: 0.8841 (mtp) REVERT: R 81 PHE cc_start: 0.8263 (t80) cc_final: 0.7974 (m-80) REVERT: S 70 MET cc_start: 0.9090 (mtp) cc_final: 0.8844 (mtp) REVERT: S 81 PHE cc_start: 0.8276 (t80) cc_final: 0.7983 (m-80) REVERT: T 70 MET cc_start: 0.9089 (mtp) cc_final: 0.8855 (mtp) REVERT: U 70 MET cc_start: 0.9088 (mtp) cc_final: 0.8858 (mtp) REVERT: V 70 MET cc_start: 0.9085 (mtp) cc_final: 0.8834 (mtp) REVERT: V 81 PHE cc_start: 0.8262 (t80) cc_final: 0.7976 (m-80) REVERT: W 70 MET cc_start: 0.9087 (mtp) cc_final: 0.8858 (mtp) REVERT: X 70 MET cc_start: 0.9086 (mtp) cc_final: 0.8838 (mtp) REVERT: X 81 PHE cc_start: 0.8296 (t80) cc_final: 0.7986 (m-80) outliers start: 0 outliers final: 0 residues processed: 665 average time/residue: 1.0859 time to fit residues: 817.5636 Evaluate side-chains 649 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 649 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 117 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 368 optimal weight: 20.0000 chunk 138 optimal weight: 7.9990 chunk 237 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 303 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 123 optimal weight: 0.9980 chunk 176 optimal weight: 10.0000 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 HIS A 112 GLN B 60 HIS B 112 GLN C 60 HIS C 112 GLN D 60 HIS D 112 GLN E 60 HIS E 112 GLN F 60 HIS F 112 GLN G 60 HIS G 112 GLN H 60 HIS H 112 GLN I 60 HIS I 112 GLN J 60 HIS J 112 GLN K 60 HIS K 112 GLN L 60 HIS L 112 GLN M 60 HIS M 112 GLN N 60 HIS N 112 GLN O 60 HIS O 112 GLN P 60 HIS P 112 GLN Q 60 HIS Q 112 GLN R 60 HIS R 112 GLN S 60 HIS S 112 GLN T 60 HIS T 112 GLN U 60 HIS U 112 GLN V 60 HIS V 112 GLN W 60 HIS W 83 GLN W 112 GLN X 60 HIS X 112 GLN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.150583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.137003 restraints weight = 11706.331| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 0.27 r_work: 0.3362 rms_B_bonded: 0.55 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 1.02 restraints_weight: 0.2500 r_work: 0.2874 rms_B_bonded: 2.86 restraints_weight: 0.1250 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 34704 Z= 0.140 Angle : 0.534 5.644 46800 Z= 0.296 Chirality : 0.036 0.145 4896 Planarity : 0.003 0.015 6144 Dihedral : 7.530 83.639 4512 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.01 (0.13), residues: 3936 helix: 3.78 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : 1.19 (0.26), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG V 156 TYR 0.020 0.002 TYR N 39 PHE 0.018 0.003 PHE A 41 TRP 0.006 0.002 TRP O 93 HIS 0.007 0.001 HIS E 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.14 (34704) covalent geometry : angle 0.53388 / 0.30 (46800) hydrogen bonds : bond 0.05312 / 3.55 ( 2664) hydrogen bonds : angle 3.54421 / 2.62 ( 7992) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 639 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.9079 (mtp) cc_final: 0.8841 (mtp) REVERT: A 81 PHE cc_start: 0.8286 (t80) cc_final: 0.8009 (m-80) REVERT: B 70 MET cc_start: 0.9077 (mtp) cc_final: 0.8833 (mtp) REVERT: C 70 MET cc_start: 0.9078 (mtp) cc_final: 0.8843 (mtp) REVERT: C 81 PHE cc_start: 0.8346 (t80) cc_final: 0.8036 (m-80) REVERT: D 70 MET cc_start: 0.9079 (mtp) cc_final: 0.8846 (mtp) REVERT: D 81 PHE cc_start: 0.8350 (t80) cc_final: 0.8028 (m-80) REVERT: E 70 MET cc_start: 0.9076 (mtp) cc_final: 0.8829 (mtp) REVERT: F 70 MET cc_start: 0.9077 (mtp) cc_final: 0.8833 (mtp) REVERT: G 70 MET cc_start: 0.9077 (mtp) cc_final: 0.8832 (mtp) REVERT: H 70 MET cc_start: 0.9074 (mtp) cc_final: 0.8828 (mtp) REVERT: I 70 MET cc_start: 0.9081 (mtp) cc_final: 0.8843 (mtp) REVERT: I 81 PHE cc_start: 0.8298 (t80) cc_final: 0.8013 (m-80) REVERT: J 70 MET cc_start: 0.9079 (mtp) cc_final: 0.8849 (mtp) REVERT: J 81 PHE cc_start: 0.8334 (t80) cc_final: 0.8030 (m-80) REVERT: K 70 MET cc_start: 0.9073 (mtp) cc_final: 0.8852 (mtp) REVERT: K 81 PHE cc_start: 0.8359 (t80) cc_final: 0.8030 (m-80) REVERT: L 70 MET cc_start: 0.9080 (mtp) cc_final: 0.8842 (mtp) REVERT: L 81 PHE cc_start: 0.8290 (t80) cc_final: 0.8004 (m-80) REVERT: M 70 MET cc_start: 0.9078 (mtp) cc_final: 0.8841 (mtp) REVERT: M 81 PHE cc_start: 0.8355 (t80) cc_final: 0.8031 (m-80) REVERT: N 70 MET cc_start: 0.9076 (mtp) cc_final: 0.8844 (mtp) REVERT: N 81 PHE cc_start: 0.8350 (t80) cc_final: 0.8041 (m-80) REVERT: O 70 MET cc_start: 0.9077 (mtp) cc_final: 0.8839 (mtp) REVERT: O 81 PHE cc_start: 0.8284 (t80) cc_final: 0.8004 (m-80) REVERT: P 70 MET cc_start: 0.9076 (mtp) cc_final: 0.8832 (mtp) REVERT: Q 70 MET cc_start: 0.9079 (mtp) cc_final: 0.8841 (mtp) REVERT: Q 81 PHE cc_start: 0.8291 (t80) cc_final: 0.8000 (m-80) REVERT: R 70 MET cc_start: 0.9076 (mtp) cc_final: 0.8842 (mtp) REVERT: R 81 PHE cc_start: 0.8351 (t80) cc_final: 0.8028 (m-80) REVERT: S 70 MET cc_start: 0.9080 (mtp) cc_final: 0.8849 (mtp) REVERT: S 81 PHE cc_start: 0.8344 (t80) cc_final: 0.8033 (m-80) REVERT: T 70 MET cc_start: 0.9076 (mtp) cc_final: 0.8830 (mtp) REVERT: U 70 MET cc_start: 0.9079 (mtp) cc_final: 0.8841 (mtp) REVERT: U 81 PHE cc_start: 0.8286 (t80) cc_final: 0.8002 (m-80) REVERT: V 70 MET cc_start: 0.9073 (mtp) cc_final: 0.8852 (mtp) REVERT: V 81 PHE cc_start: 0.8349 (t80) cc_final: 0.8028 (m-80) REVERT: W 70 MET cc_start: 0.9074 (mtp) cc_final: 0.8831 (mtp) REVERT: X 70 MET cc_start: 0.9075 (mtp) cc_final: 0.8854 (mtp) REVERT: X 81 PHE cc_start: 0.8340 (t80) cc_final: 0.8031 (m-80) outliers start: 0 outliers final: 0 residues processed: 639 average time/residue: 1.0288 time to fit residues: 746.2576 Evaluate side-chains 656 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 656 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 131 optimal weight: 0.2980 chunk 387 optimal weight: 5.9990 chunk 181 optimal weight: 0.7980 chunk 186 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 187 optimal weight: 7.9990 chunk 264 optimal weight: 30.0000 chunk 369 optimal weight: 3.9990 chunk 206 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 119 optimal weight: 20.0000 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 HIS A 112 GLN B 60 HIS B 112 GLN C 60 HIS C 112 GLN D 60 HIS D 112 GLN E 60 HIS E 112 GLN F 60 HIS F 112 GLN G 60 HIS G 112 GLN H 60 HIS H 112 GLN I 60 HIS I 112 GLN J 60 HIS J 112 GLN K 60 HIS K 112 GLN L 60 HIS L 112 GLN M 60 HIS M 112 GLN N 60 HIS N 112 GLN O 60 HIS O 112 GLN P 60 HIS P 112 GLN Q 60 HIS Q 112 GLN R 60 HIS R 112 GLN S 60 HIS S 112 GLN T 60 HIS T 112 GLN U 60 HIS U 112 GLN V 60 HIS V 112 GLN W 60 HIS W 112 GLN X 60 HIS X 112 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.150365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.136956 restraints weight = 11649.057| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 0.26 r_work: 0.3364 rms_B_bonded: 0.54 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 1.00 restraints_weight: 0.2500 r_work: 0.2876 rms_B_bonded: 2.84 restraints_weight: 0.1250 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 34704 Z= 0.140 Angle : 0.540 5.661 46800 Z= 0.298 Chirality : 0.037 0.144 4896 Planarity : 0.003 0.014 6144 Dihedral : 7.506 83.242 4512 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.02 (0.13), residues: 3936 helix: 3.78 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : 1.19 (0.26), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 156 TYR 0.020 0.002 TYR J 39 PHE 0.018 0.003 PHE I 41 TRP 0.005 0.001 TRP U 93 HIS 0.007 0.001 HIS O 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.14 (34704) covalent geometry : angle 0.53964 / 0.30 (46800) hydrogen bonds : bond 0.05313 / 3.55 ( 2664) hydrogen bonds : angle 3.52213 / 2.60 ( 7992) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 618 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.9078 (mtp) cc_final: 0.8838 (mtp) REVERT: B 70 MET cc_start: 0.9082 (mtp) cc_final: 0.8847 (mtp) REVERT: C 70 MET cc_start: 0.9079 (mtp) cc_final: 0.8837 (mtp) REVERT: C 81 PHE cc_start: 0.8334 (t80) cc_final: 0.7985 (m-80) REVERT: D 70 MET cc_start: 0.9080 (mtp) cc_final: 0.8839 (mtp) REVERT: D 81 PHE cc_start: 0.8335 (t80) cc_final: 0.7978 (m-80) REVERT: E 70 MET cc_start: 0.9077 (mtp) cc_final: 0.8838 (mtp) REVERT: F 70 MET cc_start: 0.9080 (mtp) cc_final: 0.8844 (mtp) REVERT: G 70 MET cc_start: 0.9078 (mtp) cc_final: 0.8842 (mtp) REVERT: H 70 MET cc_start: 0.9077 (mtp) cc_final: 0.8838 (mtp) REVERT: I 70 MET cc_start: 0.9078 (mtp) cc_final: 0.8838 (mtp) REVERT: J 70 MET cc_start: 0.9077 (mtp) cc_final: 0.8838 (mtp) REVERT: J 81 PHE cc_start: 0.8321 (t80) cc_final: 0.7978 (m-80) REVERT: K 70 MET cc_start: 0.9075 (mtp) cc_final: 0.8832 (mtp) REVERT: K 81 PHE cc_start: 0.8344 (t80) cc_final: 0.7979 (m-80) REVERT: L 70 MET cc_start: 0.9079 (mtp) cc_final: 0.8840 (mtp) REVERT: M 70 MET cc_start: 0.9080 (mtp) cc_final: 0.8838 (mtp) REVERT: M 81 PHE cc_start: 0.8334 (t80) cc_final: 0.7976 (m-80) REVERT: N 70 MET cc_start: 0.9075 (mtp) cc_final: 0.8836 (mtp) REVERT: N 81 PHE cc_start: 0.8335 (t80) cc_final: 0.7990 (m-80) REVERT: O 70 MET cc_start: 0.9076 (mtp) cc_final: 0.8835 (mtp) REVERT: P 70 MET cc_start: 0.9077 (mtp) cc_final: 0.8840 (mtp) REVERT: Q 70 MET cc_start: 0.9078 (mtp) cc_final: 0.8837 (mtp) REVERT: Q 81 PHE cc_start: 0.8333 (t80) cc_final: 0.7992 (m-80) REVERT: R 70 MET cc_start: 0.9076 (mtp) cc_final: 0.8833 (mtp) REVERT: R 81 PHE cc_start: 0.8335 (t80) cc_final: 0.7974 (m-80) REVERT: S 70 MET cc_start: 0.9081 (mtp) cc_final: 0.8842 (mtp) REVERT: S 81 PHE cc_start: 0.8328 (t80) cc_final: 0.7981 (m-80) REVERT: T 70 MET cc_start: 0.9079 (mtp) cc_final: 0.8840 (mtp) REVERT: U 70 MET cc_start: 0.9077 (mtp) cc_final: 0.8838 (mtp) REVERT: U 81 PHE cc_start: 0.8338 (t80) cc_final: 0.7992 (m-80) REVERT: V 70 MET cc_start: 0.9076 (mtp) cc_final: 0.8832 (mtp) REVERT: V 81 PHE cc_start: 0.8331 (t80) cc_final: 0.7975 (m-80) REVERT: W 70 MET cc_start: 0.9077 (mtp) cc_final: 0.8841 (mtp) REVERT: X 70 MET cc_start: 0.9076 (mtp) cc_final: 0.8836 (mtp) outliers start: 0 outliers final: 0 residues processed: 618 average time/residue: 1.0075 time to fit residues: 707.2785 Evaluate side-chains 622 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 622 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 386 optimal weight: 0.8980 chunk 185 optimal weight: 3.9990 chunk 363 optimal weight: 2.9990 chunk 344 optimal weight: 10.0000 chunk 258 optimal weight: 0.9990 chunk 131 optimal weight: 0.9980 chunk 249 optimal weight: 10.0000 chunk 160 optimal weight: 4.9990 chunk 291 optimal weight: 1.9990 chunk 395 optimal weight: 10.0000 chunk 330 optimal weight: 0.5980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 HIS A 83 GLN A 112 GLN B 60 HIS B 112 GLN C 60 HIS C 83 GLN C 112 GLN D 60 HIS D 83 GLN D 112 GLN E 60 HIS E 112 GLN F 60 HIS F 112 GLN G 60 HIS G 112 GLN H 60 HIS H 112 GLN I 60 HIS I 83 GLN I 112 GLN J 60 HIS J 83 GLN J 112 GLN K 60 HIS K 83 GLN K 112 GLN L 60 HIS L 83 GLN L 112 GLN M 60 HIS M 83 GLN M 112 GLN N 60 HIS N 83 GLN N 112 GLN O 60 HIS O 83 GLN O 112 GLN P 60 HIS P 112 GLN Q 60 HIS Q 112 GLN R 60 HIS R 83 GLN R 112 GLN S 60 HIS S 83 GLN S 112 GLN T 60 HIS T 112 GLN U 60 HIS U 112 GLN V 60 HIS V 83 GLN V 112 GLN W 60 HIS W 112 GLN X 60 HIS X 112 GLN Total number of N/Q/H flips: 61 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.153161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.139818 restraints weight = 11288.889| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 0.26 r_work: 0.3399 rms_B_bonded: 0.53 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 0.99 restraints_weight: 0.2500 r_work: 0.2918 rms_B_bonded: 2.83 restraints_weight: 0.1250 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 34704 Z= 0.113 Angle : 0.476 4.957 46800 Z= 0.263 Chirality : 0.035 0.137 4896 Planarity : 0.002 0.016 6144 Dihedral : 7.395 82.657 4512 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.32 (0.13), residues: 3936 helix: 4.03 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : 1.13 (0.26), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 156 TYR 0.017 0.002 TYR G 39 PHE 0.014 0.002 PHE A 41 TRP 0.007 0.001 TRP U 93 HIS 0.005 0.001 HIS O 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.11 (34704) covalent geometry : angle 0.47644 / 0.26 (46800) hydrogen bonds : bond 0.04645 / 3.11 ( 2664) hydrogen bonds : angle 3.31142 / 2.44 ( 7992) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 642 time to evaluate : 1.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.9059 (mtp) cc_final: 0.8822 (mtp) REVERT: B 70 MET cc_start: 0.9058 (mtp) cc_final: 0.8830 (mtp) REVERT: C 70 MET cc_start: 0.9054 (mtp) cc_final: 0.8823 (mtp) REVERT: D 70 MET cc_start: 0.9055 (mtp) cc_final: 0.8825 (mtp) REVERT: E 70 MET cc_start: 0.9054 (mtp) cc_final: 0.8823 (mtp) REVERT: F 70 MET cc_start: 0.9053 (mtp) cc_final: 0.8825 (mtp) REVERT: G 70 MET cc_start: 0.9054 (mtp) cc_final: 0.8826 (mtp) REVERT: H 70 MET cc_start: 0.9051 (mtp) cc_final: 0.8822 (mtp) REVERT: I 70 MET cc_start: 0.9060 (mtp) cc_final: 0.8822 (mtp) REVERT: J 70 MET cc_start: 0.9053 (mtp) cc_final: 0.8824 (mtp) REVERT: K 70 MET cc_start: 0.9049 (mtp) cc_final: 0.8818 (mtp) REVERT: L 70 MET cc_start: 0.9059 (mtp) cc_final: 0.8823 (mtp) REVERT: M 70 MET cc_start: 0.9056 (mtp) cc_final: 0.8825 (mtp) REVERT: N 70 MET cc_start: 0.9054 (mtp) cc_final: 0.8824 (mtp) REVERT: O 70 MET cc_start: 0.9056 (mtp) cc_final: 0.8820 (mtp) REVERT: P 70 MET cc_start: 0.9055 (mtp) cc_final: 0.8827 (mtp) REVERT: Q 70 MET cc_start: 0.9053 (mtp) cc_final: 0.8820 (mtp) REVERT: Q 81 PHE cc_start: 0.8309 (t80) cc_final: 0.7987 (m-80) REVERT: R 70 MET cc_start: 0.9050 (mtp) cc_final: 0.8817 (mtp) REVERT: S 70 MET cc_start: 0.9055 (mtp) cc_final: 0.8824 (mtp) REVERT: T 70 MET cc_start: 0.9056 (mtp) cc_final: 0.8827 (mtp) REVERT: U 70 MET cc_start: 0.9054 (mtp) cc_final: 0.8823 (mtp) REVERT: U 81 PHE cc_start: 0.8314 (t80) cc_final: 0.7992 (m-80) REVERT: V 70 MET cc_start: 0.9048 (mtp) cc_final: 0.8816 (mtp) REVERT: W 70 MET cc_start: 0.9053 (mtp) cc_final: 0.8826 (mtp) REVERT: X 70 MET cc_start: 0.9051 (mtp) cc_final: 0.8818 (mtp) REVERT: X 81 PHE cc_start: 0.8167 (t80) cc_final: 0.7930 (m-80) outliers start: 0 outliers final: 0 residues processed: 642 average time/residue: 1.1228 time to fit residues: 818.8520 Evaluate side-chains 647 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 647 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 18 optimal weight: 5.9990 chunk 357 optimal weight: 2.9990 chunk 402 optimal weight: 10.0000 chunk 266 optimal weight: 5.9990 chunk 158 optimal weight: 9.9990 chunk 85 optimal weight: 20.0000 chunk 21 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 348 optimal weight: 3.9990 chunk 366 optimal weight: 20.0000 chunk 97 optimal weight: 0.5980 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 HIS A 83 GLN A 112 GLN A 141 GLN B 60 HIS B 112 GLN C 60 HIS C 112 GLN D 60 HIS D 112 GLN D 141 GLN E 60 HIS E 112 GLN E 141 GLN F 60 HIS F 112 GLN G 60 HIS G 112 GLN H 60 HIS H 112 GLN I 60 HIS I 83 GLN I 112 GLN J 60 HIS J 112 GLN K 60 HIS K 112 GLN L 60 HIS L 83 GLN L 112 GLN M 60 HIS M 112 GLN N 60 HIS N 112 GLN O 60 HIS O 83 GLN O 112 GLN P 60 HIS P 112 GLN Q 60 HIS Q 112 GLN Q 141 GLN R 60 HIS R 112 GLN S 60 HIS S 112 GLN S 141 GLN T 60 HIS T 112 GLN T 141 GLN U 60 HIS U 112 GLN V 60 HIS V 112 GLN W 60 HIS W 112 GLN W 141 GLN X 60 HIS X 112 GLN X 141 GLN Total number of N/Q/H flips: 60 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.148650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.135010 restraints weight = 11962.230| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 0.27 r_work: 0.3339 rms_B_bonded: 0.55 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 1.03 restraints_weight: 0.2500 r_work: 0.2849 rms_B_bonded: 2.89 restraints_weight: 0.1250 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 34704 Z= 0.171 Angle : 0.574 6.048 46800 Z= 0.318 Chirality : 0.038 0.145 4896 Planarity : 0.003 0.018 6144 Dihedral : 7.542 83.464 4512 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.96 (0.13), residues: 3936 helix: 3.81 (0.09), residues: 3120 sheet: None (None), residues: 0 loop : 0.94 (0.26), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG X 156 TYR 0.021 0.003 TYR X 39 PHE 0.021 0.003 PHE A 41 TRP 0.003 0.001 TRP X 93 HIS 0.008 0.001 HIS E 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.17 (34704) covalent geometry : angle 0.57378 / 0.32 (46800) hydrogen bonds : bond 0.05710 / 3.82 ( 2664) hydrogen bonds : angle 3.65621 / 2.70 ( 7992) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 624 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.9086 (mtp) cc_final: 0.8855 (mtp) REVERT: B 70 MET cc_start: 0.9089 (mtp) cc_final: 0.8860 (mtp) REVERT: C 70 MET cc_start: 0.9088 (mtp) cc_final: 0.8858 (mtp) REVERT: C 81 PHE cc_start: 0.8293 (t80) cc_final: 0.8004 (m-80) REVERT: D 70 MET cc_start: 0.9089 (mtp) cc_final: 0.8859 (mtp) REVERT: D 81 PHE cc_start: 0.8297 (t80) cc_final: 0.8005 (m-80) REVERT: E 70 MET cc_start: 0.9085 (mtp) cc_final: 0.8853 (mtp) REVERT: F 70 MET cc_start: 0.9088 (mtp) cc_final: 0.8858 (mtp) REVERT: G 70 MET cc_start: 0.9086 (mtp) cc_final: 0.8857 (mtp) REVERT: H 70 MET cc_start: 0.9085 (mtp) cc_final: 0.8852 (mtp) REVERT: I 70 MET cc_start: 0.9089 (mtp) cc_final: 0.8858 (mtp) REVERT: J 70 MET cc_start: 0.9086 (mtp) cc_final: 0.8857 (mtp) REVERT: J 81 PHE cc_start: 0.8285 (t80) cc_final: 0.7999 (m-80) REVERT: K 70 MET cc_start: 0.9085 (mtp) cc_final: 0.8854 (mtp) REVERT: K 81 PHE cc_start: 0.8297 (t80) cc_final: 0.8018 (m-80) REVERT: L 70 MET cc_start: 0.9087 (mtp) cc_final: 0.8858 (mtp) REVERT: M 70 MET cc_start: 0.9088 (mtp) cc_final: 0.8859 (mtp) REVERT: M 81 PHE cc_start: 0.8297 (t80) cc_final: 0.8005 (m-80) REVERT: N 70 MET cc_start: 0.9088 (mtp) cc_final: 0.8861 (mtp) REVERT: N 81 PHE cc_start: 0.8298 (t80) cc_final: 0.8012 (m-80) REVERT: O 70 MET cc_start: 0.9086 (mtp) cc_final: 0.8858 (mtp) REVERT: P 70 MET cc_start: 0.9085 (mtp) cc_final: 0.8856 (mtp) REVERT: Q 70 MET cc_start: 0.9085 (mtp) cc_final: 0.8853 (mtp) REVERT: R 70 MET cc_start: 0.9083 (mtp) cc_final: 0.8849 (mtp) REVERT: R 81 PHE cc_start: 0.8298 (t80) cc_final: 0.8008 (m-80) REVERT: S 70 MET cc_start: 0.9087 (mtp) cc_final: 0.8856 (mtp) REVERT: S 81 PHE cc_start: 0.8288 (t80) cc_final: 0.7997 (m-80) REVERT: T 70 MET cc_start: 0.9086 (mtp) cc_final: 0.8855 (mtp) REVERT: U 70 MET cc_start: 0.9088 (mtp) cc_final: 0.8857 (mtp) REVERT: V 70 MET cc_start: 0.9084 (mtp) cc_final: 0.8852 (mtp) REVERT: V 81 PHE cc_start: 0.8298 (t80) cc_final: 0.8011 (m-80) REVERT: W 70 MET cc_start: 0.9084 (mtp) cc_final: 0.8854 (mtp) REVERT: X 70 MET cc_start: 0.9083 (mtp) cc_final: 0.8850 (mtp) outliers start: 0 outliers final: 0 residues processed: 624 average time/residue: 1.0639 time to fit residues: 755.4886 Evaluate side-chains 600 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 600 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 327 optimal weight: 10.0000 chunk 295 optimal weight: 4.9990 chunk 230 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 283 optimal weight: 9.9990 chunk 196 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 400 optimal weight: 4.9990 chunk 289 optimal weight: 8.9990 chunk 277 optimal weight: 5.9990 chunk 193 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 HIS A 112 GLN B 60 HIS B 112 GLN C 60 HIS C 112 GLN D 60 HIS D 112 GLN E 60 HIS E 112 GLN F 60 HIS F 112 GLN G 60 HIS G 112 GLN H 60 HIS H 112 GLN I 60 HIS I 112 GLN J 60 HIS J 112 GLN K 60 HIS K 112 GLN L 60 HIS L 112 GLN M 60 HIS M 112 GLN N 60 HIS N 112 GLN O 60 HIS O 112 GLN P 60 HIS P 112 GLN Q 60 HIS Q 112 GLN R 60 HIS R 112 GLN S 60 HIS S 112 GLN T 60 HIS T 112 GLN U 60 HIS U 112 GLN V 60 HIS V 112 GLN W 60 HIS W 112 GLN X 60 HIS X 112 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.147380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.133592 restraints weight = 12119.639| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 0.27 r_work: 0.3321 rms_B_bonded: 0.56 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 1.04 restraints_weight: 0.2500 r_work: 0.2830 rms_B_bonded: 2.89 restraints_weight: 0.1250 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 34704 Z= 0.217 Angle : 0.637 6.869 46800 Z= 0.355 Chirality : 0.040 0.163 4896 Planarity : 0.004 0.023 6144 Dihedral : 7.644 84.163 4512 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.28 % Allowed : 6.21 % Favored : 93.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.59 (0.13), residues: 3936 helix: 3.54 (0.09), residues: 3120 sheet: None (None), residues: 0 loop : 0.88 (0.27), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 156 TYR 0.024 0.003 TYR A 39 PHE 0.024 0.004 PHE X 41 TRP 0.006 0.002 TRP X 93 HIS 0.009 0.002 HIS E 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.22 (34704) covalent geometry : angle 0.63674 / 0.35 (46800) hydrogen bonds : bond 0.06113 / 4.09 ( 2664) hydrogen bonds : angle 3.83914 / 2.84 ( 7992) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 587 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.9094 (mtp) cc_final: 0.8852 (mtp) REVERT: B 70 MET cc_start: 0.9098 (mtp) cc_final: 0.8858 (mtp) REVERT: C 70 MET cc_start: 0.9098 (mtp) cc_final: 0.8860 (mtp) REVERT: C 81 PHE cc_start: 0.8270 (t80) cc_final: 0.7979 (m-80) REVERT: D 70 MET cc_start: 0.9099 (mtp) cc_final: 0.8859 (mtp) REVERT: D 81 PHE cc_start: 0.8273 (t80) cc_final: 0.7978 (m-80) REVERT: E 70 MET cc_start: 0.9094 (mtp) cc_final: 0.8851 (mtp) REVERT: F 70 MET cc_start: 0.9097 (mtp) cc_final: 0.8856 (mtp) REVERT: G 70 MET cc_start: 0.9095 (mtp) cc_final: 0.8855 (mtp) REVERT: H 70 MET cc_start: 0.9093 (mtp) cc_final: 0.8853 (mtp) REVERT: I 70 MET cc_start: 0.9096 (mtp) cc_final: 0.8855 (mtp) REVERT: J 70 MET cc_start: 0.9094 (mtp) cc_final: 0.8854 (mtp) REVERT: J 81 PHE cc_start: 0.8267 (t80) cc_final: 0.7980 (m-80) REVERT: K 70 MET cc_start: 0.9094 (mtp) cc_final: 0.8854 (mtp) REVERT: K 81 PHE cc_start: 0.8284 (t80) cc_final: 0.7995 (m-80) REVERT: L 70 MET cc_start: 0.9097 (mtp) cc_final: 0.8859 (mtp) REVERT: M 70 MET cc_start: 0.9096 (mtp) cc_final: 0.8855 (mtp) REVERT: M 81 PHE cc_start: 0.8287 (t80) cc_final: 0.7993 (m-80) REVERT: N 70 MET cc_start: 0.9097 (mtp) cc_final: 0.8857 (mtp) REVERT: N 81 PHE cc_start: 0.8288 (t80) cc_final: 0.7997 (m-80) REVERT: O 70 MET cc_start: 0.9096 (mtp) cc_final: 0.8856 (mtp) REVERT: P 70 MET cc_start: 0.9093 (mtp) cc_final: 0.8853 (mtp) REVERT: Q 70 MET cc_start: 0.9097 (mtp) cc_final: 0.8854 (mtp) REVERT: Q 81 PHE cc_start: 0.8304 (t80) cc_final: 0.8004 (m-80) REVERT: R 70 MET cc_start: 0.9092 (mtp) cc_final: 0.8848 (mtp) REVERT: R 81 PHE cc_start: 0.8290 (t80) cc_final: 0.7991 (m-80) REVERT: S 70 MET cc_start: 0.9097 (mtp) cc_final: 0.8856 (mtp) REVERT: S 81 PHE cc_start: 0.8269 (t80) cc_final: 0.7977 (m-80) REVERT: T 70 MET cc_start: 0.9095 (mtp) cc_final: 0.8852 (mtp) REVERT: U 70 MET cc_start: 0.9096 (mtp) cc_final: 0.8853 (mtp) REVERT: U 81 PHE cc_start: 0.8306 (t80) cc_final: 0.7997 (m-80) REVERT: V 70 MET cc_start: 0.9092 (mtp) cc_final: 0.8850 (mtp) REVERT: V 81 PHE cc_start: 0.8288 (t80) cc_final: 0.7993 (m-80) REVERT: W 70 MET cc_start: 0.9093 (mtp) cc_final: 0.8853 (mtp) REVERT: X 70 MET cc_start: 0.9093 (mtp) cc_final: 0.8849 (mtp) outliers start: 10 outliers final: 0 residues processed: 587 average time/residue: 1.0377 time to fit residues: 693.7426 Evaluate side-chains 587 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 587 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 286 optimal weight: 2.9990 chunk 324 optimal weight: 3.9990 chunk 271 optimal weight: 2.9990 chunk 219 optimal weight: 4.9990 chunk 141 optimal weight: 9.9990 chunk 213 optimal weight: 0.6980 chunk 234 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 251 optimal weight: 0.8980 chunk 349 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 HIS A 112 GLN B 60 HIS B 112 GLN C 60 HIS C 112 GLN D 60 HIS D 112 GLN E 60 HIS E 112 GLN F 60 HIS F 112 GLN G 60 HIS G 112 GLN H 60 HIS H 112 GLN I 60 HIS I 112 GLN J 60 HIS J 112 GLN K 60 HIS K 112 GLN L 60 HIS L 112 GLN M 60 HIS M 112 GLN N 60 HIS N 112 GLN O 60 HIS O 112 GLN P 60 HIS P 112 GLN Q 60 HIS Q 112 GLN R 60 HIS R 112 GLN S 60 HIS S 112 GLN T 60 HIS T 112 GLN U 60 HIS U 112 GLN V 60 HIS V 112 GLN W 60 HIS W 112 GLN X 60 HIS X 83 GLN X 112 GLN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.150010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.136511 restraints weight = 11679.621| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 0.27 r_work: 0.3357 rms_B_bonded: 0.55 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 1.02 restraints_weight: 0.2500 r_work: 0.2871 rms_B_bonded: 2.86 restraints_weight: 0.1250 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 34704 Z= 0.136 Angle : 0.528 5.504 46800 Z= 0.293 Chirality : 0.037 0.149 4896 Planarity : 0.003 0.015 6144 Dihedral : 7.477 82.899 4512 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.02 (0.14), residues: 3936 helix: 3.80 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : 1.12 (0.27), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 156 TYR 0.021 0.002 TYR G 39 PHE 0.018 0.003 PHE H 41 TRP 0.008 0.002 TRP M 93 HIS 0.007 0.001 HIS B 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.14 (34704) covalent geometry : angle 0.52772 / 0.29 (46800) hydrogen bonds : bond 0.05246 / 3.51 ( 2664) hydrogen bonds : angle 3.52987 / 2.61 ( 7992) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 576 time to evaluate : 1.544 Fit side-chains revert: symmetry clash REVERT: A 70 MET cc_start: 0.9075 (mtp) cc_final: 0.8831 (mtp) REVERT: B 70 MET cc_start: 0.9076 (mtp) cc_final: 0.8835 (mtp) REVERT: C 70 MET cc_start: 0.9073 (mtp) cc_final: 0.8832 (mtp) REVERT: C 81 PHE cc_start: 0.8221 (t80) cc_final: 0.7953 (m-80) REVERT: D 70 MET cc_start: 0.9075 (mtp) cc_final: 0.8832 (mtp) REVERT: D 81 PHE cc_start: 0.8222 (t80) cc_final: 0.7954 (m-80) REVERT: E 70 MET cc_start: 0.9071 (mtp) cc_final: 0.8829 (mtp) REVERT: F 70 MET cc_start: 0.9074 (mtp) cc_final: 0.8832 (mtp) REVERT: G 70 MET cc_start: 0.9074 (mtp) cc_final: 0.8832 (mtp) REVERT: H 70 MET cc_start: 0.9071 (mtp) cc_final: 0.8829 (mtp) REVERT: I 70 MET cc_start: 0.9075 (mtp) cc_final: 0.8833 (mtp) REVERT: J 70 MET cc_start: 0.9073 (mtp) cc_final: 0.8831 (mtp) REVERT: J 81 PHE cc_start: 0.8218 (t80) cc_final: 0.7950 (m-80) REVERT: K 70 MET cc_start: 0.9072 (mtp) cc_final: 0.8830 (mtp) REVERT: K 81 PHE cc_start: 0.8238 (t80) cc_final: 0.7973 (m-80) REVERT: L 70 MET cc_start: 0.9079 (mtp) cc_final: 0.8841 (mtp) REVERT: M 70 MET cc_start: 0.9074 (mtp) cc_final: 0.8831 (mtp) REVERT: M 81 PHE cc_start: 0.8248 (t80) cc_final: 0.7968 (m-80) REVERT: N 70 MET cc_start: 0.9075 (mtp) cc_final: 0.8834 (mtp) REVERT: N 81 PHE cc_start: 0.8245 (t80) cc_final: 0.7965 (m-80) REVERT: O 70 MET cc_start: 0.9077 (mtp) cc_final: 0.8836 (mtp) REVERT: P 70 MET cc_start: 0.9071 (mtp) cc_final: 0.8830 (mtp) REVERT: Q 70 MET cc_start: 0.9075 (mtp) cc_final: 0.8832 (mtp) REVERT: Q 81 PHE cc_start: 0.8240 (t80) cc_final: 0.7967 (m-80) REVERT: R 70 MET cc_start: 0.9071 (mtp) cc_final: 0.8828 (mtp) REVERT: R 81 PHE cc_start: 0.8256 (t80) cc_final: 0.7970 (m-80) REVERT: S 70 MET cc_start: 0.9075 (mtp) cc_final: 0.8833 (mtp) REVERT: S 81 PHE cc_start: 0.8218 (t80) cc_final: 0.7950 (m-80) REVERT: T 70 MET cc_start: 0.9075 (mtp) cc_final: 0.8832 (mtp) REVERT: U 70 MET cc_start: 0.9077 (mtp) cc_final: 0.8835 (mtp) REVERT: U 81 PHE cc_start: 0.8237 (t80) cc_final: 0.7959 (m-80) REVERT: V 70 MET cc_start: 0.9074 (mtp) cc_final: 0.8832 (mtp) REVERT: V 81 PHE cc_start: 0.8253 (t80) cc_final: 0.7970 (m-80) REVERT: W 70 MET cc_start: 0.9073 (mtp) cc_final: 0.8832 (mtp) REVERT: X 70 MET cc_start: 0.9070 (mtp) cc_final: 0.8828 (mtp) outliers start: 0 outliers final: 0 residues processed: 576 average time/residue: 1.0480 time to fit residues: 687.5582 Evaluate side-chains 623 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 623 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 168 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 133 optimal weight: 10.0000 chunk 337 optimal weight: 4.9990 chunk 316 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 368 optimal weight: 20.0000 chunk 111 optimal weight: 5.9990 chunk 96 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 HIS A 112 GLN B 60 HIS B 112 GLN C 60 HIS C 112 GLN D 60 HIS D 112 GLN E 60 HIS E 112 GLN F 60 HIS F 112 GLN G 60 HIS G 112 GLN H 60 HIS H 112 GLN I 60 HIS I 112 GLN J 60 HIS J 112 GLN K 60 HIS K 112 GLN L 60 HIS L 112 GLN M 60 HIS M 112 GLN N 60 HIS N 112 GLN O 60 HIS O 112 GLN P 60 HIS P 112 GLN Q 60 HIS Q 112 GLN R 60 HIS R 112 GLN S 60 HIS S 112 GLN T 60 HIS T 112 GLN U 60 HIS U 112 GLN V 60 HIS V 112 GLN W 60 HIS W 112 GLN X 60 HIS X 83 GLN X 112 GLN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.147189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.133367 restraints weight = 12221.882| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 0.28 r_work: 0.3316 rms_B_bonded: 0.57 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 1.05 restraints_weight: 0.2500 r_work: 0.2828 rms_B_bonded: 2.90 restraints_weight: 0.1250 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 34704 Z= 0.212 Angle : 0.630 6.641 46800 Z= 0.350 Chirality : 0.040 0.155 4896 Planarity : 0.004 0.021 6144 Dihedral : 7.667 84.262 4512 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.61 (0.13), residues: 3936 helix: 3.56 (0.09), residues: 3120 sheet: None (None), residues: 0 loop : 0.85 (0.26), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 156 TYR 0.024 0.003 TYR I 39 PHE 0.023 0.004 PHE Q 41 TRP 0.004 0.002 TRP M 93 HIS 0.009 0.002 HIS I 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.21 (34704) covalent geometry : angle 0.63002 / 0.35 (46800) hydrogen bonds : bond 0.06056 / 4.05 ( 2664) hydrogen bonds : angle 3.83840 / 2.84 ( 7992) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 603 time to evaluate : 1.496 Fit side-chains REVERT: A 70 MET cc_start: 0.9100 (mtp) cc_final: 0.8839 (mtp) REVERT: B 70 MET cc_start: 0.9096 (mtp) cc_final: 0.8848 (mtp) REVERT: C 70 MET cc_start: 0.9097 (mtp) cc_final: 0.8869 (mtp) REVERT: D 70 MET cc_start: 0.9100 (mtp) cc_final: 0.8872 (mtp) REVERT: E 70 MET cc_start: 0.9096 (mtp) cc_final: 0.8835 (mtp) REVERT: F 70 MET cc_start: 0.9097 (mtp) cc_final: 0.8849 (mtp) REVERT: G 70 MET cc_start: 0.9095 (mtp) cc_final: 0.8848 (mtp) REVERT: H 70 MET cc_start: 0.9092 (mtp) cc_final: 0.8844 (mtp) REVERT: I 70 MET cc_start: 0.9098 (mtp) cc_final: 0.8837 (mtp) REVERT: J 70 MET cc_start: 0.9097 (mtp) cc_final: 0.8838 (mtp) REVERT: K 70 MET cc_start: 0.9092 (mtp) cc_final: 0.8832 (mtp) REVERT: K 81 PHE cc_start: 0.8288 (t80) cc_final: 0.8007 (m-80) REVERT: L 70 MET cc_start: 0.9098 (mtp) cc_final: 0.8840 (mtp) REVERT: M 70 MET cc_start: 0.9098 (mtp) cc_final: 0.8871 (mtp) REVERT: M 81 PHE cc_start: 0.8292 (t80) cc_final: 0.8000 (m-80) REVERT: N 70 MET cc_start: 0.9097 (mtp) cc_final: 0.8869 (mtp) REVERT: N 81 PHE cc_start: 0.8286 (t80) cc_final: 0.7995 (m-80) REVERT: O 70 MET cc_start: 0.9097 (mtp) cc_final: 0.8838 (mtp) REVERT: P 70 MET cc_start: 0.9093 (mtp) cc_final: 0.8844 (mtp) REVERT: Q 70 MET cc_start: 0.9101 (mtp) cc_final: 0.8872 (mtp) REVERT: Q 81 PHE cc_start: 0.8326 (t80) cc_final: 0.8017 (m-80) REVERT: R 70 MET cc_start: 0.9095 (mtp) cc_final: 0.8866 (mtp) REVERT: R 81 PHE cc_start: 0.8293 (t80) cc_final: 0.7997 (m-80) REVERT: S 70 MET cc_start: 0.9099 (mtp) cc_final: 0.8871 (mtp) REVERT: T 70 MET cc_start: 0.9096 (mtp) cc_final: 0.8833 (mtp) REVERT: U 70 MET cc_start: 0.9101 (mtp) cc_final: 0.8872 (mtp) REVERT: U 81 PHE cc_start: 0.8326 (t80) cc_final: 0.8011 (m-80) REVERT: V 70 MET cc_start: 0.9094 (mtp) cc_final: 0.8865 (mtp) REVERT: V 81 PHE cc_start: 0.8293 (t80) cc_final: 0.7998 (m-80) REVERT: W 70 MET cc_start: 0.9097 (mtp) cc_final: 0.8838 (mtp) REVERT: X 70 MET cc_start: 0.9097 (mtp) cc_final: 0.8868 (mtp) outliers start: 0 outliers final: 0 residues processed: 603 average time/residue: 1.0910 time to fit residues: 748.5473 Evaluate side-chains 604 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 604 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 66 optimal weight: 7.9990 chunk 385 optimal weight: 8.9990 chunk 358 optimal weight: 4.9990 chunk 90 optimal weight: 8.9990 chunk 232 optimal weight: 8.9990 chunk 91 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 366 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 HIS A 112 GLN B 60 HIS B 112 GLN C 60 HIS C 112 GLN D 60 HIS D 112 GLN E 60 HIS E 112 GLN F 60 HIS F 112 GLN G 60 HIS G 112 GLN H 60 HIS H 112 GLN I 60 HIS I 112 GLN J 60 HIS J 112 GLN K 60 HIS K 112 GLN L 60 HIS L 112 GLN M 60 HIS M 112 GLN N 60 HIS N 112 GLN O 60 HIS O 112 GLN P 60 HIS P 112 GLN Q 60 HIS Q 112 GLN R 60 HIS R 112 GLN S 60 HIS S 112 GLN T 60 HIS T 112 GLN U 60 HIS U 112 GLN V 60 HIS V 112 GLN W 60 HIS W 83 GLN W 112 GLN X 60 HIS X 83 GLN X 112 GLN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.147300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.133539 restraints weight = 12190.016| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 0.28 r_work: 0.3319 rms_B_bonded: 0.56 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 1.04 restraints_weight: 0.2500 r_work: 0.2829 rms_B_bonded: 2.90 restraints_weight: 0.1250 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 34704 Z= 0.211 Angle : 0.632 6.856 46800 Z= 0.353 Chirality : 0.040 0.164 4896 Planarity : 0.004 0.022 6144 Dihedral : 7.676 84.412 4512 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.46 (0.13), residues: 3936 helix: 3.44 (0.09), residues: 3120 sheet: None (None), residues: 0 loop : 0.88 (0.27), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 79 TYR 0.025 0.003 TYR F 39 PHE 0.023 0.004 PHE L 41 TRP 0.006 0.002 TRP K 93 HIS 0.009 0.002 HIS H 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.21 (34704) covalent geometry : angle 0.63183 / 0.35 (46800) hydrogen bonds : bond 0.06036 / 4.03 ( 2664) hydrogen bonds : angle 3.83862 / 2.84 ( 7992) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 600 time to evaluate : 1.538 Fit side-chains REVERT: A 70 MET cc_start: 0.9097 (mtp) cc_final: 0.8860 (mtp) REVERT: B 70 MET cc_start: 0.9094 (mtp) cc_final: 0.8855 (mtp) REVERT: C 70 MET cc_start: 0.9093 (mtp) cc_final: 0.8855 (mtp) REVERT: D 70 MET cc_start: 0.9096 (mtp) cc_final: 0.8858 (mtp) REVERT: E 70 MET cc_start: 0.9093 (mtp) cc_final: 0.8853 (mtp) REVERT: F 70 MET cc_start: 0.9094 (mtp) cc_final: 0.8854 (mtp) REVERT: G 70 MET cc_start: 0.9091 (mtp) cc_final: 0.8852 (mtp) REVERT: H 70 MET cc_start: 0.9091 (mtp) cc_final: 0.8852 (mtp) REVERT: I 70 MET cc_start: 0.9097 (mtp) cc_final: 0.8860 (mtp) REVERT: J 70 MET cc_start: 0.9092 (mtp) cc_final: 0.8854 (mtp) REVERT: K 70 MET cc_start: 0.9092 (mtp) cc_final: 0.8856 (mtp) REVERT: K 81 PHE cc_start: 0.8305 (t80) cc_final: 0.8024 (m-80) REVERT: L 70 MET cc_start: 0.9096 (mtp) cc_final: 0.8860 (mtp) REVERT: M 70 MET cc_start: 0.9097 (mtp) cc_final: 0.8861 (mtp) REVERT: M 81 PHE cc_start: 0.8307 (t80) cc_final: 0.8013 (m-80) REVERT: N 70 MET cc_start: 0.9096 (mtp) cc_final: 0.8861 (mtp) REVERT: N 81 PHE cc_start: 0.8308 (t80) cc_final: 0.8018 (m-80) REVERT: O 70 MET cc_start: 0.9093 (mtp) cc_final: 0.8857 (mtp) REVERT: P 70 MET cc_start: 0.9093 (mtp) cc_final: 0.8854 (mtp) REVERT: Q 70 MET cc_start: 0.9099 (mtp) cc_final: 0.8863 (mtp) REVERT: Q 81 PHE cc_start: 0.8327 (t80) cc_final: 0.8019 (m-80) REVERT: R 70 MET cc_start: 0.9093 (mtp) cc_final: 0.8856 (mtp) REVERT: R 81 PHE cc_start: 0.8312 (t80) cc_final: 0.8016 (m-80) REVERT: S 70 MET cc_start: 0.9095 (mtp) cc_final: 0.8857 (mtp) REVERT: T 70 MET cc_start: 0.9095 (mtp) cc_final: 0.8856 (mtp) REVERT: U 70 MET cc_start: 0.9100 (mtp) cc_final: 0.8862 (mtp) REVERT: U 81 PHE cc_start: 0.8325 (t80) cc_final: 0.8015 (m-80) REVERT: V 70 MET cc_start: 0.9092 (mtp) cc_final: 0.8856 (mtp) REVERT: V 81 PHE cc_start: 0.8308 (t80) cc_final: 0.8016 (m-80) REVERT: W 70 MET cc_start: 0.9094 (mtp) cc_final: 0.8857 (mtp) REVERT: X 70 MET cc_start: 0.9093 (mtp) cc_final: 0.8856 (mtp) outliers start: 0 outliers final: 0 residues processed: 600 average time/residue: 1.0447 time to fit residues: 713.8022 Evaluate side-chains 601 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 601 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 387 optimal weight: 6.9990 chunk 143 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 244 optimal weight: 9.9990 chunk 235 optimal weight: 9.9990 chunk 265 optimal weight: 2.9990 chunk 342 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 220 optimal weight: 0.8980 chunk 108 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 HIS A 112 GLN B 60 HIS B 112 GLN C 60 HIS C 83 GLN C 112 GLN D 60 HIS D 83 GLN D 112 GLN E 60 HIS E 112 GLN F 60 HIS F 112 GLN G 60 HIS G 112 GLN H 60 HIS H 112 GLN I 60 HIS I 112 GLN J 60 HIS J 83 GLN J 112 GLN K 60 HIS K 112 GLN L 60 HIS L 112 GLN M 60 HIS M 112 GLN N 60 HIS N 112 GLN O 60 HIS O 112 GLN P 60 HIS P 112 GLN Q 60 HIS Q 112 GLN R 60 HIS R 112 GLN S 60 HIS S 83 GLN S 112 GLN T 60 HIS T 112 GLN U 60 HIS U 112 GLN V 60 HIS V 112 GLN W 60 HIS W 83 GLN W 112 GLN X 60 HIS X 83 GLN X 112 GLN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.148544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.135010 restraints weight = 11925.494| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 0.27 r_work: 0.3337 rms_B_bonded: 0.56 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 1.03 restraints_weight: 0.2500 r_work: 0.2850 rms_B_bonded: 2.88 restraints_weight: 0.1250 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 34704 Z= 0.161 Angle : 0.569 5.988 46800 Z= 0.317 Chirality : 0.038 0.154 4896 Planarity : 0.003 0.016 6144 Dihedral : 7.549 83.141 4512 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.75 (0.13), residues: 3936 helix: 3.59 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : 1.11 (0.27), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 79 TYR 0.023 0.002 TYR V 39 PHE 0.021 0.003 PHE X 41 TRP 0.008 0.002 TRP R 93 HIS 0.008 0.001 HIS H 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.16 (34704) covalent geometry : angle 0.56897 / 0.32 (46800) hydrogen bonds : bond 0.05579 / 3.73 ( 2664) hydrogen bonds : angle 3.64301 / 2.69 ( 7992) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21538.07 seconds wall clock time: 366 minutes 13.57 seconds (21973.57 seconds total)