Starting phenix.real_space_refine on Tue Aug 26 10:29:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jqe_61729/08_2025/9jqe_61729.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jqe_61729/08_2025/9jqe_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_61729/08_2025/9jqe_61729.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jqe_61729/08_2025/9jqe_61729.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jqe_61729/08_2025/9jqe_61729.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jqe_61729/08_2025/9jqe_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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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, 2 Unusual residues: {' CU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 4.61, per 1000 atoms: 0.12 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: 3.66 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.80 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: 6.78 Time building geometry restraints manager: 4.66 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 2.240 nonbonded pdb=" OE2 GLU U 62 " pdb="CU CU U 202 " model vdw 2.126 2.240 nonbonded pdb=" OE2 GLU J 62 " pdb="CU CU J 202 " model vdw 2.126 2.240 nonbonded pdb=" OE2 GLU V 62 " pdb="CU CU V 202 " model vdw 2.127 2.240 nonbonded pdb=" OE2 GLU M 62 " pdb="CU CU M 202 " model vdw 2.127 2.240 ... (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: 0.11 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: 7.600 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: 0.060 Extract box with map and model: 0.810 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 28.220 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 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 aren 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 covalent geometry : bond 0.00446 (34704) covalent geometry : angle 0.55849 (46800) hydrogen bonds : bond 0.08103 ( 2664) hydrogen bonds : angle 3.96394 ( 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 : 1.039 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: 0.8068 (mppt) REVERT: A 157 LYS cc_start: 0.8321 (mttt) cc_final: 0.8066 (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: 0.8078 (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: 0.8086 (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: 0.8443 (mmmt) cc_final: 0.8086 (mppt) REVERT: D 157 LYS cc_start: 0.8318 (mttt) cc_final: 0.8059 (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: 0.8093 (mppt) REVERT: E 157 LYS cc_start: 0.8319 (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: 0.8079 (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: 0.8068 (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: 0.8783 (mtp) REVERT: J 86 LYS cc_start: 0.8440 (mmmt) cc_final: 0.8085 (mppt) REVERT: J 157 LYS cc_start: 0.8318 (mttt) cc_final: 0.8055 (mtpt) REVERT: K 70 MET cc_start: 0.9036 (mtp) cc_final: 0.8797 (mtp) REVERT: K 86 LYS cc_start: 0.8445 (mmmt) cc_final: 0.8092 (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: 0.8065 (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: 0.8795 (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: 0.8434 (mmmt) cc_final: 0.8078 (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: 0.8324 (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: 0.8442 (mmmt) cc_final: 0.8086 (mppt) REVERT: S 157 LYS cc_start: 0.8318 (mttt) cc_final: 0.8058 (mtpt) REVERT: T 70 MET cc_start: 0.9027 (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: 0.8777 (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: 0.8798 (mtp) REVERT: V 86 LYS cc_start: 0.8445 (mmmt) cc_final: 0.8093 (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: 0.9609 time to fit residues: 1176.6178 Evaluate side-chains 878 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 878 time to evaluate : 1.348 ------------------------------------------------------------------------------- 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: 5.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 7.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3597 r_free = 0.3597 target = 0.148443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.134551 restraints weight = 12383.528| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 0.28 r_work: 0.3327 rms_B_bonded: 0.57 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 1.06 restraints_weight: 0.2500 r_work: 0.2838 rms_B_bonded: 2.91 restraints_weight: 0.1250 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 34704 Z= 0.175 Angle : 0.606 6.312 46800 Z= 0.334 Chirality : 0.038 0.151 4896 Planarity : 0.004 0.023 6144 Dihedral : 7.554 82.853 4512 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 2.35 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 aren not related in a simple way. whole: 4.81 (0.13), residues: 3936 helix: 3.72 (0.08), residues: 3120 sheet: None (None), residues: 0 loop : 0.79 (0.25), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 156 TYR 0.022 0.003 TYR D 32 PHE 0.020 0.003 PHE X 41 TRP 0.003 0.001 TRP N 93 HIS 0.008 0.001 HIS K 128 Details of bonding type rmsd covalent geometry : bond 0.00347 (34704) covalent geometry : angle 0.60576 (46800) hydrogen bonds : bond 0.05811 ( 2664) hydrogen bonds : angle 3.71221 ( 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 726 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 726 time to evaluate : 1.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.9091 (mtp) cc_final: 0.8836 (mtp) REVERT: B 70 MET cc_start: 0.9091 (mtp) cc_final: 0.8836 (mtp) REVERT: C 70 MET cc_start: 0.9090 (mtp) cc_final: 0.8864 (mtp) REVERT: C 81 PHE cc_start: 0.8282 (t80) cc_final: 0.7980 (m-80) REVERT: D 70 MET cc_start: 0.9092 (mtp) cc_final: 0.8866 (mtp) REVERT: D 81 PHE cc_start: 0.8285 (t80) cc_final: 0.7975 (m-80) REVERT: E 70 MET cc_start: 0.9089 (mtp) cc_final: 0.8831 (mtp) REVERT: F 70 MET cc_start: 0.9092 (mtp) cc_final: 0.8838 (mtp) REVERT: G 70 MET cc_start: 0.9090 (mtp) cc_final: 0.8836 (mtp) REVERT: H 70 MET cc_start: 0.9086 (mtp) cc_final: 0.8828 (mtp) REVERT: I 70 MET cc_start: 0.9093 (mtp) cc_final: 0.8839 (mtp) REVERT: J 70 MET cc_start: 0.9090 (mtp) cc_final: 0.8866 (mtp) REVERT: J 81 PHE cc_start: 0.8254 (t80) cc_final: 0.7976 (m-80) REVERT: K 70 MET cc_start: 0.9087 (mtp) cc_final: 0.8858 (mtp) REVERT: K 81 PHE cc_start: 0.8275 (t80) cc_final: 0.7976 (m-80) REVERT: L 70 MET cc_start: 0.9091 (mtp) cc_final: 0.8837 (mtp) REVERT: M 70 MET cc_start: 0.9092 (mtp) cc_final: 0.8864 (mtp) REVERT: M 81 PHE cc_start: 0.8290 (t80) cc_final: 0.7970 (m-80) REVERT: N 70 MET cc_start: 0.9089 (mtp) cc_final: 0.8863 (mtp) REVERT: N 81 PHE cc_start: 0.8294 (t80) cc_final: 0.7982 (m-80) REVERT: O 70 MET cc_start: 0.9087 (mtp) cc_final: 0.8832 (mtp) REVERT: P 70 MET cc_start: 0.9092 (mtp) cc_final: 0.8838 (mtp) REVERT: Q 70 MET cc_start: 0.9091 (mtp) cc_final: 0.8834 (mtp) REVERT: R 70 MET cc_start: 0.9090 (mtp) cc_final: 0.8862 (mtp) REVERT: R 81 PHE cc_start: 0.8271 (t80) cc_final: 0.7974 (m-80) REVERT: S 70 MET cc_start: 0.9093 (mtp) cc_final: 0.8867 (mtp) REVERT: S 81 PHE cc_start: 0.8260 (t80) cc_final: 0.7980 (m-80) REVERT: T 70 MET cc_start: 0.9090 (mtp) cc_final: 0.8832 (mtp) REVERT: U 70 MET cc_start: 0.9090 (mtp) cc_final: 0.8835 (mtp) REVERT: V 70 MET cc_start: 0.9087 (mtp) cc_final: 0.8858 (mtp) REVERT: V 81 PHE cc_start: 0.8270 (t80) cc_final: 0.7972 (m-80) REVERT: W 70 MET cc_start: 0.9091 (mtp) cc_final: 0.8836 (mtp) REVERT: X 70 MET cc_start: 0.9089 (mtp) cc_final: 0.8863 (mtp) REVERT: X 81 PHE cc_start: 0.8309 (t80) cc_final: 0.7988 (m-80) outliers start: 0 outliers final: 0 residues processed: 726 average time/residue: 1.2322 time to fit residues: 1004.8987 Evaluate side-chains 613 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 613 time to evaluate : 1.537 ------------------------------------------------------------------------------- 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: 0.8980 chunk 368 optimal weight: 20.0000 chunk 138 optimal weight: 8.9990 chunk 237 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 303 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 chunk 123 optimal weight: 0.9990 chunk 176 optimal weight: 10.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 83 GLN 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: 49 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.149083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.135378 restraints weight = 12508.017| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 0.28 r_work: 0.3339 rms_B_bonded: 0.58 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 1.07 restraints_weight: 0.2500 r_work: 0.2844 rms_B_bonded: 2.98 restraints_weight: 0.1250 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1865 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= 0.149 Angle : 0.553 5.875 46800 Z= 0.307 Chirality : 0.037 0.148 4896 Planarity : 0.003 0.017 6144 Dihedral : 7.545 83.630 4512 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 2.15 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 aren not related in a simple way. whole: 4.94 (0.13), residues: 3936 helix: 3.71 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : 1.24 (0.26), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG I 156 TYR 0.021 0.002 TYR K 39 PHE 0.019 0.003 PHE O 41 TRP 0.006 0.002 TRP U 93 HIS 0.007 0.001 HIS U 128 Details of bonding type rmsd covalent geometry : bond 0.00288 (34704) covalent geometry : angle 0.55266 (46800) hydrogen bonds : bond 0.05480 ( 2664) hydrogen bonds : angle 3.61076 ( 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 597 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 597 time to evaluate : 1.647 Fit side-chains revert: symmetry clash REVERT: A 70 MET cc_start: 0.9087 (mtp) cc_final: 0.8850 (mtp) REVERT: A 81 PHE cc_start: 0.8353 (t80) cc_final: 0.8045 (m-80) REVERT: B 70 MET cc_start: 0.9090 (mtp) cc_final: 0.8868 (mtp) REVERT: B 81 PHE cc_start: 0.8310 (t80) cc_final: 0.8011 (m-80) REVERT: C 70 MET cc_start: 0.9088 (mtp) cc_final: 0.8867 (mtp) REVERT: C 81 PHE cc_start: 0.8387 (t80) cc_final: 0.8051 (m-80) REVERT: D 70 MET cc_start: 0.9088 (mtp) cc_final: 0.8865 (mtp) REVERT: D 81 PHE cc_start: 0.8386 (t80) cc_final: 0.8050 (m-80) REVERT: E 70 MET cc_start: 0.9087 (mtp) cc_final: 0.8850 (mtp) REVERT: E 81 PHE cc_start: 0.8335 (t80) cc_final: 0.8038 (m-80) REVERT: F 70 MET cc_start: 0.9085 (mtp) cc_final: 0.8837 (mtp) REVERT: G 70 MET cc_start: 0.9087 (mtp) cc_final: 0.8869 (mtp) REVERT: H 70 MET cc_start: 0.9084 (mtp) cc_final: 0.8848 (mtp) REVERT: H 81 PHE cc_start: 0.8375 (t80) cc_final: 0.8022 (m-80) REVERT: I 70 MET cc_start: 0.9087 (mtp) cc_final: 0.8852 (mtp) REVERT: I 81 PHE cc_start: 0.8344 (t80) cc_final: 0.8042 (m-80) REVERT: J 70 MET cc_start: 0.9088 (mtp) cc_final: 0.8868 (mtp) REVERT: J 81 PHE cc_start: 0.8379 (t80) cc_final: 0.8047 (m-80) REVERT: K 70 MET cc_start: 0.9083 (mtp) cc_final: 0.8859 (mtp) REVERT: K 81 PHE cc_start: 0.8387 (t80) cc_final: 0.8045 (m-80) REVERT: L 70 MET cc_start: 0.9086 (mtp) cc_final: 0.8850 (mtp) REVERT: L 81 PHE cc_start: 0.8352 (t80) cc_final: 0.8037 (m-80) REVERT: M 70 MET cc_start: 0.9087 (mtp) cc_final: 0.8866 (mtp) REVERT: M 81 PHE cc_start: 0.8390 (t80) cc_final: 0.8045 (m-80) REVERT: N 70 MET cc_start: 0.9082 (mtp) cc_final: 0.8860 (mtp) REVERT: N 81 PHE cc_start: 0.8389 (t80) cc_final: 0.8056 (m-80) REVERT: O 70 MET cc_start: 0.9085 (mtp) cc_final: 0.8848 (mtp) REVERT: O 81 PHE cc_start: 0.8352 (t80) cc_final: 0.8043 (m-80) REVERT: P 70 MET cc_start: 0.9086 (mtp) cc_final: 0.8851 (mtp) REVERT: P 81 PHE cc_start: 0.8347 (t80) cc_final: 0.8039 (m-80) REVERT: Q 70 MET cc_start: 0.9089 (mtp) cc_final: 0.8853 (mtp) REVERT: Q 81 PHE cc_start: 0.8345 (t80) cc_final: 0.8035 (m-80) REVERT: R 70 MET cc_start: 0.9083 (mtp) cc_final: 0.8860 (mtp) REVERT: R 81 PHE cc_start: 0.8378 (t80) cc_final: 0.8047 (m-80) REVERT: S 70 MET cc_start: 0.9088 (mtp) cc_final: 0.8868 (mtp) REVERT: S 81 PHE cc_start: 0.8378 (t80) cc_final: 0.8048 (m-80) REVERT: T 70 MET cc_start: 0.9086 (mtp) cc_final: 0.8839 (mtp) REVERT: U 70 MET cc_start: 0.9086 (mtp) cc_final: 0.8850 (mtp) REVERT: U 81 PHE cc_start: 0.8344 (t80) cc_final: 0.8040 (m-80) REVERT: V 70 MET cc_start: 0.9083 (mtp) cc_final: 0.8859 (mtp) REVERT: V 81 PHE cc_start: 0.8378 (t80) cc_final: 0.8035 (m-80) REVERT: W 70 MET cc_start: 0.9086 (mtp) cc_final: 0.8839 (mtp) REVERT: X 70 MET cc_start: 0.9084 (mtp) cc_final: 0.8863 (mtp) REVERT: X 81 PHE cc_start: 0.8379 (t80) cc_final: 0.8052 (m-80) outliers start: 0 outliers final: 0 residues processed: 597 average time/residue: 1.2102 time to fit residues: 816.0649 Evaluate side-chains 619 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 619 time to evaluate : 1.145 ------------------------------------------------------------------------------- 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: 0.8980 chunk 387 optimal weight: 0.6980 chunk 181 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 187 optimal weight: 6.9990 chunk 264 optimal weight: 1.9990 chunk 369 optimal weight: 0.9990 chunk 206 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 119 optimal weight: 20.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 83 GLN A 112 GLN B 60 HIS B 83 GLN B 112 GLN C 60 HIS C 112 GLN D 60 HIS D 112 GLN E 60 HIS E 83 GLN E 112 GLN F 60 HIS F 112 GLN G 60 HIS 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 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 83 GLN P 112 GLN Q 60 HIS Q 83 GLN 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 83 GLN 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: 58 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.151302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.137636 restraints weight = 12580.390| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 0.28 r_work: 0.3368 rms_B_bonded: 0.58 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 1.08 restraints_weight: 0.2500 r_work: 0.2877 rms_B_bonded: 3.01 restraints_weight: 0.1250 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 34704 Z= 0.118 Angle : 0.497 5.199 46800 Z= 0.274 Chirality : 0.036 0.140 4896 Planarity : 0.002 0.016 6144 Dihedral : 7.414 82.469 4512 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % 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 aren not related in a simple way. whole: 5.26 (0.13), residues: 3936 helix: 3.96 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : 1.21 (0.26), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 156 TYR 0.018 0.002 TYR G 39 PHE 0.015 0.002 PHE V 41 TRP 0.006 0.001 TRP N 93 HIS 0.005 0.001 HIS S 128 Details of bonding type rmsd covalent geometry : bond 0.00220 (34704) covalent geometry : angle 0.49748 (46800) hydrogen bonds : bond 0.04829 ( 2664) hydrogen bonds : angle 3.38268 ( 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 666 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 666 time to evaluate : 1.272 Fit side-chains revert: symmetry clash REVERT: A 70 MET cc_start: 0.9069 (mtp) cc_final: 0.8829 (mtp) REVERT: A 81 PHE cc_start: 0.8361 (t80) cc_final: 0.8002 (m-80) REVERT: B 70 MET cc_start: 0.9069 (mtp) cc_final: 0.8833 (mtp) REVERT: B 81 PHE cc_start: 0.8351 (t80) cc_final: 0.8013 (m-80) REVERT: C 70 MET cc_start: 0.9068 (mtp) cc_final: 0.8811 (mtp) REVERT: C 81 PHE cc_start: 0.8359 (t80) cc_final: 0.8028 (m-80) REVERT: D 70 MET cc_start: 0.9070 (mtp) cc_final: 0.8814 (mtp) REVERT: D 81 PHE cc_start: 0.8358 (t80) cc_final: 0.8022 (m-80) REVERT: E 70 MET cc_start: 0.9069 (mtp) cc_final: 0.8830 (mtp) REVERT: E 81 PHE cc_start: 0.8341 (t80) cc_final: 0.7987 (m-80) REVERT: E 157 LYS cc_start: 0.8604 (mttm) cc_final: 0.8142 (mtpt) REVERT: F 70 MET cc_start: 0.9070 (mtp) cc_final: 0.8833 (mtp) REVERT: F 157 LYS cc_start: 0.8616 (mttm) cc_final: 0.8162 (mtpt) REVERT: G 70 MET cc_start: 0.9069 (mtp) cc_final: 0.8837 (mtp) REVERT: G 157 LYS cc_start: 0.8606 (mttm) cc_final: 0.8151 (mtpt) REVERT: H 70 MET cc_start: 0.9065 (mtp) cc_final: 0.8825 (mtp) REVERT: H 81 PHE cc_start: 0.8359 (t80) cc_final: 0.8004 (m-80) REVERT: H 157 LYS cc_start: 0.8610 (mttm) cc_final: 0.8147 (mtpt) REVERT: I 70 MET cc_start: 0.9071 (mtp) cc_final: 0.8830 (mtp) REVERT: I 81 PHE cc_start: 0.8354 (t80) cc_final: 0.8003 (m-80) REVERT: J 70 MET cc_start: 0.9066 (mtp) cc_final: 0.8811 (mtp) REVERT: J 81 PHE cc_start: 0.8345 (t80) cc_final: 0.8026 (m-80) REVERT: K 70 MET cc_start: 0.9065 (mtp) cc_final: 0.8822 (mtp) REVERT: K 81 PHE cc_start: 0.8376 (t80) cc_final: 0.8006 (m-80) REVERT: L 70 MET cc_start: 0.9070 (mtp) cc_final: 0.8829 (mtp) REVERT: L 81 PHE cc_start: 0.8355 (t80) cc_final: 0.7995 (m-80) REVERT: M 70 MET cc_start: 0.9069 (mtp) cc_final: 0.8825 (mtp) REVERT: M 81 PHE cc_start: 0.8357 (t80) cc_final: 0.7993 (m-80) REVERT: N 70 MET cc_start: 0.9065 (mtp) cc_final: 0.8821 (mtp) REVERT: N 81 PHE cc_start: 0.8363 (t80) cc_final: 0.8015 (m-80) REVERT: O 70 MET cc_start: 0.9067 (mtp) cc_final: 0.8826 (mtp) REVERT: O 81 PHE cc_start: 0.8349 (t80) cc_final: 0.7992 (m-80) REVERT: P 70 MET cc_start: 0.9066 (mtp) cc_final: 0.8812 (mtp) REVERT: P 81 PHE cc_start: 0.8345 (t80) cc_final: 0.7993 (m-80) REVERT: P 157 LYS cc_start: 0.8621 (mttm) cc_final: 0.8163 (mtpt) REVERT: Q 70 MET cc_start: 0.9071 (mtp) cc_final: 0.8832 (mtp) REVERT: Q 81 PHE cc_start: 0.8358 (t80) cc_final: 0.7998 (m-80) REVERT: Q 157 LYS cc_start: 0.8605 (mttm) cc_final: 0.8144 (mtpt) REVERT: R 70 MET cc_start: 0.9066 (mtp) cc_final: 0.8807 (mtp) REVERT: R 81 PHE cc_start: 0.8363 (t80) cc_final: 0.8004 (m-80) REVERT: S 70 MET cc_start: 0.9069 (mtp) cc_final: 0.8829 (mtp) REVERT: S 81 PHE cc_start: 0.8353 (t80) cc_final: 0.8025 (m-80) REVERT: T 70 MET cc_start: 0.9070 (mtp) cc_final: 0.8832 (mtp) REVERT: U 70 MET cc_start: 0.9069 (mtp) cc_final: 0.8830 (mtp) REVERT: U 81 PHE cc_start: 0.8355 (t80) cc_final: 0.8001 (m-80) REVERT: V 70 MET cc_start: 0.9066 (mtp) cc_final: 0.8823 (mtp) REVERT: V 81 PHE cc_start: 0.8356 (t80) cc_final: 0.7992 (m-80) REVERT: V 157 LYS cc_start: 0.8617 (mttm) cc_final: 0.8152 (mtpt) REVERT: W 70 MET cc_start: 0.9069 (mtp) cc_final: 0.8833 (mtp) REVERT: X 70 MET cc_start: 0.9066 (mtp) cc_final: 0.8830 (mtp) REVERT: X 81 PHE cc_start: 0.8352 (t80) cc_final: 0.7996 (m-80) outliers start: 0 outliers final: 0 residues processed: 666 average time/residue: 1.0397 time to fit residues: 781.0412 Evaluate side-chains 634 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 634 time to evaluate : 1.222 ------------------------------------------------------------------------------- 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: 3.9990 chunk 185 optimal weight: 9.9990 chunk 363 optimal weight: 0.9980 chunk 344 optimal weight: 10.0000 chunk 258 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 249 optimal weight: 7.9990 chunk 160 optimal weight: 6.9990 chunk 291 optimal weight: 1.9990 chunk 395 optimal weight: 10.0000 chunk 330 optimal weight: 0.0870 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 83 GLN 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 83 GLN 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: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.150062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.136456 restraints weight = 12464.501| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 0.28 r_work: 0.3356 rms_B_bonded: 0.57 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 1.07 restraints_weight: 0.2500 r_work: 0.2864 rms_B_bonded: 2.97 restraints_weight: 0.1250 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 34704 Z= 0.126 Angle : 0.508 5.304 46800 Z= 0.280 Chirality : 0.036 0.140 4896 Planarity : 0.003 0.015 6144 Dihedral : 7.401 82.169 4512 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % 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 aren not related in a simple way. whole: 5.19 (0.13), residues: 3936 helix: 3.91 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : 1.21 (0.26), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG X 156 TYR 0.018 0.002 TYR Q 39 PHE 0.016 0.002 PHE A 41 TRP 0.005 0.001 TRP O 93 HIS 0.006 0.001 HIS M 128 Details of bonding type rmsd covalent geometry : bond 0.00236 (34704) covalent geometry : angle 0.50767 (46800) hydrogen bonds : bond 0.05076 ( 2664) hydrogen bonds : angle 3.45238 ( 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 629 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 629 time to evaluate : 1.476 Fit side-chains revert: symmetry clash REVERT: A 70 MET cc_start: 0.9075 (mtp) cc_final: 0.8844 (mtp) REVERT: B 70 MET cc_start: 0.9076 (mtp) cc_final: 0.8846 (mtp) REVERT: B 81 PHE cc_start: 0.8342 (t80) cc_final: 0.8001 (m-80) REVERT: C 70 MET cc_start: 0.9073 (mtp) cc_final: 0.8843 (mtp) REVERT: D 70 MET cc_start: 0.9076 (mtp) cc_final: 0.8847 (mtp) REVERT: E 70 MET cc_start: 0.9079 (mtp) cc_final: 0.8792 (mtp) REVERT: F 70 MET cc_start: 0.9077 (mtp) cc_final: 0.8862 (mtp) REVERT: G 70 MET cc_start: 0.9074 (mtp) cc_final: 0.8858 (mtp) REVERT: H 70 MET cc_start: 0.9074 (mtp) cc_final: 0.8846 (mtp) REVERT: H 81 PHE cc_start: 0.8361 (t80) cc_final: 0.8023 (m-80) REVERT: I 70 MET cc_start: 0.9079 (mtp) cc_final: 0.8850 (mtp) REVERT: J 70 MET cc_start: 0.9071 (mtp) cc_final: 0.8841 (mtp) REVERT: K 70 MET cc_start: 0.9070 (mtp) cc_final: 0.8839 (mtp) REVERT: L 70 MET cc_start: 0.9077 (mtp) cc_final: 0.8848 (mtp) REVERT: M 70 MET cc_start: 0.9075 (mtp) cc_final: 0.8846 (mtp) REVERT: N 70 MET cc_start: 0.9073 (mtp) cc_final: 0.8845 (mtp) REVERT: O 70 MET cc_start: 0.9073 (mtp) cc_final: 0.8841 (mtp) REVERT: P 70 MET cc_start: 0.9071 (mtp) cc_final: 0.8786 (mtp) REVERT: Q 70 MET cc_start: 0.9080 (mtp) cc_final: 0.8791 (mtp) REVERT: R 70 MET cc_start: 0.9069 (mtp) cc_final: 0.8836 (mtp) REVERT: S 70 MET cc_start: 0.9076 (mtp) cc_final: 0.8848 (mtp) REVERT: T 70 MET cc_start: 0.9076 (mtp) cc_final: 0.8789 (mtp) REVERT: U 70 MET cc_start: 0.9078 (mtp) cc_final: 0.8850 (mtp) REVERT: V 70 MET cc_start: 0.9073 (mtp) cc_final: 0.8785 (mtp) REVERT: W 70 MET cc_start: 0.9073 (mtp) cc_final: 0.8784 (mtp) REVERT: X 70 MET cc_start: 0.9074 (mtp) cc_final: 0.8847 (mtp) outliers start: 0 outliers final: 0 residues processed: 629 average time/residue: 1.0422 time to fit residues: 740.8676 Evaluate side-chains 614 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 614 time to evaluate : 1.497 ------------------------------------------------------------------------------- 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: 2.9990 chunk 357 optimal weight: 2.9990 chunk 402 optimal weight: 10.0000 chunk 266 optimal weight: 10.0000 chunk 158 optimal weight: 8.9990 chunk 85 optimal weight: 20.0000 chunk 21 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 348 optimal weight: 5.9990 chunk 366 optimal weight: 9.9990 chunk 97 optimal weight: 0.7980 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 83 GLN 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: 49 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.148076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.134456 restraints weight = 12317.576| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 0.28 r_work: 0.3332 rms_B_bonded: 0.57 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 1.05 restraints_weight: 0.2500 r_work: 0.2837 rms_B_bonded: 2.93 restraints_weight: 0.1250 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 34704 Z= 0.171 Angle : 0.582 6.130 46800 Z= 0.323 Chirality : 0.038 0.151 4896 Planarity : 0.003 0.019 6144 Dihedral : 7.529 83.176 4512 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 1.97 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 aren not related in a simple way. whole: 4.90 (0.13), residues: 3936 helix: 3.75 (0.09), residues: 3120 sheet: None (None), residues: 0 loop : 1.02 (0.26), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 156 TYR 0.022 0.003 TYR T 39 PHE 0.021 0.003 PHE Q 41 TRP 0.004 0.002 TRP L 93 HIS 0.008 0.001 HIS L 128 Details of bonding type rmsd covalent geometry : bond 0.00337 (34704) covalent geometry : angle 0.58161 (46800) hydrogen bonds : bond 0.05734 ( 2664) hydrogen bonds : angle 3.68383 ( 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 615 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 615 time to evaluate : 1.600 Fit side-chains revert: symmetry clash REVERT: A 70 MET cc_start: 0.9087 (mtp) cc_final: 0.8855 (mtp) REVERT: A 81 PHE cc_start: 0.8299 (t80) cc_final: 0.7991 (m-80) REVERT: B 70 MET cc_start: 0.9091 (mtp) cc_final: 0.8863 (mtp) REVERT: C 70 MET cc_start: 0.9089 (mtp) cc_final: 0.8861 (mtp) REVERT: C 81 PHE cc_start: 0.8306 (t80) cc_final: 0.7994 (m-80) REVERT: D 70 MET cc_start: 0.9094 (mtp) cc_final: 0.8868 (mtp) REVERT: D 81 PHE cc_start: 0.8299 (t80) cc_final: 0.7991 (m-80) REVERT: E 70 MET cc_start: 0.9093 (mtp) cc_final: 0.8864 (mtp) REVERT: E 81 PHE cc_start: 0.8289 (t80) cc_final: 0.7989 (m-80) REVERT: F 70 MET cc_start: 0.9094 (mtp) cc_final: 0.8865 (mtp) REVERT: G 70 MET cc_start: 0.9090 (mtp) cc_final: 0.8862 (mtp) REVERT: H 70 MET cc_start: 0.9087 (mtp) cc_final: 0.8857 (mtp) REVERT: I 70 MET cc_start: 0.9091 (mtp) cc_final: 0.8864 (mtp) REVERT: I 81 PHE cc_start: 0.8296 (t80) cc_final: 0.7987 (m-80) REVERT: J 70 MET cc_start: 0.9086 (mtp) cc_final: 0.8856 (mtp) REVERT: J 81 PHE cc_start: 0.8314 (t80) cc_final: 0.8001 (m-80) REVERT: K 70 MET cc_start: 0.9085 (mtp) cc_final: 0.8854 (mtp) REVERT: K 81 PHE cc_start: 0.8321 (t80) cc_final: 0.8008 (m-80) REVERT: L 70 MET cc_start: 0.9093 (mtp) cc_final: 0.8867 (mtp) REVERT: L 81 PHE cc_start: 0.8299 (t80) cc_final: 0.7993 (m-80) REVERT: M 70 MET cc_start: 0.9093 (mtp) cc_final: 0.8867 (mtp) REVERT: M 81 PHE cc_start: 0.8304 (t80) cc_final: 0.7983 (m-80) REVERT: N 70 MET cc_start: 0.9089 (mtp) cc_final: 0.8862 (mtp) REVERT: N 81 PHE cc_start: 0.8312 (t80) cc_final: 0.7999 (m-80) REVERT: O 70 MET cc_start: 0.9089 (mtp) cc_final: 0.8862 (mtp) REVERT: O 81 PHE cc_start: 0.8309 (t80) cc_final: 0.7990 (m-80) REVERT: P 70 MET cc_start: 0.9090 (mtp) cc_final: 0.8863 (mtp) REVERT: P 81 PHE cc_start: 0.8311 (t80) cc_final: 0.7999 (m-80) REVERT: Q 70 MET cc_start: 0.9090 (mtp) cc_final: 0.8861 (mtp) REVERT: Q 81 PHE cc_start: 0.8299 (t80) cc_final: 0.7992 (m-80) REVERT: R 70 MET cc_start: 0.9085 (mtp) cc_final: 0.8855 (mtp) REVERT: R 81 PHE cc_start: 0.8319 (t80) cc_final: 0.7999 (m-80) REVERT: S 70 MET cc_start: 0.9090 (mtp) cc_final: 0.8863 (mtp) REVERT: S 81 PHE cc_start: 0.8305 (t80) cc_final: 0.7986 (m-80) REVERT: T 70 MET cc_start: 0.9089 (mtp) cc_final: 0.8859 (mtp) REVERT: U 70 MET cc_start: 0.9089 (mtp) cc_final: 0.8860 (mtp) REVERT: U 81 PHE cc_start: 0.8306 (t80) cc_final: 0.7991 (m-80) REVERT: V 70 MET cc_start: 0.9088 (mtp) cc_final: 0.8858 (mtp) REVERT: V 81 PHE cc_start: 0.8316 (t80) cc_final: 0.7991 (m-80) REVERT: W 70 MET cc_start: 0.9085 (mtp) cc_final: 0.8856 (mtp) REVERT: X 70 MET cc_start: 0.9091 (mtp) cc_final: 0.8863 (mtp) REVERT: X 81 PHE cc_start: 0.8308 (t80) cc_final: 0.7994 (m-80) outliers start: 0 outliers final: 0 residues processed: 615 average time/residue: 1.1737 time to fit residues: 814.6494 Evaluate side-chains 626 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 626 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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: 4.9990 chunk 128 optimal weight: 4.9990 chunk 283 optimal weight: 8.9990 chunk 196 optimal weight: 4.9990 chunk 144 optimal weight: 8.9990 chunk 400 optimal weight: 4.9990 chunk 289 optimal weight: 8.9990 chunk 277 optimal weight: 2.9990 chunk 193 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3587 r_free = 0.3587 target = 0.146984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.133355 restraints weight = 12220.963| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 0.28 r_work: 0.3319 rms_B_bonded: 0.56 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 1.04 restraints_weight: 0.2500 r_work: 0.2825 rms_B_bonded: 2.89 restraints_weight: 0.1250 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 34704 Z= 0.216 Angle : 0.640 6.850 46800 Z= 0.355 Chirality : 0.040 0.162 4896 Planarity : 0.004 0.023 6144 Dihedral : 7.667 84.398 4512 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.33 % Allowed : 6.51 % Favored : 93.16 % 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 aren not related in a simple way. whole: 4.55 (0.13), residues: 3936 helix: 3.51 (0.09), residues: 3120 sheet: None (None), residues: 0 loop : 0.89 (0.27), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 79 TYR 0.025 0.003 TYR W 39 PHE 0.024 0.004 PHE V 41 TRP 0.006 0.002 TRP X 93 HIS 0.009 0.002 HIS D 128 Details of bonding type rmsd covalent geometry : bond 0.00436 (34704) covalent geometry : angle 0.64044 (46800) hydrogen bonds : bond 0.06094 ( 2664) hydrogen bonds : angle 3.85048 ( 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 621 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 609 time to evaluate : 1.162 Fit side-chains REVERT: A 70 MET cc_start: 0.9095 (mtp) cc_final: 0.8855 (mtp) REVERT: A 81 PHE cc_start: 0.8318 (t80) cc_final: 0.8008 (m-80) REVERT: B 70 MET cc_start: 0.9108 (mtp) cc_final: 0.8872 (mtp) REVERT: B 81 PHE cc_start: 0.8286 (t80) cc_final: 0.7997 (m-80) REVERT: C 70 MET cc_start: 0.9095 (mtp) cc_final: 0.8855 (mtp) REVERT: C 81 PHE cc_start: 0.8311 (t80) cc_final: 0.8005 (m-80) REVERT: D 70 MET cc_start: 0.9097 (mtp) cc_final: 0.8856 (mtp) REVERT: D 81 PHE cc_start: 0.8311 (t80) cc_final: 0.8003 (m-80) REVERT: E 70 MET cc_start: 0.9107 (mtp) cc_final: 0.8869 (mtp) REVERT: E 81 PHE cc_start: 0.8309 (t80) cc_final: 0.7999 (m-80) REVERT: F 70 MET cc_start: 0.9107 (mtp) cc_final: 0.8871 (mtp) REVERT: G 70 MET cc_start: 0.9105 (mtp) cc_final: 0.8869 (mtp) REVERT: H 70 MET cc_start: 0.9104 (mtp) cc_final: 0.8868 (mtp) REVERT: H 81 PHE cc_start: 0.8291 (t80) cc_final: 0.7981 (m-80) REVERT: I 70 MET cc_start: 0.9107 (mtp) cc_final: 0.8872 (mtp) REVERT: I 81 PHE cc_start: 0.8312 (t80) cc_final: 0.8004 (m-80) REVERT: J 70 MET cc_start: 0.9103 (mtp) cc_final: 0.8865 (mtp) REVERT: J 81 PHE cc_start: 0.8338 (t80) cc_final: 0.8016 (m-80) REVERT: K 70 MET cc_start: 0.9102 (mtp) cc_final: 0.8864 (mtp) REVERT: K 81 PHE cc_start: 0.8319 (t80) cc_final: 0.8006 (m-80) REVERT: L 70 MET cc_start: 0.9109 (mtp) cc_final: 0.8875 (mtp) REVERT: L 81 PHE cc_start: 0.8309 (t80) cc_final: 0.8004 (m-80) REVERT: M 70 MET cc_start: 0.9108 (mtp) cc_final: 0.8871 (mtp) REVERT: M 81 PHE cc_start: 0.8302 (t80) cc_final: 0.7994 (m-80) REVERT: N 70 MET cc_start: 0.9096 (mtp) cc_final: 0.8857 (mtp) REVERT: N 81 PHE cc_start: 0.8311 (t80) cc_final: 0.8013 (m-80) REVERT: O 70 MET cc_start: 0.9094 (mtp) cc_final: 0.8854 (mtp) REVERT: O 81 PHE cc_start: 0.8310 (t80) cc_final: 0.7993 (m-80) REVERT: P 70 MET cc_start: 0.9106 (mtp) cc_final: 0.8870 (mtp) REVERT: P 81 PHE cc_start: 0.8323 (t80) cc_final: 0.8010 (m-80) REVERT: Q 70 MET cc_start: 0.9106 (mtp) cc_final: 0.8870 (mtp) REVERT: Q 81 PHE cc_start: 0.8322 (t80) cc_final: 0.8013 (m-80) REVERT: R 70 MET cc_start: 0.9103 (mtp) cc_final: 0.8865 (mtp) REVERT: R 81 PHE cc_start: 0.8317 (t80) cc_final: 0.8001 (m-80) REVERT: S 70 MET cc_start: 0.9097 (mtp) cc_final: 0.8857 (mtp) REVERT: S 81 PHE cc_start: 0.8310 (t80) cc_final: 0.7998 (m-80) REVERT: T 70 MET cc_start: 0.9105 (mtp) cc_final: 0.8869 (mtp) REVERT: U 70 MET cc_start: 0.9106 (mtp) cc_final: 0.8870 (mtp) REVERT: U 81 PHE cc_start: 0.8321 (t80) cc_final: 0.8007 (m-80) REVERT: V 70 MET cc_start: 0.9105 (mtp) cc_final: 0.8868 (mtp) REVERT: V 81 PHE cc_start: 0.8314 (t80) cc_final: 0.7995 (m-80) REVERT: W 70 MET cc_start: 0.9092 (mtp) cc_final: 0.8851 (mtp) REVERT: X 70 MET cc_start: 0.9106 (mtp) cc_final: 0.8870 (mtp) REVERT: X 81 PHE cc_start: 0.8325 (t80) cc_final: 0.8011 (m-80) outliers start: 12 outliers final: 0 residues processed: 609 average time/residue: 1.0207 time to fit residues: 704.3095 Evaluate side-chains 608 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 608 time to evaluate : 1.426 ------------------------------------------------------------------------------- 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: 8.9990 chunk 324 optimal weight: 4.9990 chunk 271 optimal weight: 2.9990 chunk 219 optimal weight: 6.9990 chunk 141 optimal weight: 9.9990 chunk 213 optimal weight: 0.9990 chunk 234 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 92 optimal weight: 0.8980 chunk 251 optimal weight: 6.9990 chunk 349 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3610 r_free = 0.3610 target = 0.149062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.135371 restraints weight = 12356.419| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 0.28 r_work: 0.3340 rms_B_bonded: 0.58 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 1.06 restraints_weight: 0.2500 r_work: 0.2847 rms_B_bonded: 2.95 restraints_weight: 0.1250 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 34704 Z= 0.143 Angle : 0.542 5.636 46800 Z= 0.301 Chirality : 0.037 0.151 4896 Planarity : 0.003 0.015 6144 Dihedral : 7.473 82.567 4512 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % 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 aren not related in a simple way. whole: 4.95 (0.13), residues: 3936 helix: 3.74 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : 1.16 (0.27), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG Q 156 TYR 0.022 0.002 TYR F 39 PHE 0.034 0.003 PHE B 81 TRP 0.008 0.002 TRP L 93 HIS 0.007 0.001 HIS Q 128 Details of bonding type rmsd covalent geometry : bond 0.00275 (34704) covalent geometry : angle 0.54193 (46800) hydrogen bonds : bond 0.05362 ( 2664) hydrogen bonds : angle 3.58049 ( 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 578 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 578 time to evaluate : 1.347 Fit side-chains REVERT: A 70 MET cc_start: 0.9084 (mtp) cc_final: 0.8840 (mtp) REVERT: A 81 PHE cc_start: 0.8238 (t80) cc_final: 0.7958 (m-80) REVERT: B 70 MET cc_start: 0.9084 (mtp) cc_final: 0.8839 (mtp) REVERT: B 81 PHE cc_start: 0.8131 (t80) cc_final: 0.7851 (m-80) REVERT: C 70 MET cc_start: 0.9082 (mtp) cc_final: 0.8840 (mtp) REVERT: C 81 PHE cc_start: 0.8230 (t80) cc_final: 0.7955 (m-80) REVERT: D 70 MET cc_start: 0.9087 (mtp) cc_final: 0.8845 (mtp) REVERT: D 81 PHE cc_start: 0.8236 (t80) cc_final: 0.7962 (m-80) REVERT: E 70 MET cc_start: 0.9084 (mtp) cc_final: 0.8841 (mtp) REVERT: E 81 PHE cc_start: 0.8229 (t80) cc_final: 0.7957 (m-80) REVERT: F 70 MET cc_start: 0.9087 (mtp) cc_final: 0.8846 (mtp) REVERT: G 70 MET cc_start: 0.9083 (mtp) cc_final: 0.8842 (mtp) REVERT: H 70 MET cc_start: 0.9081 (mtp) cc_final: 0.8837 (mtp) REVERT: H 81 PHE cc_start: 0.8109 (t80) cc_final: 0.7840 (m-80) REVERT: I 70 MET cc_start: 0.9086 (mtp) cc_final: 0.8845 (mtp) REVERT: I 81 PHE cc_start: 0.8227 (t80) cc_final: 0.7948 (m-80) REVERT: J 70 MET cc_start: 0.9079 (mtp) cc_final: 0.8835 (mtp) REVERT: J 81 PHE cc_start: 0.8256 (t80) cc_final: 0.7954 (m-80) REVERT: K 70 MET cc_start: 0.9084 (mtp) cc_final: 0.8840 (mtp) REVERT: K 81 PHE cc_start: 0.8244 (t80) cc_final: 0.7967 (m-80) REVERT: L 70 MET cc_start: 0.9086 (mtp) cc_final: 0.8847 (mtp) REVERT: L 81 PHE cc_start: 0.8228 (t80) cc_final: 0.7955 (m-80) REVERT: M 70 MET cc_start: 0.9087 (mtp) cc_final: 0.8846 (mtp) REVERT: M 81 PHE cc_start: 0.8227 (t80) cc_final: 0.7947 (m-80) REVERT: N 70 MET cc_start: 0.9082 (mtp) cc_final: 0.8840 (mtp) REVERT: N 81 PHE cc_start: 0.8228 (t80) cc_final: 0.7956 (m-80) REVERT: O 70 MET cc_start: 0.9082 (mtp) cc_final: 0.8840 (mtp) REVERT: O 81 PHE cc_start: 0.8230 (t80) cc_final: 0.7948 (m-80) REVERT: P 70 MET cc_start: 0.9081 (mtp) cc_final: 0.8838 (mtp) REVERT: P 81 PHE cc_start: 0.8240 (t80) cc_final: 0.7959 (m-80) REVERT: Q 70 MET cc_start: 0.9087 (mtp) cc_final: 0.8845 (mtp) REVERT: Q 81 PHE cc_start: 0.8234 (t80) cc_final: 0.7955 (m-80) REVERT: R 70 MET cc_start: 0.9084 (mtp) cc_final: 0.8841 (mtp) REVERT: R 81 PHE cc_start: 0.8242 (t80) cc_final: 0.7963 (m-80) REVERT: S 70 MET cc_start: 0.9085 (mtp) cc_final: 0.8842 (mtp) REVERT: S 81 PHE cc_start: 0.8233 (t80) cc_final: 0.7952 (m-80) REVERT: T 70 MET cc_start: 0.9082 (mtp) cc_final: 0.8841 (mtp) REVERT: U 70 MET cc_start: 0.9082 (mtp) cc_final: 0.8839 (mtp) REVERT: U 81 PHE cc_start: 0.8235 (t80) cc_final: 0.7953 (m-80) REVERT: V 70 MET cc_start: 0.9083 (mtp) cc_final: 0.8841 (mtp) REVERT: V 81 PHE cc_start: 0.8234 (t80) cc_final: 0.7945 (m-80) REVERT: W 70 MET cc_start: 0.9080 (mtp) cc_final: 0.8840 (mtp) REVERT: X 70 MET cc_start: 0.9081 (mtp) cc_final: 0.8838 (mtp) REVERT: X 81 PHE cc_start: 0.8252 (t80) cc_final: 0.7949 (m-80) outliers start: 0 outliers final: 0 residues processed: 578 average time/residue: 1.0401 time to fit residues: 679.1199 Evaluate side-chains 606 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 606 time to evaluate : 1.451 ------------------------------------------------------------------------------- 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: 0.6980 chunk 15 optimal weight: 0.0030 chunk 133 optimal weight: 1.9990 chunk 337 optimal weight: 2.9990 chunk 316 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 368 optimal weight: 20.0000 chunk 111 optimal weight: 10.0000 chunk 96 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 overall best weight: 1.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3612 r_free = 0.3612 target = 0.149338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.135685 restraints weight = 12441.489| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 0.28 r_work: 0.3345 rms_B_bonded: 0.57 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 1.06 restraints_weight: 0.2500 r_work: 0.2854 rms_B_bonded: 2.95 restraints_weight: 0.1250 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1948 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= 0.135 Angle : 0.529 5.419 46800 Z= 0.293 Chirality : 0.037 0.149 4896 Planarity : 0.003 0.015 6144 Dihedral : 7.419 81.961 4512 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % 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 aren not related in a simple way. whole: 5.05 (0.14), residues: 3936 helix: 3.81 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : 1.18 (0.27), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG W 79 TYR 0.020 0.002 TYR T 39 PHE 0.019 0.003 PHE H 81 TRP 0.008 0.002 TRP M 93 HIS 0.007 0.001 HIS H 128 Details of bonding type rmsd covalent geometry : bond 0.00259 (34704) covalent geometry : angle 0.52916 (46800) hydrogen bonds : bond 0.05237 ( 2664) hydrogen bonds : angle 3.51371 ( 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 645 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 645 time to evaluate : 1.473 Fit side-chains REVERT: A 70 MET cc_start: 0.9082 (mtp) cc_final: 0.8836 (mtp) REVERT: A 81 PHE cc_start: 0.8205 (t80) cc_final: 0.7941 (m-80) REVERT: B 70 MET cc_start: 0.9083 (mtp) cc_final: 0.8836 (mtp) REVERT: B 81 PHE cc_start: 0.8241 (t80) cc_final: 0.7959 (m-80) REVERT: C 70 MET cc_start: 0.9084 (mtp) cc_final: 0.8840 (mtp) REVERT: C 81 PHE cc_start: 0.8200 (t80) cc_final: 0.7940 (m-80) REVERT: D 70 MET cc_start: 0.9086 (mtp) cc_final: 0.8843 (mtp) REVERT: D 81 PHE cc_start: 0.8199 (t80) cc_final: 0.7937 (m-80) REVERT: E 70 MET cc_start: 0.9087 (mtp) cc_final: 0.8841 (mtp) REVERT: E 81 PHE cc_start: 0.8209 (t80) cc_final: 0.7944 (m-80) REVERT: F 70 MET cc_start: 0.9085 (mtp) cc_final: 0.8838 (mtp) REVERT: G 70 MET cc_start: 0.9081 (mtp) cc_final: 0.8834 (mtp) REVERT: H 70 MET cc_start: 0.9081 (mtp) cc_final: 0.8835 (mtp) REVERT: H 81 PHE cc_start: 0.8198 (t80) cc_final: 0.7927 (m-80) REVERT: I 70 MET cc_start: 0.9087 (mtp) cc_final: 0.8845 (mtp) REVERT: I 81 PHE cc_start: 0.8199 (t80) cc_final: 0.7935 (m-80) REVERT: J 70 MET cc_start: 0.9081 (mtp) cc_final: 0.8834 (mtp) REVERT: J 81 PHE cc_start: 0.8259 (t80) cc_final: 0.7964 (m-80) REVERT: K 70 MET cc_start: 0.9080 (mtp) cc_final: 0.8833 (mtp) REVERT: K 81 PHE cc_start: 0.8221 (t80) cc_final: 0.7949 (m-80) REVERT: L 70 MET cc_start: 0.9086 (mtp) cc_final: 0.8843 (mtp) REVERT: L 81 PHE cc_start: 0.8196 (t80) cc_final: 0.7941 (m-80) REVERT: M 70 MET cc_start: 0.9087 (mtp) cc_final: 0.8844 (mtp) REVERT: M 81 PHE cc_start: 0.8207 (t80) cc_final: 0.7936 (m-80) REVERT: N 70 MET cc_start: 0.9081 (mtp) cc_final: 0.8836 (mtp) REVERT: N 81 PHE cc_start: 0.8201 (t80) cc_final: 0.7934 (m-80) REVERT: O 70 MET cc_start: 0.9081 (mtp) cc_final: 0.8836 (mtp) REVERT: O 81 PHE cc_start: 0.8201 (t80) cc_final: 0.7935 (m-80) REVERT: P 70 MET cc_start: 0.9080 (mtp) cc_final: 0.8832 (mtp) REVERT: P 81 PHE cc_start: 0.8210 (t80) cc_final: 0.7942 (m-80) REVERT: Q 70 MET cc_start: 0.9088 (mtp) cc_final: 0.8841 (mtp) REVERT: Q 81 PHE cc_start: 0.8203 (t80) cc_final: 0.7943 (m-80) REVERT: R 70 MET cc_start: 0.9079 (mtp) cc_final: 0.8832 (mtp) REVERT: R 81 PHE cc_start: 0.8212 (t80) cc_final: 0.7943 (m-80) REVERT: S 70 MET cc_start: 0.9086 (mtp) cc_final: 0.8842 (mtp) REVERT: S 81 PHE cc_start: 0.8206 (t80) cc_final: 0.7936 (m-80) REVERT: T 70 MET cc_start: 0.9082 (mtp) cc_final: 0.8837 (mtp) REVERT: U 70 MET cc_start: 0.9083 (mtp) cc_final: 0.8837 (mtp) REVERT: U 81 PHE cc_start: 0.8208 (t80) cc_final: 0.7937 (m-80) REVERT: V 70 MET cc_start: 0.9081 (mtp) cc_final: 0.8833 (mtp) REVERT: V 81 PHE cc_start: 0.8212 (t80) cc_final: 0.7932 (m-80) REVERT: W 70 MET cc_start: 0.9081 (mtp) cc_final: 0.8838 (mtp) REVERT: X 70 MET cc_start: 0.9084 (mtp) cc_final: 0.8841 (mtp) REVERT: X 81 PHE cc_start: 0.8260 (t80) cc_final: 0.7970 (m-80) outliers start: 0 outliers final: 0 residues processed: 645 average time/residue: 1.0637 time to fit residues: 774.9361 Evaluate side-chains 627 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 627 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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: 1.9990 chunk 385 optimal weight: 5.9990 chunk 358 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 232 optimal weight: 0.7980 chunk 91 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 chunk 366 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3600 r_free = 0.3600 target = 0.148248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.134552 restraints weight = 12313.506| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 0.28 r_work: 0.3329 rms_B_bonded: 0.57 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 1.06 restraints_weight: 0.2500 r_work: 0.2837 rms_B_bonded: 2.93 restraints_weight: 0.1250 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1994 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= 0.160 Angle : 0.565 5.930 46800 Z= 0.315 Chirality : 0.038 0.149 4896 Planarity : 0.003 0.017 6144 Dihedral : 7.504 82.846 4512 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % 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 aren not related in a simple way. whole: 4.85 (0.13), residues: 3936 helix: 3.67 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : 1.09 (0.27), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG W 79 TYR 0.022 0.002 TYR F 39 PHE 0.021 0.004 PHE L 41 TRP 0.006 0.002 TRP F 93 HIS 0.007 0.001 HIS J 128 Details of bonding type rmsd covalent geometry : bond 0.00315 (34704) covalent geometry : angle 0.56475 (46800) hydrogen bonds : bond 0.05619 ( 2664) hydrogen bonds : angle 3.63143 ( 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 631 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 631 time to evaluate : 1.424 Fit side-chains REVERT: A 70 MET cc_start: 0.9090 (mtp) cc_final: 0.8865 (mtp) REVERT: A 81 PHE cc_start: 0.8246 (t80) cc_final: 0.7954 (m-80) REVERT: B 70 MET cc_start: 0.9089 (mtp) cc_final: 0.8866 (mtp) REVERT: B 81 PHE cc_start: 0.8298 (t80) cc_final: 0.7973 (m-80) REVERT: C 70 MET cc_start: 0.9091 (mtp) cc_final: 0.8867 (mtp) REVERT: C 81 PHE cc_start: 0.8238 (t80) cc_final: 0.7949 (m-80) REVERT: D 70 MET cc_start: 0.9096 (mtp) cc_final: 0.8871 (mtp) REVERT: D 81 PHE cc_start: 0.8238 (t80) cc_final: 0.7951 (m-80) REVERT: E 70 MET cc_start: 0.9092 (mtp) cc_final: 0.8867 (mtp) REVERT: E 81 PHE cc_start: 0.8241 (t80) cc_final: 0.7955 (m-80) REVERT: F 70 MET cc_start: 0.9092 (mtp) cc_final: 0.8838 (mtp) REVERT: G 70 MET cc_start: 0.9088 (mtp) cc_final: 0.8834 (mtp) REVERT: H 70 MET cc_start: 0.9088 (mtp) cc_final: 0.8862 (mtp) REVERT: H 81 PHE cc_start: 0.8209 (t80) cc_final: 0.7908 (m-80) REVERT: I 70 MET cc_start: 0.9094 (mtp) cc_final: 0.8873 (mtp) REVERT: I 81 PHE cc_start: 0.8231 (t80) cc_final: 0.7944 (m-80) REVERT: J 70 MET cc_start: 0.9088 (mtp) cc_final: 0.8864 (mtp) REVERT: J 81 PHE cc_start: 0.8260 (t80) cc_final: 0.7958 (m-80) REVERT: K 70 MET cc_start: 0.9088 (mtp) cc_final: 0.8862 (mtp) REVERT: K 81 PHE cc_start: 0.8256 (t80) cc_final: 0.7961 (m-80) REVERT: L 70 MET cc_start: 0.9095 (mtp) cc_final: 0.8873 (mtp) REVERT: L 81 PHE cc_start: 0.8232 (t80) cc_final: 0.7949 (m-80) REVERT: M 70 MET cc_start: 0.9091 (mtp) cc_final: 0.8869 (mtp) REVERT: M 81 PHE cc_start: 0.8242 (t80) cc_final: 0.7942 (m-80) REVERT: N 70 MET cc_start: 0.9091 (mtp) cc_final: 0.8867 (mtp) REVERT: N 81 PHE cc_start: 0.8242 (t80) cc_final: 0.7954 (m-80) REVERT: O 70 MET cc_start: 0.9089 (mtp) cc_final: 0.8864 (mtp) REVERT: O 81 PHE cc_start: 0.8241 (t80) cc_final: 0.7942 (m-80) REVERT: P 70 MET cc_start: 0.9089 (mtp) cc_final: 0.8863 (mtp) REVERT: P 81 PHE cc_start: 0.8246 (t80) cc_final: 0.7952 (m-80) REVERT: Q 70 MET cc_start: 0.9093 (mtp) cc_final: 0.8871 (mtp) REVERT: Q 81 PHE cc_start: 0.8243 (t80) cc_final: 0.7949 (m-80) REVERT: R 70 MET cc_start: 0.9088 (mtp) cc_final: 0.8862 (mtp) REVERT: R 81 PHE cc_start: 0.8248 (t80) cc_final: 0.7955 (m-80) REVERT: S 70 MET cc_start: 0.9092 (mtp) cc_final: 0.8871 (mtp) REVERT: S 81 PHE cc_start: 0.8237 (t80) cc_final: 0.7939 (m-80) REVERT: T 70 MET cc_start: 0.9088 (mtp) cc_final: 0.8833 (mtp) REVERT: U 70 MET cc_start: 0.9093 (mtp) cc_final: 0.8869 (mtp) REVERT: U 81 PHE cc_start: 0.8243 (t80) cc_final: 0.7945 (m-80) REVERT: V 70 MET cc_start: 0.9087 (mtp) cc_final: 0.8862 (mtp) REVERT: V 81 PHE cc_start: 0.8245 (t80) cc_final: 0.7945 (m-80) REVERT: W 70 MET cc_start: 0.9088 (mtp) cc_final: 0.8835 (mtp) REVERT: X 70 MET cc_start: 0.9093 (mtp) cc_final: 0.8872 (mtp) REVERT: X 81 PHE cc_start: 0.8258 (t80) cc_final: 0.7965 (m-80) outliers start: 0 outliers final: 0 residues processed: 631 average time/residue: 1.0715 time to fit residues: 764.4569 Evaluate side-chains 626 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 626 time to evaluate : 1.563 ------------------------------------------------------------------------------- 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: 5.9990 chunk 145 optimal weight: 3.9990 chunk 244 optimal weight: 9.9990 chunk 235 optimal weight: 9.9990 chunk 265 optimal weight: 5.9990 chunk 342 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 chunk 220 optimal weight: 0.9990 chunk 108 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3596 r_free = 0.3596 target = 0.147914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.134260 restraints weight = 12239.080| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 0.28 r_work: 0.3326 rms_B_bonded: 0.57 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 1.06 restraints_weight: 0.2500 r_work: 0.2834 rms_B_bonded: 2.91 restraints_weight: 0.1250 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 34704 Z= 0.173 Angle : 0.582 6.122 46800 Z= 0.325 Chirality : 0.039 0.152 4896 Planarity : 0.003 0.018 6144 Dihedral : 7.541 83.216 4512 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % 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 aren not related in a simple way. whole: 4.76 (0.13), residues: 3936 helix: 3.60 (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 0.004 0.001 ARG W 79 TYR 0.023 0.003 TYR O 39 PHE 0.022 0.004 PHE L 41 TRP 0.006 0.002 TRP F 93 HIS 0.008 0.001 HIS O 128 Details of bonding type rmsd covalent geometry : bond 0.00344 (34704) covalent geometry : angle 0.58151 (46800) hydrogen bonds : bond 0.05718 ( 2664) hydrogen bonds : angle 3.69158 ( 7992) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21129.33 seconds wall clock time: 359 minutes 2.99 seconds (21542.99 seconds total)