Starting phenix.real_space_refine on Tue Aug 26 10:21:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jqc_61727/08_2025/9jqc_61727.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jqc_61727/08_2025/9jqc_61727.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jqc_61727/08_2025/9jqc_61727.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jqc_61727/08_2025/9jqc_61727.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jqc_61727/08_2025/9jqc_61727.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jqc_61727/08_2025/9jqc_61727.map" } resolution = 1.73 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= 0.003 sd= 0.126 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: 6 Type Number sf(0) Gaussians Br 48 7.06 5 Cu 24 5.60 5 S 216 5.16 5 C 21336 2.51 5 N 5880 2.21 5 O 9360 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 36864 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: {'33W:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CU': 1} Classifications: {'undetermined': 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: 3.54, per 1000 atoms: 0.10 Number of scatterers: 36864 At special positions: 0 Unit cell: (132.84, 132.84, 132.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Br 48 34.99 Cu 24 28.99 S 216 16.00 O 9360 8.00 N 5880 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: 4.69 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 953.7 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: 0.62 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 2688 hydrogen bonds defined for protein. 8064 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.40 Time building geometry restraints manager: 4.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.37: 11760 1.37 - 1.51: 9431 1.51 - 1.66: 13105 1.66 - 1.80: 216 1.80 - 1.94: 192 Bond restraints: 34704 Sorted by residual: bond pdb=" C3 33W J 63 " pdb="BR 33W J 63 " ideal model delta sigma weight residual 1.864 1.941 -0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" C3 33W C 63 " pdb="BR 33W C 63 " ideal model delta sigma weight residual 1.864 1.941 -0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" C3 33W T 63 " pdb="BR 33W T 63 " ideal model delta sigma weight residual 1.864 1.941 -0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" C3 33W V 63 " pdb="BR 33W V 63 " ideal model delta sigma weight residual 1.864 1.941 -0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" C3 33W F 63 " pdb="BR 33W F 63 " ideal model delta sigma weight residual 1.864 1.941 -0.077 2.00e-02 2.50e+03 1.48e+01 ... (remaining 34699 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 45696 1.60 - 3.21: 600 3.21 - 4.81: 240 4.81 - 6.42: 96 6.42 - 8.02: 168 Bond angle restraints: 46800 Sorted by residual: angle pdb=" C TRP P 93 " pdb=" N GLU P 94 " pdb=" CA GLU P 94 " ideal model delta sigma weight residual 121.54 127.23 -5.69 1.91e+00 2.74e-01 8.89e+00 angle pdb=" C TRP O 93 " pdb=" N GLU O 94 " pdb=" CA GLU O 94 " ideal model delta sigma weight residual 121.54 127.23 -5.69 1.91e+00 2.74e-01 8.89e+00 angle pdb=" C TRP J 93 " pdb=" N GLU J 94 " pdb=" CA GLU J 94 " ideal model delta sigma weight residual 121.54 127.23 -5.69 1.91e+00 2.74e-01 8.89e+00 angle pdb=" C TRP N 93 " pdb=" N GLU N 94 " pdb=" CA GLU N 94 " ideal model delta sigma weight residual 121.54 127.23 -5.69 1.91e+00 2.74e-01 8.89e+00 angle pdb=" C TRP E 93 " pdb=" N GLU E 94 " pdb=" CA GLU E 94 " ideal model delta sigma weight residual 121.54 127.23 -5.69 1.91e+00 2.74e-01 8.89e+00 ... (remaining 46795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.39: 18696 16.39 - 32.77: 1440 32.77 - 49.15: 360 49.15 - 65.54: 168 65.54 - 81.92: 120 Dihedral angle restraints: 20784 sinusoidal: 8544 harmonic: 12240 Sorted by residual: dihedral pdb=" CA ASP D 171 " pdb=" CB ASP D 171 " pdb=" CG ASP D 171 " pdb=" OD1 ASP D 171 " ideal model delta sinusoidal sigma weight residual -30.00 -78.23 48.23 1 2.00e+01 2.50e-03 8.01e+00 dihedral pdb=" CA ASP G 171 " pdb=" CB ASP G 171 " pdb=" CG ASP G 171 " pdb=" OD1 ASP G 171 " ideal model delta sinusoidal sigma weight residual -30.00 -78.23 48.23 1 2.00e+01 2.50e-03 8.01e+00 dihedral pdb=" CA ASP P 171 " pdb=" CB ASP P 171 " pdb=" CG ASP P 171 " pdb=" OD1 ASP P 171 " ideal model delta sinusoidal sigma weight residual -30.00 -78.23 48.23 1 2.00e+01 2.50e-03 8.01e+00 ... (remaining 20781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 3575 0.033 - 0.066: 936 0.066 - 0.098: 241 0.098 - 0.131: 120 0.131 - 0.164: 24 Chirality restraints: 4896 Sorted by residual: chirality pdb=" CA GLU B 94 " pdb=" N GLU B 94 " pdb=" C GLU B 94 " pdb=" CB GLU B 94 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.72e-01 chirality pdb=" CA GLU M 94 " pdb=" N GLU M 94 " pdb=" C GLU M 94 " pdb=" CB GLU M 94 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.72e-01 chirality pdb=" CA GLU T 94 " pdb=" N GLU T 94 " pdb=" C GLU T 94 " pdb=" CB GLU T 94 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.72e-01 ... (remaining 4893 not shown) Planarity restraints: 6144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR X 32 " 0.039 2.00e-02 2.50e+03 3.30e-02 2.18e+01 pdb=" CG TYR X 32 " -0.080 2.00e-02 2.50e+03 pdb=" CD1 TYR X 32 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR X 32 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR X 32 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR X 32 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR X 32 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR X 32 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR Q 32 " -0.039 2.00e-02 2.50e+03 3.30e-02 2.18e+01 pdb=" CG TYR Q 32 " 0.080 2.00e-02 2.50e+03 pdb=" CD1 TYR Q 32 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR Q 32 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR Q 32 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR Q 32 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR Q 32 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR Q 32 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR S 32 " 0.039 2.00e-02 2.50e+03 3.30e-02 2.18e+01 pdb=" CG TYR S 32 " -0.080 2.00e-02 2.50e+03 pdb=" CD1 TYR S 32 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR S 32 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR S 32 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR S 32 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR S 32 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR S 32 " 0.005 2.00e-02 2.50e+03 ... (remaining 6141 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 2160 2.67 - 3.23: 38401 3.23 - 3.79: 73618 3.79 - 4.34: 97756 4.34 - 4.90: 152690 Nonbonded interactions: 364625 Sorted by model distance: nonbonded pdb=" ND1 HIS L 65 " pdb="CU CU L 201 " model vdw 2.117 2.320 nonbonded pdb=" ND1 HIS E 65 " pdb="CU CU E 201 " model vdw 2.117 2.320 nonbonded pdb=" ND1 HIS F 65 " pdb="CU CU F 201 " model vdw 2.117 2.320 nonbonded pdb=" ND1 HIS K 65 " pdb="CU CU K 201 " model vdw 2.117 2.320 nonbonded pdb=" ND1 HIS G 65 " pdb="CU CU G 201 " model vdw 2.117 2.320 ... (remaining 364620 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: 0.07 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: 5.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.600 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 27.500 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 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 : 0.005 0.077 34704 Z= 0.260 Angle : 0.732 8.019 46800 Z= 0.343 Chirality : 0.037 0.164 4896 Planarity : 0.003 0.033 6144 Dihedral : 15.288 81.923 12864 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 3.87 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: 4.70 (0.14), residues: 3936 helix: 3.53 (0.09), residues: 3096 sheet: None (None), residues: 0 loop : 1.38 (0.28), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 156 TYR 0.080 0.005 TYR H 32 PHE 0.017 0.002 PHE O 41 TRP 0.003 0.001 TRP E 93 HIS 0.006 0.001 HIS L 128 Details of bonding type rmsd covalent geometry : bond 0.00527 (34704) covalent geometry : angle 0.73163 (46800) hydrogen bonds : bond 0.09690 ( 2688) hydrogen bonds : angle 3.88165 ( 8064) *********************** 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 672 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 672 time to evaluate : 0.896 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 672 average time/residue: 0.6812 time to fit residues: 545.9378 Evaluate side-chains 544 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 544 time to evaluate : 1.359 ------------------------------------------------------------------------------- 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: 0.7980 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 8.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS B 60 HIS B 112 GLN C 60 HIS D 60 HIS E 60 HIS F 60 HIS G 60 HIS H 60 HIS I 60 HIS J 60 HIS K 60 HIS L 60 HIS M 60 HIS N 60 HIS O 60 HIS P 60 HIS P 112 GLN Q 60 HIS R 60 HIS R 112 GLN S 60 HIS T 60 HIS U 60 HIS V 60 HIS W 60 HIS X 60 HIS X 112 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.157340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.144875 restraints weight = 9703.162| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 0.33 r_work: 0.3555 rms_B_bonded: 0.34 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 0.62 restraints_weight: 0.2500 r_work: 0.3120 rms_B_bonded: 1.85 restraints_weight: 0.1250 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.0871 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= 0.164 Angle : 0.589 6.013 46800 Z= 0.323 Chirality : 0.037 0.155 4896 Planarity : 0.003 0.022 6144 Dihedral : 9.178 82.921 4512 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % 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: 3.59 (0.08), residues: 3120 sheet: None (None), residues: 0 loop : 1.59 (0.28), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 156 TYR 0.053 0.004 TYR U 32 PHE 0.020 0.002 PHE U 41 TRP 0.003 0.001 TRP G 93 HIS 0.006 0.001 HIS B 128 Details of bonding type rmsd covalent geometry : bond 0.00330 (34704) covalent geometry : angle 0.58902 (46800) hydrogen bonds : bond 0.05420 ( 2688) hydrogen bonds : angle 3.76157 ( 8064) *********************** 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 624 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 624 time to evaluate : 1.108 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 624 average time/residue: 0.8679 time to fit residues: 625.3119 Evaluate side-chains 584 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 584 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 158 optimal weight: 9.9990 chunk 129 optimal weight: 5.9990 chunk 275 optimal weight: 7.9990 chunk 150 optimal weight: 8.9990 chunk 321 optimal weight: 2.9990 chunk 197 optimal weight: 0.9990 chunk 284 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 281 optimal weight: 8.9990 chunk 78 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS B 60 HIS B 112 GLN C 60 HIS D 60 HIS E 60 HIS F 60 HIS G 60 HIS H 60 HIS I 60 HIS I 112 GLN J 60 HIS K 60 HIS L 60 HIS M 60 HIS M 112 GLN N 60 HIS O 60 HIS P 60 HIS P 112 GLN Q 60 HIS R 60 HIS R 112 GLN S 60 HIS T 60 HIS U 60 HIS U 112 GLN V 60 HIS W 60 HIS X 60 HIS X 112 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.156169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.143762 restraints weight = 9442.730| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 0.33 r_work: 0.3539 rms_B_bonded: 0.33 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 0.60 restraints_weight: 0.2500 r_work: 0.3104 rms_B_bonded: 1.82 restraints_weight: 0.1250 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 34704 Z= 0.214 Angle : 0.638 5.835 46800 Z= 0.352 Chirality : 0.039 0.158 4896 Planarity : 0.004 0.022 6144 Dihedral : 9.135 82.567 4512 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % 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: 4.63 (0.13), residues: 3936 helix: 3.40 (0.08), residues: 3120 sheet: None (None), residues: 0 loop : 1.65 (0.28), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K 9 TYR 0.036 0.004 TYR O 32 PHE 0.024 0.003 PHE K 41 TRP 0.004 0.002 TRP Q 93 HIS 0.008 0.002 HIS P 128 Details of bonding type rmsd covalent geometry : bond 0.00447 (34704) covalent geometry : angle 0.63754 (46800) hydrogen bonds : bond 0.05869 ( 2688) hydrogen bonds : angle 3.91472 ( 8064) *********************** 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 624 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 624 time to evaluate : 1.546 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 624 average time/residue: 1.0378 time to fit residues: 745.2652 Evaluate side-chains 576 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 576 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 245 optimal weight: 6.9990 chunk 272 optimal weight: 8.9990 chunk 183 optimal weight: 2.9990 chunk 204 optimal weight: 8.9990 chunk 257 optimal weight: 0.9990 chunk 264 optimal weight: 7.9990 chunk 179 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 344 optimal weight: 0.2980 chunk 337 optimal weight: 3.9990 chunk 165 optimal weight: 6.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS B 60 HIS C 60 HIS D 60 HIS E 60 HIS F 60 HIS G 60 HIS H 60 HIS I 60 HIS J 60 HIS K 60 HIS L 60 HIS M 60 HIS N 60 HIS O 60 HIS P 60 HIS Q 60 HIS R 60 HIS S 60 HIS T 60 HIS U 60 HIS V 60 HIS W 60 HIS X 60 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.156249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.143745 restraints weight = 9506.683| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 0.33 r_work: 0.3541 rms_B_bonded: 0.33 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 0.61 restraints_weight: 0.2500 r_work: 0.3109 rms_B_bonded: 1.81 restraints_weight: 0.1250 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 34704 Z= 0.183 Angle : 0.587 5.620 46800 Z= 0.326 Chirality : 0.037 0.148 4896 Planarity : 0.003 0.018 6144 Dihedral : 9.177 82.869 4512 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % 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: 4.80 (0.13), residues: 3936 helix: 3.54 (0.08), residues: 3120 sheet: None (None), residues: 0 loop : 1.64 (0.28), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 79 TYR 0.024 0.003 TYR L 39 PHE 0.022 0.002 PHE S 41 TRP 0.004 0.002 TRP E 93 HIS 0.007 0.002 HIS E 128 Details of bonding type rmsd covalent geometry : bond 0.00377 (34704) covalent geometry : angle 0.58652 (46800) hydrogen bonds : bond 0.05574 ( 2688) hydrogen bonds : angle 3.85860 ( 8064) *********************** 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 624 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 624 time to evaluate : 1.566 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 624 average time/residue: 0.9644 time to fit residues: 692.8606 Evaluate side-chains 552 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 552 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 44 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 143 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 262 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 190 optimal weight: 4.9990 chunk 182 optimal weight: 4.9990 chunk 277 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 386 optimal weight: 6.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 98 ASN B 60 HIS B 98 ASN C 60 HIS C 98 ASN D 60 HIS D 98 ASN E 60 HIS E 98 ASN F 60 HIS F 98 ASN G 60 HIS G 98 ASN H 60 HIS H 98 ASN I 60 HIS I 98 ASN J 60 HIS J 98 ASN K 60 HIS K 98 ASN L 60 HIS L 98 ASN M 60 HIS M 98 ASN N 60 HIS N 98 ASN O 60 HIS O 98 ASN P 60 HIS P 98 ASN Q 60 HIS Q 98 ASN R 60 HIS R 98 ASN S 60 HIS S 98 ASN T 60 HIS T 98 ASN U 60 HIS V 60 HIS V 98 ASN W 60 HIS W 98 ASN X 60 HIS X 98 ASN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.156106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.143820 restraints weight = 9480.448| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 0.33 r_work: 0.3541 rms_B_bonded: 0.32 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 0.60 restraints_weight: 0.2500 r_work: 0.3110 rms_B_bonded: 1.80 restraints_weight: 0.1250 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 34704 Z= 0.198 Angle : 0.610 5.376 46800 Z= 0.337 Chirality : 0.038 0.146 4896 Planarity : 0.003 0.020 6144 Dihedral : 9.170 82.703 4512 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 1.96 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: 4.69 (0.13), residues: 3936 helix: 3.46 (0.08), residues: 3120 sheet: None (None), residues: 0 loop : 1.60 (0.27), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG W 79 TYR 0.025 0.003 TYR U 39 PHE 0.023 0.003 PHE U 41 TRP 0.004 0.002 TRP R 93 HIS 0.007 0.002 HIS K 128 Details of bonding type rmsd covalent geometry : bond 0.00411 (34704) covalent geometry : angle 0.60963 (46800) hydrogen bonds : bond 0.05710 ( 2688) hydrogen bonds : angle 3.88401 ( 8064) *********************** 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 600 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 600 time to evaluate : 1.411 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 600 average time/residue: 0.9158 time to fit residues: 632.3734 Evaluate side-chains 571 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 571 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 159 optimal weight: 5.9990 chunk 292 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 354 optimal weight: 0.9980 chunk 17 optimal weight: 20.0000 chunk 378 optimal weight: 1.9990 chunk 268 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 85 optimal weight: 20.0000 chunk 291 optimal weight: 0.7980 chunk 312 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 98 ASN B 60 HIS B 98 ASN C 60 HIS C 98 ASN D 60 HIS D 98 ASN E 60 HIS E 98 ASN F 60 HIS F 98 ASN G 60 HIS G 98 ASN H 60 HIS H 98 ASN I 60 HIS I 98 ASN J 60 HIS J 98 ASN K 60 HIS K 98 ASN L 60 HIS L 98 ASN M 60 HIS M 98 ASN N 60 HIS N 98 ASN O 60 HIS O 98 ASN P 60 HIS P 98 ASN Q 60 HIS Q 98 ASN R 60 HIS R 98 ASN S 60 HIS S 98 ASN T 60 HIS T 98 ASN U 60 HIS U 98 ASN V 60 HIS V 98 ASN W 60 HIS W 98 ASN X 60 HIS X 98 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.160454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.148382 restraints weight = 9676.106| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 0.32 r_work: 0.3601 rms_B_bonded: 0.34 restraints_weight: 0.5000 r_work: 0.3485 rms_B_bonded: 0.62 restraints_weight: 0.2500 r_work: 0.3170 rms_B_bonded: 1.88 restraints_weight: 0.1250 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 34704 Z= 0.110 Angle : 0.475 5.511 46800 Z= 0.263 Chirality : 0.035 0.132 4896 Planarity : 0.002 0.019 6144 Dihedral : 9.307 83.586 4512 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 0.66 % Allowed : 6.62 % Favored : 92.72 % 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: 5.52 (0.14), residues: 3936 helix: 4.10 (0.09), residues: 3120 sheet: None (None), residues: 0 loop : 1.65 (0.28), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 79 TYR 0.019 0.002 TYR C 39 PHE 0.012 0.001 PHE J 41 TRP 0.004 0.001 TRP U 93 HIS 0.005 0.001 HIS C 128 Details of bonding type rmsd covalent geometry : bond 0.00209 (34704) covalent geometry : angle 0.47497 (46800) hydrogen bonds : bond 0.04408 ( 2688) hydrogen bonds : angle 3.46874 ( 8064) *********************** 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 696 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 672 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 24 residues processed: 696 average time/residue: 0.8351 time to fit residues: 674.0705 Evaluate side-chains 620 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 596 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain I residue 94 GLU Chi-restraints excluded: chain J residue 94 GLU Chi-restraints excluded: chain K residue 94 GLU Chi-restraints excluded: chain L residue 94 GLU Chi-restraints excluded: chain M residue 94 GLU Chi-restraints excluded: chain N residue 94 GLU Chi-restraints excluded: chain O residue 94 GLU Chi-restraints excluded: chain P residue 94 GLU Chi-restraints excluded: chain Q residue 94 GLU Chi-restraints excluded: chain R residue 94 GLU Chi-restraints excluded: chain S residue 94 GLU Chi-restraints excluded: chain T residue 94 GLU Chi-restraints excluded: chain U residue 94 GLU Chi-restraints excluded: chain V residue 94 GLU Chi-restraints excluded: chain W residue 94 GLU Chi-restraints excluded: chain X residue 94 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 232 optimal weight: 0.7980 chunk 240 optimal weight: 0.3980 chunk 157 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 245 optimal weight: 8.9990 chunk 376 optimal weight: 7.9990 chunk 372 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 368 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS B 60 HIS C 60 HIS D 60 HIS D 112 GLN E 60 HIS F 60 HIS G 60 HIS H 60 HIS I 60 HIS J 60 HIS K 60 HIS L 60 HIS M 60 HIS N 60 HIS O 60 HIS P 60 HIS Q 60 HIS R 60 HIS S 60 HIS T 60 HIS U 60 HIS V 60 HIS W 60 HIS X 60 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.156621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.144454 restraints weight = 9477.747| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 0.32 r_work: 0.3549 rms_B_bonded: 0.32 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 0.59 restraints_weight: 0.2500 r_work: 0.3121 rms_B_bonded: 1.78 restraints_weight: 0.1250 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 34704 Z= 0.194 Angle : 0.606 5.274 46800 Z= 0.335 Chirality : 0.038 0.140 4896 Planarity : 0.003 0.019 6144 Dihedral : 9.152 82.475 4512 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.66 % Allowed : 5.96 % Favored : 93.38 % 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: 4.89 (0.13), residues: 3936 helix: 3.62 (0.08), residues: 3120 sheet: None (None), residues: 0 loop : 1.62 (0.28), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 79 TYR 0.022 0.003 TYR N 39 PHE 0.022 0.003 PHE S 41 TRP 0.005 0.002 TRP U 93 HIS 0.008 0.002 HIS G 128 Details of bonding type rmsd covalent geometry : bond 0.00406 (34704) covalent geometry : angle 0.60560 (46800) hydrogen bonds : bond 0.05622 ( 2688) hydrogen bonds : angle 3.83761 ( 8064) *********************** 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 624 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 600 time to evaluate : 1.505 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 624 average time/residue: 0.9626 time to fit residues: 693.2628 Evaluate side-chains 624 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 624 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 52 optimal weight: 3.9990 chunk 296 optimal weight: 0.9980 chunk 139 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 33 optimal weight: 20.0000 chunk 87 optimal weight: 0.6980 chunk 9 optimal weight: 7.9990 chunk 137 optimal weight: 3.9990 chunk 306 optimal weight: 8.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS B 60 HIS C 60 HIS D 60 HIS E 60 HIS F 60 HIS G 60 HIS H 60 HIS I 60 HIS J 60 HIS K 60 HIS L 60 HIS M 60 HIS N 60 HIS O 60 HIS P 60 HIS Q 60 HIS R 60 HIS S 60 HIS T 60 HIS U 60 HIS V 60 HIS W 60 HIS X 60 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.156933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.144627 restraints weight = 9544.590| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 0.33 r_work: 0.3549 rms_B_bonded: 0.33 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 0.61 restraints_weight: 0.2500 r_work: 0.3120 rms_B_bonded: 1.84 restraints_weight: 0.1250 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 34704 Z= 0.180 Angle : 0.572 4.809 46800 Z= 0.320 Chirality : 0.037 0.136 4896 Planarity : 0.003 0.018 6144 Dihedral : 9.174 82.693 4512 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 3.30 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: 4.91 (0.13), residues: 3936 helix: 3.64 (0.08), residues: 3120 sheet: None (None), residues: 0 loop : 1.56 (0.27), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG T 79 TYR 0.023 0.003 TYR R 39 PHE 0.022 0.002 PHE N 41 TRP 0.006 0.002 TRP E 93 HIS 0.007 0.002 HIS K 128 Details of bonding type rmsd covalent geometry : bond 0.00372 (34704) covalent geometry : angle 0.57207 (46800) hydrogen bonds : bond 0.05519 ( 2688) hydrogen bonds : angle 3.81669 ( 8064) *********************** 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 600 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 600 time to evaluate : 1.163 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 600 average time/residue: 0.9406 time to fit residues: 649.0022 Evaluate side-chains 571 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 571 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 173 optimal weight: 3.9990 chunk 272 optimal weight: 8.9990 chunk 404 optimal weight: 10.0000 chunk 353 optimal weight: 0.9990 chunk 395 optimal weight: 7.9990 chunk 210 optimal weight: 10.0000 chunk 196 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 chunk 403 optimal weight: 4.9990 chunk 248 optimal weight: 0.6980 chunk 149 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 98 ASN B 60 HIS B 98 ASN C 60 HIS C 98 ASN D 60 HIS D 98 ASN E 60 HIS E 98 ASN F 60 HIS F 98 ASN G 60 HIS G 98 ASN H 60 HIS H 98 ASN I 60 HIS I 98 ASN J 60 HIS J 98 ASN K 60 HIS K 98 ASN L 60 HIS L 98 ASN M 60 HIS M 98 ASN N 60 HIS N 98 ASN O 60 HIS O 98 ASN P 60 HIS P 98 ASN Q 60 HIS Q 98 ASN R 60 HIS R 98 ASN S 60 HIS S 98 ASN T 60 HIS T 98 ASN U 60 HIS U 98 ASN V 60 HIS V 98 ASN W 60 HIS W 98 ASN X 60 HIS X 98 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.158994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.146828 restraints weight = 9560.182| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 0.32 r_work: 0.3578 rms_B_bonded: 0.33 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 0.62 restraints_weight: 0.2500 r_work: 0.3147 rms_B_bonded: 1.86 restraints_weight: 0.1250 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1032 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= 0.131 Angle : 0.498 4.899 46800 Z= 0.280 Chirality : 0.036 0.136 4896 Planarity : 0.003 0.019 6144 Dihedral : 9.233 82.873 4512 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % 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: 5.26 (0.13), residues: 3936 helix: 3.90 (0.08), residues: 3120 sheet: None (None), residues: 0 loop : 1.61 (0.27), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 79 TYR 0.021 0.002 TYR A 39 PHE 0.016 0.002 PHE N 41 TRP 0.005 0.001 TRP P 93 HIS 0.005 0.001 HIS S 128 Details of bonding type rmsd covalent geometry : bond 0.00263 (34704) covalent geometry : angle 0.49819 (46800) hydrogen bonds : bond 0.04911 ( 2688) hydrogen bonds : angle 3.61541 ( 8064) *********************** 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 624 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 624 time to evaluate : 1.007 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 624 average time/residue: 0.8752 time to fit residues: 629.7223 Evaluate side-chains 581 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 581 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 311 optimal weight: 10.0000 chunk 387 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 104 optimal weight: 1.9990 chunk 226 optimal weight: 9.9990 chunk 224 optimal weight: 0.7980 chunk 245 optimal weight: 6.9990 chunk 405 optimal weight: 10.0000 chunk 270 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 359 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS B 60 HIS C 60 HIS D 60 HIS E 60 HIS F 60 HIS G 60 HIS H 60 HIS I 60 HIS J 60 HIS K 60 HIS L 60 HIS M 60 HIS N 60 HIS O 60 HIS P 60 HIS Q 60 HIS R 60 HIS S 60 HIS T 60 HIS U 60 HIS V 60 HIS W 60 HIS X 60 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.158639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.146308 restraints weight = 9526.027| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 0.32 r_work: 0.3572 rms_B_bonded: 0.33 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 0.62 restraints_weight: 0.2500 r_work: 0.3139 rms_B_bonded: 1.86 restraints_weight: 0.1250 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.1030 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= 0.154 Angle : 0.584 6.742 46800 Z= 0.320 Chirality : 0.037 0.133 4896 Planarity : 0.003 0.019 6144 Dihedral : 9.186 82.559 4512 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 2.79 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: 5.05 (0.13), residues: 3936 helix: 3.75 (0.08), residues: 3120 sheet: None (None), residues: 0 loop : 1.57 (0.27), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 79 TYR 0.023 0.002 TYR M 39 PHE 0.025 0.002 PHE U 41 TRP 0.006 0.002 TRP P 93 HIS 0.006 0.002 HIS F 128 Details of bonding type rmsd covalent geometry : bond 0.00319 (34704) covalent geometry : angle 0.58445 (46800) hydrogen bonds : bond 0.05239 ( 2688) hydrogen bonds : angle 3.69920 ( 8064) ********************** 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 624 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 624 time to evaluate : 1.360 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 624 average time/residue: 0.8961 time to fit residues: 645.5828 Evaluate side-chains 617 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 617 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 172 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 253 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 387 optimal weight: 9.9990 chunk 320 optimal weight: 10.0000 chunk 127 optimal weight: 20.0000 chunk 248 optimal weight: 0.6980 chunk 395 optimal weight: 10.0000 chunk 323 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 C 60 HIS C 112 GLN D 60 HIS 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 J 60 HIS J 112 GLN K 60 HIS K 112 GLN L 60 HIS L 112 GLN M 60 HIS N 60 HIS N 112 GLN O 60 HIS O 112 GLN P 60 HIS Q 60 HIS Q 112 GLN R 60 HIS S 60 HIS S 112 GLN T 60 HIS T 112 GLN U 60 HIS V 60 HIS V 112 GLN W 60 HIS W 112 GLN X 60 HIS Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.159004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.146922 restraints weight = 9393.235| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 0.32 r_work: 0.3579 rms_B_bonded: 0.33 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 0.60 restraints_weight: 0.2500 r_work: 0.3151 rms_B_bonded: 1.82 restraints_weight: 0.1250 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 34704 Z= 0.140 Angle : 0.519 4.793 46800 Z= 0.292 Chirality : 0.036 0.135 4896 Planarity : 0.003 0.019 6144 Dihedral : 9.217 82.638 4512 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % 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: 5.14 (0.13), residues: 3936 helix: 3.80 (0.08), residues: 3120 sheet: None (None), residues: 0 loop : 1.66 (0.27), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG S 79 TYR 0.022 0.002 TYR K 39 PHE 0.018 0.002 PHE A 41 TRP 0.005 0.002 TRP W 93 HIS 0.006 0.002 HIS N 128 Details of bonding type rmsd covalent geometry : bond 0.00282 (34704) covalent geometry : angle 0.51905 (46800) hydrogen bonds : bond 0.05063 ( 2688) hydrogen bonds : angle 3.66119 ( 8064) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19710.82 seconds wall clock time: 335 minutes 58.72 seconds (20158.72 seconds total)