Starting phenix.real_space_refine on Mon Jul 6 13:36:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jqc_61727/07_2026/9jqc_61727.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jqc_61727/07_2026/9jqc_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_61727/07_2026/9jqc_61727.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jqc_61727/07_2026/9jqc_61727.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jqc_61727/07_2026/9jqc_61727.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jqc_61727/07_2026/9jqc_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-dev-6108/lib/python3.11/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, 0 Ad-hoc single atom residues: {' CU': 1} Chain breaks: 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: 4.35, per 1000 atoms: 0.12 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: 2.82 Conformation dependent library (CDL) restraints added in 1.3 seconds 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7920 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 79.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 13 through 42 Processing helix chain 'A' and resid 48 through 76 Processing helix chain 'A' and resid 95 through 124 Processing helix chain 'A' and resid 126 through 137 Processing helix chain 'A' and resid 137 through 159 Processing helix chain 'A' and resid 163 through 174 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: 7.67 Time building geometry restraints manager: 3.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.37: 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 3.060 nonbonded pdb=" ND1 HIS E 65 " pdb="CU CU E 201 " model vdw 2.117 3.060 nonbonded pdb=" ND1 HIS F 65 " pdb="CU CU F 201 " model vdw 2.117 3.060 nonbonded pdb=" ND1 HIS K 65 " pdb="CU CU K 201 " model vdw 2.117 3.060 nonbonded pdb=" ND1 HIS G 65 " pdb="CU CU G 201 " model vdw 2.117 3.060 ... (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: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.780 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 29.320 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 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 are 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/Z covalent geometry : bond 0.00527 / 0.26 (34704) covalent geometry : angle 0.73163 / 0.34 (46800) hydrogen bonds : bond 0.09690 / 6.57 ( 2688) hydrogen bonds : angle 3.88165 / 2.80 ( 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 : 1.502 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 672 average time/residue: 0.7498 time to fit residues: 604.1423 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 : 1.397 ------------------------------------------------------------------------------- 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: 8.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 9.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3833 r_free = 0.3833 target = 0.160189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.147531 restraints weight = 9472.067| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 0.32 r_work: 0.3589 rms_B_bonded: 0.33 restraints_weight: 0.5000 r_work: 0.3473 rms_B_bonded: 0.61 restraints_weight: 0.2500 r_work: 0.3157 rms_B_bonded: 1.84 restraints_weight: 0.1250 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.0948 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= 0.137 Angle : 0.546 6.001 46800 Z= 0.300 Chirality : 0.036 0.148 4896 Planarity : 0.003 0.020 6144 Dihedral : 9.222 83.291 4512 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.15 (0.13), residues: 3936 helix: 3.83 (0.09), residues: 3120 sheet: None (None), residues: 0 loop : 1.54 (0.28), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 156 TYR 0.049 0.003 TYR S 32 PHE 0.016 0.002 PHE S 41 TRP 0.003 0.001 TRP C 93 HIS 0.005 0.001 HIS I 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.14 (34704) covalent geometry : angle 0.54556 / 0.30 (46800) hydrogen bonds : bond 0.05042 / 3.39 ( 2688) hydrogen bonds : angle 3.61896 / 2.60 ( 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 : 0.970 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 624 average time/residue: 0.8935 time to fit residues: 647.1092 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 : 1.524 ------------------------------------------------------------------------------- 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: 10.0000 chunk 129 optimal weight: 5.9990 chunk 275 optimal weight: 3.9990 chunk 150 optimal weight: 10.0000 chunk 321 optimal weight: 6.9990 chunk 197 optimal weight: 0.6980 chunk 284 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 281 optimal weight: 9.9990 chunk 78 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 HIS B 60 HIS B 112 GLN C 60 HIS D 60 HIS E 60 HIS F 60 HIS G 60 HIS G 112 GLN H 60 HIS I 60 HIS J 60 HIS K 60 HIS L 60 HIS M 60 HIS N 60 HIS O 60 HIS O 112 GLN 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 Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.157143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.144677 restraints weight = 9038.081| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 0.31 r_work: 0.3553 rms_B_bonded: 0.31 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 0.58 restraints_weight: 0.2500 r_work: 0.3122 rms_B_bonded: 1.75 restraints_weight: 0.1250 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.0997 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= 0.214 Angle : 0.637 6.030 46800 Z= 0.351 Chirality : 0.039 0.157 4896 Planarity : 0.004 0.020 6144 Dihedral : 9.144 82.594 4512 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.55 % Allowed : 4.75 % 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 are not related in a simple way. whole: 4.73 (0.13), residues: 3936 helix: 3.47 (0.09), residues: 3120 sheet: None (None), residues: 0 loop : 1.70 (0.28), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 9 TYR 0.040 0.004 TYR Q 32 PHE 0.024 0.003 PHE D 41 TRP 0.004 0.002 TRP E 93 HIS 0.008 0.002 HIS V 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.21 (34704) covalent geometry : angle 0.63711 / 0.35 (46800) hydrogen bonds : bond 0.05840 / 3.93 ( 2688) hydrogen bonds : angle 3.89207 / 2.80 ( 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 644 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 624 time to evaluate : 1.536 Fit side-chains outliers start: 20 outliers final: 0 residues processed: 624 average time/residue: 0.9409 time to fit residues: 680.6823 Evaluate side-chains 558 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 558 time to evaluate : 1.115 ------------------------------------------------------------------------------- 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: 0.8980 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: 7.9990 chunk 337 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3792 r_free = 0.3792 target = 0.156710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.144073 restraints weight = 9056.677| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 0.31 r_work: 0.3545 rms_B_bonded: 0.31 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 0.58 restraints_weight: 0.2500 r_work: 0.3116 rms_B_bonded: 1.74 restraints_weight: 0.1250 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.0924 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= 0.211 Angle : 0.622 5.466 46800 Z= 0.345 Chirality : 0.038 0.152 4896 Planarity : 0.004 0.022 6144 Dihedral : 9.153 82.816 4512 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.70 (0.13), residues: 3936 helix: 3.46 (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 0.003 0.001 ARG O 9 TYR 0.025 0.003 TYR L 39 PHE 0.024 0.003 PHE K 41 TRP 0.005 0.002 TRP J 93 HIS 0.008 0.002 HIS M 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.21 (34704) covalent geometry : angle 0.62221 / 0.34 (46800) hydrogen bonds : bond 0.05819 / 3.92 ( 2688) hydrogen bonds : angle 3.92631 / 2.82 ( 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 606 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 606 time to evaluate : 1.474 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 606 average time/residue: 0.9244 time to fit residues: 647.6300 Evaluate side-chains 554 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 554 time to evaluate : 1.589 ------------------------------------------------------------------------------- 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: 0.9990 chunk 13 optimal weight: 0.8980 chunk 143 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 262 optimal weight: 5.9990 chunk 155 optimal weight: 0.9980 chunk 190 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 277 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 386 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 HIS A 98 ASN B 60 HIS B 98 ASN C 60 HIS C 98 ASN D 60 HIS 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 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 W 60 HIS W 98 ASN X 60 HIS X 98 ASN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.159224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.146783 restraints weight = 9217.458| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 0.31 r_work: 0.3585 rms_B_bonded: 0.32 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 0.59 restraints_weight: 0.2500 r_work: 0.3155 rms_B_bonded: 1.79 restraints_weight: 0.1250 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 34704 Z= 0.145 Angle : 0.528 5.554 46800 Z= 0.294 Chirality : 0.036 0.135 4896 Planarity : 0.003 0.018 6144 Dihedral : 9.234 83.103 4512 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 1.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.66 % Allowed : 5.85 % 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 are not related in a simple way. whole: 5.21 (0.14), residues: 3936 helix: 3.85 (0.09), residues: 3120 sheet: None (None), residues: 0 loop : 1.66 (0.28), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG D 79 TYR 0.022 0.002 TYR J 39 PHE 0.017 0.002 PHE L 41 TRP 0.004 0.001 TRP T 93 HIS 0.006 0.001 HIS E 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (34704) covalent geometry : angle 0.52783 / 0.29 (46800) hydrogen bonds : bond 0.05069 / 3.41 ( 2688) hydrogen bonds : angle 3.66586 / 2.64 ( 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 630 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 606 time to evaluate : 1.556 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 630 average time/residue: 1.0207 time to fit residues: 741.3336 Evaluate side-chains 556 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 556 time to evaluate : 1.499 ------------------------------------------------------------------------------- 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: 9.9990 chunk 11 optimal weight: 5.9990 chunk 354 optimal weight: 0.7980 chunk 17 optimal weight: 20.0000 chunk 378 optimal weight: 7.9990 chunk 268 optimal weight: 0.9980 chunk 112 optimal weight: 5.9990 chunk 85 optimal weight: 20.0000 chunk 291 optimal weight: 7.9990 chunk 312 optimal weight: 6.9990 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3791 r_free = 0.3791 target = 0.157078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.144583 restraints weight = 9057.519| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 0.31 r_work: 0.3548 rms_B_bonded: 0.31 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 0.58 restraints_weight: 0.2500 r_work: 0.3121 rms_B_bonded: 1.76 restraints_weight: 0.1250 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 34704 Z= 0.221 Angle : 0.630 5.056 46800 Z= 0.349 Chirality : 0.038 0.137 4896 Planarity : 0.004 0.022 6144 Dihedral : 9.143 82.590 4512 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % 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 are not related in a simple way. whole: 4.78 (0.13), residues: 3936 helix: 3.54 (0.08), residues: 3120 sheet: None (None), residues: 0 loop : 1.53 (0.27), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG V 79 TYR 0.025 0.003 TYR B 39 PHE 0.025 0.003 PHE U 41 TRP 0.006 0.002 TRP Q 93 HIS 0.008 0.002 HIS B 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.22 (34704) covalent geometry : angle 0.62987 / 0.35 (46800) hydrogen bonds : bond 0.05847 / 3.94 ( 2688) hydrogen bonds : angle 3.91068 / 2.81 ( 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 604 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 604 time to evaluate : 1.488 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 604 average time/residue: 0.9841 time to fit residues: 686.8481 Evaluate side-chains 589 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 589 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 232 optimal weight: 0.4980 chunk 240 optimal weight: 0.9990 chunk 157 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 245 optimal weight: 6.9990 chunk 376 optimal weight: 0.7980 chunk 372 optimal weight: 0.8980 chunk 107 optimal weight: 9.9990 chunk 368 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 HIS A 98 ASN B 60 HIS B 98 ASN C 60 HIS C 98 ASN D 60 HIS 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 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 W 60 HIS W 98 ASN X 60 HIS X 98 ASN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.163227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.150652 restraints weight = 9614.208| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 0.31 r_work: 0.3625 rms_B_bonded: 0.34 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 0.62 restraints_weight: 0.2500 r_work: 0.3200 rms_B_bonded: 1.89 restraints_weight: 0.1250 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.1268 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= 0.111 Angle : 0.459 5.144 46800 Z= 0.257 Chirality : 0.034 0.133 4896 Planarity : 0.002 0.019 6144 Dihedral : 9.305 83.634 4512 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.54 (0.13), residues: 3936 helix: 4.11 (0.08), residues: 3120 sheet: None (None), residues: 0 loop : 1.69 (0.28), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 79 TYR 0.019 0.002 TYR D 39 PHE 0.012 0.001 PHE V 41 TRP 0.004 0.001 TRP D 93 HIS 0.004 0.001 HIS K 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.11 (34704) covalent geometry : angle 0.45903 / 0.26 (46800) hydrogen bonds : bond 0.04332 / 2.91 ( 2688) hydrogen bonds : angle 3.43470 / 2.47 ( 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: 0 poor density : 624 time to evaluate : 1.616 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 624 average time/residue: 0.9726 time to fit residues: 704.3743 Evaluate side-chains 600 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 600 time to evaluate : 1.538 ------------------------------------------------------------------------------- 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: 5.9990 chunk 296 optimal weight: 4.9990 chunk 139 optimal weight: 0.3980 chunk 86 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 87 optimal weight: 0.6980 chunk 9 optimal weight: 7.9990 chunk 137 optimal weight: 3.9990 chunk 306 optimal weight: 10.0000 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 I 112 GLN 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 X 112 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.158886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.146405 restraints weight = 8956.889| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 0.31 r_work: 0.3571 rms_B_bonded: 0.32 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 0.58 restraints_weight: 0.2500 r_work: 0.3142 rms_B_bonded: 1.78 restraints_weight: 0.1250 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 34704 Z= 0.171 Angle : 0.563 4.725 46800 Z= 0.313 Chirality : 0.037 0.130 4896 Planarity : 0.003 0.018 6144 Dihedral : 9.168 82.558 4512 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.06 (0.13), residues: 3936 helix: 3.75 (0.08), residues: 3120 sheet: None (None), residues: 0 loop : 1.59 (0.27), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 79 TYR 0.021 0.003 TYR D 39 PHE 0.022 0.002 PHE K 41 TRP 0.005 0.002 TRP V 93 HIS 0.007 0.002 HIS L 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 (34704) covalent geometry : angle 0.56268 / 0.31 (46800) hydrogen bonds : bond 0.05396 / 3.63 ( 2688) hydrogen bonds : angle 3.74016 / 2.69 ( 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 619 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 619 time to evaluate : 1.537 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 619 average time/residue: 0.9822 time to fit residues: 703.6691 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 : 1.464 ------------------------------------------------------------------------------- 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: 0.9980 chunk 395 optimal weight: 5.9990 chunk 210 optimal weight: 2.9990 chunk 196 optimal weight: 10.0000 chunk 97 optimal weight: 0.9980 chunk 403 optimal weight: 6.9990 chunk 248 optimal weight: 0.8980 chunk 149 optimal weight: 0.8980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 HIS A 112 GLN B 60 HIS C 60 HIS C 112 GLN D 60 HIS D 112 GLN E 60 HIS F 60 HIS G 60 HIS 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 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: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.160765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.148127 restraints weight = 9307.966| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 0.31 r_work: 0.3594 rms_B_bonded: 0.33 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 0.60 restraints_weight: 0.2500 r_work: 0.3169 rms_B_bonded: 1.83 restraints_weight: 0.1250 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 34704 Z= 0.130 Angle : 0.502 4.947 46800 Z= 0.281 Chirality : 0.035 0.134 4896 Planarity : 0.003 0.019 6144 Dihedral : 9.245 82.952 4512 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 0.00 % Allowed : 6.62 % 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 are not related in a simple way. whole: 5.37 (0.13), residues: 3936 helix: 4.01 (0.08), residues: 3120 sheet: None (None), residues: 0 loop : 1.53 (0.27), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG V 79 TYR 0.020 0.002 TYR E 39 PHE 0.016 0.002 PHE F 41 TRP 0.004 0.001 TRP P 93 HIS 0.005 0.001 HIS R 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.13 (34704) covalent geometry : angle 0.50226 / 0.28 (46800) hydrogen bonds : bond 0.04813 / 3.24 ( 2688) hydrogen bonds : angle 3.56139 / 2.56 ( 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 619 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 619 time to evaluate : 1.493 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 619 average time/residue: 0.9374 time to fit residues: 672.0318 Evaluate side-chains 612 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 612 time to evaluate : 1.434 ------------------------------------------------------------------------------- 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: 5.9990 chunk 387 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 226 optimal weight: 5.9990 chunk 224 optimal weight: 0.9990 chunk 245 optimal weight: 7.9990 chunk 405 optimal weight: 10.0000 chunk 270 optimal weight: 6.9990 chunk 11 optimal weight: 0.5980 chunk 359 optimal weight: 9.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 60 HIS B 60 HIS C 60 HIS D 60 HIS E 60 HIS E 112 GLN 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 = 0.3818 r_free = 0.3818 target = 0.159251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.146763 restraints weight = 9009.603| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 0.31 r_work: 0.3577 rms_B_bonded: 0.32 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 0.59 restraints_weight: 0.2500 r_work: 0.3148 rms_B_bonded: 1.79 restraints_weight: 0.1250 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 34704 Z= 0.163 Angle : 0.556 4.898 46800 Z= 0.311 Chirality : 0.037 0.131 4896 Planarity : 0.003 0.019 6144 Dihedral : 9.172 82.548 4512 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.00 % Allowed : 6.62 % 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 are not related in a simple way. whole: 5.01 (0.13), residues: 3936 helix: 3.72 (0.08), residues: 3120 sheet: None (None), residues: 0 loop : 1.58 (0.27), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG N 79 TYR 0.021 0.002 TYR E 39 PHE 0.020 0.002 PHE C 41 TRP 0.005 0.002 TRP V 93 HIS 0.006 0.002 HIS H 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (34704) covalent geometry : angle 0.55626 / 0.31 (46800) hydrogen bonds : bond 0.05312 / 3.57 ( 2688) hydrogen bonds : angle 3.71625 / 2.67 ( 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 612 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 612 time to evaluate : 1.595 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 612 average time/residue: 0.8921 time to fit residues: 633.3222 Evaluate side-chains 604 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 604 time to evaluate : 1.489 ------------------------------------------------------------------------------- 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: 2.9990 chunk 175 optimal weight: 2.9990 chunk 253 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 387 optimal weight: 9.9990 chunk 320 optimal weight: 4.9990 chunk 127 optimal weight: 20.0000 chunk 248 optimal weight: 0.9980 chunk 395 optimal weight: 0.9990 chunk 323 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3810 r_free = 0.3810 target = 0.158667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.146168 restraints weight = 9042.833| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 0.31 r_work: 0.3568 rms_B_bonded: 0.32 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 0.59 restraints_weight: 0.2500 r_work: 0.3144 rms_B_bonded: 1.78 restraints_weight: 0.1250 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.1085 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= 0.167 Angle : 0.577 6.574 46800 Z= 0.321 Chirality : 0.037 0.133 4896 Planarity : 0.003 0.019 6144 Dihedral : 9.194 82.649 4512 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.00 % Allowed : 6.62 % 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 are not related in a simple way. whole: 5.02 (0.13), residues: 3936 helix: 3.73 (0.08), residues: 3120 sheet: None (None), residues: 0 loop : 1.52 (0.27), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG J 79 TYR 0.022 0.002 TYR D 39 PHE 0.020 0.002 PHE K 41 TRP 0.005 0.002 TRP V 93 HIS 0.006 0.002 HIS U 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.17 (34704) covalent geometry : angle 0.57743 / 0.32 (46800) hydrogen bonds : bond 0.05318 / 3.58 ( 2688) hydrogen bonds : angle 3.74708 / 2.69 ( 8064) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20186.44 seconds wall clock time: 344 minutes 15.11 seconds (20655.11 seconds total)