Starting phenix.real_space_refine on Mon Jul 6 14:32:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jqb_61726/07_2026/9jqb_61726.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jqb_61726/07_2026/9jqb_61726.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jqb_61726/07_2026/9jqb_61726.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jqb_61726/07_2026/9jqb_61726.map" model { file = "/net/cci-nas-00/data/ceres_data/9jqb_61726/07_2026/9jqb_61726.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jqb_61726/07_2026/9jqb_61726.cif" } resolution = 1.78 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= 0.002 sd= 0.147 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 S 216 5.16 5 Na 24 4.78 5 C 21336 2.51 5 N 5880 2.21 5 O 9912 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: 37416 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: {' NA': 1} Chain breaks: 1 Chain: "A" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 143 Classifications: {'water': 143} Link IDs: {None: 142} Chain: "B" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 143 Classifications: {'water': 143} Link IDs: {None: 142} Chain: "C" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 143 Classifications: {'water': 143} Link IDs: {None: 142} Chain: "D" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 143 Classifications: {'water': 143} Link IDs: {None: 142} Chain: "E" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 143 Classifications: {'water': 143} Link IDs: {None: 142} Chain: "F" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 143 Classifications: {'water': 143} Link IDs: {None: 142} Chain: "G" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 143 Classifications: {'water': 143} Link IDs: {None: 142} Chain: "H" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 143 Classifications: {'water': 143} Link IDs: {None: 142} Chain: "I" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 143 Classifications: {'water': 143} Link IDs: {None: 142} Chain: "J" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 143 Classifications: {'water': 143} Link IDs: {None: 142} Chain: "K" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 143 Classifications: {'water': 143} Link IDs: {None: 142} Chain: "L" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 143 Classifications: {'water': 143} Link IDs: {None: 142} Chain: "M" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 143 Classifications: {'water': 143} Link IDs: {None: 142} Chain: "N" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 143 Classifications: {'water': 143} Link IDs: {None: 142} Chain: "O" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 143 Classifications: {'water': 143} Link IDs: {None: 142} Chain: "P" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 143 Classifications: {'water': 143} Link IDs: {None: 142} Chain: "Q" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 143 Classifications: {'water': 143} Link IDs: {None: 142} Chain: "R" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 143 Classifications: {'water': 143} Link IDs: {None: 142} Chain: "S" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 143 Classifications: {'water': 143} Link IDs: {None: 142} Chain: "T" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 143 Classifications: {'water': 143} Link IDs: {None: 142} Chain: "U" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 143 Classifications: {'water': 143} Link IDs: {None: 142} Chain: "V" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 143 Classifications: {'water': 143} Link IDs: {None: 142} Chain: "W" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 143 Classifications: {'water': 143} Link IDs: {None: 142} Chain: "X" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 143 Classifications: {'water': 143} Link IDs: {None: 142} 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: 4.84, per 1000 atoms: 0.13 Number of scatterers: 37416 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 S 216 16.00 Na 24 11.00 O 9912 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: 3.42 Conformation dependent library (CDL) restraints added in 1.5 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: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 13 through 42 Processing helix chain 'A' and resid 48 through 76 Processing helix chain 'A' and resid 95 through 124 Processing helix chain 'A' and resid 126 through 137 Processing helix chain 'A' and resid 137 through 159 Processing helix chain 'A' and resid 163 through 174 removed outlier: 3.592A pdb=" N GLU A 167 " --> pdb=" O SER A 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 42 Processing helix chain 'B' and resid 48 through 76 Processing helix chain 'B' and resid 95 through 124 Processing helix chain 'B' and resid 126 through 137 Processing helix chain 'B' and resid 137 through 159 Processing helix chain 'B' and resid 163 through 174 removed outlier: 3.592A pdb=" N GLU B 167 " --> pdb=" O SER B 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 42 Processing helix chain 'C' and resid 48 through 76 Processing helix chain 'C' and resid 95 through 124 Processing helix chain 'C' and resid 126 through 137 Processing helix chain 'C' and resid 137 through 159 Processing helix chain 'C' and resid 163 through 174 removed outlier: 3.592A pdb=" N GLU C 167 " --> pdb=" O SER C 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 42 Processing helix chain 'D' and resid 48 through 76 Processing helix chain 'D' and resid 95 through 124 Processing helix chain 'D' and resid 126 through 137 Processing helix chain 'D' and resid 137 through 159 Processing helix chain 'D' and resid 163 through 174 removed outlier: 3.592A pdb=" N GLU D 167 " --> pdb=" O SER D 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 42 Processing helix chain 'E' and resid 48 through 76 Processing helix chain 'E' and resid 95 through 124 Processing helix chain 'E' and resid 126 through 137 Processing helix chain 'E' and resid 137 through 159 Processing helix chain 'E' and resid 163 through 174 removed outlier: 3.592A pdb=" N GLU E 167 " --> pdb=" O SER E 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 42 Processing helix chain 'F' and resid 48 through 76 Processing helix chain 'F' and resid 95 through 124 Processing helix chain 'F' and resid 126 through 137 Processing helix chain 'F' and resid 137 through 159 Processing helix chain 'F' and resid 163 through 174 removed outlier: 3.592A pdb=" N GLU F 167 " --> pdb=" O SER F 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 42 Processing helix chain 'G' and resid 48 through 76 Processing helix chain 'G' and resid 95 through 124 Processing helix chain 'G' and resid 126 through 137 Processing helix chain 'G' and resid 137 through 159 Processing helix chain 'G' and resid 163 through 174 removed outlier: 3.592A pdb=" N GLU G 167 " --> pdb=" O SER G 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 42 Processing helix chain 'H' and resid 48 through 76 Processing helix chain 'H' and resid 95 through 124 Processing helix chain 'H' and resid 126 through 137 Processing helix chain 'H' and resid 137 through 159 Processing helix chain 'H' and resid 163 through 174 removed outlier: 3.592A pdb=" N GLU H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 42 Processing helix chain 'I' and resid 48 through 76 Processing helix chain 'I' and resid 95 through 124 Processing helix chain 'I' and resid 126 through 137 Processing helix chain 'I' and resid 137 through 159 Processing helix chain 'I' and resid 163 through 174 removed outlier: 3.592A pdb=" N GLU I 167 " --> pdb=" O SER I 163 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 42 Processing helix chain 'J' and resid 48 through 76 Processing helix chain 'J' and resid 95 through 124 Processing helix chain 'J' and resid 126 through 137 Processing helix chain 'J' and resid 137 through 159 Processing helix chain 'J' and resid 163 through 174 removed outlier: 3.592A pdb=" N GLU J 167 " --> pdb=" O SER J 163 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 42 Processing helix chain 'K' and resid 48 through 76 Processing helix chain 'K' and resid 95 through 124 Processing helix chain 'K' and resid 126 through 137 Processing helix chain 'K' and resid 137 through 159 Processing helix chain 'K' and resid 163 through 174 removed outlier: 3.592A pdb=" N GLU K 167 " --> pdb=" O SER K 163 " (cutoff:3.500A) Processing helix chain 'L' and resid 13 through 42 Processing helix chain 'L' and resid 48 through 76 Processing helix chain 'L' and resid 95 through 124 Processing helix chain 'L' and resid 126 through 137 Processing helix chain 'L' and resid 137 through 159 Processing helix chain 'L' and resid 163 through 174 removed outlier: 3.592A pdb=" N GLU L 167 " --> pdb=" O SER L 163 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 42 Processing helix chain 'M' and resid 48 through 76 Processing helix chain 'M' and resid 95 through 124 Processing helix chain 'M' and resid 126 through 137 Processing helix chain 'M' and resid 137 through 159 Processing helix chain 'M' and resid 163 through 174 removed outlier: 3.592A pdb=" N GLU M 167 " --> pdb=" O SER M 163 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 42 Processing helix chain 'N' and resid 48 through 76 Processing helix chain 'N' and resid 95 through 124 Processing helix chain 'N' and resid 126 through 137 Processing helix chain 'N' and resid 137 through 159 Processing helix chain 'N' and resid 163 through 174 removed outlier: 3.592A pdb=" N GLU N 167 " --> pdb=" O SER N 163 " (cutoff:3.500A) Processing helix chain 'O' and resid 13 through 42 Processing helix chain 'O' and resid 48 through 76 Processing helix chain 'O' and resid 95 through 124 Processing helix chain 'O' and resid 126 through 137 Processing helix chain 'O' and resid 137 through 159 Processing helix chain 'O' and resid 163 through 174 removed outlier: 3.592A pdb=" N GLU O 167 " --> pdb=" O SER O 163 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 42 Processing helix chain 'P' and resid 48 through 76 Processing helix chain 'P' and resid 95 through 124 Processing helix chain 'P' and resid 126 through 137 Processing helix chain 'P' and resid 137 through 159 Processing helix chain 'P' and resid 163 through 174 removed outlier: 3.592A pdb=" N GLU P 167 " --> pdb=" O SER P 163 " (cutoff:3.500A) Processing helix chain 'Q' and resid 13 through 42 Processing helix chain 'Q' and resid 48 through 76 Processing helix chain 'Q' and resid 95 through 124 Processing helix chain 'Q' and resid 126 through 137 Processing helix chain 'Q' and resid 137 through 159 Processing helix chain 'Q' and resid 163 through 174 removed outlier: 3.592A pdb=" N GLU Q 167 " --> pdb=" O SER Q 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 13 through 42 Processing helix chain 'R' and resid 48 through 76 Processing helix chain 'R' and resid 95 through 124 Processing helix chain 'R' and resid 126 through 137 Processing helix chain 'R' and resid 137 through 159 Processing helix chain 'R' and resid 163 through 174 removed outlier: 3.592A pdb=" N GLU R 167 " --> pdb=" O SER R 163 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 42 Processing helix chain 'S' and resid 48 through 76 Processing helix chain 'S' and resid 95 through 124 Processing helix chain 'S' and resid 126 through 137 Processing helix chain 'S' and resid 137 through 159 Processing helix chain 'S' and resid 163 through 174 removed outlier: 3.592A pdb=" N GLU S 167 " --> pdb=" O SER S 163 " (cutoff:3.500A) Processing helix chain 'T' and resid 13 through 42 Processing helix chain 'T' and resid 48 through 76 Processing helix chain 'T' and resid 95 through 124 Processing helix chain 'T' and resid 126 through 137 Processing helix chain 'T' and resid 137 through 159 Processing helix chain 'T' and resid 163 through 174 removed outlier: 3.592A pdb=" N GLU T 167 " --> pdb=" O SER T 163 " (cutoff:3.500A) Processing helix chain 'U' and resid 13 through 42 Processing helix chain 'U' and resid 48 through 76 Processing helix chain 'U' and resid 95 through 124 Processing helix chain 'U' and resid 126 through 137 Processing helix chain 'U' and resid 137 through 159 Processing helix chain 'U' and resid 163 through 174 removed outlier: 3.592A pdb=" N GLU U 167 " --> pdb=" O SER U 163 " (cutoff:3.500A) Processing helix chain 'V' and resid 13 through 42 Processing helix chain 'V' and resid 48 through 76 Processing helix chain 'V' and resid 95 through 124 Processing helix chain 'V' and resid 126 through 137 Processing helix chain 'V' and resid 137 through 159 Processing helix chain 'V' and resid 163 through 174 removed outlier: 3.592A pdb=" N GLU V 167 " --> pdb=" O SER V 163 " (cutoff:3.500A) Processing helix chain 'W' and resid 13 through 42 Processing helix chain 'W' and resid 48 through 76 Processing helix chain 'W' and resid 95 through 124 Processing helix chain 'W' and resid 126 through 137 Processing helix chain 'W' and resid 137 through 159 Processing helix chain 'W' and resid 163 through 174 removed outlier: 3.592A pdb=" N GLU W 167 " --> pdb=" O SER W 163 " (cutoff:3.500A) Processing helix chain 'X' and resid 13 through 42 Processing helix chain 'X' and resid 48 through 76 Processing helix chain 'X' and resid 95 through 124 Processing helix chain 'X' and resid 126 through 137 Processing helix chain 'X' and resid 137 through 159 Processing helix chain 'X' and resid 163 through 174 removed outlier: 3.592A pdb=" N GLU X 167 " --> pdb=" O SER X 163 " (cutoff:3.500A) 2664 hydrogen bonds defined for protein. 7992 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.84 Time building geometry restraints manager: 4.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 11736 1.37 - 1.51: 9673 1.51 - 1.65: 12887 1.65 - 1.80: 216 1.80 - 1.94: 192 Bond restraints: 34704 Sorted by residual: bond pdb=" C3 33W K 67 " pdb="BR 33W K 67 " ideal model delta sigma weight residual 1.864 1.940 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C3 33W V 67 " pdb="BR 33W V 67 " ideal model delta sigma weight residual 1.864 1.940 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C3 33W H 67 " pdb="BR 33W H 67 " ideal model delta sigma weight residual 1.864 1.940 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C3 33W R 67 " pdb="BR 33W R 67 " ideal model delta sigma weight residual 1.864 1.940 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C3 33W L 67 " pdb="BR 33W L 67 " ideal model delta sigma weight residual 1.864 1.940 -0.076 2.00e-02 2.50e+03 1.46e+01 ... (remaining 34699 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 45146 1.62 - 3.23: 1222 3.23 - 4.85: 168 4.85 - 6.46: 120 6.46 - 8.08: 144 Bond angle restraints: 46800 Sorted by residual: angle pdb=" N GLU O 94 " pdb=" CA GLU O 94 " pdb=" C GLU O 94 " ideal model delta sigma weight residual 110.80 117.21 -6.41 2.13e+00 2.20e-01 9.05e+00 angle pdb=" N GLU N 94 " pdb=" CA GLU N 94 " pdb=" C GLU N 94 " ideal model delta sigma weight residual 110.80 117.21 -6.41 2.13e+00 2.20e-01 9.05e+00 angle pdb=" N GLU L 94 " pdb=" CA GLU L 94 " pdb=" C GLU L 94 " ideal model delta sigma weight residual 110.80 117.21 -6.41 2.13e+00 2.20e-01 9.05e+00 angle pdb=" N GLU M 94 " pdb=" CA GLU M 94 " pdb=" C GLU M 94 " ideal model delta sigma weight residual 110.80 117.21 -6.41 2.13e+00 2.20e-01 9.05e+00 angle pdb=" N GLU B 94 " pdb=" CA GLU B 94 " pdb=" C GLU B 94 " ideal model delta sigma weight residual 110.80 117.21 -6.41 2.13e+00 2.20e-01 9.05e+00 ... (remaining 46795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.71: 18936 15.71 - 31.43: 1272 31.43 - 47.14: 216 47.14 - 62.85: 216 62.85 - 78.57: 144 Dihedral angle restraints: 20784 sinusoidal: 8544 harmonic: 12240 Sorted by residual: dihedral pdb=" CA TRP D 93 " pdb=" C TRP D 93 " pdb=" N GLU D 94 " pdb=" CA GLU D 94 " ideal model delta harmonic sigma weight residual 180.00 160.98 19.02 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA TRP S 93 " pdb=" C TRP S 93 " pdb=" N GLU S 94 " pdb=" CA GLU S 94 " ideal model delta harmonic sigma weight residual 180.00 160.98 19.02 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA TRP C 93 " pdb=" C TRP C 93 " pdb=" N GLU C 94 " pdb=" CA GLU C 94 " ideal model delta harmonic sigma weight residual 180.00 160.98 19.02 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 20781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 3169 0.028 - 0.055: 1007 0.055 - 0.083: 455 0.083 - 0.110: 170 0.110 - 0.138: 95 Chirality restraints: 4896 Sorted by residual: chirality pdb=" CA TYR S 39 " pdb=" N TYR S 39 " pdb=" C TYR S 39 " pdb=" CB TYR S 39 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA TYR X 39 " pdb=" N TYR X 39 " pdb=" C TYR X 39 " pdb=" CB TYR X 39 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA TYR P 39 " pdb=" N TYR P 39 " pdb=" C TYR P 39 " pdb=" CB TYR P 39 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.77e-01 ... (remaining 4893 not shown) Planarity restraints: 6144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR Q 32 " -0.028 2.00e-02 2.50e+03 2.05e-02 8.43e+00 pdb=" CG TYR Q 32 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR Q 32 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR Q 32 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR Q 32 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR Q 32 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR Q 32 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR Q 32 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR S 32 " -0.028 2.00e-02 2.50e+03 2.05e-02 8.40e+00 pdb=" CG TYR S 32 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR S 32 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR S 32 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR S 32 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR S 32 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR S 32 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR S 32 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 32 " 0.028 2.00e-02 2.50e+03 2.05e-02 8.39e+00 pdb=" CG TYR G 32 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR G 32 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR G 32 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR G 32 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR G 32 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR G 32 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR G 32 " 0.003 2.00e-02 2.50e+03 ... (remaining 6141 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 10032 2.77 - 3.31: 40896 3.31 - 3.84: 78854 3.84 - 4.37: 92677 4.37 - 4.90: 150946 Nonbonded interactions: 373405 Sorted by model distance: nonbonded pdb=" O HOH H 428 " pdb=" O HOH H 435 " model vdw 2.243 3.040 nonbonded pdb=" O HOH E 428 " pdb=" O HOH E 435 " model vdw 2.243 3.040 nonbonded pdb=" O HOH X 428 " pdb=" O HOH X 435 " model vdw 2.243 3.040 nonbonded pdb=" O HOH R 428 " pdb=" O HOH R 435 " model vdw 2.243 3.040 nonbonded pdb=" O HOH W 428 " pdb=" O HOH W 435 " model vdw 2.243 3.040 ... (remaining 373400 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: 0.14 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: 5.410 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: 0.800 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 32.350 Find NCS groups from input model: 0.440 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: 0.020 Load rotamer database and sin/cos tables:6.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 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 : 0.006 0.079 34704 Z= 0.296 Angle : 0.790 8.076 46800 Z= 0.391 Chirality : 0.039 0.138 4896 Planarity : 0.005 0.034 6144 Dihedral : 14.538 78.565 12864 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 1.97 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: 3.92 (0.13), residues: 3936 helix: 3.14 (0.08), residues: 3120 sheet: None (None), residues: 0 loop : 0.30 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 156 TYR 0.049 0.004 TYR Q 32 PHE 0.021 0.004 PHE B 41 TRP 0.009 0.002 TRP K 93 HIS 0.007 0.002 HIS R 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00612 / 0.30 (34704) covalent geometry : angle 0.78980 / 0.39 (46800) hydrogen bonds : bond 0.07807 / 5.20 ( 2664) hydrogen bonds : angle 3.97737 / 2.92 ( 7992) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 876 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 876 time to evaluate : 1.413 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 876 average time/residue: 0.9462 time to fit residues: 963.6601 Evaluate side-chains 613 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 613 time to evaluate : 1.380 ------------------------------------------------------------------------------- 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: 1.9990 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.6980 chunk 401 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 10.0000 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 25 ASN A 109 ASN A 112 GLN B 25 ASN B 109 ASN B 112 GLN C 25 ASN C 109 ASN C 112 GLN D 25 ASN D 109 ASN D 112 GLN E 25 ASN E 109 ASN E 112 GLN F 25 ASN F 109 ASN F 112 GLN G 25 ASN G 109 ASN G 112 GLN H 25 ASN H 109 ASN H 112 GLN I 25 ASN I 109 ASN I 112 GLN J 25 ASN J 109 ASN J 112 GLN K 25 ASN K 109 ASN K 112 GLN L 25 ASN L 109 ASN L 112 GLN M 25 ASN M 109 ASN M 112 GLN N 25 ASN N 109 ASN N 112 GLN O 25 ASN O 109 ASN O 112 GLN P 25 ASN P 109 ASN P 112 GLN Q 25 ASN Q 109 ASN Q 112 GLN R 25 ASN R 109 ASN R 112 GLN S 25 ASN S 109 ASN S 112 GLN T 25 ASN T 109 ASN T 112 GLN U 25 ASN U 109 ASN U 112 GLN V 25 ASN V 109 ASN V 112 GLN W 25 ASN W 109 ASN W 112 GLN X 25 ASN X 109 ASN X 112 GLN Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.159511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.149235 restraints weight = 8723.675| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 0.27 r_work: 0.3556 rms_B_bonded: 0.28 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 0.54 restraints_weight: 0.2500 r_work: 0.3154 rms_B_bonded: 1.71 restraints_weight: 0.1250 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 34704 Z= 0.125 Angle : 0.510 5.758 46800 Z= 0.286 Chirality : 0.035 0.130 4896 Planarity : 0.003 0.020 6144 Dihedral : 8.859 77.758 4512 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % 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: 4.63 (0.13), residues: 3936 helix: 3.73 (0.09), residues: 3120 sheet: None (None), residues: 0 loop : 0.12 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG W 156 TYR 0.019 0.002 TYR G 39 PHE 0.015 0.002 PHE E 41 TRP 0.010 0.002 TRP R 93 HIS 0.004 0.001 HIS W 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 (34704) covalent geometry : angle 0.51033 / 0.29 (46800) hydrogen bonds : bond 0.04802 / 3.22 ( 2664) hydrogen bonds : angle 3.48942 / 2.57 ( 7992) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 618 time to evaluate : 1.381 Fit side-chains REVERT: A 86 LYS cc_start: 0.8609 (mmtp) cc_final: 0.8292 (mppt) REVERT: B 86 LYS cc_start: 0.8615 (mmtp) cc_final: 0.8290 (mppt) REVERT: C 86 LYS cc_start: 0.8617 (mmtp) cc_final: 0.8294 (mppt) REVERT: D 86 LYS cc_start: 0.8620 (mmtp) cc_final: 0.8296 (mppt) REVERT: F 86 LYS cc_start: 0.8614 (mmtp) cc_final: 0.8291 (mppt) REVERT: I 86 LYS cc_start: 0.8602 (mmtp) cc_final: 0.8287 (mppt) REVERT: J 86 LYS cc_start: 0.8621 (mmtp) cc_final: 0.8294 (mppt) REVERT: L 86 LYS cc_start: 0.8595 (mmtp) cc_final: 0.8288 (mppt) REVERT: M 86 LYS cc_start: 0.8600 (mmtp) cc_final: 0.8289 (mppt) REVERT: N 86 LYS cc_start: 0.8598 (mmtp) cc_final: 0.8286 (mppt) REVERT: O 86 LYS cc_start: 0.8605 (mmtp) cc_final: 0.8291 (mppt) REVERT: Q 86 LYS cc_start: 0.8602 (mmtp) cc_final: 0.8287 (mppt) REVERT: S 86 LYS cc_start: 0.8614 (mmtp) cc_final: 0.8291 (mppt) REVERT: U 86 LYS cc_start: 0.8607 (mmtp) cc_final: 0.8289 (mppt) outliers start: 0 outliers final: 0 residues processed: 618 average time/residue: 0.9152 time to fit residues: 658.4727 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 : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 258 optimal weight: 9.9990 chunk 395 optimal weight: 0.7980 chunk 277 optimal weight: 1.9990 chunk 403 optimal weight: 3.9990 chunk 226 optimal weight: 1.9990 chunk 211 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 399 optimal weight: 10.0000 chunk 215 optimal weight: 9.9990 chunk 108 optimal weight: 10.0000 chunk 185 optimal weight: 9.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN A 112 GLN B 109 ASN B 112 GLN C 109 ASN C 112 GLN D 109 ASN D 112 GLN E 109 ASN E 112 GLN F 109 ASN F 112 GLN G 109 ASN G 112 GLN H 109 ASN H 112 GLN I 109 ASN I 112 GLN J 109 ASN J 112 GLN K 109 ASN K 112 GLN L 109 ASN L 112 GLN M 109 ASN M 112 GLN N 109 ASN N 112 GLN O 109 ASN O 112 GLN P 109 ASN P 112 GLN Q 109 ASN Q 112 GLN R 109 ASN R 112 GLN S 109 ASN S 112 GLN T 109 ASN T 112 GLN U 109 ASN U 112 GLN V 109 ASN V 112 GLN W 109 ASN W 112 GLN X 109 ASN X 112 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.156115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.145379 restraints weight = 8537.045| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 0.26 r_work: 0.3510 rms_B_bonded: 0.27 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 0.52 restraints_weight: 0.2500 r_work: 0.3099 rms_B_bonded: 1.65 restraints_weight: 0.1250 r_work: 0.2746 rms_B_bonded: 4.76 restraints_weight: 0.0625 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 34704 Z= 0.163 Angle : 0.564 6.185 46800 Z= 0.317 Chirality : 0.037 0.138 4896 Planarity : 0.004 0.024 6144 Dihedral : 8.814 77.835 4512 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.37 (0.13), residues: 3936 helix: 3.55 (0.09), residues: 3120 sheet: None (None), residues: 0 loop : 0.02 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 22 TYR 0.023 0.002 TYR C 39 PHE 0.019 0.003 PHE M 41 TRP 0.008 0.002 TRP K 93 HIS 0.006 0.001 HIS C 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.16 (34704) covalent geometry : angle 0.56442 / 0.32 (46800) hydrogen bonds : bond 0.05414 / 3.64 ( 2664) hydrogen bonds : angle 3.65964 / 2.70 ( 7992) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 613 time to evaluate : 1.551 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 613 average time/residue: 0.8818 time to fit residues: 638.7856 Evaluate side-chains 586 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 586 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 160 optimal weight: 7.9990 chunk 108 optimal weight: 10.0000 chunk 248 optimal weight: 0.7980 chunk 132 optimal weight: 6.9990 chunk 209 optimal weight: 20.0000 chunk 364 optimal weight: 4.9990 chunk 312 optimal weight: 10.0000 chunk 117 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 chunk 358 optimal weight: 0.2980 chunk 297 optimal weight: 9.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN A 112 GLN B 109 ASN B 112 GLN C 109 ASN C 112 GLN D 109 ASN D 112 GLN E 109 ASN E 112 GLN F 109 ASN F 112 GLN G 109 ASN G 112 GLN H 109 ASN H 112 GLN I 109 ASN I 112 GLN J 109 ASN J 112 GLN K 109 ASN K 112 GLN L 109 ASN L 112 GLN M 109 ASN M 112 GLN N 109 ASN N 112 GLN O 109 ASN O 112 GLN P 109 ASN P 112 GLN Q 109 ASN Q 112 GLN R 109 ASN R 112 GLN S 109 ASN S 112 GLN T 109 ASN T 112 GLN U 109 ASN U 112 GLN V 109 ASN V 112 GLN W 109 ASN W 112 GLN X 109 ASN X 112 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.154697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.145035 restraints weight = 8363.630| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 0.23 r_work: 0.3506 rms_B_bonded: 0.24 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 0.45 restraints_weight: 0.2500 r_work: 0.3113 rms_B_bonded: 1.47 restraints_weight: 0.1250 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 34704 Z= 0.207 Angle : 0.619 6.646 46800 Z= 0.348 Chirality : 0.039 0.146 4896 Planarity : 0.004 0.034 6144 Dihedral : 8.826 78.164 4512 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % 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: 4.14 (0.13), residues: 3936 helix: 3.38 (0.08), residues: 3120 sheet: None (None), residues: 0 loop : -0.02 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 156 TYR 0.025 0.003 TYR J 39 PHE 0.024 0.004 PHE G 41 TRP 0.008 0.002 TRP G 93 HIS 0.007 0.002 HIS G 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.21 (34704) covalent geometry : angle 0.61913 / 0.35 (46800) hydrogen bonds : bond 0.05813 / 3.91 ( 2664) hydrogen bonds : angle 3.81742 / 2.81 ( 7992) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 581 time to evaluate : 1.500 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 581 average time/residue: 0.8265 time to fit residues: 570.3929 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 : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 170 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 76 optimal weight: 0.5980 chunk 127 optimal weight: 0.0370 chunk 160 optimal weight: 5.9990 chunk 243 optimal weight: 2.9990 chunk 136 optimal weight: 20.0000 chunk 39 optimal weight: 2.9990 chunk 217 optimal weight: 2.9990 chunk 189 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 overall best weight: 1.7264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN A 112 GLN B 109 ASN B 112 GLN C 109 ASN C 112 GLN D 109 ASN D 112 GLN E 109 ASN E 112 GLN F 109 ASN F 112 GLN G 109 ASN G 112 GLN H 109 ASN H 112 GLN I 109 ASN I 112 GLN J 109 ASN J 112 GLN K 109 ASN K 112 GLN L 109 ASN L 112 GLN M 109 ASN M 112 GLN N 109 ASN N 112 GLN O 109 ASN O 112 GLN P 109 ASN P 112 GLN Q 109 ASN Q 112 GLN R 109 ASN R 112 GLN S 109 ASN S 112 GLN T 109 ASN T 112 GLN U 109 ASN U 112 GLN V 109 ASN V 112 GLN W 109 ASN W 112 GLN X 109 ASN X 112 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.157719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.147352 restraints weight = 8601.083| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 0.27 r_work: 0.3530 rms_B_bonded: 0.29 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 0.54 restraints_weight: 0.2500 r_work: 0.3130 rms_B_bonded: 1.68 restraints_weight: 0.1250 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 34704 Z= 0.136 Angle : 0.522 6.727 46800 Z= 0.293 Chirality : 0.036 0.137 4896 Planarity : 0.003 0.021 6144 Dihedral : 8.894 77.698 4512 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % 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: 4.58 (0.13), residues: 3936 helix: 3.72 (0.08), residues: 3120 sheet: None (None), residues: 0 loop : -0.00 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 156 TYR 0.023 0.002 TYR T 39 PHE 0.018 0.002 PHE R 41 TRP 0.009 0.002 TRP R 93 HIS 0.005 0.001 HIS M 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.14 (34704) covalent geometry : angle 0.52202 / 0.29 (46800) hydrogen bonds : bond 0.04994 / 3.36 ( 2664) hydrogen bonds : angle 3.53201 / 2.60 ( 7992) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 577 time to evaluate : 1.582 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 577 average time/residue: 0.8482 time to fit residues: 581.8924 Evaluate side-chains 579 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 579 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 362 optimal weight: 0.9990 chunk 145 optimal weight: 0.5980 chunk 134 optimal weight: 8.9990 chunk 148 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 381 optimal weight: 8.9990 chunk 190 optimal weight: 10.0000 chunk 184 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 225 optimal weight: 8.9990 chunk 214 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN A 112 GLN B 109 ASN B 112 GLN B 136 HIS C 109 ASN C 112 GLN C 136 HIS D 109 ASN D 112 GLN D 136 HIS E 109 ASN E 112 GLN F 109 ASN F 112 GLN F 136 HIS G 109 ASN G 112 GLN H 109 ASN H 112 GLN I 109 ASN I 112 GLN J 109 ASN J 112 GLN K 109 ASN K 112 GLN K 136 HIS L 109 ASN L 112 GLN L 136 HIS M 109 ASN M 112 GLN N 109 ASN N 112 GLN O 109 ASN O 112 GLN P 109 ASN P 112 GLN P 136 HIS Q 109 ASN Q 112 GLN R 109 ASN R 112 GLN R 136 HIS S 109 ASN S 112 GLN S 136 HIS T 109 ASN T 112 GLN U 109 ASN U 112 GLN V 109 ASN V 112 GLN V 136 HIS W 109 ASN W 112 GLN W 136 HIS X 109 ASN X 112 GLN Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.161056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.150641 restraints weight = 8795.550| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 0.27 r_work: 0.3574 rms_B_bonded: 0.29 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 0.54 restraints_weight: 0.2500 r_work: 0.3181 rms_B_bonded: 1.71 restraints_weight: 0.1250 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1603 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= 0.109 Angle : 0.472 7.214 46800 Z= 0.264 Chirality : 0.035 0.128 4896 Planarity : 0.003 0.022 6144 Dihedral : 8.913 77.236 4512 Min Nonbonded Distance : 2.654 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % 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: 4.98 (0.13), residues: 3936 helix: 4.02 (0.08), residues: 3120 sheet: None (None), residues: 0 loop : 0.05 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 9 TYR 0.019 0.002 TYR O 39 PHE 0.013 0.002 PHE G 41 TRP 0.008 0.002 TRP B 93 HIS 0.004 0.001 HIS F 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.11 (34704) covalent geometry : angle 0.47214 / 0.26 (46800) hydrogen bonds : bond 0.04316 / 2.90 ( 2664) hydrogen bonds : angle 3.30909 / 2.44 ( 7992) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 568 time to evaluate : 1.530 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 568 average time/residue: 0.8474 time to fit residues: 571.7638 Evaluate side-chains 563 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 563 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 4 optimal weight: 4.9990 chunk 182 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 403 optimal weight: 3.9990 chunk 233 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 360 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 345 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 34 optimal weight: 20.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN A 112 GLN B 109 ASN B 112 GLN C 109 ASN C 112 GLN D 109 ASN D 112 GLN E 109 ASN E 112 GLN F 109 ASN F 112 GLN G 57 HIS G 109 ASN G 112 GLN H 109 ASN H 112 GLN I 109 ASN I 112 GLN J 109 ASN J 112 GLN K 109 ASN K 112 GLN L 109 ASN L 112 GLN M 109 ASN M 112 GLN N 109 ASN N 112 GLN O 109 ASN O 112 GLN P 57 HIS P 109 ASN P 112 GLN Q 109 ASN Q 112 GLN R 109 ASN R 112 GLN S 57 HIS S 109 ASN S 112 GLN T 109 ASN T 112 GLN U 109 ASN U 112 GLN V 109 ASN V 112 GLN W 109 ASN W 112 GLN X 109 ASN X 112 GLN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.158885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.148416 restraints weight = 8702.567| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 0.27 r_work: 0.3544 rms_B_bonded: 0.29 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 0.54 restraints_weight: 0.2500 r_work: 0.3143 rms_B_bonded: 1.70 restraints_weight: 0.1250 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 34704 Z= 0.127 Angle : 0.517 7.697 46800 Z= 0.287 Chirality : 0.036 0.144 4896 Planarity : 0.003 0.021 6144 Dihedral : 8.871 77.243 4512 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.47 % Allowed : 4.83 % 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: 4.90 (0.13), residues: 3936 helix: 3.93 (0.08), residues: 3120 sheet: None (None), residues: 0 loop : 0.17 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 22 TYR 0.021 0.002 TYR K 39 PHE 0.017 0.002 PHE F 41 TRP 0.008 0.002 TRP E 93 HIS 0.005 0.001 HIS U 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.13 (34704) covalent geometry : angle 0.51727 / 0.29 (46800) hydrogen bonds : bond 0.04818 / 3.24 ( 2664) hydrogen bonds : angle 3.43651 / 2.53 ( 7992) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 576 time to evaluate : 1.539 Fit side-chains REVERT: B 32 TYR cc_start: 0.9355 (OUTLIER) cc_final: 0.7666 (t80) REVERT: C 32 TYR cc_start: 0.9353 (OUTLIER) cc_final: 0.7664 (t80) REVERT: D 32 TYR cc_start: 0.9353 (OUTLIER) cc_final: 0.7661 (t80) REVERT: E 32 TYR cc_start: 0.9354 (OUTLIER) cc_final: 0.7663 (t80) REVERT: F 32 TYR cc_start: 0.9354 (OUTLIER) cc_final: 0.7660 (t80) REVERT: G 32 TYR cc_start: 0.9351 (OUTLIER) cc_final: 0.7661 (t80) REVERT: H 32 TYR cc_start: 0.9352 (OUTLIER) cc_final: 0.7660 (t80) REVERT: I 32 TYR cc_start: 0.9355 (OUTLIER) cc_final: 0.7664 (t80) REVERT: J 32 TYR cc_start: 0.9354 (OUTLIER) cc_final: 0.7661 (t80) REVERT: L 32 TYR cc_start: 0.9355 (OUTLIER) cc_final: 0.7665 (t80) REVERT: P 32 TYR cc_start: 0.9355 (OUTLIER) cc_final: 0.7665 (t80) REVERT: R 32 TYR cc_start: 0.9354 (OUTLIER) cc_final: 0.7670 (t80) REVERT: S 32 TYR cc_start: 0.9354 (OUTLIER) cc_final: 0.7663 (t80) REVERT: T 32 TYR cc_start: 0.9353 (OUTLIER) cc_final: 0.7661 (t80) REVERT: V 32 TYR cc_start: 0.9353 (OUTLIER) cc_final: 0.7662 (t80) REVERT: W 32 TYR cc_start: 0.9353 (OUTLIER) cc_final: 0.7665 (t80) REVERT: X 32 TYR cc_start: 0.9354 (OUTLIER) cc_final: 0.7665 (t80) outliers start: 17 outliers final: 0 residues processed: 593 average time/residue: 0.8050 time to fit residues: 568.5904 Evaluate side-chains 578 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 561 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 TYR Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain E residue 32 TYR Chi-restraints excluded: chain F residue 32 TYR Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain I residue 32 TYR Chi-restraints excluded: chain J residue 32 TYR Chi-restraints excluded: chain L residue 32 TYR Chi-restraints excluded: chain P residue 32 TYR Chi-restraints excluded: chain R residue 32 TYR Chi-restraints excluded: chain S residue 32 TYR Chi-restraints excluded: chain T residue 32 TYR Chi-restraints excluded: chain V residue 32 TYR Chi-restraints excluded: chain W residue 32 TYR Chi-restraints excluded: chain X residue 32 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 177 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 56 optimal weight: 9.9990 chunk 368 optimal weight: 4.9990 chunk 284 optimal weight: 0.0970 chunk 345 optimal weight: 0.8980 chunk 139 optimal weight: 3.9990 chunk 384 optimal weight: 9.9990 chunk 401 optimal weight: 10.0000 chunk 205 optimal weight: 6.9990 chunk 367 optimal weight: 9.9990 overall best weight: 3.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN A 112 GLN B 57 HIS B 109 ASN B 112 GLN C 57 HIS C 109 ASN C 112 GLN D 57 HIS D 109 ASN D 112 GLN E 109 ASN E 112 GLN F 57 HIS F 109 ASN F 112 GLN G 57 HIS G 109 ASN G 112 GLN H 109 ASN H 112 GLN I 109 ASN I 112 GLN J 57 HIS J 109 ASN J 112 GLN K 109 ASN K 112 GLN L 109 ASN L 112 GLN M 109 ASN M 112 GLN N 109 ASN N 112 GLN O 109 ASN O 112 GLN P 57 HIS P 109 ASN P 112 GLN Q 109 ASN Q 112 GLN R 109 ASN R 112 GLN S 57 HIS S 109 ASN S 112 GLN T 109 ASN T 112 GLN U 109 ASN U 112 GLN V 109 ASN V 112 GLN W 109 ASN W 112 GLN X 109 ASN X 112 GLN Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.154999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.145125 restraints weight = 8318.839| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 0.24 r_work: 0.3511 rms_B_bonded: 0.25 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 0.47 restraints_weight: 0.2500 r_work: 0.3116 rms_B_bonded: 1.51 restraints_weight: 0.1250 r_work: 0.2723 rms_B_bonded: 4.94 restraints_weight: 0.0625 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 34704 Z= 0.191 Angle : 0.613 8.157 46800 Z= 0.342 Chirality : 0.038 0.164 4896 Planarity : 0.004 0.027 6144 Dihedral : 8.816 77.788 4512 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % 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: 4.41 (0.13), residues: 3936 helix: 3.57 (0.08), residues: 3120 sheet: None (None), residues: 0 loop : 0.05 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 22 TYR 0.025 0.003 TYR C 39 PHE 0.022 0.003 PHE E 41 TRP 0.005 0.001 TRP V 93 HIS 0.007 0.002 HIS C 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.19 (34704) covalent geometry : angle 0.61328 / 0.34 (46800) hydrogen bonds : bond 0.05628 / 3.78 ( 2664) hydrogen bonds : angle 3.72384 / 2.74 ( 7992) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 568 time to evaluate : 1.495 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 568 average time/residue: 0.7855 time to fit residues: 531.4224 Evaluate side-chains 557 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 557 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 274 optimal weight: 0.5980 chunk 376 optimal weight: 0.8980 chunk 334 optimal weight: 10.0000 chunk 298 optimal weight: 0.9990 chunk 225 optimal weight: 6.9990 chunk 310 optimal weight: 6.9990 chunk 314 optimal weight: 0.0040 chunk 46 optimal weight: 0.8980 chunk 254 optimal weight: 8.9990 chunk 322 optimal weight: 0.9990 chunk 261 optimal weight: 10.0000 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN A 112 GLN A 136 HIS B 57 HIS B 109 ASN B 112 GLN B 136 HIS C 57 HIS C 109 ASN C 112 GLN C 136 HIS D 57 HIS D 109 ASN D 112 GLN D 136 HIS E 109 ASN E 112 GLN E 136 HIS F 57 HIS F 109 ASN F 112 GLN F 136 HIS G 57 HIS G 109 ASN G 112 GLN G 136 HIS H 109 ASN H 112 GLN H 136 HIS I 109 ASN I 112 GLN I 136 HIS J 57 HIS J 109 ASN J 112 GLN J 136 HIS K 109 ASN K 112 GLN K 136 HIS L 109 ASN L 112 GLN L 136 HIS M 109 ASN M 112 GLN M 136 HIS N 109 ASN N 112 GLN N 136 HIS O 109 ASN O 112 GLN O 136 HIS P 57 HIS P 109 ASN P 112 GLN P 136 HIS Q 109 ASN Q 112 GLN Q 136 HIS R 109 ASN R 112 GLN R 136 HIS S 57 HIS S 109 ASN S 112 GLN S 136 HIS T 109 ASN T 112 GLN T 136 HIS U 109 ASN U 112 GLN U 136 HIS V 109 ASN V 112 GLN V 136 HIS W 109 ASN W 112 GLN W 136 HIS X 109 ASN X 112 GLN X 136 HIS Total number of N/Q/H flips: 80 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.162823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.152394 restraints weight = 8944.024| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 0.27 r_work: 0.3591 rms_B_bonded: 0.29 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 0.55 restraints_weight: 0.2500 r_work: 0.3197 rms_B_bonded: 1.74 restraints_weight: 0.1250 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1697 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= 0.107 Angle : 0.475 7.982 46800 Z= 0.264 Chirality : 0.035 0.142 4896 Planarity : 0.003 0.023 6144 Dihedral : 8.948 77.552 4512 Min Nonbonded Distance : 2.655 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % 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: 5.07 (0.13), residues: 3936 helix: 4.07 (0.08), residues: 3120 sheet: None (None), residues: 0 loop : 0.13 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 9 TYR 0.019 0.002 TYR I 39 PHE 0.011 0.002 PHE U 41 TRP 0.008 0.002 TRP M 93 HIS 0.004 0.001 HIS P 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00196 / 0.11 (34704) covalent geometry : angle 0.47548 / 0.26 (46800) hydrogen bonds : bond 0.04131 / 2.77 ( 2664) hydrogen bonds : angle 3.26111 / 2.40 ( 7992) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 575 time to evaluate : 1.386 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 575 average time/residue: 0.8195 time to fit residues: 558.3493 Evaluate side-chains 532 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 532 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 190 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 170 optimal weight: 4.9990 chunk 375 optimal weight: 5.9990 chunk 179 optimal weight: 5.9990 chunk 289 optimal weight: 6.9990 chunk 187 optimal weight: 8.9990 chunk 368 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 268 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN A 112 GLN B 57 HIS B 109 ASN B 112 GLN C 57 HIS C 109 ASN C 112 GLN D 57 HIS D 109 ASN D 112 GLN E 109 ASN E 112 GLN F 57 HIS F 109 ASN F 112 GLN G 57 HIS G 109 ASN G 112 GLN H 109 ASN H 112 GLN I 109 ASN I 112 GLN J 57 HIS J 109 ASN J 112 GLN K 109 ASN K 112 GLN L 109 ASN L 112 GLN M 109 ASN M 112 GLN N 109 ASN N 112 GLN O 109 ASN O 112 GLN P 57 HIS P 109 ASN P 112 GLN Q 109 ASN Q 112 GLN R 109 ASN R 112 GLN S 57 HIS S 109 ASN S 112 GLN T 109 ASN T 112 GLN U 109 ASN U 112 GLN V 109 ASN V 112 GLN W 109 ASN W 112 GLN X 109 ASN X 112 GLN Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.154555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.144715 restraints weight = 8287.829| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 0.24 r_work: 0.3507 rms_B_bonded: 0.24 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 0.46 restraints_weight: 0.2500 r_work: 0.3112 rms_B_bonded: 1.49 restraints_weight: 0.1250 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 34704 Z= 0.227 Angle : 0.669 8.834 46800 Z= 0.371 Chirality : 0.040 0.184 4896 Planarity : 0.004 0.031 6144 Dihedral : 8.785 77.943 4512 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.26 (0.13), residues: 3936 helix: 3.46 (0.08), residues: 3120 sheet: None (None), residues: 0 loop : 0.01 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG T 22 TYR 0.027 0.003 TYR T 39 PHE 0.026 0.003 PHE F 41 TRP 0.005 0.001 TRP U 93 HIS 0.008 0.002 HIS G 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.23 (34704) covalent geometry : angle 0.66872 / 0.37 (46800) hydrogen bonds : bond 0.05863 / 3.94 ( 2664) hydrogen bonds : angle 3.80329 / 2.80 ( 7992) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 573 time to evaluate : 1.542 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 573 average time/residue: 0.8435 time to fit residues: 573.7904 Evaluate side-chains 573 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 573 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 91 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 290 optimal weight: 5.9990 chunk 326 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 68 optimal weight: 20.0000 chunk 376 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 226 optimal weight: 10.0000 chunk 216 optimal weight: 0.0980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN A 112 GLN B 57 HIS B 109 ASN B 112 GLN C 57 HIS C 109 ASN C 112 GLN D 57 HIS D 109 ASN D 112 GLN E 109 ASN E 112 GLN F 57 HIS F 109 ASN F 112 GLN G 57 HIS G 109 ASN G 112 GLN H 109 ASN H 112 GLN I 109 ASN I 112 GLN J 57 HIS J 109 ASN J 112 GLN K 109 ASN K 112 GLN L 109 ASN L 112 GLN M 109 ASN M 112 GLN N 109 ASN N 112 GLN O 109 ASN O 112 GLN P 57 HIS P 109 ASN P 112 GLN Q 109 ASN Q 112 GLN R 109 ASN R 112 GLN S 57 HIS S 109 ASN S 112 GLN T 109 ASN T 112 GLN U 109 ASN U 112 GLN V 109 ASN V 112 GLN W 109 ASN W 112 GLN X 109 ASN X 112 GLN Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.161523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.151196 restraints weight = 8744.517| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 0.27 r_work: 0.3580 rms_B_bonded: 0.29 restraints_weight: 0.5000 r_work: 0.3482 rms_B_bonded: 0.54 restraints_weight: 0.2500 r_work: 0.3189 rms_B_bonded: 1.70 restraints_weight: 0.1250 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 34704 Z= 0.112 Angle : 0.498 8.356 46800 Z= 0.276 Chirality : 0.036 0.149 4896 Planarity : 0.003 0.023 6144 Dihedral : 8.944 77.726 4512 Min Nonbonded Distance : 2.655 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % 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 are not related in a simple way. whole: 4.97 (0.13), residues: 3936 helix: 4.00 (0.08), residues: 3120 sheet: None (None), residues: 0 loop : 0.09 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG P 9 TYR 0.021 0.002 TYR C 39 PHE 0.013 0.002 PHE B 41 TRP 0.008 0.002 TRP X 93 HIS 0.004 0.001 HIS R 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.11 (34704) covalent geometry : angle 0.49802 / 0.28 (46800) hydrogen bonds : bond 0.04277 / 2.87 ( 2664) hydrogen bonds : angle 3.31241 / 2.44 ( 7992) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20624.49 seconds wall clock time: 351 minutes 36.37 seconds (21096.37 seconds total)