Starting phenix.real_space_refine on Tue Aug 26 11:09:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jqb_61726/08_2025/9jqb_61726.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jqb_61726/08_2025/9jqb_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 { model { file = "/net/cci-nas-00/data/ceres_data/9jqb_61726/08_2025/9jqb_61726.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jqb_61726/08_2025/9jqb_61726.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jqb_61726/08_2025/9jqb_61726.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jqb_61726/08_2025/9jqb_61726.map" } 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-2.0-5787/lib/python3.9/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, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 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: 4.99, 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: 3.89 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 1.2 microseconds 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: 0.99 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: 7.74 Time building geometry restraints manager: 4.90 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: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.290 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: 0.030 Extract box with map and model: 0.770 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 32.030 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.130 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:8.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 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 aren 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 covalent geometry : bond 0.00612 (34704) covalent geometry : angle 0.78980 (46800) hydrogen bonds : bond 0.07807 ( 2664) hydrogen bonds : angle 3.97737 ( 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 : 1.678 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 876 average time/residue: 1.0486 time to fit residues: 1058.9420 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 : 1.658 ------------------------------------------------------------------------------- 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: 9.9990 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: 9.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3747 r_free = 0.3747 target = 0.159148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.148885 restraints weight = 8800.549| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 0.27 r_work: 0.3550 rms_B_bonded: 0.29 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 0.54 restraints_weight: 0.2500 r_work: 0.3152 rms_B_bonded: 1.70 restraints_weight: 0.1250 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1246 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 5.785 46800 Z= 0.286 Chirality : 0.035 0.130 4896 Planarity : 0.003 0.020 6144 Dihedral : 8.853 77.732 4512 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 2.61 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 aren not related in a simple way. whole: 4.63 (0.13), residues: 3936 helix: 3.72 (0.09), 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 P 156 TYR 0.019 0.002 TYR G 39 PHE 0.015 0.002 PHE C 41 TRP 0.010 0.002 TRP K 93 HIS 0.004 0.001 HIS V 128 Details of bonding type rmsd covalent geometry : bond 0.00239 (34704) covalent geometry : angle 0.51004 (46800) hydrogen bonds : bond 0.04816 ( 2664) hydrogen bonds : angle 3.49336 ( 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 615 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 615 time to evaluate : 1.066 Fit side-chains REVERT: A 86 LYS cc_start: 0.8612 (mmtp) cc_final: 0.8293 (mppt) REVERT: B 86 LYS cc_start: 0.8619 (mmtp) cc_final: 0.8292 (mppt) REVERT: C 86 LYS cc_start: 0.8621 (mmtp) cc_final: 0.8297 (mppt) REVERT: D 86 LYS cc_start: 0.8623 (mmtp) cc_final: 0.8297 (mppt) REVERT: F 86 LYS cc_start: 0.8622 (mmtp) cc_final: 0.8295 (mppt) REVERT: I 86 LYS cc_start: 0.8610 (mmtp) cc_final: 0.8294 (mppt) REVERT: J 86 LYS cc_start: 0.8624 (mmtp) cc_final: 0.8294 (mppt) REVERT: L 86 LYS cc_start: 0.8605 (mmtp) cc_final: 0.8292 (mppt) REVERT: M 86 LYS cc_start: 0.8603 (mmtp) cc_final: 0.8291 (mppt) REVERT: N 86 LYS cc_start: 0.8603 (mmtp) cc_final: 0.8288 (mppt) REVERT: O 86 LYS cc_start: 0.8610 (mmtp) cc_final: 0.8294 (mppt) REVERT: Q 86 LYS cc_start: 0.8606 (mmtp) cc_final: 0.8288 (mppt) REVERT: S 86 LYS cc_start: 0.8619 (mmtp) cc_final: 0.8292 (mppt) REVERT: U 86 LYS cc_start: 0.8612 (mmtp) cc_final: 0.8292 (mppt) outliers start: 0 outliers final: 0 residues processed: 615 average time/residue: 0.9535 time to fit residues: 679.5622 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 : 1.497 ------------------------------------------------------------------------------- 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: 10.0000 chunk 395 optimal weight: 0.9990 chunk 277 optimal weight: 0.9980 chunk 403 optimal weight: 3.9990 chunk 226 optimal weight: 0.9980 chunk 211 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 399 optimal weight: 10.0000 chunk 215 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 185 optimal weight: 10.0000 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3737 r_free = 0.3737 target = 0.157981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.147744 restraints weight = 8784.413| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 0.27 r_work: 0.3541 rms_B_bonded: 0.28 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 0.53 restraints_weight: 0.2500 r_work: 0.3144 rms_B_bonded: 1.69 restraints_weight: 0.1250 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1300 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= 0.125 Angle : 0.501 5.980 46800 Z= 0.281 Chirality : 0.035 0.132 4896 Planarity : 0.003 0.021 6144 Dihedral : 8.850 77.300 4512 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.76 (0.13), residues: 3936 helix: 3.83 (0.09), residues: 3120 sheet: None (None), residues: 0 loop : 0.09 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 22 TYR 0.020 0.002 TYR D 39 PHE 0.016 0.002 PHE B 41 TRP 0.007 0.002 TRP Q 93 HIS 0.005 0.001 HIS Q 128 Details of bonding type rmsd covalent geometry : bond 0.00241 (34704) covalent geometry : angle 0.50061 (46800) hydrogen bonds : bond 0.04846 ( 2664) hydrogen bonds : angle 3.46609 ( 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 580 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 580 time to evaluate : 1.790 Fit side-chains REVERT: A 86 LYS cc_start: 0.8599 (mmtp) cc_final: 0.8294 (mppt) REVERT: B 86 LYS cc_start: 0.8600 (mmtp) cc_final: 0.8285 (mppt) REVERT: C 86 LYS cc_start: 0.8612 (mmtp) cc_final: 0.8295 (mppt) REVERT: D 86 LYS cc_start: 0.8611 (mmtp) cc_final: 0.8294 (mppt) REVERT: F 86 LYS cc_start: 0.8607 (mmtp) cc_final: 0.8290 (mppt) REVERT: I 86 LYS cc_start: 0.8599 (mmtp) cc_final: 0.8287 (mppt) REVERT: J 86 LYS cc_start: 0.8611 (mmtp) cc_final: 0.8291 (mppt) REVERT: L 86 LYS cc_start: 0.8592 (mmtp) cc_final: 0.8289 (mppt) REVERT: M 86 LYS cc_start: 0.8597 (mmtp) cc_final: 0.8288 (mppt) REVERT: N 86 LYS cc_start: 0.8596 (mmtp) cc_final: 0.8285 (mppt) REVERT: O 86 LYS cc_start: 0.8603 (mmtp) cc_final: 0.8293 (mppt) REVERT: Q 86 LYS cc_start: 0.8594 (mmtp) cc_final: 0.8290 (mppt) REVERT: S 86 LYS cc_start: 0.8608 (mmtp) cc_final: 0.8291 (mppt) REVERT: U 86 LYS cc_start: 0.8599 (mmtp) cc_final: 0.8291 (mppt) outliers start: 0 outliers final: 0 residues processed: 580 average time/residue: 0.9267 time to fit residues: 628.8322 Evaluate side-chains 580 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 580 time to evaluate : 1.320 ------------------------------------------------------------------------------- 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: 8.9990 chunk 108 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 209 optimal weight: 5.9990 chunk 364 optimal weight: 3.9990 chunk 312 optimal weight: 9.9990 chunk 117 optimal weight: 0.1980 chunk 149 optimal weight: 3.9990 chunk 358 optimal weight: 1.9990 chunk 297 optimal weight: 10.0000 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3709 r_free = 0.3709 target = 0.155369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.145563 restraints weight = 8441.978| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 0.24 r_work: 0.3515 rms_B_bonded: 0.25 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 0.47 restraints_weight: 0.2500 r_work: 0.3119 rms_B_bonded: 1.53 restraints_weight: 0.1250 r_work: 0.2733 rms_B_bonded: 4.90 restraints_weight: 0.0625 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.1162 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= 0.166 Angle : 0.571 6.976 46800 Z= 0.319 Chirality : 0.037 0.137 4896 Planarity : 0.004 0.025 6144 Dihedral : 8.832 77.601 4512 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 1.75 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 aren not related in a simple way. whole: 4.45 (0.13), residues: 3936 helix: 3.60 (0.09), 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 F 156 TYR 0.023 0.002 TYR M 39 PHE 0.020 0.003 PHE E 41 TRP 0.007 0.002 TRP K 93 HIS 0.006 0.001 HIS C 128 Details of bonding type rmsd covalent geometry : bond 0.00333 (34704) covalent geometry : angle 0.57053 (46800) hydrogen bonds : bond 0.05434 ( 2664) hydrogen bonds : angle 3.66407 ( 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 604 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 604 time to evaluate : 1.619 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 604 average time/residue: 0.8283 time to fit residues: 588.5151 Evaluate side-chains 576 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 576 time to evaluate : 1.332 ------------------------------------------------------------------------------- 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: 0.0970 chunk 63 optimal weight: 0.2980 chunk 76 optimal weight: 10.0000 chunk 127 optimal weight: 8.9990 chunk 160 optimal weight: 7.9990 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: 0.6980 chunk 132 optimal weight: 1.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3743 r_free = 0.3743 target = 0.158559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.148290 restraints weight = 8797.172| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 0.27 r_work: 0.3546 rms_B_bonded: 0.29 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 0.54 restraints_weight: 0.2500 r_work: 0.3152 rms_B_bonded: 1.68 restraints_weight: 0.1250 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1451 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= 0.120 Angle : 0.495 7.046 46800 Z= 0.277 Chirality : 0.036 0.133 4896 Planarity : 0.003 0.022 6144 Dihedral : 8.901 77.422 4512 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 2.68 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 aren not related in a simple way. whole: 4.85 (0.13), residues: 3936 helix: 3.92 (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 P 156 TYR 0.020 0.002 TYR P 39 PHE 0.016 0.002 PHE B 41 TRP 0.008 0.002 TRP K 93 HIS 0.004 0.001 HIS J 128 Details of bonding type rmsd covalent geometry : bond 0.00227 (34704) covalent geometry : angle 0.49464 (46800) hydrogen bonds : bond 0.04679 ( 2664) hydrogen bonds : angle 3.41229 ( 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 580 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 580 time to evaluate : 1.260 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 580 average time/residue: 0.7305 time to fit residues: 500.4446 Evaluate side-chains 576 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 576 time to evaluate : 1.276 ------------------------------------------------------------------------------- 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: 4.9990 chunk 134 optimal weight: 10.0000 chunk 148 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 381 optimal weight: 0.0870 chunk 190 optimal weight: 7.9990 chunk 184 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 225 optimal weight: 0.9990 chunk 214 optimal weight: 10.0000 overall best weight: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 112 GLN A 136 HIS 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 E 136 HIS F 109 ASN F 112 GLN F 136 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 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 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 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: 72 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.161236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.151078 restraints weight = 8920.402| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 0.27 r_work: 0.3579 rms_B_bonded: 0.28 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 0.54 restraints_weight: 0.2500 r_work: 0.3190 rms_B_bonded: 1.70 restraints_weight: 0.1250 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 34704 Z= 0.106 Angle : 0.469 7.553 46800 Z= 0.261 Chirality : 0.035 0.137 4896 Planarity : 0.003 0.022 6144 Dihedral : 8.912 77.128 4512 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.13 (0.13), residues: 3936 helix: 4.12 (0.08), residues: 3120 sheet: None (None), residues: 0 loop : 0.14 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG M 22 TYR 0.018 0.002 TYR R 39 PHE 0.013 0.002 PHE X 41 TRP 0.008 0.002 TRP H 93 HIS 0.004 0.001 HIS E 128 Details of bonding type rmsd covalent geometry : bond 0.00196 (34704) covalent geometry : angle 0.46936 (46800) hydrogen bonds : bond 0.04206 ( 2664) hydrogen bonds : angle 3.26256 ( 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 556 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 556 time to evaluate : 1.572 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 556 average time/residue: 0.8497 time to fit residues: 555.8155 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 : 1.332 ------------------------------------------------------------------------------- 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: 0.5980 chunk 403 optimal weight: 3.9990 chunk 233 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 360 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 345 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 34 optimal weight: 20.0000 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3708 r_free = 0.3708 target = 0.155528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.145694 restraints weight = 8567.903| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 0.24 r_work: 0.3513 rms_B_bonded: 0.25 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 0.48 restraints_weight: 0.2500 r_work: 0.3117 rms_B_bonded: 1.53 restraints_weight: 0.1250 r_work: 0.2743 rms_B_bonded: 4.73 restraints_weight: 0.0625 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8921 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 34704 Z= 0.174 Angle : 0.592 8.331 46800 Z= 0.330 Chirality : 0.038 0.166 4896 Planarity : 0.004 0.024 6144 Dihedral : 8.804 77.535 4512 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.61 (0.13), residues: 3936 helix: 3.71 (0.08), residues: 3120 sheet: None (None), residues: 0 loop : 0.14 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 22 TYR 0.023 0.002 TYR T 39 PHE 0.021 0.003 PHE B 41 TRP 0.006 0.001 TRP B 93 HIS 0.006 0.001 HIS Q 128 Details of bonding type rmsd covalent geometry : bond 0.00350 (34704) covalent geometry : angle 0.59234 (46800) hydrogen bonds : bond 0.05444 ( 2664) hydrogen bonds : angle 3.64207 ( 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 576 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 576 time to evaluate : 1.284 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 576 average time/residue: 0.7871 time to fit residues: 536.0487 Evaluate side-chains 576 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 576 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 368 optimal weight: 9.9990 chunk 284 optimal weight: 0.9990 chunk 345 optimal weight: 20.0000 chunk 139 optimal weight: 6.9990 chunk 384 optimal weight: 0.9980 chunk 401 optimal weight: 0.7980 chunk 205 optimal weight: 7.9990 chunk 367 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3744 r_free = 0.3744 target = 0.158681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.148399 restraints weight = 8764.624| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 0.27 r_work: 0.3548 rms_B_bonded: 0.28 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 0.54 restraints_weight: 0.2500 r_work: 0.3150 rms_B_bonded: 1.69 restraints_weight: 0.1250 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1494 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= 0.123 Angle : 0.512 8.089 46800 Z= 0.285 Chirality : 0.036 0.151 4896 Planarity : 0.003 0.022 6144 Dihedral : 8.893 77.448 4512 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.90 (0.13), residues: 3936 helix: 3.93 (0.08), residues: 3120 sheet: None (None), residues: 0 loop : 0.14 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG P 156 TYR 0.020 0.002 TYR U 39 PHE 0.017 0.002 PHE X 41 TRP 0.007 0.001 TRP J 93 HIS 0.005 0.001 HIS K 128 Details of bonding type rmsd covalent geometry : bond 0.00235 (34704) covalent geometry : angle 0.51221 (46800) hydrogen bonds : bond 0.04689 ( 2664) hydrogen bonds : angle 3.41213 ( 7992) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 576 time to evaluate : 1.584 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 576 average time/residue: 0.7428 time to fit residues: 506.0803 Evaluate side-chains 576 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 576 time to evaluate : 0.991 ------------------------------------------------------------------------------- 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: 0.8980 chunk 376 optimal weight: 0.8980 chunk 334 optimal weight: 3.9990 chunk 298 optimal weight: 2.9990 chunk 225 optimal weight: 8.9990 chunk 310 optimal weight: 8.9990 chunk 314 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 254 optimal weight: 1.9990 chunk 322 optimal weight: 0.7980 chunk 261 optimal weight: 10.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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 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: 54 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.159659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.149289 restraints weight = 8944.610| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 0.27 r_work: 0.3556 rms_B_bonded: 0.29 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 0.55 restraints_weight: 0.2500 r_work: 0.3159 rms_B_bonded: 1.72 restraints_weight: 0.1250 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1557 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= 0.117 Angle : 0.504 8.301 46800 Z= 0.279 Chirality : 0.036 0.151 4896 Planarity : 0.003 0.022 6144 Dihedral : 8.896 77.245 4512 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 2.62 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 aren not related in a simple way. whole: 5.01 (0.13), residues: 3936 helix: 4.02 (0.08), residues: 3120 sheet: None (None), residues: 0 loop : 0.16 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG P 22 TYR 0.021 0.002 TYR T 39 PHE 0.015 0.002 PHE X 41 TRP 0.008 0.002 TRP L 93 HIS 0.004 0.001 HIS B 128 Details of bonding type rmsd covalent geometry : bond 0.00220 (34704) covalent geometry : angle 0.50397 (46800) hydrogen bonds : bond 0.04536 ( 2664) hydrogen bonds : angle 3.35147 ( 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 570 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 570 time to evaluate : 1.469 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 570 average time/residue: 0.7613 time to fit residues: 512.6387 Evaluate side-chains 546 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 546 time to evaluate : 1.376 ------------------------------------------------------------------------------- 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: 0.0470 chunk 375 optimal weight: 5.9990 chunk 179 optimal weight: 3.9990 chunk 289 optimal weight: 9.9990 chunk 187 optimal weight: 6.9990 chunk 368 optimal weight: 9.9990 chunk 110 optimal weight: 9.9990 chunk 132 optimal weight: 9.9990 chunk 268 optimal weight: 0.9990 overall best weight: 3.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3703 r_free = 0.3703 target = 0.155046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.145223 restraints weight = 8440.141| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 0.24 r_work: 0.3507 rms_B_bonded: 0.25 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 0.47 restraints_weight: 0.2500 r_work: 0.3114 rms_B_bonded: 1.52 restraints_weight: 0.1250 r_work: 0.2722 rms_B_bonded: 4.99 restraints_weight: 0.0625 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 34704 Z= 0.198 Angle : 0.633 8.890 46800 Z= 0.352 Chirality : 0.039 0.179 4896 Planarity : 0.004 0.027 6144 Dihedral : 8.803 77.724 4512 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 2.24 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 aren not related in a simple way. whole: 4.44 (0.13), residues: 3936 helix: 3.60 (0.08), residues: 3120 sheet: None (None), residues: 0 loop : 0.07 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 22 TYR 0.025 0.003 TYR F 39 PHE 0.023 0.003 PHE I 41 TRP 0.004 0.001 TRP F 93 HIS 0.007 0.002 HIS R 128 Details of bonding type rmsd covalent geometry : bond 0.00401 (34704) covalent geometry : angle 0.63309 (46800) hydrogen bonds : bond 0.05661 ( 2664) hydrogen bonds : angle 3.71861 ( 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 576 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 576 time to evaluate : 1.520 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 576 average time/residue: 0.8145 time to fit residues: 553.9387 Evaluate side-chains 552 residues out of total 3624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 552 time to evaluate : 1.544 ------------------------------------------------------------------------------- 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: 9.9990 chunk 18 optimal weight: 5.9990 chunk 290 optimal weight: 5.9990 chunk 326 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 68 optimal weight: 20.0000 chunk 376 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 226 optimal weight: 9.9990 chunk 216 optimal weight: 0.3980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3740 r_free = 0.3740 target = 0.158252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.148015 restraints weight = 8712.701| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 0.27 r_work: 0.3544 rms_B_bonded: 0.28 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 0.53 restraints_weight: 0.2500 r_work: 0.3145 rms_B_bonded: 1.67 restraints_weight: 0.1250 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1468 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= 0.129 Angle : 0.537 8.750 46800 Z= 0.298 Chirality : 0.036 0.162 4896 Planarity : 0.003 0.022 6144 Dihedral : 8.894 77.690 4512 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 2.65 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 aren not related in a simple way. whole: 4.82 (0.13), residues: 3936 helix: 3.88 (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 W 76 TYR 0.022 0.002 TYR G 39 PHE 0.017 0.002 PHE H 41 TRP 0.007 0.001 TRP H 93 HIS 0.005 0.001 HIS U 128 Details of bonding type rmsd covalent geometry : bond 0.00247 (34704) covalent geometry : angle 0.53689 (46800) hydrogen bonds : bond 0.04781 ( 2664) hydrogen bonds : angle 3.44283 ( 7992) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20101.19 seconds wall clock time: 342 minutes 43.65 seconds (20563.65 seconds total)