Starting phenix.real_space_refine on Thu Aug 6 12:40:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vg2_43198/08_2026/8vg2_43198.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vg2_43198/08_2026/8vg2_43198.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vg2_43198/08_2026/8vg2_43198.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vg2_43198/08_2026/8vg2_43198.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vg2_43198/08_2026/8vg2_43198.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vg2_43198/08_2026/8vg2_43198.map" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 392 5.49 5 S 21 5.16 5 C 8651 2.51 5 N 2930 2.21 5 O 3695 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15689 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 819 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 858 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "D" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 754 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "F" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 936 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "H" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 774 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "I" Number of atoms: 3998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 3998 Classifications: {'DNA': 196} Link IDs: {'rna3p': 195} Chain: "J" Number of atoms: 4038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 4038 Classifications: {'DNA': 196} Link IDs: {'rna3p': 195} Chain: "O" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 856 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 7, 'TRANS': 94} Chain: "U" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 535 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Time building chain proxies: 3.15, per 1000 atoms: 0.20 Number of scatterers: 15689 At special positions: 0 Unit cell: (86.592, 121.44, 195.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 21 16.00 P 392 15.00 O 3695 8.00 N 2930 7.00 C 8651 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: 1.29 Conformation dependent library (CDL) restraints added in 501.0 milliseconds 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1800 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 12 sheets defined 68.0% alpha, 3.7% beta 187 base pairs and 339 stacking pairs defined. Time for finding SS restraints: 2.56 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.957A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.564A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.632A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.522A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.408A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 125 Processing helix chain 'E' and resid 44 through 56 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.895A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.682A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 125 Processing helix chain 'O' and resid 174 through 186 removed outlier: 3.825A pdb=" N ALA O 186 " --> pdb=" O ALA O 182 " (cutoff:3.500A) Processing helix chain 'O' and resid 192 through 204 Processing helix chain 'O' and resid 205 through 209 removed outlier: 3.801A pdb=" N GLN O 209 " --> pdb=" O TYR O 206 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 225 Processing helix chain 'O' and resid 248 through 251 Processing helix chain 'U' and resid 38 through 51 removed outlier: 3.606A pdb=" N LEU U 42 " --> pdb=" O PRO U 38 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER U 50 " --> pdb=" O ALA U 46 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS U 51 " --> pdb=" O VAL U 47 " (cutoff:3.500A) Processing helix chain 'U' and resid 58 through 69 Processing helix chain 'U' and resid 71 through 74 Processing helix chain 'U' and resid 75 through 89 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.012A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.578A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.259A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.838A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.940A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'O' and resid 228 through 231 removed outlier: 3.538A pdb=" N TYR O 243 " --> pdb=" O VAL O 231 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'U' and resid 56 through 57 486 hydrogen bonds defined for protein. 1422 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 471 hydrogen bonds 942 hydrogen bond angles 0 basepair planarities 187 basepair parallelities 339 stacking parallelities Total time for adding SS restraints: 3.62 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3115 1.33 - 1.45: 5281 1.45 - 1.57: 7566 1.57 - 1.69: 782 1.69 - 1.81: 35 Bond restraints: 16779 Sorted by residual: bond pdb=" C1' DT I 88 " pdb=" N1 DT I 88 " ideal model delta sigma weight residual 1.468 1.531 -0.063 1.40e-02 5.10e+03 2.06e+01 bond pdb=" C1' DT J 131 " pdb=" N1 DT J 131 " ideal model delta sigma weight residual 1.468 1.531 -0.063 1.40e-02 5.10e+03 2.01e+01 bond pdb=" C1' DC I 120 " pdb=" N1 DC I 120 " ideal model delta sigma weight residual 1.468 1.531 -0.063 1.40e-02 5.10e+03 2.00e+01 bond pdb=" C1' DC I 151 " pdb=" N1 DC I 151 " ideal model delta sigma weight residual 1.468 1.530 -0.062 1.40e-02 5.10e+03 1.94e+01 bond pdb=" C1' DC J 135 " pdb=" N1 DC J 135 " ideal model delta sigma weight residual 1.468 1.528 -0.060 1.40e-02 5.10e+03 1.83e+01 ... (remaining 16774 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 21635 1.16 - 2.31: 1879 2.31 - 3.47: 733 3.47 - 4.63: 69 4.63 - 5.78: 9 Bond angle restraints: 24325 Sorted by residual: angle pdb=" N3 DT J 129 " pdb=" C4 DT J 129 " pdb=" O4 DT J 129 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" N3 DT I 29 " pdb=" C4 DT I 29 " pdb=" O4 DT I 29 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT J 66 " pdb=" C4 DT J 66 " pdb=" O4 DT J 66 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.87e+01 angle pdb=" N3 DT I 75 " pdb=" C4 DT I 75 " pdb=" O4 DT I 75 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.85e+01 angle pdb=" N3 DT I 195 " pdb=" C4 DT I 195 " pdb=" O4 DT I 195 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 ... (remaining 24320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.10: 6209 17.10 - 34.21: 1286 34.21 - 51.31: 1119 51.31 - 68.41: 490 68.41 - 85.51: 21 Dihedral angle restraints: 9125 sinusoidal: 6332 harmonic: 2793 Sorted by residual: dihedral pdb=" CA PHE E 84 " pdb=" C PHE E 84 " pdb=" N GLN E 85 " pdb=" CA GLN E 85 " ideal model delta harmonic sigma weight residual 180.00 164.39 15.61 0 5.00e+00 4.00e-02 9.75e+00 dihedral pdb=" CA ARG E 128 " pdb=" CB ARG E 128 " pdb=" CG ARG E 128 " pdb=" CD ARG E 128 " ideal model delta sinusoidal sigma weight residual -180.00 -120.60 -59.40 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N LYS D 30 " pdb=" CA LYS D 30 " pdb=" CB LYS D 30 " pdb=" CG LYS D 30 " ideal model delta sinusoidal sigma weight residual -60.00 -117.86 57.86 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 9122 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1785 0.035 - 0.070: 468 0.070 - 0.105: 120 0.105 - 0.141: 242 0.141 - 0.176: 129 Chirality restraints: 2744 Sorted by residual: chirality pdb=" C3' DA J 155 " pdb=" C4' DA J 155 " pdb=" O3' DA J 155 " pdb=" C2' DA J 155 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 7.72e-01 chirality pdb=" C3' DG J 106 " pdb=" C4' DG J 106 " pdb=" O3' DG J 106 " pdb=" C2' DG J 106 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 7.49e-01 chirality pdb=" C3' DC I 122 " pdb=" C4' DC I 122 " pdb=" O3' DC I 122 " pdb=" C2' DC I 122 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 6.99e-01 ... (remaining 2741 not shown) Planarity restraints: 1712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT I 88 " 0.024 2.00e-02 2.50e+03 1.20e-02 3.62e+00 pdb=" N1 DT I 88 " -0.027 2.00e-02 2.50e+03 pdb=" C2 DT I 88 " -0.004 2.00e-02 2.50e+03 pdb=" O2 DT I 88 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DT I 88 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DT I 88 " 0.005 2.00e-02 2.50e+03 pdb=" O4 DT I 88 " 0.009 2.00e-02 2.50e+03 pdb=" C5 DT I 88 " -0.000 2.00e-02 2.50e+03 pdb=" C7 DT I 88 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DT I 88 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 86 " 0.023 2.00e-02 2.50e+03 1.17e-02 3.41e+00 pdb=" N1 DT I 86 " -0.027 2.00e-02 2.50e+03 pdb=" C2 DT I 86 " -0.003 2.00e-02 2.50e+03 pdb=" O2 DT I 86 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DT I 86 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DT I 86 " 0.003 2.00e-02 2.50e+03 pdb=" O4 DT I 86 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DT I 86 " 0.000 2.00e-02 2.50e+03 pdb=" C7 DT I 86 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DT I 86 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS O 237 " 0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO O 238 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO O 238 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO O 238 " 0.025 5.00e-02 4.00e+02 ... (remaining 1709 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1841 2.76 - 3.29: 13546 3.29 - 3.83: 30647 3.83 - 4.36: 36360 4.36 - 4.90: 51294 Nonbonded interactions: 133688 Sorted by model distance: nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.219 3.040 nonbonded pdb=" NZ LYS B 91 " pdb=" OE2 GLU H 71 " model vdw 2.235 3.120 nonbonded pdb=" OD2 ASP B 68 " pdb=" NE2 GLN B 93 " model vdw 2.313 3.120 nonbonded pdb=" OG1 THR H 90 " pdb=" OE1 GLU H 93 " model vdw 2.326 3.040 nonbonded pdb=" N GLU E 59 " pdb=" OE1 GLU E 59 " model vdw 2.340 3.120 ... (remaining 133683 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 37 through 133) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 9 through 119) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 30 through 125) } 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: 1.000 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: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.600 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 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 : 0.007 0.063 16779 Z= 0.591 Angle : 0.795 5.783 24325 Z= 0.695 Chirality : 0.059 0.176 2744 Planarity : 0.004 0.045 1712 Dihedral : 25.723 85.514 7325 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 0.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.69 % Favored : 98.20 % Rotamer: Outliers : 0.25 % Allowed : 1.86 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.46 (0.27), residues: 945 helix: 2.67 (0.21), residues: 616 sheet: -0.74 (1.27), residues: 20 loop : -0.40 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 208 TYR 0.008 0.001 TYR B 51 PHE 0.007 0.001 PHE A 67 TRP 0.017 0.002 TRP O 214 HIS 0.003 0.001 HIS O 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00698 / 0.59 (16779) covalent geometry : angle 0.79462 / 0.69 (24325) hydrogen bonds : bond 0.10685 / 6.82 ( 957) hydrogen bonds : angle 3.75018 / 2.65 ( 2364) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 190 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8675 (tt0) cc_final: 0.8297 (tt0) REVERT: A 123 ASP cc_start: 0.9411 (m-30) cc_final: 0.9149 (m-30) REVERT: D 68 ASP cc_start: 0.9004 (t0) cc_final: 0.8538 (t0) REVERT: D 72 ARG cc_start: 0.9138 (mtt180) cc_final: 0.8812 (mtt180) REVERT: F 59 LYS cc_start: 0.9227 (tttp) cc_final: 0.9014 (tttp) REVERT: G 101 THR cc_start: 0.9178 (t) cc_final: 0.8934 (t) REVERT: H 68 ASP cc_start: 0.9269 (t0) cc_final: 0.8868 (t0) REVERT: H 101 LEU cc_start: 0.9300 (mm) cc_final: 0.9006 (mm) REVERT: H 113 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8593 (mm-30) REVERT: O 201 MET cc_start: 0.6965 (ttt) cc_final: 0.6383 (tmm) REVERT: O 214 TRP cc_start: 0.7558 (p-90) cc_final: 0.7253 (p-90) outliers start: 2 outliers final: 0 residues processed: 191 average time/residue: 0.1904 time to fit residues: 48.4494 Evaluate side-chains 167 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 20.0000 chunk 55 optimal weight: 2.9990 chunk 129 optimal weight: 0.0970 overall best weight: 4.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN B 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.132500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.077680 restraints weight = 27075.888| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 1.46 r_work: 0.2771 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9025 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.087 16779 Z= 0.388 Angle : 0.762 7.736 24325 Z= 0.430 Chirality : 0.051 0.211 2744 Planarity : 0.005 0.056 1712 Dihedral : 30.042 80.721 5388 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.43 % Favored : 97.46 % Rotamer: Outliers : 1.12 % Allowed : 5.33 % Favored : 93.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.98 (0.27), residues: 945 helix: 2.26 (0.20), residues: 625 sheet: -0.74 (1.24), residues: 20 loop : -0.59 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 77 TYR 0.012 0.002 TYR H 121 PHE 0.013 0.002 PHE O 204 TRP 0.021 0.002 TRP O 214 HIS 0.004 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00837 / 0.39 (16779) covalent geometry : angle 0.76231 / 0.43 (24325) hydrogen bonds : bond 0.06308 / 4.32 ( 957) hydrogen bonds : angle 3.24304 / 2.32 ( 2364) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 164 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 13 LYS cc_start: 0.8983 (tppt) cc_final: 0.8757 (tttm) REVERT: C 99 ARG cc_start: 0.8783 (mmm160) cc_final: 0.8577 (mtp85) REVERT: D 68 ASP cc_start: 0.9095 (t0) cc_final: 0.8828 (t0) REVERT: E 73 GLU cc_start: 0.8992 (tt0) cc_final: 0.8778 (tt0) REVERT: F 35 ARG cc_start: 0.8800 (ttm-80) cc_final: 0.8471 (ttp80) REVERT: H 68 ASP cc_start: 0.9222 (t0) cc_final: 0.8798 (t0) REVERT: H 101 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.8872 (mm) REVERT: H 113 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8689 (mm-30) REVERT: O 201 MET cc_start: 0.6890 (ttt) cc_final: 0.6350 (tmm) REVERT: O 214 TRP cc_start: 0.7203 (p-90) cc_final: 0.6841 (p-90) outliers start: 9 outliers final: 6 residues processed: 168 average time/residue: 0.1835 time to fit residues: 41.6550 Evaluate side-chains 166 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 159 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 101 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 32 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 77 optimal weight: 20.0000 chunk 67 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 102 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 123 optimal weight: 20.0000 chunk 119 optimal weight: 0.3980 chunk 108 optimal weight: 10.0000 chunk 93 optimal weight: 50.0000 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN D 84 ASN E 113 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.135520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.081253 restraints weight = 27464.322| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.43 r_work: 0.2835 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16779 Z= 0.165 Angle : 0.622 6.273 24325 Z= 0.367 Chirality : 0.041 0.189 2744 Planarity : 0.004 0.058 1712 Dihedral : 30.185 82.427 5388 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.90 % Favored : 97.99 % Rotamer: Outliers : 0.37 % Allowed : 7.56 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.42 (0.27), residues: 945 helix: 2.60 (0.20), residues: 626 sheet: -0.70 (1.22), residues: 20 loop : -0.43 (0.34), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 86 TYR 0.013 0.001 TYR B 51 PHE 0.009 0.001 PHE A 67 TRP 0.019 0.002 TRP O 214 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.17 (16779) covalent geometry : angle 0.62186 / 0.37 (24325) hydrogen bonds : bond 0.04737 / 3.22 ( 957) hydrogen bonds : angle 2.93879 / 2.10 ( 2364) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 167 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.9159 (m-30) cc_final: 0.8917 (m-30) REVERT: E 73 GLU cc_start: 0.9011 (tt0) cc_final: 0.8759 (tt0) REVERT: F 35 ARG cc_start: 0.8802 (ttm-80) cc_final: 0.8492 (ttp80) REVERT: G 92 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8748 (mm-30) REVERT: G 101 THR cc_start: 0.9252 (OUTLIER) cc_final: 0.9012 (t) REVERT: H 68 ASP cc_start: 0.9194 (t0) cc_final: 0.8806 (t0) REVERT: H 101 LEU cc_start: 0.9322 (mm) cc_final: 0.8975 (mm) REVERT: H 113 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8633 (mm-30) REVERT: O 201 MET cc_start: 0.6856 (ttt) cc_final: 0.6324 (tmm) REVERT: O 214 TRP cc_start: 0.7219 (p-90) cc_final: 0.6849 (p-90) outliers start: 3 outliers final: 2 residues processed: 168 average time/residue: 0.1823 time to fit residues: 41.2817 Evaluate side-chains 167 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 164 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 71 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 66 optimal weight: 20.0000 chunk 87 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 70 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 2 optimal weight: 0.0570 chunk 30 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN B 93 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.136905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.082647 restraints weight = 27426.253| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.41 r_work: 0.2886 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8962 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16779 Z= 0.143 Angle : 0.582 7.200 24325 Z= 0.349 Chirality : 0.040 0.173 2744 Planarity : 0.004 0.058 1712 Dihedral : 30.200 81.505 5388 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.22 % Favored : 97.67 % Rotamer: Outliers : 0.87 % Allowed : 7.43 % Favored : 91.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.68 (0.27), residues: 945 helix: 2.80 (0.20), residues: 626 sheet: -0.60 (1.22), residues: 20 loop : -0.32 (0.34), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 86 TYR 0.011 0.001 TYR B 51 PHE 0.009 0.001 PHE A 67 TRP 0.017 0.002 TRP O 214 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.14 (16779) covalent geometry : angle 0.58202 / 0.35 (24325) hydrogen bonds : bond 0.04226 / 2.89 ( 957) hydrogen bonds : angle 2.77707 / 1.99 ( 2364) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 164 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 35 ARG cc_start: 0.8734 (ttm-80) cc_final: 0.8458 (ttp80) REVERT: G 101 THR cc_start: 0.9260 (OUTLIER) cc_final: 0.9022 (t) REVERT: H 68 ASP cc_start: 0.9125 (t0) cc_final: 0.8807 (t0) REVERT: H 101 LEU cc_start: 0.9321 (mm) cc_final: 0.8916 (mm) REVERT: H 113 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8538 (mm-30) REVERT: O 201 MET cc_start: 0.6892 (ttt) cc_final: 0.6334 (tmm) REVERT: O 214 TRP cc_start: 0.7262 (p-90) cc_final: 0.6880 (p-90) outliers start: 7 outliers final: 4 residues processed: 168 average time/residue: 0.1819 time to fit residues: 41.0692 Evaluate side-chains 166 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 161 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 71 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 77 optimal weight: 20.0000 chunk 14 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 119 optimal weight: 0.0050 chunk 110 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 overall best weight: 2.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN C 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.134907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.080401 restraints weight = 27252.346| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.41 r_work: 0.2806 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8981 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16779 Z= 0.216 Angle : 0.624 8.851 24325 Z= 0.360 Chirality : 0.042 0.175 2744 Planarity : 0.004 0.060 1712 Dihedral : 30.402 80.998 5388 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.33 % Favored : 97.57 % Rotamer: Outliers : 1.24 % Allowed : 8.05 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.61 (0.27), residues: 945 helix: 2.73 (0.20), residues: 626 sheet: -0.54 (1.23), residues: 20 loop : -0.33 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 86 TYR 0.011 0.001 TYR G 57 PHE 0.010 0.001 PHE A 67 TRP 0.019 0.002 TRP O 214 HIS 0.003 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.22 (16779) covalent geometry : angle 0.62352 / 0.36 (24325) hydrogen bonds : bond 0.04709 / 3.25 ( 957) hydrogen bonds : angle 2.86732 / 2.05 ( 2364) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 166 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 131 ARG cc_start: 0.9423 (OUTLIER) cc_final: 0.8747 (mtp180) REVERT: F 35 ARG cc_start: 0.8798 (ttm-80) cc_final: 0.8485 (ttp80) REVERT: G 101 THR cc_start: 0.9320 (OUTLIER) cc_final: 0.9080 (t) REVERT: H 68 ASP cc_start: 0.9252 (t0) cc_final: 0.8792 (t0) REVERT: H 101 LEU cc_start: 0.9338 (mm) cc_final: 0.8909 (mm) REVERT: H 113 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8609 (mm-30) REVERT: O 201 MET cc_start: 0.6849 (ttt) cc_final: 0.6376 (tmm) REVERT: O 214 TRP cc_start: 0.7284 (p-90) cc_final: 0.6899 (p-90) outliers start: 10 outliers final: 6 residues processed: 172 average time/residue: 0.1625 time to fit residues: 37.4791 Evaluate side-chains 174 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 166 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain U residue 93 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 63 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 97 optimal weight: 20.0000 chunk 110 optimal weight: 10.0000 chunk 8 optimal weight: 0.5980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN C 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.135701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.081239 restraints weight = 27278.050| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.40 r_work: 0.2846 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8973 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16779 Z= 0.155 Angle : 0.603 10.000 24325 Z= 0.352 Chirality : 0.041 0.207 2744 Planarity : 0.004 0.060 1712 Dihedral : 30.400 81.517 5388 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.22 % Favored : 97.67 % Rotamer: Outliers : 0.87 % Allowed : 8.92 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.64 (0.27), residues: 945 helix: 2.76 (0.20), residues: 626 sheet: -0.48 (1.23), residues: 20 loop : -0.32 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 86 TYR 0.010 0.001 TYR B 51 PHE 0.009 0.001 PHE A 67 TRP 0.019 0.002 TRP O 214 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.16 (16779) covalent geometry : angle 0.60262 / 0.35 (24325) hydrogen bonds : bond 0.04348 / 2.99 ( 957) hydrogen bonds : angle 2.81338 / 2.01 ( 2364) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 168 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 131 ARG cc_start: 0.9407 (OUTLIER) cc_final: 0.8645 (mtt180) REVERT: F 35 ARG cc_start: 0.8771 (ttm-80) cc_final: 0.8471 (ttp80) REVERT: G 101 THR cc_start: 0.9286 (OUTLIER) cc_final: 0.9045 (t) REVERT: H 68 ASP cc_start: 0.9216 (t0) cc_final: 0.8779 (t0) REVERT: H 101 LEU cc_start: 0.9332 (mm) cc_final: 0.8922 (mm) REVERT: H 113 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8545 (mm-30) REVERT: O 201 MET cc_start: 0.6827 (ttt) cc_final: 0.6367 (tmm) REVERT: O 214 TRP cc_start: 0.7283 (p-90) cc_final: 0.6899 (p-90) outliers start: 7 outliers final: 5 residues processed: 172 average time/residue: 0.1564 time to fit residues: 36.1392 Evaluate side-chains 172 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 165 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain U residue 93 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 56 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 84 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 123 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 75 optimal weight: 40.0000 chunk 112 optimal weight: 40.0000 chunk 76 optimal weight: 50.0000 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.136104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.081502 restraints weight = 27188.092| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.41 r_work: 0.2867 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16779 Z= 0.138 Angle : 0.599 10.737 24325 Z= 0.350 Chirality : 0.040 0.180 2744 Planarity : 0.004 0.060 1712 Dihedral : 30.386 81.583 5388 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.22 % Favored : 97.67 % Rotamer: Outliers : 0.74 % Allowed : 9.17 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.71 (0.27), residues: 945 helix: 2.81 (0.20), residues: 626 sheet: -0.43 (1.23), residues: 20 loop : -0.31 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 86 TYR 0.010 0.001 TYR B 51 PHE 0.009 0.001 PHE A 67 TRP 0.019 0.002 TRP O 214 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.14 (16779) covalent geometry : angle 0.59861 / 0.35 (24325) hydrogen bonds : bond 0.04233 / 2.91 ( 957) hydrogen bonds : angle 2.79997 / 2.00 ( 2364) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 166 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 59 GLU cc_start: 0.8982 (pm20) cc_final: 0.8624 (pm20) REVERT: F 35 ARG cc_start: 0.8747 (ttm-80) cc_final: 0.8463 (ttp80) REVERT: G 101 THR cc_start: 0.9272 (OUTLIER) cc_final: 0.9022 (t) REVERT: H 68 ASP cc_start: 0.9163 (t0) cc_final: 0.8765 (t0) REVERT: H 101 LEU cc_start: 0.9320 (mm) cc_final: 0.8929 (mm) REVERT: H 113 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8518 (mm-30) REVERT: O 201 MET cc_start: 0.6894 (ttt) cc_final: 0.6432 (tmm) REVERT: O 214 TRP cc_start: 0.7322 (p-90) cc_final: 0.6924 (p-90) outliers start: 6 outliers final: 4 residues processed: 170 average time/residue: 0.1553 time to fit residues: 35.6117 Evaluate side-chains 168 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 163 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain U residue 93 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 12 optimal weight: 3.9990 chunk 118 optimal weight: 30.0000 chunk 22 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 70 optimal weight: 0.9980 chunk 91 optimal weight: 20.0000 chunk 27 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 58 optimal weight: 0.9980 chunk 120 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN C 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.136633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.082481 restraints weight = 27261.438| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.41 r_work: 0.2866 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16779 Z= 0.136 Angle : 0.589 9.513 24325 Z= 0.346 Chirality : 0.040 0.177 2744 Planarity : 0.004 0.060 1712 Dihedral : 30.354 81.667 5388 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.43 % Favored : 97.46 % Rotamer: Outliers : 0.99 % Allowed : 9.05 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.78 (0.27), residues: 945 helix: 2.87 (0.20), residues: 626 sheet: -0.31 (1.23), residues: 20 loop : -0.30 (0.34), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 86 TYR 0.010 0.001 TYR B 51 PHE 0.009 0.001 PHE A 67 TRP 0.019 0.002 TRP O 214 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.14 (16779) covalent geometry : angle 0.58916 / 0.35 (24325) hydrogen bonds : bond 0.04116 / 2.83 ( 957) hydrogen bonds : angle 2.76371 / 1.98 ( 2364) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 164 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 59 GLU cc_start: 0.9053 (pm20) cc_final: 0.8655 (pm20) REVERT: E 131 ARG cc_start: 0.9385 (OUTLIER) cc_final: 0.8600 (mtt180) REVERT: F 35 ARG cc_start: 0.8772 (ttm-80) cc_final: 0.8492 (ttp80) REVERT: G 101 THR cc_start: 0.9278 (OUTLIER) cc_final: 0.9034 (t) REVERT: H 68 ASP cc_start: 0.9188 (t0) cc_final: 0.8783 (t0) REVERT: H 101 LEU cc_start: 0.9314 (mm) cc_final: 0.8920 (mm) REVERT: H 113 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8521 (mm-30) REVERT: O 201 MET cc_start: 0.6890 (ttt) cc_final: 0.6431 (tmm) REVERT: O 214 TRP cc_start: 0.7318 (p-90) cc_final: 0.6916 (p-90) outliers start: 8 outliers final: 5 residues processed: 168 average time/residue: 0.1591 time to fit residues: 35.9428 Evaluate side-chains 170 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 163 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain U residue 93 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 84 optimal weight: 10.0000 chunk 34 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 103 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 98 optimal weight: 10.0000 chunk 71 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.136851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.082648 restraints weight = 27234.341| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.42 r_work: 0.2875 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16779 Z= 0.144 Angle : 0.577 8.826 24325 Z= 0.342 Chirality : 0.039 0.167 2744 Planarity : 0.004 0.060 1712 Dihedral : 30.332 81.143 5388 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.43 % Favored : 97.46 % Rotamer: Outliers : 0.87 % Allowed : 8.92 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.83 (0.27), residues: 945 helix: 2.91 (0.20), residues: 626 sheet: -0.27 (1.24), residues: 20 loop : -0.28 (0.34), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 86 TYR 0.009 0.001 TYR G 57 PHE 0.009 0.001 PHE A 67 TRP 0.020 0.002 TRP O 214 HIS 0.003 0.000 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.14 (16779) covalent geometry : angle 0.57733 / 0.34 (24325) hydrogen bonds : bond 0.04040 / 2.78 ( 957) hydrogen bonds : angle 2.72497 / 1.95 ( 2364) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 165 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 131 ARG cc_start: 0.9381 (OUTLIER) cc_final: 0.8614 (mtt180) REVERT: F 35 ARG cc_start: 0.8766 (ttm-80) cc_final: 0.8460 (ttp80) REVERT: G 101 THR cc_start: 0.9278 (OUTLIER) cc_final: 0.9034 (t) REVERT: H 34 LYS cc_start: 0.9303 (mtmm) cc_final: 0.8987 (mmmm) REVERT: H 68 ASP cc_start: 0.9178 (t0) cc_final: 0.8815 (t0) REVERT: H 101 LEU cc_start: 0.9317 (mm) cc_final: 0.8939 (mm) REVERT: H 113 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8634 (mm-30) REVERT: O 201 MET cc_start: 0.6890 (ttt) cc_final: 0.6424 (tmm) REVERT: O 214 TRP cc_start: 0.7310 (p-90) cc_final: 0.6957 (p-90) outliers start: 7 outliers final: 5 residues processed: 169 average time/residue: 0.1516 time to fit residues: 34.3251 Evaluate side-chains 170 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 163 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain U residue 93 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 25 optimal weight: 0.9980 chunk 113 optimal weight: 8.9990 chunk 94 optimal weight: 50.0000 chunk 27 optimal weight: 0.0370 chunk 97 optimal weight: 20.0000 chunk 28 optimal weight: 0.9990 chunk 7 optimal weight: 0.2980 chunk 35 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 chunk 120 optimal weight: 20.0000 chunk 38 optimal weight: 0.7980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN C 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.137262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.083172 restraints weight = 27284.301| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.45 r_work: 0.2884 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16779 Z= 0.130 Angle : 0.577 10.403 24325 Z= 0.341 Chirality : 0.039 0.165 2744 Planarity : 0.004 0.060 1712 Dihedral : 30.324 81.161 5388 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.43 % Favored : 97.46 % Rotamer: Outliers : 0.87 % Allowed : 9.42 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.88 (0.27), residues: 945 helix: 2.95 (0.20), residues: 626 sheet: -0.25 (1.24), residues: 20 loop : -0.27 (0.34), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 86 TYR 0.010 0.001 TYR B 51 PHE 0.009 0.001 PHE A 67 TRP 0.019 0.002 TRP O 214 HIS 0.005 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.13 (16779) covalent geometry : angle 0.57740 / 0.34 (24325) hydrogen bonds : bond 0.03952 / 2.72 ( 957) hydrogen bonds : angle 2.71180 / 1.94 ( 2364) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 164 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 59 GLU cc_start: 0.9004 (pm20) cc_final: 0.8677 (pm20) REVERT: E 131 ARG cc_start: 0.9373 (OUTLIER) cc_final: 0.8634 (mtt180) REVERT: F 35 ARG cc_start: 0.8756 (ttm-80) cc_final: 0.8458 (ttp80) REVERT: G 101 THR cc_start: 0.9274 (OUTLIER) cc_final: 0.9030 (t) REVERT: H 34 LYS cc_start: 0.9304 (mtmm) cc_final: 0.8992 (mmmm) REVERT: H 68 ASP cc_start: 0.9157 (t0) cc_final: 0.8802 (t0) REVERT: H 101 LEU cc_start: 0.9314 (mm) cc_final: 0.8941 (mm) REVERT: H 113 GLU cc_start: 0.8962 (mm-30) cc_final: 0.8627 (mm-30) REVERT: O 201 MET cc_start: 0.6885 (ttt) cc_final: 0.6422 (tmm) REVERT: O 214 TRP cc_start: 0.7323 (p-90) cc_final: 0.6963 (p-90) outliers start: 7 outliers final: 5 residues processed: 168 average time/residue: 0.1651 time to fit residues: 37.1720 Evaluate side-chains 168 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 161 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain U residue 93 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 4 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 121 optimal weight: 0.0980 chunk 16 optimal weight: 0.2980 chunk 5 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.137369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.083298 restraints weight = 27293.723| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.46 r_work: 0.2889 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16779 Z= 0.128 Angle : 0.578 10.818 24325 Z= 0.342 Chirality : 0.039 0.165 2744 Planarity : 0.004 0.060 1712 Dihedral : 30.316 81.209 5388 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.43 % Favored : 97.46 % Rotamer: Outliers : 0.87 % Allowed : 9.54 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.91 (0.27), residues: 945 helix: 2.97 (0.20), residues: 626 sheet: -0.22 (1.24), residues: 20 loop : -0.26 (0.34), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 86 TYR 0.010 0.001 TYR B 51 PHE 0.009 0.001 PHE A 67 TRP 0.019 0.002 TRP O 214 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.13 (16779) covalent geometry : angle 0.57794 / 0.34 (24325) hydrogen bonds : bond 0.03926 / 2.70 ( 957) hydrogen bonds : angle 2.70436 / 1.93 ( 2364) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4761.40 seconds wall clock time: 81 minutes 35.34 seconds (4895.34 seconds total)