Starting phenix.real_space_refine on Wed Aug 5 15:22:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ube_42084/08_2026/8ube_42084.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ube_42084/08_2026/8ube_42084.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ube_42084/08_2026/8ube_42084.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ube_42084/08_2026/8ube_42084.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ube_42084/08_2026/8ube_42084.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ube_42084/08_2026/8ube_42084.map" } resolution = 3.05 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= 0.030 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 167 5.49 5 S 36 5.16 5 C 6142 2.51 5 N 1900 2.21 5 O 2368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 10613 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2562 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain breaks: 1 Chain: "B" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 976 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "C" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 888 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "D" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 879 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "E" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 876 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "F" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 879 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "G" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 243 Classifications: {'RNA': 11} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 3} Link IDs: {'rna3p': 10} Chain: "H" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 350 Classifications: {'RNA': 17} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 2, 'rna3p_pyr': 10} Link IDs: {'rna2p': 4, 'rna3p': 12} Chain: "I" Number of atoms: 2960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2960 Classifications: {'RNA': 139} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 17, 'rna3p_pur': 57, 'rna3p_pyr': 53} Link IDs: {'rna2p': 29, 'rna3p': 109} Time building chain proxies: 2.34, per 1000 atoms: 0.22 Number of scatterers: 10613 At special positions: 0 Unit cell: (86, 105, 130, 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 36 16.00 P 167 15.00 O 2368 8.00 N 1900 7.00 C 6142 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: 0.75 Conformation dependent library (CDL) restraints added in 192.7 milliseconds 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1642 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 2 sheets defined 76.8% alpha, 1.5% beta 34 base pairs and 87 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 8 through 13 Processing helix chain 'A' and resid 14 through 27 Processing helix chain 'A' and resid 32 through 40 removed outlier: 3.873A pdb=" N GLU A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 54 removed outlier: 3.576A pdb=" N LEU A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 91 Processing helix chain 'A' and resid 94 through 99 Processing helix chain 'A' and resid 114 through 126 Processing helix chain 'A' and resid 141 through 146 Processing helix chain 'A' and resid 150 through 154 removed outlier: 3.606A pdb=" N ALA A 153 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 172 Processing helix chain 'A' and resid 183 through 191 Processing helix chain 'A' and resid 194 through 199 Processing helix chain 'A' and resid 203 through 207 removed outlier: 3.598A pdb=" N LYS A 206 " --> pdb=" O ASP A 203 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLN A 207 " --> pdb=" O GLU A 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 203 through 207' Processing helix chain 'A' and resid 223 through 241 Processing helix chain 'A' and resid 275 through 289 Processing helix chain 'A' and resid 294 through 307 removed outlier: 3.906A pdb=" N ARG A 298 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'B' and resid 10 through 28 Processing helix chain 'B' and resid 38 through 50 Processing helix chain 'B' and resid 51 through 62 Processing helix chain 'B' and resid 64 through 87 removed outlier: 3.965A pdb=" N LEU B 68 " --> pdb=" O GLN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 122 Processing helix chain 'C' and resid 12 through 34 removed outlier: 3.733A pdb=" N ARG C 22 " --> pdb=" O GLU C 18 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) Proline residue: C 29 - end of helix Processing helix chain 'C' and resid 38 through 63 removed outlier: 3.834A pdb=" N VAL C 53 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU C 54 " --> pdb=" O LEU C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 88 removed outlier: 3.932A pdb=" N ALA C 86 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY C 87 " --> pdb=" O ARG C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 121 Processing helix chain 'D' and resid 14 through 34 removed outlier: 3.790A pdb=" N ARG D 22 " --> pdb=" O GLU D 18 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL D 23 " --> pdb=" O ARG D 19 " (cutoff:3.500A) Proline residue: D 29 - end of helix Processing helix chain 'D' and resid 38 through 62 removed outlier: 3.767A pdb=" N VAL D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLU D 54 " --> pdb=" O LEU D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 86 removed outlier: 3.755A pdb=" N LEU D 68 " --> pdb=" O GLN D 64 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA D 70 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA D 71 " --> pdb=" O LYS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 121 Processing helix chain 'E' and resid 13 through 34 removed outlier: 3.726A pdb=" N ARG E 22 " --> pdb=" O GLU E 18 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL E 23 " --> pdb=" O ARG E 19 " (cutoff:3.500A) Proline residue: E 29 - end of helix Processing helix chain 'E' and resid 35 through 37 No H-bonds generated for 'chain 'E' and resid 35 through 37' Processing helix chain 'E' and resid 38 through 50 Processing helix chain 'E' and resid 51 through 61 Processing helix chain 'E' and resid 65 through 86 Processing helix chain 'E' and resid 95 through 121 Processing helix chain 'F' and resid 14 through 34 removed outlier: 4.548A pdb=" N ARG F 22 " --> pdb=" O GLU F 18 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL F 23 " --> pdb=" O ARG F 19 " (cutoff:3.500A) Proline residue: F 29 - end of helix Processing helix chain 'F' and resid 35 through 37 No H-bonds generated for 'chain 'F' and resid 35 through 37' Processing helix chain 'F' and resid 38 through 61 removed outlier: 3.915A pdb=" N VAL F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLU F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 87 Processing helix chain 'F' and resid 88 through 93 Proline residue: F 91 - end of helix No H-bonds generated for 'chain 'F' and resid 88 through 93' Processing helix chain 'F' and resid 95 through 122 removed outlier: 4.410A pdb=" N LEU F 105 " --> pdb=" O THR F 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 211 through 212 Processing sheet with id=AA2, first strand: chain 'A' and resid 259 through 260 480 hydrogen bonds defined for protein. 1425 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 87 hydrogen bonds 134 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 87 stacking parallelities Total time for adding SS restraints: 1.96 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1268 1.30 - 1.43: 3903 1.43 - 1.56: 5618 1.56 - 1.70: 334 1.70 - 1.83: 61 Bond restraints: 11184 Sorted by residual: bond pdb=" C PRO E 35 " pdb=" O PRO E 35 " ideal model delta sigma weight residual 1.233 1.167 0.066 1.19e-02 7.06e+03 3.06e+01 bond pdb=" CA ARG B 36 " pdb=" CB ARG B 36 " ideal model delta sigma weight residual 1.530 1.603 -0.073 1.57e-02 4.06e+03 2.18e+01 bond pdb=" CG HIS E 38 " pdb=" CD2 HIS E 38 " ideal model delta sigma weight residual 1.354 1.305 0.049 1.10e-02 8.26e+03 2.00e+01 bond pdb=" CA SER A 186 " pdb=" CB SER A 186 " ideal model delta sigma weight residual 1.530 1.457 0.073 1.69e-02 3.50e+03 1.85e+01 bond pdb=" CG LYS A 278 " pdb=" CD LYS A 278 " ideal model delta sigma weight residual 1.520 1.401 0.119 3.00e-02 1.11e+03 1.58e+01 ... (remaining 11179 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.01: 14854 3.01 - 6.01: 934 6.01 - 9.02: 115 9.02 - 12.02: 14 12.02 - 15.03: 6 Bond angle restraints: 15923 Sorted by residual: angle pdb=" C3' C I 28 " pdb=" O3' C I 28 " pdb=" P G I 29 " ideal model delta sigma weight residual 119.70 104.67 15.03 1.20e+00 6.94e-01 1.57e+02 angle pdb=" C3' U I 106 " pdb=" O3' U I 106 " pdb=" P C I 107 " ideal model delta sigma weight residual 119.70 105.15 14.55 1.20e+00 6.94e-01 1.47e+02 angle pdb=" C3' C I 107 " pdb=" O3' C I 107 " pdb=" P G I 108 " ideal model delta sigma weight residual 119.70 106.00 13.70 1.20e+00 6.94e-01 1.30e+02 angle pdb=" C3' G I 26 " pdb=" O3' G I 26 " pdb=" P G I 27 " ideal model delta sigma weight residual 119.70 106.94 12.76 1.20e+00 6.94e-01 1.13e+02 angle pdb=" C3' C I 78 " pdb=" O3' C I 78 " pdb=" P G I 79 " ideal model delta sigma weight residual 119.70 107.01 12.69 1.20e+00 6.94e-01 1.12e+02 ... (remaining 15918 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.75: 6003 35.75 - 71.50: 855 71.50 - 107.25: 100 107.25 - 143.00: 4 143.00 - 178.75: 5 Dihedral angle restraints: 6967 sinusoidal: 4421 harmonic: 2546 Sorted by residual: dihedral pdb=" O4' C I 82 " pdb=" C1' C I 82 " pdb=" N1 C I 82 " pdb=" C2 C I 82 " ideal model delta sinusoidal sigma weight residual 232.00 53.25 178.75 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U I 94 " pdb=" C1' U I 94 " pdb=" N1 U I 94 " pdb=" C2 U I 94 " ideal model delta sinusoidal sigma weight residual 232.00 54.32 177.68 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C I 59 " pdb=" C1' C I 59 " pdb=" N1 C I 59 " pdb=" C2 C I 59 " ideal model delta sinusoidal sigma weight residual 232.00 58.83 173.17 1 1.70e+01 3.46e-03 6.62e+01 ... (remaining 6964 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 1427 0.111 - 0.223: 401 0.223 - 0.334: 37 0.334 - 0.445: 33 0.445 - 0.557: 10 Chirality restraints: 1908 Sorted by residual: chirality pdb=" P G G 371 " pdb=" OP1 G G 371 " pdb=" OP2 G G 371 " pdb=" O5' G G 371 " both_signs ideal model delta sigma weight residual True 2.41 -2.97 -0.56 2.00e-01 2.50e+01 7.75e+00 chirality pdb=" P G G 372 " pdb=" OP1 G G 372 " pdb=" OP2 G G 372 " pdb=" O5' G G 372 " both_signs ideal model delta sigma weight residual True 2.41 -2.94 -0.53 2.00e-01 2.50e+01 7.11e+00 chirality pdb=" P U H 118 " pdb=" OP1 U H 118 " pdb=" OP2 U H 118 " pdb=" O5' U H 118 " both_signs ideal model delta sigma weight residual True 2.41 -2.94 -0.53 2.00e-01 2.50e+01 6.96e+00 ... (remaining 1905 not shown) Planarity restraints: 1395 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 28 " 0.089 2.00e-02 2.50e+03 4.58e-02 4.20e+01 pdb=" CG TYR C 28 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TYR C 28 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR C 28 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR C 28 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR C 28 " -0.021 2.00e-02 2.50e+03 pdb=" CZ TYR C 28 " 0.027 2.00e-02 2.50e+03 pdb=" OH TYR C 28 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 28 " -0.062 2.00e-02 2.50e+03 3.54e-02 2.50e+01 pdb=" CG TYR D 28 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR D 28 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TYR D 28 " 0.059 2.00e-02 2.50e+03 pdb=" CE1 TYR D 28 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR D 28 " -0.023 2.00e-02 2.50e+03 pdb=" CZ TYR D 28 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR D 28 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 163 " 0.024 2.00e-02 2.50e+03 4.84e-02 2.34e+01 pdb=" C ALA A 163 " -0.084 2.00e-02 2.50e+03 pdb=" O ALA A 163 " 0.032 2.00e-02 2.50e+03 pdb=" N THR A 164 " 0.028 2.00e-02 2.50e+03 ... (remaining 1392 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.26: 2 2.26 - 2.92: 5253 2.92 - 3.58: 18827 3.58 - 4.24: 33867 4.24 - 4.90: 48219 Nonbonded interactions: 106168 Sorted by model distance: nonbonded pdb=" O3' G H 134 " pdb=" P C I 1 " model vdw 1.606 3.400 nonbonded pdb=" NE2 GLN E 98 " pdb=" O3' C I 17 " model vdw 2.261 3.120 nonbonded pdb=" NZ LYS D 47 " pdb=" OE2 GLU E 43 " model vdw 2.295 3.120 nonbonded pdb=" O ILE B 34 " pdb=" O PRO B 35 " model vdw 2.299 3.040 nonbonded pdb=" O SER A 140 " pdb=" N PHE A 142 " model vdw 2.305 3.120 ... (remaining 106163 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 'B' and resid 13 through 121) selection = (chain 'C' and resid 13 through 121) selection = (chain 'D' and resid 13 through 121) selection = (chain 'E' and resid 13 through 121) selection = (chain 'F' and resid 13 through 121) } 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=0.00 max=1.00 mean=0.99 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: 3.480 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.460 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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:0.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6342 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 : 0.012 0.119 11184 Z= 0.758 Angle : 1.630 15.031 15923 Z= 1.090 Chirality : 0.113 0.557 1908 Planarity : 0.011 0.091 1395 Dihedral : 26.943 178.748 5325 Min Nonbonded Distance : 1.606 Molprobity Statistics. All-atom Clashscore : 51.44 Ramachandran Plot: Outliers : 3.94 % Allowed : 11.48 % Favored : 84.57 % Rotamer: Outliers : 23.26 % Allowed : 12.31 % Favored : 64.43 % Cbeta Deviations : 0.12 % 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: -4.56 (0.22), residues: 862 helix: -2.25 (0.16), residues: 619 sheet: -5.97 (0.64), residues: 10 loop : -4.67 (0.29), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.003 ARG A 6 TYR 0.089 0.011 TYR C 28 PHE 0.050 0.010 PHE C 84 TRP 0.042 0.009 TRP C 116 HIS 0.016 0.004 HIS A 248 Details of bonding type rmsd/Z covalent geometry : bond 0.01210 / 0.76 (11184) covalent geometry : angle 1.63015 / 1.09 (15923) hydrogen bonds : bond 0.23218 / 14.83 ( 567) hydrogen bonds : angle 10.41068 / 7.13 ( 1559) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 293 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4776 (mmt) cc_final: 0.4575 (mpp) REVERT: A 16 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8158 (mp0) REVERT: A 22 TYR cc_start: 0.7939 (t80) cc_final: 0.7714 (t80) REVERT: A 27 HIS cc_start: 0.7733 (t70) cc_final: 0.7475 (t70) REVERT: A 39 LYS cc_start: 0.5829 (OUTLIER) cc_final: 0.5271 (ttpt) REVERT: A 58 TYR cc_start: 0.7603 (t80) cc_final: 0.7300 (t80) REVERT: A 59 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8201 (tm-30) REVERT: A 84 ARG cc_start: 0.6745 (mtm110) cc_final: 0.6534 (mtm110) REVERT: A 107 TYR cc_start: 0.8280 (m-80) cc_final: 0.7938 (m-80) REVERT: A 116 HIS cc_start: 0.8549 (m-70) cc_final: 0.8235 (t70) REVERT: A 127 ARG cc_start: 0.7191 (OUTLIER) cc_final: 0.6937 (mtp180) REVERT: A 156 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7217 (m-30) REVERT: A 165 ARG cc_start: 0.6678 (OUTLIER) cc_final: 0.6218 (mtp180) REVERT: A 220 LEU cc_start: 0.7642 (mt) cc_final: 0.7307 (mt) REVERT: A 263 TYR cc_start: 0.6669 (m-80) cc_final: 0.6416 (m-10) REVERT: A 270 LYS cc_start: 0.7534 (OUTLIER) cc_final: 0.7241 (pttp) REVERT: B 1 MET cc_start: 0.5546 (tmm) cc_final: 0.5132 (ttp) REVERT: B 54 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6787 (tt0) REVERT: B 65 VAL cc_start: 0.7958 (OUTLIER) cc_final: 0.7745 (p) REVERT: B 94 MET cc_start: 0.8043 (mtp) cc_final: 0.7762 (mtm) REVERT: B 108 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6859 (tp30) REVERT: B 116 TRP cc_start: 0.8115 (t60) cc_final: 0.7391 (t60) REVERT: C 21 GLU cc_start: 0.7387 (mm-30) cc_final: 0.6722 (tt0) REVERT: C 44 MET cc_start: 0.6906 (mtp) cc_final: 0.6472 (mtp) REVERT: C 91 PRO cc_start: 0.7729 (OUTLIER) cc_final: 0.7522 (Cg_endo) REVERT: C 94 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8155 (ttm) REVERT: D 18 GLU cc_start: 0.6274 (OUTLIER) cc_final: 0.5775 (tp30) REVERT: D 62 SER cc_start: 0.7743 (OUTLIER) cc_final: 0.6983 (p) REVERT: D 64 GLN cc_start: 0.7203 (OUTLIER) cc_final: 0.6932 (pm20) REVERT: D 77 MET cc_start: 0.8234 (tpt) cc_final: 0.7915 (tpp) REVERT: D 89 GLN cc_start: 0.7144 (OUTLIER) cc_final: 0.6633 (tp40) REVERT: D 100 GLU cc_start: 0.6732 (tm-30) cc_final: 0.6429 (mm-30) REVERT: D 103 GLN cc_start: 0.6323 (OUTLIER) cc_final: 0.6047 (mt0) REVERT: D 111 ARG cc_start: 0.6988 (mtm-85) cc_final: 0.6753 (mtt180) REVERT: E 14 MET cc_start: 0.5086 (mmt) cc_final: 0.4433 (mpp) REVERT: E 22 ARG cc_start: 0.7543 (mtp85) cc_final: 0.7253 (mtp85) REVERT: E 54 GLU cc_start: 0.7532 (tt0) cc_final: 0.7017 (tt0) REVERT: E 83 ARG cc_start: 0.7259 (OUTLIER) cc_final: 0.7047 (ttp-110) REVERT: F 14 MET cc_start: 0.5995 (OUTLIER) cc_final: 0.3848 (ttt) REVERT: F 21 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7916 (mt-10) REVERT: F 26 TYR cc_start: 0.6499 (t80) cc_final: 0.6146 (t80) REVERT: F 54 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.6371 (tp30) REVERT: F 77 MET cc_start: 0.7206 (tpt) cc_final: 0.6446 (tpt) REVERT: F 88 ILE cc_start: 0.7540 (OUTLIER) cc_final: 0.7337 (tt) REVERT: F 94 MET cc_start: 0.7789 (ttm) cc_final: 0.7586 (ttp) outliers start: 170 outliers final: 49 residues processed: 385 average time/residue: 0.1408 time to fit residues: 70.3179 Evaluate side-chains 298 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 228 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 161 CYS Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 91 PRO Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain C residue 94 MET Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 37 LYS Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 64 GLN Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain D residue 122 ARG Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 83 ARG Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 14 MET Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 113 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 50.0000 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 10.0000 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 GLN ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN C 32 GLN C 92 HIS C 97 HIS C 121 ASN D 32 GLN E 63 ASN E 103 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.221471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.159736 restraints weight = 13297.270| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 1.81 r_work: 0.3717 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 11184 Z= 0.287 Angle : 0.924 11.530 15923 Z= 0.494 Chirality : 0.053 0.266 1908 Planarity : 0.008 0.090 1395 Dihedral : 26.756 179.191 3798 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 32.85 Ramachandran Plot: Outliers : 1.28 % Allowed : 8.24 % Favored : 90.49 % Rotamer: Outliers : 10.67 % Allowed : 19.15 % Favored : 70.18 % 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 (0.25), residues: 862 helix: -0.92 (0.18), residues: 655 sheet: -5.52 (0.90), residues: 10 loop : -4.06 (0.37), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 19 TYR 0.028 0.004 TYR F 28 PHE 0.032 0.004 PHE A 231 TRP 0.022 0.003 TRP A 303 HIS 0.008 0.003 HIS D 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00639 / 0.29 (11184) covalent geometry : angle 0.92382 / 0.49 (15923) hydrogen bonds : bond 0.08390 / 5.30 ( 567) hydrogen bonds : angle 6.05556 / 4.28 ( 1559) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 227 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 ARG cc_start: 0.6460 (OUTLIER) cc_final: 0.6172 (ptm160) REVERT: A 27 HIS cc_start: 0.7904 (t70) cc_final: 0.7633 (t-90) REVERT: A 39 LYS cc_start: 0.7198 (OUTLIER) cc_final: 0.6851 (ttpt) REVERT: A 103 LEU cc_start: 0.8150 (mt) cc_final: 0.7945 (mt) REVERT: A 115 THR cc_start: 0.7895 (OUTLIER) cc_final: 0.7565 (t) REVERT: A 116 HIS cc_start: 0.8093 (m-70) cc_final: 0.7818 (t70) REVERT: A 127 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7551 (mtt90) REVERT: A 152 TYR cc_start: 0.7599 (m-80) cc_final: 0.7204 (m-80) REVERT: A 165 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7524 (mtt180) REVERT: B 2 GLU cc_start: 0.7591 (pp20) cc_final: 0.7371 (pp20) REVERT: C 43 GLU cc_start: 0.8114 (pt0) cc_final: 0.7829 (mt-10) REVERT: D 15 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7379 (pt) REVERT: D 103 GLN cc_start: 0.7374 (OUTLIER) cc_final: 0.6735 (mt0) REVERT: E 14 MET cc_start: 0.5949 (mmt) cc_final: 0.5570 (mpp) REVERT: E 50 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7564 (mt) REVERT: E 111 ARG cc_start: 0.8136 (mtm-85) cc_final: 0.7401 (mtm110) REVERT: F 13 GLN cc_start: 0.4019 (tp-100) cc_final: 0.3671 (tp-100) REVERT: F 14 MET cc_start: 0.5238 (OUTLIER) cc_final: 0.3854 (ttt) REVERT: F 20 TYR cc_start: 0.7901 (t80) cc_final: 0.7387 (t80) REVERT: F 22 ARG cc_start: 0.7819 (ptp90) cc_final: 0.7396 (ptm-80) REVERT: F 26 TYR cc_start: 0.7062 (t80) cc_final: 0.6453 (t80) outliers start: 78 outliers final: 43 residues processed: 271 average time/residue: 0.1019 time to fit residues: 37.2412 Evaluate side-chains 253 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 201 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 32 GLN Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain D residue 122 ARG Chi-restraints excluded: chain E residue 13 GLN Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain F residue 14 MET Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 113 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 75 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 33 optimal weight: 0.3980 chunk 95 optimal weight: 50.0000 chunk 2 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 77 optimal weight: 0.5980 chunk 90 optimal weight: 10.0000 chunk 9 optimal weight: 0.4980 chunk 63 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 GLN C 32 GLN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.221653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.160080 restraints weight = 13423.719| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 1.75 r_work: 0.3749 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 11184 Z= 0.233 Angle : 0.797 11.147 15923 Z= 0.426 Chirality : 0.045 0.261 1908 Planarity : 0.007 0.092 1395 Dihedral : 26.270 178.910 3710 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 29.71 Ramachandran Plot: Outliers : 1.16 % Allowed : 8.12 % Favored : 90.72 % Rotamer: Outliers : 9.03 % Allowed : 22.16 % Favored : 68.81 % 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: -1.95 (0.27), residues: 862 helix: -0.53 (0.19), residues: 656 sheet: -5.27 (1.04), residues: 10 loop : -3.39 (0.41), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 208 TYR 0.029 0.003 TYR A 105 PHE 0.029 0.004 PHE A 231 TRP 0.027 0.003 TRP A 303 HIS 0.011 0.002 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.23 (11184) covalent geometry : angle 0.79715 / 0.43 (15923) hydrogen bonds : bond 0.07078 / 4.50 ( 567) hydrogen bonds : angle 5.74101 / 4.08 ( 1559) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 222 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 HIS cc_start: 0.7874 (t70) cc_final: 0.7654 (t70) REVERT: A 39 LYS cc_start: 0.7199 (OUTLIER) cc_final: 0.6701 (ttpt) REVERT: A 127 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7654 (mtt90) REVERT: A 135 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7030 (tp) REVERT: A 152 TYR cc_start: 0.7538 (m-80) cc_final: 0.7197 (m-80) REVERT: A 165 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7525 (mtt180) REVERT: A 210 TRP cc_start: 0.8099 (p-90) cc_final: 0.7802 (p-90) REVERT: A 260 PHE cc_start: 0.7661 (t80) cc_final: 0.7438 (t80) REVERT: A 274 LYS cc_start: 0.4667 (pptt) cc_final: 0.4013 (pttm) REVERT: B 2 GLU cc_start: 0.7815 (pp20) cc_final: 0.7611 (pp20) REVERT: B 108 GLU cc_start: 0.7336 (tp30) cc_final: 0.7117 (tp30) REVERT: B 116 TRP cc_start: 0.8745 (t60) cc_final: 0.8143 (t60) REVERT: C 43 GLU cc_start: 0.8058 (pt0) cc_final: 0.7788 (mt-10) REVERT: D 103 GLN cc_start: 0.7375 (OUTLIER) cc_final: 0.6865 (mt0) REVERT: E 14 MET cc_start: 0.6280 (mmt) cc_final: 0.5736 (mpp) REVERT: E 50 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7560 (mt) REVERT: F 14 MET cc_start: 0.4767 (mmp) cc_final: 0.3791 (ttt) REVERT: F 20 TYR cc_start: 0.7979 (t80) cc_final: 0.7507 (t80) REVERT: F 22 ARG cc_start: 0.7804 (ptp90) cc_final: 0.7407 (ptm-80) REVERT: F 26 TYR cc_start: 0.7012 (t80) cc_final: 0.6316 (t80) outliers start: 66 outliers final: 38 residues processed: 260 average time/residue: 0.1049 time to fit residues: 36.6283 Evaluate side-chains 237 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 193 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain B residue 37 LYS Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain D residue 122 ARG Chi-restraints excluded: chain E residue 13 GLN Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 113 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 47 optimal weight: 0.5980 chunk 98 optimal weight: 40.0000 chunk 67 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 88 optimal weight: 50.0000 chunk 78 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 ASN ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 HIS ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 GLN E 89 GLN ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 ASN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.220483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.159111 restraints weight = 13436.836| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 1.82 r_work: 0.3731 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 11184 Z= 0.244 Angle : 0.749 7.872 15923 Z= 0.403 Chirality : 0.045 0.305 1908 Planarity : 0.006 0.078 1395 Dihedral : 25.978 178.648 3695 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 28.06 Ramachandran Plot: Outliers : 0.93 % Allowed : 7.54 % Favored : 91.53 % Rotamer: Outliers : 8.34 % Allowed : 22.44 % Favored : 69.22 % 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: -1.67 (0.27), residues: 862 helix: -0.29 (0.19), residues: 654 sheet: -5.19 (1.05), residues: 10 loop : -3.41 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 19 TYR 0.028 0.003 TYR C 28 PHE 0.027 0.003 PHE A 231 TRP 0.018 0.002 TRP A 303 HIS 0.015 0.002 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.24 (11184) covalent geometry : angle 0.74924 / 0.40 (15923) hydrogen bonds : bond 0.06674 / 4.22 ( 567) hydrogen bonds : angle 5.57988 / 3.99 ( 1559) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 209 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.7367 (OUTLIER) cc_final: 0.6947 (ttpt) REVERT: A 125 GLU cc_start: 0.5273 (OUTLIER) cc_final: 0.5041 (tp30) REVERT: A 152 TYR cc_start: 0.7686 (m-80) cc_final: 0.7419 (m-80) REVERT: A 165 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7486 (mtt180) REVERT: A 207 GLN cc_start: 0.6826 (mm-40) cc_final: 0.6519 (mm110) REVERT: A 260 PHE cc_start: 0.7638 (t80) cc_final: 0.7382 (t80) REVERT: A 274 LYS cc_start: 0.4268 (pptt) cc_final: 0.3926 (pttm) REVERT: B 77 MET cc_start: 0.8502 (tpt) cc_final: 0.7957 (tpt) REVERT: B 108 GLU cc_start: 0.7303 (tp30) cc_final: 0.7051 (tp30) REVERT: C 43 GLU cc_start: 0.8024 (pt0) cc_final: 0.7676 (mt-10) REVERT: E 14 MET cc_start: 0.6364 (mmt) cc_final: 0.5723 (mpp) REVERT: E 50 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7588 (mt) REVERT: F 14 MET cc_start: 0.4529 (mmp) cc_final: 0.3756 (ttt) REVERT: F 20 TYR cc_start: 0.7999 (t80) cc_final: 0.7530 (t80) REVERT: F 21 GLU cc_start: 0.7360 (mt-10) cc_final: 0.7129 (mt-10) REVERT: F 22 ARG cc_start: 0.7803 (ptp90) cc_final: 0.7407 (ptm-80) REVERT: F 26 TYR cc_start: 0.6892 (t80) cc_final: 0.6155 (t80) outliers start: 61 outliers final: 41 residues processed: 244 average time/residue: 0.1052 time to fit residues: 34.2229 Evaluate side-chains 234 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 189 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain B residue 37 LYS Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 100 GLU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 122 ARG Chi-restraints excluded: chain E residue 13 GLN Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 95 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 44 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 99 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.221543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.159215 restraints weight = 13446.644| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 1.77 r_work: 0.3758 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 11184 Z= 0.219 Angle : 0.724 12.034 15923 Z= 0.386 Chirality : 0.043 0.306 1908 Planarity : 0.006 0.079 1395 Dihedral : 25.687 178.410 3687 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 25.69 Ramachandran Plot: Outliers : 1.04 % Allowed : 7.54 % Favored : 91.42 % Rotamer: Outliers : 7.39 % Allowed : 22.71 % Favored : 69.90 % 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: -1.40 (0.28), residues: 862 helix: -0.13 (0.19), residues: 654 sheet: -5.01 (1.16), residues: 10 loop : -3.17 (0.43), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 22 TYR 0.026 0.003 TYR C 28 PHE 0.027 0.003 PHE A 260 TRP 0.020 0.002 TRP A 303 HIS 0.017 0.002 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.22 (11184) covalent geometry : angle 0.72424 / 0.39 (15923) hydrogen bonds : bond 0.06344 / 4.01 ( 567) hydrogen bonds : angle 5.44537 / 3.92 ( 1559) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 204 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.7430 (OUTLIER) cc_final: 0.6894 (ttpt) REVERT: A 125 GLU cc_start: 0.5428 (OUTLIER) cc_final: 0.5049 (tp30) REVERT: A 141 LYS cc_start: 0.7127 (OUTLIER) cc_final: 0.6913 (pttp) REVERT: A 152 TYR cc_start: 0.7784 (m-80) cc_final: 0.7550 (m-80) REVERT: A 165 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7166 (mtp180) REVERT: A 191 ASN cc_start: 0.8312 (m110) cc_final: 0.7775 (m-40) REVERT: A 274 LYS cc_start: 0.4031 (pptt) cc_final: 0.3761 (pttm) REVERT: B 108 GLU cc_start: 0.7193 (tp30) cc_final: 0.6842 (tp30) REVERT: B 119 ARG cc_start: 0.7474 (OUTLIER) cc_final: 0.7200 (ptt90) REVERT: C 43 GLU cc_start: 0.7950 (pt0) cc_final: 0.7509 (mt-10) REVERT: D 47 LYS cc_start: 0.8133 (mttm) cc_final: 0.7800 (mmtt) REVERT: D 103 GLN cc_start: 0.7638 (OUTLIER) cc_final: 0.7149 (mt0) REVERT: E 14 MET cc_start: 0.6249 (mmt) cc_final: 0.5669 (mpp) REVERT: E 50 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7530 (mt) REVERT: F 14 MET cc_start: 0.4173 (mmp) cc_final: 0.3443 (ttm) REVERT: F 20 TYR cc_start: 0.7997 (t80) cc_final: 0.7651 (t80) REVERT: F 21 GLU cc_start: 0.7355 (mt-10) cc_final: 0.7059 (mt-10) REVERT: F 22 ARG cc_start: 0.7816 (ptp90) cc_final: 0.7387 (ptm-80) REVERT: F 26 TYR cc_start: 0.6905 (t80) cc_final: 0.6311 (t80) outliers start: 54 outliers final: 40 residues processed: 237 average time/residue: 0.1182 time to fit residues: 37.2164 Evaluate side-chains 241 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 194 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain B residue 37 LYS Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 122 ARG Chi-restraints excluded: chain E residue 13 GLN Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 95 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 97 optimal weight: 50.0000 chunk 54 optimal weight: 0.4980 chunk 52 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 68 optimal weight: 0.0970 chunk 24 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 70 optimal weight: 0.5980 chunk 64 optimal weight: 0.0270 chunk 85 optimal weight: 0.6980 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 HIS ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.223708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.161436 restraints weight = 13539.038| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 1.95 r_work: 0.3792 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 11184 Z= 0.184 Angle : 0.682 9.035 15923 Z= 0.368 Chirality : 0.042 0.269 1908 Planarity : 0.006 0.077 1395 Dihedral : 25.430 178.303 3687 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 24.77 Ramachandran Plot: Outliers : 1.04 % Allowed : 6.50 % Favored : 92.46 % Rotamer: Outliers : 6.29 % Allowed : 25.31 % Favored : 68.40 % 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: -1.07 (0.28), residues: 862 helix: 0.08 (0.20), residues: 649 sheet: -4.84 (1.03), residues: 12 loop : -2.85 (0.45), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 19 TYR 0.024 0.002 TYR D 26 PHE 0.040 0.003 PHE A 260 TRP 0.024 0.002 TRP E 116 HIS 0.019 0.002 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (11184) covalent geometry : angle 0.68179 / 0.37 (15923) hydrogen bonds : bond 0.06070 / 3.84 ( 567) hydrogen bonds : angle 5.29510 / 3.80 ( 1559) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 204 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4350 (mpp) cc_final: 0.3755 (mpp) REVERT: A 39 LYS cc_start: 0.7348 (OUTLIER) cc_final: 0.6793 (ttpt) REVERT: A 125 GLU cc_start: 0.5250 (OUTLIER) cc_final: 0.4942 (tp30) REVERT: A 181 ILE cc_start: 0.7349 (OUTLIER) cc_final: 0.7045 (mp) REVERT: A 191 ASN cc_start: 0.8287 (m110) cc_final: 0.7764 (m-40) REVERT: B 108 GLU cc_start: 0.7082 (tp30) cc_final: 0.6769 (tp30) REVERT: B 119 ARG cc_start: 0.7427 (OUTLIER) cc_final: 0.7148 (ptt90) REVERT: C 26 TYR cc_start: 0.7571 (t80) cc_final: 0.7340 (t80) REVERT: C 43 GLU cc_start: 0.7946 (pt0) cc_final: 0.7552 (mt-10) REVERT: D 44 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7857 (mtp) REVERT: D 47 LYS cc_start: 0.8222 (mttm) cc_final: 0.7900 (mmtt) REVERT: D 103 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.7122 (mt0) REVERT: E 14 MET cc_start: 0.6250 (mmt) cc_final: 0.5666 (mpp) REVERT: E 50 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7353 (mt) REVERT: F 14 MET cc_start: 0.3991 (mmp) cc_final: 0.3597 (ttm) REVERT: F 21 GLU cc_start: 0.7429 (mt-10) cc_final: 0.7142 (mt-10) REVERT: F 22 ARG cc_start: 0.7652 (ptp90) cc_final: 0.7240 (ptm-80) REVERT: F 26 TYR cc_start: 0.6731 (t80) cc_final: 0.6194 (t80) outliers start: 46 outliers final: 32 residues processed: 231 average time/residue: 0.1107 time to fit residues: 33.9225 Evaluate side-chains 227 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 188 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain B residue 37 LYS Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain E residue 13 GLN Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 95 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 99 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 chunk 36 optimal weight: 0.4980 chunk 82 optimal weight: 0.6980 chunk 26 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 chunk 43 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 94 optimal weight: 50.0000 chunk 40 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.222484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.162014 restraints weight = 13427.526| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 1.75 r_work: 0.3773 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.5300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 11184 Z= 0.206 Angle : 0.710 8.492 15923 Z= 0.376 Chirality : 0.043 0.412 1908 Planarity : 0.006 0.064 1395 Dihedral : 25.229 178.296 3672 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 24.15 Ramachandran Plot: Outliers : 0.93 % Allowed : 6.96 % Favored : 92.11 % Rotamer: Outliers : 5.75 % Allowed : 25.31 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -1.03 (0.28), residues: 862 helix: 0.05 (0.20), residues: 658 sheet: -4.56 (1.14), residues: 12 loop : -2.74 (0.47), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 273 TYR 0.027 0.003 TYR C 28 PHE 0.041 0.003 PHE A 260 TRP 0.046 0.003 TRP E 116 HIS 0.016 0.002 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.21 (11184) covalent geometry : angle 0.70958 / 0.38 (15923) hydrogen bonds : bond 0.06024 / 3.80 ( 567) hydrogen bonds : angle 5.30186 / 3.79 ( 1559) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 196 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.7390 (OUTLIER) cc_final: 0.6872 (ttpt) REVERT: A 125 GLU cc_start: 0.5276 (OUTLIER) cc_final: 0.5007 (tp30) REVERT: A 165 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7404 (mtt180) REVERT: A 181 ILE cc_start: 0.7456 (OUTLIER) cc_final: 0.7156 (mp) REVERT: A 191 ASN cc_start: 0.8288 (m110) cc_final: 0.7882 (m-40) REVERT: B 37 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8230 (ptmm) REVERT: B 108 GLU cc_start: 0.7013 (tp30) cc_final: 0.6626 (tp30) REVERT: B 119 ARG cc_start: 0.7312 (OUTLIER) cc_final: 0.6996 (ptt90) REVERT: D 47 LYS cc_start: 0.8217 (mttm) cc_final: 0.7924 (mmtt) REVERT: D 103 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.7161 (mt0) REVERT: E 14 MET cc_start: 0.6383 (mmt) cc_final: 0.5733 (mpp) REVERT: E 50 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7398 (mt) REVERT: F 14 MET cc_start: 0.3792 (mmp) cc_final: 0.3518 (ttm) REVERT: F 21 GLU cc_start: 0.7405 (mt-10) cc_final: 0.7154 (mt-10) REVERT: F 22 ARG cc_start: 0.7713 (ptp90) cc_final: 0.7382 (ptm-80) REVERT: F 26 TYR cc_start: 0.6887 (t80) cc_final: 0.6295 (t80) outliers start: 42 outliers final: 27 residues processed: 220 average time/residue: 0.1022 time to fit residues: 30.1089 Evaluate side-chains 217 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 182 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain B residue 37 LYS Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain E residue 13 GLN Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 68 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 40 optimal weight: 0.4980 chunk 84 optimal weight: 0.6980 chunk 41 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.222955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.161085 restraints weight = 13400.834| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 1.87 r_work: 0.3781 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.5473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 11184 Z= 0.202 Angle : 0.704 9.125 15923 Z= 0.374 Chirality : 0.043 0.411 1908 Planarity : 0.006 0.066 1395 Dihedral : 25.033 178.300 3670 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 24.46 Ramachandran Plot: Outliers : 0.70 % Allowed : 6.61 % Favored : 92.69 % Rotamer: Outliers : 6.02 % Allowed : 25.85 % Favored : 68.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -1.15 (0.28), residues: 862 helix: -0.02 (0.19), residues: 657 sheet: -4.32 (1.32), residues: 12 loop : -2.84 (0.45), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 19 TYR 0.026 0.003 TYR D 26 PHE 0.040 0.003 PHE A 260 TRP 0.030 0.002 TRP E 116 HIS 0.020 0.002 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.20 (11184) covalent geometry : angle 0.70445 / 0.37 (15923) hydrogen bonds : bond 0.05946 / 3.76 ( 567) hydrogen bonds : angle 5.28898 / 3.78 ( 1559) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 195 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4373 (mpp) cc_final: 0.3719 (mpp) REVERT: A 39 LYS cc_start: 0.7403 (OUTLIER) cc_final: 0.6877 (ttpt) REVERT: A 125 GLU cc_start: 0.5460 (OUTLIER) cc_final: 0.5103 (tp30) REVERT: A 165 ARG cc_start: 0.7724 (OUTLIER) cc_final: 0.7339 (mtt180) REVERT: A 181 ILE cc_start: 0.7410 (OUTLIER) cc_final: 0.7098 (mp) REVERT: A 191 ASN cc_start: 0.8297 (m110) cc_final: 0.7894 (m-40) REVERT: B 108 GLU cc_start: 0.7012 (tp30) cc_final: 0.6648 (tp30) REVERT: B 119 ARG cc_start: 0.7306 (OUTLIER) cc_final: 0.7027 (ptt90) REVERT: C 20 TYR cc_start: 0.7692 (t80) cc_final: 0.7427 (t80) REVERT: C 43 GLU cc_start: 0.7918 (pt0) cc_final: 0.7620 (mt-10) REVERT: D 15 LEU cc_start: 0.7718 (tp) cc_final: 0.7379 (pt) REVERT: D 47 LYS cc_start: 0.8190 (mttm) cc_final: 0.7878 (mmtt) REVERT: D 103 GLN cc_start: 0.7685 (OUTLIER) cc_final: 0.7323 (tp40) REVERT: E 14 MET cc_start: 0.6415 (mmt) cc_final: 0.5722 (mpp) REVERT: E 50 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7470 (mt) REVERT: E 54 GLU cc_start: 0.7751 (tt0) cc_final: 0.7512 (tt0) REVERT: F 14 MET cc_start: 0.3844 (mmp) cc_final: 0.3624 (ttm) REVERT: F 21 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7323 (mt-10) REVERT: F 22 ARG cc_start: 0.7688 (ptp90) cc_final: 0.7361 (ptm-80) REVERT: F 26 TYR cc_start: 0.6864 (t80) cc_final: 0.6337 (t80) outliers start: 44 outliers final: 32 residues processed: 222 average time/residue: 0.1170 time to fit residues: 34.3588 Evaluate side-chains 223 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 184 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain B residue 37 LYS Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain E residue 13 GLN Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 68 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 17 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 97 optimal weight: 50.0000 chunk 59 optimal weight: 0.7980 chunk 47 optimal weight: 0.0970 chunk 99 optimal weight: 9.9990 chunk 46 optimal weight: 0.8980 chunk 101 optimal weight: 9.9990 chunk 89 optimal weight: 7.9990 chunk 93 optimal weight: 40.0000 chunk 10 optimal weight: 0.7980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 123 GLN ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.223706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.163393 restraints weight = 13406.499| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 1.84 r_work: 0.3746 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.5636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 11184 Z= 0.210 Angle : 0.711 9.919 15923 Z= 0.376 Chirality : 0.043 0.368 1908 Planarity : 0.006 0.063 1395 Dihedral : 24.907 178.459 3668 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 25.33 Ramachandran Plot: Outliers : 0.58 % Allowed : 7.08 % Favored : 92.34 % Rotamer: Outliers : 5.75 % Allowed : 26.68 % Favored : 67.58 % 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: -1.22 (0.28), residues: 862 helix: -0.09 (0.19), residues: 658 sheet: -3.94 (1.45), residues: 12 loop : -2.84 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 256 TYR 0.029 0.003 TYR A 232 PHE 0.038 0.003 PHE A 260 TRP 0.020 0.002 TRP A 303 HIS 0.024 0.002 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.21 (11184) covalent geometry : angle 0.71073 / 0.38 (15923) hydrogen bonds : bond 0.05940 / 3.77 ( 567) hydrogen bonds : angle 5.32882 / 3.82 ( 1559) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 191 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4240 (mpp) cc_final: 0.3697 (mpp) REVERT: A 39 LYS cc_start: 0.7343 (OUTLIER) cc_final: 0.6938 (ttpt) REVERT: A 125 GLU cc_start: 0.5383 (OUTLIER) cc_final: 0.5079 (tp30) REVERT: A 127 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7671 (mpt-90) REVERT: A 141 LYS cc_start: 0.7348 (pttp) cc_final: 0.7008 (pttp) REVERT: A 165 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7316 (mtt180) REVERT: A 181 ILE cc_start: 0.7400 (OUTLIER) cc_final: 0.7072 (mp) REVERT: A 191 ASN cc_start: 0.8312 (m110) cc_final: 0.7925 (m-40) REVERT: B 37 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8367 (ptmm) REVERT: B 108 GLU cc_start: 0.6950 (tp30) cc_final: 0.6566 (tp30) REVERT: B 113 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7778 (tp) REVERT: B 119 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.7163 (ptm160) REVERT: C 43 GLU cc_start: 0.7938 (pt0) cc_final: 0.7634 (mt-10) REVERT: C 92 HIS cc_start: 0.6874 (OUTLIER) cc_final: 0.6446 (m-70) REVERT: D 15 LEU cc_start: 0.7770 (tp) cc_final: 0.7462 (pt) REVERT: D 47 LYS cc_start: 0.8242 (mttm) cc_final: 0.7907 (mmtt) REVERT: D 100 GLU cc_start: 0.6861 (mm-30) cc_final: 0.6470 (mm-30) REVERT: D 103 GLN cc_start: 0.7659 (OUTLIER) cc_final: 0.7166 (mt0) REVERT: E 14 MET cc_start: 0.6520 (mmt) cc_final: 0.5675 (mpp) REVERT: E 54 GLU cc_start: 0.7633 (tt0) cc_final: 0.7338 (tt0) REVERT: F 14 MET cc_start: 0.3820 (mmp) cc_final: 0.3572 (ttm) REVERT: F 21 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7341 (mt-10) REVERT: F 22 ARG cc_start: 0.7667 (ptp90) cc_final: 0.7360 (ptm-80) REVERT: F 26 TYR cc_start: 0.6912 (t80) cc_final: 0.6402 (t80) outliers start: 42 outliers final: 29 residues processed: 217 average time/residue: 0.1218 time to fit residues: 35.2064 Evaluate side-chains 222 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 183 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 37 LYS Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 92 HIS Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain E residue 13 GLN Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 68 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 40 optimal weight: 0.3980 chunk 14 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 8.9990 chunk 69 optimal weight: 0.4980 chunk 23 optimal weight: 9.9990 chunk 60 optimal weight: 0.0970 chunk 15 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.224878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.161216 restraints weight = 13458.858| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 1.75 r_work: 0.3815 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.5904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 11184 Z= 0.183 Angle : 0.696 10.706 15923 Z= 0.367 Chirality : 0.043 0.331 1908 Planarity : 0.006 0.061 1395 Dihedral : 24.779 178.483 3665 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 24.05 Ramachandran Plot: Outliers : 0.58 % Allowed : 7.19 % Favored : 92.23 % Rotamer: Outliers : 5.75 % Allowed : 26.68 % Favored : 67.58 % 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: -1.20 (0.28), residues: 862 helix: -0.05 (0.19), residues: 658 sheet: -3.67 (1.57), residues: 12 loop : -2.94 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 19 TYR 0.022 0.002 TYR C 28 PHE 0.046 0.003 PHE A 231 TRP 0.019 0.002 TRP A 303 HIS 0.016 0.002 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (11184) covalent geometry : angle 0.69601 / 0.37 (15923) hydrogen bonds : bond 0.05778 / 3.67 ( 567) hydrogen bonds : angle 5.32540 / 3.83 ( 1559) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 195 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4243 (mpp) cc_final: 0.3729 (mpp) REVERT: A 39 LYS cc_start: 0.7312 (OUTLIER) cc_final: 0.6952 (ttpt) REVERT: A 57 ASN cc_start: 0.7448 (t0) cc_final: 0.7177 (t0) REVERT: A 125 GLU cc_start: 0.5326 (OUTLIER) cc_final: 0.5035 (tp30) REVERT: A 127 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7806 (mpt-90) REVERT: A 141 LYS cc_start: 0.7298 (pttp) cc_final: 0.7004 (pttp) REVERT: A 165 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.7289 (mtt180) REVERT: A 191 ASN cc_start: 0.8248 (m110) cc_final: 0.7889 (m-40) REVERT: A 232 TYR cc_start: 0.7366 (m-80) cc_final: 0.7099 (m-80) REVERT: B 21 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7697 (mt-10) REVERT: B 108 GLU cc_start: 0.6690 (tp30) cc_final: 0.6428 (tp30) REVERT: B 113 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7685 (tp) REVERT: B 119 ARG cc_start: 0.7391 (OUTLIER) cc_final: 0.7080 (ptt90) REVERT: C 111 ARG cc_start: 0.7604 (ttp80) cc_final: 0.6139 (mtt180) REVERT: D 47 LYS cc_start: 0.8228 (mttm) cc_final: 0.7920 (mmtt) REVERT: D 100 GLU cc_start: 0.6806 (mm-30) cc_final: 0.6432 (mm-30) REVERT: D 103 GLN cc_start: 0.7555 (OUTLIER) cc_final: 0.7238 (tp40) REVERT: E 14 MET cc_start: 0.6343 (mmt) cc_final: 0.5613 (mpp) REVERT: E 54 GLU cc_start: 0.7481 (tt0) cc_final: 0.7205 (tt0) REVERT: F 21 GLU cc_start: 0.7435 (mt-10) cc_final: 0.7185 (mt-10) REVERT: F 22 ARG cc_start: 0.7546 (ptp90) cc_final: 0.7333 (ptm-80) REVERT: F 26 TYR cc_start: 0.6784 (t80) cc_final: 0.6236 (t80) REVERT: F 43 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6640 (tp30) outliers start: 42 outliers final: 26 residues processed: 219 average time/residue: 0.1340 time to fit residues: 39.0162 Evaluate side-chains 221 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 187 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 138 ASP Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 265 ILE Chi-restraints excluded: chain B residue 37 LYS Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain E residue 13 GLN Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 30 ILE Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 68 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 66 optimal weight: 0.5980 chunk 96 optimal weight: 50.0000 chunk 42 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 29 optimal weight: 20.0000 chunk 99 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 GLN A 123 GLN ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.222565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.162727 restraints weight = 13455.370| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 1.92 r_work: 0.3716 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.5931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 11184 Z= 0.250 Angle : 0.743 9.897 15923 Z= 0.389 Chirality : 0.045 0.354 1908 Planarity : 0.006 0.082 1395 Dihedral : 24.758 178.744 3663 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 25.23 Ramachandran Plot: Outliers : 0.58 % Allowed : 6.96 % Favored : 92.46 % Rotamer: Outliers : 4.51 % Allowed : 28.18 % Favored : 67.31 % 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: -1.21 (0.28), residues: 862 helix: -0.11 (0.19), residues: 659 sheet: -3.25 (1.56), residues: 12 loop : -2.76 (0.46), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 19 TYR 0.030 0.003 TYR C 28 PHE 0.049 0.003 PHE A 231 TRP 0.018 0.002 TRP A 303 HIS 0.021 0.002 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.25 (11184) covalent geometry : angle 0.74258 / 0.39 (15923) hydrogen bonds : bond 0.06019 / 3.80 ( 567) hydrogen bonds : angle 5.43966 / 3.92 ( 1559) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2537.10 seconds wall clock time: 44 minutes 22.44 seconds (2662.44 seconds total)