Starting phenix.real_space_refine on Thu Jul 2 21:41:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ube_42084/07_2026/8ube_42084.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ube_42084/07_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_42084/07_2026/8ube_42084.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ube_42084/07_2026/8ube_42084.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ube_42084/07_2026/8ube_42084.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ube_42084/07_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-dev-6108/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: 2.87, per 1000 atoms: 0.27 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: 0.98 Conformation dependent library (CDL) restraints added in 344.8 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: 1.63 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: 2.14 Time building geometry restraints manager: 1.31 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 - 3.11: 14908 3.11 - 6.21: 882 6.21 - 9.32: 115 9.32 - 12.42: 12 12.42 - 15.53: 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 120.20 104.67 15.53 1.50e+00 4.44e-01 1.07e+02 angle pdb=" C3' U I 106 " pdb=" O3' U I 106 " pdb=" P C I 107 " ideal model delta sigma weight residual 120.20 105.15 15.05 1.50e+00 4.44e-01 1.01e+02 angle pdb=" C3' C I 107 " pdb=" O3' C I 107 " pdb=" P G I 108 " ideal model delta sigma weight residual 120.20 106.00 14.20 1.50e+00 4.44e-01 8.96e+01 angle pdb=" C3' G I 26 " pdb=" O3' G I 26 " pdb=" P G I 27 " ideal model delta sigma weight residual 120.20 106.94 13.26 1.50e+00 4.44e-01 7.82e+01 angle pdb=" C3' C I 78 " pdb=" O3' C I 78 " pdb=" P G I 79 " ideal model delta sigma weight residual 120.20 107.01 13.19 1.50e+00 4.44e-01 7.73e+01 ... (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: 1392 0.111 - 0.223: 434 0.223 - 0.334: 39 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: 2.620 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: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 13.530 Find NCS groups from input model: 0.130 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: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.040 ------------------------------------------------------------------------------- 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= 0.727 Angle : 1.654 15.531 15923 Z= 1.067 Chirality : 0.116 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 0.01209 / 0.73 (11184) covalent geometry : angle 1.65390 / 1.07 (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 : 0.324 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: 0.4574 (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: 0.7937 (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: 0.6982 (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: 0.7308 (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: 0.6445 (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: 48 residues processed: 385 average time/residue: 0.1534 time to fit residues: 76.1240 Evaluate side-chains 295 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 226 time to evaluate : 0.311 ------------------------------------------------------------------------------- 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 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: 30.0000 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 9.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4661 r_free = 0.4661 target = 0.221576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.159638 restraints weight = 13350.059| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 2.04 r_work: 0.3701 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.3055 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= 0.289 Angle : 0.901 11.980 15923 Z= 0.489 Chirality : 0.050 0.260 1908 Planarity : 0.008 0.088 1395 Dihedral : 26.843 179.910 3794 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 33.62 Ramachandran Plot: Outliers : 1.28 % Allowed : 8.47 % Favored : 90.26 % Rotamer: Outliers : 10.26 % Allowed : 19.56 % 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: -2.57 (0.26), residues: 862 helix: -0.83 (0.18), residues: 649 sheet: -5.53 (0.90), residues: 10 loop : -4.10 (0.37), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 19 TYR 0.028 0.003 TYR F 28 PHE 0.032 0.004 PHE A 231 TRP 0.021 0.003 TRP A 303 HIS 0.008 0.003 HIS D 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00649 / 0.29 (11184) covalent geometry : angle 0.90115 / 0.49 (15923) hydrogen bonds : bond 0.08149 / 5.14 ( 567) hydrogen bonds : angle 6.04100 / 4.27 ( 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 301 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 226 time to evaluate : 0.324 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: A 27 HIS cc_start: 0.7902 (t70) cc_final: 0.7619 (t-90) REVERT: A 39 LYS cc_start: 0.7215 (OUTLIER) cc_final: 0.6859 (ttpt) REVERT: A 115 THR cc_start: 0.7916 (OUTLIER) cc_final: 0.7561 (t) REVERT: A 116 HIS cc_start: 0.8061 (m-70) cc_final: 0.7746 (t70) REVERT: A 127 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7581 (mtp180) REVERT: A 152 TYR cc_start: 0.7606 (m-80) cc_final: 0.7213 (m-80) REVERT: A 165 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7482 (mtt180) REVERT: A 274 LYS cc_start: 0.4809 (OUTLIER) cc_final: 0.4561 (pttp) REVERT: B 1 MET cc_start: 0.7048 (tmm) cc_final: 0.6665 (tmm) REVERT: B 32 GLN cc_start: 0.8117 (mm110) cc_final: 0.7824 (mm-40) REVERT: C 43 GLU cc_start: 0.8132 (pt0) cc_final: 0.7797 (mt-10) REVERT: D 15 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7444 (pt) REVERT: D 103 GLN cc_start: 0.7372 (OUTLIER) cc_final: 0.6840 (mt0) REVERT: E 14 MET cc_start: 0.5979 (mmt) cc_final: 0.5558 (mpp) REVERT: E 50 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7578 (mt) REVERT: F 13 GLN cc_start: 0.4149 (tp-100) cc_final: 0.3775 (tp-100) REVERT: F 14 MET cc_start: 0.5225 (OUTLIER) cc_final: 0.3821 (ttt) REVERT: F 20 TYR cc_start: 0.7954 (t80) cc_final: 0.7350 (t80) REVERT: F 22 ARG cc_start: 0.7897 (ptp90) cc_final: 0.7448 (ptm-80) REVERT: F 26 TYR cc_start: 0.7078 (t80) cc_final: 0.6471 (t80) outliers start: 75 outliers final: 41 residues processed: 267 average time/residue: 0.1250 time to fit residues: 45.4058 Evaluate side-chains 252 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 202 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 187 GLN Chi-restraints excluded: chain A residue 197 VAL 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 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 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 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 14 MET 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 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: 0.9980 chunk 46 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 33 optimal weight: 0.1980 chunk 95 optimal weight: 40.0000 chunk 2 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 90 optimal weight: 7.9990 chunk 9 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4664 r_free = 0.4664 target = 0.221408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.161292 restraints weight = 13491.335| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 1.98 r_work: 0.3723 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 11184 Z= 0.252 Angle : 0.790 11.235 15923 Z= 0.429 Chirality : 0.046 0.259 1908 Planarity : 0.007 0.092 1395 Dihedral : 26.304 179.018 3716 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 29.14 Ramachandran Plot: Outliers : 1.16 % Allowed : 8.47 % Favored : 90.37 % Rotamer: Outliers : 9.30 % Allowed : 20.93 % Favored : 69.77 % 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: -1.94 (0.27), residues: 862 helix: -0.54 (0.19), residues: 659 sheet: -5.18 (1.14), residues: 10 loop : -3.37 (0.41), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 208 TYR 0.031 0.003 TYR D 28 PHE 0.028 0.004 PHE A 231 TRP 0.027 0.002 TRP A 303 HIS 0.010 0.002 HIS A 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.25 (11184) covalent geometry : angle 0.79049 / 0.43 (15923) hydrogen bonds : bond 0.06939 / 4.39 ( 567) hydrogen bonds : angle 5.75324 / 4.09 ( 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 283 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 215 time to evaluate : 0.341 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: 0.7970 (t70) cc_final: 0.7748 (t70) REVERT: A 39 LYS cc_start: 0.7383 (OUTLIER) cc_final: 0.6994 (ttpt) REVERT: A 135 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7107 (tp) REVERT: A 152 TYR cc_start: 0.7593 (m-80) cc_final: 0.7259 (m-80) REVERT: A 165 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7524 (mtt180) REVERT: A 210 TRP cc_start: 0.8113 (p-90) cc_final: 0.7886 (p-90) REVERT: A 260 PHE cc_start: 0.7799 (t80) cc_final: 0.7547 (t80) REVERT: B 108 GLU cc_start: 0.7405 (tp30) cc_final: 0.7192 (tp30) REVERT: B 116 TRP cc_start: 0.8809 (t60) cc_final: 0.8189 (t60) REVERT: C 43 GLU cc_start: 0.8093 (pt0) cc_final: 0.7846 (mt-10) REVERT: D 103 GLN cc_start: 0.7426 (OUTLIER) cc_final: 0.6923 (mt0) REVERT: E 14 MET cc_start: 0.6343 (mmt) cc_final: 0.5777 (mpp) REVERT: E 50 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7554 (mt) REVERT: F 14 MET cc_start: 0.4826 (mmp) cc_final: 0.3847 (ttt) REVERT: F 20 TYR cc_start: 0.8001 (t80) cc_final: 0.7463 (t80) REVERT: F 22 ARG cc_start: 0.7868 (ptp90) cc_final: 0.7477 (ptm-80) REVERT: F 26 TYR cc_start: 0.6892 (t80) cc_final: 0.6198 (t80) outliers start: 68 outliers final: 40 residues processed: 259 average time/residue: 0.1343 time to fit residues: 46.4967 Evaluate side-chains 237 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 192 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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 97 ILE Chi-restraints excluded: chain A residue 125 GLU 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 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 66 SER Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain D residue 32 GLN 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 47 optimal weight: 0.8980 chunk 98 optimal weight: 30.0000 chunk 67 optimal weight: 0.9980 chunk 31 optimal weight: 0.0000 chunk 45 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 88 optimal weight: 40.0000 chunk 78 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 overall best weight: 0.6984 ------------------------------------------------------------------------------- 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 A 290 HIS ** C 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.221560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.161827 restraints weight = 13503.476| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 2.00 r_work: 0.3725 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 11184 Z= 0.235 Angle : 0.732 8.447 15923 Z= 0.400 Chirality : 0.045 0.329 1908 Planarity : 0.006 0.078 1395 Dihedral : 25.984 178.702 3693 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 27.44 Ramachandran Plot: Outliers : 1.04 % Allowed : 7.42 % Favored : 91.53 % Rotamer: Outliers : 8.21 % Allowed : 21.89 % 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: -1.64 (0.28), residues: 862 helix: -0.30 (0.19), residues: 654 sheet: -5.08 (0.99), residues: 12 loop : -3.23 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG C 19 TYR 0.027 0.003 TYR C 28 PHE 0.026 0.003 PHE A 231 TRP 0.022 0.002 TRP E 116 HIS 0.013 0.002 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00535 / 0.23 (11184) covalent geometry : angle 0.73165 / 0.40 (15923) hydrogen bonds : bond 0.06475 / 4.09 ( 567) hydrogen bonds : angle 5.56804 / 3.98 ( 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 271 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 211 time to evaluate : 0.287 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: A 27 HIS cc_start: 0.7971 (t70) cc_final: 0.7769 (t70) REVERT: A 39 LYS cc_start: 0.7361 (OUTLIER) cc_final: 0.6955 (ttpt) REVERT: A 125 GLU cc_start: 0.5257 (OUTLIER) cc_final: 0.5035 (tp30) REVERT: A 152 TYR cc_start: 0.7778 (m-80) cc_final: 0.7541 (m-80) REVERT: A 165 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7517 (mtt180) REVERT: A 210 TRP cc_start: 0.8090 (p-90) cc_final: 0.7715 (p-90) REVERT: A 260 PHE cc_start: 0.7640 (t80) cc_final: 0.7429 (t80) REVERT: A 264 ARG cc_start: 0.7391 (ttp-110) cc_final: 0.7076 (ttm110) REVERT: B 37 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8224 (ptmm) REVERT: B 77 MET cc_start: 0.8430 (tpt) cc_final: 0.7854 (tpt) REVERT: B 108 GLU cc_start: 0.7337 (tp30) cc_final: 0.7070 (tp30) REVERT: B 119 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.7147 (ptt90) REVERT: C 43 GLU cc_start: 0.8093 (pt0) cc_final: 0.7743 (mt-10) REVERT: E 14 MET cc_start: 0.6293 (mmt) cc_final: 0.5610 (mpp) REVERT: E 50 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7603 (mt) REVERT: F 14 MET cc_start: 0.4289 (mmp) cc_final: 0.3441 (ttm) REVERT: F 20 TYR cc_start: 0.8022 (t80) cc_final: 0.7731 (t80) REVERT: F 21 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7239 (mt-10) REVERT: F 22 ARG cc_start: 0.7849 (ptp90) cc_final: 0.7460 (ptm-80) REVERT: F 26 TYR cc_start: 0.6868 (t80) cc_final: 0.6112 (t80) REVERT: F 54 GLU cc_start: 0.7235 (tp30) cc_final: 0.6992 (pt0) outliers start: 60 outliers final: 39 residues processed: 246 average time/residue: 0.1272 time to fit residues: 41.6013 Evaluate side-chains 231 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 186 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 97 ILE Chi-restraints excluded: chain A residue 125 GLU 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 191 ASN Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 259 ASN 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 32 GLN Chi-restraints excluded: chain D residue 101 THR 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 30 ILE 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: 0.4980 chunk 79 optimal weight: 0.3980 chunk 78 optimal weight: 0.4980 chunk 65 optimal weight: 0.8980 chunk 99 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 41 optimal weight: 0.3980 chunk 15 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.222415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.161527 restraints weight = 13545.381| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 1.83 r_work: 0.3768 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 11184 Z= 0.204 Angle : 0.713 8.051 15923 Z= 0.385 Chirality : 0.043 0.236 1908 Planarity : 0.006 0.079 1395 Dihedral : 25.805 178.399 3684 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 26.47 Ramachandran Plot: Outliers : 1.04 % Allowed : 7.31 % Favored : 91.65 % Rotamer: Outliers : 7.25 % Allowed : 24.21 % Favored : 68.54 % 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: -1.35 (0.28), residues: 862 helix: -0.12 (0.19), residues: 655 sheet: -4.85 (1.25), residues: 10 loop : -3.10 (0.44), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 19 TYR 0.025 0.003 TYR C 28 PHE 0.025 0.003 PHE A 231 TRP 0.024 0.002 TRP E 116 HIS 0.015 0.002 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.20 (11184) covalent geometry : angle 0.71281 / 0.39 (15923) hydrogen bonds : bond 0.06217 / 3.91 ( 567) hydrogen bonds : angle 5.48590 / 3.93 ( 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 248 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 195 time to evaluate : 0.331 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: A 39 LYS cc_start: 0.7440 (OUTLIER) cc_final: 0.6938 (ttpt) REVERT: A 125 GLU cc_start: 0.5303 (OUTLIER) cc_final: 0.5091 (tp30) REVERT: A 152 TYR cc_start: 0.7765 (m-80) cc_final: 0.7556 (m-80) REVERT: A 165 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7482 (mtt180) REVERT: A 191 ASN cc_start: 0.8181 (OUTLIER) cc_final: 0.7873 (m-40) REVERT: A 264 ARG cc_start: 0.7393 (ttp-110) cc_final: 0.7000 (ttm110) REVERT: B 77 MET cc_start: 0.8490 (tpt) cc_final: 0.7938 (tpt) REVERT: B 108 GLU cc_start: 0.7155 (tp30) cc_final: 0.6825 (tp30) REVERT: B 119 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.7181 (ptt90) REVERT: C 43 GLU cc_start: 0.8001 (pt0) cc_final: 0.7578 (mt-10) REVERT: D 47 LYS cc_start: 0.8213 (mttm) cc_final: 0.7886 (mmtt) REVERT: D 103 GLN cc_start: 0.7653 (OUTLIER) cc_final: 0.7187 (mt0) REVERT: E 14 MET cc_start: 0.6269 (mmt) cc_final: 0.5683 (mpp) REVERT: E 50 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7564 (mt) REVERT: F 14 MET cc_start: 0.4125 (mmp) cc_final: 0.3504 (ttm) REVERT: F 20 TYR cc_start: 0.8065 (t80) cc_final: 0.7702 (t80) REVERT: F 21 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7293 (mt-10) REVERT: F 22 ARG cc_start: 0.7760 (ptp90) cc_final: 0.7425 (ptm-80) REVERT: F 26 TYR cc_start: 0.6784 (t80) cc_final: 0.6143 (t80) outliers start: 53 outliers final: 35 residues processed: 227 average time/residue: 0.1310 time to fit residues: 39.9008 Evaluate side-chains 235 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 193 time to evaluate : 0.340 ------------------------------------------------------------------------------- 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 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 181 ILE Chi-restraints excluded: chain A residue 191 ASN 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 88 ILE Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 92 HIS 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 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 30 ILE 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: 40.0000 chunk 54 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 68 optimal weight: 0.2980 chunk 24 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 85 optimal weight: 0.6980 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** A 191 ASN 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.222238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.160736 restraints weight = 13575.021| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 1.90 r_work: 0.3761 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.5027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 11184 Z= 0.209 Angle : 0.690 8.287 15923 Z= 0.374 Chirality : 0.042 0.214 1908 Planarity : 0.006 0.078 1395 Dihedral : 25.608 178.338 3682 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 24.46 Ramachandran Plot: Outliers : 1.04 % Allowed : 7.08 % Favored : 91.88 % Rotamer: Outliers : 7.11 % Allowed : 23.67 % 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: -1.15 (0.28), residues: 862 helix: 0.05 (0.19), residues: 650 sheet: -4.49 (1.14), residues: 12 loop : -3.02 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 228 TYR 0.027 0.003 TYR C 28 PHE 0.044 0.003 PHE A 260 TRP 0.020 0.002 TRP A 303 HIS 0.018 0.002 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.21 (11184) covalent geometry : angle 0.69011 / 0.37 (15923) hydrogen bonds : bond 0.06093 / 3.82 ( 567) hydrogen bonds : angle 5.33296 / 3.82 ( 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 254 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 202 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.7442 (OUTLIER) cc_final: 0.6898 (ttpt) REVERT: A 57 ASN cc_start: 0.7672 (t0) cc_final: 0.7465 (t0) REVERT: A 125 GLU cc_start: 0.5420 (OUTLIER) cc_final: 0.5022 (tp30) REVERT: A 141 LYS cc_start: 0.7090 (OUTLIER) cc_final: 0.6871 (pttp) REVERT: A 165 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.7355 (mtt180) REVERT: A 181 ILE cc_start: 0.7547 (OUTLIER) cc_final: 0.7244 (mp) REVERT: B 1 MET cc_start: 0.7152 (tmm) cc_final: 0.6671 (tmm) REVERT: B 108 GLU cc_start: 0.7153 (tp30) cc_final: 0.6840 (tp30) REVERT: B 119 ARG cc_start: 0.7431 (OUTLIER) cc_final: 0.7109 (ptt90) REVERT: C 43 GLU cc_start: 0.7947 (pt0) cc_final: 0.7558 (mt-10) REVERT: D 19 ARG cc_start: 0.7710 (tpp80) cc_final: 0.7508 (mmm-85) REVERT: D 47 LYS cc_start: 0.8281 (mttm) cc_final: 0.7921 (mmtt) REVERT: D 103 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.7212 (mt0) REVERT: E 14 MET cc_start: 0.6378 (mmt) cc_final: 0.5801 (mpp) REVERT: E 43 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7303 (mm-30) REVERT: E 50 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7507 (mt) REVERT: F 14 MET cc_start: 0.3846 (mmp) cc_final: 0.3455 (ttm) REVERT: F 21 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7344 (mt-10) REVERT: F 22 ARG cc_start: 0.7740 (ptp90) cc_final: 0.7371 (ptm-80) REVERT: F 26 TYR cc_start: 0.6838 (t80) cc_final: 0.6264 (t80) outliers start: 52 outliers final: 35 residues processed: 233 average time/residue: 0.1114 time to fit residues: 34.5421 Evaluate side-chains 225 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 182 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 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 181 ILE 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 293 ASP Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain B residue 37 LYS 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 C residue 92 HIS Chi-restraints excluded: chain D residue 32 GLN 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 117 ILE 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: 10.0000 chunk 62 optimal weight: 0.6980 chunk 36 optimal weight: 0.4980 chunk 82 optimal weight: 0.5980 chunk 26 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 chunk 43 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 50 optimal weight: 0.2980 chunk 94 optimal weight: 50.0000 chunk 40 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 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 = 0.4679 r_free = 0.4679 target = 0.223158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.161277 restraints weight = 13362.284| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 1.88 r_work: 0.3764 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.5269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 11184 Z= 0.200 Angle : 0.701 8.544 15923 Z= 0.376 Chirality : 0.042 0.234 1908 Planarity : 0.006 0.079 1395 Dihedral : 25.445 178.274 3677 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 23.53 Ramachandran Plot: Outliers : 0.93 % Allowed : 7.19 % Favored : 91.88 % Rotamer: Outliers : 5.88 % Allowed : 25.85 % Favored : 68.26 % 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: -1.18 (0.28), residues: 862 helix: -0.03 (0.19), residues: 655 sheet: -3.94 (1.26), residues: 12 loop : -2.93 (0.44), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 19 TYR 0.024 0.003 TYR C 28 PHE 0.044 0.003 PHE A 260 TRP 0.034 0.002 TRP A 266 HIS 0.016 0.002 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.20 (11184) covalent geometry : angle 0.70063 / 0.38 (15923) hydrogen bonds : bond 0.05974 / 3.75 ( 567) hydrogen bonds : angle 5.36317 / 3.84 ( 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 236 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 193 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.7440 (OUTLIER) cc_final: 0.6846 (ttpt) REVERT: A 57 ASN cc_start: 0.7730 (t0) cc_final: 0.7495 (t0) REVERT: A 125 GLU cc_start: 0.5306 (OUTLIER) cc_final: 0.4971 (tp30) REVERT: A 165 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.7445 (mtt180) REVERT: A 181 ILE cc_start: 0.7443 (OUTLIER) cc_final: 0.7208 (mp) REVERT: A 191 ASN cc_start: 0.8213 (m-40) cc_final: 0.7841 (m-40) REVERT: B 108 GLU cc_start: 0.7060 (tp30) cc_final: 0.6663 (tp30) REVERT: B 119 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.6997 (ptt90) REVERT: C 26 TYR cc_start: 0.7740 (t80) cc_final: 0.7498 (t80) REVERT: C 43 GLU cc_start: 0.7993 (pt0) cc_final: 0.7656 (mt-10) REVERT: D 47 LYS cc_start: 0.8300 (mttm) cc_final: 0.7951 (mmtt) REVERT: D 79 ARG cc_start: 0.7482 (mtt90) cc_final: 0.7251 (mtt90) REVERT: D 103 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.7209 (mt0) REVERT: E 14 MET cc_start: 0.6467 (mmt) cc_final: 0.5786 (mpp) REVERT: E 43 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7338 (mm-30) REVERT: E 50 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7592 (mt) REVERT: F 14 MET cc_start: 0.3934 (mmp) cc_final: 0.3656 (ttm) REVERT: F 21 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7397 (mt-10) REVERT: F 22 ARG cc_start: 0.7731 (ptp90) cc_final: 0.7428 (ptm-80) REVERT: F 26 TYR cc_start: 0.6775 (t80) cc_final: 0.6251 (t80) outliers start: 43 outliers final: 31 residues processed: 217 average time/residue: 0.1000 time to fit residues: 29.0926 Evaluate side-chains 220 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 182 time to evaluate : 0.262 ------------------------------------------------------------------------------- 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 109 CYS Chi-restraints excluded: chain A residue 125 GLU 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 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 66 SER 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 32 GLN 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 40 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 39 optimal weight: 0.2980 chunk 22 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 43 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 GLN E 32 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.223757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.162902 restraints weight = 13383.488| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 1.73 r_work: 0.3774 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.5506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11184 Z= 0.194 Angle : 0.686 7.566 15923 Z= 0.369 Chirality : 0.042 0.219 1908 Planarity : 0.006 0.068 1395 Dihedral : 25.214 178.331 3673 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 23.38 Ramachandran Plot: Outliers : 0.70 % Allowed : 7.66 % Favored : 91.65 % Rotamer: Outliers : 6.57 % Allowed : 25.03 % 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: -1.22 (0.28), residues: 862 helix: -0.04 (0.19), residues: 657 sheet: -3.92 (1.36), residues: 12 loop : -3.05 (0.44), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 19 TYR 0.025 0.003 TYR A 232 PHE 0.034 0.003 PHE A 231 TRP 0.029 0.002 TRP A 266 HIS 0.016 0.002 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.19 (11184) covalent geometry : angle 0.68568 / 0.37 (15923) hydrogen bonds : bond 0.05830 / 3.66 ( 567) hydrogen bonds : angle 5.32504 / 3.80 ( 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 234 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 186 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4461 (mpp) cc_final: 0.3761 (mpp) REVERT: A 39 LYS cc_start: 0.7280 (OUTLIER) cc_final: 0.6772 (ttpt) REVERT: A 57 ASN cc_start: 0.7785 (t0) cc_final: 0.7545 (t0) REVERT: A 125 GLU cc_start: 0.5359 (OUTLIER) cc_final: 0.4989 (tp30) REVERT: A 165 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.7299 (mtt180) REVERT: A 181 ILE cc_start: 0.7372 (OUTLIER) cc_final: 0.7165 (mp) REVERT: A 191 ASN cc_start: 0.8266 (m-40) cc_final: 0.7888 (m-40) REVERT: A 214 MET cc_start: 0.8055 (mmm) cc_final: 0.7829 (mmm) REVERT: B 37 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8230 (ptmm) REVERT: B 108 GLU cc_start: 0.7074 (tp30) cc_final: 0.6673 (tp30) REVERT: B 113 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7708 (tp) REVERT: B 119 ARG cc_start: 0.7335 (OUTLIER) cc_final: 0.6977 (ptt90) REVERT: C 26 TYR cc_start: 0.7775 (t80) cc_final: 0.7521 (t80) REVERT: D 47 LYS cc_start: 0.8270 (mttm) cc_final: 0.7904 (mmtt) REVERT: D 79 ARG cc_start: 0.7477 (mtt90) cc_final: 0.7256 (mtt90) REVERT: D 100 GLU cc_start: 0.6848 (mm-30) cc_final: 0.6412 (mm-30) REVERT: D 103 GLN cc_start: 0.7687 (OUTLIER) cc_final: 0.7205 (mt0) REVERT: E 14 MET cc_start: 0.6468 (mmt) cc_final: 0.5726 (mpp) REVERT: E 43 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7222 (mm-30) REVERT: E 50 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7551 (mt) REVERT: F 21 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7239 (mt-10) REVERT: F 22 ARG cc_start: 0.7628 (ptp90) cc_final: 0.7310 (ptm-80) REVERT: F 26 TYR cc_start: 0.6804 (t80) cc_final: 0.6245 (t80) outliers start: 48 outliers final: 34 residues processed: 217 average time/residue: 0.1073 time to fit residues: 31.2223 Evaluate side-chains 222 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 179 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 109 CYS Chi-restraints excluded: chain A residue 125 GLU 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 197 VAL Chi-restraints excluded: chain A residue 217 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 65 VAL Chi-restraints excluded: chain B residue 89 GLN Chi-restraints excluded: chain B residue 97 HIS 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 30 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 32 GLN 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 17 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 97 optimal weight: 40.0000 chunk 59 optimal weight: 0.6980 chunk 47 optimal weight: 0.3980 chunk 99 optimal weight: 10.0000 chunk 46 optimal weight: 0.5980 chunk 101 optimal weight: 10.9990 chunk 89 optimal weight: 5.9990 chunk 93 optimal weight: 20.0000 chunk 10 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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** ** 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 = 0.4659 r_free = 0.4659 target = 0.221086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.159280 restraints weight = 13344.449| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 1.97 r_work: 0.3713 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.5558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 11184 Z= 0.257 Angle : 0.717 7.982 15923 Z= 0.383 Chirality : 0.043 0.269 1908 Planarity : 0.006 0.064 1395 Dihedral : 25.086 178.383 3671 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 25.13 Ramachandran Plot: Outliers : 0.58 % Allowed : 7.54 % Favored : 91.88 % Rotamer: Outliers : 6.02 % Allowed : 25.72 % Favored : 68.26 % 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: -1.25 (0.28), residues: 862 helix: -0.09 (0.19), residues: 657 sheet: -3.73 (1.44), residues: 12 loop : -2.97 (0.44), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 19 TYR 0.032 0.003 TYR C 28 PHE 0.047 0.004 PHE A 231 TRP 0.019 0.002 TRP A 303 HIS 0.013 0.002 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00597 / 0.26 (11184) covalent geometry : angle 0.71739 / 0.38 (15923) hydrogen bonds : bond 0.06041 / 3.80 ( 567) hydrogen bonds : angle 5.43547 / 3.88 ( 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 228 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 184 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.7329 (OUTLIER) cc_final: 0.6924 (ttpt) REVERT: A 125 GLU cc_start: 0.5193 (OUTLIER) cc_final: 0.4915 (tp30) REVERT: A 165 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.6853 (mtp180) REVERT: A 181 ILE cc_start: 0.7559 (OUTLIER) cc_final: 0.7238 (mp) REVERT: A 191 ASN cc_start: 0.8315 (m-40) cc_final: 0.7957 (m-40) REVERT: B 37 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8348 (ptmm) REVERT: B 108 GLU cc_start: 0.7116 (tp30) cc_final: 0.6705 (tp30) REVERT: B 119 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.7046 (ptm160) REVERT: D 103 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7259 (mt0) REVERT: E 14 MET cc_start: 0.6550 (mmt) cc_final: 0.5802 (mpp) REVERT: E 43 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7341 (mm-30) REVERT: E 50 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7655 (mt) REVERT: F 21 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7348 (mt-10) REVERT: F 22 ARG cc_start: 0.7717 (ptp90) cc_final: 0.7413 (ptm-80) REVERT: F 26 TYR cc_start: 0.6897 (t80) cc_final: 0.6413 (t80) REVERT: F 68 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8149 (mm) outliers start: 44 outliers final: 29 residues processed: 213 average time/residue: 0.1109 time to fit residues: 31.7508 Evaluate side-chains 214 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 176 time to evaluate : 0.218 ------------------------------------------------------------------------------- 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 109 CYS Chi-restraints excluded: chain A residue 125 GLU 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 197 VAL Chi-restraints excluded: chain A residue 217 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 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 30 ILE Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain D residue 32 GLN 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 40 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 8.9990 chunk 69 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 82 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 ASN A 123 GLN ** 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** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.223099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.160440 restraints weight = 13344.660| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 1.83 r_work: 0.3757 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.5777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11184 Z= 0.204 Angle : 0.699 8.838 15923 Z= 0.374 Chirality : 0.042 0.261 1908 Planarity : 0.006 0.063 1395 Dihedral : 24.960 178.380 3667 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 24.72 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.54 % Favored : 92.00 % Rotamer: Outliers : 5.06 % Allowed : 25.85 % Favored : 69.08 % 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: -1.23 (0.28), residues: 862 helix: -0.10 (0.19), residues: 659 sheet: -3.58 (1.50), residues: 12 loop : -2.89 (0.44), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 19 TYR 0.025 0.002 TYR F 28 PHE 0.046 0.004 PHE A 231 TRP 0.020 0.002 TRP A 303 HIS 0.018 0.002 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.20 (11184) covalent geometry : angle 0.69866 / 0.37 (15923) hydrogen bonds : bond 0.05872 / 3.69 ( 567) hydrogen bonds : angle 5.40058 / 3.86 ( 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 221 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 184 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.7332 (OUTLIER) cc_final: 0.6969 (ttpt) REVERT: A 125 GLU cc_start: 0.5383 (OUTLIER) cc_final: 0.5023 (tp30) REVERT: A 165 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.7281 (mtt180) REVERT: A 181 ILE cc_start: 0.7399 (OUTLIER) cc_final: 0.7151 (mp) REVERT: A 191 ASN cc_start: 0.8221 (m-40) cc_final: 0.7892 (m-40) REVERT: A 232 TYR cc_start: 0.7344 (m-80) cc_final: 0.7017 (m-80) REVERT: B 37 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8375 (ptmm) REVERT: B 108 GLU cc_start: 0.7040 (tp30) cc_final: 0.6652 (tp30) REVERT: B 119 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.7046 (ptm160) REVERT: C 26 TYR cc_start: 0.7794 (t80) cc_final: 0.7520 (t80) REVERT: D 103 GLN cc_start: 0.7682 (OUTLIER) cc_final: 0.7210 (mt0) REVERT: E 14 MET cc_start: 0.6530 (mmt) cc_final: 0.5708 (mpp) REVERT: E 43 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7320 (mm-30) REVERT: E 50 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7545 (mt) REVERT: F 21 GLU cc_start: 0.7475 (mt-10) cc_final: 0.7224 (mt-10) REVERT: F 22 ARG cc_start: 0.7715 (ptp90) cc_final: 0.7404 (ptm-80) REVERT: F 26 TYR cc_start: 0.6857 (t80) cc_final: 0.6312 (t80) REVERT: F 68 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8127 (mm) outliers start: 37 outliers final: 27 residues processed: 207 average time/residue: 0.1134 time to fit residues: 31.6067 Evaluate side-chains 216 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 180 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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 130 ARG 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 197 VAL Chi-restraints excluded: chain A residue 217 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 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 30 ILE Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain D residue 32 GLN 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 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 Chi-restraints excluded: chain F residue 95 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 66 optimal weight: 0.0980 chunk 96 optimal weight: 40.0000 chunk 42 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 63 optimal weight: 0.5980 chunk 29 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 chunk 59 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.2980 chunk 46 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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** ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 HIS ** 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 = 0.4681 r_free = 0.4681 target = 0.224306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.163600 restraints weight = 13508.441| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 1.69 r_work: 0.3784 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.6008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11184 Z= 0.186 Angle : 0.690 9.096 15923 Z= 0.369 Chirality : 0.041 0.270 1908 Planarity : 0.006 0.058 1395 Dihedral : 24.814 178.322 3665 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 23.33 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.42 % Favored : 92.11 % Rotamer: Outliers : 4.92 % Allowed : 25.99 % Favored : 69.08 % 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: -0.02 (0.19), residues: 663 sheet: -3.27 (1.58), residues: 12 loop : -2.76 (0.46), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 19 TYR 0.028 0.002 TYR D 26 PHE 0.045 0.003 PHE A 231 TRP 0.018 0.002 TRP A 303 HIS 0.017 0.002 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 (11184) covalent geometry : angle 0.68961 / 0.37 (15923) hydrogen bonds : bond 0.05767 / 3.64 ( 567) hydrogen bonds : angle 5.34498 / 3.82 ( 1559) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2649.12 seconds wall clock time: 46 minutes 27.01 seconds (2787.01 seconds total)