Starting phenix.real_space_refine on Wed Feb 4 11:25:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ube_42084/02_2026/8ube_42084.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ube_42084/02_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_42084/02_2026/8ube_42084.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ube_42084/02_2026/8ube_42084.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ube_42084/02_2026/8ube_42084.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ube_42084/02_2026/8ube_42084.map" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 167 5.49 5 S 36 5.16 5 C 6142 2.51 5 N 1900 2.21 5 O 2368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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: 2.30, per 1000 atoms: 0.22 Number of scatterers: 10613 At special positions: 0 Unit cell: (86, 105, 130, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 167 15.00 O 2368 8.00 N 1900 7.00 C 6142 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 474.2 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: 1.69 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: 2.05 Time building geometry restraints manager: 1.06 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: 2.940 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.490 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6229 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= 0.701 Angle : 1.654 15.531 15923 Z= 1.022 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 covalent geometry : bond 0.01209 (11184) covalent geometry : angle 1.65392 (15923) hydrogen bonds : bond 0.23218 ( 567) hydrogen bonds : angle 10.41068 ( 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 : 0.312 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: 0.1442 time to fit residues: 70.8841 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 : 0.304 ------------------------------------------------------------------------------- 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: 20.0000 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: 4.9990 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... Flipped N/Q/H residues before XYZ refinement: ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN C 97 HIS C 121 ASN D 32 GLN E 63 ASN E 103 GLN E 121 ASN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.222316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.162313 restraints weight = 13462.816| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 2.07 r_work: 0.3737 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 11184 Z= 0.239 Angle : 0.847 10.530 15923 Z= 0.429 Chirality : 0.045 0.217 1908 Planarity : 0.007 0.086 1395 Dihedral : 26.260 178.241 3794 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 26.67 Ramachandran Plot: Outliers : 1.16 % Allowed : 8.12 % Favored : 90.72 % Rotamer: Outliers : 8.62 % Allowed : 18.74 % Favored : 72.64 % 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: -1.92 (0.27), residues: 862 helix: -0.41 (0.19), residues: 658 sheet: -5.42 (0.86), residues: 10 loop : -3.80 (0.41), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 208 TYR 0.028 0.003 TYR C 28 PHE 0.029 0.004 PHE A 143 TRP 0.025 0.002 TRP A 303 HIS 0.008 0.002 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00546 (11184) covalent geometry : angle 0.84667 (15923) hydrogen bonds : bond 0.06638 ( 567) hydrogen bonds : angle 5.72204 ( 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 298 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 235 time to evaluate : 0.312 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: 0.7881 (t70) cc_final: 0.7603 (t70) REVERT: A 123 GLN cc_start: 0.7579 (tt0) cc_final: 0.7036 (tt0) REVERT: A 127 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7732 (mpp80) REVERT: A 141 LYS cc_start: 0.7087 (OUTLIER) cc_final: 0.6827 (pttp) REVERT: C 26 TYR cc_start: 0.7762 (t80) cc_final: 0.7432 (t80) REVERT: D 103 GLN cc_start: 0.7413 (OUTLIER) cc_final: 0.6948 (mt0) REVERT: E 14 MET cc_start: 0.6209 (mmt) cc_final: 0.5520 (mpp) REVERT: E 50 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7587 (mt) REVERT: F 14 MET cc_start: 0.4519 (mmp) cc_final: 0.3796 (ttt) REVERT: F 21 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7454 (mt-10) REVERT: F 22 ARG cc_start: 0.8006 (ptp90) cc_final: 0.7476 (ptm-80) REVERT: F 26 TYR cc_start: 0.6901 (t80) cc_final: 0.6087 (t80) outliers start: 63 outliers final: 31 residues processed: 270 average time/residue: 0.1007 time to fit residues: 36.6868 Evaluate side-chains 229 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 194 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 CYS Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 240 GLU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 327 CYS 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 D residue 64 GLN Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain D residue 122 ARG Chi-restraints excluded: chain E residue 13 GLN Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 33 SER Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 95 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 75 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 28 optimal weight: 6.9990 chunk 33 optimal weight: 0.1980 chunk 95 optimal weight: 20.0000 chunk 2 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 ASN ** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN E 121 ASN F 92 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.223168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.162081 restraints weight = 13577.493| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 1.88 r_work: 0.3788 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 11184 Z= 0.204 Angle : 0.745 7.643 15923 Z= 0.379 Chirality : 0.041 0.224 1908 Planarity : 0.006 0.111 1395 Dihedral : 25.601 177.874 3683 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 22.66 Ramachandran Plot: Outliers : 1.04 % Allowed : 7.77 % Favored : 91.18 % Rotamer: Outliers : 7.39 % Allowed : 19.29 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.28), residues: 862 helix: 0.02 (0.19), residues: 653 sheet: -4.65 (1.11), residues: 10 loop : -3.15 (0.43), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 42 TYR 0.023 0.002 TYR C 28 PHE 0.022 0.003 PHE A 231 TRP 0.018 0.002 TRP A 303 HIS 0.017 0.002 HIS F 92 Details of bonding type rmsd covalent geometry : bond 0.00468 (11184) covalent geometry : angle 0.74510 (15923) hydrogen bonds : bond 0.05914 ( 567) hydrogen bonds : angle 5.28391 ( 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 268 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 214 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLU cc_start: 0.5909 (OUTLIER) cc_final: 0.5357 (tp30) REVERT: A 127 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7807 (mtt180) REVERT: A 165 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7202 (mtp180) REVERT: A 191 ASN cc_start: 0.7732 (OUTLIER) cc_final: 0.7479 (m110) REVERT: A 274 LYS cc_start: 0.4141 (pptt) cc_final: 0.3868 (pttp) REVERT: A 287 PHE cc_start: 0.5943 (m-80) cc_final: 0.5663 (m-80) REVERT: B 1 MET cc_start: 0.7004 (tmm) cc_final: 0.6753 (ttp) REVERT: B 119 ARG cc_start: 0.7448 (OUTLIER) cc_final: 0.7050 (ptm160) REVERT: C 69 TYR cc_start: 0.7995 (m-80) cc_final: 0.7792 (m-80) REVERT: C 103 GLN cc_start: 0.7315 (OUTLIER) cc_final: 0.6956 (mt0) REVERT: E 14 MET cc_start: 0.6367 (mmt) cc_final: 0.5673 (mpp) REVERT: E 50 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7635 (mt) REVERT: F 14 MET cc_start: 0.4031 (mmp) cc_final: 0.3631 (tmm) REVERT: F 21 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7599 (mt-10) REVERT: F 26 TYR cc_start: 0.6902 (t80) cc_final: 0.6099 (t80) outliers start: 54 outliers final: 22 residues processed: 246 average time/residue: 0.1178 time to fit residues: 37.9371 Evaluate side-chains 222 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 193 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 191 ASN 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 66 SER 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 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 C residue 103 GLN Chi-restraints excluded: chain D residue 101 THR 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 E residue 104 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 47 optimal weight: 0.3980 chunk 98 optimal weight: 10.0000 chunk 67 optimal weight: 0.6980 chunk 31 optimal weight: 0.0040 chunk 45 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 88 optimal weight: 30.0000 chunk 78 optimal weight: 0.8980 chunk 83 optimal weight: 0.0030 chunk 11 optimal weight: 3.9990 chunk 46 optimal weight: 0.3980 overall best weight: 0.3002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN A 290 HIS A 297 GLN D 64 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.227398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.167945 restraints weight = 13612.601| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 1.74 r_work: 0.3849 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.5743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11184 Z= 0.161 Angle : 0.690 7.501 15923 Z= 0.352 Chirality : 0.040 0.369 1908 Planarity : 0.006 0.084 1395 Dihedral : 24.975 177.402 3656 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 21.57 Ramachandran Plot: Outliers : 0.81 % Allowed : 6.73 % Favored : 92.46 % Rotamer: Outliers : 5.47 % Allowed : 22.44 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.28), residues: 862 helix: 0.25 (0.20), residues: 654 sheet: -3.15 (1.55), residues: 10 loop : -3.06 (0.43), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 22 TYR 0.020 0.002 TYR C 28 PHE 0.021 0.003 PHE A 299 TRP 0.016 0.002 TRP A 303 HIS 0.013 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00354 (11184) covalent geometry : angle 0.69015 (15923) hydrogen bonds : bond 0.05514 ( 567) hydrogen bonds : angle 5.09024 ( 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 252 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 212 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 HIS cc_start: 0.7681 (t70) cc_final: 0.7479 (t70) REVERT: A 125 GLU cc_start: 0.5643 (OUTLIER) cc_final: 0.4716 (tp30) REVERT: A 127 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7644 (mtt180) REVERT: A 165 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7407 (mtt180) REVERT: A 232 TYR cc_start: 0.7547 (m-80) cc_final: 0.7325 (m-80) REVERT: A 287 PHE cc_start: 0.6430 (m-80) cc_final: 0.6216 (m-80) REVERT: B 1 MET cc_start: 0.7144 (tmm) cc_final: 0.6574 (ttp) REVERT: B 119 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.7115 (ptm160) REVERT: C 26 TYR cc_start: 0.7588 (t80) cc_final: 0.7377 (t80) REVERT: C 90 LYS cc_start: 0.6050 (OUTLIER) cc_final: 0.5838 (mptm) REVERT: C 111 ARG cc_start: 0.7418 (ttp80) cc_final: 0.6034 (mtt180) REVERT: D 19 ARG cc_start: 0.7472 (ttm-80) cc_final: 0.7256 (mmm160) REVERT: D 43 GLU cc_start: 0.7404 (mt-10) cc_final: 0.7194 (mt-10) REVERT: D 44 MET cc_start: 0.8084 (mtp) cc_final: 0.7883 (mtp) REVERT: D 103 GLN cc_start: 0.7505 (OUTLIER) cc_final: 0.7138 (mt0) REVERT: E 14 MET cc_start: 0.6322 (mmt) cc_final: 0.5641 (mpp) REVERT: E 50 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7381 (mt) REVERT: E 111 ARG cc_start: 0.7689 (ptt90) cc_final: 0.6980 (ptt90) REVERT: F 22 ARG cc_start: 0.7810 (ptm-80) cc_final: 0.7521 (ptm-80) REVERT: F 26 TYR cc_start: 0.6742 (t80) cc_final: 0.6227 (t80) REVERT: F 43 GLU cc_start: 0.7003 (OUTLIER) cc_final: 0.6644 (tp30) outliers start: 40 outliers final: 17 residues processed: 236 average time/residue: 0.1109 time to fit residues: 34.6021 Evaluate side-chains 216 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 191 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain E residue 13 GLN Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 27 LEU Chi-restraints excluded: chain F residue 43 GLU Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 68 LEU 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: 0.5980 chunk 79 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 72 optimal weight: 0.2980 chunk 37 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN B 97 HIS ** D 38 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 = 0.4687 r_free = 0.4687 target = 0.225400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.165061 restraints weight = 13503.163| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 1.73 r_work: 0.3799 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.6024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11184 Z= 0.190 Angle : 0.712 9.283 15923 Z= 0.362 Chirality : 0.039 0.248 1908 Planarity : 0.006 0.104 1395 Dihedral : 24.657 177.845 3653 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 21.99 Ramachandran Plot: Outliers : 0.58 % Allowed : 7.08 % Favored : 92.34 % Rotamer: Outliers : 5.88 % Allowed : 22.02 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.28), residues: 862 helix: 0.25 (0.19), residues: 661 sheet: -1.86 (1.85), residues: 10 loop : -3.00 (0.45), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 256 TYR 0.022 0.002 TYR C 28 PHE 0.023 0.003 PHE A 299 TRP 0.014 0.002 TRP A 303 HIS 0.013 0.002 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00433 (11184) covalent geometry : angle 0.71207 (15923) hydrogen bonds : bond 0.05556 ( 567) hydrogen bonds : angle 5.03258 ( 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 243 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 200 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLU cc_start: 0.5516 (OUTLIER) cc_final: 0.4669 (tp30) REVERT: A 127 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7565 (mpt-90) REVERT: A 141 LYS cc_start: 0.7428 (pttp) cc_final: 0.7136 (pttp) REVERT: A 154 MET cc_start: 0.7376 (ptp) cc_final: 0.7016 (ptp) REVERT: A 165 ARG cc_start: 0.7689 (OUTLIER) cc_final: 0.7379 (mtt180) REVERT: A 232 TYR cc_start: 0.7698 (m-80) cc_final: 0.7411 (m-80) REVERT: A 287 PHE cc_start: 0.6539 (m-80) cc_final: 0.6281 (m-80) REVERT: B 119 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.7156 (ptm160) REVERT: C 19 ARG cc_start: 0.6501 (tpp-160) cc_final: 0.6300 (tpp-160) REVERT: C 22 ARG cc_start: 0.6356 (ttp-110) cc_final: 0.5901 (mmp80) REVERT: C 26 TYR cc_start: 0.7692 (t80) cc_final: 0.7376 (t80) REVERT: D 103 GLN cc_start: 0.7609 (OUTLIER) cc_final: 0.7135 (mt0) REVERT: E 14 MET cc_start: 0.6428 (mmt) cc_final: 0.5647 (mpp) REVERT: E 50 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7776 (mt) REVERT: F 26 TYR cc_start: 0.6956 (t80) cc_final: 0.6415 (t80) REVERT: F 43 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6747 (tp30) REVERT: F 68 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8160 (mm) outliers start: 43 outliers final: 22 residues processed: 225 average time/residue: 0.1157 time to fit residues: 33.8878 Evaluate side-chains 214 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 184 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 127 ARG Chi-restraints excluded: chain A residue 130 ARG Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 266 TRP Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 66 SER 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 68 LEU 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 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: 30.0000 chunk 54 optimal weight: 0.3980 chunk 52 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 50 optimal weight: 0.2980 chunk 42 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 64 optimal weight: 0.4980 chunk 85 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** F 98 GLN ** 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 = 0.4688 r_free = 0.4688 target = 0.225633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.165961 restraints weight = 13664.284| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 1.70 r_work: 0.3815 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.6314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11184 Z= 0.175 Angle : 0.696 9.642 15923 Z= 0.354 Chirality : 0.039 0.222 1908 Planarity : 0.006 0.099 1395 Dihedral : 24.489 177.994 3652 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 21.11 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.08 % Favored : 92.46 % Rotamer: Outliers : 5.61 % Allowed : 22.44 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.28), residues: 862 helix: 0.29 (0.19), residues: 662 sheet: -1.37 (1.87), residues: 10 loop : -2.86 (0.46), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 19 TYR 0.022 0.002 TYR C 28 PHE 0.022 0.003 PHE A 299 TRP 0.015 0.002 TRP A 303 HIS 0.023 0.002 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00396 (11184) covalent geometry : angle 0.69648 (15923) hydrogen bonds : bond 0.05445 ( 567) hydrogen bonds : angle 5.03690 ( 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 235 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 194 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4040 (mpp) cc_final: 0.3687 (mpp) REVERT: A 59 GLU cc_start: 0.7207 (tp30) cc_final: 0.7004 (tm-30) REVERT: A 125 GLU cc_start: 0.5350 (OUTLIER) cc_final: 0.4566 (tp30) REVERT: A 141 LYS cc_start: 0.7369 (pttp) cc_final: 0.7095 (pttp) REVERT: A 154 MET cc_start: 0.7434 (ptp) cc_final: 0.7037 (ptp) REVERT: A 165 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.7331 (mtt180) REVERT: A 191 ASN cc_start: 0.8288 (m-40) cc_final: 0.7992 (m-40) REVERT: A 287 PHE cc_start: 0.6496 (m-80) cc_final: 0.6163 (m-80) REVERT: B 119 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.7117 (ptm160) REVERT: C 22 ARG cc_start: 0.6363 (ttp-110) cc_final: 0.6016 (mmp80) REVERT: C 111 ARG cc_start: 0.7608 (ttp80) cc_final: 0.6122 (mtt180) REVERT: D 100 GLU cc_start: 0.6779 (mm-30) cc_final: 0.6536 (mm-30) REVERT: D 103 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.7127 (mt0) REVERT: E 14 MET cc_start: 0.6407 (mmt) cc_final: 0.5651 (mpp) REVERT: E 50 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.8001 (mt) REVERT: F 26 TYR cc_start: 0.6901 (t80) cc_final: 0.6400 (t80) REVERT: F 43 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6711 (tp30) outliers start: 41 outliers final: 19 residues processed: 223 average time/residue: 0.1111 time to fit residues: 32.8767 Evaluate side-chains 214 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 189 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 179 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 266 TRP Chi-restraints excluded: chain B residue 65 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 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 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 43 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 99 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 36 optimal weight: 0.0770 chunk 82 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 50 optimal weight: 0.0980 chunk 94 optimal weight: 30.0000 chunk 40 optimal weight: 2.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 HIS ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.225405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.166320 restraints weight = 13472.986| |-----------------------------------------------------------------------------| r_work (start): 0.4052 rms_B_bonded: 1.68 r_work: 0.3823 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.6703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11184 Z= 0.176 Angle : 0.686 7.428 15923 Z= 0.349 Chirality : 0.039 0.241 1908 Planarity : 0.006 0.094 1395 Dihedral : 24.285 178.079 3643 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 21.32 Ramachandran Plot: Outliers : 0.58 % Allowed : 7.08 % Favored : 92.34 % Rotamer: Outliers : 4.24 % Allowed : 24.76 % Favored : 71.00 % 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: -0.58 (0.28), residues: 862 helix: 0.33 (0.19), residues: 667 sheet: -1.46 (1.83), residues: 10 loop : -2.77 (0.47), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 228 TYR 0.022 0.002 TYR D 26 PHE 0.019 0.003 PHE A 299 TRP 0.015 0.002 TRP A 303 HIS 0.014 0.002 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00397 (11184) covalent geometry : angle 0.68633 (15923) hydrogen bonds : bond 0.05420 ( 567) hydrogen bonds : angle 5.00959 ( 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 222 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 191 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLU cc_start: 0.5419 (OUTLIER) cc_final: 0.4838 (tp30) REVERT: A 154 MET cc_start: 0.7438 (ptp) cc_final: 0.7025 (ptp) REVERT: A 165 ARG cc_start: 0.7566 (OUTLIER) cc_final: 0.7296 (mtt180) REVERT: A 191 ASN cc_start: 0.8199 (m-40) cc_final: 0.7960 (m-40) REVERT: A 232 TYR cc_start: 0.7448 (m-80) cc_final: 0.7208 (m-80) REVERT: A 287 PHE cc_start: 0.6501 (m-80) cc_final: 0.6161 (m-80) REVERT: B 119 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.7067 (ptm160) REVERT: C 22 ARG cc_start: 0.6486 (ttp-110) cc_final: 0.6200 (mmp80) REVERT: C 111 ARG cc_start: 0.7585 (ttp80) cc_final: 0.6164 (mtt90) REVERT: D 43 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7232 (mt-10) REVERT: D 100 GLU cc_start: 0.6956 (mm-30) cc_final: 0.6739 (mm-30) REVERT: D 103 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.7148 (mt0) REVERT: E 14 MET cc_start: 0.6400 (mmt) cc_final: 0.5670 (mpp) REVERT: E 50 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7663 (mt) REVERT: F 26 TYR cc_start: 0.6834 (t80) cc_final: 0.6312 (t80) REVERT: F 43 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6761 (tp30) outliers start: 31 outliers final: 17 residues processed: 211 average time/residue: 0.1149 time to fit residues: 32.1714 Evaluate side-chains 204 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 181 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 266 TRP Chi-restraints excluded: chain B residue 65 VAL 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 30 ILE Chi-restraints excluded: chain C residue 88 ILE 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 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 43 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 40 optimal weight: 0.0670 chunk 84 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 78 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 HIS C 92 HIS ** D 38 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 = 0.4689 r_free = 0.4689 target = 0.225750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.166276 restraints weight = 13482.269| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 1.71 r_work: 0.3822 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.6879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11184 Z= 0.175 Angle : 0.691 8.040 15923 Z= 0.350 Chirality : 0.039 0.270 1908 Planarity : 0.006 0.094 1395 Dihedral : 24.208 178.023 3639 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 21.21 Ramachandran Plot: Outliers : 0.58 % Allowed : 6.84 % Favored : 92.58 % Rotamer: Outliers : 3.56 % Allowed : 26.27 % 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: -0.57 (0.28), residues: 862 helix: 0.34 (0.19), residues: 667 sheet: -2.05 (1.56), residues: 12 loop : -2.70 (0.48), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 228 TYR 0.023 0.002 TYR C 28 PHE 0.041 0.003 PHE A 260 TRP 0.013 0.001 TRP A 303 HIS 0.023 0.002 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00398 (11184) covalent geometry : angle 0.69084 (15923) hydrogen bonds : bond 0.05365 ( 567) hydrogen bonds : angle 5.00036 ( 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 211 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLU cc_start: 0.5448 (OUTLIER) cc_final: 0.4864 (tp30) REVERT: A 154 MET cc_start: 0.7403 (ptp) cc_final: 0.6957 (ptp) REVERT: A 165 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.7292 (mtt180) REVERT: A 224 PRO cc_start: 0.6057 (Cg_exo) cc_final: 0.5835 (Cg_endo) REVERT: A 232 TYR cc_start: 0.7477 (m-80) cc_final: 0.7273 (m-80) REVERT: A 287 PHE cc_start: 0.6488 (m-80) cc_final: 0.6143 (m-80) REVERT: B 119 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.7124 (ptm160) REVERT: C 22 ARG cc_start: 0.6404 (ttp-110) cc_final: 0.6103 (mmp80) REVERT: C 111 ARG cc_start: 0.7518 (ttp80) cc_final: 0.6169 (mtt90) REVERT: D 100 GLU cc_start: 0.6835 (mm-30) cc_final: 0.6596 (mm-30) REVERT: D 103 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.7116 (mt0) REVERT: E 14 MET cc_start: 0.6261 (mmt) cc_final: 0.5407 (mpp) REVERT: E 50 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7637 (mt) REVERT: F 26 TYR cc_start: 0.6804 (t80) cc_final: 0.6295 (t80) REVERT: F 43 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6725 (tp30) REVERT: F 44 MET cc_start: 0.7844 (ttp) cc_final: 0.7370 (ptm) outliers start: 26 outliers final: 15 residues processed: 198 average time/residue: 0.1112 time to fit residues: 29.5525 Evaluate side-chains 196 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 175 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 266 TRP 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 30 ILE Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 103 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 43 GLU Chi-restraints excluded: chain F residue 105 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 17 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 97 optimal weight: 30.0000 chunk 59 optimal weight: 1.9990 chunk 47 optimal weight: 0.1980 chunk 99 optimal weight: 5.9990 chunk 46 optimal weight: 0.5980 chunk 101 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 93 optimal weight: 20.0000 chunk 10 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 HIS ** D 38 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 = 0.4674 r_free = 0.4674 target = 0.224089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.163856 restraints weight = 13502.690| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 1.94 r_work: 0.3746 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.6935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11184 Z= 0.206 Angle : 0.717 8.900 15923 Z= 0.363 Chirality : 0.040 0.297 1908 Planarity : 0.006 0.090 1395 Dihedral : 24.186 178.240 3639 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 21.83 Ramachandran Plot: Outliers : 0.58 % Allowed : 6.84 % Favored : 92.58 % Rotamer: Outliers : 3.56 % Allowed : 26.40 % Favored : 70.04 % 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: -0.64 (0.28), residues: 862 helix: 0.28 (0.19), residues: 661 sheet: -2.49 (1.41), residues: 12 loop : -2.60 (0.47), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 228 TYR 0.027 0.002 TYR C 28 PHE 0.021 0.003 PHE D 80 TRP 0.014 0.002 TRP A 303 HIS 0.015 0.002 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00477 (11184) covalent geometry : angle 0.71684 (15923) hydrogen bonds : bond 0.05518 ( 567) hydrogen bonds : angle 5.07517 ( 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 213 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 187 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLU cc_start: 0.5540 (OUTLIER) cc_final: 0.4680 (tp30) REVERT: A 165 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.7388 (mtt180) REVERT: A 224 PRO cc_start: 0.5986 (Cg_exo) cc_final: 0.5767 (Cg_endo) REVERT: A 232 TYR cc_start: 0.7576 (m-80) cc_final: 0.7345 (m-80) REVERT: A 287 PHE cc_start: 0.6484 (m-80) cc_final: 0.6130 (m-80) REVERT: C 19 ARG cc_start: 0.6451 (tpp-160) cc_final: 0.6112 (tpp-160) REVERT: C 22 ARG cc_start: 0.6476 (ttp-110) cc_final: 0.6161 (mmp80) REVERT: C 111 ARG cc_start: 0.7698 (ttp80) cc_final: 0.6257 (mtt90) REVERT: D 43 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7279 (mt-10) REVERT: D 103 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.7256 (mt0) REVERT: E 14 MET cc_start: 0.6419 (mmt) cc_final: 0.5513 (mpp) REVERT: E 50 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7761 (mt) REVERT: F 43 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6802 (tp30) REVERT: F 44 MET cc_start: 0.7960 (ttp) cc_final: 0.7294 (ptm) outliers start: 26 outliers final: 17 residues processed: 200 average time/residue: 0.1072 time to fit residues: 28.5643 Evaluate side-chains 206 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 184 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 266 TRP Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C 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 50 LEU Chi-restraints excluded: chain E residue 62 SER 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 43 GLU Chi-restraints excluded: chain F residue 105 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 40 optimal weight: 0.1980 chunk 14 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 10.0000 chunk 69 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 82 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 ASN ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 HIS ** D 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.225062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.167279 restraints weight = 13536.421| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 1.86 r_work: 0.3773 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.7108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 11184 Z= 0.181 Angle : 0.707 8.638 15923 Z= 0.357 Chirality : 0.040 0.279 1908 Planarity : 0.006 0.089 1395 Dihedral : 24.130 178.131 3633 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 22.40 Ramachandran Plot: Outliers : 0.58 % Allowed : 7.08 % Favored : 92.34 % Rotamer: Outliers : 2.60 % Allowed : 27.63 % 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: -0.61 (0.28), residues: 862 helix: 0.30 (0.19), residues: 663 sheet: -2.19 (1.49), residues: 12 loop : -2.64 (0.48), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 228 TYR 0.022 0.002 TYR C 28 PHE 0.041 0.003 PHE A 260 TRP 0.034 0.002 TRP E 116 HIS 0.019 0.002 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00418 (11184) covalent geometry : angle 0.70694 (15923) hydrogen bonds : bond 0.05421 ( 567) hydrogen bonds : angle 5.08017 ( 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 205 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 186 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.7311 (mtt180) REVERT: A 191 ASN cc_start: 0.8212 (m-40) cc_final: 0.7968 (m-40) REVERT: A 232 TYR cc_start: 0.7509 (m-80) cc_final: 0.7298 (m-80) REVERT: A 287 PHE cc_start: 0.6487 (m-80) cc_final: 0.6133 (m-80) REVERT: C 111 ARG cc_start: 0.7652 (ttp80) cc_final: 0.6254 (mtt90) REVERT: D 100 GLU cc_start: 0.6783 (mm-30) cc_final: 0.6539 (mm-30) REVERT: D 103 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.7188 (mt0) REVERT: E 14 MET cc_start: 0.6396 (mmt) cc_final: 0.5585 (mpp) REVERT: E 50 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7677 (mt) REVERT: F 26 TYR cc_start: 0.6926 (t80) cc_final: 0.6438 (t80) REVERT: F 43 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6784 (tp30) REVERT: F 44 MET cc_start: 0.7890 (ttp) cc_final: 0.7393 (ptm) outliers start: 19 outliers final: 14 residues processed: 195 average time/residue: 0.1010 time to fit residues: 26.3054 Evaluate side-chains 201 residues out of total 731 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 183 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ARG Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 266 TRP Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain C residue 16 ILE Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 103 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 43 GLU Chi-restraints excluded: chain F residue 105 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 66 optimal weight: 0.5980 chunk 96 optimal weight: 20.0000 chunk 42 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 HIS ** D 38 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 = 0.4675 r_free = 0.4675 target = 0.224387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.159900 restraints weight = 13633.208| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 1.80 r_work: 0.3782 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.7192 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= 0.199 Angle : 0.719 8.589 15923 Z= 0.364 Chirality : 0.041 0.305 1908 Planarity : 0.006 0.088 1395 Dihedral : 24.125 178.216 3633 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 23.02 Ramachandran Plot: Outliers : 0.70 % Allowed : 6.73 % Favored : 92.58 % Rotamer: Outliers : 3.15 % Allowed : 27.77 % 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: -0.65 (0.28), residues: 862 helix: 0.27 (0.19), residues: 663 sheet: -2.03 (1.56), residues: 12 loop : -2.66 (0.47), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 22 TYR 0.024 0.002 TYR C 28 PHE 0.020 0.003 PHE D 80 TRP 0.020 0.002 TRP E 116 HIS 0.023 0.002 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00463 (11184) covalent geometry : angle 0.71873 (15923) hydrogen bonds : bond 0.05504 ( 567) hydrogen bonds : angle 5.11574 ( 1559) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2502.05 seconds wall clock time: 43 minutes 46.53 seconds (2626.53 seconds total)