Starting phenix.real_space_refine on Sat Mar 7 01:49:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vfk_21185/03_2026/6vfk_21185.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vfk_21185/03_2026/6vfk_21185.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vfk_21185/03_2026/6vfk_21185.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vfk_21185/03_2026/6vfk_21185.map" model { file = "/net/cci-nas-00/data/ceres_data/6vfk_21185/03_2026/6vfk_21185.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vfk_21185/03_2026/6vfk_21185.cif" } resolution = 4.25 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= 0.003 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: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 23580 2.51 5 N 6156 2.21 5 O 7176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 192 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37032 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2099 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 1, 'TRANS': 275} Chain: "A" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 987 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Restraints were copied for chains: C, E, G, I, K, M, O, Q, S, U, W, D, F, H, J, L, N, P, R, T, V, X Time building chain proxies: 3.88, per 1000 atoms: 0.10 Number of scatterers: 37032 At special positions: 0 Unit cell: (175.95, 177.1, 173.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 7176 8.00 N 6156 7.00 C 23580 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.57 Conformation dependent library (CDL) restraints added in 1.9 seconds 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9336 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 0 sheets defined 91.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'B' and resid 1 through 30 Processing helix chain 'B' and resid 32 through 59 removed outlier: 3.503A pdb=" N VAL B 36 " --> pdb=" O THR B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 93 Processing helix chain 'B' and resid 97 through 121 Processing helix chain 'B' and resid 125 through 153 Processing helix chain 'B' and resid 158 through 183 Processing helix chain 'B' and resid 187 through 215 Processing helix chain 'B' and resid 218 through 245 Processing helix chain 'B' and resid 249 through 277 Processing helix chain 'A' and resid 2 through 17 Processing helix chain 'A' and resid 19 through 34 Processing helix chain 'A' and resid 37 through 50 Processing helix chain 'A' and resid 53 through 68 Processing helix chain 'A' and resid 71 through 85 Processing helix chain 'A' and resid 87 through 102 Processing helix chain 'A' and resid 105 through 120 Processing helix chain 'C' and resid 1 through 30 Processing helix chain 'C' and resid 32 through 59 removed outlier: 3.503A pdb=" N VAL C 36 " --> pdb=" O THR C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 93 Processing helix chain 'C' and resid 97 through 121 Processing helix chain 'C' and resid 125 through 153 Processing helix chain 'C' and resid 158 through 183 Processing helix chain 'C' and resid 187 through 215 Processing helix chain 'C' and resid 218 through 245 Processing helix chain 'C' and resid 249 through 277 Processing helix chain 'D' and resid 2 through 17 Processing helix chain 'D' and resid 19 through 34 Processing helix chain 'D' and resid 37 through 50 Processing helix chain 'D' and resid 53 through 68 Processing helix chain 'D' and resid 71 through 85 Processing helix chain 'D' and resid 87 through 102 Processing helix chain 'D' and resid 105 through 120 Processing helix chain 'E' and resid 1 through 30 Processing helix chain 'E' and resid 32 through 59 removed outlier: 3.503A pdb=" N VAL E 36 " --> pdb=" O THR E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 93 Processing helix chain 'E' and resid 97 through 121 Processing helix chain 'E' and resid 125 through 153 Processing helix chain 'E' and resid 158 through 183 Processing helix chain 'E' and resid 187 through 215 Processing helix chain 'E' and resid 218 through 245 Processing helix chain 'E' and resid 249 through 277 Processing helix chain 'F' and resid 2 through 17 Processing helix chain 'F' and resid 19 through 34 Processing helix chain 'F' and resid 37 through 50 Processing helix chain 'F' and resid 53 through 68 Processing helix chain 'F' and resid 71 through 85 Processing helix chain 'F' and resid 87 through 102 Processing helix chain 'F' and resid 105 through 120 Processing helix chain 'G' and resid 1 through 30 Processing helix chain 'G' and resid 32 through 59 removed outlier: 3.503A pdb=" N VAL G 36 " --> pdb=" O THR G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 93 Processing helix chain 'G' and resid 97 through 121 Processing helix chain 'G' and resid 125 through 153 Processing helix chain 'G' and resid 158 through 183 Processing helix chain 'G' and resid 187 through 215 Processing helix chain 'G' and resid 218 through 245 Processing helix chain 'G' and resid 249 through 277 Processing helix chain 'H' and resid 2 through 17 Processing helix chain 'H' and resid 19 through 34 Processing helix chain 'H' and resid 37 through 50 Processing helix chain 'H' and resid 53 through 68 Processing helix chain 'H' and resid 71 through 85 Processing helix chain 'H' and resid 87 through 102 Processing helix chain 'H' and resid 105 through 120 Processing helix chain 'I' and resid 1 through 30 Processing helix chain 'I' and resid 32 through 59 removed outlier: 3.503A pdb=" N VAL I 36 " --> pdb=" O THR I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 93 Processing helix chain 'I' and resid 97 through 121 Processing helix chain 'I' and resid 125 through 153 Processing helix chain 'I' and resid 158 through 183 Processing helix chain 'I' and resid 187 through 215 Processing helix chain 'I' and resid 218 through 245 Processing helix chain 'I' and resid 249 through 277 Processing helix chain 'J' and resid 2 through 17 Processing helix chain 'J' and resid 19 through 34 Processing helix chain 'J' and resid 37 through 50 Processing helix chain 'J' and resid 53 through 68 Processing helix chain 'J' and resid 71 through 85 Processing helix chain 'J' and resid 87 through 102 Processing helix chain 'J' and resid 105 through 120 Processing helix chain 'K' and resid 1 through 30 Processing helix chain 'K' and resid 32 through 59 removed outlier: 3.502A pdb=" N VAL K 36 " --> pdb=" O THR K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 93 Processing helix chain 'K' and resid 97 through 121 Processing helix chain 'K' and resid 125 through 153 Processing helix chain 'K' and resid 158 through 183 Processing helix chain 'K' and resid 187 through 215 Processing helix chain 'K' and resid 218 through 245 Processing helix chain 'K' and resid 249 through 277 Processing helix chain 'L' and resid 2 through 17 Processing helix chain 'L' and resid 19 through 34 Processing helix chain 'L' and resid 37 through 50 Processing helix chain 'L' and resid 53 through 68 Processing helix chain 'L' and resid 71 through 85 Processing helix chain 'L' and resid 87 through 102 Processing helix chain 'L' and resid 105 through 120 Processing helix chain 'M' and resid 1 through 30 Processing helix chain 'M' and resid 32 through 59 removed outlier: 3.503A pdb=" N VAL M 36 " --> pdb=" O THR M 32 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 93 Processing helix chain 'M' and resid 97 through 121 Processing helix chain 'M' and resid 125 through 153 Processing helix chain 'M' and resid 158 through 183 Processing helix chain 'M' and resid 187 through 215 Processing helix chain 'M' and resid 218 through 245 Processing helix chain 'M' and resid 249 through 277 Processing helix chain 'N' and resid 2 through 17 Processing helix chain 'N' and resid 19 through 34 Processing helix chain 'N' and resid 37 through 50 Processing helix chain 'N' and resid 53 through 68 Processing helix chain 'N' and resid 71 through 85 Processing helix chain 'N' and resid 87 through 102 Processing helix chain 'N' and resid 105 through 120 Processing helix chain 'O' and resid 1 through 30 Processing helix chain 'O' and resid 32 through 59 removed outlier: 3.503A pdb=" N VAL O 36 " --> pdb=" O THR O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 93 Processing helix chain 'O' and resid 97 through 121 Processing helix chain 'O' and resid 125 through 153 Processing helix chain 'O' and resid 158 through 183 Processing helix chain 'O' and resid 187 through 215 Processing helix chain 'O' and resid 218 through 245 Processing helix chain 'O' and resid 249 through 277 Processing helix chain 'P' and resid 2 through 17 Processing helix chain 'P' and resid 19 through 34 Processing helix chain 'P' and resid 37 through 50 Processing helix chain 'P' and resid 53 through 68 Processing helix chain 'P' and resid 71 through 85 Processing helix chain 'P' and resid 87 through 102 Processing helix chain 'P' and resid 105 through 120 Processing helix chain 'Q' and resid 1 through 30 Processing helix chain 'Q' and resid 32 through 59 removed outlier: 3.503A pdb=" N VAL Q 36 " --> pdb=" O THR Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 63 through 93 Processing helix chain 'Q' and resid 97 through 121 Processing helix chain 'Q' and resid 125 through 153 Processing helix chain 'Q' and resid 158 through 183 Processing helix chain 'Q' and resid 187 through 215 Processing helix chain 'Q' and resid 218 through 245 Processing helix chain 'Q' and resid 249 through 277 Processing helix chain 'R' and resid 2 through 17 Processing helix chain 'R' and resid 19 through 34 Processing helix chain 'R' and resid 37 through 50 Processing helix chain 'R' and resid 53 through 68 Processing helix chain 'R' and resid 71 through 85 Processing helix chain 'R' and resid 87 through 102 Processing helix chain 'R' and resid 105 through 120 Processing helix chain 'S' and resid 1 through 30 Processing helix chain 'S' and resid 32 through 59 removed outlier: 3.503A pdb=" N VAL S 36 " --> pdb=" O THR S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 63 through 93 Processing helix chain 'S' and resid 97 through 121 Processing helix chain 'S' and resid 125 through 153 Processing helix chain 'S' and resid 158 through 183 Processing helix chain 'S' and resid 187 through 215 Processing helix chain 'S' and resid 218 through 245 Processing helix chain 'S' and resid 249 through 277 Processing helix chain 'T' and resid 2 through 17 Processing helix chain 'T' and resid 19 through 34 Processing helix chain 'T' and resid 37 through 50 Processing helix chain 'T' and resid 53 through 68 Processing helix chain 'T' and resid 71 through 85 Processing helix chain 'T' and resid 87 through 102 Processing helix chain 'T' and resid 105 through 120 Processing helix chain 'U' and resid 1 through 30 Processing helix chain 'U' and resid 32 through 59 removed outlier: 3.503A pdb=" N VAL U 36 " --> pdb=" O THR U 32 " (cutoff:3.500A) Processing helix chain 'U' and resid 63 through 93 Processing helix chain 'U' and resid 97 through 121 Processing helix chain 'U' and resid 125 through 153 Processing helix chain 'U' and resid 158 through 183 Processing helix chain 'U' and resid 187 through 215 Processing helix chain 'U' and resid 218 through 245 Processing helix chain 'U' and resid 249 through 277 Processing helix chain 'V' and resid 2 through 17 Processing helix chain 'V' and resid 19 through 34 Processing helix chain 'V' and resid 37 through 50 Processing helix chain 'V' and resid 53 through 68 Processing helix chain 'V' and resid 71 through 85 Processing helix chain 'V' and resid 87 through 102 Processing helix chain 'V' and resid 105 through 120 Processing helix chain 'W' and resid 1 through 30 Processing helix chain 'W' and resid 32 through 59 removed outlier: 3.503A pdb=" N VAL W 36 " --> pdb=" O THR W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 63 through 93 Processing helix chain 'W' and resid 97 through 121 Processing helix chain 'W' and resid 125 through 153 Processing helix chain 'W' and resid 158 through 183 Processing helix chain 'W' and resid 187 through 215 Processing helix chain 'W' and resid 218 through 245 Processing helix chain 'W' and resid 249 through 277 Processing helix chain 'X' and resid 2 through 17 Processing helix chain 'X' and resid 19 through 34 Processing helix chain 'X' and resid 37 through 50 Processing helix chain 'X' and resid 53 through 68 Processing helix chain 'X' and resid 71 through 85 Processing helix chain 'X' and resid 87 through 102 Processing helix chain 'X' and resid 105 through 120 3588 hydrogen bonds defined for protein. 10764 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.72 Time building geometry restraints manager: 4.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 7434 1.31 - 1.44: 10074 1.44 - 1.57: 19515 1.57 - 1.69: 213 1.69 - 1.82: 240 Bond restraints: 37476 Sorted by residual: bond pdb=" CB HIS K 123 " pdb=" CG HIS K 123 " ideal model delta sigma weight residual 1.497 1.370 0.127 1.40e-02 5.10e+03 8.29e+01 bond pdb=" CB HIS G 123 " pdb=" CG HIS G 123 " ideal model delta sigma weight residual 1.497 1.370 0.127 1.40e-02 5.10e+03 8.27e+01 bond pdb=" CB HIS M 123 " pdb=" CG HIS M 123 " ideal model delta sigma weight residual 1.497 1.370 0.127 1.40e-02 5.10e+03 8.27e+01 bond pdb=" CB HIS Q 123 " pdb=" CG HIS Q 123 " ideal model delta sigma weight residual 1.497 1.370 0.127 1.40e-02 5.10e+03 8.26e+01 bond pdb=" CB HIS E 123 " pdb=" CG HIS E 123 " ideal model delta sigma weight residual 1.497 1.370 0.127 1.40e-02 5.10e+03 8.25e+01 ... (remaining 37471 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 40130 1.59 - 3.19: 8562 3.19 - 4.78: 1643 4.78 - 6.37: 209 6.37 - 7.97: 84 Bond angle restraints: 50628 Sorted by residual: angle pdb=" C ASP N 34 " pdb=" N PRO N 35 " pdb=" CA PRO N 35 " ideal model delta sigma weight residual 119.82 127.79 -7.97 9.80e-01 1.04e+00 6.61e+01 angle pdb=" C ASP T 34 " pdb=" N PRO T 35 " pdb=" CA PRO T 35 " ideal model delta sigma weight residual 119.82 127.76 -7.94 9.80e-01 1.04e+00 6.56e+01 angle pdb=" C ASP H 34 " pdb=" N PRO H 35 " pdb=" CA PRO H 35 " ideal model delta sigma weight residual 119.82 127.76 -7.94 9.80e-01 1.04e+00 6.56e+01 angle pdb=" C ASP L 34 " pdb=" N PRO L 35 " pdb=" CA PRO L 35 " ideal model delta sigma weight residual 119.82 127.75 -7.93 9.80e-01 1.04e+00 6.55e+01 angle pdb=" C ASP V 34 " pdb=" N PRO V 35 " pdb=" CA PRO V 35 " ideal model delta sigma weight residual 119.82 127.75 -7.93 9.80e-01 1.04e+00 6.55e+01 ... (remaining 50623 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.11: 22252 15.11 - 30.22: 740 30.22 - 45.32: 192 45.32 - 60.43: 48 60.43 - 75.54: 48 Dihedral angle restraints: 23280 sinusoidal: 8952 harmonic: 14328 Sorted by residual: dihedral pdb=" CB GLU V 12 " pdb=" CG GLU V 12 " pdb=" CD GLU V 12 " pdb=" OE1 GLU V 12 " ideal model delta sinusoidal sigma weight residual 0.00 -75.54 75.54 1 3.00e+01 1.11e-03 8.00e+00 dihedral pdb=" CB GLU D 12 " pdb=" CG GLU D 12 " pdb=" CD GLU D 12 " pdb=" OE1 GLU D 12 " ideal model delta sinusoidal sigma weight residual 0.00 -75.52 75.52 1 3.00e+01 1.11e-03 8.00e+00 dihedral pdb=" CB GLU P 12 " pdb=" CG GLU P 12 " pdb=" CD GLU P 12 " pdb=" OE1 GLU P 12 " ideal model delta sinusoidal sigma weight residual 0.00 -75.51 75.51 1 3.00e+01 1.11e-03 8.00e+00 ... (remaining 23277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3645 0.072 - 0.145: 1729 0.145 - 0.217: 511 0.217 - 0.289: 57 0.289 - 0.361: 22 Chirality restraints: 5964 Sorted by residual: chirality pdb=" CG LEU P 106 " pdb=" CB LEU P 106 " pdb=" CD1 LEU P 106 " pdb=" CD2 LEU P 106 " both_signs ideal model delta sigma weight residual False -2.59 -2.95 0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" CG LEU T 106 " pdb=" CB LEU T 106 " pdb=" CD1 LEU T 106 " pdb=" CD2 LEU T 106 " both_signs ideal model delta sigma weight residual False -2.59 -2.95 0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CG LEU R 106 " pdb=" CB LEU R 106 " pdb=" CD1 LEU R 106 " pdb=" CD2 LEU R 106 " both_signs ideal model delta sigma weight residual False -2.59 -2.95 0.36 2.00e-01 2.50e+01 3.25e+00 ... (remaining 5961 not shown) Planarity restraints: 6444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR W 148 " 0.082 2.00e-02 2.50e+03 4.52e-02 4.08e+01 pdb=" CG TYR W 148 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR W 148 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR W 148 " -0.038 2.00e-02 2.50e+03 pdb=" CE1 TYR W 148 " -0.027 2.00e-02 2.50e+03 pdb=" CE2 TYR W 148 " -0.020 2.00e-02 2.50e+03 pdb=" CZ TYR W 148 " -0.014 2.00e-02 2.50e+03 pdb=" OH TYR W 148 " 0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR Q 148 " 0.082 2.00e-02 2.50e+03 4.50e-02 4.06e+01 pdb=" CG TYR Q 148 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR Q 148 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR Q 148 " -0.038 2.00e-02 2.50e+03 pdb=" CE1 TYR Q 148 " -0.027 2.00e-02 2.50e+03 pdb=" CE2 TYR Q 148 " -0.020 2.00e-02 2.50e+03 pdb=" CZ TYR Q 148 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR Q 148 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR S 148 " -0.082 2.00e-02 2.50e+03 4.50e-02 4.05e+01 pdb=" CG TYR S 148 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR S 148 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR S 148 " 0.038 2.00e-02 2.50e+03 pdb=" CE1 TYR S 148 " 0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR S 148 " 0.020 2.00e-02 2.50e+03 pdb=" CZ TYR S 148 " 0.013 2.00e-02 2.50e+03 pdb=" OH TYR S 148 " -0.072 2.00e-02 2.50e+03 ... (remaining 6441 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 15949 2.89 - 3.39: 42847 3.39 - 3.90: 65745 3.90 - 4.40: 79770 4.40 - 4.90: 121312 Nonbonded interactions: 325623 Sorted by model distance: nonbonded pdb=" OG1 THR W 156 " pdb=" N ASP W 157 " model vdw 2.389 3.120 nonbonded pdb=" OG1 THR I 156 " pdb=" N ASP I 157 " model vdw 2.389 3.120 nonbonded pdb=" OG1 THR U 156 " pdb=" N ASP U 157 " model vdw 2.389 3.120 nonbonded pdb=" OG1 THR O 156 " pdb=" N ASP O 157 " model vdw 2.389 3.120 nonbonded pdb=" OG1 THR E 156 " pdb=" N ASP E 157 " model vdw 2.390 3.120 ... (remaining 325618 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: 0.12 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 5.440 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: 0.050 Extract box with map and model: 0.550 Check model and map are aligned: 0.120 Set scattering table: 0.120 Process input model: 29.990 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 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 : 0.021 0.127 37476 Z= 1.249 Angle : 1.410 7.966 50628 Z= 0.968 Chirality : 0.086 0.361 5964 Planarity : 0.009 0.045 6444 Dihedral : 10.301 75.538 13944 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 0.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.59 (0.10), residues: 4716 helix: 1.80 (0.06), residues: 4344 sheet: None (None), residues: 0 loop : 1.15 (0.35), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 21 TYR 0.082 0.012 TYR S 148 PHE 0.033 0.009 PHE C 159 TRP 0.026 0.009 TRP N 41 HIS 0.016 0.007 HIS M 216 Details of bonding type rmsd covalent geometry : bond 0.02085 (37476) covalent geometry : angle 1.41029 (50628) hydrogen bonds : bond 0.11584 ( 3588) hydrogen bonds : angle 4.67082 (10764) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1316 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1316 time to evaluate : 1.403 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: 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: 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: 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: symmetry clash revert: symmetry clash REVERT: B 67 MET cc_start: 0.9138 (mtp) cc_final: 0.8650 (mtp) REVERT: B 85 ILE cc_start: 0.9698 (mt) cc_final: 0.9482 (tt) REVERT: B 160 MET cc_start: 0.7955 (ptm) cc_final: 0.7262 (ptm) REVERT: A 31 LEU cc_start: 0.9135 (mt) cc_final: 0.8886 (mt) REVERT: A 55 ASP cc_start: 0.8379 (m-30) cc_final: 0.8155 (t70) REVERT: A 102 ASP cc_start: 0.8713 (t0) cc_final: 0.8468 (t0) REVERT: A 118 LYS cc_start: 0.8731 (mmtt) cc_final: 0.8449 (mppt) REVERT: C 67 MET cc_start: 0.9080 (mtp) cc_final: 0.8878 (mtp) REVERT: C 160 MET cc_start: 0.8129 (ptm) cc_final: 0.7541 (ptm) REVERT: D 42 TYR cc_start: 0.8591 (t80) cc_final: 0.8318 (t80) REVERT: D 55 ASP cc_start: 0.8106 (m-30) cc_final: 0.7789 (t70) REVERT: D 97 LYS cc_start: 0.9313 (tppt) cc_final: 0.8867 (ttmt) REVERT: D 102 ASP cc_start: 0.8719 (t0) cc_final: 0.7220 (t0) REVERT: D 118 LYS cc_start: 0.8534 (mmtt) cc_final: 0.8285 (mppt) REVERT: E 15 SER cc_start: 0.9446 (t) cc_final: 0.9228 (p) REVERT: E 160 MET cc_start: 0.8064 (ptm) cc_final: 0.7476 (ptm) REVERT: F 31 LEU cc_start: 0.9231 (mt) cc_final: 0.8989 (mt) REVERT: F 55 ASP cc_start: 0.8550 (m-30) cc_final: 0.8071 (t0) REVERT: F 97 LYS cc_start: 0.9324 (tppt) cc_final: 0.9011 (ttmt) REVERT: F 102 ASP cc_start: 0.8701 (t0) cc_final: 0.8264 (t0) REVERT: F 117 ASP cc_start: 0.8918 (t70) cc_final: 0.7210 (t0) REVERT: F 118 LYS cc_start: 0.8660 (mmtt) cc_final: 0.8383 (mppt) REVERT: G 19 SER cc_start: 0.9295 (m) cc_final: 0.8958 (p) REVERT: G 67 MET cc_start: 0.8977 (mtp) cc_final: 0.8638 (mtp) REVERT: G 113 ILE cc_start: 0.9341 (mt) cc_final: 0.9137 (tt) REVERT: G 160 MET cc_start: 0.8034 (ptm) cc_final: 0.7671 (ptm) REVERT: G 266 LEU cc_start: 0.9430 (tt) cc_final: 0.9203 (tt) REVERT: H 31 LEU cc_start: 0.9261 (mt) cc_final: 0.9025 (mt) REVERT: H 55 ASP cc_start: 0.8382 (m-30) cc_final: 0.7983 (t70) REVERT: H 102 ASP cc_start: 0.8622 (t0) cc_final: 0.8103 (t0) REVERT: H 118 LYS cc_start: 0.8721 (mmtt) cc_final: 0.8403 (mppt) REVERT: I 15 SER cc_start: 0.9524 (t) cc_final: 0.9320 (p) REVERT: I 19 SER cc_start: 0.9331 (m) cc_final: 0.9006 (p) REVERT: I 67 MET cc_start: 0.9122 (mtp) cc_final: 0.8697 (mtp) REVERT: I 160 MET cc_start: 0.8001 (ptm) cc_final: 0.7704 (ptm) REVERT: J 36 ASN cc_start: 0.8480 (m-40) cc_final: 0.8026 (t0) REVERT: J 55 ASP cc_start: 0.8240 (m-30) cc_final: 0.7982 (t0) REVERT: J 63 LYS cc_start: 0.8782 (mmtt) cc_final: 0.8375 (ttpt) REVERT: J 97 LYS cc_start: 0.9225 (tppt) cc_final: 0.8919 (mtmt) REVERT: J 102 ASP cc_start: 0.8521 (t0) cc_final: 0.8234 (t0) REVERT: K 5 VAL cc_start: 0.9376 (t) cc_final: 0.9152 (p) REVERT: K 15 SER cc_start: 0.9482 (t) cc_final: 0.9280 (p) REVERT: K 19 SER cc_start: 0.9285 (m) cc_final: 0.8996 (p) REVERT: K 67 MET cc_start: 0.9029 (mtp) cc_final: 0.8369 (mtp) REVERT: K 160 MET cc_start: 0.8068 (ptm) cc_final: 0.7486 (ptm) REVERT: K 221 TYR cc_start: 0.7023 (m-80) cc_final: 0.6686 (m-80) REVERT: K 266 LEU cc_start: 0.9432 (tt) cc_final: 0.9151 (tt) REVERT: L 31 LEU cc_start: 0.9177 (mt) cc_final: 0.8966 (mt) REVERT: L 97 LYS cc_start: 0.9308 (tppt) cc_final: 0.9036 (mttt) REVERT: L 102 ASP cc_start: 0.8786 (t0) cc_final: 0.8200 (t0) REVERT: L 118 LYS cc_start: 0.8591 (mmtt) cc_final: 0.8252 (mppt) REVERT: M 19 SER cc_start: 0.9301 (m) cc_final: 0.8996 (p) REVERT: M 67 MET cc_start: 0.9072 (mtp) cc_final: 0.8603 (mtp) REVERT: M 160 MET cc_start: 0.7985 (ptm) cc_final: 0.7567 (ptm) REVERT: M 221 TYR cc_start: 0.6987 (m-80) cc_final: 0.6602 (m-80) REVERT: M 268 LYS cc_start: 0.9240 (tptt) cc_final: 0.9039 (tptt) REVERT: N 102 ASP cc_start: 0.8642 (t0) cc_final: 0.8027 (t0) REVERT: N 118 LYS cc_start: 0.8680 (mmtt) cc_final: 0.8339 (mppt) REVERT: O 67 MET cc_start: 0.9206 (mtp) cc_final: 0.8700 (mtp) REVERT: O 77 LEU cc_start: 0.9463 (mt) cc_final: 0.9248 (tp) REVERT: O 160 MET cc_start: 0.8227 (ptm) cc_final: 0.7793 (ptm) REVERT: P 55 ASP cc_start: 0.8167 (m-30) cc_final: 0.7842 (t0) REVERT: P 102 ASP cc_start: 0.8601 (t0) cc_final: 0.7232 (t0) REVERT: P 118 LYS cc_start: 0.8628 (mmtt) cc_final: 0.8425 (mppt) REVERT: Q 5 VAL cc_start: 0.9384 (t) cc_final: 0.9174 (p) REVERT: Q 67 MET cc_start: 0.9223 (mtp) cc_final: 0.8813 (mtp) REVERT: Q 160 MET cc_start: 0.8119 (ptm) cc_final: 0.7763 (ptm) REVERT: Q 221 TYR cc_start: 0.6985 (m-80) cc_final: 0.6577 (m-80) REVERT: R 36 ASN cc_start: 0.8592 (m-40) cc_final: 0.8069 (t0) REVERT: R 55 ASP cc_start: 0.8006 (m-30) cc_final: 0.7700 (t0) REVERT: R 102 ASP cc_start: 0.8598 (t0) cc_final: 0.7106 (t0) REVERT: R 118 LYS cc_start: 0.8712 (mmtt) cc_final: 0.8385 (mppt) REVERT: S 67 MET cc_start: 0.8995 (mtp) cc_final: 0.8571 (mtp) REVERT: S 160 MET cc_start: 0.7920 (ptm) cc_final: 0.7467 (ptm) REVERT: S 221 TYR cc_start: 0.6823 (m-80) cc_final: 0.6620 (m-80) REVERT: T 55 ASP cc_start: 0.8423 (m-30) cc_final: 0.8175 (t0) REVERT: T 63 LYS cc_start: 0.8769 (mmtt) cc_final: 0.8311 (ttpt) REVERT: T 97 LYS cc_start: 0.9356 (tppt) cc_final: 0.8953 (ttmt) REVERT: T 102 ASP cc_start: 0.8507 (t0) cc_final: 0.8104 (t0) REVERT: T 118 LYS cc_start: 0.8788 (mmtt) cc_final: 0.8471 (mppt) REVERT: U 67 MET cc_start: 0.8896 (mtp) cc_final: 0.8644 (mtp) REVERT: U 136 ILE cc_start: 0.9345 (mt) cc_final: 0.8971 (mt) REVERT: V 36 ASN cc_start: 0.8487 (m-40) cc_final: 0.8001 (t0) REVERT: V 102 ASP cc_start: 0.8669 (t0) cc_final: 0.8090 (t0) REVERT: W 67 MET cc_start: 0.9113 (mtp) cc_final: 0.8768 (mtp) REVERT: W 77 LEU cc_start: 0.9553 (mt) cc_final: 0.9347 (tp) REVERT: W 160 MET cc_start: 0.7920 (ptm) cc_final: 0.7671 (ptm) REVERT: W 221 TYR cc_start: 0.6764 (m-80) cc_final: 0.6320 (m-80) REVERT: X 36 ASN cc_start: 0.8501 (m-40) cc_final: 0.7960 (t0) REVERT: X 55 ASP cc_start: 0.8455 (m-30) cc_final: 0.8198 (t0) REVERT: X 97 LYS cc_start: 0.9353 (tppt) cc_final: 0.9109 (mmmm) REVERT: X 102 ASP cc_start: 0.8534 (t0) cc_final: 0.8213 (t0) outliers start: 0 outliers final: 0 residues processed: 1316 average time/residue: 0.2605 time to fit residues: 536.1116 Evaluate side-chains 544 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 544 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 5.9990 chunk 455 optimal weight: 0.9980 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.9990 chunk 401 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 105 ASN E 122 ASN E 277 ASN I 277 ASN K 277 ASN M 277 ASN O 277 ASN R 105 ASN W 277 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.067283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.053891 restraints weight = 164724.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.055254 restraints weight = 115296.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.056172 restraints weight = 90659.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.056754 restraints weight = 77094.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.057196 restraints weight = 69256.116| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 37476 Z= 0.165 Angle : 0.577 8.859 50628 Z= 0.315 Chirality : 0.040 0.225 5964 Planarity : 0.004 0.039 6444 Dihedral : 3.671 19.304 5172 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.03 % Allowed : 1.61 % Favored : 98.37 % 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: 4.26 (0.11), residues: 4716 helix: 3.02 (0.07), residues: 4368 sheet: None (None), residues: 0 loop : -0.43 (0.37), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 45 TYR 0.021 0.002 TYR O 221 PHE 0.018 0.003 PHE E 128 TRP 0.010 0.002 TRP T 75 HIS 0.013 0.003 HIS U 123 Details of bonding type rmsd covalent geometry : bond 0.00353 (37476) covalent geometry : angle 0.57678 (50628) hydrogen bonds : bond 0.04585 ( 3588) hydrogen bonds : angle 3.18487 (10764) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 849 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 848 time to evaluate : 1.524 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: 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: 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: symmetry clash revert: symmetry clash REVERT: B 160 MET cc_start: 0.7732 (ptm) cc_final: 0.7383 (ptm) REVERT: B 212 LEU cc_start: 0.8796 (mt) cc_final: 0.8509 (mt) REVERT: B 221 TYR cc_start: 0.7747 (m-10) cc_final: 0.7222 (m-80) REVERT: A 62 GLN cc_start: 0.9154 (mt0) cc_final: 0.8858 (mt0) REVERT: A 102 ASP cc_start: 0.8678 (t0) cc_final: 0.8192 (t0) REVERT: C 160 MET cc_start: 0.7816 (ptm) cc_final: 0.6500 (ptm) REVERT: C 221 TYR cc_start: 0.7705 (m-10) cc_final: 0.7292 (m-80) REVERT: D 34 ASP cc_start: 0.9217 (t0) cc_final: 0.8955 (t0) REVERT: D 55 ASP cc_start: 0.7993 (m-30) cc_final: 0.7661 (t0) REVERT: D 62 GLN cc_start: 0.9201 (mt0) cc_final: 0.8994 (mt0) REVERT: D 97 LYS cc_start: 0.9275 (tppt) cc_final: 0.8692 (ttmt) REVERT: D 102 ASP cc_start: 0.8726 (t0) cc_final: 0.8466 (t0) REVERT: E 160 MET cc_start: 0.7525 (ptm) cc_final: 0.7324 (ptm) REVERT: E 221 TYR cc_start: 0.7581 (m-10) cc_final: 0.6898 (m-80) REVERT: E 268 LYS cc_start: 0.9094 (tptt) cc_final: 0.8620 (tptp) REVERT: F 36 ASN cc_start: 0.8527 (m-40) cc_final: 0.8149 (t0) REVERT: F 55 ASP cc_start: 0.8276 (m-30) cc_final: 0.7957 (t0) REVERT: F 62 GLN cc_start: 0.9150 (mt0) cc_final: 0.8934 (mt0) REVERT: F 63 LYS cc_start: 0.9075 (mmtt) cc_final: 0.8785 (mttm) REVERT: F 97 LYS cc_start: 0.9359 (tppt) cc_final: 0.8904 (ttmt) REVERT: F 102 ASP cc_start: 0.8674 (t0) cc_final: 0.8385 (t0) REVERT: F 105 ASN cc_start: 0.8362 (m-40) cc_final: 0.7614 (p0) REVERT: G 19 SER cc_start: 0.9427 (m) cc_final: 0.9156 (p) REVERT: G 221 TYR cc_start: 0.7587 (m-10) cc_final: 0.7062 (m-80) REVERT: H 55 ASP cc_start: 0.8123 (m-30) cc_final: 0.7892 (t0) REVERT: H 62 GLN cc_start: 0.9074 (mt0) cc_final: 0.8803 (mt0) REVERT: H 97 LYS cc_start: 0.9354 (mmmm) cc_final: 0.8745 (mttp) REVERT: H 102 ASP cc_start: 0.8812 (t0) cc_final: 0.8489 (t0) REVERT: I 19 SER cc_start: 0.9442 (m) cc_final: 0.9131 (p) REVERT: I 67 MET cc_start: 0.8711 (mtp) cc_final: 0.8274 (mtp) REVERT: I 160 MET cc_start: 0.7421 (ptm) cc_final: 0.7025 (ptm) REVERT: I 221 TYR cc_start: 0.7924 (m-10) cc_final: 0.7285 (m-80) REVERT: I 268 LYS cc_start: 0.8988 (tptt) cc_final: 0.8704 (tptp) REVERT: J 36 ASN cc_start: 0.8380 (m-40) cc_final: 0.8117 (t0) REVERT: J 62 GLN cc_start: 0.9158 (mt0) cc_final: 0.8890 (mt0) REVERT: J 63 LYS cc_start: 0.9065 (mmtt) cc_final: 0.8840 (mttm) REVERT: J 70 ASN cc_start: 0.8271 (m110) cc_final: 0.7713 (t0) REVERT: J 97 LYS cc_start: 0.9284 (tppt) cc_final: 0.8986 (mmmm) REVERT: J 102 ASP cc_start: 0.8554 (t0) cc_final: 0.7724 (t0) REVERT: K 19 SER cc_start: 0.9412 (m) cc_final: 0.9199 (p) REVERT: K 67 MET cc_start: 0.8709 (mtp) cc_final: 0.8181 (mtp) REVERT: K 160 MET cc_start: 0.7692 (ptm) cc_final: 0.7122 (ptm) REVERT: K 212 LEU cc_start: 0.8929 (mt) cc_final: 0.8459 (mt) REVERT: L 62 GLN cc_start: 0.9151 (mt0) cc_final: 0.8907 (mt0) REVERT: L 97 LYS cc_start: 0.9297 (tppt) cc_final: 0.8926 (mttt) REVERT: L 102 ASP cc_start: 0.8908 (t0) cc_final: 0.8269 (t0) REVERT: M 19 SER cc_start: 0.9414 (m) cc_final: 0.9126 (p) REVERT: M 160 MET cc_start: 0.7519 (ptm) cc_final: 0.6883 (ptm) REVERT: N 62 GLN cc_start: 0.9169 (mt0) cc_final: 0.8873 (mt0) REVERT: N 63 LYS cc_start: 0.8999 (mmtt) cc_final: 0.8732 (mttm) REVERT: N 102 ASP cc_start: 0.8643 (t0) cc_final: 0.8236 (t0) REVERT: O 67 MET cc_start: 0.8540 (mtp) cc_final: 0.7859 (mtp) REVERT: O 160 MET cc_start: 0.7881 (ptm) cc_final: 0.7248 (ptm) REVERT: O 212 LEU cc_start: 0.8826 (mt) cc_final: 0.8504 (mt) REVERT: O 216 HIS cc_start: 0.5947 (m90) cc_final: 0.5595 (m-70) REVERT: O 221 TYR cc_start: 0.7912 (m-10) cc_final: 0.7425 (m-80) REVERT: P 22 ILE cc_start: 0.9403 (mp) cc_final: 0.9187 (mm) REVERT: P 33 ARG cc_start: 0.7874 (tpt170) cc_final: 0.7639 (tpt90) REVERT: P 36 ASN cc_start: 0.8389 (m-40) cc_final: 0.8095 (t0) REVERT: P 62 GLN cc_start: 0.9141 (mt0) cc_final: 0.8864 (mt0) REVERT: P 63 LYS cc_start: 0.9057 (mmtt) cc_final: 0.8828 (mttm) REVERT: P 102 ASP cc_start: 0.8700 (t0) cc_final: 0.8165 (t0) REVERT: P 105 ASN cc_start: 0.8254 (m-40) cc_final: 0.8033 (m110) REVERT: Q 67 MET cc_start: 0.8599 (mtp) cc_final: 0.8183 (mtp) REVERT: Q 160 MET cc_start: 0.7753 (ptm) cc_final: 0.7446 (ptm) REVERT: R 36 ASN cc_start: 0.8632 (m-40) cc_final: 0.8264 (t0) REVERT: R 55 ASP cc_start: 0.8036 (m-30) cc_final: 0.7623 (t0) REVERT: R 62 GLN cc_start: 0.9032 (mt0) cc_final: 0.8689 (mt0) REVERT: R 102 ASP cc_start: 0.8717 (t0) cc_final: 0.8350 (t0) REVERT: S 67 MET cc_start: 0.8559 (mtp) cc_final: 0.8242 (mtp) REVERT: S 160 MET cc_start: 0.7878 (ptm) cc_final: 0.7300 (ptm) REVERT: S 226 ILE cc_start: 0.9387 (mt) cc_final: 0.8868 (mm) REVERT: T 36 ASN cc_start: 0.8692 (m-40) cc_final: 0.8389 (t0) REVERT: T 62 GLN cc_start: 0.9062 (mt0) cc_final: 0.8716 (mt0) REVERT: T 63 LYS cc_start: 0.9018 (mmtt) cc_final: 0.8450 (ttpt) REVERT: T 105 ASN cc_start: 0.8143 (m-40) cc_final: 0.7854 (p0) REVERT: U 160 MET cc_start: 0.7612 (ptm) cc_final: 0.7153 (ptm) REVERT: U 221 TYR cc_start: 0.7729 (m-10) cc_final: 0.7192 (m-80) REVERT: U 252 TYR cc_start: 0.8618 (m-80) cc_final: 0.8348 (m-80) REVERT: U 268 LYS cc_start: 0.9059 (tptt) cc_final: 0.8561 (tptp) REVERT: V 36 ASN cc_start: 0.8521 (m-40) cc_final: 0.8237 (t0) REVERT: V 63 LYS cc_start: 0.9111 (mmtt) cc_final: 0.8803 (mmmm) REVERT: V 102 ASP cc_start: 0.8716 (t0) cc_final: 0.8335 (t0) REVERT: V 105 ASN cc_start: 0.8326 (m-40) cc_final: 0.7740 (p0) REVERT: V 118 LYS cc_start: 0.9055 (mmmm) cc_final: 0.8613 (mppt) REVERT: W 209 ILE cc_start: 0.9417 (mt) cc_final: 0.9207 (mm) REVERT: W 268 LYS cc_start: 0.9058 (tptt) cc_final: 0.8685 (tptp) REVERT: X 55 ASP cc_start: 0.8168 (m-30) cc_final: 0.7965 (t0) REVERT: X 63 LYS cc_start: 0.9020 (mmtt) cc_final: 0.8767 (mmmm) REVERT: X 70 ASN cc_start: 0.8008 (m110) cc_final: 0.7612 (t0) REVERT: X 97 LYS cc_start: 0.9304 (tppt) cc_final: 0.8959 (mmmm) REVERT: X 102 ASP cc_start: 0.8659 (t0) cc_final: 0.7860 (t0) REVERT: X 118 LYS cc_start: 0.9033 (mmmm) cc_final: 0.8761 (mppt) outliers start: 1 outliers final: 0 residues processed: 849 average time/residue: 0.2349 time to fit residues: 326.6407 Evaluate side-chains 470 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 470 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 71 optimal weight: 1.9990 chunk 238 optimal weight: 0.9990 chunk 161 optimal weight: 0.9980 chunk 332 optimal weight: 0.9990 chunk 380 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 314 optimal weight: 4.9990 chunk 299 optimal weight: 3.9990 chunk 357 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 331 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 GLN ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN C 277 ASN E 52 GLN G 52 GLN G 122 ASN G 185 HIS G 277 ASN ** I 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 52 GLN O 52 GLN O 92 HIS ** O 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 277 ASN U 52 GLN U 122 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.066432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.052795 restraints weight = 164865.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.054046 restraints weight = 119133.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.054931 restraints weight = 95701.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.055485 restraints weight = 82169.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.055901 restraints weight = 74297.005| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.4768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 37476 Z= 0.149 Angle : 0.530 12.018 50628 Z= 0.286 Chirality : 0.038 0.291 5964 Planarity : 0.003 0.033 6444 Dihedral : 3.578 18.730 5172 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 0.19 % Allowed : 1.77 % Favored : 98.03 % 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: 4.22 (0.11), residues: 4716 helix: 3.05 (0.07), residues: 4368 sheet: None (None), residues: 0 loop : -1.48 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Q 211 TYR 0.017 0.002 TYR Q 221 PHE 0.024 0.002 PHE E 128 TRP 0.014 0.002 TRP L 41 HIS 0.017 0.003 HIS M 123 Details of bonding type rmsd covalent geometry : bond 0.00315 (37476) covalent geometry : angle 0.52989 (50628) hydrogen bonds : bond 0.04018 ( 3588) hydrogen bonds : angle 3.07170 (10764) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 677 time to evaluate : 1.462 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: 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: 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: symmetry clash REVERT: B 160 MET cc_start: 0.7818 (ptm) cc_final: 0.7419 (ptm) REVERT: B 195 ILE cc_start: 0.8882 (mt) cc_final: 0.8678 (mt) REVERT: B 212 LEU cc_start: 0.8880 (mt) cc_final: 0.8597 (mt) REVERT: B 257 LYS cc_start: 0.8993 (mtmt) cc_final: 0.8705 (ptpp) REVERT: A 36 ASN cc_start: 0.8389 (m-40) cc_final: 0.8119 (t0) REVERT: A 62 GLN cc_start: 0.9217 (mt0) cc_final: 0.8934 (mt0) REVERT: A 63 LYS cc_start: 0.9095 (mmtt) cc_final: 0.8869 (mmmm) REVERT: A 102 ASP cc_start: 0.8847 (t0) cc_final: 0.8592 (t0) REVERT: C 160 MET cc_start: 0.7717 (ptm) cc_final: 0.6712 (ptm) REVERT: C 191 MET cc_start: 0.8052 (tpp) cc_final: 0.7489 (tpp) REVERT: C 243 LEU cc_start: 0.9302 (mp) cc_final: 0.8867 (mm) REVERT: C 257 LYS cc_start: 0.9183 (mtmt) cc_final: 0.8804 (ptpp) REVERT: D 36 ASN cc_start: 0.8487 (m-40) cc_final: 0.8182 (t0) REVERT: D 55 ASP cc_start: 0.8053 (m-30) cc_final: 0.7736 (t0) REVERT: D 58 ILE cc_start: 0.9347 (mt) cc_final: 0.9069 (mt) REVERT: D 97 LYS cc_start: 0.9296 (tppt) cc_final: 0.8862 (ttmt) REVERT: D 102 ASP cc_start: 0.8741 (t0) cc_final: 0.8414 (t0) REVERT: E 160 MET cc_start: 0.7706 (ptm) cc_final: 0.6534 (ptm) REVERT: E 209 ILE cc_start: 0.9428 (mt) cc_final: 0.9162 (mm) REVERT: E 257 LYS cc_start: 0.9085 (mtmt) cc_final: 0.8797 (ptpp) REVERT: F 32 LYS cc_start: 0.9155 (tppt) cc_final: 0.8944 (tppt) REVERT: F 36 ASN cc_start: 0.8621 (m-40) cc_final: 0.8213 (t0) REVERT: F 55 ASP cc_start: 0.8392 (m-30) cc_final: 0.7918 (t0) REVERT: F 62 GLN cc_start: 0.9167 (mt0) cc_final: 0.8922 (mt0) REVERT: F 63 LYS cc_start: 0.9191 (mmtt) cc_final: 0.8964 (mttm) REVERT: F 97 LYS cc_start: 0.9407 (tppt) cc_final: 0.8973 (ttmt) REVERT: F 102 ASP cc_start: 0.8639 (t0) cc_final: 0.8356 (t0) REVERT: F 105 ASN cc_start: 0.8295 (m-40) cc_final: 0.7765 (p0) REVERT: F 117 ASP cc_start: 0.8572 (t70) cc_final: 0.8049 (t0) REVERT: G 160 MET cc_start: 0.7745 (ptm) cc_final: 0.7522 (ptm) REVERT: G 209 ILE cc_start: 0.9494 (mt) cc_final: 0.9266 (mm) REVERT: G 221 TYR cc_start: 0.7802 (m-10) cc_final: 0.7573 (m-80) REVERT: G 257 LYS cc_start: 0.9160 (mtmt) cc_final: 0.8633 (ptpp) REVERT: H 36 ASN cc_start: 0.8511 (m-40) cc_final: 0.8202 (t0) REVERT: H 55 ASP cc_start: 0.8348 (m-30) cc_final: 0.7952 (t0) REVERT: H 62 GLN cc_start: 0.9170 (mt0) cc_final: 0.8869 (mt0) REVERT: H 63 LYS cc_start: 0.9194 (mmtt) cc_final: 0.8892 (mmmm) REVERT: H 97 LYS cc_start: 0.9303 (mmmm) cc_final: 0.8735 (mttp) REVERT: H 102 ASP cc_start: 0.8943 (t0) cc_final: 0.8637 (t0) REVERT: H 105 ASN cc_start: 0.8228 (m-40) cc_final: 0.7835 (p0) REVERT: H 118 LYS cc_start: 0.9122 (mmmm) cc_final: 0.8622 (mppt) REVERT: I 19 SER cc_start: 0.9497 (m) cc_final: 0.9235 (p) REVERT: I 67 MET cc_start: 0.8597 (mtp) cc_final: 0.8046 (mtp) REVERT: I 160 MET cc_start: 0.7393 (ptm) cc_final: 0.7026 (ptm) REVERT: I 209 ILE cc_start: 0.9337 (mt) cc_final: 0.9104 (mm) REVERT: I 221 TYR cc_start: 0.7781 (m-10) cc_final: 0.7570 (m-80) REVERT: J 62 GLN cc_start: 0.9202 (mt0) cc_final: 0.8960 (mt0) REVERT: J 70 ASN cc_start: 0.8515 (m110) cc_final: 0.7887 (t0) REVERT: J 97 LYS cc_start: 0.9337 (tppt) cc_final: 0.8993 (mmmm) REVERT: J 102 ASP cc_start: 0.8773 (t0) cc_final: 0.8418 (t0) REVERT: K 8 MET cc_start: 0.8705 (mtp) cc_final: 0.8246 (mtp) REVERT: K 67 MET cc_start: 0.8663 (mtp) cc_final: 0.8136 (mtp) REVERT: K 160 MET cc_start: 0.7650 (ptm) cc_final: 0.7224 (ptm) REVERT: K 216 HIS cc_start: 0.6442 (m90) cc_final: 0.6197 (m170) REVERT: L 62 GLN cc_start: 0.9208 (mt0) cc_final: 0.8855 (mt0) REVERT: L 63 LYS cc_start: 0.9348 (mmtt) cc_final: 0.9047 (mttm) REVERT: L 97 LYS cc_start: 0.9307 (tppt) cc_final: 0.8895 (mttt) REVERT: L 102 ASP cc_start: 0.8848 (t0) cc_final: 0.8394 (t0) REVERT: L 105 ASN cc_start: 0.8291 (m-40) cc_final: 0.7860 (p0) REVERT: L 118 LYS cc_start: 0.9206 (mmmm) cc_final: 0.8758 (mppt) REVERT: M 8 MET cc_start: 0.8303 (mtp) cc_final: 0.7950 (mtp) REVERT: M 19 SER cc_start: 0.9456 (m) cc_final: 0.9192 (p) REVERT: M 209 ILE cc_start: 0.9402 (mt) cc_final: 0.9131 (mm) REVERT: M 212 LEU cc_start: 0.8622 (mt) cc_final: 0.8229 (mt) REVERT: M 221 TYR cc_start: 0.7657 (m-10) cc_final: 0.7451 (m-80) REVERT: N 36 ASN cc_start: 0.8542 (m-40) cc_final: 0.8294 (t0) REVERT: N 62 GLN cc_start: 0.9284 (mt0) cc_final: 0.8908 (mt0) REVERT: N 63 LYS cc_start: 0.9273 (mmtt) cc_final: 0.9007 (mmmm) REVERT: N 102 ASP cc_start: 0.8720 (t0) cc_final: 0.7720 (t0) REVERT: N 105 ASN cc_start: 0.7973 (m-40) cc_final: 0.7676 (m110) REVERT: N 118 LYS cc_start: 0.9227 (mmmm) cc_final: 0.8963 (mppt) REVERT: O 67 MET cc_start: 0.8385 (mtp) cc_final: 0.7933 (mtp) REVERT: O 160 MET cc_start: 0.7934 (ptm) cc_final: 0.7417 (ptm) REVERT: O 191 MET cc_start: 0.8035 (tpp) cc_final: 0.7511 (tpp) REVERT: O 212 LEU cc_start: 0.8764 (mt) cc_final: 0.8215 (mt) REVERT: O 221 TYR cc_start: 0.8014 (m-10) cc_final: 0.7696 (m-80) REVERT: O 243 LEU cc_start: 0.9200 (mp) cc_final: 0.8970 (mm) REVERT: O 257 LYS cc_start: 0.8984 (mtmt) cc_final: 0.8699 (ptpp) REVERT: P 33 ARG cc_start: 0.7894 (tpt170) cc_final: 0.7182 (tpt170) REVERT: P 36 ASN cc_start: 0.8444 (m-40) cc_final: 0.8144 (t0) REVERT: P 62 GLN cc_start: 0.9156 (mt0) cc_final: 0.8826 (mt0) REVERT: P 102 ASP cc_start: 0.8799 (t0) cc_final: 0.8180 (t0) REVERT: P 105 ASN cc_start: 0.8292 (m-40) cc_final: 0.7851 (m110) REVERT: P 118 LYS cc_start: 0.9032 (mmmm) cc_final: 0.8643 (mppt) REVERT: Q 160 MET cc_start: 0.7894 (ptm) cc_final: 0.7260 (ptm) REVERT: Q 243 LEU cc_start: 0.9304 (mp) cc_final: 0.9070 (mp) REVERT: R 36 ASN cc_start: 0.8791 (m-40) cc_final: 0.8403 (t0) REVERT: R 55 ASP cc_start: 0.8159 (m-30) cc_final: 0.7697 (t0) REVERT: R 102 ASP cc_start: 0.8668 (t0) cc_final: 0.8268 (t0) REVERT: S 67 MET cc_start: 0.8498 (mtp) cc_final: 0.8161 (mtp) REVERT: S 160 MET cc_start: 0.7663 (ptm) cc_final: 0.6616 (ptm) REVERT: S 221 TYR cc_start: 0.7667 (m-10) cc_final: 0.7347 (m-80) REVERT: S 226 ILE cc_start: 0.9487 (mt) cc_final: 0.9241 (mm) REVERT: S 257 LYS cc_start: 0.9039 (mtmt) cc_final: 0.8762 (ptpp) REVERT: T 36 ASN cc_start: 0.8715 (m-40) cc_final: 0.8488 (t0) REVERT: T 62 GLN cc_start: 0.9213 (mt0) cc_final: 0.8844 (mt0) REVERT: T 63 LYS cc_start: 0.9108 (mmtt) cc_final: 0.8743 (mmmm) REVERT: T 87 ASP cc_start: 0.6987 (t0) cc_final: 0.5296 (t0) REVERT: T 117 ASP cc_start: 0.8802 (t70) cc_final: 0.7315 (t0) REVERT: U 160 MET cc_start: 0.7750 (ptm) cc_final: 0.7341 (ptm) REVERT: U 226 ILE cc_start: 0.9311 (mt) cc_final: 0.8639 (mm) REVERT: U 252 TYR cc_start: 0.8724 (m-80) cc_final: 0.8518 (m-80) REVERT: V 36 ASN cc_start: 0.8478 (m-40) cc_final: 0.8177 (t0) REVERT: V 63 LYS cc_start: 0.9194 (mmtt) cc_final: 0.8958 (mmmm) REVERT: V 105 ASN cc_start: 0.8202 (m-40) cc_final: 0.7789 (p0) REVERT: V 118 LYS cc_start: 0.9264 (mmmm) cc_final: 0.8799 (mppt) REVERT: W 221 TYR cc_start: 0.7785 (m-10) cc_final: 0.7296 (m-80) REVERT: X 55 ASP cc_start: 0.8395 (m-30) cc_final: 0.8094 (t0) REVERT: X 62 GLN cc_start: 0.9238 (mt0) cc_final: 0.9001 (mt0) REVERT: X 63 LYS cc_start: 0.9255 (mmtt) cc_final: 0.8961 (mmmm) REVERT: X 70 ASN cc_start: 0.8362 (m110) cc_final: 0.7933 (t0) REVERT: X 97 LYS cc_start: 0.9256 (tppt) cc_final: 0.8936 (mmmm) REVERT: X 102 ASP cc_start: 0.8682 (t0) cc_final: 0.8331 (t0) REVERT: X 118 LYS cc_start: 0.9111 (mmmm) cc_final: 0.8901 (mppt) outliers start: 7 outliers final: 3 residues processed: 684 average time/residue: 0.2267 time to fit residues: 257.5963 Evaluate side-chains 438 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 435 time to evaluate : 1.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 210 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 375 optimal weight: 0.0770 chunk 145 optimal weight: 1.9990 chunk 337 optimal weight: 1.9990 chunk 191 optimal weight: 0.9990 chunk 209 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 465 optimal weight: 0.7980 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 HIS C 52 GLN E 52 GLN G 52 GLN J 110 GLN K 185 HIS M 185 HIS Q 122 ASN U 52 GLN U 277 ASN ** W 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.065537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.051904 restraints weight = 163219.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.053149 restraints weight = 117934.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.053992 restraints weight = 94738.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.054563 restraints weight = 81641.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.054962 restraints weight = 73737.938| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.5361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 37476 Z= 0.142 Angle : 0.502 11.353 50628 Z= 0.274 Chirality : 0.037 0.256 5964 Planarity : 0.003 0.037 6444 Dihedral : 3.577 17.082 5172 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.03 % Allowed : 2.33 % Favored : 97.65 % 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: 4.12 (0.11), residues: 4716 helix: 3.00 (0.07), residues: 4380 sheet: None (None), residues: 0 loop : -1.95 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG V 21 TYR 0.017 0.001 TYR M 210 PHE 0.016 0.002 PHE O 128 TRP 0.017 0.002 TRP L 41 HIS 0.008 0.002 HIS B 123 Details of bonding type rmsd covalent geometry : bond 0.00301 (37476) covalent geometry : angle 0.50182 (50628) hydrogen bonds : bond 0.03706 ( 3588) hydrogen bonds : angle 3.01698 (10764) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 622 time to evaluate : 1.469 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: 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: 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: symmetry clash revert: symmetry clash REVERT: B 160 MET cc_start: 0.7867 (ptm) cc_final: 0.6917 (ptm) REVERT: B 212 LEU cc_start: 0.8866 (mt) cc_final: 0.8488 (mt) REVERT: B 257 LYS cc_start: 0.9017 (mtmt) cc_final: 0.8711 (ptpp) REVERT: A 36 ASN cc_start: 0.8468 (m-40) cc_final: 0.8209 (t0) REVERT: A 62 GLN cc_start: 0.9341 (mt0) cc_final: 0.8984 (mt0) REVERT: A 63 LYS cc_start: 0.9252 (mmtt) cc_final: 0.8913 (mmmm) REVERT: A 87 ASP cc_start: 0.6602 (t70) cc_final: 0.5482 (t70) REVERT: C 148 TYR cc_start: 0.7415 (t80) cc_final: 0.7189 (t80) REVERT: C 160 MET cc_start: 0.7786 (ptm) cc_final: 0.6725 (ptm) REVERT: C 191 MET cc_start: 0.8161 (tpp) cc_final: 0.7444 (tpp) REVERT: C 209 ILE cc_start: 0.9575 (mt) cc_final: 0.9338 (mm) REVERT: C 243 LEU cc_start: 0.9385 (mp) cc_final: 0.8817 (mm) REVERT: D 3 GLU cc_start: 0.7739 (tt0) cc_final: 0.7495 (tt0) REVERT: D 33 ARG cc_start: 0.8600 (mmm160) cc_final: 0.8225 (mmt180) REVERT: D 36 ASN cc_start: 0.8511 (m-40) cc_final: 0.8189 (t0) REVERT: D 55 ASP cc_start: 0.8235 (m-30) cc_final: 0.7882 (t0) REVERT: D 58 ILE cc_start: 0.9377 (mt) cc_final: 0.9114 (mt) REVERT: D 62 GLN cc_start: 0.9281 (mt0) cc_final: 0.9066 (mt0) REVERT: D 63 LYS cc_start: 0.9264 (mmtt) cc_final: 0.8961 (mmmm) REVERT: D 97 LYS cc_start: 0.9305 (tppt) cc_final: 0.8724 (ttmt) REVERT: D 102 ASP cc_start: 0.8809 (t0) cc_final: 0.8462 (t0) REVERT: E 160 MET cc_start: 0.7827 (ptm) cc_final: 0.6551 (ptm) REVERT: E 257 LYS cc_start: 0.9074 (mtmt) cc_final: 0.8727 (ptpp) REVERT: F 32 LYS cc_start: 0.9215 (tppt) cc_final: 0.9015 (tppt) REVERT: F 36 ASN cc_start: 0.8600 (m-40) cc_final: 0.8241 (t0) REVERT: F 55 ASP cc_start: 0.8618 (m-30) cc_final: 0.8165 (t0) REVERT: F 97 LYS cc_start: 0.9417 (tppt) cc_final: 0.8975 (ttmt) REVERT: F 102 ASP cc_start: 0.8638 (t0) cc_final: 0.8292 (t0) REVERT: F 105 ASN cc_start: 0.8314 (m-40) cc_final: 0.7740 (p0) REVERT: F 117 ASP cc_start: 0.8488 (t70) cc_final: 0.7594 (t0) REVERT: G 66 PHE cc_start: 0.8952 (m-80) cc_final: 0.8361 (m-80) REVERT: G 148 TYR cc_start: 0.7502 (t80) cc_final: 0.7224 (t80) REVERT: G 160 MET cc_start: 0.7956 (ptm) cc_final: 0.6958 (ptm) REVERT: G 209 ILE cc_start: 0.9542 (mt) cc_final: 0.9276 (mm) REVERT: G 257 LYS cc_start: 0.9171 (mtmt) cc_final: 0.8821 (ptpp) REVERT: H 33 ARG cc_start: 0.8560 (mmm160) cc_final: 0.7733 (mmm-85) REVERT: H 36 ASN cc_start: 0.8541 (m-40) cc_final: 0.8233 (t0) REVERT: H 55 ASP cc_start: 0.8477 (m-30) cc_final: 0.8091 (t0) REVERT: H 62 GLN cc_start: 0.9290 (mt0) cc_final: 0.8963 (mt0) REVERT: H 63 LYS cc_start: 0.9233 (mmtt) cc_final: 0.8955 (mmmm) REVERT: H 97 LYS cc_start: 0.9309 (mmmm) cc_final: 0.8802 (mttp) REVERT: H 102 ASP cc_start: 0.8962 (t0) cc_final: 0.8628 (t0) REVERT: H 105 ASN cc_start: 0.7904 (m-40) cc_final: 0.7627 (p0) REVERT: I 19 SER cc_start: 0.9569 (m) cc_final: 0.9356 (p) REVERT: I 160 MET cc_start: 0.7667 (ptm) cc_final: 0.6798 (ptm) REVERT: I 209 ILE cc_start: 0.9451 (mt) cc_final: 0.9247 (mm) REVERT: J 62 GLN cc_start: 0.9208 (mt0) cc_final: 0.8971 (mt0) REVERT: J 63 LYS cc_start: 0.9177 (mttm) cc_final: 0.8668 (ttmt) REVERT: J 70 ASN cc_start: 0.8628 (m110) cc_final: 0.8040 (t0) REVERT: J 97 LYS cc_start: 0.9317 (tppt) cc_final: 0.8954 (mmmm) REVERT: J 102 ASP cc_start: 0.8773 (t0) cc_final: 0.8448 (t0) REVERT: K 67 MET cc_start: 0.8697 (mtp) cc_final: 0.8157 (mtp) REVERT: K 160 MET cc_start: 0.7577 (ptm) cc_final: 0.6626 (ptm) REVERT: K 257 LYS cc_start: 0.9151 (mtmt) cc_final: 0.8814 (mttt) REVERT: K 268 LYS cc_start: 0.8826 (pttp) cc_final: 0.8378 (tptp) REVERT: L 33 ARG cc_start: 0.8442 (mmm160) cc_final: 0.7950 (mmt180) REVERT: L 62 GLN cc_start: 0.9223 (mt0) cc_final: 0.8920 (mt0) REVERT: L 63 LYS cc_start: 0.9349 (mmtt) cc_final: 0.8890 (mmmm) REVERT: L 97 LYS cc_start: 0.9327 (tppt) cc_final: 0.8929 (mttt) REVERT: L 102 ASP cc_start: 0.8846 (t0) cc_final: 0.8480 (t0) REVERT: L 118 LYS cc_start: 0.9208 (mmmm) cc_final: 0.8760 (mppt) REVERT: M 8 MET cc_start: 0.8203 (mtp) cc_final: 0.7857 (mtp) REVERT: M 19 SER cc_start: 0.9503 (m) cc_final: 0.9292 (p) REVERT: M 160 MET cc_start: 0.7740 (ptm) cc_final: 0.6984 (ptm) REVERT: M 212 LEU cc_start: 0.8761 (mt) cc_final: 0.8472 (mt) REVERT: N 33 ARG cc_start: 0.8572 (mmm160) cc_final: 0.7911 (mmt180) REVERT: N 36 ASN cc_start: 0.8571 (m-40) cc_final: 0.8321 (t0) REVERT: N 62 GLN cc_start: 0.9273 (mt0) cc_final: 0.8951 (mt0) REVERT: N 63 LYS cc_start: 0.9339 (mmtt) cc_final: 0.9095 (mttm) REVERT: N 102 ASP cc_start: 0.8786 (t0) cc_final: 0.7782 (t0) REVERT: N 105 ASN cc_start: 0.8060 (m-40) cc_final: 0.7744 (m110) REVERT: O 67 MET cc_start: 0.8314 (mtp) cc_final: 0.7642 (mtp) REVERT: O 160 MET cc_start: 0.7915 (ptm) cc_final: 0.7443 (ptm) REVERT: O 191 MET cc_start: 0.8188 (tpp) cc_final: 0.7264 (tpp) REVERT: O 243 LEU cc_start: 0.9214 (mp) cc_final: 0.8718 (mm) REVERT: O 257 LYS cc_start: 0.9095 (mtmt) cc_final: 0.8802 (mttt) REVERT: P 36 ASN cc_start: 0.8531 (m-40) cc_final: 0.8161 (t0) REVERT: P 63 LYS cc_start: 0.9324 (mtpp) cc_final: 0.9087 (ttmm) REVERT: P 102 ASP cc_start: 0.8882 (t0) cc_final: 0.8262 (t0) REVERT: P 105 ASN cc_start: 0.8334 (m-40) cc_final: 0.7900 (m110) REVERT: Q 160 MET cc_start: 0.7992 (ptm) cc_final: 0.7391 (ptm) REVERT: Q 191 MET cc_start: 0.7842 (tpp) cc_final: 0.7391 (tpp) REVERT: Q 243 LEU cc_start: 0.9278 (mp) cc_final: 0.8774 (mm) REVERT: R 33 ARG cc_start: 0.8585 (mmm160) cc_final: 0.7483 (tpt170) REVERT: R 36 ASN cc_start: 0.8797 (m-40) cc_final: 0.8410 (t0) REVERT: R 55 ASP cc_start: 0.8448 (m-30) cc_final: 0.7987 (t0) REVERT: R 102 ASP cc_start: 0.8790 (t0) cc_final: 0.8370 (t0) REVERT: R 118 LYS cc_start: 0.9263 (mmmm) cc_final: 0.8854 (mppt) REVERT: S 67 MET cc_start: 0.8549 (mtp) cc_final: 0.8172 (mtp) REVERT: S 160 MET cc_start: 0.7735 (ptm) cc_final: 0.6825 (ptm) REVERT: S 257 LYS cc_start: 0.9066 (mtmt) cc_final: 0.8768 (mttt) REVERT: T 33 ARG cc_start: 0.8436 (mmm160) cc_final: 0.8141 (tpt90) REVERT: T 36 ASN cc_start: 0.8697 (m-40) cc_final: 0.8478 (t0) REVERT: T 62 GLN cc_start: 0.9305 (mt0) cc_final: 0.8957 (mt0) REVERT: T 63 LYS cc_start: 0.9274 (mmtt) cc_final: 0.8959 (mttm) REVERT: U 160 MET cc_start: 0.7671 (ptm) cc_final: 0.7216 (ptm) REVERT: U 257 LYS cc_start: 0.9096 (mtmt) cc_final: 0.8768 (ptpp) REVERT: V 36 ASN cc_start: 0.8488 (m-40) cc_final: 0.8167 (t0) REVERT: V 63 LYS cc_start: 0.9309 (mmtt) cc_final: 0.9016 (mmmm) REVERT: V 105 ASN cc_start: 0.8107 (m-40) cc_final: 0.7786 (p0) REVERT: W 160 MET cc_start: 0.7209 (ptp) cc_final: 0.6971 (ptm) REVERT: W 191 MET cc_start: 0.8022 (tpp) cc_final: 0.7738 (tpp) REVERT: X 55 ASP cc_start: 0.8312 (m-30) cc_final: 0.8011 (t0) REVERT: X 58 ILE cc_start: 0.9382 (mt) cc_final: 0.9172 (mt) REVERT: X 62 GLN cc_start: 0.9272 (mt0) cc_final: 0.8979 (mt0) REVERT: X 63 LYS cc_start: 0.9225 (mmtt) cc_final: 0.8919 (mmmm) REVERT: X 70 ASN cc_start: 0.8546 (m110) cc_final: 0.8112 (t0) REVERT: X 97 LYS cc_start: 0.9319 (tppt) cc_final: 0.8991 (mmmm) REVERT: X 102 ASP cc_start: 0.8722 (t0) cc_final: 0.8454 (t0) outliers start: 1 outliers final: 0 residues processed: 623 average time/residue: 0.2243 time to fit residues: 229.1858 Evaluate side-chains 412 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 412 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 298 optimal weight: 0.7980 chunk 349 optimal weight: 5.9990 chunk 419 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 299 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 157 optimal weight: 0.9980 chunk 317 optimal weight: 0.5980 chunk 365 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 GLN G 52 GLN ** I 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 52 GLN V 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.065880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.052253 restraints weight = 165107.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.053482 restraints weight = 119794.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.054322 restraints weight = 96322.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.054792 restraints weight = 82998.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.055231 restraints weight = 75687.789| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.5746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 37476 Z= 0.130 Angle : 0.484 10.333 50628 Z= 0.267 Chirality : 0.036 0.182 5964 Planarity : 0.003 0.037 6444 Dihedral : 3.601 22.034 5172 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.17 % Allowed : 1.30 % Favored : 98.53 % 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: 4.17 (0.11), residues: 4716 helix: 3.07 (0.07), residues: 4368 sheet: None (None), residues: 0 loop : -2.31 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 21 TYR 0.016 0.001 TYR S 210 PHE 0.015 0.002 PHE W 128 TRP 0.022 0.002 TRP V 41 HIS 0.014 0.002 HIS C 123 Details of bonding type rmsd covalent geometry : bond 0.00275 (37476) covalent geometry : angle 0.48392 (50628) hydrogen bonds : bond 0.03633 ( 3588) hydrogen bonds : angle 2.98467 (10764) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 597 time to evaluate : 1.425 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: 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: 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: symmetry clash REVERT: B 160 MET cc_start: 0.7903 (ptm) cc_final: 0.6980 (ptm) REVERT: B 212 LEU cc_start: 0.8946 (mt) cc_final: 0.8561 (mt) REVERT: B 257 LYS cc_start: 0.9049 (mtmt) cc_final: 0.8711 (mttt) REVERT: A 36 ASN cc_start: 0.8521 (m-40) cc_final: 0.8265 (t0) REVERT: A 62 GLN cc_start: 0.9308 (mt0) cc_final: 0.8975 (mt0) REVERT: A 63 LYS cc_start: 0.9263 (mmtt) cc_final: 0.8924 (mttm) REVERT: C 160 MET cc_start: 0.7969 (ptm) cc_final: 0.6855 (ptm) REVERT: C 191 MET cc_start: 0.8224 (tpp) cc_final: 0.7534 (tpp) REVERT: C 209 ILE cc_start: 0.9560 (mt) cc_final: 0.9347 (mm) REVERT: C 243 LEU cc_start: 0.9390 (mp) cc_final: 0.8864 (mm) REVERT: D 3 GLU cc_start: 0.7654 (tt0) cc_final: 0.7416 (tt0) REVERT: D 33 ARG cc_start: 0.8662 (mmm160) cc_final: 0.7837 (mmt180) REVERT: D 36 ASN cc_start: 0.8488 (m-40) cc_final: 0.8125 (t0) REVERT: D 55 ASP cc_start: 0.8371 (m-30) cc_final: 0.7948 (t0) REVERT: D 58 ILE cc_start: 0.9385 (mt) cc_final: 0.9085 (mt) REVERT: D 63 LYS cc_start: 0.9271 (mmtt) cc_final: 0.9061 (mmtp) REVERT: D 97 LYS cc_start: 0.9325 (tppt) cc_final: 0.8950 (mttp) REVERT: D 102 ASP cc_start: 0.8855 (t0) cc_final: 0.8548 (t0) REVERT: E 160 MET cc_start: 0.7895 (ptm) cc_final: 0.6722 (ptm) REVERT: E 216 HIS cc_start: 0.6396 (m90) cc_final: 0.5922 (m170) REVERT: E 257 LYS cc_start: 0.9080 (mtmt) cc_final: 0.8742 (mttt) REVERT: F 36 ASN cc_start: 0.8613 (m-40) cc_final: 0.8219 (t0) REVERT: F 55 ASP cc_start: 0.8578 (m-30) cc_final: 0.8064 (t0) REVERT: F 63 LYS cc_start: 0.9256 (mttm) cc_final: 0.8724 (ttmm) REVERT: F 97 LYS cc_start: 0.9418 (tppt) cc_final: 0.8949 (ttmt) REVERT: F 102 ASP cc_start: 0.8648 (t0) cc_final: 0.7941 (t0) REVERT: F 117 ASP cc_start: 0.8305 (t70) cc_final: 0.7863 (t0) REVERT: F 118 LYS cc_start: 0.8983 (mmpt) cc_final: 0.8782 (mmmm) REVERT: G 63 SER cc_start: 0.8062 (t) cc_final: 0.7781 (t) REVERT: G 148 TYR cc_start: 0.7689 (t80) cc_final: 0.7407 (t80) REVERT: G 160 MET cc_start: 0.7975 (ptm) cc_final: 0.7031 (ptm) REVERT: G 257 LYS cc_start: 0.9196 (mtmt) cc_final: 0.8832 (ptpp) REVERT: H 36 ASN cc_start: 0.8500 (m-40) cc_final: 0.8182 (t0) REVERT: H 55 ASP cc_start: 0.8553 (m-30) cc_final: 0.8116 (t0) REVERT: H 62 GLN cc_start: 0.9236 (mt0) cc_final: 0.8917 (mt0) REVERT: H 63 LYS cc_start: 0.9177 (mmtt) cc_final: 0.8823 (mmmm) REVERT: H 87 ASP cc_start: 0.7061 (t0) cc_final: 0.6664 (t70) REVERT: H 97 LYS cc_start: 0.9304 (mmmm) cc_final: 0.8797 (mttp) REVERT: H 102 ASP cc_start: 0.8963 (t0) cc_final: 0.8589 (t0) REVERT: H 105 ASN cc_start: 0.7947 (m-40) cc_final: 0.7640 (p0) REVERT: I 19 SER cc_start: 0.9606 (m) cc_final: 0.9400 (p) REVERT: I 160 MET cc_start: 0.7738 (ptm) cc_final: 0.6859 (ptm) REVERT: I 209 ILE cc_start: 0.9459 (mt) cc_final: 0.9248 (mm) REVERT: J 55 ASP cc_start: 0.8216 (t0) cc_final: 0.7884 (t0) REVERT: J 62 GLN cc_start: 0.9133 (mt0) cc_final: 0.8882 (mt0) REVERT: J 63 LYS cc_start: 0.9203 (mttm) cc_final: 0.8587 (ttmt) REVERT: J 70 ASN cc_start: 0.8577 (m110) cc_final: 0.8070 (t0) REVERT: J 97 LYS cc_start: 0.9310 (tppt) cc_final: 0.8912 (mmmm) REVERT: J 102 ASP cc_start: 0.8675 (t0) cc_final: 0.8355 (t0) REVERT: K 67 MET cc_start: 0.8661 (mtp) cc_final: 0.8115 (mtp) REVERT: K 160 MET cc_start: 0.7729 (ptm) cc_final: 0.6859 (ptm) REVERT: K 216 HIS cc_start: 0.6397 (m90) cc_final: 0.6077 (m170) REVERT: K 257 LYS cc_start: 0.9165 (mtmt) cc_final: 0.8847 (mttt) REVERT: L 62 GLN cc_start: 0.9214 (mt0) cc_final: 0.8942 (mt0) REVERT: L 63 LYS cc_start: 0.9372 (mmtt) cc_final: 0.8963 (mmmm) REVERT: L 97 LYS cc_start: 0.9325 (tppt) cc_final: 0.8919 (mttt) REVERT: L 102 ASP cc_start: 0.8955 (t0) cc_final: 0.8689 (t0) REVERT: L 118 LYS cc_start: 0.9198 (mmmm) cc_final: 0.8716 (mppt) REVERT: M 8 MET cc_start: 0.8122 (mtp) cc_final: 0.7774 (mtp) REVERT: M 160 MET cc_start: 0.7767 (ptm) cc_final: 0.6839 (ttm) REVERT: M 212 LEU cc_start: 0.8850 (mt) cc_final: 0.8609 (mt) REVERT: N 36 ASN cc_start: 0.8601 (m-40) cc_final: 0.8339 (t0) REVERT: N 62 GLN cc_start: 0.9249 (mt0) cc_final: 0.8847 (mt0) REVERT: N 63 LYS cc_start: 0.9295 (mmtt) cc_final: 0.9092 (mmtp) REVERT: N 102 ASP cc_start: 0.8768 (t0) cc_final: 0.7873 (t0) REVERT: N 105 ASN cc_start: 0.8094 (m-40) cc_final: 0.7776 (m110) REVERT: O 67 MET cc_start: 0.8368 (mtp) cc_final: 0.7802 (mtp) REVERT: O 98 MET cc_start: 0.8240 (mmm) cc_final: 0.7825 (mmp) REVERT: O 160 MET cc_start: 0.7948 (ptm) cc_final: 0.7426 (ptm) REVERT: O 191 MET cc_start: 0.8131 (tpp) cc_final: 0.7337 (tpp) REVERT: O 243 LEU cc_start: 0.9242 (mp) cc_final: 0.8812 (mm) REVERT: O 257 LYS cc_start: 0.9120 (mtmt) cc_final: 0.8836 (mtmm) REVERT: P 36 ASN cc_start: 0.8553 (m-40) cc_final: 0.8147 (t0) REVERT: P 102 ASP cc_start: 0.8882 (t0) cc_final: 0.8242 (t0) REVERT: P 105 ASN cc_start: 0.8340 (m-40) cc_final: 0.7921 (m110) REVERT: Q 52 GLN cc_start: 0.8751 (mt0) cc_final: 0.8458 (mt0) REVERT: Q 160 MET cc_start: 0.8032 (ptm) cc_final: 0.7483 (ptm) REVERT: Q 191 MET cc_start: 0.7832 (tpp) cc_final: 0.7390 (tpp) REVERT: Q 216 HIS cc_start: 0.6178 (m90) cc_final: 0.5797 (m170) REVERT: Q 243 LEU cc_start: 0.9281 (mp) cc_final: 0.8779 (mm) REVERT: R 36 ASN cc_start: 0.8841 (m-40) cc_final: 0.8460 (t0) REVERT: R 55 ASP cc_start: 0.8541 (m-30) cc_final: 0.8022 (t0) REVERT: R 87 ASP cc_start: 0.6794 (t0) cc_final: 0.5265 (t0) REVERT: R 90 GLU cc_start: 0.8922 (mp0) cc_final: 0.8577 (mp0) REVERT: R 102 ASP cc_start: 0.8785 (t0) cc_final: 0.8347 (t0) REVERT: R 118 LYS cc_start: 0.9265 (mmmm) cc_final: 0.8845 (mppt) REVERT: S 67 MET cc_start: 0.8498 (mtp) cc_final: 0.8126 (mtp) REVERT: S 148 TYR cc_start: 0.7947 (t80) cc_final: 0.7678 (t80) REVERT: S 160 MET cc_start: 0.7773 (ptm) cc_final: 0.6816 (ptm) REVERT: S 196 MET cc_start: 0.7861 (tmm) cc_final: 0.7127 (tmm) REVERT: S 257 LYS cc_start: 0.9072 (mtmt) cc_final: 0.8768 (mttt) REVERT: T 36 ASN cc_start: 0.8630 (m-40) cc_final: 0.8424 (t0) REVERT: T 62 GLN cc_start: 0.9254 (mt0) cc_final: 0.8944 (mt0) REVERT: T 102 ASP cc_start: 0.8826 (t70) cc_final: 0.8618 (t0) REVERT: T 117 ASP cc_start: 0.8372 (t70) cc_final: 0.7792 (t0) REVERT: U 160 MET cc_start: 0.7848 (ptm) cc_final: 0.6934 (ptm) REVERT: U 257 LYS cc_start: 0.9137 (mtmt) cc_final: 0.8750 (ptpp) REVERT: V 33 ARG cc_start: 0.8132 (tpp-160) cc_final: 0.7711 (tpt90) REVERT: V 36 ASN cc_start: 0.8523 (m-40) cc_final: 0.8115 (t0) REVERT: V 63 LYS cc_start: 0.9266 (mmtt) cc_final: 0.8912 (mmmm) REVERT: V 118 LYS cc_start: 0.9283 (mmmm) cc_final: 0.8891 (mppt) REVERT: W 191 MET cc_start: 0.8082 (tpp) cc_final: 0.7788 (tpp) REVERT: W 242 MET cc_start: 0.8278 (ttm) cc_final: 0.8034 (ttt) REVERT: X 55 ASP cc_start: 0.8294 (m-30) cc_final: 0.7948 (t0) REVERT: X 58 ILE cc_start: 0.9379 (mt) cc_final: 0.9155 (mt) REVERT: X 62 GLN cc_start: 0.9226 (mt0) cc_final: 0.8962 (mt0) REVERT: X 70 ASN cc_start: 0.8580 (m110) cc_final: 0.8081 (t0) REVERT: X 97 LYS cc_start: 0.9320 (tppt) cc_final: 0.9012 (mmmm) REVERT: X 102 ASP cc_start: 0.8731 (t0) cc_final: 0.8484 (t0) outliers start: 6 outliers final: 1 residues processed: 603 average time/residue: 0.2192 time to fit residues: 217.1235 Evaluate side-chains 418 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 417 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 346 optimal weight: 1.9990 chunk 304 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 449 optimal weight: 2.9990 chunk 380 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 276 optimal weight: 10.0000 chunk 396 optimal weight: 5.9990 chunk 230 optimal weight: 0.9990 chunk 261 optimal weight: 7.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 GLN E 122 ASN G 52 GLN ** I 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 GLN ** M 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 215 ASN S 92 HIS S 277 ASN U 52 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.064494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.050604 restraints weight = 166360.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.051750 restraints weight = 123815.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.052527 restraints weight = 101476.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.053036 restraints weight = 88605.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.053427 restraints weight = 80928.875| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.6087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 37476 Z= 0.175 Angle : 0.535 8.126 50628 Z= 0.294 Chirality : 0.037 0.219 5964 Planarity : 0.003 0.046 6444 Dihedral : 3.644 25.465 5172 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.08 % Allowed : 1.33 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.02 (0.11), residues: 4716 helix: 2.99 (0.07), residues: 4356 sheet: None (None), residues: 0 loop : -2.40 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG R 21 TYR 0.018 0.001 TYR M 210 PHE 0.023 0.002 PHE M 128 TRP 0.022 0.002 TRP A 41 HIS 0.011 0.002 HIS B 123 Details of bonding type rmsd covalent geometry : bond 0.00377 (37476) covalent geometry : angle 0.53489 (50628) hydrogen bonds : bond 0.03771 ( 3588) hydrogen bonds : angle 3.13704 (10764) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 539 time to evaluate : 1.368 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 MET cc_start: 0.7711 (mmm) cc_final: 0.7468 (mmp) REVERT: B 160 MET cc_start: 0.8050 (ptm) cc_final: 0.7077 (ptm) REVERT: B 212 LEU cc_start: 0.8971 (mt) cc_final: 0.8605 (mt) REVERT: A 36 ASN cc_start: 0.8608 (m-40) cc_final: 0.8355 (t0) REVERT: A 62 GLN cc_start: 0.9317 (mt0) cc_final: 0.8988 (mt0) REVERT: C 160 MET cc_start: 0.8111 (ptm) cc_final: 0.6965 (ptm) REVERT: C 191 MET cc_start: 0.8197 (tpp) cc_final: 0.7805 (tpp) REVERT: D 33 ARG cc_start: 0.8671 (mmm160) cc_final: 0.8303 (tpt170) REVERT: D 36 ASN cc_start: 0.8545 (m-40) cc_final: 0.8242 (t0) REVERT: D 55 ASP cc_start: 0.8256 (m-30) cc_final: 0.7925 (t0) REVERT: D 58 ILE cc_start: 0.9414 (mt) cc_final: 0.9149 (mt) REVERT: D 62 GLN cc_start: 0.9292 (mt0) cc_final: 0.9041 (mt0) REVERT: D 63 LYS cc_start: 0.9360 (mmtt) cc_final: 0.9153 (mttm) REVERT: D 97 LYS cc_start: 0.9407 (tppt) cc_final: 0.8948 (ttmt) REVERT: D 102 ASP cc_start: 0.8746 (t0) cc_final: 0.8267 (t0) REVERT: E 160 MET cc_start: 0.8075 (ptm) cc_final: 0.6916 (ptm) REVERT: E 257 LYS cc_start: 0.9123 (mtmt) cc_final: 0.8701 (ptpp) REVERT: F 36 ASN cc_start: 0.8584 (m-40) cc_final: 0.8270 (t0) REVERT: F 55 ASP cc_start: 0.8604 (m-30) cc_final: 0.8058 (t0) REVERT: F 63 LYS cc_start: 0.9287 (mttm) cc_final: 0.8866 (ttmm) REVERT: F 97 LYS cc_start: 0.9408 (tppt) cc_final: 0.8990 (ttmt) REVERT: F 102 ASP cc_start: 0.8706 (t0) cc_final: 0.8213 (t0) REVERT: F 117 ASP cc_start: 0.8810 (t70) cc_final: 0.8017 (t0) REVERT: G 160 MET cc_start: 0.8196 (ptm) cc_final: 0.7295 (ptm) REVERT: G 257 LYS cc_start: 0.9216 (mtmt) cc_final: 0.8813 (ptpp) REVERT: H 55 ASP cc_start: 0.8465 (m-30) cc_final: 0.7939 (t0) REVERT: H 62 GLN cc_start: 0.9251 (mt0) cc_final: 0.9037 (mt0) REVERT: H 63 LYS cc_start: 0.9217 (mmtt) cc_final: 0.8984 (mmmm) REVERT: H 87 ASP cc_start: 0.7055 (t0) cc_final: 0.5615 (t70) REVERT: H 90 GLU cc_start: 0.8904 (mp0) cc_final: 0.8547 (mp0) REVERT: H 97 LYS cc_start: 0.9329 (mmmm) cc_final: 0.8890 (mttp) REVERT: H 102 ASP cc_start: 0.8879 (t0) cc_final: 0.8487 (t0) REVERT: H 105 ASN cc_start: 0.8009 (m-40) cc_final: 0.7732 (p0) REVERT: I 98 MET cc_start: 0.8169 (mmm) cc_final: 0.7909 (mmp) REVERT: I 160 MET cc_start: 0.8007 (ptm) cc_final: 0.7090 (ptm) REVERT: J 62 GLN cc_start: 0.9163 (mt0) cc_final: 0.8891 (mt0) REVERT: J 63 LYS cc_start: 0.9282 (mttm) cc_final: 0.9071 (ttmm) REVERT: J 70 ASN cc_start: 0.8784 (m110) cc_final: 0.8265 (t0) REVERT: J 97 LYS cc_start: 0.9321 (tppt) cc_final: 0.8883 (mtmt) REVERT: J 102 ASP cc_start: 0.8730 (t0) cc_final: 0.8458 (t0) REVERT: K 67 MET cc_start: 0.8644 (mtp) cc_final: 0.8162 (mtp) REVERT: K 160 MET cc_start: 0.7954 (ptm) cc_final: 0.7121 (ptm) REVERT: K 216 HIS cc_start: 0.6652 (m90) cc_final: 0.6215 (m170) REVERT: K 257 LYS cc_start: 0.9210 (mtmt) cc_final: 0.8878 (ptpp) REVERT: L 62 GLN cc_start: 0.9250 (mt0) cc_final: 0.8981 (mt0) REVERT: L 63 LYS cc_start: 0.9425 (mmtt) cc_final: 0.9156 (mmmm) REVERT: L 87 ASP cc_start: 0.7442 (t0) cc_final: 0.7229 (t0) REVERT: L 97 LYS cc_start: 0.9304 (tppt) cc_final: 0.8896 (mttt) REVERT: L 102 ASP cc_start: 0.8992 (t0) cc_final: 0.8730 (t0) REVERT: M 8 MET cc_start: 0.8229 (mtp) cc_final: 0.7831 (mtp) REVERT: M 160 MET cc_start: 0.7909 (ptm) cc_final: 0.7203 (ttp) REVERT: N 62 GLN cc_start: 0.9217 (mt0) cc_final: 0.8913 (mt0) REVERT: N 63 LYS cc_start: 0.9351 (mmtt) cc_final: 0.9079 (mmmm) REVERT: N 102 ASP cc_start: 0.8839 (t0) cc_final: 0.7925 (t0) REVERT: N 105 ASN cc_start: 0.8119 (m-40) cc_final: 0.7828 (m110) REVERT: O 67 MET cc_start: 0.8096 (mtp) cc_final: 0.7749 (mtp) REVERT: O 98 MET cc_start: 0.8345 (mmm) cc_final: 0.8086 (mmp) REVERT: O 191 MET cc_start: 0.8366 (tpp) cc_final: 0.8106 (tpp) REVERT: O 216 HIS cc_start: 0.5889 (m90) cc_final: 0.5568 (m90) REVERT: O 257 LYS cc_start: 0.9169 (mtmt) cc_final: 0.8874 (mtmm) REVERT: P 36 ASN cc_start: 0.8528 (m-40) cc_final: 0.8197 (t0) REVERT: P 70 ASN cc_start: 0.8724 (m-40) cc_final: 0.8101 (t0) REVERT: P 102 ASP cc_start: 0.8915 (t0) cc_final: 0.8230 (t0) REVERT: P 105 ASN cc_start: 0.8316 (m-40) cc_final: 0.7970 (m110) REVERT: Q 160 MET cc_start: 0.8174 (ptm) cc_final: 0.7418 (ptm) REVERT: Q 271 ILE cc_start: 0.8865 (pt) cc_final: 0.8636 (tt) REVERT: R 36 ASN cc_start: 0.8786 (m-40) cc_final: 0.8380 (t0) REVERT: R 55 ASP cc_start: 0.8607 (m-30) cc_final: 0.8068 (t0) REVERT: R 87 ASP cc_start: 0.7242 (t0) cc_final: 0.5713 (t0) REVERT: R 90 GLU cc_start: 0.9030 (mp0) cc_final: 0.8671 (mp0) REVERT: R 102 ASP cc_start: 0.8831 (t0) cc_final: 0.8422 (t0) REVERT: S 67 MET cc_start: 0.8516 (mtp) cc_final: 0.8162 (mtp) REVERT: S 160 MET cc_start: 0.7861 (ptm) cc_final: 0.7103 (ptm) REVERT: S 196 MET cc_start: 0.8037 (tmm) cc_final: 0.7603 (tmm) REVERT: S 257 LYS cc_start: 0.9111 (mtmt) cc_final: 0.8785 (mttt) REVERT: T 36 ASN cc_start: 0.8630 (m-40) cc_final: 0.8331 (t0) REVERT: T 62 GLN cc_start: 0.9306 (mt0) cc_final: 0.9077 (mt0) REVERT: T 87 ASP cc_start: 0.7462 (t0) cc_final: 0.6597 (t0) REVERT: T 102 ASP cc_start: 0.8835 (t70) cc_final: 0.8619 (t0) REVERT: T 116 MET cc_start: 0.8636 (tpp) cc_final: 0.8397 (tpp) REVERT: T 117 ASP cc_start: 0.8311 (t70) cc_final: 0.7866 (t0) REVERT: T 118 LYS cc_start: 0.8961 (mmmm) cc_final: 0.8711 (mmmt) REVERT: U 160 MET cc_start: 0.8012 (ptm) cc_final: 0.7090 (ptm) REVERT: U 257 LYS cc_start: 0.9123 (mtmt) cc_final: 0.8771 (ptpp) REVERT: V 33 ARG cc_start: 0.8162 (tpp-160) cc_final: 0.7918 (tpt90) REVERT: V 36 ASN cc_start: 0.8524 (m-40) cc_final: 0.8118 (t0) REVERT: W 160 MET cc_start: 0.7789 (ptm) cc_final: 0.7280 (mtp) REVERT: X 55 ASP cc_start: 0.8353 (m-30) cc_final: 0.7929 (t0) REVERT: X 58 ILE cc_start: 0.9487 (mt) cc_final: 0.9239 (mt) REVERT: X 62 GLN cc_start: 0.9262 (mt0) cc_final: 0.9035 (mt0) REVERT: X 70 ASN cc_start: 0.8727 (m110) cc_final: 0.8267 (t0) REVERT: X 97 LYS cc_start: 0.9330 (tppt) cc_final: 0.9020 (mmmm) REVERT: X 102 ASP cc_start: 0.8817 (t0) cc_final: 0.8590 (t0) outliers start: 3 outliers final: 2 residues processed: 542 average time/residue: 0.2224 time to fit residues: 196.9718 Evaluate side-chains 363 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 361 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 389 optimal weight: 0.9980 chunk 393 optimal weight: 0.0980 chunk 347 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 212 optimal weight: 0.5980 chunk 95 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 chunk 256 optimal weight: 0.9990 chunk 125 optimal weight: 0.5980 chunk 309 optimal weight: 3.9990 chunk 6 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: ** B 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN C 185 HIS G 92 HIS I 92 HIS I 122 ASN K 123 HIS S 185 HIS U 92 HIS V 62 GLN W 92 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.065944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.052281 restraints weight = 165588.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.053467 restraints weight = 121480.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.054271 restraints weight = 98457.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.054828 restraints weight = 85343.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.055184 restraints weight = 77284.772| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.6344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 37476 Z= 0.121 Angle : 0.497 16.770 50628 Z= 0.273 Chirality : 0.036 0.177 5964 Planarity : 0.003 0.040 6444 Dihedral : 3.626 26.586 5172 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.11 % Allowed : 1.44 % Favored : 98.45 % 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: 4.22 (0.11), residues: 4716 helix: 3.16 (0.07), residues: 4332 sheet: None (None), residues: 0 loop : -2.44 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 211 TYR 0.021 0.001 TYR U 210 PHE 0.017 0.002 PHE I 128 TRP 0.023 0.002 TRP R 41 HIS 0.015 0.002 HIS C 123 Details of bonding type rmsd covalent geometry : bond 0.00250 (37476) covalent geometry : angle 0.49724 (50628) hydrogen bonds : bond 0.03533 ( 3588) hydrogen bonds : angle 2.97299 (10764) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 580 time to evaluate : 1.372 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 160 MET cc_start: 0.7991 (ptm) cc_final: 0.6828 (ptm) REVERT: B 252 TYR cc_start: 0.8678 (m-80) cc_final: 0.8447 (m-80) REVERT: A 62 GLN cc_start: 0.9237 (mt0) cc_final: 0.8882 (mt0) REVERT: A 63 LYS cc_start: 0.9158 (mmtp) cc_final: 0.8840 (mttm) REVERT: C 147 ILE cc_start: 0.9492 (mt) cc_final: 0.9092 (tp) REVERT: C 160 MET cc_start: 0.8153 (ptm) cc_final: 0.7147 (ptm) REVERT: C 191 MET cc_start: 0.8266 (tpp) cc_final: 0.7923 (tpp) REVERT: C 216 HIS cc_start: 0.6637 (m90) cc_final: 0.6203 (m90) REVERT: D 6 LEU cc_start: 0.9225 (mt) cc_final: 0.8989 (tt) REVERT: D 36 ASN cc_start: 0.8537 (m-40) cc_final: 0.8188 (t0) REVERT: D 55 ASP cc_start: 0.8343 (m-30) cc_final: 0.8072 (t0) REVERT: D 58 ILE cc_start: 0.9384 (mt) cc_final: 0.9110 (mt) REVERT: D 63 LYS cc_start: 0.9358 (mmtt) cc_final: 0.9011 (mttm) REVERT: D 97 LYS cc_start: 0.9447 (tppt) cc_final: 0.8990 (ttmt) REVERT: D 102 ASP cc_start: 0.8843 (t0) cc_final: 0.8510 (t0) REVERT: D 118 LYS cc_start: 0.9242 (mmmm) cc_final: 0.8870 (mppt) REVERT: E 30 LYS cc_start: 0.7918 (mtmt) cc_final: 0.7179 (mmtt) REVERT: E 147 ILE cc_start: 0.9477 (mt) cc_final: 0.9230 (tp) REVERT: E 160 MET cc_start: 0.8031 (ptm) cc_final: 0.7540 (ptm) REVERT: E 200 ILE cc_start: 0.9102 (mm) cc_final: 0.8861 (mm) REVERT: F 36 ASN cc_start: 0.8608 (m-40) cc_final: 0.8280 (t0) REVERT: F 55 ASP cc_start: 0.8546 (m-30) cc_final: 0.7988 (t0) REVERT: F 63 LYS cc_start: 0.9252 (mttm) cc_final: 0.8665 (ttmm) REVERT: F 97 LYS cc_start: 0.9418 (tppt) cc_final: 0.8953 (ttmt) REVERT: F 102 ASP cc_start: 0.8670 (t0) cc_final: 0.8154 (t0) REVERT: F 117 ASP cc_start: 0.8599 (t70) cc_final: 0.7780 (t0) REVERT: G 147 ILE cc_start: 0.9462 (mt) cc_final: 0.9168 (tp) REVERT: G 160 MET cc_start: 0.8205 (ptm) cc_final: 0.7317 (ptm) REVERT: H 55 ASP cc_start: 0.8543 (m-30) cc_final: 0.8005 (t0) REVERT: H 63 LYS cc_start: 0.9164 (mmtt) cc_final: 0.8840 (mmmm) REVERT: H 87 ASP cc_start: 0.6948 (t0) cc_final: 0.5508 (t70) REVERT: H 90 GLU cc_start: 0.8885 (mp0) cc_final: 0.8464 (mp0) REVERT: H 97 LYS cc_start: 0.9317 (mmmm) cc_final: 0.8865 (mttp) REVERT: H 102 ASP cc_start: 0.8945 (t0) cc_final: 0.8640 (t0) REVERT: H 105 ASN cc_start: 0.7988 (m-40) cc_final: 0.7517 (p0) REVERT: I 147 ILE cc_start: 0.9509 (mt) cc_final: 0.9244 (tp) REVERT: I 160 MET cc_start: 0.8095 (ptm) cc_final: 0.7252 (ptm) REVERT: I 216 HIS cc_start: 0.6300 (m90) cc_final: 0.6094 (m170) REVERT: J 33 ARG cc_start: 0.8490 (mmm160) cc_final: 0.7935 (tpt90) REVERT: J 70 ASN cc_start: 0.8773 (m110) cc_final: 0.8294 (t0) REVERT: J 97 LYS cc_start: 0.9315 (tppt) cc_final: 0.8833 (mtmt) REVERT: J 102 ASP cc_start: 0.8731 (t0) cc_final: 0.8425 (t0) REVERT: K 67 MET cc_start: 0.8664 (mtp) cc_final: 0.8207 (mtp) REVERT: K 160 MET cc_start: 0.7980 (ptm) cc_final: 0.7124 (ptm) REVERT: K 216 HIS cc_start: 0.6464 (m90) cc_final: 0.6058 (m170) REVERT: K 257 LYS cc_start: 0.9166 (mtmt) cc_final: 0.8813 (mttt) REVERT: L 55 ASP cc_start: 0.8054 (t0) cc_final: 0.7664 (t0) REVERT: L 62 GLN cc_start: 0.9128 (mt0) cc_final: 0.8873 (mt0) REVERT: L 63 LYS cc_start: 0.9368 (mmtt) cc_final: 0.9093 (mmmm) REVERT: L 70 ASN cc_start: 0.8825 (m-40) cc_final: 0.8385 (t0) REVERT: L 97 LYS cc_start: 0.9312 (tppt) cc_final: 0.8896 (mttt) REVERT: L 102 ASP cc_start: 0.8961 (t0) cc_final: 0.8677 (t0) REVERT: M 8 MET cc_start: 0.7998 (mtp) cc_final: 0.7746 (mtp) REVERT: M 147 ILE cc_start: 0.9452 (mt) cc_final: 0.9191 (tp) REVERT: M 160 MET cc_start: 0.7821 (ptm) cc_final: 0.7206 (ttp) REVERT: N 63 LYS cc_start: 0.9282 (mmtt) cc_final: 0.8983 (mmmm) REVERT: N 102 ASP cc_start: 0.8834 (t0) cc_final: 0.8365 (t0) REVERT: N 105 ASN cc_start: 0.8023 (m-40) cc_final: 0.7326 (p0) REVERT: O 67 MET cc_start: 0.8160 (mtp) cc_final: 0.7758 (mtp) REVERT: O 98 MET cc_start: 0.8289 (mmm) cc_final: 0.8003 (mmp) REVERT: O 191 MET cc_start: 0.8252 (tpp) cc_final: 0.7615 (tpp) REVERT: O 216 HIS cc_start: 0.5417 (m90) cc_final: 0.5037 (m90) REVERT: O 243 LEU cc_start: 0.9325 (mp) cc_final: 0.8960 (mm) REVERT: O 257 LYS cc_start: 0.9126 (mtmt) cc_final: 0.8802 (mtmm) REVERT: P 70 ASN cc_start: 0.8683 (m-40) cc_final: 0.8178 (t0) REVERT: P 102 ASP cc_start: 0.8906 (t0) cc_final: 0.8609 (t0) REVERT: Q 147 ILE cc_start: 0.9453 (mt) cc_final: 0.9164 (tp) REVERT: Q 160 MET cc_start: 0.8129 (ptm) cc_final: 0.7553 (ptm) REVERT: Q 191 MET cc_start: 0.8033 (tpp) cc_final: 0.7683 (tpp) REVERT: Q 216 HIS cc_start: 0.6144 (m90) cc_final: 0.5932 (m90) REVERT: R 36 ASN cc_start: 0.8763 (m-40) cc_final: 0.8311 (t0) REVERT: R 55 ASP cc_start: 0.8597 (m-30) cc_final: 0.8045 (t0) REVERT: R 87 ASP cc_start: 0.7037 (t0) cc_final: 0.5180 (t0) REVERT: R 90 GLU cc_start: 0.8939 (mp0) cc_final: 0.8488 (mp0) REVERT: R 102 ASP cc_start: 0.8847 (t0) cc_final: 0.8394 (t0) REVERT: S 67 MET cc_start: 0.8526 (mtp) cc_final: 0.7996 (mtp) REVERT: S 160 MET cc_start: 0.7960 (ptm) cc_final: 0.7071 (ptm) REVERT: S 196 MET cc_start: 0.8116 (tmm) cc_final: 0.7735 (tmm) REVERT: T 36 ASN cc_start: 0.8630 (m-40) cc_final: 0.8215 (t0) REVERT: T 62 GLN cc_start: 0.9246 (mt0) cc_final: 0.8931 (mt0) REVERT: T 102 ASP cc_start: 0.8813 (t70) cc_final: 0.8580 (t0) REVERT: T 116 MET cc_start: 0.8596 (tpp) cc_final: 0.8367 (tpp) REVERT: T 117 ASP cc_start: 0.8310 (t70) cc_final: 0.7826 (t0) REVERT: U 147 ILE cc_start: 0.9461 (mt) cc_final: 0.9184 (tp) REVERT: U 160 MET cc_start: 0.7930 (ptm) cc_final: 0.7043 (ptm) REVERT: V 33 ARG cc_start: 0.8136 (tpp-160) cc_final: 0.7921 (tpt90) REVERT: V 63 LYS cc_start: 0.9224 (mmmm) cc_final: 0.8989 (ttmt) REVERT: V 118 LYS cc_start: 0.9373 (mmmm) cc_final: 0.9022 (mppt) REVERT: W 67 MET cc_start: 0.7881 (mtp) cc_final: 0.7632 (tpt) REVERT: X 55 ASP cc_start: 0.8273 (m-30) cc_final: 0.7839 (t0) REVERT: X 58 ILE cc_start: 0.9432 (mt) cc_final: 0.9136 (mt) REVERT: X 62 GLN cc_start: 0.9130 (mt0) cc_final: 0.8884 (mt0) REVERT: X 70 ASN cc_start: 0.8678 (m110) cc_final: 0.8273 (t0) REVERT: X 102 ASP cc_start: 0.8715 (t0) cc_final: 0.8465 (t0) outliers start: 4 outliers final: 0 residues processed: 584 average time/residue: 0.2231 time to fit residues: 213.6790 Evaluate side-chains 406 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 406 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 384 optimal weight: 2.9990 chunk 390 optimal weight: 0.9990 chunk 213 optimal weight: 5.9990 chunk 227 optimal weight: 3.9990 chunk 157 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 399 optimal weight: 0.0570 chunk 263 optimal weight: 0.5980 chunk 129 optimal weight: 3.9990 chunk 279 optimal weight: 2.9990 overall best weight: 1.1304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 277 ASN C 52 GLN G 52 GLN ** G 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 92 HIS ** Q 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 52 GLN U 92 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.065232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.051360 restraints weight = 165923.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.052481 restraints weight = 124377.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.053247 restraints weight = 102346.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.053777 restraints weight = 89557.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.054051 restraints weight = 81628.770| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.6530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 37476 Z= 0.147 Angle : 0.517 9.044 50628 Z= 0.286 Chirality : 0.037 0.184 5964 Planarity : 0.004 0.059 6444 Dihedral : 3.630 24.922 5172 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % 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: 4.09 (0.11), residues: 4716 helix: 3.07 (0.07), residues: 4356 sheet: None (None), residues: 0 loop : -2.79 (0.29), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 21 TYR 0.018 0.001 TYR X 42 PHE 0.017 0.002 PHE K 128 TRP 0.021 0.002 TRP R 41 HIS 0.011 0.002 HIS M 123 Details of bonding type rmsd covalent geometry : bond 0.00316 (37476) covalent geometry : angle 0.51741 (50628) hydrogen bonds : bond 0.03659 ( 3588) hydrogen bonds : angle 3.07476 (10764) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 543 time to evaluate : 1.435 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: 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: 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: B 98 MET cc_start: 0.7764 (mmm) cc_final: 0.7544 (mmp) REVERT: B 160 MET cc_start: 0.7873 (ptm) cc_final: 0.6900 (ptm) REVERT: B 252 TYR cc_start: 0.8791 (m-80) cc_final: 0.8541 (m-80) REVERT: A 62 GLN cc_start: 0.9264 (mt0) cc_final: 0.8897 (mt0) REVERT: A 63 LYS cc_start: 0.9277 (mmtp) cc_final: 0.8991 (mttm) REVERT: A 70 ASN cc_start: 0.8832 (m-40) cc_final: 0.8501 (t0) REVERT: C 147 ILE cc_start: 0.9485 (mt) cc_final: 0.9131 (tp) REVERT: C 160 MET cc_start: 0.8166 (ptm) cc_final: 0.7176 (ptm) REVERT: C 191 MET cc_start: 0.8181 (tpp) cc_final: 0.7833 (tpp) REVERT: C 216 HIS cc_start: 0.6384 (m90) cc_final: 0.5893 (m170) REVERT: D 36 ASN cc_start: 0.8551 (m-40) cc_final: 0.8190 (t0) REVERT: D 55 ASP cc_start: 0.8342 (m-30) cc_final: 0.7998 (t0) REVERT: D 58 ILE cc_start: 0.9410 (mt) cc_final: 0.9095 (mt) REVERT: D 62 GLN cc_start: 0.9225 (mt0) cc_final: 0.8980 (mt0) REVERT: D 63 LYS cc_start: 0.9383 (mmtt) cc_final: 0.9154 (mttm) REVERT: D 97 LYS cc_start: 0.9448 (tppt) cc_final: 0.9009 (ttmt) REVERT: D 102 ASP cc_start: 0.8829 (t0) cc_final: 0.8504 (t0) REVERT: E 30 LYS cc_start: 0.7892 (mtmt) cc_final: 0.7174 (mmtt) REVERT: E 147 ILE cc_start: 0.9474 (mt) cc_final: 0.9240 (tp) REVERT: E 160 MET cc_start: 0.8104 (ptm) cc_final: 0.7496 (ptm) REVERT: F 36 ASN cc_start: 0.8544 (m-40) cc_final: 0.8321 (t0) REVERT: F 55 ASP cc_start: 0.8537 (m-30) cc_final: 0.7930 (t0) REVERT: F 63 LYS cc_start: 0.9283 (mttm) cc_final: 0.8838 (ttmm) REVERT: F 70 ASN cc_start: 0.8784 (m-40) cc_final: 0.8399 (t0) REVERT: F 97 LYS cc_start: 0.9393 (tppt) cc_final: 0.8939 (ttmt) REVERT: F 102 ASP cc_start: 0.8739 (t0) cc_final: 0.8205 (t0) REVERT: F 117 ASP cc_start: 0.8546 (t70) cc_final: 0.8140 (t0) REVERT: G 147 ILE cc_start: 0.9440 (mt) cc_final: 0.9206 (tp) REVERT: G 160 MET cc_start: 0.8242 (ptm) cc_final: 0.7338 (ptm) REVERT: H 55 ASP cc_start: 0.8493 (m-30) cc_final: 0.7875 (t0) REVERT: H 87 ASP cc_start: 0.7197 (t0) cc_final: 0.6866 (t0) REVERT: H 97 LYS cc_start: 0.9319 (mmmm) cc_final: 0.8862 (mttp) REVERT: H 102 ASP cc_start: 0.8872 (t0) cc_final: 0.8538 (t0) REVERT: H 105 ASN cc_start: 0.8035 (m-40) cc_final: 0.7566 (p0) REVERT: I 147 ILE cc_start: 0.9479 (mt) cc_final: 0.9231 (tp) REVERT: I 160 MET cc_start: 0.8259 (ptm) cc_final: 0.7351 (ptm) REVERT: J 33 ARG cc_start: 0.8420 (mmm160) cc_final: 0.7882 (tpt90) REVERT: J 70 ASN cc_start: 0.8745 (m110) cc_final: 0.8350 (t0) REVERT: J 97 LYS cc_start: 0.9330 (tppt) cc_final: 0.8856 (ttmt) REVERT: J 102 ASP cc_start: 0.8747 (t0) cc_final: 0.8473 (t0) REVERT: J 116 MET cc_start: 0.8798 (tpp) cc_final: 0.8560 (tpp) REVERT: K 67 MET cc_start: 0.8617 (mtp) cc_final: 0.8185 (mtp) REVERT: K 147 ILE cc_start: 0.9496 (mt) cc_final: 0.9281 (tp) REVERT: K 160 MET cc_start: 0.8045 (ptm) cc_final: 0.7154 (ptm) REVERT: K 216 HIS cc_start: 0.6489 (m90) cc_final: 0.5965 (m170) REVERT: L 62 GLN cc_start: 0.9224 (mt0) cc_final: 0.8911 (mt0) REVERT: L 63 LYS cc_start: 0.9394 (mmtt) cc_final: 0.9175 (mmmm) REVERT: L 70 ASN cc_start: 0.8881 (m-40) cc_final: 0.8425 (t0) REVERT: L 97 LYS cc_start: 0.9324 (tppt) cc_final: 0.8909 (mttt) REVERT: L 102 ASP cc_start: 0.9010 (t0) cc_final: 0.8704 (t0) REVERT: M 8 MET cc_start: 0.7935 (mtp) cc_final: 0.7673 (mtp) REVERT: M 147 ILE cc_start: 0.9459 (mt) cc_final: 0.9243 (tp) REVERT: M 160 MET cc_start: 0.7899 (ptm) cc_final: 0.7473 (ttp) REVERT: N 22 ILE cc_start: 0.9440 (mp) cc_final: 0.9096 (mt) REVERT: N 63 LYS cc_start: 0.9416 (mmtt) cc_final: 0.9089 (mmmm) REVERT: N 102 ASP cc_start: 0.8793 (t0) cc_final: 0.7860 (t0) REVERT: N 105 ASN cc_start: 0.8019 (m-40) cc_final: 0.7628 (m110) REVERT: O 67 MET cc_start: 0.8116 (mtp) cc_final: 0.7742 (mtp) REVERT: O 98 MET cc_start: 0.8354 (mmm) cc_final: 0.7865 (mmp) REVERT: O 160 MET cc_start: 0.8098 (ptm) cc_final: 0.7705 (ptm) REVERT: O 191 MET cc_start: 0.8308 (tpp) cc_final: 0.8061 (tpp) REVERT: O 216 HIS cc_start: 0.6165 (m90) cc_final: 0.5603 (m-70) REVERT: P 70 ASN cc_start: 0.8801 (m-40) cc_final: 0.8316 (t0) REVERT: P 102 ASP cc_start: 0.8970 (t0) cc_final: 0.8526 (t0) REVERT: Q 147 ILE cc_start: 0.9484 (mt) cc_final: 0.9183 (tp) REVERT: Q 160 MET cc_start: 0.8163 (ptm) cc_final: 0.7569 (ptm) REVERT: Q 216 HIS cc_start: 0.6280 (m90) cc_final: 0.5951 (m90) REVERT: R 36 ASN cc_start: 0.8784 (m-40) cc_final: 0.8255 (t0) REVERT: R 55 ASP cc_start: 0.8615 (m-30) cc_final: 0.8043 (t0) REVERT: R 87 ASP cc_start: 0.7183 (t0) cc_final: 0.6112 (t0) REVERT: R 90 GLU cc_start: 0.9015 (mp0) cc_final: 0.8713 (mp0) REVERT: R 102 ASP cc_start: 0.8894 (t0) cc_final: 0.8464 (t0) REVERT: S 63 SER cc_start: 0.8303 (t) cc_final: 0.8035 (t) REVERT: S 160 MET cc_start: 0.8012 (ptm) cc_final: 0.7152 (ptm) REVERT: S 196 MET cc_start: 0.8118 (tmm) cc_final: 0.7710 (tmm) REVERT: T 36 ASN cc_start: 0.8520 (m-40) cc_final: 0.8239 (t0) REVERT: T 62 GLN cc_start: 0.9291 (mt0) cc_final: 0.8980 (mt0) REVERT: T 102 ASP cc_start: 0.8743 (t70) cc_final: 0.8522 (t0) REVERT: T 116 MET cc_start: 0.8515 (tpp) cc_final: 0.8279 (tpp) REVERT: T 117 ASP cc_start: 0.8318 (t70) cc_final: 0.7705 (t0) REVERT: T 118 LYS cc_start: 0.8781 (mmmt) cc_final: 0.8108 (mppt) REVERT: U 63 SER cc_start: 0.8697 (t) cc_final: 0.8191 (t) REVERT: U 147 ILE cc_start: 0.9479 (mt) cc_final: 0.9209 (tp) REVERT: U 160 MET cc_start: 0.8042 (ptm) cc_final: 0.7142 (ptm) REVERT: V 118 LYS cc_start: 0.9398 (mmmm) cc_final: 0.9010 (mppt) REVERT: W 63 SER cc_start: 0.8358 (t) cc_final: 0.7955 (t) REVERT: W 147 ILE cc_start: 0.9475 (mt) cc_final: 0.9158 (tp) REVERT: W 191 MET cc_start: 0.8210 (tpp) cc_final: 0.7957 (tpp) REVERT: X 55 ASP cc_start: 0.8297 (m-30) cc_final: 0.7783 (t0) REVERT: X 58 ILE cc_start: 0.9485 (mt) cc_final: 0.9152 (mt) REVERT: X 70 ASN cc_start: 0.8826 (m110) cc_final: 0.8376 (t0) REVERT: X 97 LYS cc_start: 0.9466 (mmmt) cc_final: 0.8631 (ttmt) REVERT: X 102 ASP cc_start: 0.8720 (t0) cc_final: 0.8507 (t0) outliers start: 0 outliers final: 0 residues processed: 543 average time/residue: 0.2249 time to fit residues: 201.6115 Evaluate side-chains 379 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 379 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 25 optimal weight: 1.9990 chunk 234 optimal weight: 1.9990 chunk 167 optimal weight: 0.3980 chunk 186 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 370 optimal weight: 0.9990 chunk 21 optimal weight: 0.2980 chunk 112 optimal weight: 4.9990 chunk 231 optimal weight: 0.8980 chunk 220 optimal weight: 3.9990 chunk 420 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 GLN ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 GLN ** G 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 GLN O 92 HIS O 215 ASN W 92 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.065707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.051891 restraints weight = 166959.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.053090 restraints weight = 121771.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.053902 restraints weight = 98344.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.054456 restraints weight = 85231.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.054833 restraints weight = 77205.573| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.6678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 37476 Z= 0.129 Angle : 0.522 11.113 50628 Z= 0.285 Chirality : 0.036 0.163 5964 Planarity : 0.003 0.061 6444 Dihedral : 3.649 24.399 5172 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.57 % Favored : 98.41 % Rotamer: Outliers : 0.03 % Allowed : 0.36 % Favored : 99.61 % 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: 4.10 (0.11), residues: 4716 helix: 3.11 (0.07), residues: 4332 sheet: None (None), residues: 0 loop : -2.79 (0.29), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG L 21 TYR 0.020 0.001 TYR U 210 PHE 0.024 0.002 PHE I 128 TRP 0.017 0.002 TRP A 41 HIS 0.010 0.002 HIS W 92 Details of bonding type rmsd covalent geometry : bond 0.00274 (37476) covalent geometry : angle 0.52241 (50628) hydrogen bonds : bond 0.03560 ( 3588) hydrogen bonds : angle 3.04792 (10764) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 538 time to evaluate : 1.569 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 160 MET cc_start: 0.7884 (ptm) cc_final: 0.7175 (ptm) REVERT: B 252 TYR cc_start: 0.8815 (m-80) cc_final: 0.8550 (m-80) REVERT: A 62 GLN cc_start: 0.9249 (mt0) cc_final: 0.8900 (mt0) REVERT: A 63 LYS cc_start: 0.9242 (mmtp) cc_final: 0.8747 (mtmm) REVERT: A 70 ASN cc_start: 0.8847 (m-40) cc_final: 0.8533 (t0) REVERT: A 118 LYS cc_start: 0.9080 (mmmm) cc_final: 0.8530 (mppt) REVERT: C 8 MET cc_start: 0.8106 (mtt) cc_final: 0.7759 (mtp) REVERT: C 147 ILE cc_start: 0.9459 (mt) cc_final: 0.9217 (tp) REVERT: C 160 MET cc_start: 0.8185 (ptm) cc_final: 0.7645 (ptm) REVERT: C 191 MET cc_start: 0.8228 (tpp) cc_final: 0.7866 (tpp) REVERT: D 36 ASN cc_start: 0.8600 (m-40) cc_final: 0.8275 (t0) REVERT: D 55 ASP cc_start: 0.8276 (m-30) cc_final: 0.7962 (t0) REVERT: D 58 ILE cc_start: 0.9404 (mt) cc_final: 0.9088 (mt) REVERT: D 63 LYS cc_start: 0.9356 (mmtt) cc_final: 0.9126 (mmtp) REVERT: D 97 LYS cc_start: 0.9449 (tppt) cc_final: 0.8999 (ttmt) REVERT: D 102 ASP cc_start: 0.8853 (t0) cc_final: 0.8498 (t0) REVERT: E 30 LYS cc_start: 0.7794 (mtmt) cc_final: 0.7114 (mmtt) REVERT: E 147 ILE cc_start: 0.9471 (mt) cc_final: 0.9234 (tp) REVERT: E 160 MET cc_start: 0.8032 (ptm) cc_final: 0.7536 (ptm) REVERT: E 200 ILE cc_start: 0.9153 (mm) cc_final: 0.8894 (mm) REVERT: F 36 ASN cc_start: 0.8527 (m-40) cc_final: 0.8244 (t0) REVERT: F 55 ASP cc_start: 0.8405 (m-30) cc_final: 0.7873 (t0) REVERT: F 63 LYS cc_start: 0.9300 (mttm) cc_final: 0.8732 (ttmm) REVERT: F 70 ASN cc_start: 0.8762 (m-40) cc_final: 0.8403 (t0) REVERT: F 97 LYS cc_start: 0.9375 (tppt) cc_final: 0.8922 (ttmt) REVERT: F 102 ASP cc_start: 0.8760 (t0) cc_final: 0.8184 (t0) REVERT: F 117 ASP cc_start: 0.8674 (t70) cc_final: 0.7928 (t0) REVERT: G 147 ILE cc_start: 0.9431 (mt) cc_final: 0.9207 (tp) REVERT: H 55 ASP cc_start: 0.8458 (m-30) cc_final: 0.7899 (t0) REVERT: H 63 LYS cc_start: 0.9174 (mmmm) cc_final: 0.8860 (mmmm) REVERT: H 70 ASN cc_start: 0.8600 (m-40) cc_final: 0.8244 (t0) REVERT: H 97 LYS cc_start: 0.9307 (mmmm) cc_final: 0.8853 (mttp) REVERT: H 102 ASP cc_start: 0.8893 (t0) cc_final: 0.8231 (t0) REVERT: I 147 ILE cc_start: 0.9463 (mt) cc_final: 0.9206 (tp) REVERT: I 160 MET cc_start: 0.8138 (ptm) cc_final: 0.7620 (ptm) REVERT: I 191 MET cc_start: 0.8284 (tpp) cc_final: 0.8028 (tpp) REVERT: J 33 ARG cc_start: 0.8424 (mmm160) cc_final: 0.7904 (tpt90) REVERT: J 70 ASN cc_start: 0.8781 (m110) cc_final: 0.8418 (t0) REVERT: J 97 LYS cc_start: 0.9318 (tppt) cc_final: 0.8837 (ttmt) REVERT: J 102 ASP cc_start: 0.8759 (t0) cc_final: 0.8492 (t0) REVERT: K 67 MET cc_start: 0.8670 (mtp) cc_final: 0.8205 (mtp) REVERT: K 147 ILE cc_start: 0.9483 (mt) cc_final: 0.9266 (tp) REVERT: K 160 MET cc_start: 0.8103 (ptm) cc_final: 0.7406 (ptm) REVERT: K 216 HIS cc_start: 0.6597 (m90) cc_final: 0.6038 (m170) REVERT: K 257 LYS cc_start: 0.9200 (mtmt) cc_final: 0.8782 (mttt) REVERT: L 58 ILE cc_start: 0.9571 (pt) cc_final: 0.9267 (pt) REVERT: L 62 GLN cc_start: 0.9174 (mt0) cc_final: 0.8911 (mt0) REVERT: L 63 LYS cc_start: 0.9380 (mmtt) cc_final: 0.9161 (mmmm) REVERT: L 97 LYS cc_start: 0.9312 (tppt) cc_final: 0.8884 (mttt) REVERT: L 102 ASP cc_start: 0.8995 (t0) cc_final: 0.8721 (t0) REVERT: M 8 MET cc_start: 0.8014 (mtp) cc_final: 0.7810 (mtp) REVERT: M 147 ILE cc_start: 0.9458 (mt) cc_final: 0.9248 (tp) REVERT: M 160 MET cc_start: 0.7949 (ptm) cc_final: 0.7505 (ttp) REVERT: N 22 ILE cc_start: 0.9410 (mp) cc_final: 0.9072 (mt) REVERT: N 63 LYS cc_start: 0.9359 (mmtt) cc_final: 0.8974 (mmmm) REVERT: N 70 ASN cc_start: 0.8839 (m-40) cc_final: 0.8371 (t0) REVERT: N 102 ASP cc_start: 0.8737 (t0) cc_final: 0.8314 (t0) REVERT: N 105 ASN cc_start: 0.8052 (m-40) cc_final: 0.7290 (p0) REVERT: O 67 MET cc_start: 0.8195 (mtp) cc_final: 0.7714 (mtp) REVERT: O 98 MET cc_start: 0.8384 (mmm) cc_final: 0.7906 (mmp) REVERT: O 160 MET cc_start: 0.8115 (ptm) cc_final: 0.7734 (ptm) REVERT: O 191 MET cc_start: 0.8300 (tpp) cc_final: 0.8055 (tpp) REVERT: O 216 HIS cc_start: 0.6140 (m90) cc_final: 0.5664 (m-70) REVERT: P 36 ASN cc_start: 0.8614 (m-40) cc_final: 0.8098 (t0) REVERT: P 102 ASP cc_start: 0.8982 (t0) cc_final: 0.8543 (t0) REVERT: Q 147 ILE cc_start: 0.9456 (mt) cc_final: 0.9167 (tp) REVERT: Q 160 MET cc_start: 0.8126 (ptm) cc_final: 0.7495 (ptm) REVERT: Q 191 MET cc_start: 0.8123 (tpp) cc_final: 0.7775 (tpp) REVERT: Q 216 HIS cc_start: 0.6420 (m90) cc_final: 0.6159 (m90) REVERT: R 36 ASN cc_start: 0.8824 (m-40) cc_final: 0.8226 (t0) REVERT: R 55 ASP cc_start: 0.8509 (m-30) cc_final: 0.7926 (t0) REVERT: R 87 ASP cc_start: 0.7113 (t0) cc_final: 0.6064 (t0) REVERT: R 90 GLU cc_start: 0.9021 (mp0) cc_final: 0.8747 (mp0) REVERT: R 102 ASP cc_start: 0.8844 (t0) cc_final: 0.8395 (t0) REVERT: S 147 ILE cc_start: 0.9427 (mt) cc_final: 0.9162 (tp) REVERT: S 160 MET cc_start: 0.8069 (ptm) cc_final: 0.7758 (ptp) REVERT: S 196 MET cc_start: 0.8146 (tmm) cc_final: 0.7717 (tmm) REVERT: T 36 ASN cc_start: 0.8641 (m-40) cc_final: 0.8224 (t0) REVERT: T 58 ILE cc_start: 0.9546 (pt) cc_final: 0.9313 (pt) REVERT: T 62 GLN cc_start: 0.9284 (mt0) cc_final: 0.8926 (mt0) REVERT: T 102 ASP cc_start: 0.8762 (t70) cc_final: 0.8523 (t0) REVERT: T 116 MET cc_start: 0.8574 (tpp) cc_final: 0.8340 (tpp) REVERT: T 117 ASP cc_start: 0.8340 (t70) cc_final: 0.7835 (t0) REVERT: U 147 ILE cc_start: 0.9477 (mt) cc_final: 0.9201 (tp) REVERT: U 160 MET cc_start: 0.8104 (ptm) cc_final: 0.7192 (ptm) REVERT: V 118 LYS cc_start: 0.9388 (mmmm) cc_final: 0.9001 (mppt) REVERT: W 147 ILE cc_start: 0.9485 (mt) cc_final: 0.9184 (tp) REVERT: W 160 MET cc_start: 0.7892 (ptm) cc_final: 0.7247 (mtp) REVERT: W 191 MET cc_start: 0.8213 (tpp) cc_final: 0.7948 (tpp) REVERT: X 55 ASP cc_start: 0.8281 (m-30) cc_final: 0.7774 (t0) REVERT: X 58 ILE cc_start: 0.9447 (mt) cc_final: 0.9088 (mt) REVERT: X 70 ASN cc_start: 0.8861 (m110) cc_final: 0.8406 (t0) REVERT: X 102 ASP cc_start: 0.8712 (t0) cc_final: 0.8476 (t0) outliers start: 1 outliers final: 1 residues processed: 539 average time/residue: 0.2292 time to fit residues: 202.7075 Evaluate side-chains 378 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 377 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 9 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 283 optimal weight: 0.9980 chunk 198 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 157 optimal weight: 0.6980 chunk 320 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 243 optimal weight: 5.9990 chunk 387 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 GLN C 52 GLN G 52 GLN O 92 HIS ** Q 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 92 HIS U 52 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.065634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.051808 restraints weight = 165587.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.052987 restraints weight = 121617.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.053777 restraints weight = 98714.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.054295 restraints weight = 85801.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.054674 restraints weight = 78032.144| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.6804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 37476 Z= 0.135 Angle : 0.522 8.582 50628 Z= 0.286 Chirality : 0.037 0.185 5964 Planarity : 0.003 0.067 6444 Dihedral : 3.618 24.245 5172 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.72 % Favored : 98.26 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: 4.08 (0.12), residues: 4716 helix: 3.10 (0.07), residues: 4332 sheet: None (None), residues: 0 loop : -2.95 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG H 21 TYR 0.021 0.001 TYR A 48 PHE 0.020 0.002 PHE I 128 TRP 0.015 0.002 TRP R 41 HIS 0.009 0.002 HIS M 123 Details of bonding type rmsd covalent geometry : bond 0.00290 (37476) covalent geometry : angle 0.52183 (50628) hydrogen bonds : bond 0.03546 ( 3588) hydrogen bonds : angle 3.04107 (10764) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 520 time to evaluate : 1.452 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 MET cc_start: 0.7734 (mmm) cc_final: 0.7374 (mmp) REVERT: B 160 MET cc_start: 0.7930 (ptm) cc_final: 0.7223 (ptm) REVERT: B 252 TYR cc_start: 0.8776 (m-80) cc_final: 0.8548 (m-80) REVERT: A 55 ASP cc_start: 0.8239 (t70) cc_final: 0.8035 (t0) REVERT: A 58 ILE cc_start: 0.9487 (pt) cc_final: 0.9237 (pt) REVERT: A 62 GLN cc_start: 0.9233 (mt0) cc_final: 0.8870 (mt0) REVERT: C 8 MET cc_start: 0.8170 (mtt) cc_final: 0.7817 (mtp) REVERT: C 147 ILE cc_start: 0.9480 (mt) cc_final: 0.9236 (tp) REVERT: C 160 MET cc_start: 0.8184 (ptm) cc_final: 0.7633 (ptm) REVERT: C 191 MET cc_start: 0.8272 (tpp) cc_final: 0.7941 (tpp) REVERT: D 36 ASN cc_start: 0.8588 (m-40) cc_final: 0.8232 (t0) REVERT: D 55 ASP cc_start: 0.8293 (m-30) cc_final: 0.7938 (t0) REVERT: D 63 LYS cc_start: 0.9351 (mmtt) cc_final: 0.9033 (mttm) REVERT: D 97 LYS cc_start: 0.9496 (tppt) cc_final: 0.9174 (mtmt) REVERT: D 102 ASP cc_start: 0.8866 (t0) cc_final: 0.8525 (t0) REVERT: E 30 LYS cc_start: 0.7779 (mtmt) cc_final: 0.7151 (mmtt) REVERT: E 147 ILE cc_start: 0.9474 (mt) cc_final: 0.9261 (tp) REVERT: E 160 MET cc_start: 0.8026 (ptm) cc_final: 0.7560 (ptm) REVERT: F 36 ASN cc_start: 0.8588 (m-40) cc_final: 0.8264 (t0) REVERT: F 55 ASP cc_start: 0.8505 (m-30) cc_final: 0.7824 (t0) REVERT: F 63 LYS cc_start: 0.9307 (mttm) cc_final: 0.8731 (ttmm) REVERT: F 70 ASN cc_start: 0.8793 (m-40) cc_final: 0.8418 (t0) REVERT: F 90 GLU cc_start: 0.8950 (mp0) cc_final: 0.8448 (mp0) REVERT: F 97 LYS cc_start: 0.9400 (tppt) cc_final: 0.8975 (ttmt) REVERT: F 102 ASP cc_start: 0.8785 (t0) cc_final: 0.8203 (t0) REVERT: F 117 ASP cc_start: 0.8559 (t70) cc_final: 0.8327 (t0) REVERT: G 147 ILE cc_start: 0.9430 (mt) cc_final: 0.9207 (tp) REVERT: G 160 MET cc_start: 0.8110 (ptm) cc_final: 0.7522 (ptm) REVERT: H 55 ASP cc_start: 0.8461 (m-30) cc_final: 0.7871 (t0) REVERT: H 63 LYS cc_start: 0.9220 (mmmm) cc_final: 0.8870 (mmmm) REVERT: H 70 ASN cc_start: 0.8597 (m-40) cc_final: 0.8245 (t0) REVERT: H 97 LYS cc_start: 0.9299 (mmmm) cc_final: 0.8895 (mttp) REVERT: H 102 ASP cc_start: 0.8903 (t0) cc_final: 0.8550 (t0) REVERT: H 105 ASN cc_start: 0.8102 (m-40) cc_final: 0.7594 (p0) REVERT: I 147 ILE cc_start: 0.9451 (mt) cc_final: 0.9194 (tp) REVERT: I 191 MET cc_start: 0.8291 (tpp) cc_final: 0.8007 (tpp) REVERT: J 33 ARG cc_start: 0.8416 (mmm160) cc_final: 0.7877 (tpt90) REVERT: J 58 ILE cc_start: 0.9504 (pt) cc_final: 0.9304 (pt) REVERT: J 70 ASN cc_start: 0.8750 (m110) cc_final: 0.8486 (t0) REVERT: J 97 LYS cc_start: 0.9325 (tppt) cc_final: 0.8855 (ttmt) REVERT: J 102 ASP cc_start: 0.8819 (t0) cc_final: 0.8544 (t0) REVERT: K 67 MET cc_start: 0.8674 (mtp) cc_final: 0.8196 (mtp) REVERT: K 147 ILE cc_start: 0.9485 (mt) cc_final: 0.9266 (tp) REVERT: K 160 MET cc_start: 0.8094 (ptm) cc_final: 0.7409 (ptm) REVERT: L 58 ILE cc_start: 0.9572 (pt) cc_final: 0.9363 (pt) REVERT: L 63 LYS cc_start: 0.9383 (mmtt) cc_final: 0.9180 (mmmm) REVERT: L 97 LYS cc_start: 0.9279 (tppt) cc_final: 0.8831 (mttt) REVERT: L 102 ASP cc_start: 0.9022 (t0) cc_final: 0.8722 (t0) REVERT: M 160 MET cc_start: 0.7916 (ptm) cc_final: 0.7703 (ttm) REVERT: N 22 ILE cc_start: 0.9426 (mp) cc_final: 0.9166 (mt) REVERT: N 70 ASN cc_start: 0.8899 (m-40) cc_final: 0.8436 (t0) REVERT: N 102 ASP cc_start: 0.8721 (t0) cc_final: 0.8267 (t0) REVERT: N 105 ASN cc_start: 0.8178 (m-40) cc_final: 0.7378 (p0) REVERT: N 118 LYS cc_start: 0.8873 (mppt) cc_final: 0.8651 (mppt) REVERT: O 98 MET cc_start: 0.8394 (mmm) cc_final: 0.7949 (mmp) REVERT: O 160 MET cc_start: 0.8165 (ptm) cc_final: 0.7744 (ttp) REVERT: O 191 MET cc_start: 0.8283 (tpp) cc_final: 0.8055 (tpp) REVERT: O 216 HIS cc_start: 0.6114 (m90) cc_final: 0.5585 (m170) REVERT: P 90 GLU cc_start: 0.8989 (mp0) cc_final: 0.8538 (mp0) REVERT: P 102 ASP cc_start: 0.8989 (t0) cc_final: 0.8573 (t0) REVERT: Q 147 ILE cc_start: 0.9457 (mt) cc_final: 0.9166 (tp) REVERT: Q 160 MET cc_start: 0.8228 (ptm) cc_final: 0.7735 (ptm) REVERT: Q 216 HIS cc_start: 0.6883 (m90) cc_final: 0.6658 (m-70) REVERT: R 36 ASN cc_start: 0.8829 (m-40) cc_final: 0.8431 (t0) REVERT: R 55 ASP cc_start: 0.8426 (m-30) cc_final: 0.7975 (t0) REVERT: R 87 ASP cc_start: 0.7193 (t0) cc_final: 0.6170 (t0) REVERT: R 90 GLU cc_start: 0.9001 (mp0) cc_final: 0.8725 (mp0) REVERT: R 102 ASP cc_start: 0.8901 (t0) cc_final: 0.8456 (t0) REVERT: S 147 ILE cc_start: 0.9437 (mt) cc_final: 0.9172 (tp) REVERT: S 160 MET cc_start: 0.8130 (ptm) cc_final: 0.7555 (ptm) REVERT: S 196 MET cc_start: 0.8125 (tmm) cc_final: 0.7744 (tmm) REVERT: T 36 ASN cc_start: 0.8653 (m-40) cc_final: 0.8202 (t0) REVERT: T 58 ILE cc_start: 0.9535 (pt) cc_final: 0.9326 (pt) REVERT: T 62 GLN cc_start: 0.9258 (mt0) cc_final: 0.8966 (mt0) REVERT: T 70 ASN cc_start: 0.8788 (m-40) cc_final: 0.8315 (t0) REVERT: T 87 ASP cc_start: 0.6369 (t70) cc_final: 0.5956 (t70) REVERT: T 102 ASP cc_start: 0.8750 (t70) cc_final: 0.8492 (t0) REVERT: T 116 MET cc_start: 0.8558 (tpp) cc_final: 0.8312 (tpp) REVERT: T 117 ASP cc_start: 0.8263 (t70) cc_final: 0.7840 (t0) REVERT: U 160 MET cc_start: 0.8137 (ptm) cc_final: 0.7168 (ptm) REVERT: V 118 LYS cc_start: 0.9417 (mmmm) cc_final: 0.9006 (mppt) REVERT: W 147 ILE cc_start: 0.9484 (mt) cc_final: 0.9185 (tp) REVERT: W 160 MET cc_start: 0.7954 (ptm) cc_final: 0.7343 (mtp) REVERT: W 191 MET cc_start: 0.8213 (tpp) cc_final: 0.7948 (tpp) REVERT: X 55 ASP cc_start: 0.8339 (m-30) cc_final: 0.7839 (t0) REVERT: X 58 ILE cc_start: 0.9449 (mt) cc_final: 0.9095 (mt) REVERT: X 70 ASN cc_start: 0.8872 (m110) cc_final: 0.8418 (t0) REVERT: X 102 ASP cc_start: 0.8661 (t0) cc_final: 0.8461 (t0) outliers start: 0 outliers final: 0 residues processed: 520 average time/residue: 0.2170 time to fit residues: 187.7986 Evaluate side-chains 385 residues out of total 3612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 385 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 381 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 351 optimal weight: 1.9990 chunk 306 optimal weight: 0.9990 chunk 462 optimal weight: 2.9990 chunk 353 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 355 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 315 optimal weight: 5.9990 chunk 246 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN C 52 GLN G 52 GLN I 92 HIS M 122 ASN O 92 HIS U 52 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.065911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.051891 restraints weight = 165888.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.052976 restraints weight = 125815.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.053707 restraints weight = 104357.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.054203 restraints weight = 91894.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.054564 restraints weight = 84255.074| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.6940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 37476 Z= 0.137 Angle : 0.529 8.878 50628 Z= 0.290 Chirality : 0.037 0.182 5964 Planarity : 0.003 0.060 6444 Dihedral : 3.670 23.406 5172 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.80 % Favored : 98.16 % Rotamer: Outliers : 0.08 % Allowed : 0.22 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.04 (0.12), residues: 4716 helix: 3.08 (0.07), residues: 4344 sheet: None (None), residues: 0 loop : -3.15 (0.28), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG N 21 TYR 0.017 0.001 TYR X 42 PHE 0.023 0.002 PHE I 128 TRP 0.016 0.002 TRP R 41 HIS 0.012 0.002 HIS I 92 Details of bonding type rmsd covalent geometry : bond 0.00295 (37476) covalent geometry : angle 0.52860 (50628) hydrogen bonds : bond 0.03555 ( 3588) hydrogen bonds : angle 3.05639 (10764) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6257.42 seconds wall clock time: 109 minutes 15.00 seconds (6555.00 seconds total)