Starting phenix.real_space_refine on Fri Jul 3 18:30:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dyl_47308/07_2026/9dyl_47308.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dyl_47308/07_2026/9dyl_47308.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dyl_47308/07_2026/9dyl_47308.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dyl_47308/07_2026/9dyl_47308.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dyl_47308/07_2026/9dyl_47308.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dyl_47308/07_2026/9dyl_47308.map" } resolution = 2.6 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= 0.003 sd= 0.095 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 5 9.91 5 S 80 5.16 5 C 10295 2.51 5 N 2555 2.21 5 O 2710 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15645 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3118 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 20, 'TRANS': 355} Chain: "E" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3118 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 20, 'TRANS': 355} Chain: "B" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3118 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 20, 'TRANS': 355} Chain: "D" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3118 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 20, 'TRANS': 355} Chain: "C" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3118 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 20, 'TRANS': 355} Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'PAB': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "E" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'PAB': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'PAB': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "D" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'PAB': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Chain: "C" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'PAB': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Time building chain proxies: 3.13, per 1000 atoms: 0.20 Number of scatterers: 15645 At special positions: 0 Unit cell: (105.41, 107.07, 112.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 5 19.99 S 80 16.00 O 2710 8.00 N 2555 7.00 C 10295 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 419.1 milliseconds 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3590 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 0 sheets defined 72.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 15 through 21 removed outlier: 3.902A pdb=" N LEU A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 53 removed outlier: 3.597A pdb=" N LEU A 31 " --> pdb=" O SER A 27 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N GLY A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N GLU A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 73 Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'A' and resid 77 through 99 Processing helix chain 'A' and resid 103 through 114 Processing helix chain 'A' and resid 118 through 144 Processing helix chain 'A' and resid 144 through 151 Processing helix chain 'A' and resid 153 through 160 Processing helix chain 'A' and resid 164 through 175 Processing helix chain 'A' and resid 179 through 181 No H-bonds generated for 'chain 'A' and resid 179 through 181' Processing helix chain 'A' and resid 182 through 198 removed outlier: 3.713A pdb=" N VAL A 186 " --> pdb=" O TRP A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 230 Processing helix chain 'A' and resid 233 through 255 removed outlier: 4.001A pdb=" N VAL A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 274 through 296 removed outlier: 4.603A pdb=" N ASN A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 324 Processing helix chain 'A' and resid 351 through 355 Processing helix chain 'A' and resid 369 through 374 removed outlier: 3.618A pdb=" N GLU A 374 " --> pdb=" O LYS A 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 21 removed outlier: 3.913A pdb=" N LEU E 20 " --> pdb=" O SER E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 53 removed outlier: 3.601A pdb=" N LEU E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N GLY E 34 " --> pdb=" O LYS E 30 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N GLU E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 73 Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 77 through 99 Processing helix chain 'E' and resid 103 through 114 Processing helix chain 'E' and resid 118 through 144 Processing helix chain 'E' and resid 144 through 151 Processing helix chain 'E' and resid 153 through 160 Processing helix chain 'E' and resid 164 through 175 Processing helix chain 'E' and resid 182 through 198 removed outlier: 3.713A pdb=" N VAL E 186 " --> pdb=" O TRP E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 230 Processing helix chain 'E' and resid 233 through 255 removed outlier: 4.008A pdb=" N VAL E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 263 Processing helix chain 'E' and resid 274 through 296 removed outlier: 4.589A pdb=" N ASN E 296 " --> pdb=" O GLU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 324 Processing helix chain 'E' and resid 351 through 355 Processing helix chain 'E' and resid 369 through 374 removed outlier: 3.615A pdb=" N GLU E 374 " --> pdb=" O LYS E 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 21 removed outlier: 3.906A pdb=" N LEU B 20 " --> pdb=" O SER B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 53 removed outlier: 3.594A pdb=" N LEU B 31 " --> pdb=" O SER B 27 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N GLY B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N GLU B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 73 Processing helix chain 'B' and resid 74 through 76 No H-bonds generated for 'chain 'B' and resid 74 through 76' Processing helix chain 'B' and resid 77 through 99 Processing helix chain 'B' and resid 103 through 114 Processing helix chain 'B' and resid 118 through 144 Processing helix chain 'B' and resid 144 through 151 Processing helix chain 'B' and resid 153 through 160 Processing helix chain 'B' and resid 164 through 175 Processing helix chain 'B' and resid 182 through 198 removed outlier: 3.713A pdb=" N VAL B 186 " --> pdb=" O TRP B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 230 Processing helix chain 'B' and resid 233 through 255 removed outlier: 4.008A pdb=" N VAL B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 274 through 296 removed outlier: 4.591A pdb=" N ASN B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 324 Processing helix chain 'B' and resid 351 through 355 Processing helix chain 'B' and resid 369 through 374 removed outlier: 3.615A pdb=" N GLU B 374 " --> pdb=" O LYS B 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 21 removed outlier: 3.902A pdb=" N LEU D 20 " --> pdb=" O SER D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 53 removed outlier: 3.596A pdb=" N LEU D 31 " --> pdb=" O SER D 27 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N GLY D 34 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N GLU D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 73 Processing helix chain 'D' and resid 74 through 76 No H-bonds generated for 'chain 'D' and resid 74 through 76' Processing helix chain 'D' and resid 77 through 99 Processing helix chain 'D' and resid 103 through 114 Processing helix chain 'D' and resid 118 through 144 Processing helix chain 'D' and resid 144 through 151 Processing helix chain 'D' and resid 153 through 160 Processing helix chain 'D' and resid 164 through 175 Processing helix chain 'D' and resid 182 through 198 removed outlier: 3.712A pdb=" N VAL D 186 " --> pdb=" O TRP D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 230 Processing helix chain 'D' and resid 233 through 255 removed outlier: 4.002A pdb=" N VAL D 253 " --> pdb=" O LEU D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 Processing helix chain 'D' and resid 274 through 296 removed outlier: 4.591A pdb=" N ASN D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 324 Processing helix chain 'D' and resid 351 through 355 Processing helix chain 'D' and resid 369 through 374 removed outlier: 3.618A pdb=" N GLU D 374 " --> pdb=" O LYS D 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 21 removed outlier: 3.907A pdb=" N LEU C 20 " --> pdb=" O SER C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 53 removed outlier: 3.600A pdb=" N LEU C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N GLY C 34 " --> pdb=" O LYS C 30 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLU C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 73 Processing helix chain 'C' and resid 74 through 76 No H-bonds generated for 'chain 'C' and resid 74 through 76' Processing helix chain 'C' and resid 77 through 99 Processing helix chain 'C' and resid 103 through 114 Processing helix chain 'C' and resid 118 through 144 Processing helix chain 'C' and resid 144 through 151 Processing helix chain 'C' and resid 153 through 160 Processing helix chain 'C' and resid 164 through 175 Processing helix chain 'C' and resid 179 through 181 No H-bonds generated for 'chain 'C' and resid 179 through 181' Processing helix chain 'C' and resid 182 through 198 removed outlier: 3.713A pdb=" N VAL C 186 " --> pdb=" O TRP C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 230 Processing helix chain 'C' and resid 233 through 255 removed outlier: 4.003A pdb=" N VAL C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 263 Processing helix chain 'C' and resid 274 through 296 removed outlier: 4.594A pdb=" N ASN C 296 " --> pdb=" O GLU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 324 Processing helix chain 'C' and resid 351 through 355 Processing helix chain 'C' and resid 369 through 374 removed outlier: 3.618A pdb=" N GLU C 374 " --> pdb=" O LYS C 370 " (cutoff:3.500A) 975 hydrogen bonds defined for protein. 2865 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: 2.05 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3912 1.32 - 1.46: 3399 1.46 - 1.59: 8669 1.59 - 1.72: 0 1.72 - 1.85: 135 Bond restraints: 16115 Sorted by residual: bond pdb=" C ARG C 105 " pdb=" O ARG C 105 " ideal model delta sigma weight residual 1.236 1.289 -0.052 1.15e-02 7.56e+03 2.08e+01 bond pdb=" C VAL B 110 " pdb=" O VAL B 110 " ideal model delta sigma weight residual 1.237 1.287 -0.050 1.12e-02 7.97e+03 2.00e+01 bond pdb=" C ARG D 105 " pdb=" O ARG D 105 " ideal model delta sigma weight residual 1.236 1.285 -0.049 1.15e-02 7.56e+03 1.79e+01 bond pdb=" C VAL E 110 " pdb=" O VAL E 110 " ideal model delta sigma weight residual 1.237 1.284 -0.047 1.12e-02 7.97e+03 1.77e+01 bond pdb=" C VAL D 110 " pdb=" O VAL D 110 " ideal model delta sigma weight residual 1.237 1.283 -0.047 1.12e-02 7.97e+03 1.74e+01 ... (remaining 16110 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 16186 1.37 - 2.74: 5080 2.74 - 4.11: 620 4.11 - 5.48: 50 5.48 - 6.85: 14 Bond angle restraints: 21950 Sorted by residual: angle pdb=" N THR C 91 " pdb=" CA THR C 91 " pdb=" C THR C 91 " ideal model delta sigma weight residual 111.14 106.07 5.07 1.08e+00 8.57e-01 2.20e+01 angle pdb=" CA GLU A 300 " pdb=" C GLU A 300 " pdb=" O GLU A 300 " ideal model delta sigma weight residual 119.95 115.52 4.43 1.21e+00 6.83e-01 1.34e+01 angle pdb=" CA GLU D 300 " pdb=" C GLU D 300 " pdb=" O GLU D 300 " ideal model delta sigma weight residual 119.95 115.73 4.22 1.21e+00 6.83e-01 1.21e+01 angle pdb=" N ILE A 232 " pdb=" CA ILE A 232 " pdb=" C ILE A 232 " ideal model delta sigma weight residual 108.96 105.13 3.83 1.10e+00 8.26e-01 1.21e+01 angle pdb=" N PHE C 281 " pdb=" CA PHE C 281 " pdb=" C PHE C 281 " ideal model delta sigma weight residual 110.97 107.18 3.79 1.09e+00 8.42e-01 1.21e+01 ... (remaining 21945 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 8499 17.87 - 35.73: 732 35.73 - 53.60: 89 53.60 - 71.46: 25 71.46 - 89.33: 35 Dihedral angle restraints: 9380 sinusoidal: 3815 harmonic: 5565 Sorted by residual: dihedral pdb=" CA LEU C 32 " pdb=" C LEU C 32 " pdb=" N TYR C 33 " pdb=" CA TYR C 33 " ideal model delta harmonic sigma weight residual -180.00 -154.91 -25.09 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA LEU B 32 " pdb=" C LEU B 32 " pdb=" N TYR B 33 " pdb=" CA TYR B 33 " ideal model delta harmonic sigma weight residual 180.00 -155.20 -24.80 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA LEU D 32 " pdb=" C LEU D 32 " pdb=" N TYR D 33 " pdb=" CA TYR D 33 " ideal model delta harmonic sigma weight residual -180.00 -155.33 -24.67 0 5.00e+00 4.00e-02 2.43e+01 ... (remaining 9377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1091 0.048 - 0.097: 829 0.097 - 0.145: 354 0.145 - 0.193: 74 0.193 - 0.241: 27 Chirality restraints: 2375 Sorted by residual: chirality pdb=" CA ILE E 232 " pdb=" N ILE E 232 " pdb=" C ILE E 232 " pdb=" CB ILE E 232 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA ILE A 28 " pdb=" N ILE A 28 " pdb=" C ILE A 28 " pdb=" CB ILE A 28 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA ILE C 232 " pdb=" N ILE C 232 " pdb=" C ILE C 232 " pdb=" CB ILE C 232 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 2372 not shown) Planarity restraints: 2760 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 276 " -0.046 2.00e-02 2.50e+03 3.03e-02 1.60e+01 pdb=" CG PHE E 276 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE E 276 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 PHE E 276 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE E 276 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 PHE E 276 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE E 276 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 276 " 0.045 2.00e-02 2.50e+03 2.80e-02 1.37e+01 pdb=" CG PHE C 276 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE C 276 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 PHE C 276 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE C 276 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE C 276 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE C 276 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 185 " 0.024 2.00e-02 2.50e+03 2.34e-02 1.37e+01 pdb=" CG TRP D 185 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP D 185 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP D 185 " 0.017 2.00e-02 2.50e+03 pdb=" NE1 TRP D 185 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TRP D 185 " 0.014 2.00e-02 2.50e+03 pdb=" CE3 TRP D 185 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 185 " 0.041 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 185 " -0.037 2.00e-02 2.50e+03 pdb=" CH2 TRP D 185 " -0.008 2.00e-02 2.50e+03 ... (remaining 2757 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1208 2.75 - 3.29: 17240 3.29 - 3.82: 27192 3.82 - 4.36: 35947 4.36 - 4.90: 57248 Nonbonded interactions: 138835 Sorted by model distance: nonbonded pdb=" OH TYR E 5 " pdb=" O ILE D 232 " model vdw 2.211 3.040 nonbonded pdb=" OH TYR D 5 " pdb=" O ILE C 232 " model vdw 2.216 3.040 nonbonded pdb=" O ILE B 232 " pdb=" OH TYR C 5 " model vdw 2.244 3.040 nonbonded pdb=" OH TYR A 5 " pdb=" O ILE E 232 " model vdw 2.250 3.040 nonbonded pdb=" O ILE A 232 " pdb=" OH TYR B 5 " model vdw 2.256 3.040 ... (remaining 138830 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'B' selection = chain 'D' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.300 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: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 12.220 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9199 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 : 0.013 0.059 16115 Z= 0.927 Angle : 1.249 6.855 21950 Z= 0.919 Chirality : 0.074 0.241 2375 Planarity : 0.007 0.033 2760 Dihedral : 14.396 89.329 5790 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % 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: 1.22 (0.18), residues: 1870 helix: 1.20 (0.14), residues: 1235 sheet: None (None), residues: 0 loop : 0.22 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG E 218 TYR 0.043 0.008 TYR A 97 PHE 0.046 0.007 PHE E 276 TRP 0.041 0.011 TRP D 185 HIS 0.011 0.005 HIS B 178 Details of bonding type rmsd/Z covalent geometry : bond 0.01306 / 0.93 (16115) covalent geometry : angle 1.24893 / 0.92 (21950) hydrogen bonds : bond 0.10361 / 6.86 ( 975) hydrogen bonds : angle 4.73803 / 3.41 ( 2865) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.633 Fit side-chains revert: symmetry clash REVERT: A 25 ARG cc_start: 0.8408 (ttp-170) cc_final: 0.7224 (pmt170) REVERT: E 25 ARG cc_start: 0.8216 (ttp-170) cc_final: 0.7013 (mpp-170) REVERT: E 57 GLU cc_start: 0.7963 (mp0) cc_final: 0.7734 (pt0) REVERT: E 119 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8436 (tt0) REVERT: E 325 MET cc_start: 0.9198 (mtp) cc_final: 0.8766 (mtp) REVERT: E 340 LYS cc_start: 0.6675 (mmtm) cc_final: 0.5868 (mtmt) REVERT: E 369 ASN cc_start: 0.7296 (m110) cc_final: 0.7090 (m-40) REVERT: B 57 GLU cc_start: 0.8092 (mp0) cc_final: 0.7644 (pt0) REVERT: B 331 ARG cc_start: 0.9021 (ttp-170) cc_final: 0.8690 (ttp-170) REVERT: D 25 ARG cc_start: 0.8360 (ttp-170) cc_final: 0.7314 (pmt170) REVERT: D 119 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8465 (tt0) REVERT: D 173 LYS cc_start: 0.8346 (mttp) cc_final: 0.8084 (mttp) REVERT: D 369 ASN cc_start: 0.7047 (m110) cc_final: 0.6802 (m-40) REVERT: C 25 ARG cc_start: 0.8299 (ttp-170) cc_final: 0.6951 (mpp-170) REVERT: C 57 GLU cc_start: 0.7936 (mp0) cc_final: 0.7647 (pt0) REVERT: C 119 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8376 (tt0) REVERT: C 344 GLN cc_start: 0.8997 (mt0) cc_final: 0.8564 (mm110) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.7773 time to fit residues: 179.4868 Evaluate side-chains 165 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 369 ASN ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 ASN ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 ASN D 96 GLN ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.104556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.084277 restraints weight = 20933.471| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 1.86 r_work: 0.2855 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16115 Z= 0.148 Angle : 0.525 4.928 21950 Z= 0.290 Chirality : 0.038 0.152 2375 Planarity : 0.004 0.032 2760 Dihedral : 5.873 80.295 2085 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.18 % Allowed : 5.96 % Favored : 92.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.18), residues: 1870 helix: 1.37 (0.14), residues: 1260 sheet: None (None), residues: 0 loop : 0.13 (0.23), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 126 TYR 0.022 0.002 TYR D 97 PHE 0.028 0.002 PHE A 248 TRP 0.015 0.002 TRP A 309 HIS 0.002 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (16115) covalent geometry : angle 0.52498 / 0.29 (21950) hydrogen bonds : bond 0.06109 / 4.00 ( 975) hydrogen bonds : angle 4.61975 / 3.32 ( 2865) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 179 time to evaluate : 0.548 Fit side-chains REVERT: A 25 ARG cc_start: 0.7973 (ttp-170) cc_final: 0.6669 (pmt170) REVERT: A 119 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7438 (tp30) REVERT: A 301 ASP cc_start: 0.8258 (m-30) cc_final: 0.7820 (m-30) REVERT: E 25 ARG cc_start: 0.7871 (ttp-170) cc_final: 0.6634 (mpp-170) REVERT: E 119 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7618 (tt0) REVERT: E 268 GLU cc_start: 0.7796 (mp0) cc_final: 0.7529 (mp0) REVERT: E 290 VAL cc_start: 0.8201 (t) cc_final: 0.7827 (m) REVERT: E 293 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7050 (tm-30) REVERT: E 325 MET cc_start: 0.9157 (mtp) cc_final: 0.8749 (mtp) REVERT: E 340 LYS cc_start: 0.6604 (mmtm) cc_final: 0.5561 (mtmt) REVERT: B 56 GLU cc_start: 0.7549 (tt0) cc_final: 0.7122 (tp30) REVERT: B 57 GLU cc_start: 0.7452 (mp0) cc_final: 0.7048 (pt0) REVERT: B 74 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.8148 (pp30) REVERT: B 301 ASP cc_start: 0.8047 (m-30) cc_final: 0.7641 (m-30) REVERT: B 374 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6194 (mp0) REVERT: D 25 ARG cc_start: 0.7933 (ttp-170) cc_final: 0.6813 (pmt170) REVERT: D 301 ASP cc_start: 0.7940 (m-30) cc_final: 0.7557 (m-30) REVERT: D 355 ARG cc_start: 0.7363 (ttp-170) cc_final: 0.7011 (ttm110) REVERT: C 25 ARG cc_start: 0.7915 (ttp-170) cc_final: 0.6399 (mpp-170) REVERT: C 56 GLU cc_start: 0.7406 (tt0) cc_final: 0.6963 (tp30) REVERT: C 119 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7750 (tt0) REVERT: C 290 VAL cc_start: 0.8421 (t) cc_final: 0.8118 (m) REVERT: C 344 GLN cc_start: 0.8697 (mt0) cc_final: 0.8064 (mm110) outliers start: 20 outliers final: 6 residues processed: 190 average time/residue: 0.6981 time to fit residues: 144.2391 Evaluate side-chains 173 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 163 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 293 GLN Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 74 GLN Chi-restraints excluded: chain C residue 60 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 103 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 80 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 100 optimal weight: 7.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 GLN ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 GLN ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 ASN B 96 GLN ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 GLN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.104560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.084207 restraints weight = 21109.815| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.87 r_work: 0.2857 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16115 Z= 0.151 Angle : 0.502 8.757 21950 Z= 0.275 Chirality : 0.038 0.153 2375 Planarity : 0.004 0.035 2760 Dihedral : 5.685 80.781 2085 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.71 % Allowed : 7.61 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.18), residues: 1870 helix: 1.39 (0.14), residues: 1265 sheet: None (None), residues: 0 loop : 0.19 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 51 TYR 0.021 0.002 TYR D 97 PHE 0.024 0.002 PHE A 248 TRP 0.014 0.001 TRP A 309 HIS 0.003 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (16115) covalent geometry : angle 0.50227 / 0.27 (21950) hydrogen bonds : bond 0.05922 / 3.88 ( 975) hydrogen bonds : angle 4.52980 / 3.25 ( 2865) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 0.567 Fit side-chains REVERT: A 25 ARG cc_start: 0.7911 (ttp-170) cc_final: 0.6605 (pmt170) REVERT: A 119 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7410 (tp30) REVERT: A 268 GLU cc_start: 0.7843 (mp0) cc_final: 0.7372 (mp0) REVERT: E 25 ARG cc_start: 0.7911 (ttp-170) cc_final: 0.6622 (mpp-170) REVERT: E 119 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7669 (tt0) REVERT: E 173 LYS cc_start: 0.7900 (mttp) cc_final: 0.7564 (mttp) REVERT: E 268 GLU cc_start: 0.7926 (mp0) cc_final: 0.7585 (mp0) REVERT: E 290 VAL cc_start: 0.8207 (t) cc_final: 0.7865 (m) REVERT: E 293 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7190 (tm-30) REVERT: E 325 MET cc_start: 0.9123 (mtp) cc_final: 0.8824 (mtp) REVERT: E 340 LYS cc_start: 0.6649 (mmtm) cc_final: 0.5586 (mtmt) REVERT: E 344 GLN cc_start: 0.8538 (mt0) cc_final: 0.8163 (mm110) REVERT: E 374 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6637 (mm-30) REVERT: B 56 GLU cc_start: 0.7504 (tt0) cc_final: 0.7117 (tp30) REVERT: B 57 GLU cc_start: 0.7494 (mp0) cc_final: 0.7113 (pt0) REVERT: B 74 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.8177 (pp30) REVERT: B 331 ARG cc_start: 0.8332 (ttp-170) cc_final: 0.7646 (ttt180) REVERT: B 344 GLN cc_start: 0.8790 (mt0) cc_final: 0.8489 (mt0) REVERT: B 374 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6155 (mp0) REVERT: D 25 ARG cc_start: 0.7971 (ttp-170) cc_final: 0.6725 (pmt170) REVERT: D 355 ARG cc_start: 0.7290 (ttp-170) cc_final: 0.6932 (ttm110) REVERT: D 374 GLU cc_start: 0.7017 (mm-30) cc_final: 0.6804 (mm-30) REVERT: C 25 ARG cc_start: 0.7959 (ttp-170) cc_final: 0.6369 (mpp-170) REVERT: C 56 GLU cc_start: 0.7369 (tt0) cc_final: 0.6921 (pm20) REVERT: C 57 GLU cc_start: 0.7382 (mt-10) cc_final: 0.6759 (pt0) REVERT: C 119 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7695 (tt0) REVERT: C 290 VAL cc_start: 0.8389 (t) cc_final: 0.8113 (m) REVERT: C 344 GLN cc_start: 0.8675 (mt0) cc_final: 0.8058 (mm110) REVERT: C 374 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6723 (mm-30) outliers start: 29 outliers final: 7 residues processed: 188 average time/residue: 0.6652 time to fit residues: 136.0221 Evaluate side-chains 175 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 162 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 293 GLN Chi-restraints excluded: chain E residue 374 GLU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain D residue 74 GLN Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 374 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 6 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 0.0980 chunk 33 optimal weight: 0.0370 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 182 optimal weight: 2.9990 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 ASN ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 GLN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.105347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.085021 restraints weight = 20937.031| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.86 r_work: 0.2870 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16115 Z= 0.143 Angle : 0.483 7.457 21950 Z= 0.264 Chirality : 0.037 0.152 2375 Planarity : 0.004 0.036 2760 Dihedral : 5.570 80.191 2085 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.77 % Allowed : 8.73 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.18), residues: 1870 helix: 1.45 (0.14), residues: 1265 sheet: None (None), residues: 0 loop : 0.15 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 25 TYR 0.020 0.001 TYR D 97 PHE 0.023 0.001 PHE B 248 TRP 0.013 0.001 TRP E 309 HIS 0.003 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (16115) covalent geometry : angle 0.48311 / 0.26 (21950) hydrogen bonds : bond 0.05717 / 3.75 ( 975) hydrogen bonds : angle 4.50580 / 3.23 ( 2865) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 168 time to evaluate : 0.624 Fit side-chains REVERT: A 25 ARG cc_start: 0.7887 (ttp-170) cc_final: 0.6565 (pmt170) REVERT: A 119 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7464 (tp30) REVERT: E 25 ARG cc_start: 0.7899 (ttp-170) cc_final: 0.6523 (mpp-170) REVERT: E 119 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7614 (tt0) REVERT: E 268 GLU cc_start: 0.7984 (mp0) cc_final: 0.7627 (mp0) REVERT: E 290 VAL cc_start: 0.8228 (t) cc_final: 0.7907 (m) REVERT: E 325 MET cc_start: 0.9113 (mtp) cc_final: 0.8751 (mtp) REVERT: E 340 LYS cc_start: 0.6624 (mmtm) cc_final: 0.5548 (mtmt) REVERT: E 344 GLN cc_start: 0.8542 (mt0) cc_final: 0.8199 (mm110) REVERT: B 56 GLU cc_start: 0.7488 (tt0) cc_final: 0.7128 (tp30) REVERT: B 57 GLU cc_start: 0.7553 (mp0) cc_final: 0.7135 (pt0) REVERT: B 74 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.8169 (pp30) REVERT: B 331 ARG cc_start: 0.8357 (ttp-170) cc_final: 0.7787 (ttp-170) REVERT: B 344 GLN cc_start: 0.8785 (mt0) cc_final: 0.8471 (mt0) REVERT: B 374 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6121 (mp0) REVERT: D 25 ARG cc_start: 0.7921 (ttp-170) cc_final: 0.7578 (mmm-85) REVERT: D 355 ARG cc_start: 0.7325 (ttp-170) cc_final: 0.6972 (ttm110) REVERT: D 374 GLU cc_start: 0.6872 (mm-30) cc_final: 0.6625 (mm-30) REVERT: C 25 ARG cc_start: 0.7964 (ttp-170) cc_final: 0.6366 (mpp-170) REVERT: C 56 GLU cc_start: 0.7361 (tt0) cc_final: 0.6908 (pm20) REVERT: C 57 GLU cc_start: 0.7358 (mt-10) cc_final: 0.6746 (pt0) REVERT: C 119 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7707 (tt0) REVERT: C 287 TRP cc_start: 0.8592 (OUTLIER) cc_final: 0.8061 (t-100) REVERT: C 290 VAL cc_start: 0.8353 (t) cc_final: 0.8087 (m) REVERT: C 344 GLN cc_start: 0.8659 (mt0) cc_final: 0.8083 (mm110) REVERT: C 374 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6752 (mm-30) outliers start: 30 outliers final: 10 residues processed: 185 average time/residue: 0.6756 time to fit residues: 136.2899 Evaluate side-chains 177 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 74 GLN Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 287 TRP Chi-restraints excluded: chain C residue 374 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 26 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 147 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 112 optimal weight: 0.9990 chunk 91 optimal weight: 0.0000 chunk 33 optimal weight: 0.6980 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN A 365 ASN ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 ASN ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 GLN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.106832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.086541 restraints weight = 20938.640| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.86 r_work: 0.2892 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16115 Z= 0.126 Angle : 0.460 6.647 21950 Z= 0.252 Chirality : 0.036 0.151 2375 Planarity : 0.004 0.041 2760 Dihedral : 5.479 79.911 2085 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.95 % Allowed : 9.38 % Favored : 88.67 % 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: 1.56 (0.18), residues: 1870 helix: 1.54 (0.14), residues: 1265 sheet: None (None), residues: 0 loop : 0.10 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 25 TYR 0.018 0.001 TYR D 97 PHE 0.021 0.001 PHE B 248 TRP 0.012 0.001 TRP E 309 HIS 0.002 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (16115) covalent geometry : angle 0.46000 / 0.25 (21950) hydrogen bonds : bond 0.05418 / 3.55 ( 975) hydrogen bonds : angle 4.43978 / 3.19 ( 2865) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 187 time to evaluate : 0.626 Fit side-chains REVERT: A 25 ARG cc_start: 0.7907 (ttp-170) cc_final: 0.6627 (pmt170) REVERT: A 119 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7446 (tp30) REVERT: A 268 GLU cc_start: 0.7866 (mp0) cc_final: 0.7409 (mp0) REVERT: E 25 ARG cc_start: 0.7909 (ttp-170) cc_final: 0.6556 (mpp-170) REVERT: E 119 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7601 (tt0) REVERT: E 268 GLU cc_start: 0.7957 (mp0) cc_final: 0.7615 (mp0) REVERT: E 290 VAL cc_start: 0.8222 (t) cc_final: 0.7882 (m) REVERT: E 293 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.7189 (tm-30) REVERT: E 325 MET cc_start: 0.9112 (mtp) cc_final: 0.8772 (mtp) REVERT: E 340 LYS cc_start: 0.6606 (mmtm) cc_final: 0.5500 (mtmt) REVERT: E 344 GLN cc_start: 0.8531 (mt0) cc_final: 0.8181 (mm110) REVERT: B 57 GLU cc_start: 0.7571 (mp0) cc_final: 0.7127 (pt0) REVERT: B 74 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8132 (pp30) REVERT: B 331 ARG cc_start: 0.8376 (ttp-170) cc_final: 0.7803 (ttp-170) REVERT: B 344 GLN cc_start: 0.8766 (mt0) cc_final: 0.8449 (mt0) REVERT: B 374 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6022 (mp0) REVERT: D 25 ARG cc_start: 0.7930 (ttp-170) cc_final: 0.7597 (mmm-85) REVERT: D 61 MET cc_start: 0.7613 (tpt) cc_final: 0.6987 (ttp) REVERT: D 355 ARG cc_start: 0.7345 (ttp-170) cc_final: 0.6984 (ttm110) REVERT: D 374 GLU cc_start: 0.6856 (mm-30) cc_final: 0.6592 (mm-30) REVERT: C 25 ARG cc_start: 0.7958 (ttp-170) cc_final: 0.6352 (mpp-170) REVERT: C 56 GLU cc_start: 0.7311 (tt0) cc_final: 0.6878 (pm20) REVERT: C 57 GLU cc_start: 0.7346 (mt-10) cc_final: 0.6749 (pt0) REVERT: C 119 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7705 (tt0) REVERT: C 268 GLU cc_start: 0.8016 (mp0) cc_final: 0.7627 (mp0) REVERT: C 290 VAL cc_start: 0.8303 (t) cc_final: 0.8048 (m) REVERT: C 344 GLN cc_start: 0.8618 (mt0) cc_final: 0.8060 (mm110) REVERT: C 374 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6670 (mm-30) outliers start: 33 outliers final: 9 residues processed: 207 average time/residue: 0.6912 time to fit residues: 156.4689 Evaluate side-chains 184 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 170 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 293 GLN Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 74 GLN Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 374 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 174 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 112 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 178 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN A 365 ASN ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 ASN ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 ASN C 159 GLN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.103444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.083221 restraints weight = 20910.129| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 1.85 r_work: 0.2842 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16115 Z= 0.184 Angle : 0.505 5.419 21950 Z= 0.277 Chirality : 0.039 0.150 2375 Planarity : 0.005 0.044 2760 Dihedral : 5.567 80.572 2085 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.24 % Allowed : 9.79 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.18), residues: 1870 helix: 1.41 (0.14), residues: 1265 sheet: None (None), residues: 0 loop : 0.07 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 356 TYR 0.025 0.002 TYR D 97 PHE 0.024 0.002 PHE B 248 TRP 0.013 0.002 TRP E 309 HIS 0.004 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 (16115) covalent geometry : angle 0.50481 / 0.28 (21950) hydrogen bonds : bond 0.06150 / 4.03 ( 975) hydrogen bonds : angle 4.51856 / 3.24 ( 2865) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 171 time to evaluate : 0.642 Fit side-chains REVERT: A 25 ARG cc_start: 0.7918 (ttp-170) cc_final: 0.6549 (pmt170) REVERT: A 119 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7444 (tp30) REVERT: A 268 GLU cc_start: 0.7874 (mp0) cc_final: 0.7321 (mp0) REVERT: A 287 TRP cc_start: 0.8601 (OUTLIER) cc_final: 0.8252 (m-90) REVERT: E 25 ARG cc_start: 0.7892 (ttp-170) cc_final: 0.6576 (mpp-170) REVERT: E 119 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7600 (tt0) REVERT: E 268 GLU cc_start: 0.7978 (mp0) cc_final: 0.7678 (mp0) REVERT: E 293 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7252 (tm-30) REVERT: E 325 MET cc_start: 0.9113 (mtp) cc_final: 0.8774 (mtp) REVERT: E 344 GLN cc_start: 0.8579 (mt0) cc_final: 0.8213 (mm110) REVERT: E 374 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6753 (mp0) REVERT: B 57 GLU cc_start: 0.7598 (mp0) cc_final: 0.7182 (pt0) REVERT: B 74 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.8170 (pp30) REVERT: B 331 ARG cc_start: 0.8347 (ttp-170) cc_final: 0.7919 (ttp-170) REVERT: B 344 GLN cc_start: 0.8816 (mt0) cc_final: 0.8517 (mt0) REVERT: B 374 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6031 (mp0) REVERT: D 25 ARG cc_start: 0.7914 (ttp-170) cc_final: 0.7570 (mmm-85) REVERT: D 203 ASP cc_start: 0.8455 (OUTLIER) cc_final: 0.8252 (t70) REVERT: D 287 TRP cc_start: 0.8753 (OUTLIER) cc_final: 0.8483 (t-100) REVERT: D 355 ARG cc_start: 0.7309 (ttp-170) cc_final: 0.6953 (ttm110) REVERT: D 374 GLU cc_start: 0.6909 (mm-30) cc_final: 0.6631 (mm-30) REVERT: C 25 ARG cc_start: 0.8026 (ttp-170) cc_final: 0.6369 (mpp-170) REVERT: C 56 GLU cc_start: 0.7383 (tt0) cc_final: 0.6917 (pm20) REVERT: C 57 GLU cc_start: 0.7377 (mt-10) cc_final: 0.6769 (pt0) REVERT: C 119 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7736 (tt0) REVERT: C 268 GLU cc_start: 0.8012 (mp0) cc_final: 0.7718 (mp0) REVERT: C 287 TRP cc_start: 0.8620 (OUTLIER) cc_final: 0.8106 (t-100) REVERT: C 290 VAL cc_start: 0.8403 (t) cc_final: 0.8156 (m) REVERT: C 344 GLN cc_start: 0.8679 (mt0) cc_final: 0.8097 (mm110) REVERT: C 374 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6659 (mm-30) outliers start: 38 outliers final: 13 residues processed: 194 average time/residue: 0.7101 time to fit residues: 150.3796 Evaluate side-chains 190 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 167 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 287 TRP Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 293 GLN Chi-restraints excluded: chain E residue 374 GLU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 287 TRP Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 287 TRP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 374 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 68 optimal weight: 1.9990 chunk 145 optimal weight: 0.7980 chunk 126 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN A 365 ASN ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 ASN ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 ASN C 159 GLN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.103300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.083107 restraints weight = 20892.986| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 1.84 r_work: 0.2826 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16115 Z= 0.182 Angle : 0.505 5.335 21950 Z= 0.278 Chirality : 0.038 0.153 2375 Planarity : 0.005 0.045 2760 Dihedral : 5.620 81.400 2085 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.95 % Allowed : 10.32 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.18), residues: 1870 helix: 1.35 (0.14), residues: 1265 sheet: None (None), residues: 0 loop : 0.03 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 356 TYR 0.023 0.002 TYR D 97 PHE 0.024 0.002 PHE B 248 TRP 0.013 0.002 TRP E 309 HIS 0.004 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.18 (16115) covalent geometry : angle 0.50547 / 0.28 (21950) hydrogen bonds : bond 0.06159 / 4.04 ( 975) hydrogen bonds : angle 4.52136 / 3.25 ( 2865) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 167 time to evaluate : 0.618 Fit side-chains REVERT: A 25 ARG cc_start: 0.7915 (ttp-170) cc_final: 0.6538 (pmt170) REVERT: A 119 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7420 (tp30) REVERT: A 268 GLU cc_start: 0.7869 (mp0) cc_final: 0.7302 (mp0) REVERT: A 287 TRP cc_start: 0.8594 (OUTLIER) cc_final: 0.8348 (t-100) REVERT: E 25 ARG cc_start: 0.7886 (ttp-170) cc_final: 0.6570 (mpp-170) REVERT: E 119 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7561 (tt0) REVERT: E 268 GLU cc_start: 0.7977 (mp0) cc_final: 0.7678 (mp0) REVERT: E 293 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7207 (tm-30) REVERT: E 325 MET cc_start: 0.9094 (mtp) cc_final: 0.8766 (mtp) REVERT: E 344 GLN cc_start: 0.8565 (mt0) cc_final: 0.8181 (mm110) REVERT: E 374 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6666 (mp0) REVERT: B 57 GLU cc_start: 0.7602 (mp0) cc_final: 0.7187 (pt0) REVERT: B 74 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8208 (pp30) REVERT: B 331 ARG cc_start: 0.8336 (ttp-170) cc_final: 0.7906 (ttp-170) REVERT: B 344 GLN cc_start: 0.8810 (mt0) cc_final: 0.8511 (mt0) REVERT: B 374 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.5982 (mp0) REVERT: D 25 ARG cc_start: 0.7968 (ttp-170) cc_final: 0.7610 (mmm-85) REVERT: D 203 ASP cc_start: 0.8490 (OUTLIER) cc_final: 0.8237 (t70) REVERT: D 287 TRP cc_start: 0.8749 (OUTLIER) cc_final: 0.8547 (t-100) REVERT: D 355 ARG cc_start: 0.7294 (ttp-170) cc_final: 0.6925 (ttm110) REVERT: D 374 GLU cc_start: 0.6868 (mm-30) cc_final: 0.6593 (mm-30) REVERT: C 25 ARG cc_start: 0.8018 (ttp-170) cc_final: 0.6335 (mpp-170) REVERT: C 56 GLU cc_start: 0.7362 (tt0) cc_final: 0.6909 (pm20) REVERT: C 57 GLU cc_start: 0.7347 (mt-10) cc_final: 0.6718 (pt0) REVERT: C 119 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7710 (tt0) REVERT: C 268 GLU cc_start: 0.8032 (mp0) cc_final: 0.7744 (mp0) REVERT: C 287 TRP cc_start: 0.8620 (OUTLIER) cc_final: 0.8102 (t-100) REVERT: C 290 VAL cc_start: 0.8383 (t) cc_final: 0.8128 (m) REVERT: C 344 GLN cc_start: 0.8667 (mt0) cc_final: 0.8079 (mm110) REVERT: C 374 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6620 (mm-30) outliers start: 33 outliers final: 14 residues processed: 185 average time/residue: 0.7208 time to fit residues: 145.7657 Evaluate side-chains 187 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 169 LYS Chi-restraints excluded: chain A residue 287 TRP Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 169 LYS Chi-restraints excluded: chain E residue 293 GLN Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 374 GLU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 287 TRP Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 287 TRP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 374 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 29 optimal weight: 0.1980 chunk 152 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 145 optimal weight: 0.0980 chunk 181 optimal weight: 3.9990 chunk 101 optimal weight: 0.3980 chunk 65 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 134 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 overall best weight: 0.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN A 365 ASN ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 ASN ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 ASN C 159 GLN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.108360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.088239 restraints weight = 20610.728| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.85 r_work: 0.2913 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16115 Z= 0.112 Angle : 0.449 5.505 21950 Z= 0.246 Chirality : 0.035 0.151 2375 Planarity : 0.004 0.047 2760 Dihedral : 5.425 80.114 2085 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.59 % Allowed : 10.86 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.18), residues: 1870 helix: 1.62 (0.14), residues: 1240 sheet: None (None), residues: 0 loop : 0.04 (0.22), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 356 TYR 0.014 0.001 TYR D 97 PHE 0.020 0.001 PHE B 248 TRP 0.013 0.001 TRP E 94 HIS 0.001 0.000 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (16115) covalent geometry : angle 0.44917 / 0.25 (21950) hydrogen bonds : bond 0.05156 / 3.39 ( 975) hydrogen bonds : angle 4.40730 / 3.16 ( 2865) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 185 time to evaluate : 0.536 Fit side-chains REVERT: A 25 ARG cc_start: 0.7893 (ttp-170) cc_final: 0.6529 (pmt170) REVERT: A 119 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7389 (tp30) REVERT: A 268 GLU cc_start: 0.7845 (mp0) cc_final: 0.7370 (mp0) REVERT: E 25 ARG cc_start: 0.7859 (ttp-170) cc_final: 0.6522 (mpp-170) REVERT: E 119 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7503 (tt0) REVERT: E 268 GLU cc_start: 0.7958 (mp0) cc_final: 0.7609 (mp0) REVERT: E 293 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7165 (tm-30) REVERT: E 325 MET cc_start: 0.9078 (mtp) cc_final: 0.8782 (mtp) REVERT: E 344 GLN cc_start: 0.8478 (mt0) cc_final: 0.8112 (mm110) REVERT: E 374 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6676 (mp0) REVERT: B 57 GLU cc_start: 0.7546 (mp0) cc_final: 0.7133 (pt0) REVERT: B 74 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8183 (pp30) REVERT: B 331 ARG cc_start: 0.8364 (ttp-170) cc_final: 0.7797 (ttp-170) REVERT: B 344 GLN cc_start: 0.8796 (mt0) cc_final: 0.8496 (mt0) REVERT: B 374 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.6030 (mp0) REVERT: D 25 ARG cc_start: 0.7910 (ttp-170) cc_final: 0.7567 (mmm-85) REVERT: D 61 MET cc_start: 0.7578 (tpt) cc_final: 0.6950 (ttp) REVERT: D 287 TRP cc_start: 0.8699 (OUTLIER) cc_final: 0.8468 (t-100) REVERT: D 300 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8401 (mt-10) REVERT: D 355 ARG cc_start: 0.7303 (ttp-170) cc_final: 0.6938 (ttm110) REVERT: D 374 GLU cc_start: 0.6828 (mm-30) cc_final: 0.6540 (mm-30) REVERT: C 25 ARG cc_start: 0.7962 (ttp-170) cc_final: 0.6324 (mpp-170) REVERT: C 56 GLU cc_start: 0.7289 (tt0) cc_final: 0.6847 (pm20) REVERT: C 57 GLU cc_start: 0.7266 (mt-10) cc_final: 0.6674 (pt0) REVERT: C 119 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7690 (tt0) REVERT: C 268 GLU cc_start: 0.8070 (mp0) cc_final: 0.7771 (mp0) REVERT: C 290 VAL cc_start: 0.8247 (t) cc_final: 0.7982 (m) REVERT: C 344 GLN cc_start: 0.8591 (mt0) cc_final: 0.8026 (mm110) REVERT: C 374 GLU cc_start: 0.6983 (OUTLIER) cc_final: 0.6595 (mm-30) outliers start: 27 outliers final: 9 residues processed: 200 average time/residue: 0.7276 time to fit residues: 158.8356 Evaluate side-chains 187 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 171 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 293 GLN Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 374 GLU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 287 TRP Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 374 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 180 optimal weight: 0.4980 chunk 120 optimal weight: 3.9990 chunk 143 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN A 365 ASN ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 ASN ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 ASN C 159 GLN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.106389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.086209 restraints weight = 20866.249| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.85 r_work: 0.2888 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16115 Z= 0.133 Angle : 0.463 5.639 21950 Z= 0.254 Chirality : 0.036 0.151 2375 Planarity : 0.004 0.047 2760 Dihedral : 5.417 80.331 2085 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.42 % Allowed : 11.62 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.19), residues: 1870 helix: 1.63 (0.14), residues: 1240 sheet: None (None), residues: 0 loop : 0.08 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 25 TYR 0.014 0.001 TYR E 236 PHE 0.021 0.001 PHE B 248 TRP 0.012 0.001 TRP E 309 HIS 0.003 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (16115) covalent geometry : angle 0.46251 / 0.25 (21950) hydrogen bonds : bond 0.05467 / 3.59 ( 975) hydrogen bonds : angle 4.42004 / 3.17 ( 2865) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 169 time to evaluate : 0.630 Fit side-chains REVERT: A 25 ARG cc_start: 0.7904 (ttp-170) cc_final: 0.6519 (pmt170) REVERT: A 119 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7318 (tp30) REVERT: A 268 GLU cc_start: 0.7854 (mp0) cc_final: 0.7385 (mp0) REVERT: E 25 ARG cc_start: 0.7902 (ttp-170) cc_final: 0.6537 (mpp-170) REVERT: E 119 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7530 (tt0) REVERT: E 268 GLU cc_start: 0.7989 (mp0) cc_final: 0.7719 (mp0) REVERT: E 290 VAL cc_start: 0.8229 (t) cc_final: 0.7910 (m) REVERT: E 325 MET cc_start: 0.9090 (mtp) cc_final: 0.8788 (mtp) REVERT: E 344 GLN cc_start: 0.8507 (mt0) cc_final: 0.8141 (mm110) REVERT: E 374 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6731 (mp0) REVERT: B 57 GLU cc_start: 0.7559 (mp0) cc_final: 0.7142 (pt0) REVERT: B 74 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8176 (pp30) REVERT: B 331 ARG cc_start: 0.8349 (ttp-170) cc_final: 0.7796 (ttp-170) REVERT: B 374 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.6094 (mp0) REVERT: D 25 ARG cc_start: 0.7924 (ttp-170) cc_final: 0.7588 (mmm-85) REVERT: D 61 MET cc_start: 0.7597 (tpt) cc_final: 0.6963 (ttp) REVERT: D 287 TRP cc_start: 0.8722 (OUTLIER) cc_final: 0.8481 (t-100) REVERT: D 355 ARG cc_start: 0.7322 (ttp-170) cc_final: 0.6974 (ttm110) REVERT: D 374 GLU cc_start: 0.6826 (mm-30) cc_final: 0.6530 (mm-30) REVERT: C 25 ARG cc_start: 0.7990 (ttp-170) cc_final: 0.6345 (mpp-170) REVERT: C 56 GLU cc_start: 0.7312 (tt0) cc_final: 0.6852 (pm20) REVERT: C 57 GLU cc_start: 0.7311 (mt-10) cc_final: 0.6710 (pt0) REVERT: C 119 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7697 (tt0) REVERT: C 268 GLU cc_start: 0.8081 (mp0) cc_final: 0.7786 (mp0) REVERT: C 290 VAL cc_start: 0.8292 (t) cc_final: 0.8031 (m) REVERT: C 344 GLN cc_start: 0.8609 (mt0) cc_final: 0.8034 (mm110) REVERT: C 374 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6666 (mm-30) outliers start: 24 outliers final: 10 residues processed: 181 average time/residue: 0.7463 time to fit residues: 147.2759 Evaluate side-chains 183 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 167 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 374 GLU Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 287 TRP Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 374 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 115 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 139 optimal weight: 3.9990 chunk 170 optimal weight: 0.6980 chunk 158 optimal weight: 0.9980 chunk 137 optimal weight: 0.0670 chunk 18 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 119 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 chunk 165 optimal weight: 0.5980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN A 365 ASN ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 ASN ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 ASN C 159 GLN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.108002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.087844 restraints weight = 20735.177| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.85 r_work: 0.2911 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16115 Z= 0.118 Angle : 0.448 5.751 21950 Z= 0.246 Chirality : 0.035 0.152 2375 Planarity : 0.004 0.047 2760 Dihedral : 5.353 80.101 2085 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.30 % Allowed : 11.86 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.19), residues: 1870 helix: 1.82 (0.14), residues: 1210 sheet: None (None), residues: 0 loop : 0.14 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 356 TYR 0.033 0.001 TYR E 97 PHE 0.019 0.001 PHE B 248 TRP 0.012 0.001 TRP A 185 HIS 0.002 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (16115) covalent geometry : angle 0.44794 / 0.25 (21950) hydrogen bonds : bond 0.05182 / 3.41 ( 975) hydrogen bonds : angle 4.37451 / 3.14 ( 2865) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 172 time to evaluate : 0.657 Fit side-chains REVERT: A 25 ARG cc_start: 0.7910 (ttp-170) cc_final: 0.6541 (pmt170) REVERT: A 119 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7333 (tp30) REVERT: A 173 LYS cc_start: 0.7993 (mttm) cc_final: 0.7678 (mttt) REVERT: A 268 GLU cc_start: 0.7879 (mp0) cc_final: 0.7411 (mp0) REVERT: A 331 ARG cc_start: 0.8597 (ttp-170) cc_final: 0.8167 (ptt180) REVERT: E 25 ARG cc_start: 0.7915 (ttp-170) cc_final: 0.6573 (mpp-170) REVERT: E 72 TYR cc_start: 0.8529 (m-80) cc_final: 0.8247 (m-80) REVERT: E 107 MET cc_start: 0.8937 (ptt) cc_final: 0.8591 (ptt) REVERT: E 119 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7549 (tt0) REVERT: E 268 GLU cc_start: 0.8004 (mp0) cc_final: 0.7726 (mp0) REVERT: E 325 MET cc_start: 0.9110 (mtp) cc_final: 0.8814 (mtp) REVERT: E 344 GLN cc_start: 0.8525 (mt0) cc_final: 0.8177 (mm110) REVERT: E 374 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6747 (mp0) REVERT: B 57 GLU cc_start: 0.7567 (mp0) cc_final: 0.7127 (pt0) REVERT: B 74 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.8209 (pp30) REVERT: B 331 ARG cc_start: 0.8388 (ttp-170) cc_final: 0.7836 (ttp-170) REVERT: B 374 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.6133 (mp0) REVERT: D 25 ARG cc_start: 0.7932 (ttp-170) cc_final: 0.7615 (mmm-85) REVERT: D 61 MET cc_start: 0.7656 (tpt) cc_final: 0.7019 (ttp) REVERT: D 268 GLU cc_start: 0.8082 (mp0) cc_final: 0.7620 (mp0) REVERT: D 287 TRP cc_start: 0.8735 (OUTLIER) cc_final: 0.8497 (t-100) REVERT: D 300 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8465 (mt-10) REVERT: D 355 ARG cc_start: 0.7374 (ttp-170) cc_final: 0.7018 (ttm110) REVERT: D 374 GLU cc_start: 0.6837 (mm-30) cc_final: 0.6538 (mm-30) REVERT: C 25 ARG cc_start: 0.7983 (ttp-170) cc_final: 0.6365 (mpp-170) REVERT: C 56 GLU cc_start: 0.7302 (tt0) cc_final: 0.6846 (pm20) REVERT: C 119 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7736 (tt0) REVERT: C 268 GLU cc_start: 0.8103 (mp0) cc_final: 0.7719 (mp0) REVERT: C 290 VAL cc_start: 0.8291 (t) cc_final: 0.8029 (m) REVERT: C 344 GLN cc_start: 0.8600 (mt0) cc_final: 0.8042 (mm110) REVERT: C 374 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6649 (mm-30) outliers start: 22 outliers final: 10 residues processed: 183 average time/residue: 0.6927 time to fit residues: 138.3667 Evaluate side-chains 181 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 374 GLU Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 287 TRP Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 374 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 30 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 54 optimal weight: 0.3980 chunk 154 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 146 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 339 ASN ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 ASN C 159 GLN ** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.107074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.086959 restraints weight = 20784.174| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.84 r_work: 0.2897 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16115 Z= 0.128 Angle : 0.457 5.590 21950 Z= 0.251 Chirality : 0.036 0.150 2375 Planarity : 0.004 0.047 2760 Dihedral : 5.357 80.180 2085 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.42 % Allowed : 11.68 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.19), residues: 1870 helix: 1.70 (0.14), residues: 1240 sheet: None (None), residues: 0 loop : 0.11 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 356 TYR 0.032 0.001 TYR E 97 PHE 0.019 0.001 PHE B 248 TRP 0.012 0.001 TRP A 185 HIS 0.002 0.001 HIS A 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (16115) covalent geometry : angle 0.45744 / 0.25 (21950) hydrogen bonds : bond 0.05358 / 3.52 ( 975) hydrogen bonds : angle 4.38491 / 3.15 ( 2865) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4829.74 seconds wall clock time: 83 minutes 23.21 seconds (5003.21 seconds total)