Starting phenix.real_space_refine on Sat May 17 10:07:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dyl_47308/05_2025/9dyl_47308.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dyl_47308/05_2025/9dyl_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9dyl_47308/05_2025/9dyl_47308.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dyl_47308/05_2025/9dyl_47308.map" model { file = "/net/cci-nas-00/data/ceres_data/9dyl_47308/05_2025/9dyl_47308.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dyl_47308/05_2025/9dyl_47308.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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, 11 Unusual residues: {' CA': 1, 'PAB': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 11 Unusual residues: {' CA': 1, 'PAB': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 11 Unusual residues: {' CA': 1, 'PAB': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 11 Unusual residues: {' CA': 1, 'PAB': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 11 Unusual residues: {' CA': 1, 'PAB': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.94, per 1000 atoms: 0.57 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: 4.04 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.38 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: 4.25 Time building geometry restraints manager: 4.65 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } 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: 4.840 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: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 33.850 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.060 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:11.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.041 0.011 TRP D 185 HIS 0.011 0.005 HIS B 178 PHE 0.046 0.007 PHE E 276 TYR 0.043 0.008 TYR A 97 ARG 0.020 0.002 ARG E 218 Details of bonding type rmsd hydrogen bonds : bond 0.10361 ( 975) hydrogen bonds : angle 4.73803 ( 2865) covalent geometry : bond 0.01306 (16115) covalent geometry : angle 1.24893 (21950) *********************** 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 : 1.935 Fit side-chains revert: symmetry clash REVERT: A 25 ARG cc_start: 0.8408 (ttp-170) cc_final: 0.7225 (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: 1.6861 time to fit residues: 390.0309 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 : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.9990 chunk 140 optimal weight: 0.3980 chunk 77 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 74 optimal weight: 0.4980 chunk 145 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 168 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 96 GLN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.105838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.085681 restraints weight = 20589.383| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.85 r_work: 0.2861 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16115 Z= 0.134 Angle : 0.515 4.982 21950 Z= 0.282 Chirality : 0.037 0.151 2375 Planarity : 0.004 0.031 2760 Dihedral : 5.872 80.753 2085 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.12 % Allowed : 6.14 % Favored : 92.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.18), residues: 1870 helix: 1.42 (0.14), residues: 1260 sheet: None (None), residues: 0 loop : 0.12 (0.23), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 309 HIS 0.002 0.001 HIS E 326 PHE 0.028 0.002 PHE A 248 TYR 0.020 0.002 TYR D 97 ARG 0.003 0.001 ARG C 126 Details of bonding type rmsd hydrogen bonds : bond 0.05887 ( 975) hydrogen bonds : angle 4.60266 ( 2865) covalent geometry : bond 0.00278 (16115) covalent geometry : angle 0.51528 (21950) *********************** 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 207 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 188 time to evaluate : 1.610 Fit side-chains REVERT: A 25 ARG cc_start: 0.7908 (ttp-170) cc_final: 0.6642 (pmt170) REVERT: A 119 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7418 (tp30) REVERT: A 268 GLU cc_start: 0.7822 (mp0) cc_final: 0.7234 (mp0) REVERT: E 25 ARG cc_start: 0.7849 (ttp-170) cc_final: 0.6646 (mpp-170) REVERT: E 119 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7561 (tt0) REVERT: E 268 GLU cc_start: 0.7791 (mp0) cc_final: 0.7515 (mp0) REVERT: E 290 VAL cc_start: 0.8134 (t) cc_final: 0.7767 (m) REVERT: E 293 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7192 (tm-30) REVERT: E 325 MET cc_start: 0.9131 (mtp) cc_final: 0.8717 (mtp) REVERT: E 340 LYS cc_start: 0.6515 (mmtm) cc_final: 0.5485 (mtmt) REVERT: B 56 GLU cc_start: 0.7458 (tt0) cc_final: 0.7045 (tp30) REVERT: B 57 GLU cc_start: 0.7427 (mp0) cc_final: 0.6996 (pt0) REVERT: B 74 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.8104 (pp30) REVERT: B 374 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6145 (mp0) REVERT: D 25 ARG cc_start: 0.7894 (ttp-170) cc_final: 0.6786 (pmt170) REVERT: D 119 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7731 (tt0) REVERT: D 355 ARG cc_start: 0.7279 (ttp-170) cc_final: 0.6861 (ttm110) REVERT: C 25 ARG cc_start: 0.7853 (ttp-170) cc_final: 0.6376 (mpp-170) REVERT: C 56 GLU cc_start: 0.7363 (tt0) cc_final: 0.7155 (mm-30) REVERT: C 119 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7693 (tt0) REVERT: C 159 GLN cc_start: 0.7134 (mt0) cc_final: 0.6800 (mp10) REVERT: C 290 VAL cc_start: 0.8365 (t) cc_final: 0.8064 (m) REVERT: C 344 GLN cc_start: 0.8657 (mt0) cc_final: 0.8031 (mm110) outliers start: 19 outliers final: 6 residues processed: 198 average time/residue: 1.5371 time to fit residues: 331.0933 Evaluate side-chains 172 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 162 time to evaluate : 1.781 ------------------------------------------------------------------------------- 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 155 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 110 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 176 optimal weight: 0.6980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.100849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.080533 restraints weight = 20899.456| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 1.85 r_work: 0.2794 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 16115 Z= 0.237 Angle : 0.573 9.559 21950 Z= 0.313 Chirality : 0.041 0.154 2375 Planarity : 0.005 0.056 2760 Dihedral : 5.837 81.648 2085 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.01 % Allowed : 7.49 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.18), residues: 1870 helix: 1.24 (0.14), residues: 1260 sheet: None (None), residues: 0 loop : 0.16 (0.23), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 309 HIS 0.006 0.002 HIS A 168 PHE 0.028 0.002 PHE A 248 TYR 0.026 0.002 TYR D 97 ARG 0.004 0.001 ARG C 51 Details of bonding type rmsd hydrogen bonds : bond 0.06875 ( 975) hydrogen bonds : angle 4.64502 ( 2865) covalent geometry : bond 0.00566 (16115) covalent geometry : angle 0.57329 (21950) *********************** 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 194 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 160 time to evaluate : 1.678 Fit side-chains REVERT: A 25 ARG cc_start: 0.7932 (ttp-170) cc_final: 0.6622 (pmt170) REVERT: A 119 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7443 (tp30) REVERT: A 268 GLU cc_start: 0.7793 (mp0) cc_final: 0.7293 (mp0) REVERT: E 25 ARG cc_start: 0.7850 (ttp-170) cc_final: 0.6567 (mpp-170) REVERT: E 119 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7636 (tt0) REVERT: E 268 GLU cc_start: 0.7873 (mp0) cc_final: 0.7517 (mp0) REVERT: E 293 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7446 (tm-30) REVERT: E 325 MET cc_start: 0.9119 (mtp) cc_final: 0.8717 (mtp) REVERT: E 340 LYS cc_start: 0.6705 (mmtm) cc_final: 0.5597 (mtmt) REVERT: E 344 GLN cc_start: 0.8614 (mt0) cc_final: 0.8196 (mm110) REVERT: E 374 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6647 (mm-30) REVERT: B 56 GLU cc_start: 0.7569 (tt0) cc_final: 0.7153 (tp30) REVERT: B 57 GLU cc_start: 0.7573 (mp0) cc_final: 0.7210 (pt0) REVERT: B 74 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8211 (pp30) REVERT: B 331 ARG cc_start: 0.8394 (ttp-170) cc_final: 0.7888 (ttp-170) REVERT: B 344 GLN cc_start: 0.8802 (mt0) cc_final: 0.8483 (mt0) REVERT: B 374 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6157 (mp0) REVERT: D 25 ARG cc_start: 0.7993 (ttp-170) cc_final: 0.7652 (mmm-85) REVERT: D 119 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7689 (tt0) REVERT: D 355 ARG cc_start: 0.7341 (ttp-170) cc_final: 0.6875 (ttm110) REVERT: D 374 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6841 (mm-30) REVERT: C 25 ARG cc_start: 0.8029 (ttp-170) cc_final: 0.6383 (mpp-170) REVERT: C 56 GLU cc_start: 0.7498 (tt0) cc_final: 0.7022 (pm20) REVERT: C 57 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.6441 (pp20) REVERT: C 119 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7696 (tt0) REVERT: C 290 VAL cc_start: 0.8418 (t) cc_final: 0.8140 (m) REVERT: C 344 GLN cc_start: 0.8674 (mt0) cc_final: 0.7984 (mm110) REVERT: C 374 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6444 (mp0) outliers start: 34 outliers final: 9 residues processed: 182 average time/residue: 1.6384 time to fit residues: 323.2794 Evaluate side-chains 167 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 1.805 ------------------------------------------------------------------------------- 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 333 GLU Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain C residue 57 GLU 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 51 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 178 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 151 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN E 96 GLN ** 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 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 = 0.3231 r_free = 0.3231 target = 0.104911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.084889 restraints weight = 20714.567| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 1.83 r_work: 0.2863 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16115 Z= 0.136 Angle : 0.483 7.988 21950 Z= 0.264 Chirality : 0.037 0.154 2375 Planarity : 0.004 0.040 2760 Dihedral : 5.640 80.935 2085 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.01 % Allowed : 8.73 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.18), residues: 1870 helix: 1.39 (0.14), residues: 1265 sheet: None (None), residues: 0 loop : 0.09 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 309 HIS 0.002 0.001 HIS A 168 PHE 0.024 0.001 PHE B 248 TYR 0.020 0.001 TYR D 97 ARG 0.004 0.000 ARG B 51 Details of bonding type rmsd hydrogen bonds : bond 0.05682 ( 975) hydrogen bonds : angle 4.51266 ( 2865) covalent geometry : bond 0.00296 (16115) covalent geometry : angle 0.48332 (21950) *********************** 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 203 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 169 time to evaluate : 1.832 Fit side-chains REVERT: A 25 ARG cc_start: 0.7932 (ttp-170) cc_final: 0.6656 (pmt170) REVERT: A 119 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7510 (tp30) REVERT: A 268 GLU cc_start: 0.7823 (mp0) cc_final: 0.7351 (mp0) REVERT: E 25 ARG cc_start: 0.7870 (ttp-170) cc_final: 0.6591 (mpp-170) REVERT: E 119 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7634 (tt0) REVERT: E 173 LYS cc_start: 0.7881 (mttp) cc_final: 0.7573 (mttm) REVERT: E 268 GLU cc_start: 0.7955 (mp0) cc_final: 0.7625 (mp0) REVERT: E 325 MET cc_start: 0.9105 (mtp) cc_final: 0.8767 (mtp) REVERT: E 340 LYS cc_start: 0.6683 (mmtm) cc_final: 0.5570 (mtmt) REVERT: E 344 GLN cc_start: 0.8528 (mt0) cc_final: 0.8198 (mm110) REVERT: B 56 GLU cc_start: 0.7539 (tt0) cc_final: 0.7175 (tp30) REVERT: B 57 GLU cc_start: 0.7534 (mp0) cc_final: 0.7160 (pt0) REVERT: B 74 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8155 (pp30) REVERT: B 331 ARG cc_start: 0.8423 (ttp-170) cc_final: 0.8084 (tmm160) REVERT: B 344 GLN cc_start: 0.8772 (mt0) cc_final: 0.8463 (mt0) REVERT: B 374 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6149 (mp0) REVERT: D 25 ARG cc_start: 0.7928 (ttp-170) cc_final: 0.7591 (mmm-85) REVERT: D 119 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7686 (tt0) REVERT: D 355 ARG cc_start: 0.7339 (ttp-170) cc_final: 0.6988 (ttm110) REVERT: D 374 GLU cc_start: 0.6876 (mm-30) cc_final: 0.6638 (mm-30) REVERT: C 25 ARG cc_start: 0.7975 (ttp-170) cc_final: 0.6371 (mpp-170) REVERT: C 56 GLU cc_start: 0.7371 (tt0) cc_final: 0.6915 (pm20) REVERT: C 57 GLU cc_start: 0.6803 (pt0) cc_final: 0.6438 (pp20) REVERT: C 119 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7692 (tt0) REVERT: C 287 TRP cc_start: 0.8615 (OUTLIER) cc_final: 0.8003 (t-100) REVERT: C 290 VAL cc_start: 0.8388 (t) cc_final: 0.8135 (m) REVERT: C 344 GLN cc_start: 0.8679 (mt0) cc_final: 0.8052 (mm110) REVERT: C 374 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6761 (mm-30) outliers start: 34 outliers final: 12 residues processed: 189 average time/residue: 1.5653 time to fit residues: 322.4898 Evaluate side-chains 179 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 1.651 ------------------------------------------------------------------------------- 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 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 169 LYS Chi-restraints excluded: chain B residue 333 GLU 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 129 ILE Chi-restraints excluded: chain C residue 169 LYS 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 165 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 89 optimal weight: 0.2980 chunk 159 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 171 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3213 r_free = 0.3213 target = 0.103678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.083412 restraints weight = 20855.909| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.85 r_work: 0.2845 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16115 Z= 0.159 Angle : 0.494 7.318 21950 Z= 0.271 Chirality : 0.038 0.152 2375 Planarity : 0.004 0.044 2760 Dihedral : 5.620 80.940 2085 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.48 % Allowed : 8.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.18), residues: 1870 helix: 1.42 (0.14), residues: 1265 sheet: None (None), residues: 0 loop : 0.05 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 309 HIS 0.004 0.001 HIS A 168 PHE 0.023 0.002 PHE B 248 TYR 0.022 0.002 TYR D 97 ARG 0.003 0.000 ARG B 25 Details of bonding type rmsd hydrogen bonds : bond 0.05940 ( 975) hydrogen bonds : angle 4.51032 ( 2865) covalent geometry : bond 0.00362 (16115) covalent geometry : angle 0.49418 (21950) *********************** 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 205 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 163 time to evaluate : 1.841 Fit side-chains REVERT: A 25 ARG cc_start: 0.7910 (ttp-170) cc_final: 0.6607 (pmt170) REVERT: A 119 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7453 (tp30) REVERT: A 268 GLU cc_start: 0.7879 (mp0) cc_final: 0.7400 (mp0) REVERT: A 287 TRP cc_start: 0.8608 (OUTLIER) cc_final: 0.8283 (m-90) REVERT: E 25 ARG cc_start: 0.7894 (ttp-170) cc_final: 0.6574 (mpp-170) REVERT: E 119 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7619 (tt0) REVERT: E 268 GLU cc_start: 0.7931 (mp0) cc_final: 0.7627 (mp0) REVERT: E 293 GLN cc_start: 0.8032 (OUTLIER) cc_final: 0.7377 (tm-30) REVERT: E 325 MET cc_start: 0.9117 (mtp) cc_final: 0.8806 (mtp) REVERT: E 340 LYS cc_start: 0.6643 (mmtm) cc_final: 0.5529 (mtmt) REVERT: E 344 GLN cc_start: 0.8567 (mt0) cc_final: 0.8204 (mm110) REVERT: B 56 GLU cc_start: 0.7561 (tt0) cc_final: 0.7196 (tp30) REVERT: B 57 GLU cc_start: 0.7582 (mp0) cc_final: 0.7157 (pt0) REVERT: B 74 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.8167 (pp30) REVERT: B 331 ARG cc_start: 0.8454 (ttp-170) cc_final: 0.8109 (tmm160) REVERT: B 344 GLN cc_start: 0.8777 (mt0) cc_final: 0.8462 (mt0) REVERT: B 374 GLU cc_start: 0.7015 (OUTLIER) cc_final: 0.6109 (mp0) REVERT: D 25 ARG cc_start: 0.7917 (ttp-170) cc_final: 0.7560 (mmm-85) REVERT: D 119 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7700 (tt0) REVERT: D 355 ARG cc_start: 0.7303 (ttp-170) cc_final: 0.6953 (ttm110) REVERT: D 374 GLU cc_start: 0.6888 (mm-30) cc_final: 0.6673 (mm-30) REVERT: C 25 ARG cc_start: 0.8025 (ttp-170) cc_final: 0.6374 (mpp-170) REVERT: C 56 GLU cc_start: 0.7411 (tt0) cc_final: 0.6941 (pm20) REVERT: C 57 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6445 (pp20) REVERT: C 119 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7704 (tt0) REVERT: C 287 TRP cc_start: 0.8628 (OUTLIER) cc_final: 0.8112 (t-100) REVERT: C 290 VAL cc_start: 0.8403 (t) cc_final: 0.8155 (m) REVERT: C 344 GLN cc_start: 0.8680 (mt0) cc_final: 0.8034 (mm110) REVERT: C 374 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6661 (mm-30) outliers start: 42 outliers final: 17 residues processed: 189 average time/residue: 1.5277 time to fit residues: 314.2852 Evaluate side-chains 186 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 1.656 ------------------------------------------------------------------------------- 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 287 TRP Chi-restraints excluded: chain E residue 293 GLN Chi-restraints excluded: chain E residue 307 THR 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 333 GLU 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 57 GLU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 169 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 112 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 135 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3222 r_free = 0.3222 target = 0.104416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.084124 restraints weight = 20856.778| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.85 r_work: 0.2855 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1742 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= 0.148 Angle : 0.484 6.755 21950 Z= 0.265 Chirality : 0.037 0.151 2375 Planarity : 0.004 0.046 2760 Dihedral : 5.564 80.854 2085 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.36 % Allowed : 9.50 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.18), residues: 1870 helix: 1.46 (0.14), residues: 1265 sheet: None (None), residues: 0 loop : 0.02 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 309 HIS 0.003 0.001 HIS A 168 PHE 0.023 0.001 PHE B 248 TYR 0.021 0.001 TYR D 97 ARG 0.003 0.000 ARG B 25 Details of bonding type rmsd hydrogen bonds : bond 0.05768 ( 975) hydrogen bonds : angle 4.48656 ( 2865) covalent geometry : bond 0.00333 (16115) covalent geometry : angle 0.48366 (21950) *********************** 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 202 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 162 time to evaluate : 1.801 Fit side-chains REVERT: A 25 ARG cc_start: 0.7912 (ttp-170) cc_final: 0.6559 (pmt170) REVERT: A 119 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7455 (tp30) REVERT: A 268 GLU cc_start: 0.7847 (mp0) cc_final: 0.7281 (mp0) REVERT: A 287 TRP cc_start: 0.8604 (OUTLIER) cc_final: 0.8279 (m-90) REVERT: E 25 ARG cc_start: 0.7909 (ttp-170) cc_final: 0.6600 (mpp-170) REVERT: E 119 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7613 (tt0) REVERT: E 268 GLU cc_start: 0.7952 (mp0) cc_final: 0.7646 (mp0) REVERT: E 325 MET cc_start: 0.9102 (mtp) cc_final: 0.8800 (mtp) REVERT: E 344 GLN cc_start: 0.8553 (mt0) cc_final: 0.8203 (mm110) REVERT: E 374 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6653 (mp0) REVERT: B 56 GLU cc_start: 0.7534 (tt0) cc_final: 0.7213 (tp30) REVERT: B 57 GLU cc_start: 0.7581 (mp0) cc_final: 0.7149 (pt0) REVERT: B 74 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8173 (pp30) REVERT: B 331 ARG cc_start: 0.8421 (ttp-170) cc_final: 0.8078 (tmm160) REVERT: B 344 GLN cc_start: 0.8784 (mt0) cc_final: 0.8478 (mt0) REVERT: B 374 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6015 (mp0) REVERT: D 25 ARG cc_start: 0.7924 (ttp-170) cc_final: 0.7568 (mmm-85) REVERT: D 119 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7692 (tt0) REVERT: D 287 TRP cc_start: 0.8758 (OUTLIER) cc_final: 0.8492 (t-100) REVERT: D 355 ARG cc_start: 0.7315 (ttp-170) cc_final: 0.6962 (ttm110) REVERT: D 374 GLU cc_start: 0.6888 (mm-30) cc_final: 0.6618 (mm-30) REVERT: C 25 ARG cc_start: 0.8021 (ttp-170) cc_final: 0.6370 (mpp-170) REVERT: C 56 GLU cc_start: 0.7398 (tt0) cc_final: 0.6922 (pm20) REVERT: C 57 GLU cc_start: 0.6808 (pt0) cc_final: 0.6426 (pp20) REVERT: C 119 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7705 (tt0) REVERT: C 287 TRP cc_start: 0.8615 (OUTLIER) cc_final: 0.8077 (t-100) REVERT: C 290 VAL cc_start: 0.8390 (t) cc_final: 0.8139 (m) REVERT: C 344 GLN cc_start: 0.8664 (mt0) cc_final: 0.8013 (mm110) REVERT: C 374 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6665 (mm-30) outliers start: 40 outliers final: 16 residues processed: 185 average time/residue: 1.5256 time to fit residues: 308.1465 Evaluate side-chains 182 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 1.887 ------------------------------------------------------------------------------- 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 169 LYS Chi-restraints excluded: chain E residue 287 TRP 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 169 LYS Chi-restraints excluded: chain B residue 333 GLU 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 287 TRP Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 169 LYS 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 90 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 171 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 chunk 71 optimal weight: 0.0270 chunk 82 optimal weight: 3.9990 overall best weight: 0.9842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3226 r_free = 0.3226 target = 0.104687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.084579 restraints weight = 20877.291| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.83 r_work: 0.2850 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1783 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= 0.143 Angle : 0.478 6.309 21950 Z= 0.262 Chirality : 0.037 0.151 2375 Planarity : 0.004 0.047 2760 Dihedral : 5.537 80.872 2085 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.30 % Allowed : 9.91 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.18), residues: 1870 helix: 1.57 (0.14), residues: 1240 sheet: None (None), residues: 0 loop : 0.02 (0.22), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 309 HIS 0.003 0.001 HIS A 168 PHE 0.022 0.001 PHE B 248 TYR 0.020 0.001 TYR D 97 ARG 0.002 0.000 ARG B 130 Details of bonding type rmsd hydrogen bonds : bond 0.05695 ( 975) hydrogen bonds : angle 4.46741 ( 2865) covalent geometry : bond 0.00319 (16115) covalent geometry : angle 0.47771 (21950) *********************** 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 214 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 175 time to evaluate : 1.659 Fit side-chains REVERT: A 25 ARG cc_start: 0.7908 (ttp-170) cc_final: 0.6570 (pmt170) REVERT: A 119 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7419 (tp30) REVERT: A 268 GLU cc_start: 0.7855 (mp0) cc_final: 0.7285 (mp0) REVERT: A 287 TRP cc_start: 0.8602 (OUTLIER) cc_final: 0.8370 (t-100) REVERT: E 25 ARG cc_start: 0.7892 (ttp-170) cc_final: 0.6590 (mpp-170) REVERT: E 119 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7572 (tt0) REVERT: E 268 GLU cc_start: 0.7966 (mp0) cc_final: 0.7670 (mp0) REVERT: E 293 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7418 (tt0) REVERT: E 325 MET cc_start: 0.9097 (mtp) cc_final: 0.8809 (mtp) REVERT: E 344 GLN cc_start: 0.8545 (mt0) cc_final: 0.8199 (mm110) REVERT: E 374 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6710 (mp0) REVERT: B 56 GLU cc_start: 0.7492 (tt0) cc_final: 0.7177 (tp30) REVERT: B 57 GLU cc_start: 0.7584 (mp0) cc_final: 0.7141 (pt0) REVERT: B 74 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8147 (pp30) REVERT: B 331 ARG cc_start: 0.8458 (ttp-170) cc_final: 0.8113 (tmm160) REVERT: B 344 GLN cc_start: 0.8808 (mt0) cc_final: 0.8519 (mt0) REVERT: B 374 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.5999 (mp0) REVERT: D 25 ARG cc_start: 0.7932 (ttp-170) cc_final: 0.7571 (mmm-85) REVERT: D 61 MET cc_start: 0.7636 (tpt) cc_final: 0.6986 (ttp) REVERT: D 119 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7682 (tt0) REVERT: D 355 ARG cc_start: 0.7341 (ttp-170) cc_final: 0.7004 (ttm110) REVERT: D 374 GLU cc_start: 0.6852 (mm-30) cc_final: 0.6569 (mm-30) REVERT: C 25 ARG cc_start: 0.8020 (ttp-170) cc_final: 0.6344 (mpp-170) REVERT: C 56 GLU cc_start: 0.7380 (tt0) cc_final: 0.6911 (pm20) REVERT: C 57 GLU cc_start: 0.6797 (OUTLIER) cc_final: 0.6437 (pp20) REVERT: C 119 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7694 (tt0) REVERT: C 287 TRP cc_start: 0.8596 (OUTLIER) cc_final: 0.8076 (t-100) REVERT: C 290 VAL cc_start: 0.8350 (t) cc_final: 0.8085 (m) REVERT: C 344 GLN cc_start: 0.8614 (mt0) cc_final: 0.7982 (mm110) REVERT: C 374 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6667 (mm-30) outliers start: 39 outliers final: 18 residues processed: 196 average time/residue: 1.5240 time to fit residues: 325.9016 Evaluate side-chains 195 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 1.778 ------------------------------------------------------------------------------- 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 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 287 TRP 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 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 333 GLU 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 C residue 57 GLU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 169 LYS 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 23 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 159 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 158 optimal weight: 0.5980 chunk 80 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3240 r_free = 0.3240 target = 0.105403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.085066 restraints weight = 20574.202| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.86 r_work: 0.2861 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1842 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= 0.142 Angle : 0.474 5.361 21950 Z= 0.260 Chirality : 0.037 0.151 2375 Planarity : 0.004 0.048 2760 Dihedral : 5.511 80.917 2085 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.30 % Allowed : 9.91 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.18), residues: 1870 helix: 1.59 (0.14), residues: 1240 sheet: None (None), residues: 0 loop : 0.04 (0.22), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 309 HIS 0.003 0.001 HIS A 168 PHE 0.022 0.001 PHE B 248 TYR 0.020 0.001 TYR D 97 ARG 0.005 0.000 ARG B 356 Details of bonding type rmsd hydrogen bonds : bond 0.05649 ( 975) hydrogen bonds : angle 4.44959 ( 2865) covalent geometry : bond 0.00317 (16115) covalent geometry : angle 0.47353 (21950) *********************** 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 208 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 169 time to evaluate : 1.786 Fit side-chains REVERT: A 25 ARG cc_start: 0.7925 (ttp-170) cc_final: 0.6566 (pmt170) REVERT: A 119 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7429 (tp30) REVERT: A 268 GLU cc_start: 0.7847 (mp0) cc_final: 0.7285 (mp0) REVERT: A 287 TRP cc_start: 0.8597 (OUTLIER) cc_final: 0.8370 (t-100) REVERT: E 25 ARG cc_start: 0.7906 (ttp-170) cc_final: 0.6605 (mpp-170) REVERT: E 119 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7578 (tt0) REVERT: E 268 GLU cc_start: 0.7994 (mp0) cc_final: 0.7729 (mp0) REVERT: E 293 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7434 (tt0) REVERT: E 325 MET cc_start: 0.9093 (mtp) cc_final: 0.8807 (mtp) REVERT: E 344 GLN cc_start: 0.8539 (mt0) cc_final: 0.8204 (mm110) REVERT: E 374 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6725 (mp0) REVERT: B 56 GLU cc_start: 0.7442 (tt0) cc_final: 0.7162 (tp30) REVERT: B 57 GLU cc_start: 0.7606 (mp0) cc_final: 0.7147 (pt0) REVERT: B 74 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.8175 (pp30) REVERT: B 331 ARG cc_start: 0.8479 (ttp-170) cc_final: 0.8137 (tmm160) REVERT: B 344 GLN cc_start: 0.8832 (mt0) cc_final: 0.8536 (mt0) REVERT: B 374 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.6090 (mp0) REVERT: D 25 ARG cc_start: 0.7934 (ttp-170) cc_final: 0.7591 (mmm-85) REVERT: D 61 MET cc_start: 0.7632 (tpt) cc_final: 0.6986 (ttp) REVERT: D 355 ARG cc_start: 0.7360 (ttp-170) cc_final: 0.7020 (ttm110) REVERT: D 374 GLU cc_start: 0.6860 (mm-30) cc_final: 0.6572 (mm-30) REVERT: C 25 ARG cc_start: 0.8007 (ttp-170) cc_final: 0.6348 (mpp-170) REVERT: C 56 GLU cc_start: 0.7376 (tt0) cc_final: 0.6908 (pm20) REVERT: C 57 GLU cc_start: 0.6796 (OUTLIER) cc_final: 0.6430 (pp20) REVERT: C 119 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7719 (tt0) REVERT: C 287 TRP cc_start: 0.8609 (OUTLIER) cc_final: 0.8084 (t-100) REVERT: C 290 VAL cc_start: 0.8340 (t) cc_final: 0.8090 (m) REVERT: C 344 GLN cc_start: 0.8617 (mt0) cc_final: 0.7999 (mm110) REVERT: C 374 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6669 (mm-30) outliers start: 39 outliers final: 19 residues processed: 189 average time/residue: 1.4751 time to fit residues: 305.3047 Evaluate side-chains 194 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 1.634 ------------------------------------------------------------------------------- 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 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 287 TRP 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 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 333 GLU 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 C residue 49 ILE Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 169 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 92 optimal weight: 0.0980 chunk 54 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 147 optimal weight: 6.9990 chunk 37 optimal weight: 0.0270 chunk 170 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3280 r_free = 0.3280 target = 0.108591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.088584 restraints weight = 20606.878| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.83 r_work: 0.2923 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16115 Z= 0.109 Angle : 0.441 5.779 21950 Z= 0.241 Chirality : 0.035 0.154 2375 Planarity : 0.004 0.048 2760 Dihedral : 5.366 80.336 2085 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.89 % Allowed : 10.44 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.18), residues: 1870 helix: 1.86 (0.14), residues: 1210 sheet: None (None), residues: 0 loop : 0.09 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 94 HIS 0.001 0.000 HIS B 168 PHE 0.018 0.001 PHE B 248 TYR 0.016 0.001 TYR B 236 ARG 0.004 0.000 ARG B 356 Details of bonding type rmsd hydrogen bonds : bond 0.04961 ( 975) hydrogen bonds : angle 4.35490 ( 2865) covalent geometry : bond 0.00223 (16115) covalent geometry : angle 0.44110 (21950) *********************** 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 219 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 187 time to evaluate : 1.662 Fit side-chains REVERT: A 25 ARG cc_start: 0.7940 (ttp-170) cc_final: 0.6641 (mpp-170) REVERT: A 119 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7352 (tp30) REVERT: A 268 GLU cc_start: 0.7856 (mp0) cc_final: 0.7386 (mp0) REVERT: A 331 ARG cc_start: 0.8576 (ttp-170) cc_final: 0.8144 (ptt180) REVERT: E 25 ARG cc_start: 0.7882 (ttp-170) cc_final: 0.6613 (mpp-170) REVERT: E 119 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7564 (tt0) REVERT: E 268 GLU cc_start: 0.7983 (mp0) cc_final: 0.7676 (mp0) REVERT: E 325 MET cc_start: 0.9086 (mtp) cc_final: 0.8665 (mtp) REVERT: E 344 GLN cc_start: 0.8441 (mt0) cc_final: 0.8135 (mm110) REVERT: E 374 GLU cc_start: 0.7123 (OUTLIER) cc_final: 0.6735 (mp0) REVERT: B 56 GLU cc_start: 0.7437 (tt0) cc_final: 0.7207 (tp30) REVERT: B 57 GLU cc_start: 0.7556 (mp0) cc_final: 0.7116 (pt0) REVERT: B 74 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8190 (pp30) REVERT: B 331 ARG cc_start: 0.8459 (ttp-170) cc_final: 0.8114 (tmm160) REVERT: B 344 GLN cc_start: 0.8794 (mt0) cc_final: 0.8493 (mt0) REVERT: B 374 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6072 (mp0) REVERT: D 25 ARG cc_start: 0.7946 (ttp-170) cc_final: 0.7606 (mmm-85) REVERT: D 61 MET cc_start: 0.7589 (tpt) cc_final: 0.6982 (ttp) REVERT: D 355 ARG cc_start: 0.7397 (ttp-170) cc_final: 0.7055 (ttm110) REVERT: D 374 GLU cc_start: 0.6828 (mm-30) cc_final: 0.6528 (mm-30) REVERT: C 19 ARG cc_start: 0.8005 (mtt90) cc_final: 0.7308 (mtt90) REVERT: C 25 ARG cc_start: 0.8004 (ttp-170) cc_final: 0.6376 (mpp-170) REVERT: C 56 GLU cc_start: 0.7256 (tt0) cc_final: 0.6794 (pm20) REVERT: C 57 GLU cc_start: 0.6782 (pt0) cc_final: 0.6489 (pp20) REVERT: C 119 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7711 (tt0) REVERT: C 290 VAL cc_start: 0.8310 (t) cc_final: 0.8040 (m) REVERT: C 344 GLN cc_start: 0.8566 (mt0) cc_final: 0.7983 (mm110) REVERT: C 374 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6689 (mm-30) outliers start: 32 outliers final: 10 residues processed: 204 average time/residue: 1.5253 time to fit residues: 339.1028 Evaluate side-chains 185 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 170 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 374 GLU 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 333 GLU Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain D residue 52 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 141 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 110 optimal weight: 7.9990 chunk 18 optimal weight: 0.7980 chunk 178 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 184 optimal weight: 8.9990 chunk 171 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3217 r_free = 0.3217 target = 0.104161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.083994 restraints weight = 20939.051| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.85 r_work: 0.2842 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1894 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= 0.167 Angle : 0.495 5.423 21950 Z= 0.272 Chirality : 0.038 0.151 2375 Planarity : 0.005 0.048 2760 Dihedral : 5.462 80.535 2085 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 1.65 % Allowed : 11.21 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.18), 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 TRP 0.014 0.002 TRP D 287 HIS 0.004 0.001 HIS A 168 PHE 0.022 0.001 PHE B 248 TYR 0.039 0.002 TYR E 97 ARG 0.006 0.000 ARG D 356 Details of bonding type rmsd hydrogen bonds : bond 0.05904 ( 975) hydrogen bonds : angle 4.46146 ( 2865) covalent geometry : bond 0.00386 (16115) covalent geometry : angle 0.49546 (21950) ********************** 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 199 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 1.772 Fit side-chains REVERT: A 25 ARG cc_start: 0.7923 (ttp-170) cc_final: 0.6556 (pmt170) REVERT: A 119 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7396 (tp30) REVERT: A 268 GLU cc_start: 0.7839 (mp0) cc_final: 0.7363 (mp0) REVERT: A 331 ARG cc_start: 0.8606 (ttp-170) cc_final: 0.8165 (ptt180) REVERT: E 25 ARG cc_start: 0.7906 (ttp-170) cc_final: 0.6501 (mpp-170) REVERT: E 119 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7577 (tt0) REVERT: E 268 GLU cc_start: 0.7975 (mp0) cc_final: 0.7705 (mp0) REVERT: E 325 MET cc_start: 0.9083 (mtp) cc_final: 0.8790 (mtp) REVERT: E 344 GLN cc_start: 0.8520 (mt0) cc_final: 0.8178 (mm110) REVERT: E 374 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6731 (mp0) REVERT: B 57 GLU cc_start: 0.7608 (mp0) cc_final: 0.7153 (pt0) REVERT: B 74 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8213 (pp30) REVERT: B 331 ARG cc_start: 0.8489 (ttp-170) cc_final: 0.8146 (tmm160) REVERT: B 374 GLU cc_start: 0.6992 (OUTLIER) cc_final: 0.6125 (mp0) REVERT: D 25 ARG cc_start: 0.7956 (ttp-170) cc_final: 0.7590 (mmm-85) REVERT: D 355 ARG cc_start: 0.7350 (ttp-170) cc_final: 0.6999 (ttm110) REVERT: D 374 GLU cc_start: 0.6824 (mm-30) cc_final: 0.6595 (mm-30) REVERT: C 19 ARG cc_start: 0.8022 (mtt90) cc_final: 0.7346 (mtt90) REVERT: C 25 ARG cc_start: 0.7999 (ttp-170) cc_final: 0.6328 (mpp-170) REVERT: C 56 GLU cc_start: 0.7358 (tt0) cc_final: 0.6877 (pm20) REVERT: C 119 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7714 (tt0) REVERT: C 268 GLU cc_start: 0.8093 (mp0) cc_final: 0.7797 (mp0) REVERT: C 290 VAL cc_start: 0.8357 (t) cc_final: 0.8080 (m) REVERT: C 344 GLN cc_start: 0.8601 (mt0) cc_final: 0.8013 (mm110) REVERT: C 374 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6678 (mm-30) outliers start: 28 outliers final: 10 residues processed: 185 average time/residue: 1.5306 time to fit residues: 308.8970 Evaluate side-chains 179 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 164 time to evaluate : 1.626 ------------------------------------------------------------------------------- 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 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 333 GLU Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain D residue 52 LEU 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 141 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 142 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 89 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 64 optimal weight: 0.3980 chunk 88 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3244 r_free = 0.3244 target = 0.106030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.086026 restraints weight = 20710.093| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.83 r_work: 0.2882 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2007 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= 0.129 Angle : 0.465 5.675 21950 Z= 0.255 Chirality : 0.036 0.152 2375 Planarity : 0.004 0.048 2760 Dihedral : 5.422 80.633 2085 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.18 % Allowed : 11.80 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.18), residues: 1870 helix: 1.67 (0.14), residues: 1240 sheet: None (None), residues: 0 loop : 0.08 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 287 HIS 0.002 0.001 HIS A 168 PHE 0.021 0.001 PHE B 248 TYR 0.031 0.001 TYR E 97 ARG 0.007 0.000 ARG D 356 Details of bonding type rmsd hydrogen bonds : bond 0.05442 ( 975) hydrogen bonds : angle 4.41158 ( 2865) covalent geometry : bond 0.00279 (16115) covalent geometry : angle 0.46542 (21950) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10073.24 seconds wall clock time: 175 minutes 22.46 seconds (10522.46 seconds total)