Starting phenix.real_space_refine on Fri Jun 13 23:53:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dyl_47308/06_2025/9dyl_47308.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dyl_47308/06_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_47308/06_2025/9dyl_47308.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dyl_47308/06_2025/9dyl_47308.map" model { file = "/net/cci-nas-00/data/ceres_data/9dyl_47308/06_2025/9dyl_47308.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dyl_47308/06_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 10.49, per 1000 atoms: 0.67 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: 4.06 Conformation dependent library (CDL) restraints added in 1.7 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: 1.40 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: 4.86 Time building geometry restraints manager: 4.75 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: 4.990 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: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 37.760 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:15.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.610 ------------------------------------------------------------------------------- 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 : 1.661 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: 1.6888 time to fit residues: 390.3191 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 : 1.664 ------------------------------------------------------------------------------- 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 = 37)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.085681 restraints weight = 20589.523| |-----------------------------------------------------------------------------| 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: 0.8220 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 4.60265 ( 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 : 1.621 Fit side-chains REVERT: A 25 ARG cc_start: 0.7906 (ttp-170) cc_final: 0.6641 (pmt170) REVERT: A 119 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7418 (tp30) REVERT: A 268 GLU cc_start: 0.7821 (mp0) cc_final: 0.7233 (mp0) REVERT: E 25 ARG cc_start: 0.7848 (ttp-170) cc_final: 0.6646 (mpp-170) REVERT: E 119 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7562 (tt0) REVERT: E 268 GLU cc_start: 0.7791 (mp0) cc_final: 0.7514 (mp0) REVERT: E 290 VAL cc_start: 0.8132 (t) cc_final: 0.7765 (m) REVERT: E 293 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.7193 (tm-30) REVERT: E 325 MET cc_start: 0.9131 (mtp) cc_final: 0.8718 (mtp) REVERT: E 340 LYS cc_start: 0.6516 (mmtm) cc_final: 0.5485 (mtmt) REVERT: B 56 GLU cc_start: 0.7457 (tt0) cc_final: 0.7044 (tp30) REVERT: B 57 GLU cc_start: 0.7427 (mp0) cc_final: 0.6995 (pt0) REVERT: B 74 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8103 (pp30) REVERT: B 374 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6140 (mp0) REVERT: D 25 ARG cc_start: 0.7893 (ttp-170) cc_final: 0.6786 (pmt170) REVERT: D 119 GLU cc_start: 0.7944 (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: 0.7852 (ttp-170) cc_final: 0.6376 (mpp-170) REVERT: C 56 GLU cc_start: 0.7361 (tt0) cc_final: 0.7154 (mm-30) REVERT: C 119 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7693 (tt0) REVERT: C 159 GLN cc_start: 0.7132 (mt0) cc_final: 0.6798 (mp10) REVERT: C 290 VAL cc_start: 0.8364 (t) cc_final: 0.8063 (m) REVERT: C 344 GLN cc_start: 0.8657 (mt0) cc_final: 0.8030 (mm110) outliers start: 19 outliers final: 6 residues processed: 198 average time/residue: 1.5596 time to fit residues: 335.7034 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 : 1.704 ------------------------------------------------------------------------------- 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: 2.9990 chunk 110 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 137 optimal weight: 8.9990 chunk 176 optimal weight: 0.8980 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.101501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.081184 restraints weight = 20859.715| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 1.85 r_work: 0.2807 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 16115 Z= 0.224 Angle : 0.559 9.472 21950 Z= 0.305 Chirality : 0.041 0.153 2375 Planarity : 0.005 0.050 2760 Dihedral : 5.815 81.311 2085 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.95 % Allowed : 7.55 % 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: 1.30 (0.18), residues: 1870 helix: 1.28 (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 0.005 0.002 HIS A 168 PHE 0.027 0.002 PHE A 248 TYR 0.025 0.002 TYR D 97 ARG 0.003 0.001 ARG C 92 Details of bonding type rmsd hydrogen bonds : bond 0.06706 ( 975) hydrogen bonds : angle 4.61688 ( 2865) covalent geometry : bond 0.00534 (16115) covalent geometry : angle 0.55902 (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 196 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 163 time to evaluate : 1.696 Fit side-chains REVERT: A 25 ARG cc_start: 0.7928 (ttp-170) cc_final: 0.6642 (pmt170) REVERT: A 119 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7468 (tp30) REVERT: A 268 GLU cc_start: 0.7808 (mp0) cc_final: 0.7318 (mp0) REVERT: E 25 ARG cc_start: 0.7901 (ttp-170) cc_final: 0.6615 (mpp-170) REVERT: E 119 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7642 (tt0) REVERT: E 268 GLU cc_start: 0.7906 (mp0) cc_final: 0.7561 (mp0) REVERT: E 293 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7440 (tm-30) REVERT: E 325 MET cc_start: 0.9131 (mtp) cc_final: 0.8728 (mtp) REVERT: E 340 LYS cc_start: 0.6714 (mmtm) cc_final: 0.5610 (mtmt) REVERT: E 344 GLN cc_start: 0.8595 (mt0) cc_final: 0.8189 (mm110) REVERT: E 374 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6647 (mm-30) REVERT: B 56 GLU cc_start: 0.7537 (tt0) cc_final: 0.7134 (tp30) REVERT: B 57 GLU cc_start: 0.7519 (mp0) cc_final: 0.7120 (pt0) REVERT: B 74 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8219 (pp30) REVERT: B 331 ARG cc_start: 0.8387 (ttp-170) cc_final: 0.7875 (ttp-170) REVERT: B 344 GLN cc_start: 0.8804 (mt0) cc_final: 0.8488 (mt0) REVERT: B 374 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6168 (mp0) REVERT: D 25 ARG cc_start: 0.7978 (ttp-170) cc_final: 0.6791 (pmt170) REVERT: D 119 GLU cc_start: 0.7960 (mm-30) cc_final: 0.7693 (tt0) REVERT: D 355 ARG cc_start: 0.7352 (ttp-170) cc_final: 0.6988 (ttm110) REVERT: C 25 ARG cc_start: 0.7997 (ttp-170) cc_final: 0.6386 (mpp-170) REVERT: C 56 GLU cc_start: 0.7420 (tt0) cc_final: 0.6966 (pm20) REVERT: C 57 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.6414 (pp20) REVERT: C 119 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7700 (tt0) REVERT: C 290 VAL cc_start: 0.8423 (t) cc_final: 0.8154 (m) REVERT: C 344 GLN cc_start: 0.8678 (mt0) cc_final: 0.7993 (mm110) REVERT: C 374 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.6433 (mp0) outliers start: 33 outliers final: 9 residues processed: 185 average time/residue: 1.6942 time to fit residues: 339.6137 Evaluate side-chains 171 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 1.873 ------------------------------------------------------------------------------- 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 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 74 GLN 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: 0.7980 chunk 47 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 178 optimal weight: 0.0980 chunk 2 optimal weight: 0.7980 chunk 151 optimal weight: 3.9990 chunk 159 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.105984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.085841 restraints weight = 20619.726| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.83 r_work: 0.2875 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16115 Z= 0.125 Angle : 0.471 7.972 21950 Z= 0.257 Chirality : 0.036 0.153 2375 Planarity : 0.004 0.040 2760 Dihedral : 5.591 80.669 2085 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.06 % Allowed : 8.55 % Favored : 89.38 % 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: 1.47 (0.18), residues: 1870 helix: 1.46 (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 B 168 PHE 0.023 0.001 PHE B 248 TYR 0.018 0.001 TYR D 97 ARG 0.003 0.000 ARG B 25 Details of bonding type rmsd hydrogen bonds : bond 0.05485 ( 975) hydrogen bonds : angle 4.48528 ( 2865) covalent geometry : bond 0.00262 (16115) covalent geometry : angle 0.47079 (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 208 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 173 time to evaluate : 1.418 Fit side-chains REVERT: A 25 ARG cc_start: 0.7917 (ttp-170) cc_final: 0.6662 (pmt170) REVERT: A 119 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7486 (tp30) REVERT: A 268 GLU cc_start: 0.7823 (mp0) cc_final: 0.7321 (mp0) REVERT: E 25 ARG cc_start: 0.7849 (ttp-170) cc_final: 0.6526 (mpp-170) REVERT: E 119 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7605 (tt0) REVERT: E 173 LYS cc_start: 0.7875 (mttp) cc_final: 0.7561 (mttm) REVERT: E 268 GLU cc_start: 0.7920 (mp0) cc_final: 0.7552 (mp0) REVERT: E 325 MET cc_start: 0.9095 (mtp) cc_final: 0.8740 (mtp) REVERT: E 340 LYS cc_start: 0.6651 (mmtm) cc_final: 0.5538 (mtmt) REVERT: E 344 GLN cc_start: 0.8510 (mt0) cc_final: 0.8176 (mm110) REVERT: B 56 GLU cc_start: 0.7480 (tt0) cc_final: 0.7121 (tp30) REVERT: B 57 GLU cc_start: 0.7446 (mp0) cc_final: 0.7032 (pt0) REVERT: B 74 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8175 (pp30) REVERT: B 331 ARG cc_start: 0.8406 (ttp-170) cc_final: 0.8062 (tmm160) REVERT: B 344 GLN cc_start: 0.8755 (mt0) cc_final: 0.8446 (mt0) REVERT: B 374 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6104 (mp0) REVERT: D 25 ARG cc_start: 0.7892 (ttp-170) cc_final: 0.7570 (mmm-85) REVERT: D 119 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7651 (tt0) REVERT: D 300 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8444 (mt-10) REVERT: D 355 ARG cc_start: 0.7343 (ttp-170) cc_final: 0.6992 (ttm110) REVERT: D 374 GLU cc_start: 0.6957 (mm-30) cc_final: 0.6729 (mm-30) REVERT: C 25 ARG cc_start: 0.7924 (ttp-170) cc_final: 0.6355 (mpp-170) REVERT: C 56 GLU cc_start: 0.7329 (tt0) cc_final: 0.6880 (pm20) REVERT: C 57 GLU cc_start: 0.6775 (pt0) cc_final: 0.6412 (pp20) REVERT: C 119 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7694 (tt0) REVERT: C 290 VAL cc_start: 0.8348 (t) cc_final: 0.8092 (m) REVERT: C 344 GLN cc_start: 0.8652 (mt0) cc_final: 0.8024 (mm110) REVERT: C 374 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.6726 (mm-30) outliers start: 35 outliers final: 10 residues processed: 192 average time/residue: 1.6433 time to fit residues: 343.0144 Evaluate side-chains 177 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 163 time to evaluate : 1.709 ------------------------------------------------------------------------------- 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 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 333 GLU Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 74 GLN Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 374 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 165 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 chunk 45 optimal weight: 0.6980 chunk 120 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 171 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3223 r_free = 0.3223 target = 0.104457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.084190 restraints weight = 20795.155| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.85 r_work: 0.2850 rms_B_bonded: 2.44 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: 0.8294 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16115 Z= 0.151 Angle : 0.485 7.272 21950 Z= 0.266 Chirality : 0.037 0.152 2375 Planarity : 0.004 0.045 2760 Dihedral : 5.574 80.603 2085 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.30 % Allowed : 9.03 % 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: 1.48 (0.18), residues: 1870 helix: 1.47 (0.14), residues: 1265 sheet: None (None), residues: 0 loop : 0.08 (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 0.002 0.000 ARG B 51 Details of bonding type rmsd hydrogen bonds : bond 0.05808 ( 975) hydrogen bonds : angle 4.48265 ( 2865) covalent geometry : bond 0.00341 (16115) covalent geometry : angle 0.48493 (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 203 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 164 time to evaluate : 1.825 Fit side-chains REVERT: A 25 ARG cc_start: 0.7886 (ttp-170) cc_final: 0.6593 (pmt170) REVERT: A 119 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7426 (tp30) REVERT: A 268 GLU cc_start: 0.7841 (mp0) cc_final: 0.7377 (mp0) REVERT: A 287 TRP cc_start: 0.8584 (OUTLIER) cc_final: 0.8258 (t-100) REVERT: E 25 ARG cc_start: 0.7863 (ttp-170) cc_final: 0.6540 (mpp-170) REVERT: E 119 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7598 (tt0) REVERT: E 268 GLU cc_start: 0.7918 (mp0) cc_final: 0.7609 (mp0) REVERT: E 325 MET cc_start: 0.9105 (mtp) cc_final: 0.8770 (mtp) REVERT: E 344 GLN cc_start: 0.8545 (mt0) cc_final: 0.8181 (mm110) REVERT: E 374 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6688 (mp0) REVERT: B 56 GLU cc_start: 0.7511 (tt0) cc_final: 0.7139 (tp30) REVERT: B 57 GLU cc_start: 0.7560 (mp0) cc_final: 0.7125 (pt0) REVERT: B 74 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8143 (pp30) REVERT: B 331 ARG cc_start: 0.8413 (ttp-170) cc_final: 0.8065 (tmm160) REVERT: B 344 GLN cc_start: 0.8764 (mt0) cc_final: 0.8444 (mt0) REVERT: B 374 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6067 (mp0) REVERT: D 25 ARG cc_start: 0.7903 (ttp-170) cc_final: 0.7555 (mmm-85) REVERT: D 119 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7674 (tt0) REVERT: D 355 ARG cc_start: 0.7290 (ttp-170) cc_final: 0.6945 (ttm110) REVERT: D 374 GLU cc_start: 0.6915 (mm-30) cc_final: 0.6698 (mm-30) REVERT: C 25 ARG cc_start: 0.7977 (ttp-170) cc_final: 0.6365 (mpp-170) REVERT: C 56 GLU cc_start: 0.7328 (tt0) cc_final: 0.6868 (pm20) REVERT: C 57 GLU cc_start: 0.6802 (pt0) cc_final: 0.6407 (pp20) REVERT: C 119 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7684 (tt0) REVERT: C 268 GLU cc_start: 0.8001 (mp0) cc_final: 0.7689 (mp0) REVERT: C 287 TRP cc_start: 0.8610 (OUTLIER) cc_final: 0.8092 (t-100) REVERT: C 290 VAL cc_start: 0.8366 (t) cc_final: 0.8119 (m) REVERT: C 344 GLN cc_start: 0.8635 (mt0) cc_final: 0.7989 (mm110) REVERT: C 374 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6706 (mm-30) outliers start: 39 outliers final: 16 residues processed: 187 average time/residue: 1.5761 time to fit residues: 320.9865 Evaluate side-chains 185 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 1.678 ------------------------------------------------------------------------------- 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 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 74 GLN Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 287 TRP Chi-restraints excluded: chain C residue 374 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 112 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3250 r_free = 0.3250 target = 0.106027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.085627 restraints weight = 20594.042| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.87 r_work: 0.2872 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16115 Z= 0.134 Angle : 0.470 6.612 21950 Z= 0.258 Chirality : 0.036 0.150 2375 Planarity : 0.004 0.047 2760 Dihedral : 5.507 80.418 2085 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.30 % Allowed : 9.50 % Favored : 88.20 % 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: 1.53 (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 0.012 0.001 TRP E 309 HIS 0.003 0.001 HIS A 168 PHE 0.022 0.001 PHE B 248 TYR 0.019 0.001 TYR D 97 ARG 0.002 0.000 ARG B 130 Details of bonding type rmsd hydrogen bonds : bond 0.05566 ( 975) hydrogen bonds : angle 4.45139 ( 2865) covalent geometry : bond 0.00295 (16115) covalent geometry : angle 0.46998 (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 213 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 174 time to evaluate : 1.817 Fit side-chains REVERT: A 25 ARG cc_start: 0.7877 (ttp-170) cc_final: 0.6574 (pmt170) REVERT: A 119 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7427 (tp30) REVERT: A 268 GLU cc_start: 0.7855 (mp0) cc_final: 0.7378 (mp0) REVERT: E 25 ARG cc_start: 0.7892 (ttp-170) cc_final: 0.6549 (mpp-170) REVERT: E 119 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7592 (tt0) REVERT: E 268 GLU cc_start: 0.7945 (mp0) cc_final: 0.7633 (mp0) REVERT: E 293 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7406 (tt0) REVERT: E 325 MET cc_start: 0.9103 (mtp) cc_final: 0.8784 (mtp) REVERT: E 344 GLN cc_start: 0.8535 (mt0) cc_final: 0.8195 (mm110) REVERT: E 374 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6669 (mp0) REVERT: B 56 GLU cc_start: 0.7447 (tt0) cc_final: 0.7096 (tp30) REVERT: B 57 GLU cc_start: 0.7572 (mp0) cc_final: 0.7123 (pt0) REVERT: B 74 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8138 (pp30) REVERT: B 331 ARG cc_start: 0.8454 (ttp-170) cc_final: 0.8101 (tmm160) REVERT: B 344 GLN cc_start: 0.8755 (mt0) cc_final: 0.8437 (mt0) REVERT: B 374 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6020 (mp0) REVERT: D 25 ARG cc_start: 0.7910 (ttp-170) cc_final: 0.7567 (mmm-85) REVERT: D 119 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7669 (tt0) REVERT: D 287 TRP cc_start: 0.8752 (OUTLIER) cc_final: 0.8502 (t-100) REVERT: D 355 ARG cc_start: 0.7317 (ttp-170) cc_final: 0.6966 (ttm110) REVERT: D 374 GLU cc_start: 0.6821 (mm-30) cc_final: 0.6557 (mm-30) REVERT: C 25 ARG cc_start: 0.7986 (ttp-170) cc_final: 0.6353 (mpp-170) REVERT: C 56 GLU cc_start: 0.7311 (tt0) cc_final: 0.6855 (pm20) REVERT: C 57 GLU cc_start: 0.6801 (OUTLIER) cc_final: 0.6445 (pp20) REVERT: C 119 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7707 (tt0) REVERT: C 268 GLU cc_start: 0.8003 (mp0) cc_final: 0.7600 (mp0) REVERT: C 287 TRP cc_start: 0.8616 (OUTLIER) cc_final: 0.8064 (t-100) REVERT: C 290 VAL cc_start: 0.8314 (t) cc_final: 0.8069 (m) REVERT: C 344 GLN cc_start: 0.8618 (mt0) cc_final: 0.7990 (mm110) REVERT: C 374 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6648 (mm-30) outliers start: 39 outliers final: 11 residues processed: 199 average time/residue: 1.5567 time to fit residues: 337.6229 Evaluate side-chains 185 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 1.797 ------------------------------------------------------------------------------- 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 129 ILE Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 293 GLN Chi-restraints excluded: chain E residue 374 GLU Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 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 D residue 287 TRP Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 287 TRP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 374 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 90 optimal weight: 0.9990 chunk 178 optimal weight: 0.9990 chunk 129 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 171 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3238 r_free = 0.3238 target = 0.105625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.085359 restraints weight = 20810.142| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.85 r_work: 0.2873 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16115 Z= 0.135 Angle : 0.467 5.582 21950 Z= 0.256 Chirality : 0.036 0.151 2375 Planarity : 0.004 0.048 2760 Dihedral : 5.475 80.374 2085 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.12 % Allowed : 10.15 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.72 (0.18), residues: 1870 helix: 1.75 (0.14), residues: 1210 sheet: None (None), residues: 0 loop : 0.08 (0.22), residues: 660 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 0.021 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 0.05548 ( 975) hydrogen bonds : angle 4.43015 ( 2865) covalent geometry : bond 0.00298 (16115) covalent geometry : angle 0.46694 (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 213 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 177 time to evaluate : 1.770 Fit side-chains REVERT: A 25 ARG cc_start: 0.7895 (ttp-170) cc_final: 0.6589 (pmt170) REVERT: A 119 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7406 (tp30) REVERT: A 268 GLU cc_start: 0.7838 (mp0) cc_final: 0.7279 (mp0) REVERT: A 287 TRP cc_start: 0.8576 (OUTLIER) cc_final: 0.8316 (m-90) REVERT: A 374 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6965 (mp0) REVERT: E 25 ARG cc_start: 0.7904 (ttp-170) cc_final: 0.6553 (mpp-170) REVERT: E 119 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7601 (tt0) REVERT: E 268 GLU cc_start: 0.7956 (mp0) cc_final: 0.7652 (mp0) REVERT: E 293 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7421 (tt0) REVERT: E 325 MET cc_start: 0.9100 (mtp) cc_final: 0.8781 (mtp) REVERT: E 344 GLN cc_start: 0.8512 (mt0) cc_final: 0.8173 (mm110) REVERT: E 374 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.6723 (mp0) REVERT: B 56 GLU cc_start: 0.7466 (tt0) cc_final: 0.7179 (tp30) REVERT: B 57 GLU cc_start: 0.7592 (mp0) cc_final: 0.7135 (pt0) REVERT: B 74 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8168 (pp30) REVERT: B 331 ARG cc_start: 0.8476 (ttp-170) cc_final: 0.8128 (tmm160) REVERT: B 344 GLN cc_start: 0.8807 (mt0) cc_final: 0.8516 (mt0) REVERT: B 374 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6102 (mp0) REVERT: D 25 ARG cc_start: 0.7923 (ttp-170) cc_final: 0.7584 (mmm-85) REVERT: D 61 MET cc_start: 0.7629 (tpt) cc_final: 0.6984 (ttp) REVERT: D 119 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7684 (tt0) REVERT: D 300 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8329 (mt-10) REVERT: D 355 ARG cc_start: 0.7363 (ttp-170) cc_final: 0.7028 (ttm110) REVERT: D 374 GLU cc_start: 0.6835 (mm-30) cc_final: 0.6577 (mm-30) REVERT: C 25 ARG cc_start: 0.7993 (ttp-170) cc_final: 0.6366 (mpp-170) REVERT: C 56 GLU cc_start: 0.7336 (tt0) cc_final: 0.6863 (pm20) REVERT: C 57 GLU cc_start: 0.6789 (OUTLIER) cc_final: 0.6421 (pp20) REVERT: C 119 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7727 (tt0) REVERT: C 268 GLU cc_start: 0.8032 (mp0) cc_final: 0.7714 (mp0) REVERT: C 290 VAL cc_start: 0.8316 (t) cc_final: 0.8067 (m) REVERT: C 344 GLN cc_start: 0.8606 (mt0) cc_final: 0.7985 (mm110) REVERT: C 374 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6661 (mm-30) outliers start: 36 outliers final: 16 residues processed: 196 average time/residue: 1.4964 time to fit residues: 320.6828 Evaluate side-chains 195 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 1.852 ------------------------------------------------------------------------------- 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 A residue 169 LYS Chi-restraints excluded: chain A residue 287 TRP Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 169 LYS Chi-restraints excluded: chain E residue 293 GLN Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 374 GLU Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 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 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 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: 2.9990 chunk 76 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 159 optimal weight: 6.9990 chunk 116 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 141 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3242 r_free = 0.3242 target = 0.105865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.085670 restraints weight = 20745.101| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.85 r_work: 0.2878 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1903 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= 0.132 Angle : 0.466 6.349 21950 Z= 0.255 Chirality : 0.036 0.150 2375 Planarity : 0.004 0.048 2760 Dihedral : 5.454 80.336 2085 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.12 % Allowed : 10.38 % Favored : 87.49 % 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: 1.64 (0.18), residues: 1870 helix: 1.66 (0.14), residues: 1240 sheet: None (None), residues: 0 loop : 0.05 (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 0.021 0.001 PHE B 248 TYR 0.019 0.001 TYR D 97 ARG 0.004 0.000 ARG B 356 Details of bonding type rmsd hydrogen bonds : bond 0.05484 ( 975) hydrogen bonds : angle 4.42302 ( 2865) covalent geometry : bond 0.00290 (16115) covalent geometry : angle 0.46622 (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 209 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 173 time to evaluate : 2.774 Fit side-chains REVERT: A 25 ARG cc_start: 0.7937 (ttp-170) cc_final: 0.6622 (pmt170) REVERT: A 119 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7413 (tp30) REVERT: A 268 GLU cc_start: 0.7851 (mp0) cc_final: 0.7290 (mp0) REVERT: A 287 TRP cc_start: 0.8583 (OUTLIER) cc_final: 0.8329 (m-90) REVERT: A 374 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6937 (mp0) REVERT: E 25 ARG cc_start: 0.7906 (ttp-170) cc_final: 0.6559 (mpp-170) REVERT: E 119 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7582 (tt0) REVERT: E 268 GLU cc_start: 0.7991 (mp0) cc_final: 0.7679 (mp0) REVERT: E 293 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7418 (tt0) REVERT: E 325 MET cc_start: 0.9103 (mtp) cc_final: 0.8796 (mtp) REVERT: E 344 GLN cc_start: 0.8504 (mt0) cc_final: 0.8171 (mm110) REVERT: E 374 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6728 (mp0) REVERT: B 56 GLU cc_start: 0.7445 (tt0) cc_final: 0.7210 (tp30) REVERT: B 57 GLU cc_start: 0.7593 (mp0) cc_final: 0.7136 (pt0) REVERT: B 74 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.8144 (pp30) REVERT: B 331 ARG cc_start: 0.8487 (ttp-170) cc_final: 0.8142 (tmm160) REVERT: B 344 GLN cc_start: 0.8819 (mt0) cc_final: 0.8522 (mt0) REVERT: B 374 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6073 (mp0) REVERT: D 25 ARG cc_start: 0.7930 (ttp-170) cc_final: 0.7593 (mmm-85) REVERT: D 61 MET cc_start: 0.7624 (tpt) cc_final: 0.6981 (ttp) REVERT: D 119 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7678 (tt0) REVERT: D 300 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8393 (mt-10) REVERT: D 355 ARG cc_start: 0.7353 (ttp-170) cc_final: 0.7017 (ttm110) REVERT: D 374 GLU cc_start: 0.6822 (mm-30) cc_final: 0.6549 (mm-30) REVERT: C 25 ARG cc_start: 0.7996 (ttp-170) cc_final: 0.6366 (mpp-170) REVERT: C 56 GLU cc_start: 0.7324 (tt0) cc_final: 0.6845 (pm20) REVERT: C 57 GLU cc_start: 0.6784 (OUTLIER) cc_final: 0.6423 (pp20) REVERT: C 119 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7723 (tt0) REVERT: C 268 GLU cc_start: 0.8066 (mp0) cc_final: 0.7760 (mp0) REVERT: C 290 VAL cc_start: 0.8339 (t) cc_final: 0.8070 (m) REVERT: C 344 GLN cc_start: 0.8609 (mt0) cc_final: 0.7990 (mm110) REVERT: C 374 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6707 (mm-30) outliers start: 36 outliers final: 17 residues processed: 192 average time/residue: 1.9418 time to fit residues: 408.3682 Evaluate side-chains 196 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 170 time to evaluate : 1.688 ------------------------------------------------------------------------------- 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 129 ILE Chi-restraints excluded: chain A residue 287 TRP Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 169 LYS Chi-restraints excluded: chain E residue 293 GLN Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 374 GLU Chi-restraints excluded: chain B residue 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 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 203 ASP 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: 0.0970 chunk 54 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 147 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 170 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 19 optimal weight: 0.0980 chunk 126 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 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 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 = 0.108576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.088576 restraints weight = 20552.020| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.83 r_work: 0.2925 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16115 Z= 0.110 Angle : 0.441 5.473 21950 Z= 0.241 Chirality : 0.035 0.152 2375 Planarity : 0.004 0.048 2760 Dihedral : 5.347 79.885 2085 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.01 % Allowed : 10.68 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.87 (0.18), residues: 1870 helix: 1.89 (0.14), residues: 1210 sheet: None (None), residues: 0 loop : 0.10 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 287 HIS 0.001 0.000 HIS A 168 PHE 0.018 0.001 PHE A 248 TYR 0.015 0.001 TYR B 236 ARG 0.004 0.000 ARG E 356 Details of bonding type rmsd hydrogen bonds : bond 0.05005 ( 975) hydrogen bonds : angle 4.35226 ( 2865) covalent geometry : bond 0.00227 (16115) covalent geometry : angle 0.44075 (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 221 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 187 time to evaluate : 1.685 Fit side-chains REVERT: A 25 ARG cc_start: 0.7935 (ttp-170) cc_final: 0.6639 (mpp-170) REVERT: A 119 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7341 (tp30) REVERT: A 268 GLU cc_start: 0.7819 (mp0) cc_final: 0.7353 (mp0) REVERT: A 331 ARG cc_start: 0.8603 (ttp-170) cc_final: 0.8181 (ptt180) REVERT: A 374 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6899 (mp0) REVERT: E 25 ARG cc_start: 0.7878 (ttp-170) cc_final: 0.6615 (mpp-170) REVERT: E 119 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7567 (tt0) REVERT: E 268 GLU cc_start: 0.7960 (mp0) cc_final: 0.7666 (mp0) REVERT: E 325 MET cc_start: 0.9093 (mtp) cc_final: 0.8774 (mtp) REVERT: E 344 GLN cc_start: 0.8453 (mt0) cc_final: 0.8141 (mm110) REVERT: E 374 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6740 (mp0) REVERT: B 56 GLU cc_start: 0.7419 (tt0) cc_final: 0.7197 (tp30) REVERT: B 57 GLU cc_start: 0.7568 (mp0) cc_final: 0.7103 (pt0) REVERT: B 74 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.8147 (pp30) REVERT: B 331 ARG cc_start: 0.8466 (ttp-170) cc_final: 0.8119 (tmm160) REVERT: B 374 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6116 (mp0) REVERT: B 376 GLN cc_start: 0.7111 (mt0) cc_final: 0.6884 (mt0) REVERT: D 25 ARG cc_start: 0.7923 (ttp-170) cc_final: 0.7608 (mmm-85) REVERT: D 61 MET cc_start: 0.7597 (tpt) cc_final: 0.7000 (ttp) REVERT: D 268 GLU cc_start: 0.8062 (mp0) cc_final: 0.7580 (mp0) REVERT: D 300 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8334 (mt-10) REVERT: D 355 ARG cc_start: 0.7380 (ttp-170) cc_final: 0.7041 (ttm110) REVERT: D 374 GLU cc_start: 0.6813 (mm-30) cc_final: 0.6530 (mm-30) REVERT: C 25 ARG cc_start: 0.7974 (ttp-170) cc_final: 0.6371 (mpp-170) REVERT: C 56 GLU cc_start: 0.7282 (tt0) cc_final: 0.6808 (pm20) REVERT: C 119 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7737 (tt0) REVERT: C 268 GLU cc_start: 0.8062 (mp0) cc_final: 0.7758 (mp0) REVERT: C 290 VAL cc_start: 0.8320 (t) cc_final: 0.8041 (m) REVERT: C 344 GLN cc_start: 0.8544 (mt0) cc_final: 0.7969 (mm110) REVERT: C 374 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6670 (mm-30) outliers start: 34 outliers final: 12 residues processed: 207 average time/residue: 1.4778 time to fit residues: 334.2296 Evaluate side-chains 195 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 177 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 374 GLU Chi-restraints excluded: chain B residue 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 273 VAL Chi-restraints excluded: chain C residue 60 LEU 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: 5.9990 chunk 24 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 178 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 184 optimal weight: 8.9990 chunk 171 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3206 r_free = 0.3206 target = 0.103283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.083116 restraints weight = 20961.113| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 1.85 r_work: 0.2819 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16115 Z= 0.187 Angle : 0.511 5.383 21950 Z= 0.280 Chirality : 0.038 0.150 2375 Planarity : 0.005 0.047 2760 Dihedral : 5.504 80.416 2085 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.59 % Allowed : 11.33 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.19), residues: 1870 helix: 1.51 (0.14), residues: 1265 sheet: None (None), residues: 0 loop : 0.08 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 287 HIS 0.004 0.001 HIS A 168 PHE 0.023 0.002 PHE C 248 TYR 0.038 0.002 TYR E 97 ARG 0.006 0.001 ARG D 356 Details of bonding type rmsd hydrogen bonds : bond 0.06159 ( 975) hydrogen bonds : angle 4.49184 ( 2865) covalent geometry : bond 0.00438 (16115) covalent geometry : angle 0.51054 (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 201 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 174 time to evaluate : 1.928 Fit side-chains REVERT: A 25 ARG cc_start: 0.7906 (ttp-170) cc_final: 0.6526 (pmt170) REVERT: A 119 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7372 (tp30) REVERT: A 268 GLU cc_start: 0.7819 (mp0) cc_final: 0.7338 (mp0) REVERT: A 331 ARG cc_start: 0.8598 (ttp-170) cc_final: 0.8161 (ptt180) REVERT: A 374 GLU cc_start: 0.6976 (OUTLIER) cc_final: 0.6738 (mp0) REVERT: E 25 ARG cc_start: 0.7899 (ttp-170) cc_final: 0.6524 (mpp-170) REVERT: E 119 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7530 (tt0) REVERT: E 268 GLU cc_start: 0.7967 (mp0) cc_final: 0.7680 (mp0) REVERT: E 290 VAL cc_start: 0.8199 (t) cc_final: 0.7862 (m) REVERT: E 325 MET cc_start: 0.9074 (mtp) cc_final: 0.8743 (mtp) REVERT: E 344 GLN cc_start: 0.8516 (mt0) cc_final: 0.8161 (mm110) REVERT: E 374 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6652 (mp0) REVERT: B 57 GLU cc_start: 0.7603 (mp0) cc_final: 0.7139 (pt0) REVERT: B 74 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.8183 (pp30) REVERT: B 331 ARG cc_start: 0.8468 (ttp-170) cc_final: 0.8110 (tmm160) REVERT: B 374 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.6075 (mp0) REVERT: D 25 ARG cc_start: 0.7928 (ttp-170) cc_final: 0.7556 (mmm-85) REVERT: D 355 ARG cc_start: 0.7296 (ttp-170) cc_final: 0.6944 (ttm110) REVERT: D 374 GLU cc_start: 0.6782 (mm-30) cc_final: 0.6489 (mm-30) REVERT: C 19 ARG cc_start: 0.7973 (mtt90) cc_final: 0.7287 (mtt90) REVERT: C 25 ARG cc_start: 0.7993 (ttp-170) cc_final: 0.6309 (mpp-170) REVERT: C 56 GLU cc_start: 0.7332 (tt0) cc_final: 0.7060 (tp30) REVERT: C 57 GLU cc_start: 0.6630 (pt0) cc_final: 0.6297 (pp20) REVERT: C 119 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7687 (tt0) REVERT: C 268 GLU cc_start: 0.8086 (mp0) cc_final: 0.7782 (mp0) REVERT: C 290 VAL cc_start: 0.8345 (t) cc_final: 0.8064 (m) REVERT: C 344 GLN cc_start: 0.8583 (mt0) cc_final: 0.7945 (mm110) REVERT: C 374 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6641 (mm-30) outliers start: 27 outliers final: 11 residues processed: 186 average time/residue: 1.6204 time to fit residues: 328.8272 Evaluate side-chains 186 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 1.872 ------------------------------------------------------------------------------- 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 374 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 74 GLN Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 374 GLU Chi-restraints excluded: chain B residue 74 GLN Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 169 LYS Chi-restraints excluded: chain B residue 333 GLU Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain D residue 273 VAL Chi-restraints excluded: chain D residue 287 TRP Chi-restraints excluded: chain C residue 60 LEU 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: 0.8980 chunk 46 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3234 r_free = 0.3234 target = 0.105335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.085330 restraints weight = 20720.348| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.84 r_work: 0.2871 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1939 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= 0.136 Angle : 0.470 5.653 21950 Z= 0.258 Chirality : 0.036 0.152 2375 Planarity : 0.004 0.048 2760 Dihedral : 5.454 80.427 2085 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.59 % Allowed : 11.39 % 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: 1.62 (0.18), residues: 1870 helix: 1.64 (0.14), residues: 1240 sheet: None (None), residues: 0 loop : 0.05 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 287 HIS 0.003 0.001 HIS A 168 PHE 0.022 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 0.05592 ( 975) hydrogen bonds : angle 4.42945 ( 2865) covalent geometry : bond 0.00300 (16115) covalent geometry : angle 0.47026 (21950) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11625.35 seconds wall clock time: 205 minutes 42.27 seconds (12342.27 seconds total)