Starting phenix.real_space_refine on Fri Jul 3 18:19:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ctt_45918/07_2026/9ctt_45918.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ctt_45918/07_2026/9ctt_45918.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ctt_45918/07_2026/9ctt_45918.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ctt_45918/07_2026/9ctt_45918.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ctt_45918/07_2026/9ctt_45918.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ctt_45918/07_2026/9ctt_45918.map" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.097 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 10260 2.51 5 N 2550 2.21 5 O 2700 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15595 Number of models: 1 Model: "" Number of chains: 10 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: "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: "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: "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: "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: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Time building chain proxies: 3.68, per 1000 atoms: 0.24 Number of scatterers: 15595 At special positions: 0 Unit cell: (107.07, 108.73, 112.88, 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 2700 8.00 N 2550 7.00 C 10260 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 674.4 milliseconds 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3590 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 3 sheets defined 70.2% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'D' and resid 18 through 23 removed outlier: 3.735A pdb=" N LEU D 22 " --> pdb=" O ARG D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 53 removed outlier: 5.817A pdb=" N GLY D 34 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N GLU D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 71 removed outlier: 3.954A pdb=" N SER D 71 " --> pdb=" O LEU D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 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: 3.689A 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: 3.779A pdb=" N LEU D 252 " --> pdb=" O PHE D 248 " (cutoff:3.500A) removed outlier: 4.123A 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 264 through 268 removed outlier: 4.107A pdb=" N GLU D 268 " --> pdb=" O PRO D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 295 removed outlier: 3.775A pdb=" N ALA D 291 " --> pdb=" O TRP D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 324 Processing helix chain 'D' and resid 348 through 355 removed outlier: 3.685A pdb=" N ALA D 352 " --> pdb=" O ALA D 349 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N GLN D 353 " --> pdb=" O ALA D 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 23 removed outlier: 3.704A pdb=" N LEU B 22 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N CYS B 23 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 53 removed outlier: 5.686A pdb=" N GLY B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N GLU B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 70 Processing helix chain 'B' and resid 75 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 179 through 181 No H-bonds generated for 'chain 'B' and resid 179 through 181' Processing helix chain 'B' and resid 182 through 198 removed outlier: 3.695A 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: 3.941A pdb=" N LEU B 252 " --> pdb=" O PHE B 248 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 295 removed outlier: 3.784A pdb=" N ALA B 291 " --> pdb=" O TRP B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 324 Processing helix chain 'B' and resid 351 through 355 Processing helix chain 'E' and resid 17 through 23 removed outlier: 3.714A pdb=" N LEU E 22 " --> pdb=" O ARG E 19 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N CYS E 23 " --> pdb=" O LEU E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 52 removed outlier: 5.713A pdb=" N GLY E 34 " --> pdb=" O LYS E 30 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N GLU E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 71 removed outlier: 3.668A pdb=" N SER E 71 " --> pdb=" O LEU E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 99 removed outlier: 4.524A pdb=" N ILE E 78 " --> pdb=" O GLN E 74 " (cutoff:3.500A) 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: 3.679A 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: 3.761A pdb=" N LEU E 252 " --> pdb=" O PHE E 248 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 263 removed outlier: 3.579A pdb=" N LYS E 262 " --> pdb=" O ASN E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 295 removed outlier: 3.774A pdb=" N ALA E 291 " --> pdb=" O TRP E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 324 Processing helix chain 'E' and resid 351 through 355 removed outlier: 3.650A pdb=" N ARG E 355 " --> pdb=" O ALA E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 374 removed outlier: 3.527A pdb=" N GLU E 374 " --> pdb=" O GLU E 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 23 removed outlier: 3.576A pdb=" N LEU A 22 " --> pdb=" O ARG A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 53 removed outlier: 5.789A pdb=" N GLY A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N GLU A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 72 removed outlier: 4.003A pdb=" N SER A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TYR A 72 " --> pdb=" O TYR A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 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 174 Processing helix chain 'A' and resid 182 through 198 removed outlier: 3.676A 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: 3.898A pdb=" N LEU A 252 " --> pdb=" O PHE A 248 " (cutoff:3.500A) removed outlier: 4.136A 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 295 removed outlier: 3.789A pdb=" N ALA A 291 " --> pdb=" O TRP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 324 Processing helix chain 'A' and resid 351 through 355 removed outlier: 3.552A pdb=" N ARG A 355 " --> pdb=" O ALA A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 373 Processing helix chain 'C' and resid 18 through 23 removed outlier: 3.672A pdb=" N LEU C 22 " --> pdb=" O ARG C 19 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS C 23 " --> pdb=" O LEU C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 52 removed outlier: 5.771A pdb=" N GLY C 34 " --> pdb=" O LYS C 30 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N GLU C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 71 removed outlier: 3.818A pdb=" N SER C 71 " --> pdb=" O LEU C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 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 174 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: 3.707A 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: 3.523A pdb=" N PHE C 247 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU C 252 " --> pdb=" O PHE C 248 " (cutoff:3.500A) removed outlier: 4.207A 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 295 removed outlier: 3.793A pdb=" N ALA C 291 " --> pdb=" O TRP C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 324 Processing helix chain 'C' and resid 351 through 355 Processing sheet with id=AA1, first strand: chain 'D' and resid 375 through 376 removed outlier: 4.453A pdb=" N TYR C 347 " --> pdb=" O GLN D 376 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 347 through 348 removed outlier: 4.396A pdb=" N TYR B 347 " --> pdb=" O GLN C 376 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 347 through 348 removed outlier: 4.398A pdb=" N TYR E 347 " --> pdb=" O GLN A 376 " (cutoff:3.500A) 953 hydrogen bonds defined for protein. 2778 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.62 Time building geometry restraints manager: 1.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4827 1.34 - 1.46: 4122 1.46 - 1.58: 6981 1.58 - 1.70: 0 1.70 - 1.82: 135 Bond restraints: 16065 Sorted by residual: bond pdb=" N LYS B 64 " pdb=" CA LYS B 64 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.20e-02 6.94e+03 7.98e+00 bond pdb=" N TYR C 50 " pdb=" CA TYR C 50 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.21e-02 6.83e+03 7.55e+00 bond pdb=" N ASP B 303 " pdb=" CA ASP B 303 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.26e-02 6.30e+03 7.35e+00 bond pdb=" N LYS C 262 " pdb=" CA LYS C 262 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.35e-02 5.49e+03 7.18e+00 bond pdb=" CA LYS B 64 " pdb=" C LYS B 64 " ideal model delta sigma weight residual 1.524 1.558 -0.034 1.32e-02 5.74e+03 6.76e+00 ... (remaining 16060 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 21354 1.57 - 3.14: 431 3.14 - 4.70: 70 4.70 - 6.27: 23 6.27 - 7.84: 7 Bond angle restraints: 21885 Sorted by residual: angle pdb=" C LEU D 75 " pdb=" N ILE D 76 " pdb=" CA ILE D 76 " ideal model delta sigma weight residual 120.33 123.51 -3.18 8.00e-01 1.56e+00 1.58e+01 angle pdb=" N LEU B 52 " pdb=" CA LEU B 52 " pdb=" CB LEU B 52 " ideal model delta sigma weight residual 110.49 115.58 -5.09 1.48e+00 4.57e-01 1.18e+01 angle pdb=" CA MET B 214 " pdb=" C MET B 214 " pdb=" O MET B 214 " ideal model delta sigma weight residual 120.55 117.14 3.41 1.06e+00 8.90e-01 1.04e+01 angle pdb=" O PHE B 62 " pdb=" C PHE B 62 " pdb=" N GLU B 63 " ideal model delta sigma weight residual 122.12 125.38 -3.26 1.06e+00 8.90e-01 9.43e+00 angle pdb=" CA TYR C 50 " pdb=" C TYR C 50 " pdb=" O TYR C 50 " ideal model delta sigma weight residual 120.55 117.30 3.25 1.06e+00 8.90e-01 9.40e+00 ... (remaining 21880 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 8217 17.90 - 35.81: 869 35.81 - 53.71: 222 53.71 - 71.62: 43 71.62 - 89.52: 24 Dihedral angle restraints: 9375 sinusoidal: 3810 harmonic: 5565 Sorted by residual: dihedral pdb=" CA LEU E 52 " pdb=" C LEU E 52 " pdb=" N ALA E 53 " pdb=" CA ALA E 53 " ideal model delta harmonic sigma weight residual 180.00 160.66 19.34 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CG ARG D 13 " pdb=" CD ARG D 13 " pdb=" NE ARG D 13 " pdb=" CZ ARG D 13 " ideal model delta sinusoidal sigma weight residual -90.00 -41.94 -48.06 2 1.50e+01 4.44e-03 1.18e+01 dihedral pdb=" CB GLU C 119 " pdb=" CG GLU C 119 " pdb=" CD GLU C 119 " pdb=" OE1 GLU C 119 " ideal model delta sinusoidal sigma weight residual 0.00 88.76 -88.76 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 9372 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1780 0.040 - 0.080: 472 0.080 - 0.120: 109 0.120 - 0.160: 12 0.160 - 0.200: 2 Chirality restraints: 2375 Sorted by residual: chirality pdb=" CA LEU B 52 " pdb=" N LEU B 52 " pdb=" C LEU B 52 " pdb=" CB LEU B 52 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.97e-01 chirality pdb=" CA LEU C 52 " pdb=" N LEU C 52 " pdb=" C LEU C 52 " pdb=" CB LEU C 52 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.91e-01 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 2.59 -0.15 2.00e-01 2.50e+01 5.95e-01 ... (remaining 2372 not shown) Planarity restraints: 2750 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 80 " 0.013 2.00e-02 2.50e+03 1.57e-02 4.29e+00 pdb=" CG PHE E 80 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE E 80 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE E 80 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE E 80 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE E 80 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE E 80 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 164 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.74e+00 pdb=" N PRO B 165 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 165 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 165 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 164 " -0.032 5.00e-02 4.00e+02 4.82e-02 3.71e+00 pdb=" N PRO A 165 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 165 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 165 " -0.027 5.00e-02 4.00e+02 ... (remaining 2747 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 175 2.63 - 3.20: 13753 3.20 - 3.76: 26577 3.76 - 4.33: 37133 4.33 - 4.90: 60170 Nonbonded interactions: 137808 Sorted by model distance: nonbonded pdb=" O LEU C 52 " pdb=" CD1 LEU C 52 " model vdw 2.059 3.460 nonbonded pdb=" NH2 ARG B 51 " pdb=" O PHE B 257 " model vdw 2.163 3.120 nonbonded pdb=" OE1 GLU D 292 " pdb=" OG SER E 16 " model vdw 2.196 3.040 nonbonded pdb=" OH TYR E 43 " pdb=" O ARG E 255 " model vdw 2.213 3.040 nonbonded pdb=" O GLN A 353 " pdb=" NH1 ARG A 356 " model vdw 2.236 3.120 ... (remaining 137803 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.520 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: 0.030 Extract box with map and model: 0.290 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.180 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 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 : 0.003 0.036 16065 Z= 0.165 Angle : 0.564 7.838 21885 Z= 0.319 Chirality : 0.039 0.200 2375 Planarity : 0.004 0.048 2750 Dihedral : 16.167 89.523 5785 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.66 % Favored : 98.29 % Rotamer: Outliers : 1.53 % Allowed : 15.63 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.18), residues: 1870 helix: 1.47 (0.14), residues: 1225 sheet: None (None), residues: 0 loop : -0.39 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 13 TYR 0.024 0.001 TYR D 97 PHE 0.036 0.001 PHE E 80 TRP 0.013 0.001 TRP A 93 HIS 0.002 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.16 (16065) covalent geometry : angle 0.56419 / 0.32 (21885) hydrogen bonds : bond 0.08688 / 5.63 ( 953) hydrogen bonds : angle 4.45357 / 3.33 ( 2778) *********************** 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 231 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 205 time to evaluate : 0.618 Fit side-chains revert: symmetry clash REVERT: D 25 ARG cc_start: 0.8187 (mmm-85) cc_final: 0.6529 (mtm-85) REVERT: D 374 GLU cc_start: 0.7589 (tm-30) cc_final: 0.7286 (tm-30) REVERT: B 13 ARG cc_start: 0.7923 (ptt180) cc_final: 0.7683 (ptt90) REVERT: E 169 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8083 (tptp) REVERT: A 25 ARG cc_start: 0.8030 (mtp-110) cc_final: 0.6909 (mtm-85) REVERT: A 374 GLU cc_start: 0.7949 (mp0) cc_final: 0.7451 (mp0) REVERT: C 119 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7230 (tp30) REVERT: C 169 LYS cc_start: 0.8334 (mttp) cc_final: 0.8057 (mmmt) outliers start: 26 outliers final: 17 residues processed: 222 average time/residue: 0.6853 time to fit residues: 166.6407 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 : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 169 LYS Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 344 GLN Chi-restraints excluded: chain C residue 367 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.4980 chunk 149 optimal weight: 3.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 376 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.114127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.093331 restraints weight = 19359.031| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.46 r_work: 0.2979 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.0593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16065 Z= 0.186 Angle : 0.548 7.944 21885 Z= 0.288 Chirality : 0.041 0.157 2375 Planarity : 0.005 0.051 2750 Dihedral : 5.773 82.034 2119 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.01 % Allowed : 14.51 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.18), residues: 1870 helix: 1.21 (0.14), residues: 1255 sheet: None (None), residues: 0 loop : -0.59 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 25 TYR 0.025 0.002 TYR D 97 PHE 0.025 0.002 PHE E 80 TRP 0.015 0.002 TRP C 309 HIS 0.003 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.19 (16065) covalent geometry : angle 0.54823 / 0.29 (21885) hydrogen bonds : bond 0.06044 / 3.99 ( 953) hydrogen bonds : angle 4.31698 / 3.21 ( 2778) *********************** 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 253 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 202 time to evaluate : 0.717 Fit side-chains REVERT: D 25 ARG cc_start: 0.8273 (mmm-85) cc_final: 0.6574 (mtm-85) REVERT: D 374 GLU cc_start: 0.7599 (tm-30) cc_final: 0.7224 (tm-30) REVERT: B 13 ARG cc_start: 0.7966 (ptt180) cc_final: 0.7605 (ptt90) REVERT: B 376 GLN cc_start: 0.7333 (mt0) cc_final: 0.7107 (mt0) REVERT: E 119 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7511 (tp30) REVERT: E 203 ASP cc_start: 0.8537 (OUTLIER) cc_final: 0.8329 (t70) REVERT: A 25 ARG cc_start: 0.8284 (mtp-110) cc_final: 0.6830 (mtm-85) REVERT: A 203 ASP cc_start: 0.8752 (OUTLIER) cc_final: 0.8517 (t70) REVERT: C 169 LYS cc_start: 0.8463 (mttp) cc_final: 0.8033 (mmmt) REVERT: C 331 ARG cc_start: 0.8161 (ttp-110) cc_final: 0.7431 (ttp-170) outliers start: 51 outliers final: 23 residues processed: 237 average time/residue: 0.6515 time to fit residues: 170.0131 Evaluate side-chains 217 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 191 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 344 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 9 optimal weight: 0.5980 chunk 129 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 103 optimal weight: 0.4980 chunk 178 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 168 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 GLN E 296 ASN A 259 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.116914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.096207 restraints weight = 19461.979| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.46 r_work: 0.3001 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.0675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16065 Z= 0.125 Angle : 0.488 7.227 21885 Z= 0.257 Chirality : 0.038 0.152 2375 Planarity : 0.004 0.050 2750 Dihedral : 4.627 46.585 2092 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.48 % Allowed : 15.34 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.18), residues: 1870 helix: 1.41 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.40 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 51 TYR 0.018 0.001 TYR A 97 PHE 0.016 0.001 PHE D 80 TRP 0.013 0.001 TRP A 309 HIS 0.002 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (16065) covalent geometry : angle 0.48840 / 0.26 (21885) hydrogen bonds : bond 0.05280 / 3.48 ( 953) hydrogen bonds : angle 4.22913 / 3.14 ( 2778) *********************** 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 249 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 207 time to evaluate : 0.629 Fit side-chains revert: symmetry clash REVERT: D 25 ARG cc_start: 0.8267 (mmm-85) cc_final: 0.6582 (mtm-85) REVERT: D 374 GLU cc_start: 0.7521 (tm-30) cc_final: 0.7104 (tm-30) REVERT: B 67 LEU cc_start: 0.7851 (mp) cc_final: 0.7624 (mm) REVERT: B 203 ASP cc_start: 0.8418 (OUTLIER) cc_final: 0.8169 (t70) REVERT: E 119 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7469 (tp30) REVERT: E 374 GLU cc_start: 0.8379 (mp0) cc_final: 0.8099 (mp0) REVERT: A 25 ARG cc_start: 0.8284 (mtp-110) cc_final: 0.6799 (mtm-85) REVERT: A 80 PHE cc_start: 0.7604 (OUTLIER) cc_final: 0.7226 (m-80) REVERT: A 172 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7476 (pt0) REVERT: A 203 ASP cc_start: 0.8660 (OUTLIER) cc_final: 0.8402 (t70) REVERT: C 51 ARG cc_start: 0.7723 (mmt90) cc_final: 0.7351 (mmt90) REVERT: C 119 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7465 (tp30) REVERT: C 169 LYS cc_start: 0.8424 (mttp) cc_final: 0.8003 (mmmt) outliers start: 42 outliers final: 22 residues processed: 239 average time/residue: 0.6555 time to fit residues: 172.0969 Evaluate side-chains 215 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 188 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain E residue 367 SER Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 269 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 153 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 chunk 145 optimal weight: 0.3980 chunk 140 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 GLN C 259 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.113757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.092908 restraints weight = 19349.193| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.45 r_work: 0.2974 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.0798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16065 Z= 0.189 Angle : 0.537 7.719 21885 Z= 0.283 Chirality : 0.040 0.157 2375 Planarity : 0.005 0.049 2750 Dihedral : 4.571 46.424 2089 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.19 % Allowed : 15.22 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.18), residues: 1870 helix: 1.16 (0.14), residues: 1255 sheet: None (None), residues: 0 loop : -0.62 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 331 TYR 0.024 0.002 TYR C 44 PHE 0.028 0.002 PHE E 80 TRP 0.015 0.002 TRP A 309 HIS 0.003 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 (16065) covalent geometry : angle 0.53717 / 0.28 (21885) hydrogen bonds : bond 0.06081 / 4.02 ( 953) hydrogen bonds : angle 4.30618 / 3.20 ( 2778) *********************** 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 251 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 197 time to evaluate : 0.624 Fit side-chains REVERT: D 25 ARG cc_start: 0.8294 (mmm-85) cc_final: 0.6658 (mtm-85) REVERT: D 374 GLU cc_start: 0.7576 (tm-30) cc_final: 0.7180 (tm-30) REVERT: B 67 LEU cc_start: 0.7845 (mp) cc_final: 0.7617 (mm) REVERT: E 119 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7458 (tp30) REVERT: E 374 GLU cc_start: 0.8392 (mp0) cc_final: 0.8047 (mp0) REVERT: A 25 ARG cc_start: 0.8308 (mtp-110) cc_final: 0.6787 (mtm-85) REVERT: A 172 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7537 (pt0) REVERT: A 203 ASP cc_start: 0.8777 (OUTLIER) cc_final: 0.8539 (t70) REVERT: C 119 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7410 (tp30) REVERT: C 169 LYS cc_start: 0.8418 (mttp) cc_final: 0.7999 (mmmt) REVERT: C 331 ARG cc_start: 0.8152 (ttp-110) cc_final: 0.7509 (ttp-170) outliers start: 54 outliers final: 28 residues processed: 237 average time/residue: 0.6359 time to fit residues: 166.1943 Evaluate side-chains 220 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 189 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain E residue 367 SER Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 344 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 53 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 144 optimal weight: 0.0270 chunk 58 optimal weight: 3.9990 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN B 369 ASN E 155 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.116901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.096117 restraints weight = 19407.466| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.46 r_work: 0.3000 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.0786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16065 Z= 0.123 Angle : 0.486 7.187 21885 Z= 0.255 Chirality : 0.037 0.152 2375 Planarity : 0.004 0.052 2750 Dihedral : 4.383 46.491 2089 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.65 % Allowed : 15.69 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.18), residues: 1870 helix: 1.38 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.42 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 331 TYR 0.020 0.001 TYR A 97 PHE 0.018 0.001 PHE D 80 TRP 0.013 0.001 TRP C 93 HIS 0.002 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (16065) covalent geometry : angle 0.48634 / 0.26 (21885) hydrogen bonds : bond 0.05275 / 3.48 ( 953) hydrogen bonds : angle 4.22791 / 3.14 ( 2778) *********************** 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 243 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 198 time to evaluate : 0.601 Fit side-chains REVERT: D 25 ARG cc_start: 0.8265 (mmm-85) cc_final: 0.6631 (mtm-85) REVERT: D 374 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7127 (tm-30) REVERT: B 203 ASP cc_start: 0.8382 (OUTLIER) cc_final: 0.8156 (t70) REVERT: E 119 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7397 (tp30) REVERT: E 374 GLU cc_start: 0.8382 (mp0) cc_final: 0.7996 (mp0) REVERT: A 25 ARG cc_start: 0.8280 (mtp-110) cc_final: 0.6779 (mtm-85) REVERT: A 172 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7503 (pt0) REVERT: A 203 ASP cc_start: 0.8662 (OUTLIER) cc_final: 0.8403 (t70) REVERT: A 373 MET cc_start: 0.8232 (mtp) cc_final: 0.8002 (mtt) REVERT: A 374 GLU cc_start: 0.8131 (mp0) cc_final: 0.7575 (mp0) REVERT: C 119 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7430 (tp30) REVERT: C 169 LYS cc_start: 0.8413 (mttp) cc_final: 0.7988 (mmmt) REVERT: C 331 ARG cc_start: 0.8137 (ttp-110) cc_final: 0.7737 (ttp-170) REVERT: C 373 MET cc_start: 0.8684 (mtm) cc_final: 0.8404 (mtm) outliers start: 45 outliers final: 25 residues processed: 236 average time/residue: 0.6229 time to fit residues: 162.2291 Evaluate side-chains 215 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 185 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 374 GLU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain E residue 367 SER Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 311 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 64 optimal weight: 0.2980 chunk 150 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 153 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 144 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 GLN E 376 GLN C 259 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.116082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.095329 restraints weight = 19265.943| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.45 r_work: 0.3010 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.0838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16065 Z= 0.139 Angle : 0.501 7.196 21885 Z= 0.262 Chirality : 0.038 0.152 2375 Planarity : 0.004 0.051 2750 Dihedral : 4.410 46.421 2089 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.71 % Allowed : 16.05 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.18), residues: 1870 helix: 1.37 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.40 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 25 TYR 0.021 0.001 TYR D 97 PHE 0.029 0.001 PHE E 80 TRP 0.014 0.001 TRP A 309 HIS 0.003 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (16065) covalent geometry : angle 0.50128 / 0.26 (21885) hydrogen bonds : bond 0.05476 / 3.62 ( 953) hydrogen bonds : angle 4.22652 / 3.14 ( 2778) *********************** 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 235 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 189 time to evaluate : 0.628 Fit side-chains REVERT: D 25 ARG cc_start: 0.8252 (mmm-85) cc_final: 0.6587 (mtm-85) REVERT: D 374 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7129 (tm-30) REVERT: B 203 ASP cc_start: 0.8442 (OUTLIER) cc_final: 0.8202 (t70) REVERT: E 119 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7380 (tp30) REVERT: E 203 ASP cc_start: 0.8526 (OUTLIER) cc_final: 0.8325 (t70) REVERT: E 374 GLU cc_start: 0.8389 (mp0) cc_final: 0.8012 (mp0) REVERT: A 25 ARG cc_start: 0.8305 (mtp-110) cc_final: 0.6807 (mtm-85) REVERT: A 203 ASP cc_start: 0.8679 (OUTLIER) cc_final: 0.8473 (t70) REVERT: C 119 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7406 (tp30) REVERT: C 169 LYS cc_start: 0.8418 (mttp) cc_final: 0.7987 (mmmt) REVERT: C 331 ARG cc_start: 0.8161 (ttp-110) cc_final: 0.7568 (ttp-170) REVERT: C 373 MET cc_start: 0.8685 (mtm) cc_final: 0.8412 (mtm) outliers start: 46 outliers final: 25 residues processed: 225 average time/residue: 0.6280 time to fit residues: 156.1321 Evaluate side-chains 217 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 186 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain D residue 374 GLU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain E residue 367 SER Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 311 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 115 optimal weight: 0.9980 chunk 43 optimal weight: 0.1980 chunk 108 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 146 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 113 optimal weight: 0.2980 chunk 49 optimal weight: 1.9990 chunk 15 optimal weight: 0.0470 chunk 71 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 ASN E 155 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.118808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.098149 restraints weight = 19152.805| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.45 r_work: 0.3041 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 16065 Z= 0.111 Angle : 0.475 6.677 21885 Z= 0.247 Chirality : 0.037 0.150 2375 Planarity : 0.004 0.051 2750 Dihedral : 4.271 46.815 2089 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.65 % Allowed : 16.34 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.19), residues: 1870 helix: 1.48 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.39 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 25 TYR 0.022 0.001 TYR A 33 PHE 0.019 0.001 PHE D 80 TRP 0.013 0.001 TRP A 93 HIS 0.002 0.000 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (16065) covalent geometry : angle 0.47450 / 0.25 (21885) hydrogen bonds : bond 0.04959 / 3.27 ( 953) hydrogen bonds : angle 4.16881 / 3.10 ( 2778) *********************** 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 237 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 192 time to evaluate : 0.791 Fit side-chains REVERT: D 25 ARG cc_start: 0.8224 (mmm-85) cc_final: 0.6590 (mtm-85) REVERT: D 374 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7081 (tm-30) REVERT: B 203 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.8142 (t70) REVERT: E 119 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7326 (tp30) REVERT: E 374 GLU cc_start: 0.8467 (mp0) cc_final: 0.8041 (mp0) REVERT: A 25 ARG cc_start: 0.8282 (mtp-110) cc_final: 0.6783 (mtm-85) REVERT: A 203 ASP cc_start: 0.8602 (OUTLIER) cc_final: 0.8384 (t70) REVERT: A 271 LEU cc_start: 0.6532 (OUTLIER) cc_final: 0.6283 (mp) REVERT: A 374 GLU cc_start: 0.8121 (mp0) cc_final: 0.7617 (mp0) REVERT: C 119 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7403 (tp30) REVERT: C 123 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8338 (tt) REVERT: C 169 LYS cc_start: 0.8437 (mttp) cc_final: 0.8027 (mmmt) REVERT: C 331 ARG cc_start: 0.8152 (ttp-110) cc_final: 0.7754 (ttp-170) REVERT: C 373 MET cc_start: 0.8676 (mtm) cc_final: 0.8448 (mtt) outliers start: 45 outliers final: 23 residues processed: 229 average time/residue: 0.6090 time to fit residues: 154.4906 Evaluate side-chains 213 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 183 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain D residue 374 GLU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain E residue 344 GLN Chi-restraints excluded: chain E residue 367 SER Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 172 GLU Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 344 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 146 optimal weight: 0.5980 chunk 151 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 178 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 259 ASN E 155 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.111960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.091146 restraints weight = 19419.525| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.45 r_work: 0.2947 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 16065 Z= 0.268 Angle : 0.595 7.894 21885 Z= 0.312 Chirality : 0.044 0.166 2375 Planarity : 0.005 0.050 2750 Dihedral : 4.696 45.774 2089 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.83 % Allowed : 15.87 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.18), residues: 1870 helix: 1.00 (0.14), residues: 1255 sheet: None (None), residues: 0 loop : -0.64 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 25 TYR 0.027 0.002 TYR D 97 PHE 0.037 0.002 PHE E 80 TRP 0.016 0.002 TRP B 309 HIS 0.004 0.001 HIS D 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00641 / 0.27 (16065) covalent geometry : angle 0.59535 / 0.31 (21885) hydrogen bonds : bond 0.06726 / 4.45 ( 953) hydrogen bonds : angle 4.39003 / 3.26 ( 2778) *********************** 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 238 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 190 time to evaluate : 0.617 Fit side-chains REVERT: D 25 ARG cc_start: 0.8278 (mmm-85) cc_final: 0.6635 (mtm-85) REVERT: D 374 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7225 (tm-30) REVERT: B 203 ASP cc_start: 0.8567 (OUTLIER) cc_final: 0.8275 (t70) REVERT: E 119 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7494 (tp30) REVERT: A 25 ARG cc_start: 0.8308 (mtp-110) cc_final: 0.6765 (mtm-85) REVERT: A 203 ASP cc_start: 0.8830 (OUTLIER) cc_final: 0.8572 (t70) REVERT: A 271 LEU cc_start: 0.6612 (OUTLIER) cc_final: 0.6348 (mp) REVERT: A 374 GLU cc_start: 0.8132 (mp0) cc_final: 0.7519 (mp0) REVERT: C 119 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7399 (tp30) REVERT: C 169 LYS cc_start: 0.8420 (mttp) cc_final: 0.8001 (mmmt) REVERT: C 331 ARG cc_start: 0.8179 (ttp-110) cc_final: 0.7507 (ttp-170) REVERT: C 373 MET cc_start: 0.8640 (mtm) cc_final: 0.8359 (mtm) outliers start: 48 outliers final: 24 residues processed: 228 average time/residue: 0.6068 time to fit residues: 152.6106 Evaluate side-chains 216 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 186 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain D residue 374 GLU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain E residue 367 SER Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 367 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 94 optimal weight: 0.6980 chunk 145 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 144 optimal weight: 0.0060 chunk 35 optimal weight: 0.7980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 376 GLN B 369 ASN E 155 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.117308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.096628 restraints weight = 19267.499| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.45 r_work: 0.3008 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 16065 Z= 0.119 Angle : 0.496 6.923 21885 Z= 0.259 Chirality : 0.037 0.152 2375 Planarity : 0.004 0.051 2750 Dihedral : 4.393 46.621 2089 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.83 % Allowed : 16.99 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.18), residues: 1870 helix: 1.31 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.44 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 25 TYR 0.026 0.001 TYR D 97 PHE 0.026 0.001 PHE D 80 TRP 0.014 0.002 TRP E 93 HIS 0.002 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (16065) covalent geometry : angle 0.49616 / 0.26 (21885) hydrogen bonds : bond 0.05217 / 3.43 ( 953) hydrogen bonds : angle 4.24485 / 3.15 ( 2778) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 188 time to evaluate : 0.556 Fit side-chains REVERT: D 25 ARG cc_start: 0.8235 (mmm-85) cc_final: 0.6632 (mtm-85) REVERT: D 374 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7079 (tm-30) REVERT: B 203 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.8081 (t70) REVERT: E 119 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7373 (tp30) REVERT: A 25 ARG cc_start: 0.8284 (mtp-110) cc_final: 0.6786 (mtm-85) REVERT: A 203 ASP cc_start: 0.8639 (OUTLIER) cc_final: 0.8432 (t70) REVERT: A 374 GLU cc_start: 0.8164 (mp0) cc_final: 0.7560 (mp0) REVERT: C 80 PHE cc_start: 0.6958 (m-80) cc_final: 0.6717 (m-80) REVERT: C 119 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7390 (tp30) REVERT: C 169 LYS cc_start: 0.8407 (mttp) cc_final: 0.7966 (mmmt) REVERT: C 331 ARG cc_start: 0.8141 (ttp-110) cc_final: 0.7538 (ttp-170) REVERT: C 373 MET cc_start: 0.8661 (mtm) cc_final: 0.8390 (mtt) outliers start: 31 outliers final: 23 residues processed: 215 average time/residue: 0.6240 time to fit residues: 147.8980 Evaluate side-chains 212 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain D residue 374 GLU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain E residue 367 SER Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 311 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 37 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 139 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 147 optimal weight: 7.9990 chunk 161 optimal weight: 0.9980 chunk 165 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 259 ASN D 369 ASN D 376 GLN B 369 ASN E 155 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.114476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.093697 restraints weight = 19230.250| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.44 r_work: 0.2986 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8863 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16065 Z= 0.179 Angle : 0.540 7.514 21885 Z= 0.283 Chirality : 0.040 0.156 2375 Planarity : 0.004 0.051 2750 Dihedral : 4.526 45.992 2089 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.89 % Allowed : 17.29 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.18), residues: 1870 helix: 1.12 (0.14), residues: 1260 sheet: None (None), residues: 0 loop : -0.60 (0.23), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 331 TYR 0.029 0.002 TYR D 97 PHE 0.041 0.002 PHE E 80 TRP 0.015 0.002 TRP A 309 HIS 0.003 0.001 HIS A 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (16065) covalent geometry : angle 0.54023 / 0.28 (21885) hydrogen bonds : bond 0.05912 / 3.90 ( 953) hydrogen bonds : angle 4.29559 / 3.19 ( 2778) ********************** 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 219 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 187 time to evaluate : 0.680 Fit side-chains REVERT: D 25 ARG cc_start: 0.8266 (mmm-85) cc_final: 0.6636 (mtm-85) REVERT: D 374 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7156 (tm-30) REVERT: B 203 ASP cc_start: 0.8439 (OUTLIER) cc_final: 0.8183 (t70) REVERT: E 119 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7381 (tp30) REVERT: A 25 ARG cc_start: 0.8282 (mtp-110) cc_final: 0.6770 (mtm-85) REVERT: A 203 ASP cc_start: 0.8763 (OUTLIER) cc_final: 0.8522 (t70) REVERT: A 271 LEU cc_start: 0.6629 (OUTLIER) cc_final: 0.6393 (mp) REVERT: A 374 GLU cc_start: 0.8159 (mp0) cc_final: 0.7540 (mp0) REVERT: C 119 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7380 (tp30) REVERT: C 169 LYS cc_start: 0.8409 (mttp) cc_final: 0.7980 (mmmt) REVERT: C 331 ARG cc_start: 0.8153 (ttp-110) cc_final: 0.7535 (ttp-170) REVERT: C 373 MET cc_start: 0.8668 (mtm) cc_final: 0.8407 (mtm) outliers start: 32 outliers final: 23 residues processed: 214 average time/residue: 0.6056 time to fit residues: 143.2908 Evaluate side-chains 214 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 185 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain D residue 374 GLU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain E residue 367 SER Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 311 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 34 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 144 optimal weight: 0.4980 chunk 101 optimal weight: 0.0770 chunk 61 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 369 ASN D 376 GLN B 369 ASN E 155 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.118505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.097860 restraints weight = 19174.123| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.45 r_work: 0.3037 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 16065 Z= 0.115 Angle : 0.488 7.309 21885 Z= 0.254 Chirality : 0.037 0.151 2375 Planarity : 0.004 0.051 2750 Dihedral : 4.309 46.735 2089 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.82 % Favored : 98.13 % Rotamer: Outliers : 1.83 % Allowed : 17.35 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.18), residues: 1870 helix: 1.39 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.41 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 331 TYR 0.025 0.001 TYR D 97 PHE 0.026 0.001 PHE D 80 TRP 0.015 0.001 TRP D 185 HIS 0.002 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (16065) covalent geometry : angle 0.48790 / 0.25 (21885) hydrogen bonds : bond 0.05026 / 3.30 ( 953) hydrogen bonds : angle 4.20947 / 3.12 ( 2778) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5098.83 seconds wall clock time: 88 minutes 0.71 seconds (5280.71 seconds total)