Starting phenix.real_space_refine on Fri Jun 13 22:55:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ctt_45918/06_2025/9ctt_45918.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ctt_45918/06_2025/9ctt_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ctt_45918/06_2025/9ctt_45918.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ctt_45918/06_2025/9ctt_45918.map" model { file = "/net/cci-nas-00/data/ceres_data/9ctt_45918/06_2025/9ctt_45918.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ctt_45918/06_2025/9ctt_45918.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.47, per 1000 atoms: 0.61 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: 4.25 Conformation dependent library (CDL) restraints added in 2.0 seconds 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3590 Finding SS restraints... Secondary structure from input PDB file: 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: 1.30 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: 4.27 Time building geometry restraints manager: 4.70 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: 0.02 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: 6.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 34.820 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (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 TRP 0.013 0.001 TRP A 93 HIS 0.002 0.001 HIS B 267 PHE 0.036 0.001 PHE E 80 TYR 0.024 0.001 TYR D 97 ARG 0.010 0.000 ARG D 13 Details of bonding type rmsd hydrogen bonds : bond 0.08688 ( 953) hydrogen bonds : angle 4.45357 ( 2778) covalent geometry : bond 0.00316 (16065) covalent geometry : angle 0.56419 (21885) *********************** 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 : 1.639 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: 0.8056 (mmmt) outliers start: 26 outliers final: 17 residues processed: 222 average time/residue: 1.4940 time to fit residues: 362.3036 Evaluate side-chains 207 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 188 time to evaluate : 1.727 ------------------------------------------------------------------------------- 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 156 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 168 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 376 GLN A 259 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.115508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.094764 restraints weight = 19264.258| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.46 r_work: 0.3001 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.0517 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= 0.150 Angle : 0.521 7.691 21885 Z= 0.272 Chirality : 0.039 0.152 2375 Planarity : 0.004 0.050 2750 Dihedral : 5.652 80.529 2119 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.60 % Allowed : 15.10 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.18), residues: 1870 helix: 1.45 (0.14), residues: 1225 sheet: None (None), residues: 0 loop : -0.40 (0.22), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 309 HIS 0.003 0.001 HIS A 326 PHE 0.025 0.001 PHE E 80 TYR 0.022 0.001 TYR D 97 ARG 0.008 0.001 ARG C 25 Details of bonding type rmsd hydrogen bonds : bond 0.05660 ( 953) hydrogen bonds : angle 4.26242 ( 2778) covalent geometry : bond 0.00335 (16065) covalent geometry : angle 0.52071 (21885) *********************** 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 245 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 201 time to evaluate : 1.800 Fit side-chains REVERT: D 25 ARG cc_start: 0.8290 (mmm-85) cc_final: 0.6637 (mtm-85) REVERT: D 374 GLU cc_start: 0.7589 (tm-30) cc_final: 0.7210 (tm-30) REVERT: B 13 ARG cc_start: 0.7953 (ptt180) cc_final: 0.7623 (ptt90) REVERT: B 376 GLN cc_start: 0.7358 (mt0) cc_final: 0.7104 (mt0) REVERT: E 119 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7498 (tp30) REVERT: A 25 ARG cc_start: 0.8290 (mtp-110) cc_final: 0.6868 (mtm-85) REVERT: A 172 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7507 (pt0) REVERT: C 169 LYS cc_start: 0.8468 (mttp) cc_final: 0.8043 (mmmt) REVERT: C 331 ARG cc_start: 0.8167 (ttp-110) cc_final: 0.7411 (ttp-170) REVERT: C 333 GLU cc_start: 0.8478 (pt0) cc_final: 0.8104 (pt0) outliers start: 44 outliers final: 19 residues processed: 233 average time/residue: 1.5382 time to fit residues: 391.8419 Evaluate side-chains 214 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 194 time to evaluate : 1.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 THR 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 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 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 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 344 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 33 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 177 optimal weight: 0.0170 chunk 69 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 overall best weight: 2.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.112554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.091748 restraints weight = 19305.959| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.45 r_work: 0.2955 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.0792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 16065 Z= 0.213 Angle : 0.563 7.923 21885 Z= 0.296 Chirality : 0.042 0.160 2375 Planarity : 0.005 0.050 2750 Dihedral : 4.928 46.161 2092 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.83 % Allowed : 15.22 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.18), residues: 1870 helix: 1.13 (0.14), residues: 1255 sheet: None (None), residues: 0 loop : -0.65 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 309 HIS 0.004 0.001 HIS B 267 PHE 0.024 0.002 PHE E 248 TYR 0.026 0.002 TYR C 44 ARG 0.006 0.000 ARG C 51 Details of bonding type rmsd hydrogen bonds : bond 0.06412 ( 953) hydrogen bonds : angle 4.37402 ( 2778) covalent geometry : bond 0.00500 (16065) covalent geometry : angle 0.56292 (21885) *********************** 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: 48 poor density : 201 time to evaluate : 1.794 Fit side-chains REVERT: D 25 ARG cc_start: 0.8309 (mmm-85) cc_final: 0.6670 (mtm-85) REVERT: D 374 GLU cc_start: 0.7581 (tm-30) cc_final: 0.7209 (tm-30) REVERT: B 203 ASP cc_start: 0.8520 (OUTLIER) cc_final: 0.8242 (t70) REVERT: E 119 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7505 (tp30) REVERT: E 374 GLU cc_start: 0.8373 (mp0) cc_final: 0.8083 (mp0) REVERT: A 25 ARG cc_start: 0.8278 (mtp-110) cc_final: 0.6770 (mtm-85) REVERT: A 172 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7546 (pt0) REVERT: C 119 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7443 (tp30) REVERT: C 169 LYS cc_start: 0.8429 (mttp) cc_final: 0.7993 (mmmt) REVERT: C 331 ARG cc_start: 0.8183 (ttp-110) cc_final: 0.7417 (ttp-170) REVERT: C 333 GLU cc_start: 0.8614 (pt0) cc_final: 0.8204 (pt0) outliers start: 48 outliers final: 27 residues processed: 234 average time/residue: 1.5265 time to fit residues: 391.4278 Evaluate side-chains 220 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 190 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 344 GLN 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 9 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 137 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3351 r_free = 0.3351 target = 0.112460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.091650 restraints weight = 19233.150| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.45 r_work: 0.2953 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 16065 Z= 0.212 Angle : 0.560 7.993 21885 Z= 0.294 Chirality : 0.042 0.161 2375 Planarity : 0.005 0.049 2750 Dihedral : 4.953 45.633 2092 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.48 % Allowed : 14.63 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.18), residues: 1870 helix: 1.04 (0.14), residues: 1255 sheet: None (None), residues: 0 loop : -0.67 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 309 HIS 0.003 0.001 HIS A 326 PHE 0.028 0.002 PHE E 80 TYR 0.025 0.002 TYR A 97 ARG 0.007 0.000 ARG C 51 Details of bonding type rmsd hydrogen bonds : bond 0.06358 ( 953) hydrogen bonds : angle 4.39362 ( 2778) covalent geometry : bond 0.00499 (16065) covalent geometry : angle 0.55978 (21885) *********************** 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 256 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 197 time to evaluate : 1.668 Fit side-chains REVERT: D 25 ARG cc_start: 0.8309 (mmm-85) cc_final: 0.6682 (mtm-85) REVERT: D 374 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7237 (tm-30) REVERT: B 67 LEU cc_start: 0.7863 (mp) cc_final: 0.7610 (mm) REVERT: B 203 ASP cc_start: 0.8502 (OUTLIER) cc_final: 0.8211 (t70) REVERT: E 119 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7495 (tp30) REVERT: E 203 ASP cc_start: 0.8539 (OUTLIER) cc_final: 0.8331 (t70) REVERT: E 374 GLU cc_start: 0.8370 (mp0) cc_final: 0.8024 (mp0) REVERT: A 25 ARG cc_start: 0.8278 (mtp-110) cc_final: 0.6772 (mtm-85) REVERT: A 203 ASP cc_start: 0.8848 (OUTLIER) cc_final: 0.8612 (t70) REVERT: C 119 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7474 (tp30) REVERT: C 169 LYS cc_start: 0.8415 (mttp) cc_final: 0.7989 (mmmt) REVERT: C 331 ARG cc_start: 0.8167 (ttp-110) cc_final: 0.7399 (ttp-170) REVERT: C 333 GLU cc_start: 0.8569 (pt0) cc_final: 0.8035 (pt0) REVERT: C 373 MET cc_start: 0.8638 (mtm) cc_final: 0.8376 (mtm) outliers start: 59 outliers final: 28 residues processed: 240 average time/residue: 1.5547 time to fit residues: 417.3670 Evaluate side-chains 223 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 189 time to evaluate : 1.729 ------------------------------------------------------------------------------- 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 275 VAL 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 B residue 275 VAL Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 344 GLN 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 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 249 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 64 optimal weight: 0.9980 chunk 155 optimal weight: 0.7980 chunk 174 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 176 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 129 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 369 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.115751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.095053 restraints weight = 19370.705| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.45 r_work: 0.3005 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.0801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16065 Z= 0.128 Angle : 0.497 7.315 21885 Z= 0.261 Chirality : 0.038 0.153 2375 Planarity : 0.004 0.052 2750 Dihedral : 4.478 45.942 2089 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.77 % Allowed : 15.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.18), residues: 1870 helix: 1.34 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.48 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 309 HIS 0.002 0.001 HIS A 326 PHE 0.019 0.001 PHE D 80 TYR 0.022 0.001 TYR D 97 ARG 0.010 0.000 ARG E 25 Details of bonding type rmsd hydrogen bonds : bond 0.05400 ( 953) hydrogen bonds : angle 4.27690 ( 2778) covalent geometry : bond 0.00272 (16065) covalent geometry : angle 0.49748 (21885) *********************** 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 242 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 195 time to evaluate : 1.756 Fit side-chains revert: symmetry clash REVERT: D 25 ARG cc_start: 0.8264 (mmm-85) cc_final: 0.6644 (mtm-85) REVERT: D 374 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7127 (tm-30) REVERT: B 203 ASP cc_start: 0.8414 (OUTLIER) cc_final: 0.8166 (t70) REVERT: E 119 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7401 (tp30) REVERT: E 374 GLU cc_start: 0.8365 (mp0) cc_final: 0.7958 (mp0) REVERT: A 25 ARG cc_start: 0.8286 (mtp-110) cc_final: 0.6795 (mtm-85) REVERT: A 271 LEU cc_start: 0.6570 (OUTLIER) cc_final: 0.6358 (mp) REVERT: A 373 MET cc_start: 0.8262 (mtp) cc_final: 0.7991 (mtt) REVERT: A 374 GLU cc_start: 0.8131 (mp0) cc_final: 0.7561 (mp0) REVERT: C 119 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7456 (tp30) REVERT: C 169 LYS cc_start: 0.8397 (mttp) cc_final: 0.7977 (mmmt) REVERT: C 373 MET cc_start: 0.8672 (mtm) cc_final: 0.8435 (mtm) outliers start: 47 outliers final: 24 residues processed: 234 average time/residue: 1.3151 time to fit residues: 339.6588 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 : 1.803 ------------------------------------------------------------------------------- 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 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 A residue 108 SER Chi-restraints excluded: chain A residue 129 ILE 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 344 GLN 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 249 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 344 GLN Chi-restraints excluded: chain C residue 367 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 107 optimal weight: 0.0670 chunk 108 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 164 optimal weight: 1.9990 chunk 147 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 ASN E 155 GLN E 376 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.115898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.095119 restraints weight = 19351.691| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.46 r_work: 0.3006 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.0853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16065 Z= 0.133 Angle : 0.499 7.195 21885 Z= 0.260 Chirality : 0.038 0.152 2375 Planarity : 0.004 0.052 2750 Dihedral : 4.430 46.023 2089 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.89 % Allowed : 15.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.18), residues: 1870 helix: 1.39 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.43 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 309 HIS 0.003 0.001 HIS A 326 PHE 0.026 0.001 PHE E 80 TYR 0.022 0.001 TYR C 68 ARG 0.007 0.000 ARG B 331 Details of bonding type rmsd hydrogen bonds : bond 0.05414 ( 953) hydrogen bonds : angle 4.24569 ( 2778) covalent geometry : bond 0.00288 (16065) covalent geometry : angle 0.49942 (21885) *********************** 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 239 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 190 time to evaluate : 1.689 Fit side-chains REVERT: D 25 ARG cc_start: 0.8266 (mmm-85) cc_final: 0.6659 (mtm-85) REVERT: D 374 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7142 (tm-30) REVERT: E 119 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7382 (tp30) REVERT: E 374 GLU cc_start: 0.8412 (mp0) cc_final: 0.7986 (mp0) REVERT: A 25 ARG cc_start: 0.8281 (mtp-110) cc_final: 0.6792 (mtm-85) REVERT: A 80 PHE cc_start: 0.7617 (OUTLIER) cc_final: 0.7220 (m-80) REVERT: C 119 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7411 (tp30) REVERT: C 169 LYS cc_start: 0.8410 (mttp) cc_final: 0.7989 (mmmt) REVERT: C 331 ARG cc_start: 0.8146 (ttp-110) cc_final: 0.7688 (ttp-170) REVERT: C 373 MET cc_start: 0.8628 (mtm) cc_final: 0.8378 (mtm) outliers start: 49 outliers final: 28 residues processed: 228 average time/residue: 1.3459 time to fit residues: 338.6042 Evaluate side-chains 217 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 185 time to evaluate : 1.756 ------------------------------------------------------------------------------- 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 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 344 GLN 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 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 269 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 344 GLN Chi-restraints excluded: chain C residue 367 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 14 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 128 optimal weight: 0.4980 chunk 101 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3378 r_free = 0.3378 target = 0.114481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.093680 restraints weight = 19290.477| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.45 r_work: 0.2985 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.0890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 16065 Z= 0.161 Angle : 0.523 7.459 21885 Z= 0.273 Chirality : 0.039 0.155 2375 Planarity : 0.004 0.052 2750 Dihedral : 4.515 46.289 2089 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.77 % Allowed : 15.81 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.18), residues: 1870 helix: 1.21 (0.14), residues: 1260 sheet: None (None), residues: 0 loop : -0.61 (0.23), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 309 HIS 0.003 0.001 HIS A 326 PHE 0.026 0.002 PHE D 80 TYR 0.024 0.001 TYR D 97 ARG 0.007 0.000 ARG B 331 Details of bonding type rmsd hydrogen bonds : bond 0.05762 ( 953) hydrogen bonds : angle 4.27585 ( 2778) covalent geometry : bond 0.00365 (16065) covalent geometry : angle 0.52290 (21885) *********************** 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 236 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 189 time to evaluate : 1.823 Fit side-chains REVERT: D 25 ARG cc_start: 0.8272 (mmm-85) cc_final: 0.6620 (mtm-85) REVERT: D 374 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7128 (tm-30) REVERT: B 203 ASP cc_start: 0.8391 (OUTLIER) cc_final: 0.8136 (t70) REVERT: E 119 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7388 (tp30) REVERT: E 374 GLU cc_start: 0.8448 (mp0) cc_final: 0.7981 (mp0) REVERT: A 25 ARG cc_start: 0.8294 (mtp-110) cc_final: 0.6788 (mtm-85) REVERT: A 271 LEU cc_start: 0.6626 (OUTLIER) cc_final: 0.6414 (mp) REVERT: A 374 GLU cc_start: 0.8129 (mp0) cc_final: 0.7522 (mp0) REVERT: C 119 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7400 (tp30) REVERT: C 169 LYS cc_start: 0.8416 (mttp) cc_final: 0.8000 (mmmt) REVERT: C 331 ARG cc_start: 0.8157 (ttp-110) cc_final: 0.7769 (ttp-170) REVERT: C 373 MET cc_start: 0.8631 (mtm) cc_final: 0.8411 (mtm) outliers start: 47 outliers final: 29 residues processed: 229 average time/residue: 1.3510 time to fit residues: 341.6684 Evaluate side-chains 216 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 182 time to evaluate : 1.832 ------------------------------------------------------------------------------- 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 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 B residue 303 ASP Chi-restraints excluded: chain B residue 344 GLN 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 242 VAL 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 249 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 344 GLN Chi-restraints excluded: chain C residue 367 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 78 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 169 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 chunk 174 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 131 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3380 r_free = 0.3380 target = 0.114640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.093893 restraints weight = 19126.727| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.45 r_work: 0.2987 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.0924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 16065 Z= 0.157 Angle : 0.521 7.475 21885 Z= 0.272 Chirality : 0.039 0.156 2375 Planarity : 0.004 0.052 2750 Dihedral : 4.512 46.417 2089 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.65 % Allowed : 15.81 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.18), residues: 1870 helix: 1.20 (0.14), residues: 1260 sheet: None (None), residues: 0 loop : -0.61 (0.23), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 309 HIS 0.003 0.001 HIS A 326 PHE 0.033 0.002 PHE E 80 TYR 0.023 0.001 TYR D 97 ARG 0.007 0.000 ARG B 331 Details of bonding type rmsd hydrogen bonds : bond 0.05723 ( 953) hydrogen bonds : angle 4.27957 ( 2778) covalent geometry : bond 0.00355 (16065) covalent geometry : angle 0.52053 (21885) *********************** 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 233 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 188 time to evaluate : 1.912 Fit side-chains REVERT: D 25 ARG cc_start: 0.8280 (mmm-85) cc_final: 0.6668 (mtm-85) REVERT: D 374 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7108 (tm-30) REVERT: B 203 ASP cc_start: 0.8392 (OUTLIER) cc_final: 0.8157 (t70) REVERT: E 119 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7393 (tp30) REVERT: E 374 GLU cc_start: 0.8466 (mp0) cc_final: 0.8067 (mp0) REVERT: A 25 ARG cc_start: 0.8283 (mtp-110) cc_final: 0.6767 (mtm-85) REVERT: A 374 GLU cc_start: 0.8156 (mp0) cc_final: 0.7570 (mp0) REVERT: C 119 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7397 (tp30) REVERT: C 169 LYS cc_start: 0.8423 (mttp) cc_final: 0.8000 (mmmt) REVERT: C 331 ARG cc_start: 0.8154 (ttp-110) cc_final: 0.7578 (ttp-170) outliers start: 45 outliers final: 29 residues processed: 224 average time/residue: 1.7666 time to fit residues: 439.1219 Evaluate side-chains 215 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 182 time to evaluate : 1.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 123 LEU 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 123 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 344 GLN 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 173 LYS 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 Chi-restraints excluded: chain C residue 344 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 24 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 136 optimal weight: 0.0570 chunk 40 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 overall best weight: 0.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3392 r_free = 0.3392 target = 0.115558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.094823 restraints weight = 19174.018| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.45 r_work: 0.3003 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16065 Z= 0.137 Angle : 0.509 7.293 21885 Z= 0.266 Chirality : 0.038 0.153 2375 Planarity : 0.004 0.052 2750 Dihedral : 4.455 46.246 2089 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.42 % Allowed : 16.17 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.18), residues: 1870 helix: 1.24 (0.14), residues: 1260 sheet: None (None), residues: 0 loop : -0.61 (0.23), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 309 HIS 0.003 0.001 HIS A 326 PHE 0.029 0.001 PHE D 80 TYR 0.025 0.001 TYR D 97 ARG 0.007 0.000 ARG B 331 Details of bonding type rmsd hydrogen bonds : bond 0.05486 ( 953) hydrogen bonds : angle 4.25516 ( 2778) covalent geometry : bond 0.00301 (16065) covalent geometry : angle 0.50897 (21885) *********************** 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 227 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 186 time to evaluate : 1.774 Fit side-chains REVERT: D 25 ARG cc_start: 0.8263 (mmm-85) cc_final: 0.6657 (mtm-85) REVERT: D 374 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7087 (tm-30) REVERT: B 203 ASP cc_start: 0.8358 (OUTLIER) cc_final: 0.8122 (t70) REVERT: E 119 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7384 (tp30) REVERT: E 374 GLU cc_start: 0.8431 (mp0) cc_final: 0.8028 (mp0) REVERT: A 25 ARG cc_start: 0.8286 (mtp-110) cc_final: 0.6782 (mtm-85) REVERT: A 374 GLU cc_start: 0.8153 (mp0) cc_final: 0.7559 (mp0) REVERT: C 119 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7406 (tp30) REVERT: C 169 LYS cc_start: 0.8421 (mttp) cc_final: 0.7993 (mmmt) REVERT: C 331 ARG cc_start: 0.8148 (ttp-110) cc_final: 0.7590 (ttp-170) REVERT: C 373 MET cc_start: 0.8670 (mtm) cc_final: 0.8455 (mtt) outliers start: 41 outliers final: 30 residues processed: 221 average time/residue: 1.3862 time to fit residues: 337.0645 Evaluate side-chains 218 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 184 time to evaluate : 1.813 ------------------------------------------------------------------------------- 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 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 B residue 344 GLN 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 242 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 311 VAL 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 Chi-restraints excluded: chain C residue 344 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 127 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 134 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 139 optimal weight: 0.8980 chunk 138 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 152 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 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 = 0.3403 r_free = 0.3403 target = 0.116331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.095569 restraints weight = 19375.736| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.46 r_work: 0.3013 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.0922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16065 Z= 0.132 Angle : 0.504 7.190 21885 Z= 0.263 Chirality : 0.038 0.151 2375 Planarity : 0.004 0.052 2750 Dihedral : 4.410 46.261 2089 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.06 % Allowed : 16.46 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.18), residues: 1870 helix: 1.39 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.42 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 309 HIS 0.003 0.001 HIS A 326 PHE 0.028 0.001 PHE D 80 TYR 0.024 0.001 TYR D 97 ARG 0.007 0.000 ARG B 331 Details of bonding type rmsd hydrogen bonds : bond 0.05359 ( 953) hydrogen bonds : angle 4.23216 ( 2778) covalent geometry : bond 0.00286 (16065) covalent geometry : angle 0.50413 (21885) ********************** 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 224 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 189 time to evaluate : 1.674 Fit side-chains REVERT: D 25 ARG cc_start: 0.8264 (mmm-85) cc_final: 0.6659 (mtm-85) REVERT: D 374 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.7062 (tm-30) REVERT: B 203 ASP cc_start: 0.8363 (OUTLIER) cc_final: 0.8145 (t70) REVERT: E 119 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7363 (tp30) REVERT: E 374 GLU cc_start: 0.8456 (mp0) cc_final: 0.8049 (mp0) REVERT: A 25 ARG cc_start: 0.8275 (mtp-110) cc_final: 0.6772 (mtm-85) REVERT: A 80 PHE cc_start: 0.7668 (OUTLIER) cc_final: 0.7230 (m-80) REVERT: A 374 GLU cc_start: 0.8166 (mp0) cc_final: 0.7565 (mp0) REVERT: C 123 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8324 (tt) REVERT: C 169 LYS cc_start: 0.8405 (mttp) cc_final: 0.7989 (mmmt) REVERT: C 331 ARG cc_start: 0.8173 (ttp-110) cc_final: 0.7714 (ttp-170) outliers start: 35 outliers final: 28 residues processed: 217 average time/residue: 1.3441 time to fit residues: 320.9240 Evaluate side-chains 219 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 186 time to evaluate : 1.626 ------------------------------------------------------------------------------- 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 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 B residue 344 GLN 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 344 GLN 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 242 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain C residue 78 ILE 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 344 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 149 optimal weight: 0.0050 chunk 124 optimal weight: 0.8980 chunk 156 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 164 optimal weight: 0.8980 chunk 169 optimal weight: 4.9990 chunk 131 optimal weight: 0.6980 chunk 109 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 369 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 = 0.3420 r_free = 0.3420 target = 0.117655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.096945 restraints weight = 19230.674| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.45 r_work: 0.3013 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 16065 Z= 0.118 Angle : 0.493 7.329 21885 Z= 0.256 Chirality : 0.037 0.150 2375 Planarity : 0.004 0.052 2750 Dihedral : 4.328 46.181 2089 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.71 % Favored : 98.24 % Rotamer: Outliers : 1.95 % Allowed : 16.64 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.18), residues: 1870 helix: 1.45 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.40 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 93 HIS 0.002 0.001 HIS B 326 PHE 0.023 0.001 PHE D 80 TYR 0.023 0.001 TYR D 97 ARG 0.007 0.000 ARG B 331 Details of bonding type rmsd hydrogen bonds : bond 0.05107 ( 953) hydrogen bonds : angle 4.19665 ( 2778) covalent geometry : bond 0.00248 (16065) covalent geometry : angle 0.49258 (21885) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11603.95 seconds wall clock time: 202 minutes 32.14 seconds (12152.14 seconds total)