Starting phenix.real_space_refine on Thu Sep 18 08:55:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ctt_45918/09_2025/9ctt_45918.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ctt_45918/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9ctt_45918/09_2025/9ctt_45918.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ctt_45918/09_2025/9ctt_45918.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ctt_45918/09_2025/9ctt_45918.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ctt_45918/09_2025/9ctt_45918.map" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.097 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 5 9.91 5 S 80 5.16 5 C 10260 2.51 5 N 2550 2.21 5 O 2700 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15595 Number of models: 1 Model: "" Number of chains: 10 Chain: "D" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3118 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 20, 'TRANS': 355} Chain: "B" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3118 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 20, 'TRANS': 355} Chain: "E" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3118 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 20, 'TRANS': 355} Chain: "A" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3118 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 20, 'TRANS': 355} Chain: "C" Number of atoms: 3118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3118 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 20, 'TRANS': 355} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 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: 3.97, per 1000 atoms: 0.25 Number of scatterers: 15595 At special positions: 0 Unit cell: (107.07, 108.73, 112.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 5 19.99 S 80 16.00 O 2700 8.00 N 2550 7.00 C 10260 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 648.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3590 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 3 sheets defined 70.2% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'D' and resid 18 through 23 removed outlier: 3.735A pdb=" N LEU D 22 " --> pdb=" O ARG D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 53 removed outlier: 5.817A pdb=" N GLY D 34 " --> pdb=" O LYS D 30 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N GLU D 35 " --> pdb=" O LEU D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 71 removed outlier: 3.954A pdb=" N SER D 71 " --> pdb=" O LEU D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 99 Processing helix chain 'D' and resid 103 through 114 Processing helix chain 'D' and resid 118 through 144 Processing helix chain 'D' and resid 144 through 151 Processing helix chain 'D' and resid 153 through 160 Processing helix chain 'D' and resid 164 through 175 Processing helix chain 'D' and resid 182 through 198 removed outlier: 3.689A pdb=" N VAL D 186 " --> pdb=" O TRP D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 230 Processing helix chain 'D' and resid 233 through 255 removed outlier: 3.779A pdb=" N LEU D 252 " --> pdb=" O PHE D 248 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL D 253 " --> pdb=" O LEU D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 263 Processing helix chain 'D' and resid 264 through 268 removed outlier: 4.107A pdb=" N GLU D 268 " --> pdb=" O PRO D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 295 removed outlier: 3.775A pdb=" N ALA D 291 " --> pdb=" O TRP D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 324 Processing helix chain 'D' and resid 348 through 355 removed outlier: 3.685A pdb=" N ALA D 352 " --> pdb=" O ALA D 349 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N GLN D 353 " --> pdb=" O ALA D 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 23 removed outlier: 3.704A pdb=" N LEU B 22 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N CYS B 23 " --> pdb=" O LEU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 53 removed outlier: 5.686A pdb=" N GLY B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N GLU B 35 " --> pdb=" O LEU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 70 Processing helix chain 'B' and resid 75 through 99 Processing helix chain 'B' and resid 103 through 114 Processing helix chain 'B' and resid 118 through 144 Processing helix chain 'B' and resid 144 through 151 Processing helix chain 'B' and resid 153 through 160 Processing helix chain 'B' and resid 164 through 175 Processing helix chain 'B' and resid 179 through 181 No H-bonds generated for 'chain 'B' and resid 179 through 181' Processing helix chain 'B' and resid 182 through 198 removed outlier: 3.695A pdb=" N VAL B 186 " --> pdb=" O TRP B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 230 Processing helix chain 'B' and resid 233 through 255 removed outlier: 3.941A pdb=" N LEU B 252 " --> pdb=" O PHE B 248 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 295 removed outlier: 3.784A pdb=" N ALA B 291 " --> pdb=" O TRP B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 324 Processing helix chain 'B' and resid 351 through 355 Processing helix chain 'E' and resid 17 through 23 removed outlier: 3.714A pdb=" N LEU E 22 " --> pdb=" O ARG E 19 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N CYS E 23 " --> pdb=" O LEU E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 52 removed outlier: 5.713A pdb=" N GLY E 34 " --> pdb=" O LYS E 30 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N GLU E 35 " --> pdb=" O LEU E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 71 removed outlier: 3.668A pdb=" N SER E 71 " --> pdb=" O LEU E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 99 removed outlier: 4.524A pdb=" N ILE E 78 " --> pdb=" O GLN E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 114 Processing helix chain 'E' and resid 118 through 144 Processing helix chain 'E' and resid 144 through 151 Processing helix chain 'E' and resid 153 through 160 Processing helix chain 'E' and resid 164 through 175 Processing helix chain 'E' and resid 182 through 198 removed outlier: 3.679A pdb=" N VAL E 186 " --> pdb=" O TRP E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 230 Processing helix chain 'E' and resid 233 through 255 removed outlier: 3.761A pdb=" N LEU E 252 " --> pdb=" O PHE E 248 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 263 removed outlier: 3.579A pdb=" N LYS E 262 " --> pdb=" O ASN E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 295 removed outlier: 3.774A pdb=" N ALA E 291 " --> pdb=" O TRP E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 324 Processing helix chain 'E' and resid 351 through 355 removed outlier: 3.650A pdb=" N ARG E 355 " --> pdb=" O ALA E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 374 removed outlier: 3.527A pdb=" N GLU E 374 " --> pdb=" O GLU E 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 23 removed outlier: 3.576A pdb=" N LEU A 22 " --> pdb=" O ARG A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 53 removed outlier: 5.789A pdb=" N GLY A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N GLU A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 72 removed outlier: 4.003A pdb=" N SER A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TYR A 72 " --> pdb=" O TYR A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 99 Processing helix chain 'A' and resid 103 through 114 Processing helix chain 'A' and resid 118 through 144 Processing helix chain 'A' and resid 144 through 151 Processing helix chain 'A' and resid 153 through 160 Processing helix chain 'A' and resid 164 through 174 Processing helix chain 'A' and resid 182 through 198 removed outlier: 3.676A pdb=" N VAL A 186 " --> pdb=" O TRP A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 230 Processing helix chain 'A' and resid 233 through 255 removed outlier: 3.898A pdb=" N LEU A 252 " --> pdb=" O PHE A 248 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 274 through 295 removed outlier: 3.789A pdb=" N ALA A 291 " --> pdb=" O TRP A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 324 Processing helix chain 'A' and resid 351 through 355 removed outlier: 3.552A pdb=" N ARG A 355 " --> pdb=" O ALA A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 373 Processing helix chain 'C' and resid 18 through 23 removed outlier: 3.672A pdb=" N LEU C 22 " --> pdb=" O ARG C 19 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS C 23 " --> pdb=" O LEU C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 52 removed outlier: 5.771A pdb=" N GLY C 34 " --> pdb=" O LYS C 30 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N GLU C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 71 removed outlier: 3.818A pdb=" N SER C 71 " --> pdb=" O LEU C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 99 Processing helix chain 'C' and resid 103 through 114 Processing helix chain 'C' and resid 118 through 144 Processing helix chain 'C' and resid 144 through 151 Processing helix chain 'C' and resid 153 through 160 Processing helix chain 'C' and resid 164 through 174 Processing helix chain 'C' and resid 179 through 181 No H-bonds generated for 'chain 'C' and resid 179 through 181' Processing helix chain 'C' and resid 182 through 198 removed outlier: 3.707A pdb=" N VAL C 186 " --> pdb=" O TRP C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 230 Processing helix chain 'C' and resid 233 through 255 removed outlier: 3.523A pdb=" N PHE C 247 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU C 252 " --> pdb=" O PHE C 248 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 263 Processing helix chain 'C' and resid 274 through 295 removed outlier: 3.793A pdb=" N ALA C 291 " --> pdb=" O TRP C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 324 Processing helix chain 'C' and resid 351 through 355 Processing sheet with id=AA1, first strand: chain 'D' and resid 375 through 376 removed outlier: 4.453A pdb=" N TYR C 347 " --> pdb=" O GLN D 376 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 347 through 348 removed outlier: 4.396A pdb=" N TYR B 347 " --> pdb=" O GLN C 376 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 347 through 348 removed outlier: 4.398A pdb=" N TYR E 347 " --> pdb=" O GLN A 376 " (cutoff:3.500A) 953 hydrogen bonds defined for protein. 2778 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.49 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4827 1.34 - 1.46: 4122 1.46 - 1.58: 6981 1.58 - 1.70: 0 1.70 - 1.82: 135 Bond restraints: 16065 Sorted by residual: bond pdb=" N LYS B 64 " pdb=" CA LYS B 64 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.20e-02 6.94e+03 7.98e+00 bond pdb=" N TYR C 50 " pdb=" CA TYR C 50 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.21e-02 6.83e+03 7.55e+00 bond pdb=" N ASP B 303 " pdb=" CA ASP B 303 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.26e-02 6.30e+03 7.35e+00 bond pdb=" N LYS C 262 " pdb=" CA LYS C 262 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.35e-02 5.49e+03 7.18e+00 bond pdb=" CA LYS B 64 " pdb=" C LYS B 64 " ideal model delta sigma weight residual 1.524 1.558 -0.034 1.32e-02 5.74e+03 6.76e+00 ... (remaining 16060 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 21354 1.57 - 3.14: 431 3.14 - 4.70: 70 4.70 - 6.27: 23 6.27 - 7.84: 7 Bond angle restraints: 21885 Sorted by residual: angle pdb=" C LEU D 75 " pdb=" N ILE D 76 " pdb=" CA ILE D 76 " ideal model delta sigma weight residual 120.33 123.51 -3.18 8.00e-01 1.56e+00 1.58e+01 angle pdb=" N LEU B 52 " pdb=" CA LEU B 52 " pdb=" CB LEU B 52 " ideal model delta sigma weight residual 110.49 115.58 -5.09 1.48e+00 4.57e-01 1.18e+01 angle pdb=" CA MET B 214 " pdb=" C MET B 214 " pdb=" O MET B 214 " ideal model delta sigma weight residual 120.55 117.14 3.41 1.06e+00 8.90e-01 1.04e+01 angle pdb=" O PHE B 62 " pdb=" C PHE B 62 " pdb=" N GLU B 63 " ideal model delta sigma weight residual 122.12 125.38 -3.26 1.06e+00 8.90e-01 9.43e+00 angle pdb=" CA TYR C 50 " pdb=" C TYR C 50 " pdb=" O TYR C 50 " ideal model delta sigma weight residual 120.55 117.30 3.25 1.06e+00 8.90e-01 9.40e+00 ... (remaining 21880 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 8217 17.90 - 35.81: 869 35.81 - 53.71: 222 53.71 - 71.62: 43 71.62 - 89.52: 24 Dihedral angle restraints: 9375 sinusoidal: 3810 harmonic: 5565 Sorted by residual: dihedral pdb=" CA LEU E 52 " pdb=" C LEU E 52 " pdb=" N ALA E 53 " pdb=" CA ALA E 53 " ideal model delta harmonic sigma weight residual 180.00 160.66 19.34 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CG ARG D 13 " pdb=" CD ARG D 13 " pdb=" NE ARG D 13 " pdb=" CZ ARG D 13 " ideal model delta sinusoidal sigma weight residual -90.00 -41.94 -48.06 2 1.50e+01 4.44e-03 1.18e+01 dihedral pdb=" CB GLU C 119 " pdb=" CG GLU C 119 " pdb=" CD GLU C 119 " pdb=" OE1 GLU C 119 " ideal model delta sinusoidal sigma weight residual 0.00 88.76 -88.76 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 9372 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1780 0.040 - 0.080: 472 0.080 - 0.120: 109 0.120 - 0.160: 12 0.160 - 0.200: 2 Chirality restraints: 2375 Sorted by residual: chirality pdb=" CA LEU B 52 " pdb=" N LEU B 52 " pdb=" C LEU B 52 " pdb=" CB LEU B 52 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.97e-01 chirality pdb=" CA LEU C 52 " pdb=" N LEU C 52 " pdb=" C LEU C 52 " pdb=" CB LEU C 52 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.91e-01 chirality pdb=" CA ILE C 232 " pdb=" N ILE C 232 " pdb=" C ILE C 232 " pdb=" CB ILE C 232 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.95e-01 ... (remaining 2372 not shown) Planarity restraints: 2750 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 80 " 0.013 2.00e-02 2.50e+03 1.57e-02 4.29e+00 pdb=" CG PHE E 80 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE E 80 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE E 80 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE E 80 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE E 80 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE E 80 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 164 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.74e+00 pdb=" N PRO B 165 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 165 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 165 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 164 " -0.032 5.00e-02 4.00e+02 4.82e-02 3.71e+00 pdb=" N PRO A 165 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 165 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 165 " -0.027 5.00e-02 4.00e+02 ... (remaining 2747 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 175 2.63 - 3.20: 13753 3.20 - 3.76: 26577 3.76 - 4.33: 37133 4.33 - 4.90: 60170 Nonbonded interactions: 137808 Sorted by model distance: nonbonded pdb=" O LEU C 52 " pdb=" CD1 LEU C 52 " model vdw 2.059 3.460 nonbonded pdb=" NH2 ARG B 51 " pdb=" O PHE B 257 " model vdw 2.163 3.120 nonbonded pdb=" OE1 GLU D 292 " pdb=" OG SER E 16 " model vdw 2.196 3.040 nonbonded pdb=" OH TYR E 43 " pdb=" O ARG E 255 " model vdw 2.213 3.040 nonbonded pdb=" O GLN A 353 " pdb=" NH1 ARG A 356 " model vdw 2.236 3.120 ... (remaining 137803 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.160 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.310 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 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:7.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.800 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.18), residues: 1870 helix: 1.47 (0.14), residues: 1225 sheet: None (None), residues: 0 loop : -0.39 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 13 TYR 0.024 0.001 TYR D 97 PHE 0.036 0.001 PHE E 80 TRP 0.013 0.001 TRP A 93 HIS 0.002 0.001 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00316 (16065) covalent geometry : angle 0.56419 (21885) hydrogen bonds : bond 0.08688 ( 953) hydrogen bonds : angle 4.45357 ( 2778) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 205 time to evaluate : 0.607 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: 0.7368 time to fit residues: 178.4672 Evaluate side-chains 207 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 188 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 169 LYS Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 344 GLN Chi-restraints excluded: chain C residue 367 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.4980 chunk 149 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 376 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.113874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.093057 restraints weight = 19323.439| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.46 r_work: 0.2975 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.0601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16065 Z= 0.188 Angle : 0.550 7.975 21885 Z= 0.288 Chirality : 0.041 0.156 2375 Planarity : 0.005 0.051 2750 Dihedral : 5.785 81.625 2119 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.95 % Allowed : 14.57 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.18), residues: 1870 helix: 1.22 (0.14), residues: 1255 sheet: None (None), residues: 0 loop : -0.60 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 25 TYR 0.023 0.002 TYR A 97 PHE 0.027 0.002 PHE E 80 TRP 0.015 0.002 TRP C 309 HIS 0.003 0.001 HIS B 267 Details of bonding type rmsd covalent geometry : bond 0.00438 (16065) covalent geometry : angle 0.54980 (21885) hydrogen bonds : bond 0.06095 ( 953) hydrogen bonds : angle 4.32845 ( 2778) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 201 time to evaluate : 0.601 Fit side-chains REVERT: D 25 ARG cc_start: 0.8277 (mmm-85) cc_final: 0.6582 (mtm-85) REVERT: D 374 GLU cc_start: 0.7599 (tm-30) cc_final: 0.7213 (tm-30) REVERT: B 13 ARG cc_start: 0.7938 (ptt180) cc_final: 0.7589 (ptt90) REVERT: B 376 GLN cc_start: 0.7349 (mt0) cc_final: 0.7089 (mt0) REVERT: E 119 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7529 (tp30) REVERT: E 203 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.8336 (t70) REVERT: A 25 ARG cc_start: 0.8279 (mtp-110) cc_final: 0.6822 (mtm-85) REVERT: A 203 ASP cc_start: 0.8761 (OUTLIER) cc_final: 0.8526 (t70) REVERT: C 169 LYS cc_start: 0.8444 (mttp) cc_final: 0.8012 (mmmt) REVERT: C 331 ARG cc_start: 0.8194 (ttp-110) cc_final: 0.7432 (ttp-170) outliers start: 50 outliers final: 23 residues processed: 236 average time/residue: 0.6949 time to fit residues: 179.5865 Evaluate side-chains 219 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 193 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 80 PHE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 269 LEU Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 344 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 9 optimal weight: 0.5980 chunk 129 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 103 optimal weight: 0.4980 chunk 178 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 168 optimal weight: 0.1980 chunk 92 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 A 259 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.116135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.095351 restraints weight = 19426.999| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.46 r_work: 0.3008 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.0645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16065 Z= 0.130 Angle : 0.495 7.350 21885 Z= 0.260 Chirality : 0.038 0.153 2375 Planarity : 0.004 0.050 2750 Dihedral : 4.672 46.497 2092 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.48 % Allowed : 15.28 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.18), residues: 1870 helix: 1.41 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.41 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 51 TYR 0.019 0.001 TYR A 97 PHE 0.015 0.001 PHE D 80 TRP 0.013 0.001 TRP A 309 HIS 0.003 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00281 (16065) covalent geometry : angle 0.49451 (21885) hydrogen bonds : bond 0.05398 ( 953) hydrogen bonds : angle 4.24707 ( 2778) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 202 time to evaluate : 0.636 Fit side-chains revert: symmetry clash REVERT: D 25 ARG cc_start: 0.8281 (mmm-85) cc_final: 0.6596 (mtm-85) REVERT: D 374 GLU cc_start: 0.7533 (tm-30) cc_final: 0.7120 (tm-30) REVERT: B 13 ARG cc_start: 0.7946 (ptt180) cc_final: 0.7531 (ptt90) REVERT: B 67 LEU cc_start: 0.7864 (mp) cc_final: 0.7638 (mm) REVERT: B 203 ASP cc_start: 0.8405 (OUTLIER) cc_final: 0.8156 (t70) REVERT: E 119 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7468 (tp30) REVERT: E 374 GLU cc_start: 0.8379 (mp0) cc_final: 0.8084 (mp0) REVERT: A 25 ARG cc_start: 0.8265 (mtp-110) cc_final: 0.6771 (mtm-85) REVERT: A 80 PHE cc_start: 0.7603 (OUTLIER) cc_final: 0.7192 (m-80) REVERT: A 172 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7474 (pt0) REVERT: A 203 ASP cc_start: 0.8687 (OUTLIER) cc_final: 0.8431 (t70) REVERT: A 374 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7913 (mp0) REVERT: C 119 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7458 (tp30) REVERT: C 169 LYS cc_start: 0.8417 (mttp) cc_final: 0.8000 (mmmt) REVERT: C 373 MET cc_start: 0.8641 (mtm) cc_final: 0.8370 (mtm) outliers start: 42 outliers final: 23 residues processed: 235 average time/residue: 0.7088 time to fit residues: 182.2882 Evaluate side-chains 216 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain E residue 367 SER Chi-restraints excluded: chain A residue 80 PHE Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain A residue 374 GLU 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 367 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 153 optimal weight: 6.9990 chunk 161 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 145 optimal weight: 0.0670 chunk 140 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 overall best weight: 1.3924 ------------------------------------------------------------------------------- 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** E 155 GLN ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.114299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.093413 restraints weight = 19294.469| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.46 r_work: 0.2980 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.0772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 16065 Z= 0.168 Angle : 0.521 7.671 21885 Z= 0.274 Chirality : 0.039 0.156 2375 Planarity : 0.004 0.049 2750 Dihedral : 4.534 46.548 2089 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.01 % Allowed : 15.46 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.18), residues: 1870 helix: 1.22 (0.14), residues: 1260 sheet: None (None), residues: 0 loop : -0.59 (0.23), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 51 TYR 0.022 0.002 TYR D 97 PHE 0.028 0.002 PHE E 80 TRP 0.015 0.002 TRP A 309 HIS 0.004 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00385 (16065) covalent geometry : angle 0.52095 (21885) hydrogen bonds : bond 0.05861 ( 953) hydrogen bonds : angle 4.28037 ( 2778) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 192 time to evaluate : 0.661 Fit side-chains REVERT: D 25 ARG cc_start: 0.8279 (mmm-85) cc_final: 0.6630 (mtm-85) REVERT: D 374 GLU cc_start: 0.7540 (tm-30) cc_final: 0.7143 (tm-30) REVERT: B 67 LEU cc_start: 0.7830 (mp) cc_final: 0.7606 (mm) REVERT: E 119 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7419 (tp30) REVERT: E 374 GLU cc_start: 0.8367 (mp0) cc_final: 0.8013 (mp0) REVERT: A 25 ARG cc_start: 0.8303 (mtp-110) cc_final: 0.6799 (mtm-85) REVERT: A 172 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7534 (pt0) REVERT: A 203 ASP cc_start: 0.8758 (OUTLIER) cc_final: 0.8515 (t70) REVERT: A 373 MET cc_start: 0.8326 (mtp) cc_final: 0.8111 (mtt) REVERT: C 119 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7458 (tp30) REVERT: C 169 LYS cc_start: 0.8419 (mttp) cc_final: 0.8008 (mmmt) REVERT: C 331 ARG cc_start: 0.8134 (ttp-110) cc_final: 0.7721 (ttp-170) outliers start: 51 outliers final: 30 residues processed: 232 average time/residue: 0.6796 time to fit residues: 173.0607 Evaluate side-chains 216 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 183 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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 249 LEU Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain E residue 367 SER Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 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 344 GLN 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 53 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 67 optimal weight: 0.3980 chunk 17 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 144 optimal weight: 0.0070 chunk 58 optimal weight: 0.8980 overall best weight: 0.8200 ------------------------------------------------------------------------------- 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** E 155 GLN E 376 GLN ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.116209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.095407 restraints weight = 19367.920| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.46 r_work: 0.3010 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.0761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16065 Z= 0.128 Angle : 0.490 7.241 21885 Z= 0.257 Chirality : 0.038 0.152 2375 Planarity : 0.004 0.052 2750 Dihedral : 4.412 46.304 2089 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.89 % Allowed : 15.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.18), residues: 1870 helix: 1.42 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.42 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 331 TYR 0.022 0.001 TYR D 97 PHE 0.017 0.001 PHE D 80 TRP 0.013 0.001 TRP A 309 HIS 0.002 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00274 (16065) covalent geometry : angle 0.49034 (21885) hydrogen bonds : bond 0.05350 ( 953) hydrogen bonds : angle 4.22432 ( 2778) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 194 time to evaluate : 0.652 Fit side-chains REVERT: D 25 ARG cc_start: 0.8268 (mmm-85) cc_final: 0.6643 (mtm-85) REVERT: D 374 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7119 (tm-30) REVERT: B 203 ASP cc_start: 0.8399 (OUTLIER) cc_final: 0.8143 (t70) REVERT: E 119 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7399 (tp30) REVERT: E 374 GLU cc_start: 0.8372 (mp0) cc_final: 0.8001 (mp0) REVERT: A 25 ARG cc_start: 0.8310 (mtp-110) cc_final: 0.6820 (mtm-85) REVERT: A 172 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7507 (pt0) REVERT: A 203 ASP cc_start: 0.8684 (OUTLIER) cc_final: 0.8426 (t70) REVERT: A 373 MET cc_start: 0.8278 (mtp) cc_final: 0.8021 (mtt) REVERT: A 374 GLU cc_start: 0.8151 (mp0) cc_final: 0.7588 (mp0) REVERT: C 119 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7432 (tp30) REVERT: C 169 LYS cc_start: 0.8415 (mttp) cc_final: 0.8000 (mmmt) REVERT: C 331 ARG cc_start: 0.8133 (ttp-110) cc_final: 0.7726 (ttp-170) REVERT: C 373 MET cc_start: 0.8665 (mtm) cc_final: 0.8413 (mtm) outliers start: 49 outliers final: 26 residues processed: 236 average time/residue: 0.6657 time to fit residues: 172.7419 Evaluate side-chains 215 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 184 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 374 GLU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain E residue 367 SER Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 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 367 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 64 optimal weight: 0.0870 chunk 150 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 153 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 144 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 154 optimal weight: 4.9990 chunk 111 optimal weight: 0.4980 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.117198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.096411 restraints weight = 19225.610| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.46 r_work: 0.3026 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.0866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 16065 Z= 0.120 Angle : 0.485 6.888 21885 Z= 0.252 Chirality : 0.037 0.150 2375 Planarity : 0.004 0.051 2750 Dihedral : 4.340 46.186 2089 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.13 % Allowed : 15.46 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.18), residues: 1870 helix: 1.47 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.39 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 25 TYR 0.020 0.001 TYR D 97 PHE 0.029 0.001 PHE E 80 TRP 0.013 0.001 TRP C 93 HIS 0.002 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00252 (16065) covalent geometry : angle 0.48476 (21885) hydrogen bonds : bond 0.05166 ( 953) hydrogen bonds : angle 4.18842 ( 2778) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 191 time to evaluate : 0.596 Fit side-chains REVERT: D 25 ARG cc_start: 0.8250 (mmm-85) cc_final: 0.6645 (mtm-85) REVERT: D 374 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7084 (tm-30) REVERT: B 203 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.8172 (t70) REVERT: E 119 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7375 (tp30) REVERT: E 374 GLU cc_start: 0.8417 (mp0) cc_final: 0.8011 (mp0) REVERT: A 25 ARG cc_start: 0.8306 (mtp-110) cc_final: 0.6821 (mtm-85) REVERT: A 80 PHE cc_start: 0.7578 (OUTLIER) cc_final: 0.7344 (m-80) REVERT: A 172 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7503 (pt0) REVERT: A 203 ASP cc_start: 0.8640 (OUTLIER) cc_final: 0.8402 (t70) REVERT: C 119 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7405 (tp30) REVERT: C 123 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8341 (tt) REVERT: C 169 LYS cc_start: 0.8453 (mttp) cc_final: 0.8047 (mmmt) REVERT: C 331 ARG cc_start: 0.8140 (ttp-110) cc_final: 0.7727 (ttp-170) REVERT: C 373 MET cc_start: 0.8678 (mtm) cc_final: 0.8402 (mtm) outliers start: 53 outliers final: 24 residues processed: 231 average time/residue: 0.6525 time to fit residues: 166.2722 Evaluate side-chains 217 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 186 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain D residue 374 GLU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 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 173 LYS Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 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 115 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 146 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 113 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 15 optimal weight: 0.0980 chunk 71 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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** ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.116460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.095648 restraints weight = 19139.173| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.45 r_work: 0.3014 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.0866 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= 0.134 Angle : 0.497 7.121 21885 Z= 0.259 Chirality : 0.038 0.153 2375 Planarity : 0.004 0.051 2750 Dihedral : 4.377 46.509 2089 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.48 % Allowed : 15.99 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.18), residues: 1870 helix: 1.45 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.38 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 25 TYR 0.021 0.001 TYR A 33 PHE 0.023 0.001 PHE D 80 TRP 0.013 0.001 TRP B 309 HIS 0.003 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00292 (16065) covalent geometry : angle 0.49701 (21885) hydrogen bonds : bond 0.05361 ( 953) hydrogen bonds : angle 4.20267 ( 2778) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 190 time to evaluate : 0.651 Fit side-chains REVERT: D 25 ARG cc_start: 0.8256 (mmm-85) cc_final: 0.6602 (mtm-85) REVERT: D 374 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7098 (tm-30) REVERT: B 203 ASP cc_start: 0.8382 (OUTLIER) cc_final: 0.8143 (t70) REVERT: E 119 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7375 (tp30) REVERT: E 374 GLU cc_start: 0.8437 (mp0) cc_final: 0.7986 (mp0) REVERT: A 25 ARG cc_start: 0.8291 (mtp-110) cc_final: 0.6808 (mtm-85) REVERT: A 172 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7517 (pt0) REVERT: A 203 ASP cc_start: 0.8662 (OUTLIER) cc_final: 0.8402 (t70) REVERT: A 271 LEU cc_start: 0.6736 (OUTLIER) cc_final: 0.6472 (mp) REVERT: A 374 GLU cc_start: 0.8101 (mp0) cc_final: 0.7511 (mp0) REVERT: C 119 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7421 (tp30) REVERT: C 123 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8343 (tt) REVERT: C 169 LYS cc_start: 0.8450 (mttp) cc_final: 0.8042 (mmmt) REVERT: C 331 ARG cc_start: 0.8160 (ttp-110) cc_final: 0.7541 (ttp-170) REVERT: C 373 MET cc_start: 0.8668 (mtm) cc_final: 0.8397 (mtm) outliers start: 42 outliers final: 27 residues processed: 225 average time/residue: 0.6525 time to fit residues: 161.8266 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 : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain D residue 374 GLU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain E residue 344 GLN Chi-restraints excluded: chain E residue 367 SER Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain 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 367 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 0.0970 chunk 20 optimal weight: 0.0170 chunk 46 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 146 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 overall best weight: 0.5216 ------------------------------------------------------------------------------- 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 ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.118522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.097719 restraints weight = 19239.422| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.46 r_work: 0.3032 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 16065 Z= 0.112 Angle : 0.475 6.769 21885 Z= 0.247 Chirality : 0.037 0.150 2375 Planarity : 0.004 0.051 2750 Dihedral : 4.266 46.697 2089 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.30 % Allowed : 16.17 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.19), residues: 1870 helix: 1.54 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.35 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 25 TYR 0.022 0.001 TYR C 68 PHE 0.025 0.001 PHE E 80 TRP 0.013 0.001 TRP A 93 HIS 0.002 0.000 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00229 (16065) covalent geometry : angle 0.47513 (21885) hydrogen bonds : bond 0.04946 ( 953) hydrogen bonds : angle 4.15559 ( 2778) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 191 time to evaluate : 0.620 Fit side-chains REVERT: D 25 ARG cc_start: 0.8233 (mmm-85) cc_final: 0.6591 (mtm-85) REVERT: D 374 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7054 (tm-30) REVERT: B 203 ASP cc_start: 0.8342 (OUTLIER) cc_final: 0.8139 (t70) REVERT: E 119 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7344 (tp30) REVERT: E 374 GLU cc_start: 0.8503 (mp0) cc_final: 0.8131 (mp0) REVERT: A 25 ARG cc_start: 0.8301 (mtp-110) cc_final: 0.6801 (mtm-85) REVERT: A 172 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7527 (pt0) REVERT: A 203 ASP cc_start: 0.8621 (OUTLIER) cc_final: 0.8382 (t70) REVERT: A 271 LEU cc_start: 0.6786 (OUTLIER) cc_final: 0.6525 (mp) REVERT: A 374 GLU cc_start: 0.8145 (mp0) cc_final: 0.7610 (mp0) REVERT: C 119 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7404 (tp30) REVERT: C 169 LYS cc_start: 0.8441 (mttp) cc_final: 0.8035 (mmmt) REVERT: C 331 ARG cc_start: 0.8152 (ttp-110) cc_final: 0.7563 (ttp-170) REVERT: C 373 MET cc_start: 0.8669 (mtm) cc_final: 0.8448 (mtt) outliers start: 39 outliers final: 26 residues processed: 223 average time/residue: 0.6543 time to fit residues: 161.0542 Evaluate side-chains 218 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 0.644 ------------------------------------------------------------------------------- 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 129 ILE Chi-restraints excluded: chain B residue 203 ASP Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain E residue 344 GLN Chi-restraints excluded: chain E residue 367 SER Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 94 optimal weight: 0.8980 chunk 145 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 36 optimal weight: 0.0770 chunk 115 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 144 optimal weight: 0.1980 chunk 35 optimal weight: 3.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 259 ASN E 155 GLN ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.118141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.097338 restraints weight = 19236.300| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.46 r_work: 0.3026 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 16065 Z= 0.118 Angle : 0.483 7.087 21885 Z= 0.251 Chirality : 0.037 0.154 2375 Planarity : 0.004 0.051 2750 Dihedral : 4.270 46.699 2089 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.71 % Favored : 98.24 % Rotamer: Outliers : 2.30 % Allowed : 16.28 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.19), residues: 1870 helix: 1.55 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.32 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 25 TYR 0.021 0.001 TYR D 97 PHE 0.021 0.001 PHE D 80 TRP 0.012 0.001 TRP B 309 HIS 0.002 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00246 (16065) covalent geometry : angle 0.48298 (21885) hydrogen bonds : bond 0.05035 ( 953) hydrogen bonds : angle 4.15343 ( 2778) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 195 time to evaluate : 0.551 Fit side-chains REVERT: D 25 ARG cc_start: 0.8231 (mmm-85) cc_final: 0.6589 (mtm-85) REVERT: D 169 LYS cc_start: 0.8083 (mtmm) cc_final: 0.7570 (tppt) REVERT: D 374 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7060 (tm-30) REVERT: E 119 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7347 (tp30) REVERT: E 374 GLU cc_start: 0.8494 (mp0) cc_final: 0.8107 (mp0) REVERT: A 25 ARG cc_start: 0.8297 (mtp-110) cc_final: 0.6813 (mtm-85) REVERT: A 172 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7533 (pt0) REVERT: A 203 ASP cc_start: 0.8625 (OUTLIER) cc_final: 0.8389 (t70) REVERT: A 374 GLU cc_start: 0.8170 (mp0) cc_final: 0.7649 (mp0) REVERT: C 119 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7384 (tp30) REVERT: C 123 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8300 (tt) REVERT: C 169 LYS cc_start: 0.8438 (mttp) cc_final: 0.8032 (mmmt) REVERT: C 331 ARG cc_start: 0.8161 (ttp-110) cc_final: 0.7547 (ttp-170) REVERT: C 373 MET cc_start: 0.8678 (mtm) cc_final: 0.8464 (mtt) outliers start: 39 outliers final: 27 residues processed: 228 average time/residue: 0.6598 time to fit residues: 165.4396 Evaluate side-chains 220 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 188 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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 129 ILE 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 123 LEU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain E residue 344 GLN Chi-restraints excluded: chain E residue 367 SER Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 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 93 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 139 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 161 optimal weight: 0.9980 chunk 165 optimal weight: 2.9990 chunk 146 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 259 ASN D 376 GLN E 155 GLN ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.117188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.096385 restraints weight = 19177.679| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.46 r_work: 0.3002 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16065 Z= 0.133 Angle : 0.499 7.035 21885 Z= 0.260 Chirality : 0.038 0.162 2375 Planarity : 0.004 0.051 2750 Dihedral : 4.334 46.923 2089 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.71 % Favored : 98.24 % Rotamer: Outliers : 1.89 % Allowed : 16.93 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.19), residues: 1870 helix: 1.50 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.32 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 356 TYR 0.024 0.001 TYR D 97 PHE 0.027 0.001 PHE B 80 TRP 0.013 0.001 TRP B 309 HIS 0.003 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00292 (16065) covalent geometry : angle 0.49927 (21885) hydrogen bonds : bond 0.05275 ( 953) hydrogen bonds : angle 4.18676 ( 2778) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3740 Ramachandran restraints generated. 1870 Oldfield, 0 Emsley, 1870 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 190 time to evaluate : 0.490 Fit side-chains REVERT: D 25 ARG cc_start: 0.8219 (mmm-85) cc_final: 0.6641 (mtm-85) REVERT: D 169 LYS cc_start: 0.8056 (mtmm) cc_final: 0.7542 (tppt) REVERT: D 374 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7069 (tm-30) REVERT: E 119 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7356 (tp30) REVERT: E 374 GLU cc_start: 0.8494 (mp0) cc_final: 0.8103 (mp0) REVERT: A 25 ARG cc_start: 0.8287 (mtp-110) cc_final: 0.6814 (mtm-85) REVERT: A 172 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7541 (pt0) REVERT: A 203 ASP cc_start: 0.8640 (OUTLIER) cc_final: 0.8390 (t70) REVERT: A 374 GLU cc_start: 0.8176 (mp0) cc_final: 0.7582 (mp0) REVERT: C 119 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7414 (tp30) REVERT: C 123 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8302 (tt) REVERT: C 169 LYS cc_start: 0.8446 (mttp) cc_final: 0.8045 (mmmt) REVERT: C 331 ARG cc_start: 0.8139 (ttp-110) cc_final: 0.7550 (ttp-170) REVERT: C 373 MET cc_start: 0.8665 (mtm) cc_final: 0.8447 (mtt) outliers start: 32 outliers final: 25 residues processed: 216 average time/residue: 0.6662 time to fit residues: 158.1946 Evaluate side-chains 221 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 191 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 367 SER Chi-restraints excluded: chain D residue 374 GLU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain 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 123 LEU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain E residue 344 GLN Chi-restraints excluded: chain E residue 367 SER Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 344 GLN Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 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 34 optimal weight: 0.2980 chunk 45 optimal weight: 2.9990 chunk 144 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 259 ASN D 369 ASN D 376 GLN B 369 ASN E 155 GLN ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.118321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.097473 restraints weight = 19114.054| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.46 r_work: 0.3018 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16065 Z= 0.118 Angle : 0.487 6.784 21885 Z= 0.254 Chirality : 0.037 0.164 2375 Planarity : 0.004 0.051 2750 Dihedral : 4.283 46.834 2089 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.82 % Favored : 98.13 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.19), residues: 1870 helix: 1.54 (0.14), residues: 1230 sheet: None (None), residues: 0 loop : -0.31 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 356 TYR 0.023 0.001 TYR D 97 PHE 0.029 0.001 PHE B 80 TRP 0.013 0.001 TRP A 93 HIS 0.002 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00250 (16065) covalent geometry : angle 0.48699 (21885) hydrogen bonds : bond 0.05058 ( 953) hydrogen bonds : angle 4.16915 ( 2778) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5638.36 seconds wall clock time: 97 minutes 2.36 seconds (5822.36 seconds total)