Starting phenix.real_space_refine on Wed Mar 4 03:21:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d44_27174/03_2026/8d44_27174.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d44_27174/03_2026/8d44_27174.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8d44_27174/03_2026/8d44_27174.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d44_27174/03_2026/8d44_27174.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d44_27174/03_2026/8d44_27174.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d44_27174/03_2026/8d44_27174.map" } resolution = 2.8 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= 0.055 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: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 6568 2.51 5 N 1864 2.21 5 O 1984 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10472 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 329} Chain: "C" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 329} Chain: "B" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 329} Chain: "A" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2618 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 329} Time building chain proxies: 2.63, per 1000 atoms: 0.25 Number of scatterers: 10472 At special positions: 0 Unit cell: (105.93, 82.39, 99.51, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1984 8.00 N 1864 7.00 C 6568 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: 0.73 Conformation dependent library (CDL) restraints added in 529.3 milliseconds 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2528 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 8 sheets defined 52.3% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'D' and resid 9 through 24 removed outlier: 3.783A pdb=" N VAL D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 46 removed outlier: 4.040A pdb=" N ARG D 46 " --> pdb=" O ASN D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 64 Processing helix chain 'D' and resid 80 through 85 removed outlier: 3.882A pdb=" N TYR D 85 " --> pdb=" O HIS D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 101 Processing helix chain 'D' and resid 130 through 141 removed outlier: 3.793A pdb=" N ARG D 134 " --> pdb=" O GLY D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 182 Processing helix chain 'D' and resid 198 through 220 Processing helix chain 'D' and resid 223 through 227 removed outlier: 3.560A pdb=" N THR D 227 " --> pdb=" O LEU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 259 Processing helix chain 'D' and resid 276 through 289 Processing helix chain 'D' and resid 308 through 315 Processing helix chain 'D' and resid 320 through 338 removed outlier: 3.686A pdb=" N ARG D 331 " --> pdb=" O ALA D 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 24 removed outlier: 3.786A pdb=" N VAL C 24 " --> pdb=" O ALA C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 45 Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 52 through 65 Processing helix chain 'C' and resid 80 through 85 removed outlier: 4.004A pdb=" N TYR C 85 " --> pdb=" O HIS C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 101 Processing helix chain 'C' and resid 130 through 141 Processing helix chain 'C' and resid 160 through 182 Processing helix chain 'C' and resid 198 through 220 Processing helix chain 'C' and resid 223 through 227 removed outlier: 3.719A pdb=" N THR C 227 " --> pdb=" O LEU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 261 removed outlier: 3.547A pdb=" N ARG C 259 " --> pdb=" O THR C 255 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR C 260 " --> pdb=" O ALA C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 289 Processing helix chain 'C' and resid 308 through 315 Processing helix chain 'C' and resid 320 through 338 Processing helix chain 'B' and resid 9 through 24 removed outlier: 3.794A pdb=" N VAL B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 45 Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 52 through 65 Processing helix chain 'B' and resid 67 through 72 removed outlier: 3.712A pdb=" N ASN B 71 " --> pdb=" O SER B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 85 removed outlier: 4.083A pdb=" N TYR B 85 " --> pdb=" O HIS B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 101 Processing helix chain 'B' and resid 130 through 141 Processing helix chain 'B' and resid 160 through 181 Processing helix chain 'B' and resid 198 through 220 Processing helix chain 'B' and resid 223 through 227 removed outlier: 3.723A pdb=" N THR B 227 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 259 removed outlier: 3.625A pdb=" N ARG B 259 " --> pdb=" O THR B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 289 Processing helix chain 'B' and resid 308 through 315 Processing helix chain 'B' and resid 321 through 340 Processing helix chain 'A' and resid 9 through 24 removed outlier: 3.771A pdb=" N VAL A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 45 Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 52 through 65 Processing helix chain 'A' and resid 67 through 72 removed outlier: 3.676A pdb=" N ASN A 71 " --> pdb=" O SER A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 85 removed outlier: 3.961A pdb=" N TYR A 85 " --> pdb=" O HIS A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 101 Processing helix chain 'A' and resid 130 through 141 Processing helix chain 'A' and resid 160 through 182 Processing helix chain 'A' and resid 198 through 220 Processing helix chain 'A' and resid 223 through 227 removed outlier: 3.720A pdb=" N THR A 227 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 259 removed outlier: 3.617A pdb=" N ARG A 259 " --> pdb=" O THR A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 289 Processing helix chain 'A' and resid 308 through 315 Processing helix chain 'A' and resid 321 through 338 Processing sheet with id=AA1, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.970A pdb=" N GLY D 29 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N VAL D 77 " --> pdb=" O GLY D 29 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU D 31 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N LEU D 79 " --> pdb=" O LEU D 31 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N GLY D 75 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N GLY D 106 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL D 77 " --> pdb=" O GLY D 106 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N LYS D 108 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N LEU D 79 " --> pdb=" O LYS D 108 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL D 105 " --> pdb=" O PHE D 145 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N LYS D 147 " --> pdb=" O VAL D 105 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE D 107 " --> pdb=" O LYS D 147 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N ARG D 149 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N LEU D 229 " --> pdb=" O CYS D 269 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ILE D 268 " --> pdb=" O SER D 299 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N SER D 301 " --> pdb=" O ILE D 268 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N PHE D 270 " --> pdb=" O SER D 301 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 112 through 115 Processing sheet with id=AA3, first strand: chain 'C' and resid 29 through 32 removed outlier: 7.067A pdb=" N GLY C 29 " --> pdb=" O GLY C 75 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N VAL C 77 " --> pdb=" O GLY C 29 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU C 31 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU C 79 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLY C 75 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N GLY C 106 " --> pdb=" O GLY C 75 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL C 77 " --> pdb=" O GLY C 106 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N LYS C 108 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LEU C 79 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL C 105 " --> pdb=" O PHE C 145 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N LYS C 147 " --> pdb=" O VAL C 105 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE C 107 " --> pdb=" O LYS C 147 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N ARG C 149 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N LEU C 229 " --> pdb=" O CYS C 269 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE C 268 " --> pdb=" O SER C 299 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N SER C 301 " --> pdb=" O ILE C 268 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N PHE C 270 " --> pdb=" O SER C 301 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 112 through 115 Processing sheet with id=AA5, first strand: chain 'B' and resid 29 through 32 removed outlier: 7.088A pdb=" N GLY B 29 " --> pdb=" O GLY B 75 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N VAL B 77 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU B 31 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N LEU B 79 " --> pdb=" O LEU B 31 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL B 105 " --> pdb=" O PHE B 145 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N LYS B 147 " --> pdb=" O VAL B 105 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE B 107 " --> pdb=" O LYS B 147 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N ARG B 149 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N LEU B 229 " --> pdb=" O CYS B 269 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE B 268 " --> pdb=" O SER B 299 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N SER B 301 " --> pdb=" O ILE B 268 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N PHE B 270 " --> pdb=" O SER B 301 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 112 through 115 Processing sheet with id=AA7, first strand: chain 'A' and resid 29 through 32 removed outlier: 7.059A pdb=" N GLY A 29 " --> pdb=" O GLY A 75 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N VAL A 77 " --> pdb=" O GLY A 29 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU A 31 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LEU A 79 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL A 105 " --> pdb=" O PHE A 145 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N LYS A 147 " --> pdb=" O VAL A 105 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE A 107 " --> pdb=" O LYS A 147 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N ARG A 149 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N LEU A 229 " --> pdb=" O CYS A 269 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILE A 268 " --> pdb=" O SER A 299 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N SER A 301 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N PHE A 270 " --> pdb=" O SER A 301 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 112 through 115 551 hydrogen bonds defined for protein. 1611 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: 1.70 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2220 1.33 - 1.45: 2245 1.45 - 1.57: 6103 1.57 - 1.69: 0 1.69 - 1.81: 80 Bond restraints: 10648 Sorted by residual: bond pdb=" C MET B 251 " pdb=" O MET B 251 " ideal model delta sigma weight residual 1.236 1.206 0.031 1.15e-02 7.56e+03 7.20e+00 bond pdb=" CA ALA B 250 " pdb=" C ALA B 250 " ideal model delta sigma weight residual 1.524 1.495 0.029 1.27e-02 6.20e+03 5.05e+00 bond pdb=" CA MET B 251 " pdb=" C MET B 251 " ideal model delta sigma weight residual 1.524 1.497 0.026 1.27e-02 6.20e+03 4.33e+00 bond pdb=" C THR B 253 " pdb=" O THR B 253 " ideal model delta sigma weight residual 1.236 1.216 0.021 1.15e-02 7.56e+03 3.33e+00 bond pdb=" CA ALA B 250 " pdb=" CB ALA B 250 " ideal model delta sigma weight residual 1.529 1.506 0.023 1.55e-02 4.16e+03 2.25e+00 ... (remaining 10643 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 14174 2.13 - 4.25: 197 4.25 - 6.38: 22 6.38 - 8.51: 2 8.51 - 10.63: 1 Bond angle restraints: 14396 Sorted by residual: angle pdb=" CB MET A 251 " pdb=" CG MET A 251 " pdb=" SD MET A 251 " ideal model delta sigma weight residual 112.70 123.33 -10.63 3.00e+00 1.11e-01 1.26e+01 angle pdb=" CA GLN C 90 " pdb=" CB GLN C 90 " pdb=" CG GLN C 90 " ideal model delta sigma weight residual 114.10 120.93 -6.83 2.00e+00 2.50e-01 1.17e+01 angle pdb=" CB GLN B 58 " pdb=" CG GLN B 58 " pdb=" CD GLN B 58 " ideal model delta sigma weight residual 112.60 117.75 -5.15 1.70e+00 3.46e-01 9.19e+00 angle pdb=" CB GLU D 322 " pdb=" CG GLU D 322 " pdb=" CD GLU D 322 " ideal model delta sigma weight residual 112.60 117.59 -4.99 1.70e+00 3.46e-01 8.62e+00 angle pdb=" CB GLU D 326 " pdb=" CG GLU D 326 " pdb=" CD GLU D 326 " ideal model delta sigma weight residual 112.60 117.53 -4.93 1.70e+00 3.46e-01 8.40e+00 ... (remaining 14391 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 5621 17.79 - 35.59: 623 35.59 - 53.38: 196 53.38 - 71.17: 33 71.17 - 88.97: 15 Dihedral angle restraints: 6488 sinusoidal: 2556 harmonic: 3932 Sorted by residual: dihedral pdb=" CA ALA C 338 " pdb=" C ALA C 338 " pdb=" N ALA C 339 " pdb=" CA ALA C 339 " ideal model delta harmonic sigma weight residual 180.00 162.37 17.63 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA GLN A 111 " pdb=" C GLN A 111 " pdb=" N GLY A 112 " pdb=" CA GLY A 112 " ideal model delta harmonic sigma weight residual 180.00 163.26 16.74 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA VAL C 24 " pdb=" C VAL C 24 " pdb=" N ALA C 25 " pdb=" CA ALA C 25 " ideal model delta harmonic sigma weight residual -180.00 -163.58 -16.42 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 6485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 940 0.027 - 0.055: 387 0.055 - 0.082: 158 0.082 - 0.110: 106 0.110 - 0.137: 33 Chirality restraints: 1624 Sorted by residual: chirality pdb=" CA TYR D 214 " pdb=" N TYR D 214 " pdb=" C TYR D 214 " pdb=" CB TYR D 214 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" CA VAL C 187 " pdb=" N VAL C 187 " pdb=" C VAL C 187 " pdb=" CB VAL C 187 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA VAL A 187 " pdb=" N VAL A 187 " pdb=" C VAL A 187 " pdb=" CB VAL A 187 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 ... (remaining 1621 not shown) Planarity restraints: 1888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 114 " -0.047 5.00e-02 4.00e+02 7.14e-02 8.15e+00 pdb=" N PRO B 115 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 115 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 115 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 114 " -0.045 5.00e-02 4.00e+02 6.84e-02 7.49e+00 pdb=" N PRO C 115 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO C 115 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 115 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 114 " 0.042 5.00e-02 4.00e+02 6.47e-02 6.69e+00 pdb=" N PRO A 115 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 115 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 115 " 0.035 5.00e-02 4.00e+02 ... (remaining 1885 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1770 2.77 - 3.30: 9787 3.30 - 3.83: 18980 3.83 - 4.37: 22189 4.37 - 4.90: 37800 Nonbonded interactions: 90526 Sorted by model distance: nonbonded pdb=" O GLU D 61 " pdb=" OG SER D 65 " model vdw 2.232 3.040 nonbonded pdb=" O LEU A 116 " pdb=" OG1 THR A 119 " model vdw 2.244 3.040 nonbonded pdb=" O LEU B 116 " pdb=" OG1 THR B 119 " model vdw 2.250 3.040 nonbonded pdb=" NH1 ARG B 149 " pdb=" OE1 GLU B 190 " model vdw 2.254 3.120 nonbonded pdb=" O LEU D 116 " pdb=" OG1 THR D 119 " model vdw 2.272 3.040 ... (remaining 90521 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' } 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: 1.940 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.290 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 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 : 0.004 0.039 10648 Z= 0.170 Angle : 0.628 10.635 14396 Z= 0.353 Chirality : 0.043 0.137 1624 Planarity : 0.006 0.071 1888 Dihedral : 16.987 88.965 3960 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.73 % Allowed : 15.82 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.23), residues: 1364 helix: 1.65 (0.19), residues: 668 sheet: -1.68 (0.29), residues: 248 loop : -0.60 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 57 TYR 0.019 0.002 TYR B 174 PHE 0.012 0.002 PHE C 145 TRP 0.021 0.002 TRP C 148 HIS 0.006 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00373 (10648) covalent geometry : angle 0.62792 (14396) hydrogen bonds : bond 0.11027 ( 551) hydrogen bonds : angle 4.76125 ( 1611) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.410 Fit side-chains REVERT: D 110 ASP cc_start: 0.8200 (p0) cc_final: 0.7981 (p0) REVERT: C 296 TRP cc_start: 0.8654 (OUTLIER) cc_final: 0.8367 (m-90) REVERT: B 110 ASP cc_start: 0.8277 (p0) cc_final: 0.7942 (p0) REVERT: A 110 ASP cc_start: 0.8345 (p0) cc_final: 0.8119 (p0) outliers start: 19 outliers final: 12 residues processed: 138 average time/residue: 0.5921 time to fit residues: 88.0488 Evaluate side-chains 129 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 129 ASP Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 296 TRP Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 202 CYS Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain C residue 296 TRP Chi-restraints excluded: chain B residue 296 TRP Chi-restraints excluded: chain A residue 129 ASP Chi-restraints excluded: chain A residue 202 CYS Chi-restraints excluded: chain A residue 296 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 GLN C 258 HIS C 335 ASN B 258 HIS A 258 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.183604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.142628 restraints weight = 9954.872| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 1.54 r_work: 0.3502 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.0752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 10648 Z= 0.159 Angle : 0.544 5.246 14396 Z= 0.292 Chirality : 0.042 0.134 1624 Planarity : 0.005 0.051 1888 Dihedral : 5.449 48.637 1486 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.73 % Allowed : 15.45 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.23), residues: 1364 helix: 2.00 (0.19), residues: 672 sheet: -1.74 (0.29), residues: 248 loop : -0.45 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 149 TYR 0.015 0.002 TYR A 214 PHE 0.013 0.002 PHE B 145 TRP 0.018 0.002 TRP C 148 HIS 0.005 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00380 (10648) covalent geometry : angle 0.54419 (14396) hydrogen bonds : bond 0.03932 ( 551) hydrogen bonds : angle 4.07650 ( 1611) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.388 Fit side-chains REVERT: C 110 ASP cc_start: 0.8295 (p0) cc_final: 0.8065 (p0) REVERT: C 174 TYR cc_start: 0.8602 (OUTLIER) cc_final: 0.7821 (t80) REVERT: C 251 MET cc_start: 0.7708 (tpp) cc_final: 0.7379 (tpp) REVERT: B 110 ASP cc_start: 0.8288 (p0) cc_final: 0.7924 (p0) REVERT: B 174 TYR cc_start: 0.8628 (OUTLIER) cc_final: 0.7896 (t80) REVERT: A 110 ASP cc_start: 0.8125 (p0) cc_final: 0.7826 (p0) REVERT: A 174 TYR cc_start: 0.8607 (OUTLIER) cc_final: 0.7819 (t80) outliers start: 19 outliers final: 6 residues processed: 143 average time/residue: 0.5733 time to fit residues: 88.3857 Evaluate side-chains 126 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 296 TRP Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain C residue 296 TRP Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 296 TRP Chi-restraints excluded: chain A residue 174 TYR Chi-restraints excluded: chain A residue 296 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 1.9990 chunk 2 optimal weight: 0.0470 chunk 118 optimal weight: 0.6980 chunk 133 optimal weight: 7.9990 chunk 102 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 90 GLN D 258 HIS C 258 HIS B 258 HIS A 258 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.176962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.132846 restraints weight = 10033.957| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.95 r_work: 0.3425 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10648 Z= 0.131 Angle : 0.503 5.399 14396 Z= 0.270 Chirality : 0.041 0.132 1624 Planarity : 0.005 0.047 1888 Dihedral : 4.840 44.926 1468 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.18 % Allowed : 15.82 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.23), residues: 1364 helix: 2.26 (0.19), residues: 672 sheet: -1.53 (0.30), residues: 228 loop : -0.37 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 149 TYR 0.014 0.002 TYR B 214 PHE 0.013 0.001 PHE B 145 TRP 0.016 0.002 TRP C 148 HIS 0.004 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00312 (10648) covalent geometry : angle 0.50255 (14396) hydrogen bonds : bond 0.03564 ( 551) hydrogen bonds : angle 3.88509 ( 1611) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.472 Fit side-chains REVERT: C 80 PHE cc_start: 0.7017 (t80) cc_final: 0.6785 (t80) REVERT: C 174 TYR cc_start: 0.8499 (OUTLIER) cc_final: 0.7766 (t80) REVERT: C 248 GLN cc_start: 0.7890 (mt0) cc_final: 0.7624 (mt0) REVERT: C 251 MET cc_start: 0.7539 (tpp) cc_final: 0.6998 (tpp) REVERT: B 110 ASP cc_start: 0.8151 (p0) cc_final: 0.7906 (p0) REVERT: B 174 TYR cc_start: 0.8500 (OUTLIER) cc_final: 0.7816 (t80) REVERT: A 110 ASP cc_start: 0.7891 (p0) cc_final: 0.7654 (p0) REVERT: A 174 TYR cc_start: 0.8430 (OUTLIER) cc_final: 0.7683 (t80) REVERT: A 251 MET cc_start: 0.7556 (tpp) cc_final: 0.7290 (tpp) outliers start: 24 outliers final: 10 residues processed: 156 average time/residue: 0.5950 time to fit residues: 99.8068 Evaluate side-chains 132 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 126 GLN Chi-restraints excluded: chain D residue 296 TRP Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain C residue 296 TRP Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 296 TRP Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 174 TYR Chi-restraints excluded: chain A residue 296 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 95 optimal weight: 0.0570 chunk 59 optimal weight: 0.8980 chunk 78 optimal weight: 0.4980 chunk 41 optimal weight: 0.6980 chunk 127 optimal weight: 0.1980 chunk 36 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 90 GLN C 90 GLN C 258 HIS B 258 HIS A 258 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.177890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.135110 restraints weight = 10070.813| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.80 r_work: 0.3441 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10648 Z= 0.114 Angle : 0.479 5.408 14396 Z= 0.257 Chirality : 0.040 0.128 1624 Planarity : 0.004 0.047 1888 Dihedral : 4.730 45.895 1468 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.36 % Allowed : 16.55 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.23), residues: 1364 helix: 2.48 (0.19), residues: 672 sheet: -1.48 (0.30), residues: 228 loop : -0.31 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 57 TYR 0.011 0.001 TYR D 214 PHE 0.013 0.001 PHE D 59 TRP 0.015 0.002 TRP C 148 HIS 0.008 0.001 HIS D 258 Details of bonding type rmsd covalent geometry : bond 0.00270 (10648) covalent geometry : angle 0.47897 (14396) hydrogen bonds : bond 0.03287 ( 551) hydrogen bonds : angle 3.79276 ( 1611) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.413 Fit side-chains REVERT: C 174 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.7766 (t80) REVERT: C 248 GLN cc_start: 0.7931 (mt0) cc_final: 0.7648 (mt0) REVERT: C 251 MET cc_start: 0.7536 (tpp) cc_final: 0.6997 (tpp) REVERT: B 110 ASP cc_start: 0.8078 (p0) cc_final: 0.7834 (p0) REVERT: B 174 TYR cc_start: 0.8386 (OUTLIER) cc_final: 0.7773 (t80) REVERT: B 251 MET cc_start: 0.7107 (tpp) cc_final: 0.6655 (tpp) REVERT: A 110 ASP cc_start: 0.7860 (p0) cc_final: 0.7652 (p0) REVERT: A 140 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7663 (mtpt) REVERT: A 200 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7661 (mp0) REVERT: A 251 MET cc_start: 0.7682 (tpp) cc_final: 0.7382 (tpp) outliers start: 26 outliers final: 6 residues processed: 154 average time/residue: 0.5970 time to fit residues: 98.8300 Evaluate side-chains 126 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 296 TRP Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 296 TRP Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 296 TRP Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 296 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 4.9990 chunk 45 optimal weight: 0.0010 chunk 26 optimal weight: 0.9990 chunk 91 optimal weight: 0.0370 chunk 30 optimal weight: 0.0870 chunk 128 optimal weight: 0.2980 chunk 28 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 overall best weight: 0.2842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 90 GLN C 258 HIS B 258 HIS A 258 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.179521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.134176 restraints weight = 10051.949| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.85 r_work: 0.3465 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10648 Z= 0.097 Angle : 0.456 5.444 14396 Z= 0.245 Chirality : 0.039 0.124 1624 Planarity : 0.004 0.047 1888 Dihedral : 4.577 46.211 1468 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.00 % Allowed : 17.09 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.23), residues: 1364 helix: 2.69 (0.19), residues: 672 sheet: -1.42 (0.30), residues: 228 loop : -0.28 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 57 TYR 0.011 0.001 TYR A 204 PHE 0.012 0.001 PHE D 59 TRP 0.013 0.001 TRP C 148 HIS 0.006 0.001 HIS D 258 Details of bonding type rmsd covalent geometry : bond 0.00228 (10648) covalent geometry : angle 0.45607 (14396) hydrogen bonds : bond 0.03017 ( 551) hydrogen bonds : angle 3.68275 ( 1611) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.295 Fit side-chains REVERT: D 110 ASP cc_start: 0.7975 (p0) cc_final: 0.7671 (p0) REVERT: C 100 GLU cc_start: 0.6959 (mt-10) cc_final: 0.6706 (mp0) REVERT: C 110 ASP cc_start: 0.7957 (p0) cc_final: 0.7664 (p0) REVERT: C 248 GLN cc_start: 0.7904 (mt0) cc_final: 0.7589 (mt0) REVERT: C 251 MET cc_start: 0.7501 (tpp) cc_final: 0.7022 (tpp) REVERT: B 110 ASP cc_start: 0.8012 (p0) cc_final: 0.7742 (p0) REVERT: B 174 TYR cc_start: 0.8344 (OUTLIER) cc_final: 0.7803 (t80) REVERT: B 251 MET cc_start: 0.7065 (tpp) cc_final: 0.6671 (tpp) REVERT: A 140 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7605 (mtpt) REVERT: A 174 TYR cc_start: 0.8329 (OUTLIER) cc_final: 0.7724 (t80) REVERT: A 251 MET cc_start: 0.7710 (tpp) cc_final: 0.7486 (tpp) outliers start: 22 outliers final: 8 residues processed: 150 average time/residue: 0.5705 time to fit residues: 92.4287 Evaluate side-chains 128 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 296 TRP Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain C residue 296 TRP Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 296 TRP Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain A residue 174 TYR Chi-restraints excluded: chain A residue 296 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 110 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 83 optimal weight: 0.3980 chunk 23 optimal weight: 0.9990 chunk 85 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 258 HIS B 86 GLN B 258 HIS A 258 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.176138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.132260 restraints weight = 10124.992| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.13 r_work: 0.3418 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10648 Z= 0.142 Angle : 0.508 5.060 14396 Z= 0.271 Chirality : 0.041 0.132 1624 Planarity : 0.004 0.047 1888 Dihedral : 4.797 47.262 1468 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.82 % Allowed : 17.73 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.23), residues: 1364 helix: 2.58 (0.19), residues: 672 sheet: -1.35 (0.30), residues: 224 loop : -0.40 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 57 TYR 0.016 0.002 TYR A 214 PHE 0.013 0.002 PHE A 59 TRP 0.015 0.002 TRP C 148 HIS 0.007 0.001 HIS D 258 Details of bonding type rmsd covalent geometry : bond 0.00342 (10648) covalent geometry : angle 0.50759 (14396) hydrogen bonds : bond 0.03543 ( 551) hydrogen bonds : angle 3.80864 ( 1611) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.413 Fit side-chains REVERT: D 42 ASN cc_start: 0.7997 (OUTLIER) cc_final: 0.7686 (t0) REVERT: D 174 TYR cc_start: 0.8529 (OUTLIER) cc_final: 0.7743 (t80) REVERT: C 174 TYR cc_start: 0.8514 (OUTLIER) cc_final: 0.7815 (t80) REVERT: C 251 MET cc_start: 0.7556 (tpp) cc_final: 0.7009 (tpp) REVERT: B 110 ASP cc_start: 0.8149 (p0) cc_final: 0.7882 (p0) REVERT: B 174 TYR cc_start: 0.8556 (OUTLIER) cc_final: 0.7919 (t80) REVERT: B 251 MET cc_start: 0.7113 (tpp) cc_final: 0.6701 (tpp) REVERT: A 110 ASP cc_start: 0.7859 (p0) cc_final: 0.7569 (p0) REVERT: A 174 TYR cc_start: 0.8480 (OUTLIER) cc_final: 0.7785 (t80) REVERT: A 251 MET cc_start: 0.7740 (tpp) cc_final: 0.7383 (tpp) outliers start: 20 outliers final: 8 residues processed: 143 average time/residue: 0.5776 time to fit residues: 89.3060 Evaluate side-chains 133 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 42 ASN Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 296 TRP Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 296 TRP Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 296 TRP Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 174 TYR Chi-restraints excluded: chain A residue 296 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 64 optimal weight: 1.9990 chunk 116 optimal weight: 0.5980 chunk 129 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 90 GLN C 258 HIS B 258 HIS A 258 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.175833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.131876 restraints weight = 10011.968| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.17 r_work: 0.3408 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 10648 Z= 0.146 Angle : 0.511 5.102 14396 Z= 0.274 Chirality : 0.041 0.132 1624 Planarity : 0.004 0.046 1888 Dihedral : 4.845 48.712 1468 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.45 % Allowed : 17.82 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.23), residues: 1364 helix: 2.55 (0.19), residues: 672 sheet: -1.38 (0.30), residues: 224 loop : -0.43 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 60 TYR 0.014 0.002 TYR A 204 PHE 0.013 0.002 PHE B 145 TRP 0.016 0.002 TRP C 148 HIS 0.008 0.001 HIS D 258 Details of bonding type rmsd covalent geometry : bond 0.00354 (10648) covalent geometry : angle 0.51082 (14396) hydrogen bonds : bond 0.03571 ( 551) hydrogen bonds : angle 3.84639 ( 1611) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.449 Fit side-chains REVERT: D 110 ASP cc_start: 0.8106 (p0) cc_final: 0.7900 (p0) REVERT: D 174 TYR cc_start: 0.8537 (OUTLIER) cc_final: 0.7769 (t80) REVERT: C 174 TYR cc_start: 0.8514 (OUTLIER) cc_final: 0.7825 (t80) REVERT: C 251 MET cc_start: 0.7559 (tpp) cc_final: 0.7059 (tpp) REVERT: B 97 ILE cc_start: 0.7151 (OUTLIER) cc_final: 0.6839 (mm) REVERT: B 110 ASP cc_start: 0.8206 (p0) cc_final: 0.7939 (p0) REVERT: B 111 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.6680 (mp10) REVERT: B 174 TYR cc_start: 0.8542 (OUTLIER) cc_final: 0.7845 (t80) REVERT: B 251 MET cc_start: 0.7172 (tpp) cc_final: 0.6716 (tpp) REVERT: A 110 ASP cc_start: 0.7859 (p0) cc_final: 0.7542 (p0) REVERT: A 174 TYR cc_start: 0.8468 (OUTLIER) cc_final: 0.7791 (t80) REVERT: A 251 MET cc_start: 0.7750 (tpp) cc_final: 0.7386 (tpp) outliers start: 27 outliers final: 9 residues processed: 146 average time/residue: 0.5518 time to fit residues: 87.1868 Evaluate side-chains 135 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 129 ASP Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 296 TRP Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain C residue 296 TRP Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 296 TRP Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 174 TYR Chi-restraints excluded: chain A residue 296 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 129 optimal weight: 0.7980 chunk 27 optimal weight: 0.0870 chunk 0 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 115 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 74 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 258 HIS C 258 HIS B 258 HIS A 258 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.176463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.132437 restraints weight = 9989.201| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.23 r_work: 0.3418 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10648 Z= 0.129 Angle : 0.496 5.061 14396 Z= 0.266 Chirality : 0.041 0.131 1624 Planarity : 0.004 0.046 1888 Dihedral : 4.807 49.600 1468 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.27 % Allowed : 18.00 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.23), residues: 1364 helix: 2.60 (0.19), residues: 672 sheet: -1.39 (0.30), residues: 224 loop : -0.42 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 60 TYR 0.013 0.002 TYR A 204 PHE 0.013 0.001 PHE B 145 TRP 0.016 0.002 TRP C 148 HIS 0.005 0.001 HIS D 258 Details of bonding type rmsd covalent geometry : bond 0.00311 (10648) covalent geometry : angle 0.49592 (14396) hydrogen bonds : bond 0.03426 ( 551) hydrogen bonds : angle 3.79674 ( 1611) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.405 Fit side-chains REVERT: D 110 ASP cc_start: 0.8131 (p0) cc_final: 0.7929 (p0) REVERT: D 174 TYR cc_start: 0.8496 (OUTLIER) cc_final: 0.7732 (t80) REVERT: C 110 ASP cc_start: 0.8079 (p0) cc_final: 0.7760 (p0) REVERT: C 174 TYR cc_start: 0.8476 (OUTLIER) cc_final: 0.7807 (t80) REVERT: C 248 GLN cc_start: 0.7997 (mt0) cc_final: 0.7694 (mt0) REVERT: C 251 MET cc_start: 0.7539 (tpp) cc_final: 0.7168 (tpp) REVERT: C 329 MET cc_start: 0.7480 (tpt) cc_final: 0.7233 (mmm) REVERT: B 110 ASP cc_start: 0.8199 (p0) cc_final: 0.7923 (p0) REVERT: B 111 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.6669 (mp10) REVERT: B 140 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7668 (mtpt) REVERT: B 174 TYR cc_start: 0.8459 (OUTLIER) cc_final: 0.7775 (t80) REVERT: B 251 MET cc_start: 0.7162 (tpp) cc_final: 0.6711 (tpp) REVERT: A 110 ASP cc_start: 0.7874 (p0) cc_final: 0.7558 (p0) REVERT: A 174 TYR cc_start: 0.8410 (OUTLIER) cc_final: 0.7725 (t80) REVERT: A 200 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7669 (mp0) REVERT: A 251 MET cc_start: 0.7753 (tpp) cc_final: 0.7382 (tpp) outliers start: 25 outliers final: 10 residues processed: 147 average time/residue: 0.5917 time to fit residues: 93.7371 Evaluate side-chains 137 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 129 ASP Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 296 TRP Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain C residue 296 TRP Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 296 TRP Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 174 TYR Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 296 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 45 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 115 optimal weight: 0.6980 chunk 122 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 128 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 258 HIS C 90 GLN C 258 HIS B 258 HIS A 258 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.175768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.132682 restraints weight = 10085.337| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.87 r_work: 0.3420 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10648 Z= 0.143 Angle : 0.513 5.011 14396 Z= 0.275 Chirality : 0.041 0.132 1624 Planarity : 0.004 0.046 1888 Dihedral : 4.867 50.133 1468 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.18 % Allowed : 17.82 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.23), residues: 1364 helix: 2.56 (0.19), residues: 672 sheet: -1.40 (0.31), residues: 224 loop : -0.43 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 57 TYR 0.013 0.002 TYR D 214 PHE 0.013 0.002 PHE B 145 TRP 0.016 0.002 TRP C 148 HIS 0.004 0.001 HIS D 258 Details of bonding type rmsd covalent geometry : bond 0.00348 (10648) covalent geometry : angle 0.51305 (14396) hydrogen bonds : bond 0.03559 ( 551) hydrogen bonds : angle 3.83571 ( 1611) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.394 Fit side-chains REVERT: D 174 TYR cc_start: 0.8519 (OUTLIER) cc_final: 0.7750 (t80) REVERT: C 110 ASP cc_start: 0.8059 (p0) cc_final: 0.7706 (p0) REVERT: C 174 TYR cc_start: 0.8501 (OUTLIER) cc_final: 0.7812 (t80) REVERT: C 251 MET cc_start: 0.7527 (tpp) cc_final: 0.7148 (tpp) REVERT: B 97 ILE cc_start: 0.7246 (OUTLIER) cc_final: 0.6930 (mm) REVERT: B 111 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.6599 (mp10) REVERT: B 140 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7665 (mtpt) REVERT: B 174 TYR cc_start: 0.8524 (OUTLIER) cc_final: 0.7831 (t80) REVERT: B 251 MET cc_start: 0.7141 (tpp) cc_final: 0.6675 (tpp) REVERT: A 110 ASP cc_start: 0.7885 (p0) cc_final: 0.7580 (p0) REVERT: A 174 TYR cc_start: 0.8455 (OUTLIER) cc_final: 0.7775 (t80) REVERT: A 200 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7660 (mp0) REVERT: A 251 MET cc_start: 0.7735 (tpp) cc_final: 0.7360 (tpp) outliers start: 24 outliers final: 9 residues processed: 139 average time/residue: 0.5456 time to fit residues: 82.0709 Evaluate side-chains 137 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 129 ASP Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 296 TRP Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 275 MET Chi-restraints excluded: chain C residue 296 TRP Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 111 GLN Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 296 TRP Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 174 TYR Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 296 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 41 optimal weight: 1.9990 chunk 94 optimal weight: 0.4980 chunk 68 optimal weight: 2.9990 chunk 131 optimal weight: 0.0470 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 125 optimal weight: 0.0670 chunk 15 optimal weight: 0.0970 overall best weight: 0.2814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 258 HIS C 90 GLN C 258 HIS B 258 HIS A 258 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.179487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.134071 restraints weight = 9898.536| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.83 r_work: 0.3449 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10648 Z= 0.099 Angle : 0.462 5.158 14396 Z= 0.249 Chirality : 0.039 0.126 1624 Planarity : 0.004 0.047 1888 Dihedral : 4.616 50.084 1468 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.64 % Allowed : 19.00 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.23), residues: 1364 helix: 2.75 (0.19), residues: 672 sheet: -1.36 (0.31), residues: 224 loop : -0.36 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 57 TYR 0.012 0.001 TYR A 204 PHE 0.012 0.001 PHE B 145 TRP 0.014 0.001 TRP C 148 HIS 0.003 0.001 HIS D 258 Details of bonding type rmsd covalent geometry : bond 0.00235 (10648) covalent geometry : angle 0.46218 (14396) hydrogen bonds : bond 0.03007 ( 551) hydrogen bonds : angle 3.68675 ( 1611) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2728 Ramachandran restraints generated. 1364 Oldfield, 0 Emsley, 1364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.385 Fit side-chains REVERT: C 100 GLU cc_start: 0.7092 (mt-10) cc_final: 0.6823 (mp0) REVERT: C 248 GLN cc_start: 0.7972 (mt0) cc_final: 0.7657 (mt0) REVERT: C 251 MET cc_start: 0.7528 (tpp) cc_final: 0.7008 (tpp) REVERT: C 329 MET cc_start: 0.7298 (tpt) cc_final: 0.7020 (mmm) REVERT: B 174 TYR cc_start: 0.8350 (OUTLIER) cc_final: 0.7806 (t80) REVERT: B 251 MET cc_start: 0.7185 (tpp) cc_final: 0.6774 (tpp) REVERT: A 110 ASP cc_start: 0.7770 (p0) cc_final: 0.7444 (p0) REVERT: A 174 TYR cc_start: 0.8299 (OUTLIER) cc_final: 0.7751 (t80) REVERT: A 251 MET cc_start: 0.7800 (tpp) cc_final: 0.7424 (tpp) outliers start: 18 outliers final: 9 residues processed: 146 average time/residue: 0.5995 time to fit residues: 94.1683 Evaluate side-chains 131 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 129 ASP Chi-restraints excluded: chain D residue 296 TRP Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 296 TRP Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 296 TRP Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 174 TYR Chi-restraints excluded: chain A residue 296 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 87 optimal weight: 0.0020 chunk 63 optimal weight: 0.0970 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 0.2980 chunk 73 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 67 optimal weight: 0.0470 chunk 54 optimal weight: 0.6980 overall best weight: 0.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 258 HIS C 90 GLN C 258 HIS B 86 GLN B 258 HIS A 258 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.180766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.136160 restraints weight = 10066.911| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.17 r_work: 0.3462 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10648 Z= 0.095 Angle : 0.458 5.007 14396 Z= 0.246 Chirality : 0.039 0.122 1624 Planarity : 0.004 0.047 1888 Dihedral : 4.526 49.088 1468 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.27 % Allowed : 19.18 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.23), residues: 1364 helix: 2.81 (0.19), residues: 672 sheet: -1.27 (0.31), residues: 224 loop : -0.33 (0.31), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 57 TYR 0.015 0.001 TYR A 204 PHE 0.011 0.001 PHE B 145 TRP 0.014 0.001 TRP C 148 HIS 0.003 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00225 (10648) covalent geometry : angle 0.45825 (14396) hydrogen bonds : bond 0.02934 ( 551) hydrogen bonds : angle 3.63091 ( 1611) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3771.72 seconds wall clock time: 65 minutes 5.07 seconds (3905.07 seconds total)