Starting phenix.real_space_refine on Mon Jul 28 14:48:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d44_27174/07_2025/8d44_27174.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d44_27174/07_2025/8d44_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8d44_27174/07_2025/8d44_27174.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d44_27174/07_2025/8d44_27174.map" model { file = "/net/cci-nas-00/data/ceres_data/8d44_27174/07_2025/8d44_27174.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d44_27174/07_2025/8d44_27174.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.055 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.46, per 1000 atoms: 0.62 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: 2.42 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.35 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: 3.38 Time building geometry restraints manager: 2.89 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: 0.03 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: 1.910 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.340 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.530 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (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 TRP 0.021 0.002 TRP C 148 HIS 0.006 0.001 HIS C 197 PHE 0.012 0.002 PHE C 145 TYR 0.019 0.002 TYR B 174 ARG 0.003 0.000 ARG B 57 Details of bonding type rmsd hydrogen bonds : bond 0.11027 ( 551) hydrogen bonds : angle 4.76125 ( 1611) covalent geometry : bond 0.00373 (10648) covalent geometry : angle 0.62792 (14396) *********************** 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 : 1.112 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: 1.2241 time to fit residues: 182.7402 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 : 1.160 ------------------------------------------------------------------------------- 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 114 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 64 optimal weight: 0.0970 chunk 79 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.4060 r_free = 0.4060 target = 0.182704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.141816 restraints weight = 9867.588| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 1.52 r_work: 0.3493 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.0781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10648 Z= 0.178 Angle : 0.564 5.254 14396 Z= 0.302 Chirality : 0.043 0.137 1624 Planarity : 0.005 0.052 1888 Dihedral : 5.542 47.661 1486 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.00 % Allowed : 15.09 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.23), residues: 1364 helix: 1.94 (0.19), residues: 672 sheet: -1.75 (0.29), residues: 248 loop : -0.47 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 148 HIS 0.005 0.001 HIS C 197 PHE 0.013 0.002 PHE A 145 TYR 0.017 0.002 TYR C 214 ARG 0.005 0.000 ARG B 149 Details of bonding type rmsd hydrogen bonds : bond 0.04121 ( 551) hydrogen bonds : angle 4.12712 ( 1611) covalent geometry : bond 0.00428 (10648) covalent geometry : angle 0.56414 (14396) *********************** 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 152 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 1.502 Fit side-chains REVERT: D 110 ASP cc_start: 0.8138 (p0) cc_final: 0.7893 (p0) REVERT: C 110 ASP cc_start: 0.8321 (p0) cc_final: 0.8100 (p0) REVERT: C 174 TYR cc_start: 0.8618 (OUTLIER) cc_final: 0.7842 (t80) REVERT: C 251 MET cc_start: 0.7727 (tpp) cc_final: 0.7337 (tpp) REVERT: B 110 ASP cc_start: 0.8312 (p0) cc_final: 0.8074 (p0) REVERT: B 174 TYR cc_start: 0.8650 (OUTLIER) cc_final: 0.7927 (t80) REVERT: A 110 ASP cc_start: 0.8136 (p0) cc_final: 0.7873 (p0) REVERT: A 174 TYR cc_start: 0.8622 (OUTLIER) cc_final: 0.7834 (t80) outliers start: 22 outliers final: 7 residues processed: 145 average time/residue: 1.1490 time to fit residues: 180.5684 Evaluate side-chains 127 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 1.188 ------------------------------------------------------------------------------- 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 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 126 optimal weight: 0.8980 chunk 105 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 chunk 96 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 53 optimal weight: 0.0670 chunk 2 optimal weight: 0.9980 chunk 45 optimal weight: 0.0570 overall best weight: 0.5236 ------------------------------------------------------------------------------- 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 = 0.3973 r_free = 0.3973 target = 0.177249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.135100 restraints weight = 10088.262| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.66 r_work: 0.3418 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.0896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10648 Z= 0.121 Angle : 0.493 5.370 14396 Z= 0.265 Chirality : 0.040 0.129 1624 Planarity : 0.005 0.048 1888 Dihedral : 4.876 44.979 1470 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.00 % Allowed : 16.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.23), residues: 1364 helix: 2.26 (0.19), residues: 672 sheet: -1.54 (0.30), residues: 228 loop : -0.37 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 148 HIS 0.004 0.001 HIS C 197 PHE 0.013 0.001 PHE B 145 TYR 0.011 0.001 TYR C 214 ARG 0.003 0.000 ARG D 57 Details of bonding type rmsd hydrogen bonds : bond 0.03486 ( 551) hydrogen bonds : angle 3.86713 ( 1611) covalent geometry : bond 0.00284 (10648) covalent geometry : angle 0.49281 (14396) *********************** 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 159 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 1.089 Fit side-chains REVERT: D 174 TYR cc_start: 0.8506 (OUTLIER) cc_final: 0.7757 (t80) REVERT: C 80 PHE cc_start: 0.7053 (t80) cc_final: 0.6817 (t80) REVERT: C 174 TYR cc_start: 0.8486 (OUTLIER) cc_final: 0.7769 (t80) REVERT: C 248 GLN cc_start: 0.7934 (mt0) cc_final: 0.7672 (mt0) REVERT: C 251 MET cc_start: 0.7578 (tpp) cc_final: 0.7071 (tpp) REVERT: B 110 ASP cc_start: 0.8185 (p0) cc_final: 0.7919 (p0) REVERT: B 174 TYR cc_start: 0.8495 (OUTLIER) cc_final: 0.7819 (t80) REVERT: A 110 ASP cc_start: 0.7916 (p0) cc_final: 0.7681 (p0) REVERT: A 174 TYR cc_start: 0.8422 (OUTLIER) cc_final: 0.7692 (t80) outliers start: 22 outliers final: 7 residues processed: 154 average time/residue: 1.2419 time to fit residues: 207.2928 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 : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 174 TYR 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 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 52 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 106 optimal weight: 8.9990 chunk 126 optimal weight: 0.9990 chunk 68 optimal weight: 0.2980 chunk 125 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3961 r_free = 0.3961 target = 0.175832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.133358 restraints weight = 9952.670| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.98 r_work: 0.3400 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 10648 Z= 0.150 Angle : 0.520 5.230 14396 Z= 0.278 Chirality : 0.041 0.134 1624 Planarity : 0.005 0.048 1888 Dihedral : 4.922 46.505 1468 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.18 % Allowed : 17.09 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.23), residues: 1364 helix: 2.27 (0.19), residues: 676 sheet: -1.54 (0.30), residues: 228 loop : -0.44 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 148 HIS 0.009 0.001 HIS D 258 PHE 0.013 0.002 PHE B 145 TYR 0.016 0.002 TYR D 214 ARG 0.003 0.000 ARG D 57 Details of bonding type rmsd hydrogen bonds : bond 0.03673 ( 551) hydrogen bonds : angle 3.91791 ( 1611) covalent geometry : bond 0.00362 (10648) covalent geometry : angle 0.52039 (14396) *********************** 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 151 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 1.069 Fit side-chains REVERT: D 174 TYR cc_start: 0.8567 (OUTLIER) cc_final: 0.7799 (t80) REVERT: C 110 ASP cc_start: 0.8226 (p0) cc_final: 0.8025 (p0) REVERT: C 174 TYR cc_start: 0.8542 (OUTLIER) cc_final: 0.7796 (t80) REVERT: C 251 MET cc_start: 0.7608 (tpp) cc_final: 0.7217 (tpp) REVERT: B 110 ASP cc_start: 0.8184 (p0) cc_final: 0.7905 (p0) REVERT: B 174 TYR cc_start: 0.8583 (OUTLIER) cc_final: 0.7890 (t80) REVERT: B 190 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7913 (tt0) REVERT: B 251 MET cc_start: 0.7134 (tpp) cc_final: 0.6649 (tpp) REVERT: A 110 ASP cc_start: 0.7980 (p0) cc_final: 0.7748 (p0) REVERT: A 174 TYR cc_start: 0.8529 (OUTLIER) cc_final: 0.7775 (t80) REVERT: A 251 MET cc_start: 0.7616 (tpp) cc_final: 0.7405 (tpp) outliers start: 24 outliers final: 7 residues processed: 145 average time/residue: 1.1339 time to fit residues: 178.1366 Evaluate side-chains 129 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 174 TYR 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 190 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 83 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 115 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 22 optimal weight: 0.2980 chunk 94 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 258 HIS B 258 HIS A 258 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.175401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.131682 restraints weight = 10037.172| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.88 r_work: 0.3402 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 10648 Z= 0.149 Angle : 0.518 5.281 14396 Z= 0.277 Chirality : 0.041 0.133 1624 Planarity : 0.004 0.047 1888 Dihedral : 4.958 48.661 1468 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.45 % Allowed : 17.00 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.23), residues: 1364 helix: 2.35 (0.19), residues: 676 sheet: -1.45 (0.30), residues: 224 loop : -0.48 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 148 HIS 0.008 0.001 HIS D 258 PHE 0.014 0.002 PHE B 145 TYR 0.015 0.002 TYR D 214 ARG 0.002 0.000 ARG B 43 Details of bonding type rmsd hydrogen bonds : bond 0.03635 ( 551) hydrogen bonds : angle 3.89904 ( 1611) covalent geometry : bond 0.00361 (10648) covalent geometry : angle 0.51781 (14396) *********************** 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 157 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 1.206 Fit side-chains REVERT: D 42 ASN cc_start: 0.7977 (OUTLIER) cc_final: 0.7676 (t0) REVERT: D 174 TYR cc_start: 0.8540 (OUTLIER) cc_final: 0.7773 (t80) REVERT: C 174 TYR cc_start: 0.8530 (OUTLIER) cc_final: 0.7792 (t80) REVERT: C 251 MET cc_start: 0.7551 (tpp) cc_final: 0.7154 (tpp) REVERT: C 329 MET cc_start: 0.7517 (tpt) cc_final: 0.7219 (mmm) REVERT: B 174 TYR cc_start: 0.8556 (OUTLIER) cc_final: 0.7870 (t80) REVERT: B 251 MET cc_start: 0.7068 (tpp) cc_final: 0.6588 (tpp) REVERT: A 110 ASP cc_start: 0.7926 (p0) cc_final: 0.7711 (p0) REVERT: A 174 TYR cc_start: 0.8501 (OUTLIER) cc_final: 0.7734 (t80) REVERT: A 200 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7602 (mp0) outliers start: 27 outliers final: 10 residues processed: 149 average time/residue: 1.2227 time to fit residues: 196.5554 Evaluate side-chains 134 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 1.191 ------------------------------------------------------------------------------- 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 140 LYS 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 82 GLU Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain B residue 174 TYR Chi-restraints excluded: chain B residue 275 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 89 optimal weight: 0.5980 chunk 53 optimal weight: 0.0870 chunk 27 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 125 optimal weight: 7.9990 chunk 132 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 48 optimal weight: 0.3980 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.3964 r_free = 0.3964 target = 0.176390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.133316 restraints weight = 10044.069| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.83 r_work: 0.3422 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1198 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= 0.122 Angle : 0.492 5.294 14396 Z= 0.264 Chirality : 0.040 0.130 1624 Planarity : 0.004 0.048 1888 Dihedral : 4.839 49.219 1468 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.18 % Allowed : 17.27 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.23), residues: 1364 helix: 2.55 (0.19), residues: 672 sheet: -1.45 (0.30), residues: 224 loop : -0.39 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 148 HIS 0.006 0.001 HIS D 258 PHE 0.013 0.001 PHE B 145 TYR 0.012 0.001 TYR C 214 ARG 0.003 0.000 ARG D 57 Details of bonding type rmsd hydrogen bonds : bond 0.03351 ( 551) hydrogen bonds : angle 3.79960 ( 1611) covalent geometry : bond 0.00294 (10648) covalent geometry : angle 0.49178 (14396) *********************** 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 154 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 1.181 Fit side-chains REVERT: D 174 TYR cc_start: 0.8480 (OUTLIER) cc_final: 0.7787 (t80) REVERT: D 251 MET cc_start: 0.7101 (tpp) cc_final: 0.6631 (tpp) REVERT: C 174 TYR cc_start: 0.8471 (OUTLIER) cc_final: 0.7733 (t80) REVERT: C 248 GLN cc_start: 0.7961 (mt0) cc_final: 0.7658 (mt0) REVERT: C 251 MET cc_start: 0.7536 (tpp) cc_final: 0.7158 (tpp) REVERT: B 111 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.6665 (mp10) REVERT: B 140 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7710 (mtpt) REVERT: B 174 TYR cc_start: 0.8421 (OUTLIER) cc_final: 0.7802 (t80) REVERT: B 251 MET cc_start: 0.7150 (tpp) cc_final: 0.6681 (tpp) REVERT: A 174 TYR cc_start: 0.8390 (OUTLIER) cc_final: 0.7716 (t80) REVERT: A 200 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7625 (mp0) REVERT: A 251 MET cc_start: 0.7623 (tpp) cc_final: 0.7356 (tpp) outliers start: 24 outliers final: 7 residues processed: 149 average time/residue: 1.2541 time to fit residues: 201.7250 Evaluate side-chains 132 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 118 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 296 TRP 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 60 optimal weight: 0.8980 chunk 3 optimal weight: 8.9990 chunk 21 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 109 optimal weight: 0.1980 chunk 65 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3958 r_free = 0.3958 target = 0.175752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.131596 restraints weight = 10142.128| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.17 r_work: 0.3409 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1261 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= 0.138 Angle : 0.508 5.191 14396 Z= 0.272 Chirality : 0.041 0.132 1624 Planarity : 0.004 0.047 1888 Dihedral : 4.888 49.602 1468 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.27 % Allowed : 17.45 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.23), residues: 1364 helix: 2.54 (0.19), residues: 672 sheet: -1.44 (0.30), residues: 224 loop : -0.40 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 148 HIS 0.005 0.001 HIS D 258 PHE 0.013 0.002 PHE A 145 TYR 0.014 0.002 TYR B 214 ARG 0.003 0.000 ARG D 57 Details of bonding type rmsd hydrogen bonds : bond 0.03517 ( 551) hydrogen bonds : angle 3.83401 ( 1611) covalent geometry : bond 0.00335 (10648) covalent geometry : angle 0.50839 (14396) *********************** 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 147 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 1.167 Fit side-chains REVERT: D 110 ASP cc_start: 0.8081 (p0) cc_final: 0.7837 (p0) REVERT: D 174 TYR cc_start: 0.8528 (OUTLIER) cc_final: 0.7755 (t80) REVERT: C 110 ASP cc_start: 0.8101 (p0) cc_final: 0.7854 (p0) REVERT: C 174 TYR cc_start: 0.8507 (OUTLIER) cc_final: 0.7755 (t80) REVERT: C 248 GLN cc_start: 0.7927 (mt0) cc_final: 0.7651 (mt0) REVERT: C 251 MET cc_start: 0.7551 (tpp) cc_final: 0.7163 (tpp) REVERT: B 97 ILE cc_start: 0.7133 (OUTLIER) cc_final: 0.6819 (mm) REVERT: B 111 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.6541 (mp10) REVERT: B 140 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7715 (mtpt) REVERT: B 174 TYR cc_start: 0.8530 (OUTLIER) cc_final: 0.7828 (t80) REVERT: B 251 MET cc_start: 0.7191 (tpp) cc_final: 0.6719 (tpp) REVERT: A 110 ASP cc_start: 0.7978 (p0) cc_final: 0.7750 (p0) REVERT: A 174 TYR cc_start: 0.8456 (OUTLIER) cc_final: 0.7692 (t80) REVERT: A 200 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7657 (mp0) REVERT: A 251 MET cc_start: 0.7751 (tpp) cc_final: 0.7434 (tpp) outliers start: 25 outliers final: 9 residues processed: 140 average time/residue: 1.2283 time to fit residues: 186.6294 Evaluate side-chains 138 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 296 TRP Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 296 TRP Chi-restraints excluded: chain B residue 82 GLU 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 275 MET Chi-restraints excluded: chain B residue 296 TRP Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 82 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 10 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 119 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 90 GLN C 258 HIS 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 = 0.3942 r_free = 0.3942 target = 0.174059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.128914 restraints weight = 10024.558| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.14 r_work: 0.3378 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10648 Z= 0.178 Angle : 0.548 5.235 14396 Z= 0.293 Chirality : 0.043 0.138 1624 Planarity : 0.005 0.046 1888 Dihedral : 5.078 50.339 1468 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.55 % Allowed : 17.36 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.23), residues: 1364 helix: 2.37 (0.19), residues: 676 sheet: -1.50 (0.30), residues: 224 loop : -0.50 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 148 HIS 0.004 0.001 HIS D 258 PHE 0.014 0.002 PHE B 145 TYR 0.015 0.002 TYR D 214 ARG 0.003 0.000 ARG B 149 Details of bonding type rmsd hydrogen bonds : bond 0.03882 ( 551) hydrogen bonds : angle 3.97140 ( 1611) covalent geometry : bond 0.00436 (10648) covalent geometry : angle 0.54779 (14396) *********************** 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: 28 poor density : 124 time to evaluate : 0.979 Fit side-chains REVERT: D 110 ASP cc_start: 0.8149 (p0) cc_final: 0.7931 (p0) REVERT: D 174 TYR cc_start: 0.8623 (OUTLIER) cc_final: 0.7808 (t80) REVERT: C 110 ASP cc_start: 0.8234 (p0) cc_final: 0.8008 (p0) REVERT: C 174 TYR cc_start: 0.8622 (OUTLIER) cc_final: 0.7812 (t80) REVERT: C 251 MET cc_start: 0.7555 (tpp) cc_final: 0.7087 (tpp) REVERT: C 329 MET cc_start: 0.7596 (tpt) cc_final: 0.7312 (mmm) REVERT: B 97 ILE cc_start: 0.7279 (OUTLIER) cc_final: 0.6895 (mm) REVERT: B 111 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.6521 (mp10) REVERT: B 174 TYR cc_start: 0.8626 (OUTLIER) cc_final: 0.7865 (t80) REVERT: B 251 MET cc_start: 0.7207 (tpp) cc_final: 0.6719 (tpp) REVERT: A 35 GLU cc_start: 0.8182 (mp0) cc_final: 0.7977 (mp0) REVERT: A 110 ASP cc_start: 0.7956 (p0) cc_final: 0.7734 (p0) REVERT: A 174 TYR cc_start: 0.8599 (OUTLIER) cc_final: 0.7784 (t80) REVERT: A 200 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7629 (mp0) REVERT: A 251 MET cc_start: 0.7770 (tpp) cc_final: 0.7433 (tpp) outliers start: 28 outliers final: 11 residues processed: 142 average time/residue: 1.6358 time to fit residues: 249.5817 Evaluate side-chains 139 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 2.134 ------------------------------------------------------------------------------- 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 140 LYS Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 296 TRP Chi-restraints excluded: chain B residue 82 GLU 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 275 MET Chi-restraints excluded: chain B residue 296 TRP Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 82 GLU 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 94 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 132 optimal weight: 0.0970 chunk 123 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 90 GLN C 258 HIS 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 = 0.3959 r_free = 0.3959 target = 0.175844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.132628 restraints weight = 10075.926| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.91 r_work: 0.3404 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1333 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= 0.137 Angle : 0.509 5.136 14396 Z= 0.274 Chirality : 0.041 0.132 1624 Planarity : 0.004 0.047 1888 Dihedral : 4.949 50.868 1468 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.36 % Allowed : 18.18 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.23), residues: 1364 helix: 2.49 (0.19), residues: 672 sheet: -1.49 (0.30), residues: 224 loop : -0.44 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 148 HIS 0.004 0.001 HIS C 197 PHE 0.014 0.002 PHE B 145 TYR 0.012 0.002 TYR B 214 ARG 0.005 0.000 ARG D 57 Details of bonding type rmsd hydrogen bonds : bond 0.03524 ( 551) hydrogen bonds : angle 3.87011 ( 1611) covalent geometry : bond 0.00331 (10648) covalent geometry : angle 0.50936 (14396) *********************** 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 160 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 1.084 Fit side-chains REVERT: D 110 ASP cc_start: 0.8128 (p0) cc_final: 0.7900 (p0) REVERT: D 174 TYR cc_start: 0.8535 (OUTLIER) cc_final: 0.7776 (t80) REVERT: C 110 ASP cc_start: 0.8107 (p0) cc_final: 0.7906 (p0) REVERT: C 174 TYR cc_start: 0.8512 (OUTLIER) cc_final: 0.7772 (t80) REVERT: C 251 MET cc_start: 0.7543 (tpp) cc_final: 0.7084 (tpp) REVERT: C 329 MET cc_start: 0.7586 (tpt) cc_final: 0.7259 (mmm) REVERT: B 97 ILE cc_start: 0.7157 (OUTLIER) cc_final: 0.6825 (mm) REVERT: B 111 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.6663 (mp10) REVERT: B 174 TYR cc_start: 0.8526 (OUTLIER) cc_final: 0.7841 (t80) REVERT: B 251 MET cc_start: 0.7184 (tpp) cc_final: 0.6712 (tpp) REVERT: A 110 ASP cc_start: 0.7996 (p0) cc_final: 0.7776 (p0) REVERT: A 174 TYR cc_start: 0.8453 (OUTLIER) cc_final: 0.7692 (t80) REVERT: A 200 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7632 (mp0) REVERT: A 251 MET cc_start: 0.7765 (tpp) cc_final: 0.7422 (tpp) outliers start: 26 outliers final: 10 residues processed: 151 average time/residue: 1.2556 time to fit residues: 204.3630 Evaluate side-chains 142 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 1.185 ------------------------------------------------------------------------------- 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 140 LYS Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 296 TRP Chi-restraints excluded: chain B residue 82 GLU 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 275 MET 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 93 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 9 optimal weight: 0.0980 chunk 56 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3952 r_free = 0.3952 target = 0.175200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.130856 restraints weight = 10026.432| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.99 r_work: 0.3407 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10648 Z= 0.147 Angle : 0.523 5.060 14396 Z= 0.281 Chirality : 0.041 0.133 1624 Planarity : 0.004 0.047 1888 Dihedral : 4.981 51.115 1468 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.00 % Allowed : 18.55 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.23), residues: 1364 helix: 2.49 (0.19), residues: 672 sheet: -1.62 (0.29), residues: 244 loop : -0.39 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 148 HIS 0.004 0.001 HIS C 197 PHE 0.014 0.002 PHE B 145 TYR 0.012 0.002 TYR B 214 ARG 0.004 0.000 ARG D 57 Details of bonding type rmsd hydrogen bonds : bond 0.03635 ( 551) hydrogen bonds : angle 3.89601 ( 1611) covalent geometry : bond 0.00358 (10648) covalent geometry : angle 0.52336 (14396) ********************** 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 147 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 1.077 Fit side-chains REVERT: D 110 ASP cc_start: 0.8135 (p0) cc_final: 0.7914 (p0) REVERT: D 174 TYR cc_start: 0.8552 (OUTLIER) cc_final: 0.7785 (t80) REVERT: C 110 ASP cc_start: 0.8171 (p0) cc_final: 0.7930 (p0) REVERT: C 174 TYR cc_start: 0.8530 (OUTLIER) cc_final: 0.7776 (t80) REVERT: C 251 MET cc_start: 0.7562 (tpp) cc_final: 0.7107 (tpp) REVERT: C 329 MET cc_start: 0.7544 (tpt) cc_final: 0.7285 (mmm) REVERT: B 97 ILE cc_start: 0.7208 (OUTLIER) cc_final: 0.6864 (mm) REVERT: B 111 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.6559 (mp10) REVERT: B 174 TYR cc_start: 0.8544 (OUTLIER) cc_final: 0.7849 (t80) REVERT: B 251 MET cc_start: 0.7171 (tpp) cc_final: 0.6689 (tpp) REVERT: A 110 ASP cc_start: 0.8018 (p0) cc_final: 0.7810 (p0) REVERT: A 174 TYR cc_start: 0.8500 (OUTLIER) cc_final: 0.7729 (t80) REVERT: A 200 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7658 (mp0) REVERT: A 251 MET cc_start: 0.7787 (tpp) cc_final: 0.7457 (tpp) outliers start: 22 outliers final: 10 residues processed: 140 average time/residue: 1.1561 time to fit residues: 175.4411 Evaluate side-chains 139 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 1.213 ------------------------------------------------------------------------------- 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 140 LYS Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 296 TRP Chi-restraints excluded: chain B residue 82 GLU 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 275 MET 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 5 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 58 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 45 optimal weight: 0.0050 chunk 21 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- 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 90 GLN C 258 HIS 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 = 0.3967 r_free = 0.3967 target = 0.176611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.132674 restraints weight = 10008.106| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.69 r_work: 0.3376 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1377 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= 0.127 Angle : 0.503 5.107 14396 Z= 0.270 Chirality : 0.041 0.131 1624 Planarity : 0.004 0.047 1888 Dihedral : 4.886 51.257 1468 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.09 % Allowed : 18.64 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.23), residues: 1364 helix: 2.56 (0.19), residues: 672 sheet: -1.59 (0.29), residues: 244 loop : -0.36 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 148 HIS 0.004 0.001 HIS C 197 PHE 0.013 0.001 PHE A 145 TYR 0.012 0.001 TYR B 214 ARG 0.004 0.000 ARG D 57 Details of bonding type rmsd hydrogen bonds : bond 0.03428 ( 551) hydrogen bonds : angle 3.82765 ( 1611) covalent geometry : bond 0.00307 (10648) covalent geometry : angle 0.50293 (14396) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7695.63 seconds wall clock time: 134 minutes 38.73 seconds (8078.73 seconds total)