Starting phenix.real_space_refine on Sat Aug 23 07:58:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hvt_35048/08_2025/8hvt_35048.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hvt_35048/08_2025/8hvt_35048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hvt_35048/08_2025/8hvt_35048.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hvt_35048/08_2025/8hvt_35048.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hvt_35048/08_2025/8hvt_35048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hvt_35048/08_2025/8hvt_35048.map" } resolution = 3.6 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= 0.001 sd= 0.004 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 80 5.16 5 C 6952 2.51 5 N 1730 2.21 5 O 1940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10702 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3653 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 17, 'TRANS': 462} Chain breaks: 1 Chain: "B" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1617 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 8, 'TRANS': 194} Chain breaks: 2 Chain: "C" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3653 Classifications: {'peptide': 480} Link IDs: {'PTRANS': 17, 'TRANS': 462} Chain breaks: 1 Chain: "D" Number of atoms: 1617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1617 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 8, 'TRANS': 194} Chain breaks: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.84, per 1000 atoms: 0.27 Number of scatterers: 10702 At special positions: 0 Unit cell: (90.47, 115.37, 103.75, 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 80 16.00 O 1940 8.00 N 1730 7.00 C 6952 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 438 " - pdb=" SG CYS A 454 " distance=2.03 Simple disulfide: pdb=" SG CYS B 101 " - pdb=" SG CYS B 115 " distance=2.04 Simple disulfide: pdb=" SG CYS B 112 " - pdb=" SG CYS B 171 " distance=2.03 Simple disulfide: pdb=" SG CYS B 174 " - pdb=" SG CYS B 255 " distance=2.03 Simple disulfide: pdb=" SG CYS C 438 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS D 101 " - pdb=" SG CYS D 115 " distance=2.04 Simple disulfide: pdb=" SG CYS D 112 " - pdb=" SG CYS D 171 " distance=2.03 Simple disulfide: pdb=" SG CYS D 174 " - pdb=" SG CYS D 255 " distance=2.03 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " NAG-ASN " NAG B 401 " - " ASN B 128 " " NAG B 402 " - " ASN B 163 " " NAG B 403 " - " ASN B 194 " " NAG D 401 " - " ASN D 128 " " NAG D 402 " - " ASN D 163 " " NAG D 403 " - " ASN D 194 " " NAG E 1 " - " ASN D 263 " " NAG F 1 " - " ASN B 263 " Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 444.0 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 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: 60 helices and 2 sheets defined 75.3% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 119 through 164 Processing helix chain 'A' and resid 172 through 197 removed outlier: 3.693A pdb=" N LEU A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A 196 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 197 " --> pdb=" O ILE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 202 removed outlier: 3.622A pdb=" N ALA A 202 " --> pdb=" O PRO A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 215 Processing helix chain 'A' and resid 223 through 239 removed outlier: 3.842A pdb=" N LEU A 227 " --> pdb=" O ARG A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 262 removed outlier: 3.675A pdb=" N SER A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 302 removed outlier: 3.596A pdb=" N ASP A 287 " --> pdb=" O THR A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 314 removed outlier: 4.046A pdb=" N GLU A 314 " --> pdb=" O PHE A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 346 Processing helix chain 'A' and resid 365 through 369 removed outlier: 3.569A pdb=" N MET A 368 " --> pdb=" O SER A 365 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA A 369 " --> pdb=" O GLU A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 369' Processing helix chain 'A' and resid 374 through 406 Processing helix chain 'A' and resid 409 through 434 Processing helix chain 'A' and resid 462 through 467 removed outlier: 3.652A pdb=" N PHE A 466 " --> pdb=" O MET A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 480 removed outlier: 3.591A pdb=" N VAL A 474 " --> pdb=" O PRO A 470 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VAL A 475 " --> pdb=" O GLU A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 506 removed outlier: 4.663A pdb=" N GLY A 506 " --> pdb=" O CYS A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 536 Processing helix chain 'A' and resid 543 through 560 removed outlier: 3.570A pdb=" N TYR A 547 " --> pdb=" O ASP A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 573 Processing helix chain 'A' and resid 580 through 596 Processing helix chain 'A' and resid 600 through 605 Processing helix chain 'B' and resid 81 through 105 Processing helix chain 'B' and resid 110 through 115 Processing helix chain 'B' and resid 115 through 130 Processing helix chain 'B' and resid 144 through 148 removed outlier: 4.058A pdb=" N MET B 148 " --> pdb=" O ARG B 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 144 through 148' Processing helix chain 'B' and resid 153 through 170 Processing helix chain 'B' and resid 171 through 175 removed outlier: 3.572A pdb=" N LEU B 175 " --> pdb=" O ALA B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 201 removed outlier: 3.719A pdb=" N VAL B 187 " --> pdb=" O SER B 183 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR B 188 " --> pdb=" O ASN B 184 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE B 189 " --> pdb=" O SER B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 245 removed outlier: 3.683A pdb=" N GLU B 243 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU B 244 " --> pdb=" O LYS B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 270 Processing helix chain 'B' and resid 281 through 305 removed outlier: 3.803A pdb=" N VAL B 285 " --> pdb=" O ASP B 281 " (cutoff:3.500A) Proline residue: B 296 - end of helix Processing helix chain 'C' and resid 119 through 164 Processing helix chain 'C' and resid 172 through 197 removed outlier: 3.693A pdb=" N LEU C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE C 196 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE C 197 " --> pdb=" O ILE C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 202 removed outlier: 3.622A pdb=" N ALA C 202 " --> pdb=" O PRO C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 215 Processing helix chain 'C' and resid 223 through 239 removed outlier: 3.842A pdb=" N LEU C 227 " --> pdb=" O ARG C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 262 removed outlier: 3.675A pdb=" N SER C 262 " --> pdb=" O ALA C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 302 removed outlier: 3.596A pdb=" N ASP C 287 " --> pdb=" O THR C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 314 removed outlier: 4.046A pdb=" N GLU C 314 " --> pdb=" O PHE C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 346 Processing helix chain 'C' and resid 365 through 369 removed outlier: 3.569A pdb=" N MET C 368 " --> pdb=" O SER C 365 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA C 369 " --> pdb=" O GLU C 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 369' Processing helix chain 'C' and resid 374 through 406 Processing helix chain 'C' and resid 409 through 434 Processing helix chain 'C' and resid 462 through 467 removed outlier: 3.652A pdb=" N PHE C 466 " --> pdb=" O MET C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 480 removed outlier: 3.591A pdb=" N VAL C 474 " --> pdb=" O PRO C 470 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VAL C 475 " --> pdb=" O GLU C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 506 removed outlier: 4.663A pdb=" N GLY C 506 " --> pdb=" O CYS C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 536 Processing helix chain 'C' and resid 543 through 560 removed outlier: 3.570A pdb=" N TYR C 547 " --> pdb=" O ASP C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 573 Processing helix chain 'C' and resid 580 through 596 Processing helix chain 'C' and resid 600 through 605 Processing helix chain 'D' and resid 81 through 105 Processing helix chain 'D' and resid 110 through 115 Processing helix chain 'D' and resid 115 through 130 Processing helix chain 'D' and resid 144 through 148 removed outlier: 4.058A pdb=" N MET D 148 " --> pdb=" O ARG D 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 144 through 148' Processing helix chain 'D' and resid 153 through 170 Processing helix chain 'D' and resid 171 through 175 removed outlier: 3.572A pdb=" N LEU D 175 " --> pdb=" O ALA D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 201 removed outlier: 3.719A pdb=" N VAL D 187 " --> pdb=" O SER D 183 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR D 188 " --> pdb=" O ASN D 184 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE D 189 " --> pdb=" O SER D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 245 removed outlier: 3.683A pdb=" N GLU D 243 " --> pdb=" O GLN D 239 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU D 244 " --> pdb=" O LYS D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 270 Processing helix chain 'D' and resid 281 through 305 removed outlier: 3.803A pdb=" N VAL D 285 " --> pdb=" O ASP D 281 " (cutoff:3.500A) Proline residue: D 296 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 438 through 439 Processing sheet with id=AA2, first strand: chain 'C' and resid 438 through 439 746 hydrogen bonds defined for protein. 2220 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.04 Time building geometry restraints manager: 1.60 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: 2870 1.33 - 1.46: 2832 1.46 - 1.58: 5118 1.58 - 1.71: 0 1.71 - 1.83: 122 Bond restraints: 10942 Sorted by residual: bond pdb=" C1 NAG B 402 " pdb=" O5 NAG B 402 " ideal model delta sigma weight residual 1.406 1.505 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" C1 NAG D 402 " pdb=" O5 NAG D 402 " ideal model delta sigma weight residual 1.406 1.505 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" CG LEU A 587 " pdb=" CD1 LEU A 587 " ideal model delta sigma weight residual 1.521 1.440 0.081 3.30e-02 9.18e+02 5.98e+00 bond pdb=" CG LEU C 587 " pdb=" CD1 LEU C 587 " ideal model delta sigma weight residual 1.521 1.440 0.081 3.30e-02 9.18e+02 5.98e+00 bond pdb=" CB ASN C 339 " pdb=" CG ASN C 339 " ideal model delta sigma weight residual 1.516 1.466 0.050 2.50e-02 1.60e+03 4.07e+00 ... (remaining 10937 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 13988 2.08 - 4.16: 708 4.16 - 6.25: 114 6.25 - 8.33: 40 8.33 - 10.41: 16 Bond angle restraints: 14866 Sorted by residual: angle pdb=" CA ARG D 104 " pdb=" CB ARG D 104 " pdb=" CG ARG D 104 " ideal model delta sigma weight residual 114.10 123.35 -9.25 2.00e+00 2.50e-01 2.14e+01 angle pdb=" CA ARG B 104 " pdb=" CB ARG B 104 " pdb=" CG ARG B 104 " ideal model delta sigma weight residual 114.10 123.35 -9.25 2.00e+00 2.50e-01 2.14e+01 angle pdb=" C ARG D 107 " pdb=" N PRO D 108 " pdb=" CA PRO D 108 " ideal model delta sigma weight residual 119.84 114.96 4.88 1.25e+00 6.40e-01 1.52e+01 angle pdb=" C ARG B 107 " pdb=" N PRO B 108 " pdb=" CA PRO B 108 " ideal model delta sigma weight residual 119.84 114.96 4.88 1.25e+00 6.40e-01 1.52e+01 angle pdb=" C SER D 276 " pdb=" N VAL D 277 " pdb=" CA VAL D 277 " ideal model delta sigma weight residual 122.13 129.04 -6.91 1.85e+00 2.92e-01 1.40e+01 ... (remaining 14861 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.20: 6112 23.20 - 46.41: 382 46.41 - 69.61: 38 69.61 - 92.81: 28 92.81 - 116.01: 10 Dihedral angle restraints: 6570 sinusoidal: 2644 harmonic: 3926 Sorted by residual: dihedral pdb=" CA PRO D 108 " pdb=" C PRO D 108 " pdb=" N VAL D 109 " pdb=" CA VAL D 109 " ideal model delta harmonic sigma weight residual 180.00 -155.02 -24.98 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA PRO B 108 " pdb=" C PRO B 108 " pdb=" N VAL B 109 " pdb=" CA VAL B 109 " ideal model delta harmonic sigma weight residual 180.00 -155.02 -24.98 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA ASN D 177 " pdb=" C ASN D 177 " pdb=" N ASN D 178 " pdb=" CA ASN D 178 " ideal model delta harmonic sigma weight residual 180.00 155.57 24.43 0 5.00e+00 4.00e-02 2.39e+01 ... (remaining 6567 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1320 0.063 - 0.125: 352 0.125 - 0.188: 76 0.188 - 0.250: 20 0.250 - 0.313: 4 Chirality restraints: 1772 Sorted by residual: chirality pdb=" CB VAL C 513 " pdb=" CA VAL C 513 " pdb=" CG1 VAL C 513 " pdb=" CG2 VAL C 513 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CB VAL A 513 " pdb=" CA VAL A 513 " pdb=" CG1 VAL A 513 " pdb=" CG2 VAL A 513 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 1769 not shown) Planarity restraints: 1846 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 515 " -0.054 5.00e-02 4.00e+02 8.09e-02 1.05e+01 pdb=" N PRO C 516 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO C 516 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 516 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 515 " -0.054 5.00e-02 4.00e+02 8.09e-02 1.05e+01 pdb=" N PRO A 516 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 516 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 516 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 81 " -0.038 5.00e-02 4.00e+02 5.73e-02 5.25e+00 pdb=" N PRO B 82 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 82 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 82 " -0.032 5.00e-02 4.00e+02 ... (remaining 1843 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2960 2.80 - 3.33: 10308 3.33 - 3.85: 17728 3.85 - 4.38: 19636 4.38 - 4.90: 34707 Nonbonded interactions: 85339 Sorted by model distance: nonbonded pdb=" OG SER A 290 " pdb=" OG SER A 311 " model vdw 2.279 3.040 nonbonded pdb=" OG SER C 290 " pdb=" OG SER C 311 " model vdw 2.279 3.040 nonbonded pdb=" OG1 THR B 176 " pdb=" O ASN B 178 " model vdw 2.284 3.040 nonbonded pdb=" OG1 THR D 176 " pdb=" O ASN D 178 " model vdw 2.284 3.040 nonbonded pdb=" OG SER C 476 " pdb=" OD2 ASP C 480 " model vdw 2.289 3.040 ... (remaining 85334 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } 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 group one per residue 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: 1.800 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.660 Find NCS groups from input model: 0.100 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: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 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 : 0.009 0.099 10962 Z= 0.374 Angle : 1.158 15.906 14918 Z= 0.590 Chirality : 0.064 0.313 1772 Planarity : 0.007 0.081 1838 Dihedral : 16.297 116.015 4018 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.49 (0.18), residues: 1346 helix: -1.04 (0.14), residues: 932 sheet: None (None), residues: 0 loop : -2.88 (0.24), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 362 TYR 0.018 0.002 TYR A 448 PHE 0.028 0.002 PHE A 363 TRP 0.018 0.002 TRP C 524 HIS 0.011 0.003 HIS C 479 Details of bonding type rmsd covalent geometry : bond 0.00903 (10942) covalent geometry : angle 1.10832 (14866) SS BOND : bond 0.00434 ( 8) SS BOND : angle 1.82953 ( 16) hydrogen bonds : bond 0.13830 ( 746) hydrogen bonds : angle 6.03744 ( 2220) link_BETA1-4 : bond 0.00740 ( 4) link_BETA1-4 : angle 3.36246 ( 12) link_NAG-ASN : bond 0.00983 ( 8) link_NAG-ASN : angle 8.04532 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 367 LYS cc_start: 0.6427 (mttp) cc_final: 0.5278 (pttp) REVERT: A 471 GLU cc_start: 0.8171 (mp0) cc_final: 0.7800 (mp0) REVERT: C 367 LYS cc_start: 0.6465 (mttp) cc_final: 0.5303 (pttp) REVERT: C 471 GLU cc_start: 0.8173 (mp0) cc_final: 0.7792 (mp0) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.1021 time to fit residues: 32.1811 Evaluate side-chains 168 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 10 optimal weight: 0.0980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.0050 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN C 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.128769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.097210 restraints weight = 14347.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.100534 restraints weight = 8497.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.102703 restraints weight = 6187.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.104138 restraints weight = 5062.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.104650 restraints weight = 4455.189| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10962 Z= 0.132 Angle : 0.702 13.138 14918 Z= 0.345 Chirality : 0.042 0.152 1772 Planarity : 0.005 0.065 1838 Dihedral : 10.820 101.471 1698 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.70 % Allowed : 10.30 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.22), residues: 1346 helix: 1.01 (0.16), residues: 948 sheet: None (None), residues: 0 loop : -2.64 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 281 TYR 0.013 0.001 TYR A 505 PHE 0.014 0.001 PHE C 392 TRP 0.015 0.001 TRP C 524 HIS 0.004 0.001 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00269 (10942) covalent geometry : angle 0.64801 (14866) SS BOND : bond 0.00373 ( 8) SS BOND : angle 1.68194 ( 16) hydrogen bonds : bond 0.04591 ( 746) hydrogen bonds : angle 3.77695 ( 2220) link_BETA1-4 : bond 0.00554 ( 4) link_BETA1-4 : angle 2.70141 ( 12) link_NAG-ASN : bond 0.00615 ( 8) link_NAG-ASN : angle 6.36241 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 210 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 281 ASP cc_start: 0.7890 (p0) cc_final: 0.7332 (t70) REVERT: D 281 ASP cc_start: 0.7894 (p0) cc_final: 0.7338 (t70) outliers start: 8 outliers final: 6 residues processed: 212 average time/residue: 0.0918 time to fit residues: 29.2028 Evaluate side-chains 188 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 182 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 282 ASP Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 282 ASP Chi-restraints excluded: chain C residue 359 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 5 optimal weight: 0.0370 chunk 36 optimal weight: 0.7980 chunk 113 optimal weight: 0.6980 chunk 129 optimal weight: 8.9990 chunk 117 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 125 optimal weight: 0.8980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.131412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.100388 restraints weight = 14366.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.103820 restraints weight = 8387.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.106183 restraints weight = 6055.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.107683 restraints weight = 4882.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.108683 restraints weight = 4244.633| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10962 Z= 0.122 Angle : 0.660 12.619 14918 Z= 0.321 Chirality : 0.041 0.164 1772 Planarity : 0.004 0.059 1838 Dihedral : 9.376 99.170 1698 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.22 % Allowed : 13.61 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.23), residues: 1346 helix: 1.79 (0.16), residues: 946 sheet: None (None), residues: 0 loop : -2.54 (0.28), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 281 TYR 0.014 0.001 TYR A 505 PHE 0.013 0.001 PHE C 392 TRP 0.018 0.001 TRP C 524 HIS 0.004 0.001 HIS C 605 Details of bonding type rmsd covalent geometry : bond 0.00253 (10942) covalent geometry : angle 0.60496 (14866) SS BOND : bond 0.00478 ( 8) SS BOND : angle 3.03672 ( 16) hydrogen bonds : bond 0.04120 ( 746) hydrogen bonds : angle 3.54863 ( 2220) link_BETA1-4 : bond 0.00630 ( 4) link_BETA1-4 : angle 2.43256 ( 12) link_NAG-ASN : bond 0.00636 ( 8) link_NAG-ASN : angle 5.89170 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 196 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 550 MET cc_start: 0.8783 (mmt) cc_final: 0.8505 (mmt) REVERT: B 195 HIS cc_start: 0.8279 (t70) cc_final: 0.8034 (t70) REVERT: C 550 MET cc_start: 0.8763 (mmt) cc_final: 0.8487 (mmt) REVERT: D 195 HIS cc_start: 0.8276 (t70) cc_final: 0.8032 (t70) outliers start: 14 outliers final: 10 residues processed: 200 average time/residue: 0.1026 time to fit residues: 30.2266 Evaluate side-chains 192 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 182 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain D residue 127 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 87 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 133 optimal weight: 0.2980 chunk 74 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 92 optimal weight: 9.9990 chunk 55 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 125 optimal weight: 10.0000 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.131936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.101532 restraints weight = 14451.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.104943 restraints weight = 8419.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.107146 restraints weight = 6044.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.108636 restraints weight = 4915.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.109551 restraints weight = 4282.646| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10962 Z= 0.148 Angle : 0.672 12.421 14918 Z= 0.326 Chirality : 0.042 0.194 1772 Planarity : 0.005 0.059 1838 Dihedral : 8.628 97.503 1698 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.57 % Allowed : 14.66 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.23), residues: 1346 helix: 2.02 (0.16), residues: 952 sheet: None (None), residues: 0 loop : -2.62 (0.27), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 281 TYR 0.012 0.001 TYR A 505 PHE 0.026 0.001 PHE D 200 TRP 0.015 0.001 TRP C 524 HIS 0.004 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00337 (10942) covalent geometry : angle 0.62003 (14866) SS BOND : bond 0.00854 ( 8) SS BOND : angle 3.27212 ( 16) hydrogen bonds : bond 0.04015 ( 746) hydrogen bonds : angle 3.47593 ( 2220) link_BETA1-4 : bond 0.00461 ( 4) link_BETA1-4 : angle 2.19791 ( 12) link_NAG-ASN : bond 0.00604 ( 8) link_NAG-ASN : angle 5.72117 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 188 time to evaluate : 0.417 Fit side-chains REVERT: A 368 MET cc_start: 0.6652 (ptm) cc_final: 0.6273 (ptp) REVERT: B 168 GLU cc_start: 0.8442 (tp30) cc_final: 0.7915 (mm-30) REVERT: C 368 MET cc_start: 0.6642 (ptm) cc_final: 0.6261 (ptp) REVERT: D 168 GLU cc_start: 0.8434 (tp30) cc_final: 0.7909 (mm-30) outliers start: 18 outliers final: 8 residues processed: 198 average time/residue: 0.0997 time to fit residues: 28.8122 Evaluate side-chains 190 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 182 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 199 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 76 optimal weight: 6.9990 chunk 123 optimal weight: 0.6980 chunk 15 optimal weight: 10.0000 chunk 92 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 7 optimal weight: 0.6980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 HIS D 195 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.134269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.104242 restraints weight = 14332.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.107656 restraints weight = 8359.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.109953 restraints weight = 5998.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.111435 restraints weight = 4833.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.112245 restraints weight = 4211.593| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10962 Z= 0.137 Angle : 0.653 12.235 14918 Z= 0.317 Chirality : 0.042 0.168 1772 Planarity : 0.005 0.059 1838 Dihedral : 8.235 95.920 1698 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.09 % Allowed : 15.01 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.23), residues: 1346 helix: 2.26 (0.16), residues: 950 sheet: None (None), residues: 0 loop : -2.42 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 281 TYR 0.011 0.001 TYR A 505 PHE 0.019 0.001 PHE D 200 TRP 0.017 0.001 TRP A 524 HIS 0.006 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00306 (10942) covalent geometry : angle 0.60489 (14866) SS BOND : bond 0.00615 ( 8) SS BOND : angle 2.99585 ( 16) hydrogen bonds : bond 0.03862 ( 746) hydrogen bonds : angle 3.40761 ( 2220) link_BETA1-4 : bond 0.00521 ( 4) link_BETA1-4 : angle 1.94839 ( 12) link_NAG-ASN : bond 0.00605 ( 8) link_NAG-ASN : angle 5.51555 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 190 time to evaluate : 0.420 Fit side-chains REVERT: A 368 MET cc_start: 0.6611 (ptm) cc_final: 0.6244 (ptp) REVERT: A 451 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8371 (pt0) REVERT: B 168 GLU cc_start: 0.8402 (tp30) cc_final: 0.7921 (mm-30) REVERT: B 174 CYS cc_start: 0.5949 (OUTLIER) cc_final: 0.5570 (m) REVERT: B 197 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8818 (mm) REVERT: C 368 MET cc_start: 0.6610 (ptm) cc_final: 0.6245 (ptp) REVERT: C 451 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8367 (pt0) REVERT: D 168 GLU cc_start: 0.8397 (tp30) cc_final: 0.7913 (mm-30) REVERT: D 174 CYS cc_start: 0.5952 (OUTLIER) cc_final: 0.5569 (m) REVERT: D 197 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8827 (mm) outliers start: 24 outliers final: 10 residues processed: 204 average time/residue: 0.0980 time to fit residues: 29.3520 Evaluate side-chains 194 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 178 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 174 CYS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 451 GLN Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 199 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 39 optimal weight: 3.9990 chunk 116 optimal weight: 8.9990 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 135 optimal weight: 0.9980 chunk 32 optimal weight: 0.3980 chunk 96 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 HIS D 195 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.135857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.105398 restraints weight = 14390.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.108862 restraints weight = 8367.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.111172 restraints weight = 6022.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.112632 restraints weight = 4873.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.113366 restraints weight = 4245.394| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10962 Z= 0.121 Angle : 0.635 11.998 14918 Z= 0.308 Chirality : 0.041 0.157 1772 Planarity : 0.004 0.057 1838 Dihedral : 7.938 94.123 1698 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.01 % Allowed : 16.32 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.23), residues: 1346 helix: 2.43 (0.16), residues: 956 sheet: None (None), residues: 0 loop : -2.36 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 281 TYR 0.010 0.001 TYR C 505 PHE 0.013 0.001 PHE A 392 TRP 0.015 0.001 TRP A 524 HIS 0.006 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00257 (10942) covalent geometry : angle 0.58793 (14866) SS BOND : bond 0.00396 ( 8) SS BOND : angle 3.05669 ( 16) hydrogen bonds : bond 0.03694 ( 746) hydrogen bonds : angle 3.32166 ( 2220) link_BETA1-4 : bond 0.00569 ( 4) link_BETA1-4 : angle 1.77275 ( 12) link_NAG-ASN : bond 0.00610 ( 8) link_NAG-ASN : angle 5.33543 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 182 time to evaluate : 0.409 Fit side-chains REVERT: A 198 GLU cc_start: 0.7909 (tp30) cc_final: 0.7699 (tp30) REVERT: A 332 MET cc_start: 0.8603 (tpt) cc_final: 0.8237 (tpt) REVERT: A 368 MET cc_start: 0.6550 (ptm) cc_final: 0.6158 (ptp) REVERT: A 451 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8362 (pt0) REVERT: B 168 GLU cc_start: 0.8392 (tp30) cc_final: 0.7933 (mm-30) REVERT: B 174 CYS cc_start: 0.5864 (OUTLIER) cc_final: 0.5546 (m) REVERT: B 197 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8796 (mm) REVERT: B 262 MET cc_start: 0.8426 (mmm) cc_final: 0.7938 (tmm) REVERT: B 281 ASP cc_start: 0.7708 (p0) cc_final: 0.7247 (t70) REVERT: C 198 GLU cc_start: 0.7908 (tp30) cc_final: 0.7696 (tp30) REVERT: C 332 MET cc_start: 0.8605 (tpt) cc_final: 0.8245 (tpt) REVERT: C 368 MET cc_start: 0.6550 (ptm) cc_final: 0.6156 (ptp) REVERT: C 451 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8363 (pt0) REVERT: D 168 GLU cc_start: 0.8387 (tp30) cc_final: 0.7927 (mm-30) REVERT: D 174 CYS cc_start: 0.5856 (OUTLIER) cc_final: 0.5542 (m) REVERT: D 197 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8796 (mm) REVERT: D 262 MET cc_start: 0.8425 (mmm) cc_final: 0.7937 (tmm) REVERT: D 281 ASP cc_start: 0.7706 (p0) cc_final: 0.7250 (t70) outliers start: 23 outliers final: 16 residues processed: 193 average time/residue: 0.0927 time to fit residues: 26.6198 Evaluate side-chains 198 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 176 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 174 CYS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 451 GLN Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 174 CYS Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 199 CYS Chi-restraints excluded: chain D residue 283 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 61 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 59 optimal weight: 0.0470 chunk 106 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 overall best weight: 1.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 HIS D 195 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.133681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.103284 restraints weight = 14306.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.106620 restraints weight = 8449.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.108822 restraints weight = 6119.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.110286 restraints weight = 4989.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.111000 restraints weight = 4357.329| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10962 Z= 0.142 Angle : 0.647 11.870 14918 Z= 0.315 Chirality : 0.042 0.158 1772 Planarity : 0.004 0.057 1838 Dihedral : 7.845 93.037 1698 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.57 % Allowed : 17.98 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.87 (0.23), residues: 1346 helix: 2.57 (0.16), residues: 944 sheet: None (None), residues: 0 loop : -2.25 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 281 TYR 0.010 0.001 TYR A 505 PHE 0.014 0.001 PHE A 392 TRP 0.014 0.001 TRP C 524 HIS 0.004 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00325 (10942) covalent geometry : angle 0.60139 (14866) SS BOND : bond 0.00588 ( 8) SS BOND : angle 3.22652 ( 16) hydrogen bonds : bond 0.03778 ( 746) hydrogen bonds : angle 3.34644 ( 2220) link_BETA1-4 : bond 0.00432 ( 4) link_BETA1-4 : angle 1.69941 ( 12) link_NAG-ASN : bond 0.00611 ( 8) link_NAG-ASN : angle 5.25957 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 190 time to evaluate : 0.390 Fit side-chains REVERT: A 368 MET cc_start: 0.6563 (ptm) cc_final: 0.6152 (ptp) REVERT: A 451 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8350 (pt0) REVERT: B 168 GLU cc_start: 0.8411 (tp30) cc_final: 0.7937 (mm-30) REVERT: B 197 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8778 (mm) REVERT: C 368 MET cc_start: 0.6558 (ptm) cc_final: 0.6149 (ptp) REVERT: C 451 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8349 (pt0) REVERT: D 168 GLU cc_start: 0.8406 (tp30) cc_final: 0.7935 (mm-30) REVERT: D 197 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8782 (mm) outliers start: 18 outliers final: 10 residues processed: 198 average time/residue: 0.0942 time to fit residues: 27.3720 Evaluate side-chains 200 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 186 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 451 GLN Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 283 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 128 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 116 optimal weight: 0.0870 chunk 34 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 121 optimal weight: 9.9990 chunk 107 optimal weight: 0.6980 chunk 92 optimal weight: 7.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 HIS D 195 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.136953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.106804 restraints weight = 14268.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.110243 restraints weight = 8412.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.112430 restraints weight = 6049.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.113967 restraints weight = 4921.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.114655 restraints weight = 4285.626| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10962 Z= 0.116 Angle : 0.644 11.662 14918 Z= 0.311 Chirality : 0.040 0.155 1772 Planarity : 0.004 0.055 1838 Dihedral : 7.682 91.196 1698 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.13 % Allowed : 18.76 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.01 (0.23), residues: 1346 helix: 2.65 (0.16), residues: 944 sheet: None (None), residues: 0 loop : -2.14 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 281 TYR 0.010 0.001 TYR C 448 PHE 0.012 0.001 PHE A 392 TRP 0.017 0.001 TRP A 524 HIS 0.005 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00246 (10942) covalent geometry : angle 0.60297 (14866) SS BOND : bond 0.00383 ( 8) SS BOND : angle 2.58197 ( 16) hydrogen bonds : bond 0.03584 ( 746) hydrogen bonds : angle 3.28255 ( 2220) link_BETA1-4 : bond 0.00538 ( 4) link_BETA1-4 : angle 1.64328 ( 12) link_NAG-ASN : bond 0.00620 ( 8) link_NAG-ASN : angle 5.16443 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 190 time to evaluate : 0.415 Fit side-chains REVERT: A 332 MET cc_start: 0.8545 (tpt) cc_final: 0.8197 (tpt) REVERT: A 368 MET cc_start: 0.6535 (ptm) cc_final: 0.6103 (ptp) REVERT: A 451 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.8298 (pt0) REVERT: B 168 GLU cc_start: 0.8384 (tp30) cc_final: 0.7823 (mm-30) REVERT: B 197 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8785 (mm) REVERT: B 262 MET cc_start: 0.8427 (mmm) cc_final: 0.8054 (tmm) REVERT: B 281 ASP cc_start: 0.7613 (p0) cc_final: 0.7242 (t70) REVERT: C 332 MET cc_start: 0.8546 (tpt) cc_final: 0.8206 (tpt) REVERT: C 368 MET cc_start: 0.6537 (ptm) cc_final: 0.6104 (ptp) REVERT: C 451 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8294 (pt0) REVERT: D 168 GLU cc_start: 0.8383 (tp30) cc_final: 0.7820 (mm-30) REVERT: D 197 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8785 (mm) REVERT: D 262 MET cc_start: 0.8428 (mmm) cc_final: 0.8055 (tmm) REVERT: D 281 ASP cc_start: 0.7614 (p0) cc_final: 0.7246 (t70) outliers start: 13 outliers final: 8 residues processed: 197 average time/residue: 0.0973 time to fit residues: 28.1090 Evaluate side-chains 198 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 186 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 451 GLN Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 283 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 80 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 35 optimal weight: 0.0670 chunk 131 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 128 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 115 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 HIS D 195 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.135624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.105449 restraints weight = 14320.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.108792 restraints weight = 8416.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.111043 restraints weight = 6069.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.112405 restraints weight = 4926.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.113453 restraints weight = 4319.010| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10962 Z= 0.119 Angle : 0.660 11.503 14918 Z= 0.317 Chirality : 0.040 0.155 1772 Planarity : 0.004 0.055 1838 Dihedral : 7.578 89.411 1698 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.05 % Allowed : 19.55 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.09 (0.23), residues: 1346 helix: 2.68 (0.16), residues: 948 sheet: None (None), residues: 0 loop : -2.04 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 281 TYR 0.010 0.001 TYR A 448 PHE 0.012 0.001 PHE C 392 TRP 0.017 0.001 TRP A 524 HIS 0.005 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00257 (10942) covalent geometry : angle 0.62186 (14866) SS BOND : bond 0.00290 ( 8) SS BOND : angle 2.55182 ( 16) hydrogen bonds : bond 0.03546 ( 746) hydrogen bonds : angle 3.28117 ( 2220) link_BETA1-4 : bond 0.00518 ( 4) link_BETA1-4 : angle 1.61599 ( 12) link_NAG-ASN : bond 0.00627 ( 8) link_NAG-ASN : angle 5.08621 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 190 time to evaluate : 0.439 Fit side-chains REVERT: A 332 MET cc_start: 0.8548 (tpt) cc_final: 0.8210 (tpt) REVERT: A 368 MET cc_start: 0.6500 (ptm) cc_final: 0.6085 (ptp) REVERT: A 451 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8307 (pt0) REVERT: B 168 GLU cc_start: 0.8346 (tp30) cc_final: 0.7969 (mm-30) REVERT: B 262 MET cc_start: 0.8427 (mmm) cc_final: 0.7958 (tmm) REVERT: B 281 ASP cc_start: 0.7583 (p0) cc_final: 0.7137 (t70) REVERT: C 332 MET cc_start: 0.8549 (tpt) cc_final: 0.8223 (tpt) REVERT: C 368 MET cc_start: 0.6503 (ptm) cc_final: 0.6087 (ptp) REVERT: C 451 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8304 (pt0) REVERT: D 168 GLU cc_start: 0.8342 (tp30) cc_final: 0.7967 (mm-30) REVERT: D 262 MET cc_start: 0.8426 (mmm) cc_final: 0.7959 (tmm) REVERT: D 281 ASP cc_start: 0.7585 (p0) cc_final: 0.7141 (t70) outliers start: 12 outliers final: 8 residues processed: 196 average time/residue: 0.1020 time to fit residues: 29.2333 Evaluate side-chains 196 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 186 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 451 GLN Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 283 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 65 optimal weight: 0.0470 chunk 72 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 64 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 105 optimal weight: 0.7980 chunk 128 optimal weight: 7.9990 chunk 131 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 HIS D 195 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.134820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.104739 restraints weight = 14354.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.108054 restraints weight = 8499.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.110263 restraints weight = 6148.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.111678 restraints weight = 5007.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.112665 restraints weight = 4373.677| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10962 Z= 0.132 Angle : 0.656 11.402 14918 Z= 0.318 Chirality : 0.041 0.155 1772 Planarity : 0.004 0.055 1838 Dihedral : 7.521 88.174 1698 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.87 % Allowed : 19.90 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.06 (0.23), residues: 1346 helix: 2.65 (0.16), residues: 948 sheet: None (None), residues: 0 loop : -2.03 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 281 TYR 0.015 0.001 TYR C 448 PHE 0.022 0.001 PHE D 193 TRP 0.015 0.001 TRP C 524 HIS 0.004 0.001 HIS D 195 Details of bonding type rmsd covalent geometry : bond 0.00298 (10942) covalent geometry : angle 0.61650 (14866) SS BOND : bond 0.00339 ( 8) SS BOND : angle 2.54547 ( 16) hydrogen bonds : bond 0.03596 ( 746) hydrogen bonds : angle 3.32421 ( 2220) link_BETA1-4 : bond 0.00502 ( 4) link_BETA1-4 : angle 1.65377 ( 12) link_NAG-ASN : bond 0.00600 ( 8) link_NAG-ASN : angle 5.10478 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2692 Ramachandran restraints generated. 1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 188 time to evaluate : 0.406 Fit side-chains REVERT: A 332 MET cc_start: 0.8541 (tpt) cc_final: 0.8209 (tpt) REVERT: A 368 MET cc_start: 0.6517 (ptm) cc_final: 0.6080 (ptp) REVERT: A 451 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8278 (pt0) REVERT: B 168 GLU cc_start: 0.8347 (tp30) cc_final: 0.7966 (mm-30) REVERT: B 262 MET cc_start: 0.8432 (mmm) cc_final: 0.7972 (tmm) REVERT: C 332 MET cc_start: 0.8537 (tpt) cc_final: 0.8215 (tpt) REVERT: C 368 MET cc_start: 0.6518 (ptm) cc_final: 0.6082 (ptp) REVERT: C 451 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8275 (pt0) REVERT: D 168 GLU cc_start: 0.8341 (tp30) cc_final: 0.7963 (mm-30) REVERT: D 262 MET cc_start: 0.8427 (mmm) cc_final: 0.7967 (tmm) outliers start: 10 outliers final: 8 residues processed: 192 average time/residue: 0.0946 time to fit residues: 27.1512 Evaluate side-chains 196 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 186 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 451 GLN Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 451 GLN Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 283 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 31 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 118 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 78 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 HIS D 195 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.135073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.105512 restraints weight = 14409.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.108865 restraints weight = 8618.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.111047 restraints weight = 6223.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.112541 restraints weight = 5039.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.113444 restraints weight = 4390.055| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10962 Z= 0.119 Angle : 0.644 11.239 14918 Z= 0.312 Chirality : 0.041 0.151 1772 Planarity : 0.004 0.055 1838 Dihedral : 7.391 85.617 1698 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.87 % Allowed : 19.90 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.10 (0.23), residues: 1346 helix: 2.65 (0.16), residues: 954 sheet: None (None), residues: 0 loop : -2.01 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 281 TYR 0.014 0.001 TYR A 448 PHE 0.018 0.001 PHE D 193 TRP 0.017 0.001 TRP A 524 HIS 0.005 0.001 HIS B 195 Details of bonding type rmsd covalent geometry : bond 0.00259 (10942) covalent geometry : angle 0.60632 (14866) SS BOND : bond 0.00274 ( 8) SS BOND : angle 2.40133 ( 16) hydrogen bonds : bond 0.03520 ( 746) hydrogen bonds : angle 3.30829 ( 2220) link_BETA1-4 : bond 0.00525 ( 4) link_BETA1-4 : angle 1.60548 ( 12) link_NAG-ASN : bond 0.00620 ( 8) link_NAG-ASN : angle 5.00556 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1755.59 seconds wall clock time: 31 minutes 13.86 seconds (1873.86 seconds total)