Starting phenix.real_space_refine on Fri Feb 14 22:25:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hvt_35048/02_2025/8hvt_35048.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hvt_35048/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hvt_35048/02_2025/8hvt_35048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hvt_35048/02_2025/8hvt_35048.map" model { file = "/net/cci-nas-00/data/ceres_data/8hvt_35048/02_2025/8hvt_35048.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hvt_35048/02_2025/8hvt_35048.cif" } resolution = 3.6 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= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 6.58, per 1000 atoms: 0.61 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: 3.28 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 0.95 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: 3.35 Time building geometry restraints manager: 3.32 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: 0.06 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'A' selection = chain 'C' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 26.830 Find NCS groups from input model: 0.200 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.680 ------------------------------------------------------------------------------- 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 10942 Z= 0.566 Angle : 1.108 10.411 14866 Z= 0.579 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 (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: -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 TRP 0.018 0.002 TRP C 524 HIS 0.011 0.003 HIS C 479 PHE 0.028 0.002 PHE A 363 TYR 0.018 0.002 TYR A 448 ARG 0.009 0.001 ARG C 362 *********************** 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 : 1.129 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: 0.2144 time to fit residues: 66.8942 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 : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 123 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3350 r_free = 0.3350 target = 0.128139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.097420 restraints weight = 14238.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.100528 restraints weight = 8731.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.102538 restraints weight = 6468.077| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10942 Z= 0.179 Angle : 0.661 8.342 14866 Z= 0.341 Chirality : 0.042 0.154 1772 Planarity : 0.005 0.067 1838 Dihedral : 11.281 102.404 1698 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.87 % Allowed : 9.95 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.11 (0.22), residues: 1346 helix: 0.96 (0.16), residues: 948 sheet: None (None), residues: 0 loop : -2.66 (0.27), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 524 HIS 0.004 0.001 HIS A 479 PHE 0.014 0.001 PHE C 392 TYR 0.013 0.001 TYR A 505 ARG 0.005 0.000 ARG A 281 *********************** 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: 10 poor density : 208 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 210 average time/residue: 0.2090 time to fit residues: 65.3650 Evaluate side-chains 186 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 178 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL 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 192 VAL 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 2 optimal weight: 0.8980 chunk 116 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 30 optimal weight: 0.2980 chunk 98 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 109 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3446 r_free = 0.3446 target = 0.135269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.105337 restraints weight = 14331.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.108804 restraints weight = 8296.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.111105 restraints weight = 5933.522| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10942 Z= 0.179 Angle : 0.616 8.519 14866 Z= 0.314 Chirality : 0.042 0.163 1772 Planarity : 0.005 0.061 1838 Dihedral : 9.700 99.834 1698 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.40 % Allowed : 12.57 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.23), residues: 1346 helix: 1.70 (0.16), residues: 950 sheet: None (None), residues: 0 loop : -2.59 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 524 HIS 0.003 0.001 HIS A 605 PHE 0.014 0.001 PHE C 392 TYR 0.014 0.001 TYR A 505 ARG 0.008 0.000 ARG A 281 *********************** 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 222 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 206 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 195 HIS cc_start: 0.8349 (t70) cc_final: 0.8072 (t70) REVERT: D 195 HIS cc_start: 0.8346 (t70) cc_final: 0.8067 (t70) outliers start: 16 outliers final: 12 residues processed: 208 average time/residue: 0.2029 time to fit residues: 61.6501 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 : 1.230 ------------------------------------------------------------------------------- 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 A residue 359 ASN 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 C residue 359 ASN 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 13 optimal weight: 1.9990 chunk 5 optimal weight: 0.0070 chunk 71 optimal weight: 0.8980 chunk 65 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.9602 ------------------------------------------------------------------------------- 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 = 0.3445 r_free = 0.3445 target = 0.134937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.104843 restraints weight = 14182.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.108279 restraints weight = 8244.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.110454 restraints weight = 5909.756| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10942 Z= 0.176 Angle : 0.608 8.655 14866 Z= 0.306 Chirality : 0.041 0.171 1772 Planarity : 0.004 0.058 1838 Dihedral : 8.834 98.050 1698 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.48 % Allowed : 14.75 % 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 (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: 1346 helix: 2.10 (0.16), residues: 938 sheet: None (None), residues: 0 loop : -2.45 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 524 HIS 0.004 0.001 HIS C 605 PHE 0.013 0.001 PHE C 392 TYR 0.013 0.001 TYR A 505 ARG 0.007 0.000 ARG A 281 *********************** 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 217 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 200 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 195 HIS cc_start: 0.8282 (t70) cc_final: 0.8047 (t70) REVERT: D 195 HIS cc_start: 0.8274 (t70) cc_final: 0.8042 (t70) outliers start: 17 outliers final: 10 residues processed: 207 average time/residue: 0.2071 time to fit residues: 62.3354 Evaluate side-chains 200 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 190 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain D residue 127 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 40 optimal weight: 5.9990 chunk 92 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 116 optimal weight: 0.0030 chunk 66 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 overall best weight: 1.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN B 195 HIS C 359 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.133835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.103731 restraints weight = 14241.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.107179 restraints weight = 8305.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.109438 restraints weight = 5960.844| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10942 Z= 0.221 Angle : 0.610 8.694 14866 Z= 0.309 Chirality : 0.042 0.189 1772 Planarity : 0.005 0.058 1838 Dihedral : 8.479 97.042 1698 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.18 % Allowed : 14.40 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.23), residues: 1346 helix: 2.12 (0.16), residues: 952 sheet: None (None), residues: 0 loop : -2.55 (0.27), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 524 HIS 0.003 0.001 HIS B 195 PHE 0.026 0.001 PHE D 200 TYR 0.011 0.001 TYR A 505 ARG 0.010 0.000 ARG C 281 *********************** 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 211 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 186 time to evaluate : 1.170 Fit side-chains REVERT: A 368 MET cc_start: 0.6673 (ptm) cc_final: 0.6374 (ptp) REVERT: B 168 GLU cc_start: 0.8409 (tp30) cc_final: 0.7883 (mm-30) REVERT: B 174 CYS cc_start: 0.6071 (OUTLIER) cc_final: 0.5673 (m) REVERT: C 368 MET cc_start: 0.6667 (ptm) cc_final: 0.6366 (ptp) REVERT: D 168 GLU cc_start: 0.8399 (tp30) cc_final: 0.7877 (mm-30) REVERT: D 174 CYS cc_start: 0.6062 (OUTLIER) cc_final: 0.5666 (m) outliers start: 25 outliers final: 14 residues processed: 197 average time/residue: 0.2091 time to fit residues: 59.9333 Evaluate side-chains 198 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 182 time to evaluate : 1.222 ------------------------------------------------------------------------------- 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 333 ILE Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 174 CYS Chi-restraints excluded: chain B residue 199 CYS 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 359 ASN Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 174 CYS 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 74 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 chunk 114 optimal weight: 0.9980 chunk 35 optimal weight: 0.0970 chunk 108 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN B 195 HIS C 359 ASN D 195 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.134826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.104638 restraints weight = 14331.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.108125 restraints weight = 8350.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.110388 restraints weight = 5973.641| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10942 Z= 0.209 Angle : 0.621 8.761 14866 Z= 0.310 Chirality : 0.042 0.170 1772 Planarity : 0.005 0.058 1838 Dihedral : 8.241 96.069 1698 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.01 % Allowed : 15.79 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.23), residues: 1346 helix: 2.23 (0.16), residues: 956 sheet: None (None), residues: 0 loop : -2.44 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 524 HIS 0.006 0.001 HIS D 195 PHE 0.020 0.001 PHE D 200 TYR 0.011 0.001 TYR A 505 ARG 0.010 0.000 ARG A 281 *********************** 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 : 0.927 Fit side-chains REVERT: A 368 MET cc_start: 0.6639 (ptm) cc_final: 0.6366 (ptp) REVERT: A 451 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8364 (pt0) REVERT: B 168 GLU cc_start: 0.8399 (tp30) cc_final: 0.7923 (mm-30) REVERT: B 174 CYS cc_start: 0.6124 (OUTLIER) cc_final: 0.5812 (m) REVERT: C 368 MET cc_start: 0.6638 (ptm) cc_final: 0.6360 (ptp) REVERT: C 451 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.8362 (pt0) REVERT: D 168 GLU cc_start: 0.8394 (tp30) cc_final: 0.7918 (mm-30) REVERT: D 174 CYS cc_start: 0.6105 (OUTLIER) cc_final: 0.5805 (m) outliers start: 23 outliers final: 16 residues processed: 191 average time/residue: 0.2117 time to fit residues: 59.4143 Evaluate side-chains 196 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 1.187 ------------------------------------------------------------------------------- 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 359 ASN 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 199 CYS 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 359 ASN 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 199 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 88 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 chunk 117 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 122 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN B 195 HIS C 359 ASN D 195 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.134553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.104163 restraints weight = 14441.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.107565 restraints weight = 8413.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.109903 restraints weight = 6044.881| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10942 Z= 0.174 Angle : 0.600 8.867 14866 Z= 0.301 Chirality : 0.041 0.155 1772 Planarity : 0.004 0.057 1838 Dihedral : 8.037 94.914 1698 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.92 % Allowed : 16.75 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.23), residues: 1346 helix: 2.36 (0.16), residues: 956 sheet: None (None), residues: 0 loop : -2.42 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 524 HIS 0.006 0.001 HIS B 195 PHE 0.013 0.001 PHE A 392 TYR 0.011 0.001 TYR A 505 ARG 0.012 0.000 ARG A 281 *********************** 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 210 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 1.121 Fit side-chains REVERT: A 368 MET cc_start: 0.6617 (ptm) cc_final: 0.6314 (ptp) REVERT: A 451 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8349 (pt0) REVERT: B 168 GLU cc_start: 0.8400 (tp30) cc_final: 0.7880 (mm-30) REVERT: B 174 CYS cc_start: 0.5934 (OUTLIER) cc_final: 0.5613 (m) REVERT: B 262 MET cc_start: 0.8493 (mmm) cc_final: 0.8045 (tmm) REVERT: B 281 ASP cc_start: 0.7743 (p0) cc_final: 0.7262 (t70) REVERT: C 368 MET cc_start: 0.6618 (ptm) cc_final: 0.6310 (ptp) REVERT: C 451 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8353 (pt0) REVERT: D 168 GLU cc_start: 0.8398 (tp30) cc_final: 0.7875 (mm-30) REVERT: D 174 CYS cc_start: 0.5918 (OUTLIER) cc_final: 0.5600 (m) REVERT: D 262 MET cc_start: 0.8491 (mmm) cc_final: 0.8045 (tmm) REVERT: D 281 ASP cc_start: 0.7745 (p0) cc_final: 0.7268 (t70) outliers start: 22 outliers final: 18 residues processed: 196 average time/residue: 0.2158 time to fit residues: 61.3453 Evaluate side-chains 202 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 180 time to evaluate : 1.178 ------------------------------------------------------------------------------- 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 333 ILE Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 365 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 174 CYS 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 333 ILE Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain C residue 365 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 174 CYS Chi-restraints excluded: chain D residue 199 CYS 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 87 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 92 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN B 195 HIS C 359 ASN D 195 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.135807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.105717 restraints weight = 14194.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.109134 restraints weight = 8325.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.111270 restraints weight = 5979.757| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10942 Z= 0.182 Angle : 0.608 8.925 14866 Z= 0.303 Chirality : 0.041 0.157 1772 Planarity : 0.005 0.057 1838 Dihedral : 7.904 93.931 1698 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.57 % Allowed : 17.89 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.23), residues: 1346 helix: 2.49 (0.16), residues: 950 sheet: None (None), residues: 0 loop : -2.33 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 524 HIS 0.005 0.001 HIS B 195 PHE 0.013 0.001 PHE C 392 TYR 0.010 0.001 TYR A 505 ARG 0.013 0.000 ARG C 281 *********************** 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 204 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 186 time to evaluate : 1.155 Fit side-chains REVERT: A 368 MET cc_start: 0.6618 (ptm) cc_final: 0.6264 (ptp) REVERT: A 451 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.8348 (pt0) REVERT: B 168 GLU cc_start: 0.8395 (tp30) cc_final: 0.7899 (mm-30) REVERT: C 368 MET cc_start: 0.6613 (ptm) cc_final: 0.6256 (ptp) REVERT: C 451 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8330 (pt0) REVERT: D 168 GLU cc_start: 0.8393 (tp30) cc_final: 0.7896 (mm-30) outliers start: 18 outliers final: 12 residues processed: 192 average time/residue: 0.2163 time to fit residues: 59.7456 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 : 1.167 ------------------------------------------------------------------------------- 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 365 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 283 VAL Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 365 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 283 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 109 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 120 optimal weight: 0.9980 chunk 92 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 121 optimal weight: 4.9990 chunk 100 optimal weight: 0.2980 chunk 128 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3470 r_free = 0.3470 target = 0.137265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.106702 restraints weight = 14375.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.110217 restraints weight = 8328.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.112516 restraints weight = 5946.122| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10942 Z= 0.163 Angle : 0.604 9.117 14866 Z= 0.300 Chirality : 0.041 0.158 1772 Planarity : 0.004 0.055 1838 Dihedral : 7.704 91.661 1698 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.22 % Allowed : 18.15 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: 1.99 (0.23), residues: 1346 helix: 2.66 (0.16), residues: 944 sheet: None (None), residues: 0 loop : -2.19 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 524 HIS 0.005 0.001 HIS B 195 PHE 0.012 0.001 PHE C 392 TYR 0.009 0.001 TYR C 505 ARG 0.007 0.000 ARG A 281 *********************** 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: 14 poor density : 188 time to evaluate : 1.259 Fit side-chains REVERT: A 332 MET cc_start: 0.8612 (tpt) cc_final: 0.8267 (tpt) REVERT: A 368 MET cc_start: 0.6583 (ptm) cc_final: 0.6250 (ptp) REVERT: A 451 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.8289 (pt0) REVERT: B 168 GLU cc_start: 0.8402 (tp30) cc_final: 0.7800 (mm-30) REVERT: B 262 MET cc_start: 0.8410 (mmm) cc_final: 0.8099 (tmm) REVERT: B 281 ASP cc_start: 0.7586 (p0) cc_final: 0.7343 (t70) REVERT: C 332 MET cc_start: 0.8610 (tpt) cc_final: 0.8267 (tpt) REVERT: C 368 MET cc_start: 0.6580 (ptm) cc_final: 0.6246 (ptp) REVERT: C 451 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8290 (pt0) REVERT: D 168 GLU cc_start: 0.8398 (tp30) cc_final: 0.7794 (mm-30) REVERT: D 262 MET cc_start: 0.8409 (mmm) cc_final: 0.8101 (tmm) REVERT: D 281 ASP cc_start: 0.7587 (p0) cc_final: 0.7342 (t70) outliers start: 14 outliers final: 10 residues processed: 192 average time/residue: 0.2224 time to fit residues: 62.2851 Evaluate side-chains 186 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 174 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 365 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 283 VAL Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 365 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 283 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 91 optimal weight: 0.7980 chunk 37 optimal weight: 0.2980 chunk 70 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 26 optimal weight: 0.0670 chunk 16 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- 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 = 0.3436 r_free = 0.3436 target = 0.134902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.105343 restraints weight = 14296.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.108675 restraints weight = 8505.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.110892 restraints weight = 6139.649| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10942 Z= 0.161 Angle : 0.623 10.836 14866 Z= 0.307 Chirality : 0.040 0.155 1772 Planarity : 0.004 0.055 1838 Dihedral : 7.610 89.936 1698 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.87 % Allowed : 19.55 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.24), residues: 1346 helix: 2.71 (0.16), residues: 946 sheet: None (None), residues: 0 loop : -2.10 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 524 HIS 0.005 0.001 HIS B 195 PHE 0.012 0.001 PHE C 392 TYR 0.015 0.001 TYR C 448 ARG 0.008 0.000 ARG A 281 ********************** 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 : 1.098 Fit side-chains REVERT: A 332 MET cc_start: 0.8599 (tpt) cc_final: 0.8272 (tpt) REVERT: A 368 MET cc_start: 0.6560 (ptm) cc_final: 0.6213 (ptp) REVERT: A 451 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.8284 (pt0) REVERT: B 168 GLU cc_start: 0.8296 (tp30) cc_final: 0.7941 (mm-30) REVERT: B 262 MET cc_start: 0.8423 (mmm) cc_final: 0.8009 (tmm) REVERT: B 281 ASP cc_start: 0.7567 (p0) cc_final: 0.7212 (t70) REVERT: C 332 MET cc_start: 0.8596 (tpt) cc_final: 0.8272 (tpt) REVERT: C 368 MET cc_start: 0.6564 (ptm) cc_final: 0.6213 (ptp) REVERT: C 451 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.8286 (pt0) REVERT: D 168 GLU cc_start: 0.8288 (tp30) cc_final: 0.7934 (mm-30) REVERT: D 262 MET cc_start: 0.8424 (mmm) cc_final: 0.8006 (tmm) REVERT: D 281 ASP cc_start: 0.7569 (p0) cc_final: 0.7213 (t70) outliers start: 10 outliers final: 8 residues processed: 192 average time/residue: 0.2058 time to fit residues: 57.3222 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 : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain A residue 365 SER 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 365 SER 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 112 optimal weight: 0.9990 chunk 66 optimal weight: 0.4980 chunk 63 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 110 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 99 optimal weight: 0.0040 chunk 35 optimal weight: 0.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- 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 = 0.3466 r_free = 0.3466 target = 0.137125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.107652 restraints weight = 14278.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.111102 restraints weight = 8403.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.113349 restraints weight = 6011.984| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10942 Z= 0.158 Angle : 0.607 10.337 14866 Z= 0.300 Chirality : 0.040 0.155 1772 Planarity : 0.004 0.055 1838 Dihedral : 7.453 87.618 1698 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.87 % Allowed : 19.37 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.24), residues: 1346 helix: 2.67 (0.16), residues: 954 sheet: None (None), residues: 0 loop : -2.02 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 524 HIS 0.003 0.001 HIS B 195 PHE 0.012 0.001 PHE A 392 TYR 0.014 0.001 TYR A 534 ARG 0.008 0.000 ARG A 281 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3008.99 seconds wall clock time: 54 minutes 55.76 seconds (3295.76 seconds total)