Starting phenix.real_space_refine on Mon Jun 9 15:03:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hvt_35048/06_2025/8hvt_35048.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hvt_35048/06_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_35048/06_2025/8hvt_35048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hvt_35048/06_2025/8hvt_35048.map" model { file = "/net/cci-nas-00/data/ceres_data/8hvt_35048/06_2025/8hvt_35048.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hvt_35048/06_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-5710/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: 7.67, per 1000 atoms: 0.72 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: 3.11 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: 0.85 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: 3.87 Time building geometry restraints manager: 3.43 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.600 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 31.020 Find NCS groups from input model: 0.230 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:4.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.610 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd link_NAG-ASN : bond 0.00983 ( 8) link_NAG-ASN : angle 8.04532 ( 24) link_BETA1-4 : bond 0.00740 ( 4) link_BETA1-4 : angle 3.36246 ( 12) hydrogen bonds : bond 0.13830 ( 746) hydrogen bonds : angle 6.03744 ( 2220) SS BOND : bond 0.00434 ( 8) SS BOND : angle 1.82953 ( 16) covalent geometry : bond 0.00903 (10942) covalent geometry : angle 1.10832 (14866) *********************** 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 : 1.179 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: 0.2822 time to fit residues: 88.5721 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 : 1.583 ------------------------------------------------------------------------------- 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 = 0.128145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.097408 restraints weight = 14238.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.100518 restraints weight = 8734.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.102456 restraints weight = 6476.400| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 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 10962 Z= 0.136 Angle : 0.716 13.243 14918 Z= 0.353 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00646 ( 8) link_NAG-ASN : angle 6.55091 ( 24) link_BETA1-4 : bond 0.00683 ( 4) link_BETA1-4 : angle 2.62400 ( 12) hydrogen bonds : bond 0.04836 ( 746) hydrogen bonds : angle 3.85794 ( 2220) SS BOND : bond 0.00424 ( 8) SS BOND : angle 1.64669 ( 16) covalent geometry : bond 0.00278 (10942) covalent geometry : angle 0.66119 (14866) *********************** 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 : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 8 residues processed: 210 average time/residue: 0.2579 time to fit residues: 82.2657 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 : 1.120 ------------------------------------------------------------------------------- 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: 0.6980 chunk 116 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 30 optimal weight: 0.1980 chunk 98 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3439 r_free = 0.3439 target = 0.134690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.104729 restraints weight = 14363.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.108163 restraints weight = 8324.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.110459 restraints weight = 5964.148| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1397 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= 0.139 Angle : 0.681 12.709 14918 Z= 0.332 Chirality : 0.042 0.162 1772 Planarity : 0.005 0.061 1838 Dihedral : 9.810 99.970 1698 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.57 % Allowed : 12.39 % 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: 0.74 (0.23), residues: 1346 helix: 1.67 (0.16), residues: 950 sheet: None (None), residues: 0 loop : -2.60 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 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 0.006 0.000 ARG C 281 Details of bonding type rmsd link_NAG-ASN : bond 0.00596 ( 8) link_NAG-ASN : angle 6.03659 ( 24) link_BETA1-4 : bond 0.00637 ( 4) link_BETA1-4 : angle 2.49878 ( 12) hydrogen bonds : bond 0.04310 ( 746) hydrogen bonds : angle 3.61122 ( 2220) SS BOND : bond 0.00579 ( 8) SS BOND : angle 3.39813 ( 16) covalent geometry : bond 0.00308 (10942) covalent geometry : angle 0.62344 (14866) *********************** 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: 18 poor density : 204 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 195 HIS cc_start: 0.8367 (t70) cc_final: 0.8091 (t70) REVERT: D 195 HIS cc_start: 0.8365 (t70) cc_final: 0.8090 (t70) outliers start: 18 outliers final: 12 residues processed: 208 average time/residue: 0.2349 time to fit residues: 71.2029 Evaluate side-chains 200 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 188 time to evaluate : 1.072 ------------------------------------------------------------------------------- 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: 2.9990 chunk 5 optimal weight: 0.5980 chunk 71 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3428 r_free = 0.3428 target = 0.133588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.103289 restraints weight = 14235.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.106697 restraints weight = 8297.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.109001 restraints weight = 5972.327| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1589 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= 0.126 Angle : 0.669 12.479 14918 Z= 0.323 Chirality : 0.042 0.191 1772 Planarity : 0.004 0.058 1838 Dihedral : 8.924 98.265 1698 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.40 % Allowed : 14.66 % Favored : 83.94 % 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: 1.20 (0.23), residues: 1346 helix: 2.08 (0.16), residues: 938 sheet: None (None), residues: 0 loop : -2.46 (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 0.008 0.000 ARG A 281 Details of bonding type rmsd link_NAG-ASN : bond 0.00588 ( 8) link_NAG-ASN : angle 5.84185 ( 24) link_BETA1-4 : bond 0.00589 ( 4) link_BETA1-4 : angle 2.28345 ( 12) hydrogen bonds : bond 0.03996 ( 746) hydrogen bonds : angle 3.49664 ( 2220) SS BOND : bond 0.00619 ( 8) SS BOND : angle 3.29158 ( 16) covalent geometry : bond 0.00270 (10942) covalent geometry : angle 0.61478 (14866) *********************** 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 214 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 198 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 195 HIS cc_start: 0.8280 (t70) cc_final: 0.8047 (t70) REVERT: C 437 ASP cc_start: 0.8025 (t0) cc_final: 0.7825 (t0) REVERT: D 195 HIS cc_start: 0.8277 (t70) cc_final: 0.8045 (t70) outliers start: 16 outliers final: 8 residues processed: 204 average time/residue: 0.2259 time to fit residues: 68.0739 Evaluate side-chains 192 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 184 time to evaluate : 1.216 ------------------------------------------------------------------------------- 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 359 ASN Chi-restraints excluded: chain B residue 127 ASP 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: 3.9990 chunk 124 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.3389 r_free = 0.3389 target = 0.130332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.099892 restraints weight = 14345.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.103226 restraints weight = 8415.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.105470 restraints weight = 6075.187| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10962 Z= 0.172 Angle : 0.682 12.396 14918 Z= 0.332 Chirality : 0.043 0.176 1772 Planarity : 0.005 0.060 1838 Dihedral : 8.564 97.433 1698 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.09 % Allowed : 14.75 % Favored : 83.16 % 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: 1.24 (0.23), residues: 1346 helix: 2.08 (0.16), residues: 950 sheet: None (None), residues: 0 loop : -2.49 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 524 HIS 0.004 0.001 HIS B 195 PHE 0.027 0.001 PHE D 200 TYR 0.011 0.001 TYR A 505 ARG 0.010 0.000 ARG C 281 Details of bonding type rmsd link_NAG-ASN : bond 0.00581 ( 8) link_NAG-ASN : angle 5.65365 ( 24) link_BETA1-4 : bond 0.00473 ( 4) link_BETA1-4 : angle 2.15893 ( 12) hydrogen bonds : bond 0.04073 ( 746) hydrogen bonds : angle 3.49334 ( 2220) SS BOND : bond 0.00725 ( 8) SS BOND : angle 3.27649 ( 16) covalent geometry : bond 0.00400 (10942) covalent geometry : angle 0.63219 (14866) *********************** 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 210 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 186 time to evaluate : 1.392 Fit side-chains REVERT: A 368 MET cc_start: 0.6682 (ptm) cc_final: 0.6377 (ptp) REVERT: B 174 CYS cc_start: 0.6043 (OUTLIER) cc_final: 0.5627 (m) REVERT: C 368 MET cc_start: 0.6676 (ptm) cc_final: 0.6369 (ptp) REVERT: C 437 ASP cc_start: 0.8074 (t0) cc_final: 0.7847 (t0) REVERT: D 174 CYS cc_start: 0.6030 (OUTLIER) cc_final: 0.5620 (m) outliers start: 24 outliers final: 14 residues processed: 198 average time/residue: 0.2236 time to fit residues: 64.8661 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 : 1.172 ------------------------------------------------------------------------------- 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: 0.9980 chunk 99 optimal weight: 8.9990 chunk 114 optimal weight: 4.9990 chunk 35 optimal weight: 0.0470 chunk 108 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 overall best weight: 2.0084 ------------------------------------------------------------------------------- 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 = 0.3335 r_free = 0.3335 target = 0.126372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.095398 restraints weight = 14514.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.098472 restraints weight = 9004.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.100382 restraints weight = 6713.743| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10962 Z= 0.175 Angle : 0.689 12.301 14918 Z= 0.334 Chirality : 0.043 0.157 1772 Planarity : 0.005 0.060 1838 Dihedral : 8.364 96.562 1698 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.18 % Allowed : 15.53 % Favored : 82.29 % 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: 1.36 (0.23), residues: 1346 helix: 2.15 (0.16), residues: 956 sheet: None (None), residues: 0 loop : -2.48 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 524 HIS 0.006 0.001 HIS B 195 PHE 0.020 0.001 PHE D 200 TYR 0.011 0.001 TYR C 505 ARG 0.011 0.000 ARG A 281 Details of bonding type rmsd link_NAG-ASN : bond 0.00585 ( 8) link_NAG-ASN : angle 5.57828 ( 24) link_BETA1-4 : bond 0.00498 ( 4) link_BETA1-4 : angle 2.04811 ( 12) hydrogen bonds : bond 0.04059 ( 746) hydrogen bonds : angle 3.48501 ( 2220) SS BOND : bond 0.00809 ( 8) SS BOND : angle 3.28588 ( 16) covalent geometry : bond 0.00411 (10942) covalent geometry : angle 0.64071 (14866) *********************** 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 208 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 1.046 Fit side-chains REVERT: A 198 GLU cc_start: 0.8162 (tp30) cc_final: 0.7834 (tp30) REVERT: A 368 MET cc_start: 0.6636 (ptm) cc_final: 0.6318 (ptp) REVERT: A 451 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8347 (pt0) REVERT: B 174 CYS cc_start: 0.6270 (OUTLIER) cc_final: 0.5904 (m) REVERT: B 197 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8730 (mm) REVERT: C 198 GLU cc_start: 0.8172 (tp30) cc_final: 0.7841 (tp30) REVERT: C 368 MET cc_start: 0.6627 (ptm) cc_final: 0.6303 (ptp) REVERT: C 451 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8342 (pt0) REVERT: D 174 CYS cc_start: 0.6258 (OUTLIER) cc_final: 0.5890 (m) REVERT: D 197 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8737 (mm) outliers start: 25 outliers final: 16 residues processed: 194 average time/residue: 0.2175 time to fit residues: 60.6313 Evaluate side-chains 199 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 177 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL 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 197 LEU Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain C residue 192 VAL 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 197 LEU 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: 0.6980 chunk 11 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 23 optimal weight: 0.3980 chunk 97 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3442 r_free = 0.3442 target = 0.134868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.104612 restraints weight = 14414.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.108078 restraints weight = 8470.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.110341 restraints weight = 6071.818| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10962 Z= 0.122 Angle : 0.651 12.100 14918 Z= 0.316 Chirality : 0.041 0.150 1772 Planarity : 0.005 0.058 1838 Dihedral : 8.100 95.250 1698 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.92 % Allowed : 17.28 % Favored : 80.80 % 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: 1.56 (0.23), residues: 1346 helix: 2.31 (0.16), residues: 956 sheet: None (None), residues: 0 loop : -2.45 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 524 HIS 0.006 0.001 HIS B 195 PHE 0.013 0.001 PHE A 392 TYR 0.012 0.001 TYR C 505 ARG 0.012 0.001 ARG A 281 Details of bonding type rmsd link_NAG-ASN : bond 0.00597 ( 8) link_NAG-ASN : angle 5.42300 ( 24) link_BETA1-4 : bond 0.00530 ( 4) link_BETA1-4 : angle 1.83798 ( 12) hydrogen bonds : bond 0.03797 ( 746) hydrogen bonds : angle 3.40138 ( 2220) SS BOND : bond 0.00578 ( 8) SS BOND : angle 3.13456 ( 16) covalent geometry : bond 0.00260 (10942) covalent geometry : angle 0.60417 (14866) *********************** 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 214 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 192 time to evaluate : 1.224 Fit side-chains REVERT: A 368 MET cc_start: 0.6626 (ptm) cc_final: 0.6330 (ptp) REVERT: A 451 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8349 (pt0) REVERT: A 585 LEU cc_start: 0.8443 (mt) cc_final: 0.8183 (mt) REVERT: B 168 GLU cc_start: 0.8402 (tp30) cc_final: 0.7896 (mm-30) REVERT: B 174 CYS cc_start: 0.6187 (OUTLIER) cc_final: 0.5863 (m) REVERT: B 197 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8755 (mm) REVERT: B 262 MET cc_start: 0.8495 (mmm) cc_final: 0.8051 (tmm) REVERT: B 281 ASP cc_start: 0.7736 (p0) cc_final: 0.7290 (t70) REVERT: C 368 MET cc_start: 0.6621 (ptm) cc_final: 0.6322 (ptp) REVERT: C 451 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8327 (pt0) REVERT: C 585 LEU cc_start: 0.8447 (mt) cc_final: 0.8198 (mt) REVERT: D 168 GLU cc_start: 0.8399 (tp30) cc_final: 0.7889 (mm-30) REVERT: D 174 CYS cc_start: 0.6177 (OUTLIER) cc_final: 0.5860 (m) REVERT: D 197 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8763 (mm) REVERT: D 262 MET cc_start: 0.8495 (mmm) cc_final: 0.8054 (tmm) REVERT: D 281 ASP cc_start: 0.7736 (p0) cc_final: 0.7295 (t70) outliers start: 22 outliers final: 16 residues processed: 200 average time/residue: 0.2170 time to fit residues: 62.7330 Evaluate side-chains 204 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 182 time to evaluate : 1.181 ------------------------------------------------------------------------------- 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 197 LEU 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 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 87 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 103 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.3402 r_free = 0.3402 target = 0.131596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.100933 restraints weight = 14304.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.104230 restraints weight = 8529.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.106269 restraints weight = 6206.144| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10962 Z= 0.173 Angle : 0.682 12.077 14918 Z= 0.333 Chirality : 0.043 0.156 1772 Planarity : 0.005 0.058 1838 Dihedral : 8.056 94.789 1698 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.01 % Allowed : 17.28 % Favored : 80.72 % 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: 1.58 (0.23), residues: 1346 helix: 2.35 (0.16), residues: 950 sheet: None (None), residues: 0 loop : -2.40 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 524 HIS 0.005 0.001 HIS B 195 PHE 0.015 0.001 PHE A 392 TYR 0.011 0.001 TYR A 505 ARG 0.013 0.001 ARG C 281 Details of bonding type rmsd link_NAG-ASN : bond 0.00594 ( 8) link_NAG-ASN : angle 5.40209 ( 24) link_BETA1-4 : bond 0.00477 ( 4) link_BETA1-4 : angle 1.86403 ( 12) hydrogen bonds : bond 0.03941 ( 746) hydrogen bonds : angle 3.43248 ( 2220) SS BOND : bond 0.00714 ( 8) SS BOND : angle 3.32191 ( 16) covalent geometry : bond 0.00408 (10942) covalent geometry : angle 0.63631 (14866) *********************** 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: 23 poor density : 180 time to evaluate : 1.063 Fit side-chains REVERT: A 368 MET cc_start: 0.6662 (ptm) cc_final: 0.6358 (ptp) REVERT: A 451 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8361 (pt0) REVERT: B 168 GLU cc_start: 0.8407 (tp30) cc_final: 0.7930 (mm-30) REVERT: B 174 CYS cc_start: 0.6050 (OUTLIER) cc_final: 0.5810 (m) REVERT: B 197 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8762 (mm) REVERT: C 368 MET cc_start: 0.6653 (ptm) cc_final: 0.6349 (ptp) REVERT: C 451 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8358 (pt0) REVERT: D 168 GLU cc_start: 0.8407 (tp30) cc_final: 0.7924 (mm-30) REVERT: D 174 CYS cc_start: 0.6039 (OUTLIER) cc_final: 0.5801 (m) REVERT: D 197 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8764 (mm) outliers start: 23 outliers final: 16 residues processed: 191 average time/residue: 0.2128 time to fit residues: 58.3276 Evaluate side-chains 200 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 178 time to evaluate : 1.108 ------------------------------------------------------------------------------- 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 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 197 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 285 VAL 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 197 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 285 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 109 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 121 optimal weight: 8.9990 chunk 100 optimal weight: 0.6980 chunk 128 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.3428 r_free = 0.3428 target = 0.133735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.103334 restraints weight = 14422.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.106667 restraints weight = 8485.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.108814 restraints weight = 6133.158| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2004 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= 0.141 Angle : 0.665 11.952 14918 Z= 0.323 Chirality : 0.042 0.152 1772 Planarity : 0.005 0.059 1838 Dihedral : 7.956 93.920 1698 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 1.92 % Allowed : 17.80 % Favored : 80.28 % 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: 1.66 (0.23), residues: 1346 helix: 2.37 (0.16), residues: 956 sheet: None (None), residues: 0 loop : -2.37 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 524 HIS 0.005 0.001 HIS B 195 PHE 0.014 0.001 PHE A 392 TYR 0.014 0.001 TYR A 448 ARG 0.013 0.001 ARG A 281 Details of bonding type rmsd link_NAG-ASN : bond 0.00598 ( 8) link_NAG-ASN : angle 5.34529 ( 24) link_BETA1-4 : bond 0.00518 ( 4) link_BETA1-4 : angle 1.79947 ( 12) hydrogen bonds : bond 0.03830 ( 746) hydrogen bonds : angle 3.38653 ( 2220) SS BOND : bond 0.00729 ( 8) SS BOND : angle 3.21828 ( 16) covalent geometry : bond 0.00323 (10942) covalent geometry : angle 0.61910 (14866) *********************** 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 200 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 178 time to evaluate : 1.046 Fit side-chains REVERT: A 368 MET cc_start: 0.6675 (ptm) cc_final: 0.6348 (ptp) REVERT: A 451 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8344 (pt0) REVERT: B 168 GLU cc_start: 0.8400 (tp30) cc_final: 0.7899 (mm-30) REVERT: B 174 CYS cc_start: 0.6007 (OUTLIER) cc_final: 0.5775 (m) REVERT: B 197 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8768 (mm) REVERT: B 262 MET cc_start: 0.8510 (mmm) cc_final: 0.8130 (tmm) REVERT: B 281 ASP cc_start: 0.7741 (p0) cc_final: 0.7332 (t70) REVERT: C 368 MET cc_start: 0.6668 (ptm) cc_final: 0.6338 (ptp) REVERT: C 451 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.8338 (pt0) REVERT: D 168 GLU cc_start: 0.8399 (tp30) cc_final: 0.7893 (mm-30) REVERT: D 174 CYS cc_start: 0.5986 (OUTLIER) cc_final: 0.5756 (m) REVERT: D 197 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8768 (mm) REVERT: D 262 MET cc_start: 0.8510 (mmm) cc_final: 0.8133 (tmm) REVERT: D 281 ASP cc_start: 0.7744 (p0) cc_final: 0.7337 (t70) outliers start: 22 outliers final: 14 residues processed: 186 average time/residue: 0.2134 time to fit residues: 57.9997 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 : 1.093 ------------------------------------------------------------------------------- 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 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 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 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 197 LEU 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: 1.9990 chunk 37 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 = 0.3362 r_free = 0.3362 target = 0.128368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.097106 restraints weight = 14378.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.100323 restraints weight = 8579.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.102476 restraints weight = 6274.717| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10962 Z= 0.153 Angle : 0.666 11.867 14918 Z= 0.324 Chirality : 0.042 0.153 1772 Planarity : 0.005 0.061 1838 Dihedral : 7.920 93.438 1698 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.92 % Allowed : 18.32 % 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: 1.70 (0.23), residues: 1346 helix: 2.41 (0.16), residues: 956 sheet: None (None), residues: 0 loop : -2.38 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 524 HIS 0.005 0.001 HIS B 195 PHE 0.016 0.001 PHE A 360 TYR 0.013 0.001 TYR A 448 ARG 0.015 0.001 ARG A 281 Details of bonding type rmsd link_NAG-ASN : bond 0.00593 ( 8) link_NAG-ASN : angle 5.31081 ( 24) link_BETA1-4 : bond 0.00487 ( 4) link_BETA1-4 : angle 1.81213 ( 12) hydrogen bonds : bond 0.03839 ( 746) hydrogen bonds : angle 3.39293 ( 2220) SS BOND : bond 0.00685 ( 8) SS BOND : angle 3.27221 ( 16) covalent geometry : bond 0.00358 (10942) covalent geometry : angle 0.62126 (14866) ********************** 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 202 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 180 time to evaluate : 1.413 Fit side-chains REVERT: A 368 MET cc_start: 0.6670 (ptm) cc_final: 0.6319 (ptp) REVERT: A 451 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8323 (pt0) REVERT: B 104 ARG cc_start: 0.8616 (tpp80) cc_final: 0.8205 (mmt90) REVERT: B 168 GLU cc_start: 0.8403 (tp30) cc_final: 0.7908 (mm-30) REVERT: B 174 CYS cc_start: 0.5935 (OUTLIER) cc_final: 0.5719 (m) REVERT: B 197 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8770 (mm) REVERT: B 262 MET cc_start: 0.8521 (mmm) cc_final: 0.8124 (tmm) REVERT: B 281 ASP cc_start: 0.7740 (p0) cc_final: 0.7302 (t70) REVERT: C 368 MET cc_start: 0.6663 (ptm) cc_final: 0.6307 (ptp) REVERT: C 451 GLN cc_start: 0.8758 (OUTLIER) cc_final: 0.8319 (pt0) REVERT: D 104 ARG cc_start: 0.8618 (tpp80) cc_final: 0.8208 (mmt90) REVERT: D 168 GLU cc_start: 0.8404 (tp30) cc_final: 0.7901 (mm-30) REVERT: D 174 CYS cc_start: 0.5927 (OUTLIER) cc_final: 0.5709 (m) REVERT: D 197 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8770 (mm) REVERT: D 262 MET cc_start: 0.8521 (mmm) cc_final: 0.8126 (tmm) REVERT: D 281 ASP cc_start: 0.7722 (p0) cc_final: 0.7291 (t70) outliers start: 22 outliers final: 14 residues processed: 190 average time/residue: 0.2161 time to fit residues: 60.7155 Evaluate side-chains 200 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 1.056 ------------------------------------------------------------------------------- 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 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 197 LEU Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 298 SER 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 197 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 285 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: 0.0270 chunk 63 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 chunk 110 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 95 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- 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 = 0.3405 r_free = 0.3405 target = 0.132453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.102466 restraints weight = 14288.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.105791 restraints weight = 8553.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.108019 restraints weight = 6196.508| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2241 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= 0.117 Angle : 0.637 11.643 14918 Z= 0.308 Chirality : 0.041 0.153 1772 Planarity : 0.004 0.057 1838 Dihedral : 7.646 90.645 1698 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.22 % Allowed : 18.85 % Favored : 79.93 % 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: 1.94 (0.23), residues: 1346 helix: 2.55 (0.16), residues: 964 sheet: None (None), residues: 0 loop : -2.25 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 524 HIS 0.005 0.001 HIS B 195 PHE 0.012 0.001 PHE A 392 TYR 0.013 0.001 TYR C 448 ARG 0.015 0.001 ARG A 281 Details of bonding type rmsd link_NAG-ASN : bond 0.00615 ( 8) link_NAG-ASN : angle 5.14574 ( 24) link_BETA1-4 : bond 0.00537 ( 4) link_BETA1-4 : angle 1.59936 ( 12) hydrogen bonds : bond 0.03530 ( 746) hydrogen bonds : angle 3.29438 ( 2220) SS BOND : bond 0.00437 ( 8) SS BOND : angle 3.03985 ( 16) covalent geometry : bond 0.00251 (10942) covalent geometry : angle 0.59327 (14866) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3597.78 seconds wall clock time: 65 minutes 52.95 seconds (3952.95 seconds total)