Starting phenix.real_space_refine on Sun Apr 27 21:24:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bcl_44429/04_2025/9bcl_44429.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bcl_44429/04_2025/9bcl_44429.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bcl_44429/04_2025/9bcl_44429.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bcl_44429/04_2025/9bcl_44429.map" model { file = "/net/cci-nas-00/data/ceres_data/9bcl_44429/04_2025/9bcl_44429.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bcl_44429/04_2025/9bcl_44429.cif" } resolution = 2.9 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= 0.004 sd= 0.254 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: 5 Type Number sf(0) Gaussians S 26 5.16 5 Cl 2 4.86 5 C 4310 2.51 5 N 1145 2.21 5 O 1236 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 6719 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3254 Classifications: {'peptide': 425} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 27, 'TRANS': 397} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 3, 'GLU:plan': 6, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 61 Chain: "B" Number of atoms: 3257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3257 Classifications: {'peptide': 425} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 27, 'TRANS': 397} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 3, 'GLU:plan': 6, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 56 Chain: "C" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CL': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CL': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.21, per 1000 atoms: 0.63 Number of scatterers: 6719 At special positions: 0 Unit cell: (106.095, 77.9472, 84.4428, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 26 16.00 O 1236 8.00 N 1145 7.00 C 4310 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 86 " distance=2.03 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 213 " distance=2.04 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 86 " distance=2.04 Simple disulfide: pdb=" SG CYS B 164 " - pdb=" SG CYS B 213 " distance=2.04 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 ALPHA1-3 " NAG C 2 " - " MAN C 3 " " NAG D 2 " - " MAN D 3 " " NAG E 2 " - " MAN E 3 " " NAG F 2 " - " MAN F 3 " ALPHA1-6 " MAN C 3 " - " MAN C 4 " " MAN E 3 " - " MAN E 4 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1102 " - " ASN A 354 " " NAG B1102 " - " ASN B 354 " " NAG C 1 " - " ASN A 13 " " NAG D 1 " - " ASN A 395 " " NAG E 1 " - " ASN B 13 " " NAG F 1 " - " ASN B 395 " Time building additional restraints: 2.03 Conformation dependent library (CDL) restraints added in 914.5 milliseconds 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1548 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 6 sheets defined 42.8% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 19 through 36 Proline residue: A 25 - end of helix Processing helix chain 'A' and resid 64 through 77 Processing helix chain 'A' and resid 86 through 101 removed outlier: 3.889A pdb=" N ALA A 91 " --> pdb=" O VAL A 87 " (cutoff:3.500A) Proline residue: A 92 - end of helix Processing helix chain 'A' and resid 112 through 116 removed outlier: 3.623A pdb=" N VAL A 116 " --> pdb=" O GLY A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 145 removed outlier: 4.040A pdb=" N GLY A 134 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE A 136 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG A 143 " --> pdb=" O ALA A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 179 Processing helix chain 'A' and resid 192 through 207 removed outlier: 3.693A pdb=" N TYR A 196 " --> pdb=" O ASP A 192 " (cutoff:3.500A) Proline residue: A 204 - end of helix Processing helix chain 'A' and resid 215 through 230 removed outlier: 3.565A pdb=" N LEU A 225 " --> pdb=" O THR A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 249 removed outlier: 3.912A pdb=" N GLN A 249 " --> pdb=" O GLN A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 274 removed outlier: 3.793A pdb=" N GLN A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 306 removed outlier: 3.564A pdb=" N LEU A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N HIS A 299 " --> pdb=" O LYS A 295 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A 300 " --> pdb=" O GLN A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 338 Processing helix chain 'A' and resid 344 through 350 Processing helix chain 'B' and resid 19 through 35 Proline residue: B 25 - end of helix Processing helix chain 'B' and resid 64 through 77 Processing helix chain 'B' and resid 86 through 101 removed outlier: 3.868A pdb=" N ALA B 91 " --> pdb=" O VAL B 87 " (cutoff:3.500A) Proline residue: B 92 - end of helix Processing helix chain 'B' and resid 112 through 116 removed outlier: 3.647A pdb=" N VAL B 116 " --> pdb=" O GLY B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 145 removed outlier: 3.765A pdb=" N ASP B 135 " --> pdb=" O ALA B 131 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE B 136 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL B 137 " --> pdb=" O LEU B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 179 removed outlier: 3.532A pdb=" N ASP B 177 " --> pdb=" O MET B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 203 Processing helix chain 'B' and resid 204 through 206 No H-bonds generated for 'chain 'B' and resid 204 through 206' Processing helix chain 'B' and resid 215 through 230 Processing helix chain 'B' and resid 245 through 249 removed outlier: 3.814A pdb=" N GLN B 249 " --> pdb=" O GLN B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 274 removed outlier: 4.086A pdb=" N GLN B 272 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA B 273 " --> pdb=" O SER B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 304 removed outlier: 3.671A pdb=" N LEU B 291 " --> pdb=" O ASN B 287 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N HIS B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU B 300 " --> pdb=" O GLN B 296 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR B 302 " --> pdb=" O LYS B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 338 removed outlier: 3.542A pdb=" N HIS B 322 " --> pdb=" O PRO B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 351 Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 51 removed outlier: 9.101A pdb=" N VAL A 80 " --> pdb=" O ASN A 2 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR A 4 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N LEU A 82 " --> pdb=" O THR A 4 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA A 6 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N PHE A 81 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU A 104 " --> pdb=" O THR A 124 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 182 through 189 removed outlier: 5.240A pdb=" N VAL A 209 " --> pdb=" O GLN A 149 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE A 210 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N LEU A 241 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N ILE A 212 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N PHE A 238 " --> pdb=" O LYS A 278 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ILE A 280 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N HIS A 240 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N TYR A 282 " --> pdb=" O HIS A 240 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N ALA A 277 " --> pdb=" O MET A 381 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N MET A 381 " --> pdb=" O ALA A 277 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ASP A 380 " --> pdb=" O VAL A 390 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N VAL A 390 " --> pdb=" O ASP A 380 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLU A 400 " --> pdb=" O ASN A 395 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 355 through 359 removed outlier: 3.726A pdb=" N GLY A 362 " --> pdb=" O GLY A 359 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 45 through 51 removed outlier: 6.273A pdb=" N LEU B 3 " --> pdb=" O ARG B 47 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N VAL B 49 " --> pdb=" O LEU B 3 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N VAL B 5 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N GLY B 51 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N VAL B 7 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N LEU B 82 " --> pdb=" O THR B 4 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ALA B 6 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N PHE B 81 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LEU B 104 " --> pdb=" O THR B 124 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 182 through 189 removed outlier: 6.933A pdb=" N ALA B 150 " --> pdb=" O ASP B 184 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N LEU B 186 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N MET B 152 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N PHE B 188 " --> pdb=" O MET B 152 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N TYR B 154 " --> pdb=" O PHE B 188 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N VAL B 209 " --> pdb=" O GLN B 149 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N PHE B 238 " --> pdb=" O LYS B 278 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ILE B 280 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N HIS B 240 " --> pdb=" O ILE B 280 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N TYR B 282 " --> pdb=" O HIS B 240 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N ALA B 277 " --> pdb=" O MET B 381 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N MET B 381 " --> pdb=" O ALA B 277 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N PHE B 376 " --> pdb=" O ASN B 393 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ASN B 393 " --> pdb=" O PHE B 376 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU B 378 " --> pdb=" O VAL B 391 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 355 through 359 removed outlier: 3.663A pdb=" N GLY B 362 " --> pdb=" O GLY B 359 " (cutoff:3.500A) 277 hydrogen bonds defined for protein. 807 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.90 Time building geometry restraints manager: 2.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 1054 1.29 - 1.42: 1897 1.42 - 1.56: 3909 1.56 - 1.69: 3 1.69 - 1.83: 40 Bond restraints: 6903 Sorted by residual: bond pdb=" C ASP B 375 " pdb=" O ASP B 375 " ideal model delta sigma weight residual 1.235 1.155 0.080 1.18e-02 7.18e+03 4.56e+01 bond pdb=" C HIS A 185 " pdb=" O HIS A 185 " ideal model delta sigma weight residual 1.236 1.181 0.055 1.14e-02 7.69e+03 2.32e+01 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.481 -0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C GLU B 373 " pdb=" O GLU B 373 " ideal model delta sigma weight residual 1.236 1.197 0.039 1.17e-02 7.31e+03 1.10e+01 bond pdb=" C GLU A 373 " pdb=" O GLU A 373 " ideal model delta sigma weight residual 1.236 1.199 0.037 1.21e-02 6.83e+03 9.20e+00 ... (remaining 6898 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 9208 2.19 - 4.38: 174 4.38 - 6.57: 34 6.57 - 8.76: 2 8.76 - 10.94: 3 Bond angle restraints: 9421 Sorted by residual: angle pdb=" CA HIS A 185 " pdb=" CB HIS A 185 " pdb=" CG HIS A 185 " ideal model delta sigma weight residual 113.80 120.56 -6.76 1.00e+00 1.00e+00 4.58e+01 angle pdb=" CA THR A 14 " pdb=" CB THR A 14 " pdb=" CG2 THR A 14 " ideal model delta sigma weight residual 110.50 119.84 -9.34 1.70e+00 3.46e-01 3.02e+01 angle pdb=" OG1 THR A 14 " pdb=" CB THR A 14 " pdb=" CG2 THR A 14 " ideal model delta sigma weight residual 109.30 120.24 -10.94 2.00e+00 2.50e-01 2.99e+01 angle pdb=" CA HIS A 185 " pdb=" C HIS A 185 " pdb=" O HIS A 185 " ideal model delta sigma weight residual 120.40 115.38 5.02 1.05e+00 9.07e-01 2.29e+01 angle pdb=" CA GLN B 252 " pdb=" CB GLN B 252 " pdb=" CG GLN B 252 " ideal model delta sigma weight residual 114.10 123.42 -9.32 2.00e+00 2.50e-01 2.17e+01 ... (remaining 9416 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.51: 4004 23.51 - 47.02: 181 47.02 - 70.52: 25 70.52 - 94.03: 18 94.03 - 117.54: 3 Dihedral angle restraints: 4231 sinusoidal: 1803 harmonic: 2428 Sorted by residual: dihedral pdb=" CA LEU A 82 " pdb=" C LEU A 82 " pdb=" N GLY A 83 " pdb=" CA GLY A 83 " ideal model delta harmonic sigma weight residual -180.00 -154.87 -25.13 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" N GLU B 373 " pdb=" C GLU B 373 " pdb=" CA GLU B 373 " pdb=" CB GLU B 373 " ideal model delta harmonic sigma weight residual 122.80 111.15 11.65 0 2.50e+00 1.60e-01 2.17e+01 dihedral pdb=" CB CYS B 60 " pdb=" SG CYS B 60 " pdb=" SG CYS B 86 " pdb=" CB CYS B 86 " ideal model delta sinusoidal sigma weight residual 93.00 129.58 -36.58 1 1.00e+01 1.00e-02 1.89e+01 ... (remaining 4228 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.300: 1074 0.300 - 0.599: 2 0.599 - 0.899: 0 0.899 - 1.198: 0 1.198 - 1.498: 1 Chirality restraints: 1077 Sorted by residual: chirality pdb=" CB THR A 14 " pdb=" CA THR A 14 " pdb=" OG1 THR A 14 " pdb=" CG2 THR A 14 " both_signs ideal model delta sigma weight residual False 2.55 1.05 1.50 2.00e-01 2.50e+01 5.61e+01 chirality pdb=" CA GLU B 373 " pdb=" N GLU B 373 " pdb=" C GLU B 373 " pdb=" CB GLU B 373 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" C4 NAG F 1 " pdb=" C3 NAG F 1 " pdb=" C5 NAG F 1 " pdb=" O4 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.17 -0.36 2.00e-01 2.50e+01 3.20e+00 ... (remaining 1074 not shown) Planarity restraints: 1205 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 420 " 0.047 5.00e-02 4.00e+02 7.23e-02 8.37e+00 pdb=" N PRO A 421 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 421 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 421 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 372 " 0.010 2.00e-02 2.50e+03 1.91e-02 3.66e+00 pdb=" C ARG B 372 " -0.033 2.00e-02 2.50e+03 pdb=" O ARG B 372 " 0.012 2.00e-02 2.50e+03 pdb=" N GLU B 373 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 317 " 0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO B 318 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 318 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 318 " 0.026 5.00e-02 4.00e+02 ... (remaining 1202 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 143 2.70 - 3.25: 6459 3.25 - 3.80: 10202 3.80 - 4.35: 14131 4.35 - 4.90: 23658 Nonbonded interactions: 54593 Sorted by model distance: nonbonded pdb=" O3 NAG E 2 " pdb=" O7 NAG E 2 " model vdw 2.149 3.040 nonbonded pdb=" O ARG B 257 " pdb=" N PHE B 388 " model vdw 2.295 3.120 nonbonded pdb=" O4 NAG C 1 " pdb=" O7 NAG C 2 " model vdw 2.363 3.040 nonbonded pdb=" O ARG B 176 " pdb=" O LEU B 179 " model vdw 2.368 3.040 nonbonded pdb=" O ASN A 13 " pdb=" OG SER A 19 " model vdw 2.409 3.040 ... (remaining 54588 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 419 or (resid 420 and (name N or name CA or name \ C or name O or name CB )) or resid 421 through 425 or resid 1101 through 1102)) \ selection = (chain 'B' and (resid 1 through 204 or (resid 205 and (name N or name CA or name \ C or name O or name CB )) or resid 206 through 425 or resid 1101 through 1102)) \ } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.410 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: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 19.360 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 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 : 0.005 0.080 6923 Z= 0.265 Angle : 0.845 17.537 9477 Z= 0.424 Chirality : 0.067 1.498 1077 Planarity : 0.005 0.072 1199 Dihedral : 14.783 117.541 2671 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.31 % Allowed : 0.15 % Favored : 99.54 % Cbeta Deviations : 0.13 % 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: -1.41 (0.28), residues: 846 helix: 0.12 (0.30), residues: 310 sheet: -1.49 (0.36), residues: 190 loop : -1.47 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 379 HIS 0.017 0.002 HIS A 185 PHE 0.021 0.001 PHE B 172 TYR 0.026 0.001 TYR B 236 ARG 0.005 0.000 ARG B 208 Details of bonding type rmsd link_NAG-ASN : bond 0.00351 ( 6) link_NAG-ASN : angle 2.87377 ( 18) link_ALPHA1-6 : bond 0.00302 ( 2) link_ALPHA1-6 : angle 1.79351 ( 6) link_BETA1-4 : bond 0.02395 ( 4) link_BETA1-4 : angle 9.20520 ( 12) link_ALPHA1-3 : bond 0.00915 ( 4) link_ALPHA1-3 : angle 3.94213 ( 12) hydrogen bonds : bond 0.17838 ( 277) hydrogen bonds : angle 7.13113 ( 807) SS BOND : bond 0.00488 ( 4) SS BOND : angle 1.37837 ( 8) covalent geometry : bond 0.00504 ( 6903) covalent geometry : angle 0.75565 ( 9421) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 108 time to evaluate : 0.759 Fit side-chains REVERT: A 2 ASN cc_start: 0.8268 (m-40) cc_final: 0.8010 (m-40) REVERT: A 161 GLU cc_start: 0.7636 (mp0) cc_final: 0.7367 (mp0) REVERT: A 182 THR cc_start: 0.8198 (m) cc_final: 0.7941 (p) REVERT: A 185 HIS cc_start: 0.7865 (OUTLIER) cc_final: 0.7553 (p90) REVERT: A 192 ASP cc_start: 0.7377 (t70) cc_final: 0.7125 (OUTLIER) REVERT: B 298 LYS cc_start: 0.8122 (mttm) cc_final: 0.7897 (mptm) outliers start: 2 outliers final: 1 residues processed: 109 average time/residue: 1.1904 time to fit residues: 137.2140 Evaluate side-chains 79 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 76 optimal weight: 0.3980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 HIS A 185 HIS B 163 HIS B 322 HIS B 338 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.145392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.114248 restraints weight = 7441.239| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.18 r_work: 0.3152 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6923 Z= 0.143 Angle : 0.726 12.149 9477 Z= 0.329 Chirality : 0.044 0.322 1077 Planarity : 0.005 0.046 1199 Dihedral : 10.915 110.086 1257 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.55 % Allowed : 7.28 % Favored : 91.18 % 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: -0.64 (0.29), residues: 846 helix: 1.10 (0.30), residues: 314 sheet: -1.27 (0.35), residues: 190 loop : -1.30 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 379 HIS 0.008 0.001 HIS A 322 PHE 0.019 0.001 PHE B 172 TYR 0.013 0.001 TYR B 154 ARG 0.006 0.000 ARG A 198 Details of bonding type rmsd link_NAG-ASN : bond 0.00358 ( 6) link_NAG-ASN : angle 1.81228 ( 18) link_ALPHA1-6 : bond 0.00520 ( 2) link_ALPHA1-6 : angle 1.53791 ( 6) link_BETA1-4 : bond 0.01820 ( 4) link_BETA1-4 : angle 6.58013 ( 12) link_ALPHA1-3 : bond 0.01651 ( 4) link_ALPHA1-3 : angle 3.41338 ( 12) hydrogen bonds : bond 0.04406 ( 277) hydrogen bonds : angle 4.78933 ( 807) SS BOND : bond 0.00464 ( 4) SS BOND : angle 1.99343 ( 8) covalent geometry : bond 0.00314 ( 6903) covalent geometry : angle 0.66998 ( 9421) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.846 Fit side-chains REVERT: A 2 ASN cc_start: 0.8380 (m-40) cc_final: 0.8144 (m-40) REVERT: A 161 GLU cc_start: 0.8090 (mp0) cc_final: 0.7831 (mp0) REVERT: A 182 THR cc_start: 0.7975 (m) cc_final: 0.7667 (p) REVERT: A 232 CYS cc_start: 0.8344 (p) cc_final: 0.7941 (p) REVERT: A 234 GLU cc_start: 0.8321 (mp0) cc_final: 0.7809 (mp0) REVERT: A 419 ASP cc_start: 0.8020 (p0) cc_final: 0.7364 (t0) REVERT: B 179 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7789 (mt) outliers start: 10 outliers final: 1 residues processed: 84 average time/residue: 1.2411 time to fit residues: 113.0231 Evaluate side-chains 70 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain B residue 179 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 81 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A 195 HIS B 338 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.139870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.107972 restraints weight = 7552.718| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.21 r_work: 0.3088 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 6923 Z= 0.231 Angle : 0.784 11.884 9477 Z= 0.355 Chirality : 0.048 0.341 1077 Planarity : 0.005 0.040 1199 Dihedral : 10.120 102.180 1255 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.70 % Allowed : 9.60 % Favored : 88.70 % 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: -0.47 (0.29), residues: 846 helix: 1.22 (0.30), residues: 314 sheet: -1.02 (0.36), residues: 190 loop : -1.27 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 379 HIS 0.008 0.002 HIS B 322 PHE 0.019 0.002 PHE B 172 TYR 0.016 0.002 TYR B 154 ARG 0.008 0.001 ARG A 198 Details of bonding type rmsd link_NAG-ASN : bond 0.00291 ( 6) link_NAG-ASN : angle 1.81096 ( 18) link_ALPHA1-6 : bond 0.00251 ( 2) link_ALPHA1-6 : angle 1.71975 ( 6) link_BETA1-4 : bond 0.01612 ( 4) link_BETA1-4 : angle 6.42790 ( 12) link_ALPHA1-3 : bond 0.01610 ( 4) link_ALPHA1-3 : angle 3.67631 ( 12) hydrogen bonds : bond 0.05185 ( 277) hydrogen bonds : angle 4.64748 ( 807) SS BOND : bond 0.00738 ( 4) SS BOND : angle 2.37876 ( 8) covalent geometry : bond 0.00579 ( 6903) covalent geometry : angle 0.73204 ( 9421) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.732 Fit side-chains revert: symmetry clash REVERT: A 2 ASN cc_start: 0.8372 (m-40) cc_final: 0.8141 (m-40) REVERT: A 161 GLU cc_start: 0.8092 (mp0) cc_final: 0.7809 (mp0) REVERT: A 192 ASP cc_start: 0.7110 (t70) cc_final: 0.6678 (t0) REVERT: A 232 CYS cc_start: 0.8444 (p) cc_final: 0.8243 (p) REVERT: B 152 MET cc_start: 0.8988 (OUTLIER) cc_final: 0.8516 (mtt) outliers start: 11 outliers final: 4 residues processed: 81 average time/residue: 1.0504 time to fit residues: 90.8879 Evaluate side-chains 77 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 237 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS B 338 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.142900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.111237 restraints weight = 7543.935| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.20 r_work: 0.3134 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 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 : 0.004 0.039 6923 Z= 0.149 Angle : 0.707 11.728 9477 Z= 0.316 Chirality : 0.044 0.310 1077 Planarity : 0.005 0.039 1199 Dihedral : 9.314 99.820 1255 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.24 % Allowed : 12.54 % Favored : 86.22 % 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: -0.18 (0.29), residues: 846 helix: 1.51 (0.30), residues: 314 sheet: -0.71 (0.37), residues: 178 loop : -1.27 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 379 HIS 0.012 0.001 HIS A 185 PHE 0.015 0.001 PHE B 172 TYR 0.013 0.001 TYR A 154 ARG 0.006 0.000 ARG A 198 Details of bonding type rmsd link_NAG-ASN : bond 0.00306 ( 6) link_NAG-ASN : angle 1.79493 ( 18) link_ALPHA1-6 : bond 0.00345 ( 2) link_ALPHA1-6 : angle 1.57637 ( 6) link_BETA1-4 : bond 0.01669 ( 4) link_BETA1-4 : angle 6.06646 ( 12) link_ALPHA1-3 : bond 0.01727 ( 4) link_ALPHA1-3 : angle 3.52788 ( 12) hydrogen bonds : bond 0.03956 ( 277) hydrogen bonds : angle 4.45676 ( 807) SS BOND : bond 0.00364 ( 4) SS BOND : angle 1.83859 ( 8) covalent geometry : bond 0.00357 ( 6903) covalent geometry : angle 0.65565 ( 9421) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.687 Fit side-chains revert: symmetry clash REVERT: A 2 ASN cc_start: 0.8373 (m-40) cc_final: 0.8145 (m-40) REVERT: A 161 GLU cc_start: 0.7959 (mp0) cc_final: 0.7744 (mp0) REVERT: A 232 CYS cc_start: 0.8370 (p) cc_final: 0.8159 (p) REVERT: A 419 ASP cc_start: 0.7986 (p0) cc_final: 0.7352 (t0) REVERT: B 75 GLU cc_start: 0.8428 (tt0) cc_final: 0.7890 (tp30) REVERT: B 232 CYS cc_start: 0.8470 (p) cc_final: 0.8190 (p) outliers start: 8 outliers final: 3 residues processed: 82 average time/residue: 1.0643 time to fit residues: 93.3579 Evaluate side-chains 79 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 76 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 182 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 17 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 47 optimal weight: 0.0570 chunk 32 optimal weight: 1.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS A 322 HIS B 338 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.144950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.113321 restraints weight = 7523.304| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.23 r_work: 0.3144 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6923 Z= 0.117 Angle : 0.649 11.144 9477 Z= 0.289 Chirality : 0.042 0.274 1077 Planarity : 0.004 0.037 1199 Dihedral : 8.797 99.757 1255 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.86 % Allowed : 13.00 % Favored : 85.14 % 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: 0.05 (0.29), residues: 846 helix: 1.79 (0.31), residues: 314 sheet: -0.75 (0.36), residues: 178 loop : -1.14 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 379 HIS 0.009 0.001 HIS A 185 PHE 0.022 0.001 PHE A 172 TYR 0.012 0.001 TYR A 154 ARG 0.005 0.000 ARG A 198 Details of bonding type rmsd link_NAG-ASN : bond 0.00434 ( 6) link_NAG-ASN : angle 1.79848 ( 18) link_ALPHA1-6 : bond 0.00410 ( 2) link_ALPHA1-6 : angle 1.48839 ( 6) link_BETA1-4 : bond 0.01628 ( 4) link_BETA1-4 : angle 5.72072 ( 12) link_ALPHA1-3 : bond 0.01589 ( 4) link_ALPHA1-3 : angle 3.23066 ( 12) hydrogen bonds : bond 0.03347 ( 277) hydrogen bonds : angle 4.29580 ( 807) SS BOND : bond 0.00278 ( 4) SS BOND : angle 1.34295 ( 8) covalent geometry : bond 0.00267 ( 6903) covalent geometry : angle 0.59918 ( 9421) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.752 Fit side-chains revert: symmetry clash REVERT: A 2 ASN cc_start: 0.8372 (m-40) cc_final: 0.8163 (m-40) REVERT: A 75 GLU cc_start: 0.8225 (tt0) cc_final: 0.7713 (tp30) REVERT: A 152 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8588 (mtt) REVERT: A 232 CYS cc_start: 0.8343 (p) cc_final: 0.8130 (p) REVERT: B 75 GLU cc_start: 0.8321 (tt0) cc_final: 0.7804 (tp30) REVERT: B 232 CYS cc_start: 0.8462 (p) cc_final: 0.8159 (p) outliers start: 12 outliers final: 6 residues processed: 94 average time/residue: 0.8485 time to fit residues: 86.0930 Evaluate side-chains 87 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain B residue 47 ARG Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 237 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 43 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS A 299 HIS B 338 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.146482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.115438 restraints weight = 7610.182| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.20 r_work: 0.3173 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6923 Z= 0.123 Angle : 0.653 11.024 9477 Z= 0.292 Chirality : 0.043 0.264 1077 Planarity : 0.004 0.037 1199 Dihedral : 8.532 97.391 1255 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.70 % Allowed : 13.62 % Favored : 84.67 % 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 (0.29), residues: 846 helix: 1.85 (0.31), residues: 316 sheet: -0.74 (0.36), residues: 178 loop : -1.11 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 379 HIS 0.007 0.001 HIS A 185 PHE 0.011 0.001 PHE A 172 TYR 0.013 0.001 TYR A 236 ARG 0.004 0.000 ARG A 198 Details of bonding type rmsd link_NAG-ASN : bond 0.00325 ( 6) link_NAG-ASN : angle 1.79152 ( 18) link_ALPHA1-6 : bond 0.00370 ( 2) link_ALPHA1-6 : angle 1.51809 ( 6) link_BETA1-4 : bond 0.01543 ( 4) link_BETA1-4 : angle 5.55334 ( 12) link_ALPHA1-3 : bond 0.01515 ( 4) link_ALPHA1-3 : angle 3.21020 ( 12) hydrogen bonds : bond 0.03399 ( 277) hydrogen bonds : angle 4.23585 ( 807) SS BOND : bond 0.00268 ( 4) SS BOND : angle 1.25715 ( 8) covalent geometry : bond 0.00289 ( 6903) covalent geometry : angle 0.60580 ( 9421) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.741 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8227 (tt0) cc_final: 0.7696 (tp30) REVERT: A 152 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8582 (mtt) REVERT: A 232 CYS cc_start: 0.8296 (p) cc_final: 0.8075 (p) REVERT: B 75 GLU cc_start: 0.8298 (tt0) cc_final: 0.7786 (tp30) REVERT: B 232 CYS cc_start: 0.8409 (p) cc_final: 0.8111 (p) outliers start: 11 outliers final: 7 residues processed: 87 average time/residue: 0.9714 time to fit residues: 90.6923 Evaluate side-chains 85 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain B residue 47 ARG Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 237 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 82 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS A 299 HIS B 338 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.144289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.112901 restraints weight = 7412.515| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.18 r_work: 0.3127 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6923 Z= 0.149 Angle : 0.677 11.183 9477 Z= 0.304 Chirality : 0.044 0.272 1077 Planarity : 0.004 0.035 1199 Dihedral : 8.317 93.902 1255 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.17 % Allowed : 14.09 % Favored : 83.75 % 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 (0.29), residues: 846 helix: 1.83 (0.31), residues: 316 sheet: -0.73 (0.36), residues: 178 loop : -1.11 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 379 HIS 0.007 0.001 HIS A 299 PHE 0.013 0.001 PHE A 172 TYR 0.014 0.001 TYR A 154 ARG 0.005 0.000 ARG B 198 Details of bonding type rmsd link_NAG-ASN : bond 0.00281 ( 6) link_NAG-ASN : angle 1.76731 ( 18) link_ALPHA1-6 : bond 0.00283 ( 2) link_ALPHA1-6 : angle 1.55275 ( 6) link_BETA1-4 : bond 0.01519 ( 4) link_BETA1-4 : angle 5.62192 ( 12) link_ALPHA1-3 : bond 0.01531 ( 4) link_ALPHA1-3 : angle 3.34057 ( 12) hydrogen bonds : bond 0.03758 ( 277) hydrogen bonds : angle 4.23485 ( 807) SS BOND : bond 0.00354 ( 4) SS BOND : angle 1.62756 ( 8) covalent geometry : bond 0.00364 ( 6903) covalent geometry : angle 0.62964 ( 9421) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 1.212 Fit side-chains REVERT: A 75 GLU cc_start: 0.8241 (tt0) cc_final: 0.7714 (tp30) REVERT: A 152 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.8577 (mtt) REVERT: A 232 CYS cc_start: 0.8264 (p) cc_final: 0.7882 (t) REVERT: A 234 GLU cc_start: 0.8332 (mp0) cc_final: 0.7416 (mp0) REVERT: B 75 GLU cc_start: 0.8335 (tt0) cc_final: 0.7819 (tp30) REVERT: B 232 CYS cc_start: 0.8420 (p) cc_final: 0.8119 (p) REVERT: B 341 THR cc_start: 0.8726 (p) cc_final: 0.8424 (t) outliers start: 14 outliers final: 8 residues processed: 87 average time/residue: 0.8724 time to fit residues: 81.6854 Evaluate side-chains 84 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 47 ARG Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 237 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 8 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 47 optimal weight: 0.0970 chunk 83 optimal weight: 10.0000 chunk 71 optimal weight: 0.0870 chunk 13 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 46 optimal weight: 6.9990 chunk 14 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS A 299 HIS B 338 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.146988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.115312 restraints weight = 7469.601| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.22 r_work: 0.3197 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 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 0.036 6923 Z= 0.110 Angle : 0.630 10.866 9477 Z= 0.280 Chirality : 0.041 0.235 1077 Planarity : 0.004 0.037 1199 Dihedral : 7.932 94.881 1255 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.86 % Allowed : 15.17 % Favored : 82.97 % 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: 0.16 (0.29), residues: 846 helix: 1.78 (0.30), residues: 326 sheet: -0.76 (0.36), residues: 178 loop : -1.02 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 379 HIS 0.007 0.001 HIS A 299 PHE 0.014 0.001 PHE A 172 TYR 0.014 0.001 TYR A 236 ARG 0.004 0.000 ARG B 198 Details of bonding type rmsd link_NAG-ASN : bond 0.00388 ( 6) link_NAG-ASN : angle 1.82474 ( 18) link_ALPHA1-6 : bond 0.00409 ( 2) link_ALPHA1-6 : angle 1.47758 ( 6) link_BETA1-4 : bond 0.01555 ( 4) link_BETA1-4 : angle 5.27174 ( 12) link_ALPHA1-3 : bond 0.01543 ( 4) link_ALPHA1-3 : angle 3.15731 ( 12) hydrogen bonds : bond 0.02968 ( 277) hydrogen bonds : angle 4.14112 ( 807) SS BOND : bond 0.00272 ( 4) SS BOND : angle 1.05712 ( 8) covalent geometry : bond 0.00248 ( 6903) covalent geometry : angle 0.58569 ( 9421) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.730 Fit side-chains REVERT: A 45 THR cc_start: 0.8589 (m) cc_final: 0.8133 (p) REVERT: A 75 GLU cc_start: 0.8214 (tt0) cc_final: 0.7698 (tp30) REVERT: A 232 CYS cc_start: 0.8233 (p) cc_final: 0.7894 (t) REVERT: A 234 GLU cc_start: 0.8249 (mp0) cc_final: 0.7328 (mp0) REVERT: B 75 GLU cc_start: 0.8243 (tt0) cc_final: 0.7769 (tp30) REVERT: B 173 MET cc_start: 0.8544 (mmt) cc_final: 0.8297 (mmm) REVERT: B 232 CYS cc_start: 0.8455 (p) cc_final: 0.8173 (p) REVERT: B 341 THR cc_start: 0.8724 (p) cc_final: 0.8427 (t) outliers start: 12 outliers final: 6 residues processed: 92 average time/residue: 0.9972 time to fit residues: 98.1586 Evaluate side-chains 83 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 47 ARG Chi-restraints excluded: chain B residue 200 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 15 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS A 299 HIS B 77 ASN B 338 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.146631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.114689 restraints weight = 7539.750| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.24 r_work: 0.3185 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6923 Z= 0.119 Angle : 0.644 10.638 9477 Z= 0.287 Chirality : 0.042 0.232 1077 Planarity : 0.004 0.036 1199 Dihedral : 7.577 92.693 1255 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.55 % Allowed : 16.41 % Favored : 82.04 % 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: 0.24 (0.29), residues: 846 helix: 1.82 (0.30), residues: 326 sheet: -0.69 (0.36), residues: 178 loop : -0.97 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 379 HIS 0.008 0.001 HIS A 299 PHE 0.013 0.001 PHE A 172 TYR 0.012 0.001 TYR A 154 ARG 0.003 0.000 ARG A 198 Details of bonding type rmsd link_NAG-ASN : bond 0.00283 ( 6) link_NAG-ASN : angle 1.79908 ( 18) link_ALPHA1-6 : bond 0.00351 ( 2) link_ALPHA1-6 : angle 1.48854 ( 6) link_BETA1-4 : bond 0.01428 ( 4) link_BETA1-4 : angle 5.16859 ( 12) link_ALPHA1-3 : bond 0.01567 ( 4) link_ALPHA1-3 : angle 3.23164 ( 12) hydrogen bonds : bond 0.03223 ( 277) hydrogen bonds : angle 4.10105 ( 807) SS BOND : bond 0.00308 ( 4) SS BOND : angle 1.26116 ( 8) covalent geometry : bond 0.00279 ( 6903) covalent geometry : angle 0.60087 ( 9421) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.658 Fit side-chains REVERT: A 45 THR cc_start: 0.8591 (m) cc_final: 0.8139 (p) REVERT: A 75 GLU cc_start: 0.8163 (tt0) cc_final: 0.7688 (tp30) REVERT: A 152 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8602 (mtt) REVERT: A 161 GLU cc_start: 0.8261 (mp0) cc_final: 0.6953 (pp20) REVERT: A 232 CYS cc_start: 0.8257 (p) cc_final: 0.7896 (t) REVERT: A 234 GLU cc_start: 0.8262 (mp0) cc_final: 0.7283 (mp0) REVERT: B 75 GLU cc_start: 0.8238 (tt0) cc_final: 0.7768 (tp30) REVERT: B 232 CYS cc_start: 0.8502 (p) cc_final: 0.8206 (p) REVERT: B 341 THR cc_start: 0.8698 (p) cc_final: 0.8420 (t) outliers start: 10 outliers final: 7 residues processed: 84 average time/residue: 0.8900 time to fit residues: 80.2553 Evaluate side-chains 87 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain B residue 47 ARG Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 200 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 4 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS A 299 HIS B 338 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.142670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.111308 restraints weight = 7619.928| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.18 r_work: 0.3132 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6923 Z= 0.174 Angle : 0.697 11.149 9477 Z= 0.313 Chirality : 0.045 0.264 1077 Planarity : 0.004 0.035 1199 Dihedral : 7.451 87.247 1255 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.24 % Allowed : 16.87 % Favored : 81.89 % 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: 0.12 (0.29), residues: 846 helix: 1.68 (0.30), residues: 326 sheet: -0.64 (0.36), residues: 178 loop : -1.06 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 379 HIS 0.008 0.002 HIS A 299 PHE 0.013 0.001 PHE A 172 TYR 0.014 0.001 TYR A 154 ARG 0.003 0.000 ARG A 95 Details of bonding type rmsd link_NAG-ASN : bond 0.00227 ( 6) link_NAG-ASN : angle 1.79821 ( 18) link_ALPHA1-6 : bond 0.00243 ( 2) link_ALPHA1-6 : angle 1.57513 ( 6) link_BETA1-4 : bond 0.01425 ( 4) link_BETA1-4 : angle 5.48910 ( 12) link_ALPHA1-3 : bond 0.01560 ( 4) link_ALPHA1-3 : angle 3.44009 ( 12) hydrogen bonds : bond 0.03959 ( 277) hydrogen bonds : angle 4.20703 ( 807) SS BOND : bond 0.00416 ( 4) SS BOND : angle 1.69752 ( 8) covalent geometry : bond 0.00433 ( 6903) covalent geometry : angle 0.65204 ( 9421) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.681 Fit side-chains REVERT: A 75 GLU cc_start: 0.8306 (tt0) cc_final: 0.7787 (tp30) REVERT: A 161 GLU cc_start: 0.8264 (mp0) cc_final: 0.6948 (pp20) REVERT: A 232 CYS cc_start: 0.8243 (p) cc_final: 0.7843 (t) REVERT: A 234 GLU cc_start: 0.8270 (mp0) cc_final: 0.7304 (mp0) REVERT: B 75 GLU cc_start: 0.8332 (tt0) cc_final: 0.7813 (tp30) REVERT: B 77 ASN cc_start: 0.8209 (t0) cc_final: 0.7676 (t0) REVERT: B 232 CYS cc_start: 0.8512 (p) cc_final: 0.8223 (p) REVERT: B 341 THR cc_start: 0.8747 (p) cc_final: 0.8461 (t) outliers start: 8 outliers final: 5 residues processed: 83 average time/residue: 0.9671 time to fit residues: 86.2582 Evaluate side-chains 79 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain B residue 200 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 24 optimal weight: 0.0570 chunk 3 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 68 optimal weight: 0.0870 chunk 15 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 overall best weight: 1.0278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS A 299 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.144877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.113378 restraints weight = 7592.586| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.21 r_work: 0.3168 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6923 Z= 0.125 Angle : 0.660 11.000 9477 Z= 0.295 Chirality : 0.042 0.248 1077 Planarity : 0.004 0.036 1199 Dihedral : 7.233 87.002 1255 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.24 % Allowed : 17.34 % Favored : 81.42 % 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: 0.18 (0.29), residues: 846 helix: 1.74 (0.30), residues: 326 sheet: -0.63 (0.36), residues: 178 loop : -1.03 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 379 HIS 0.007 0.001 HIS A 299 PHE 0.014 0.001 PHE A 172 TYR 0.013 0.001 TYR A 154 ARG 0.007 0.000 ARG B 198 Details of bonding type rmsd link_NAG-ASN : bond 0.00315 ( 6) link_NAG-ASN : angle 1.76886 ( 18) link_ALPHA1-6 : bond 0.00319 ( 2) link_ALPHA1-6 : angle 1.51531 ( 6) link_BETA1-4 : bond 0.01498 ( 4) link_BETA1-4 : angle 5.36116 ( 12) link_ALPHA1-3 : bond 0.01521 ( 4) link_ALPHA1-3 : angle 3.35977 ( 12) hydrogen bonds : bond 0.03352 ( 277) hydrogen bonds : angle 4.16662 ( 807) SS BOND : bond 0.00355 ( 4) SS BOND : angle 1.20529 ( 8) covalent geometry : bond 0.00297 ( 6903) covalent geometry : angle 0.61513 ( 9421) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4552.44 seconds wall clock time: 80 minutes 46.16 seconds (4846.16 seconds total)