Starting phenix.real_space_refine on Tue Jan 14 11:23:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bcl_44429/01_2025/9bcl_44429.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bcl_44429/01_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_44429/01_2025/9bcl_44429.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bcl_44429/01_2025/9bcl_44429.map" model { file = "/net/cci-nas-00/data/ceres_data/9bcl_44429/01_2025/9bcl_44429.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bcl_44429/01_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-5571/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: 4.63, per 1000 atoms: 0.69 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: 2.24 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.75 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: 1.84 Time building geometry restraints manager: 2.17 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: 0.000 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: 0.220 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 19.540 Find NCS groups from input model: 0.260 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:12.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.180 ------------------------------------------------------------------------------- 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 6903 Z= 0.346 Angle : 0.756 10.945 9421 Z= 0.405 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 *********************** 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 : 0.611 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: 1.1621 time to fit residues: 133.6629 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 : 0.684 ------------------------------------------------------------------------------- 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 = 0.114251 restraints weight = 7441.240| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.18 r_work: 0.3158 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 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 6903 Z= 0.213 Angle : 0.670 9.828 9421 Z= 0.316 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 *********************** 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 : 0.707 Fit side-chains REVERT: A 2 ASN cc_start: 0.8366 (m-40) cc_final: 0.8127 (m-40) REVERT: A 161 GLU cc_start: 0.8056 (mp0) cc_final: 0.7812 (mp0) REVERT: A 182 THR cc_start: 0.8020 (m) cc_final: 0.7723 (p) REVERT: A 232 CYS cc_start: 0.8354 (p) cc_final: 0.7958 (p) REVERT: A 234 GLU cc_start: 0.8314 (mp0) cc_final: 0.7820 (mp0) REVERT: A 419 ASP cc_start: 0.8038 (p0) cc_final: 0.7397 (t0) REVERT: B 179 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7815 (mt) outliers start: 10 outliers final: 1 residues processed: 84 average time/residue: 1.1068 time to fit residues: 98.9307 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 : 0.709 ------------------------------------------------------------------------------- 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: 7.9990 chunk 4 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.3657 r_free = 0.3657 target = 0.139974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.108701 restraints weight = 7667.940| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.21 r_work: 0.3078 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 6903 Z= 0.467 Angle : 0.760 10.054 9421 Z= 0.356 Chirality : 0.050 0.354 1077 Planarity : 0.005 0.041 1199 Dihedral : 10.185 101.113 1255 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.01 % Allowed : 9.44 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.29), residues: 846 helix: 1.12 (0.30), residues: 314 sheet: -1.06 (0.36), residues: 190 loop : -1.32 (0.32), 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 0.021 0.002 PHE B 172 TYR 0.017 0.002 TYR B 154 ARG 0.005 0.001 ARG A 198 *********************** 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 90 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.732 Fit side-chains revert: symmetry clash REVERT: A 2 ASN cc_start: 0.8385 (m-40) cc_final: 0.8153 (m-40) REVERT: A 161 GLU cc_start: 0.8128 (mp0) cc_final: 0.7822 (mp0) REVERT: A 192 ASP cc_start: 0.7254 (t70) cc_final: 0.6809 (t0) REVERT: A 232 CYS cc_start: 0.8503 (p) cc_final: 0.8287 (p) REVERT: B 232 CYS cc_start: 0.8472 (p) cc_final: 0.8212 (p) outliers start: 13 outliers final: 6 residues processed: 84 average time/residue: 0.9942 time to fit residues: 89.4188 Evaluate side-chains 78 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain B residue 59 VAL 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: 0.9990 chunk 18 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3712 r_free = 0.3712 target = 0.144191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.112425 restraints weight = 7536.273| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.23 r_work: 0.3154 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6903 Z= 0.198 Angle : 0.637 8.459 9421 Z= 0.294 Chirality : 0.043 0.299 1077 Planarity : 0.004 0.040 1199 Dihedral : 9.304 101.152 1255 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.93 % Allowed : 13.00 % Favored : 86.07 % 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: 1.55 (0.30), residues: 314 sheet: -0.74 (0.37), residues: 178 loop : -1.26 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 379 HIS 0.013 0.001 HIS A 185 PHE 0.014 0.001 PHE B 172 TYR 0.012 0.001 TYR A 154 ARG 0.007 0.000 ARG A 198 *********************** 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: 6 poor density : 81 time to evaluate : 0.764 Fit side-chains revert: symmetry clash REVERT: A 2 ASN cc_start: 0.8374 (m-40) cc_final: 0.8147 (m-40) REVERT: A 75 GLU cc_start: 0.8253 (tt0) cc_final: 0.7676 (tp30) REVERT: A 161 GLU cc_start: 0.7930 (mp0) cc_final: 0.7726 (mp0) REVERT: A 232 CYS cc_start: 0.8356 (p) cc_final: 0.8143 (p) REVERT: A 419 ASP cc_start: 0.7991 (p0) cc_final: 0.7358 (t0) REVERT: B 75 GLU cc_start: 0.8362 (tt0) cc_final: 0.7825 (tp30) REVERT: B 152 MET cc_start: 0.8972 (OUTLIER) cc_final: 0.8444 (mtt) REVERT: B 232 CYS cc_start: 0.8429 (p) cc_final: 0.8137 (p) outliers start: 6 outliers final: 3 residues processed: 84 average time/residue: 0.9440 time to fit residues: 84.9391 Evaluate side-chains 79 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 311 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 17 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.3687 r_free = 0.3687 target = 0.142172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.110292 restraints weight = 7553.676| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.21 r_work: 0.3120 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6903 Z= 0.288 Angle : 0.659 9.520 9421 Z= 0.306 Chirality : 0.045 0.313 1077 Planarity : 0.005 0.037 1199 Dihedral : 9.022 97.843 1255 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.48 % Allowed : 12.38 % 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: -0.12 (0.29), residues: 846 helix: 1.60 (0.30), residues: 314 sheet: -0.72 (0.36), residues: 178 loop : -1.26 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 379 HIS 0.007 0.002 HIS A 185 PHE 0.022 0.001 PHE A 172 TYR 0.014 0.001 TYR A 154 ARG 0.004 0.000 ARG B 205 *********************** 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 93 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.774 Fit side-chains revert: symmetry clash REVERT: A 2 ASN cc_start: 0.8361 (m-40) cc_final: 0.8145 (m-40) REVERT: A 152 MET cc_start: 0.8960 (OUTLIER) cc_final: 0.8572 (mtt) REVERT: A 161 GLU cc_start: 0.8002 (mp0) cc_final: 0.7778 (mp0) REVERT: A 223 MET cc_start: 0.8679 (tpp) cc_final: 0.8398 (tpp) REVERT: A 232 CYS cc_start: 0.8348 (p) cc_final: 0.8104 (p) REVERT: B 75 GLU cc_start: 0.8407 (tt0) cc_final: 0.7888 (tp30) REVERT: B 232 CYS cc_start: 0.8470 (p) cc_final: 0.8175 (p) outliers start: 16 outliers final: 6 residues processed: 85 average time/residue: 1.0375 time to fit residues: 94.5493 Evaluate side-chains 83 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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 47 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 43 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 52 optimal weight: 0.4980 chunk 3 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3720 r_free = 0.3720 target = 0.144723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.113667 restraints weight = 7499.145| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.17 r_work: 0.3172 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6903 Z= 0.185 Angle : 0.602 8.492 9421 Z= 0.279 Chirality : 0.043 0.273 1077 Planarity : 0.004 0.037 1199 Dihedral : 8.632 97.999 1255 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.39 % Allowed : 13.47 % 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: 1.83 (0.31), residues: 314 sheet: -0.74 (0.36), residues: 178 loop : -1.19 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 379 HIS 0.008 0.001 HIS A 185 PHE 0.011 0.001 PHE A 172 TYR 0.013 0.001 TYR A 154 ARG 0.005 0.000 ARG B 198 *********************** 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 95 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.761 Fit side-chains revert: symmetry clash REVERT: A 2 ASN cc_start: 0.8377 (m-40) cc_final: 0.8168 (m-40) REVERT: A 75 GLU cc_start: 0.8205 (tt0) cc_final: 0.7722 (tp30) REVERT: A 152 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8603 (mtt) REVERT: A 232 CYS cc_start: 0.8311 (p) cc_final: 0.8079 (p) REVERT: B 75 GLU cc_start: 0.8317 (tt0) cc_final: 0.7811 (tp30) REVERT: B 232 CYS cc_start: 0.8473 (p) cc_final: 0.8182 (p) outliers start: 9 outliers final: 5 residues processed: 92 average time/residue: 0.8573 time to fit residues: 85.0222 Evaluate side-chains 85 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.718 ------------------------------------------------------------------------------- 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 86 CYS Chi-restraints excluded: chain B residue 200 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 82 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 = 0.3668 r_free = 0.3668 target = 0.140451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.108916 restraints weight = 7462.464| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.17 r_work: 0.3078 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 6903 Z= 0.399 Angle : 0.707 9.773 9421 Z= 0.329 Chirality : 0.047 0.323 1077 Planarity : 0.005 0.035 1199 Dihedral : 8.562 91.906 1255 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.17 % Allowed : 13.47 % Favored : 84.37 % 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: -0.10 (0.29), residues: 846 helix: 1.61 (0.30), residues: 314 sheet: -0.71 (0.36), residues: 178 loop : -1.23 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 379 HIS 0.008 0.001 HIS B 322 PHE 0.015 0.002 PHE A 172 TYR 0.016 0.002 TYR A 154 ARG 0.004 0.000 ARG A 95 *********************** 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 87 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.701 Fit side-chains REVERT: A 232 CYS cc_start: 0.8286 (p) cc_final: 0.7883 (t) REVERT: A 234 GLU cc_start: 0.8405 (mp0) cc_final: 0.7493 (mp0) REVERT: B 75 GLU cc_start: 0.8398 (tt0) cc_final: 0.7884 (tp30) REVERT: B 232 CYS cc_start: 0.8479 (p) cc_final: 0.8193 (p) outliers start: 14 outliers final: 7 residues processed: 82 average time/residue: 0.9642 time to fit residues: 84.7078 Evaluate side-chains 79 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR 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 59 VAL Chi-restraints excluded: chain B residue 182 THR 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: 0.3980 chunk 73 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3721 r_free = 0.3721 target = 0.144810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.113719 restraints weight = 7473.542| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.17 r_work: 0.3170 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 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 : 0.003 0.037 6903 Z= 0.183 Angle : 0.611 8.496 9421 Z= 0.283 Chirality : 0.042 0.262 1077 Planarity : 0.004 0.037 1199 Dihedral : 8.195 94.645 1255 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.08 % Allowed : 14.71 % Favored : 84.21 % 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: 0.08 (0.29), residues: 846 helix: 1.82 (0.31), residues: 316 sheet: -0.70 (0.36), residues: 178 loop : -1.16 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 379 HIS 0.006 0.001 HIS B 322 PHE 0.014 0.001 PHE A 172 TYR 0.013 0.001 TYR A 236 ARG 0.005 0.000 ARG B 198 *********************** 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 89 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.683 Fit side-chains REVERT: A 75 GLU cc_start: 0.8212 (tt0) cc_final: 0.7744 (tp30) REVERT: A 232 CYS cc_start: 0.8283 (p) cc_final: 0.7926 (t) REVERT: A 234 GLU cc_start: 0.8261 (mp0) cc_final: 0.7324 (mp0) REVERT: B 75 GLU cc_start: 0.8326 (tt0) cc_final: 0.7800 (tp30) REVERT: B 232 CYS cc_start: 0.8494 (p) cc_final: 0.8220 (p) REVERT: B 341 THR cc_start: 0.8748 (p) cc_final: 0.8413 (t) outliers start: 7 outliers final: 5 residues processed: 86 average time/residue: 0.9387 time to fit residues: 86.9770 Evaluate side-chains 83 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 47 ARG Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 182 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 15 optimal weight: 0.0270 chunk 81 optimal weight: 0.0770 chunk 49 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 10 optimal weight: 0.0270 chunk 42 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 overall best weight: 0.3054 ------------------------------------------------------------------------------- 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 = 0.3768 r_free = 0.3768 target = 0.148755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.117051 restraints weight = 7532.614| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.24 r_work: 0.3215 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 6903 Z= 0.155 Angle : 0.575 7.547 9421 Z= 0.264 Chirality : 0.041 0.212 1077 Planarity : 0.004 0.038 1199 Dihedral : 7.483 95.655 1255 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.08 % Allowed : 15.33 % Favored : 83.59 % 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: 0.30 (0.29), residues: 846 helix: 1.98 (0.31), residues: 318 sheet: -0.73 (0.36), residues: 182 loop : -0.95 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 379 HIS 0.005 0.001 HIS B 322 PHE 0.014 0.001 PHE A 172 TYR 0.013 0.001 TYR A 236 ARG 0.004 0.000 ARG A 198 *********************** 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 98 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.694 Fit side-chains REVERT: A 45 THR cc_start: 0.8594 (m) cc_final: 0.8217 (p) REVERT: A 61 SER cc_start: 0.8427 (p) cc_final: 0.8219 (t) REVERT: A 75 GLU cc_start: 0.8167 (tt0) cc_final: 0.7689 (tp30) REVERT: A 232 CYS cc_start: 0.8243 (p) cc_final: 0.7882 (t) REVERT: A 234 GLU cc_start: 0.8230 (mp0) cc_final: 0.7244 (mp0) REVERT: B 75 GLU cc_start: 0.8220 (tt0) cc_final: 0.7744 (tp30) REVERT: B 173 MET cc_start: 0.8501 (mmt) cc_final: 0.8261 (mmm) REVERT: B 232 CYS cc_start: 0.8482 (p) cc_final: 0.8187 (p) REVERT: B 341 THR cc_start: 0.8634 (p) cc_final: 0.8351 (t) outliers start: 7 outliers final: 5 residues processed: 93 average time/residue: 0.8953 time to fit residues: 89.5269 Evaluate side-chains 85 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain B residue 47 ARG Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 182 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 4 optimal weight: 0.5980 chunk 83 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 31 optimal weight: 0.0670 chunk 12 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 overall best weight: 1.5322 ------------------------------------------------------------------------------- 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 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 = 0.144175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.112750 restraints weight = 7630.567| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.22 r_work: 0.3158 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6903 Z= 0.242 Angle : 0.633 7.681 9421 Z= 0.292 Chirality : 0.043 0.240 1077 Planarity : 0.004 0.036 1199 Dihedral : 7.291 89.689 1255 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.08 % Allowed : 16.10 % Favored : 82.82 % 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: 0.33 (0.29), residues: 846 helix: 1.95 (0.31), residues: 318 sheet: -0.55 (0.36), residues: 178 loop : -0.96 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 379 HIS 0.008 0.001 HIS A 299 PHE 0.013 0.001 PHE A 172 TYR 0.013 0.001 TYR A 236 ARG 0.006 0.000 ARG B 198 ********************** 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 84 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.672 Fit side-chains REVERT: A 45 THR cc_start: 0.8579 (m) cc_final: 0.8132 (p) REVERT: A 75 GLU cc_start: 0.8191 (tt0) cc_final: 0.7709 (tp30) REVERT: A 161 GLU cc_start: 0.8311 (mp0) cc_final: 0.6889 (pp20) REVERT: A 232 CYS cc_start: 0.8210 (p) cc_final: 0.7848 (t) REVERT: A 234 GLU cc_start: 0.8234 (mp0) cc_final: 0.7252 (mp0) REVERT: B 75 GLU cc_start: 0.8259 (tt0) cc_final: 0.7786 (tp30) REVERT: B 341 THR cc_start: 0.8710 (p) cc_final: 0.8420 (t) outliers start: 7 outliers final: 4 residues processed: 81 average time/residue: 0.9711 time to fit residues: 84.2157 Evaluate side-chains 77 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 182 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 68 optimal weight: 0.3980 chunk 15 optimal weight: 0.3980 chunk 0 optimal weight: 8.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.146326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.115060 restraints weight = 7619.873| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.20 r_work: 0.3199 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6903 Z= 0.171 Angle : 0.597 7.462 9421 Z= 0.276 Chirality : 0.042 0.224 1077 Planarity : 0.004 0.037 1199 Dihedral : 7.110 89.031 1255 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.08 % Allowed : 16.56 % Favored : 82.35 % 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: 0.43 (0.29), residues: 846 helix: 2.06 (0.30), residues: 318 sheet: -0.55 (0.36), residues: 178 loop : -0.91 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 379 HIS 0.007 0.001 HIS A 299 PHE 0.013 0.001 PHE A 172 TYR 0.012 0.001 TYR A 236 ARG 0.007 0.000 ARG B 198 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4187.34 seconds wall clock time: 75 minutes 47.48 seconds (4547.48 seconds total)