Starting phenix.real_space_refine on Sun Aug 24 06:27:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tmb_41383/08_2025/8tmb_41383.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tmb_41383/08_2025/8tmb_41383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tmb_41383/08_2025/8tmb_41383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tmb_41383/08_2025/8tmb_41383.map" model { file = "/net/cci-nas-00/data/ceres_data/8tmb_41383/08_2025/8tmb_41383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tmb_41383/08_2025/8tmb_41383.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1821 atoms to isotropic. 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 Mg 6 5.21 5 S 59 5.16 5 C 10556 2.51 5 N 2639 2.21 5 O 2969 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16229 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2830 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 14, 'TRANS': 324} Chain: "B" Number of atoms: 2805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2805 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 13, 'TRANS': 321} Chain: "C" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2917 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 15, 'TRANS': 334} Chain: "D" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2925 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 15, 'TRANS': 335} Chain: "E" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2925 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 15, 'TRANS': 335} Chain: "H" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 998 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 4, 'TRANS': 122} Chain: "L" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 823 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.68, per 1000 atoms: 0.23 Number of scatterers: 16229 At special positions: 0 Unit cell: (113.3, 139.05, 167.89, 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) S 59 16.00 Mg 6 11.99 O 2969 8.00 N 2639 7.00 C 10556 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.04 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 797.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3758 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 12 sheets defined 51.1% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 50 through 54 Processing helix chain 'A' and resid 69 through 81 removed outlier: 3.563A pdb=" N VAL A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 92 Processing helix chain 'A' and resid 147 through 156 Processing helix chain 'A' and resid 160 through 163 removed outlier: 3.684A pdb=" N LYS A 163 " --> pdb=" O ILE A 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 160 through 163' Processing helix chain 'A' and resid 164 through 199 removed outlier: 3.805A pdb=" N TYR A 168 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 238 removed outlier: 4.067A pdb=" N VAL A 208 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) Proline residue: A 227 - end of helix removed outlier: 3.774A pdb=" N GLU A 230 " --> pdb=" O TRP A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 246 No H-bonds generated for 'chain 'A' and resid 244 through 246' Processing helix chain 'A' and resid 247 through 302 removed outlier: 3.671A pdb=" N LEU A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ASP A 277 " --> pdb=" O SER A 273 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL A 290 " --> pdb=" O LYS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 325 through 347 Processing helix chain 'B' and resid 46 through 54 removed outlier: 4.206A pdb=" N LEU B 51 " --> pdb=" O GLU B 48 " (cutoff:3.500A) Proline residue: B 52 - end of helix Processing helix chain 'B' and resid 69 through 80 removed outlier: 4.090A pdb=" N VAL B 73 " --> pdb=" O ARG B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 removed outlier: 3.508A pdb=" N LEU B 87 " --> pdb=" O HIS B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 156 Processing helix chain 'B' and resid 165 through 202 Processing helix chain 'B' and resid 205 through 238 removed outlier: 3.897A pdb=" N GLN B 209 " --> pdb=" O LYS B 205 " (cutoff:3.500A) Proline residue: B 227 - end of helix removed outlier: 3.611A pdb=" N ASP B 238 " --> pdb=" O SER B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 311 removed outlier: 4.148A pdb=" N ASP B 277 " --> pdb=" O SER B 273 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LEU B 280 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN B 288 " --> pdb=" O SER B 284 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 329 through 349 removed outlier: 3.975A pdb=" N LYS B 348 " --> pdb=" O TYR B 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 50 Processing helix chain 'C' and resid 51 through 56 removed outlier: 4.363A pdb=" N ASP C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 81 removed outlier: 3.764A pdb=" N VAL C 73 " --> pdb=" O ARG C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 92 removed outlier: 3.627A pdb=" N LEU C 87 " --> pdb=" O HIS C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 153 Processing helix chain 'C' and resid 165 through 201 Processing helix chain 'C' and resid 206 through 238 removed outlier: 3.912A pdb=" N THR C 224 " --> pdb=" O GLU C 220 " (cutoff:3.500A) Proline residue: C 227 - end of helix removed outlier: 4.144A pdb=" N TYR C 236 " --> pdb=" O LEU C 232 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ASP C 238 " --> pdb=" O SER C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 298 removed outlier: 3.832A pdb=" N ASP C 277 " --> pdb=" O SER C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 312 removed outlier: 3.687A pdb=" N ILE C 307 " --> pdb=" O PRO C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 345 removed outlier: 3.958A pdb=" N VAL C 330 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL C 333 " --> pdb=" O VAL C 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 56 removed outlier: 3.530A pdb=" N SER D 49 " --> pdb=" O ASP D 46 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL D 50 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU D 51 " --> pdb=" O GLU D 48 " (cutoff:3.500A) Proline residue: D 52 - end of helix removed outlier: 3.604A pdb=" N ASP D 55 " --> pdb=" O PRO D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 81 Processing helix chain 'D' and resid 83 through 92 Processing helix chain 'D' and resid 147 through 156 Processing helix chain 'D' and resid 160 through 164 removed outlier: 3.555A pdb=" N LYS D 164 " --> pdb=" O ILE D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 201 removed outlier: 3.528A pdb=" N LEU D 169 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU D 201 " --> pdb=" O GLU D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 238 removed outlier: 4.052A pdb=" N ARG D 210 " --> pdb=" O GLU D 206 " (cutoff:3.500A) Proline residue: D 227 - end of helix removed outlier: 4.250A pdb=" N ASP D 238 " --> pdb=" O SER D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 311 removed outlier: 3.546A pdb=" N PHE D 251 " --> pdb=" O THR D 247 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU D 276 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ASP D 277 " --> pdb=" O SER D 273 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA D 298 " --> pdb=" O LEU D 294 " (cutoff:3.500A) Proline residue: D 303 - end of helix Processing helix chain 'D' and resid 327 through 349 removed outlier: 4.496A pdb=" N VAL D 333 " --> pdb=" O VAL D 329 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N MET D 334 " --> pdb=" O VAL D 330 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS D 348 " --> pdb=" O TYR D 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 54 Proline residue: E 52 - end of helix Processing helix chain 'E' and resid 69 through 80 removed outlier: 3.613A pdb=" N VAL E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 91 Processing helix chain 'E' and resid 147 through 156 Processing helix chain 'E' and resid 165 through 202 Processing helix chain 'E' and resid 205 through 237 removed outlier: 4.152A pdb=" N GLN E 209 " --> pdb=" O LYS E 205 " (cutoff:3.500A) Proline residue: E 227 - end of helix removed outlier: 3.947A pdb=" N GLU E 230 " --> pdb=" O TRP E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 246 No H-bonds generated for 'chain 'E' and resid 244 through 246' Processing helix chain 'E' and resid 247 through 298 Processing helix chain 'E' and resid 301 through 312 Processing helix chain 'E' and resid 330 through 348 Processing helix chain 'H' and resid 65 through 68 Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA2, first strand: chain 'B' and resid 39 through 44 removed outlier: 3.786A pdb=" N GLU B 28 " --> pdb=" O THR B 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 39 through 42 removed outlier: 4.058A pdb=" N GLU C 121 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASP C 116 " --> pdb=" O GLU C 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 39 through 41 removed outlier: 7.110A pdb=" N THR D 60 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N MET D 138 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE D 62 " --> pdb=" O MET D 138 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N GLN D 140 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ILE D 64 " --> pdb=" O GLN D 140 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 39 through 44 removed outlier: 6.800A pdb=" N THR E 60 " --> pdb=" O VAL E 136 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N MET E 138 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE E 62 " --> pdb=" O MET E 138 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N GLN E 140 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ILE E 64 " --> pdb=" O GLN E 140 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 6 through 10 removed outlier: 3.619A pdb=" N SER H 24 " --> pdb=" O SER H 10 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 13 through 14 removed outlier: 6.426A pdb=" N GLY H 13 " --> pdb=" O THR H 130 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N SER H 36 " --> pdb=" O SER H 102 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 13 through 14 removed outlier: 6.426A pdb=" N GLY H 13 " --> pdb=" O THR H 130 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR H 122 " --> pdb=" O ARG H 101 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N PHE H 103 " --> pdb=" O MET H 120 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N MET H 120 " --> pdb=" O PHE H 103 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 106 through 107 removed outlier: 3.709A pdb=" N TYR H 114 " --> pdb=" O LYS H 107 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 5 through 8 removed outlier: 3.781A pdb=" N THR L 73 " --> pdb=" O SER L 66 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 11 through 14 removed outlier: 3.579A pdb=" N LEU L 12 " --> pdb=" O LYS L 104 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLU L 106 " --> pdb=" O LEU L 12 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ALA L 14 " --> pdb=" O GLU L 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'L' and resid 54 through 55 removed outlier: 3.522A pdb=" N TYR L 50 " --> pdb=" O SER L 54 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 949 hydrogen bonds defined for protein. 2727 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.80 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5076 1.34 - 1.46: 3235 1.46 - 1.58: 8178 1.58 - 1.70: 0 1.70 - 1.82: 109 Bond restraints: 16598 Sorted by residual: bond pdb=" CA ARG D 202 " pdb=" CB ARG D 202 " ideal model delta sigma weight residual 1.525 1.539 -0.015 8.30e-03 1.45e+04 3.09e+00 bond pdb=" C TYR E 327 " pdb=" N PRO E 328 " ideal model delta sigma weight residual 1.334 1.370 -0.036 2.34e-02 1.83e+03 2.32e+00 bond pdb=" CB PRO L 45 " pdb=" CG PRO L 45 " ideal model delta sigma weight residual 1.492 1.559 -0.067 5.00e-02 4.00e+02 1.78e+00 bond pdb=" CA TYR D 327 " pdb=" C TYR D 327 " ideal model delta sigma weight residual 1.532 1.523 0.009 6.50e-03 2.37e+04 1.78e+00 bond pdb=" C ASP A 148 " pdb=" N PRO A 149 " ideal model delta sigma weight residual 1.335 1.351 -0.016 1.30e-02 5.92e+03 1.55e+00 ... (remaining 16593 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 22212 2.71 - 5.41: 266 5.41 - 8.12: 25 8.12 - 10.82: 1 10.82 - 13.53: 1 Bond angle restraints: 22505 Sorted by residual: angle pdb=" C LEU C 321 " pdb=" CA LEU C 321 " pdb=" CB LEU C 321 " ideal model delta sigma weight residual 117.23 111.19 6.04 1.36e+00 5.41e-01 1.97e+01 angle pdb=" C LEU D 235 " pdb=" N TYR D 236 " pdb=" CA TYR D 236 " ideal model delta sigma weight residual 122.09 114.78 7.31 1.79e+00 3.12e-01 1.67e+01 angle pdb=" N VAL D 290 " pdb=" CA VAL D 290 " pdb=" C VAL D 290 " ideal model delta sigma weight residual 110.42 106.58 3.84 9.60e-01 1.09e+00 1.60e+01 angle pdb=" N VAL A 93 " pdb=" CA VAL A 93 " pdb=" C VAL A 93 " ideal model delta sigma weight residual 112.17 108.40 3.77 9.50e-01 1.11e+00 1.57e+01 angle pdb=" C LEU B 235 " pdb=" N TYR B 236 " pdb=" CA TYR B 236 " ideal model delta sigma weight residual 122.53 114.94 7.59 1.92e+00 2.71e-01 1.56e+01 ... (remaining 22500 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 8887 17.94 - 35.87: 888 35.87 - 53.81: 164 53.81 - 71.74: 27 71.74 - 89.68: 17 Dihedral angle restraints: 9983 sinusoidal: 4164 harmonic: 5819 Sorted by residual: dihedral pdb=" CB CYS H 25 " pdb=" SG CYS H 25 " pdb=" SG CYS H 99 " pdb=" CB CYS H 99 " ideal model delta sinusoidal sigma weight residual 93.00 39.00 54.00 1 1.00e+01 1.00e-02 3.96e+01 dihedral pdb=" CA ILE A 307 " pdb=" C ILE A 307 " pdb=" N ALA A 308 " pdb=" CA ALA A 308 " ideal model delta harmonic sigma weight residual 180.00 157.88 22.12 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA PHE B 315 " pdb=" C PHE B 315 " pdb=" N GLU B 316 " pdb=" CA GLU B 316 " ideal model delta harmonic sigma weight residual -180.00 -159.03 -20.97 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 9980 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1902 0.048 - 0.096: 527 0.096 - 0.145: 112 0.145 - 0.193: 9 0.193 - 0.241: 1 Chirality restraints: 2551 Sorted by residual: chirality pdb=" CA PRO L 45 " pdb=" N PRO L 45 " pdb=" C PRO L 45 " pdb=" CB PRO L 45 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CG LEU A 304 " pdb=" CB LEU A 304 " pdb=" CD1 LEU A 304 " pdb=" CD2 LEU A 304 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 7.59e-01 chirality pdb=" CB ILE D 296 " pdb=" CA ILE D 296 " pdb=" CG1 ILE D 296 " pdb=" CG2 ILE D 296 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.69e-01 ... (remaining 2548 not shown) Planarity restraints: 2816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA L 44 " 0.074 5.00e-02 4.00e+02 1.12e-01 2.01e+01 pdb=" N PRO L 45 " -0.194 5.00e-02 4.00e+02 pdb=" CA PRO L 45 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO L 45 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 306 " -0.028 2.00e-02 2.50e+03 2.28e-02 9.10e+00 pdb=" CG PHE E 306 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE E 306 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE E 306 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE E 306 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE E 306 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE E 306 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER L 8 " -0.038 5.00e-02 4.00e+02 5.84e-02 5.46e+00 pdb=" N PRO L 9 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO L 9 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO L 9 " -0.030 5.00e-02 4.00e+02 ... (remaining 2813 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 201 2.66 - 3.22: 16161 3.22 - 3.78: 25581 3.78 - 4.34: 34069 4.34 - 4.90: 55918 Nonbonded interactions: 131930 Sorted by model distance: nonbonded pdb=" OE1 GLU D 186 " pdb=" OG SER E 7 " model vdw 2.100 3.040 nonbonded pdb=" O THR C 295 " pdb=" OG1 THR C 299 " model vdw 2.142 3.040 nonbonded pdb=" OE2 GLU E 30 " pdb=" NZ LYS E 43 " model vdw 2.164 3.120 nonbonded pdb=" ND2 ASN B 314 " pdb=" OD1 ASN C 314 " model vdw 2.201 3.120 nonbonded pdb=" OG SER A 35 " pdb=" O GLU A 38 " model vdw 2.216 3.040 ... (remaining 131925 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 17 through 351) selection = (chain 'B' and resid 17 through 351) selection = (chain 'C' and resid 17 through 351) selection = (chain 'D' and resid 17 through 351) selection = (chain 'E' and resid 17 through 351) } 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=0.49 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.550 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 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 : 0.004 0.067 16600 Z= 0.166 Angle : 0.706 13.530 22509 Z= 0.378 Chirality : 0.045 0.241 2551 Planarity : 0.006 0.112 2816 Dihedral : 14.696 89.679 6219 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.39 % Favored : 94.25 % Rotamer: Outliers : 0.05 % Allowed : 0.38 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.19), residues: 1947 helix: 1.22 (0.17), residues: 929 sheet: -0.66 (0.28), residues: 345 loop : -2.09 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 5 TYR 0.023 0.001 TYR A 236 PHE 0.052 0.002 PHE E 306 TRP 0.023 0.002 TRP B 350 HIS 0.004 0.001 HIS C 212 Details of bonding type rmsd covalent geometry : bond 0.00372 (16598) covalent geometry : angle 0.70552 (22505) SS BOND : bond 0.00541 ( 2) SS BOND : angle 1.23855 ( 4) hydrogen bonds : bond 0.13366 ( 945) hydrogen bonds : angle 6.33738 ( 2727) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 432 time to evaluate : 0.584 Fit side-chains REVERT: A 100 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8428 (mt-10) REVERT: A 174 ILE cc_start: 0.8583 (mm) cc_final: 0.8382 (mm) REVERT: A 186 GLU cc_start: 0.6192 (mm-30) cc_final: 0.5783 (mm-30) REVERT: A 286 LYS cc_start: 0.7954 (tptt) cc_final: 0.7091 (tmtt) REVERT: A 317 TYR cc_start: 0.5759 (t80) cc_final: 0.5398 (t80) REVERT: A 334 MET cc_start: 0.5044 (mmp) cc_final: 0.4813 (tpp) REVERT: B 96 ARG cc_start: 0.8286 (ttp-110) cc_final: 0.7468 (ttm170) REVERT: B 155 ARG cc_start: 0.7445 (mmm160) cc_final: 0.7027 (tpp80) REVERT: B 186 GLU cc_start: 0.7554 (tm-30) cc_final: 0.6891 (tm-30) REVERT: B 197 GLU cc_start: 0.6798 (mm-30) cc_final: 0.6552 (mm-30) REVERT: B 313 MET cc_start: 0.5462 (mtp) cc_final: 0.5132 (mtp) REVERT: B 318 MET cc_start: 0.0792 (tpt) cc_final: -0.0651 (tpt) REVERT: C 22 LYS cc_start: 0.7524 (pttm) cc_final: 0.7301 (pttm) REVERT: C 35 SER cc_start: 0.8753 (t) cc_final: 0.8422 (t) REVERT: D 23 TYR cc_start: 0.7675 (m-10) cc_final: 0.7364 (m-80) REVERT: D 163 LYS cc_start: 0.8110 (mtpp) cc_final: 0.7887 (mtmt) REVERT: D 318 MET cc_start: 0.5639 (ttp) cc_final: 0.4553 (ttt) REVERT: E 104 ASN cc_start: 0.8103 (t0) cc_final: 0.7716 (t0) REVERT: E 174 ILE cc_start: 0.8047 (mm) cc_final: 0.7841 (mm) REVERT: H 46 LYS cc_start: 0.6357 (mmmt) cc_final: 0.6019 (mmmm) REVERT: H 66 SER cc_start: 0.7174 (p) cc_final: 0.6410 (m) REVERT: H 83 TYR cc_start: 0.6849 (m-10) cc_final: 0.6378 (m-10) outliers start: 1 outliers final: 1 residues processed: 433 average time/residue: 0.1184 time to fit residues: 75.8255 Evaluate side-chains 372 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 371 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 98 optimal weight: 0.3980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 GLN A 288 ASN ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 ASN ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.177797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.152759 restraints weight = 21817.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.157293 restraints weight = 11100.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.160233 restraints weight = 6958.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.162409 restraints weight = 5007.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.163828 restraints weight = 3910.235| |-----------------------------------------------------------------------------| r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3716 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3716 r_free = 0.3716 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3714 r_free = 0.3714 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3714 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16600 Z= 0.181 Angle : 0.649 9.604 22509 Z= 0.338 Chirality : 0.045 0.243 2551 Planarity : 0.005 0.114 2816 Dihedral : 4.748 31.796 2181 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.75 % Favored : 93.94 % Rotamer: Outliers : 2.03 % Allowed : 10.64 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.19), residues: 1947 helix: 1.60 (0.17), residues: 939 sheet: -0.70 (0.28), residues: 339 loop : -2.09 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 40 TYR 0.023 0.002 TYR E 236 PHE 0.039 0.002 PHE C 301 TRP 0.025 0.001 TRP B 350 HIS 0.005 0.001 HIS C 83 Details of bonding type rmsd covalent geometry : bond 0.00421 (16598) covalent geometry : angle 0.64848 (22505) SS BOND : bond 0.00530 ( 2) SS BOND : angle 2.18915 ( 4) hydrogen bonds : bond 0.04642 ( 945) hydrogen bonds : angle 4.98385 ( 2727) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 406 time to evaluate : 0.631 Fit side-chains revert: symmetry clash REVERT: A 174 ILE cc_start: 0.8514 (mm) cc_final: 0.8281 (mm) REVERT: A 186 GLU cc_start: 0.6193 (mm-30) cc_final: 0.5804 (mm-30) REVERT: A 237 ARG cc_start: 0.6295 (mmm-85) cc_final: 0.5922 (mtm-85) REVERT: A 286 LYS cc_start: 0.7823 (tptt) cc_final: 0.6885 (tmtt) REVERT: B 96 ARG cc_start: 0.8399 (ttp-110) cc_final: 0.7480 (ttp-170) REVERT: B 130 ILE cc_start: 0.8503 (mt) cc_final: 0.8299 (mt) REVERT: B 155 ARG cc_start: 0.7375 (mmm160) cc_final: 0.6944 (tpp80) REVERT: B 186 GLU cc_start: 0.7412 (tm-30) cc_final: 0.6898 (tm-30) REVERT: B 187 LYS cc_start: 0.7614 (tttt) cc_final: 0.7210 (tttt) REVERT: B 197 GLU cc_start: 0.6812 (mm-30) cc_final: 0.6467 (mm-30) REVERT: B 313 MET cc_start: 0.6196 (mtp) cc_final: 0.5576 (mtp) REVERT: B 318 MET cc_start: 0.0818 (tpt) cc_final: -0.0803 (tpt) REVERT: C 75 ARG cc_start: 0.8024 (tpp-160) cc_final: 0.7686 (tpp-160) REVERT: C 291 MET cc_start: 0.7547 (tpp) cc_final: 0.7117 (tpp) REVERT: C 327 TYR cc_start: 0.5647 (OUTLIER) cc_final: 0.5022 (t80) REVERT: D 41 GLU cc_start: 0.6276 (mt-10) cc_final: 0.6075 (tt0) REVERT: D 163 LYS cc_start: 0.8133 (mtpp) cc_final: 0.7841 (mtmm) REVERT: D 318 MET cc_start: 0.5699 (ttp) cc_final: 0.4590 (ttt) REVERT: E 104 ASN cc_start: 0.8205 (t0) cc_final: 0.7873 (t0) REVERT: E 125 GLU cc_start: 0.7712 (tt0) cc_final: 0.7487 (tt0) REVERT: E 162 ARG cc_start: 0.6946 (tpt90) cc_final: 0.6636 (tpt90) REVERT: E 174 ILE cc_start: 0.8009 (mm) cc_final: 0.7747 (mm) REVERT: E 252 ARG cc_start: 0.7321 (mtp85) cc_final: 0.7114 (mtp85) REVERT: H 46 LYS cc_start: 0.6766 (mmmt) cc_final: 0.6377 (mmmm) REVERT: H 66 SER cc_start: 0.7188 (p) cc_final: 0.6499 (m) outliers start: 37 outliers final: 30 residues processed: 418 average time/residue: 0.1238 time to fit residues: 77.3888 Evaluate side-chains 412 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 381 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 327 TYR Chi-restraints excluded: chain D residue 126 GLN Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain L residue 21 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 70 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 3 optimal weight: 0.0370 chunk 118 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 163 optimal weight: 0.9980 chunk 139 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 ASN C 134 ASN D 95 GLN L 7 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.175444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.151300 restraints weight = 21974.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.155497 restraints weight = 11744.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.158304 restraints weight = 7573.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.160112 restraints weight = 5535.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.161495 restraints weight = 4422.288| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3689 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3689 r_free = 0.3689 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3689 r_free = 0.3689 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3689 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16600 Z= 0.176 Angle : 0.636 8.868 22509 Z= 0.328 Chirality : 0.044 0.245 2551 Planarity : 0.005 0.115 2816 Dihedral : 4.696 32.101 2181 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.06 % Favored : 93.68 % Rotamer: Outliers : 2.63 % Allowed : 15.85 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.19), residues: 1947 helix: 1.70 (0.17), residues: 933 sheet: -0.68 (0.28), residues: 348 loop : -2.10 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 40 TYR 0.020 0.001 TYR E 236 PHE 0.026 0.002 PHE E 306 TRP 0.024 0.001 TRP B 350 HIS 0.006 0.001 HIS C 83 Details of bonding type rmsd covalent geometry : bond 0.00417 (16598) covalent geometry : angle 0.63555 (22505) SS BOND : bond 0.00380 ( 2) SS BOND : angle 1.77972 ( 4) hydrogen bonds : bond 0.04389 ( 945) hydrogen bonds : angle 4.83561 ( 2727) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 405 time to evaluate : 0.635 Fit side-chains REVERT: A 138 MET cc_start: 0.6574 (mtm) cc_final: 0.6323 (mtm) REVERT: A 174 ILE cc_start: 0.8431 (mm) cc_final: 0.8204 (mm) REVERT: A 186 GLU cc_start: 0.6300 (mm-30) cc_final: 0.5645 (mm-30) REVERT: A 237 ARG cc_start: 0.6248 (mmm-85) cc_final: 0.5932 (mtm-85) REVERT: A 247 THR cc_start: 0.8158 (OUTLIER) cc_final: 0.7888 (m) REVERT: A 286 LYS cc_start: 0.7918 (tptt) cc_final: 0.6973 (tmtt) REVERT: A 291 MET cc_start: 0.7937 (tpp) cc_final: 0.7666 (tpt) REVERT: A 318 MET cc_start: 0.5049 (mtt) cc_final: 0.4664 (mpp) REVERT: B 96 ARG cc_start: 0.8425 (ttp-110) cc_final: 0.7498 (ttp-170) REVERT: B 155 ARG cc_start: 0.7376 (mmm160) cc_final: 0.6963 (tpp80) REVERT: B 186 GLU cc_start: 0.7390 (tm-30) cc_final: 0.6863 (tm-30) REVERT: B 187 LYS cc_start: 0.7646 (tttt) cc_final: 0.7271 (tttt) REVERT: B 197 GLU cc_start: 0.6821 (mm-30) cc_final: 0.6489 (mm-30) REVERT: B 275 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7086 (mm) REVERT: B 313 MET cc_start: 0.6386 (mtp) cc_final: 0.5996 (mtp) REVERT: B 318 MET cc_start: 0.0344 (tpt) cc_final: -0.1239 (tpt) REVERT: C 225 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8565 (tt) REVERT: C 291 MET cc_start: 0.7754 (tpp) cc_final: 0.7440 (tpp) REVERT: C 327 TYR cc_start: 0.5643 (OUTLIER) cc_final: 0.5002 (t80) REVERT: D 41 GLU cc_start: 0.6370 (mt-10) cc_final: 0.6152 (tt0) REVERT: D 163 LYS cc_start: 0.8139 (mtpp) cc_final: 0.7824 (mtmm) REVERT: D 318 MET cc_start: 0.5692 (ttp) cc_final: 0.4623 (ttt) REVERT: E 146 VAL cc_start: 0.8475 (m) cc_final: 0.8075 (p) REVERT: E 252 ARG cc_start: 0.7354 (mtp85) cc_final: 0.6846 (ttm-80) REVERT: E 313 MET cc_start: 0.5218 (tpp) cc_final: 0.4717 (tpp) REVERT: H 46 LYS cc_start: 0.6670 (mmmt) cc_final: 0.6256 (mmmm) REVERT: H 66 SER cc_start: 0.7240 (p) cc_final: 0.6552 (m) REVERT: L 2 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.7541 (t0) REVERT: L 91 GLN cc_start: 0.8192 (pp30) cc_final: 0.7801 (pp30) outliers start: 48 outliers final: 36 residues processed: 419 average time/residue: 0.1224 time to fit residues: 77.3206 Evaluate side-chains 423 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 382 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 257 HIS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 327 TYR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain L residue 2 ASP Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 21 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 118 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 134 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.172711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.148442 restraints weight = 22016.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.152558 restraints weight = 11831.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.155345 restraints weight = 7705.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.157242 restraints weight = 5672.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.158556 restraints weight = 4526.045| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3655 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3655 r_free = 0.3655 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3655 r_free = 0.3655 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3655 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 16600 Z= 0.203 Angle : 0.650 8.865 22509 Z= 0.336 Chirality : 0.045 0.248 2551 Planarity : 0.005 0.116 2816 Dihedral : 4.741 31.949 2181 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.42 % Favored : 93.32 % Rotamer: Outliers : 3.73 % Allowed : 17.72 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.19), residues: 1947 helix: 1.65 (0.17), residues: 933 sheet: -0.66 (0.28), residues: 342 loop : -2.13 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 40 TYR 0.020 0.002 TYR D 23 PHE 0.023 0.002 PHE E 306 TRP 0.026 0.001 TRP B 350 HIS 0.005 0.001 HIS C 83 Details of bonding type rmsd covalent geometry : bond 0.00482 (16598) covalent geometry : angle 0.64969 (22505) SS BOND : bond 0.00568 ( 2) SS BOND : angle 1.49286 ( 4) hydrogen bonds : bond 0.04435 ( 945) hydrogen bonds : angle 4.80734 ( 2727) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 404 time to evaluate : 0.652 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7330 (tp30) cc_final: 0.7125 (tp30) REVERT: A 173 LEU cc_start: 0.7662 (mt) cc_final: 0.7461 (mt) REVERT: A 174 ILE cc_start: 0.8438 (mm) cc_final: 0.8194 (mm) REVERT: A 186 GLU cc_start: 0.6203 (mm-30) cc_final: 0.5732 (mm-30) REVERT: A 237 ARG cc_start: 0.6227 (mmm-85) cc_final: 0.5919 (mtm-85) REVERT: A 247 THR cc_start: 0.8284 (OUTLIER) cc_final: 0.8029 (m) REVERT: A 286 LYS cc_start: 0.7969 (tptt) cc_final: 0.7024 (tmtt) REVERT: A 317 TYR cc_start: 0.5679 (t80) cc_final: 0.5412 (t80) REVERT: A 334 MET cc_start: 0.6148 (tpp) cc_final: 0.5907 (mmt) REVERT: B 96 ARG cc_start: 0.8437 (ttp-110) cc_final: 0.7522 (ttp-170) REVERT: B 155 ARG cc_start: 0.7420 (mmm160) cc_final: 0.6977 (tpp80) REVERT: B 163 LYS cc_start: 0.7714 (mttm) cc_final: 0.7426 (mttm) REVERT: B 186 GLU cc_start: 0.7389 (tm-30) cc_final: 0.6858 (tm-30) REVERT: B 187 LYS cc_start: 0.7671 (tttt) cc_final: 0.7270 (tttt) REVERT: B 197 GLU cc_start: 0.6755 (mm-30) cc_final: 0.6495 (mm-30) REVERT: B 275 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7094 (mm) REVERT: B 313 MET cc_start: 0.6598 (mtp) cc_final: 0.6302 (mtp) REVERT: B 318 MET cc_start: 0.0594 (tpt) cc_final: -0.1137 (tpt) REVERT: C 23 TYR cc_start: 0.6849 (m-80) cc_final: 0.6376 (m-80) REVERT: C 225 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8645 (tt) REVERT: C 244 GLU cc_start: 0.7684 (mp0) cc_final: 0.7461 (mp0) REVERT: C 263 ASP cc_start: 0.7510 (m-30) cc_final: 0.7170 (m-30) REVERT: C 291 MET cc_start: 0.7956 (tpp) cc_final: 0.7713 (tpp) REVERT: C 318 MET cc_start: 0.3479 (mmm) cc_final: 0.3118 (mmm) REVERT: C 327 TYR cc_start: 0.5610 (OUTLIER) cc_final: 0.4875 (t80) REVERT: D 23 TYR cc_start: 0.7999 (m-80) cc_final: 0.7749 (m-80) REVERT: D 41 GLU cc_start: 0.6378 (mt-10) cc_final: 0.6109 (tt0) REVERT: D 121 GLU cc_start: 0.7074 (pm20) cc_final: 0.6734 (pm20) REVERT: D 154 ILE cc_start: 0.8931 (mt) cc_final: 0.8724 (mm) REVERT: D 163 LYS cc_start: 0.8171 (mtpp) cc_final: 0.7815 (mtmt) REVERT: D 318 MET cc_start: 0.5669 (ttp) cc_final: 0.4817 (ttt) REVERT: E 90 ILE cc_start: 0.8197 (mm) cc_final: 0.7933 (mm) REVERT: E 131 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.7112 (tt) REVERT: E 174 ILE cc_start: 0.8042 (mm) cc_final: 0.7760 (mm) REVERT: E 177 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8612 (mm) REVERT: E 252 ARG cc_start: 0.7375 (mtp85) cc_final: 0.6877 (ttm-80) REVERT: H 46 LYS cc_start: 0.6516 (mmmt) cc_final: 0.6064 (mmmm) REVERT: H 66 SER cc_start: 0.7229 (p) cc_final: 0.6562 (m) REVERT: L 2 ASP cc_start: 0.7846 (OUTLIER) cc_final: 0.7566 (t0) outliers start: 68 outliers final: 46 residues processed: 431 average time/residue: 0.1250 time to fit residues: 80.9284 Evaluate side-chains 442 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 389 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 257 HIS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 291 MET Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 101 PHE Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 327 TYR Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 147 PHE Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain L residue 2 ASP Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 73 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 154 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 7 optimal weight: 0.2980 chunk 107 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 78 optimal weight: 0.0770 chunk 174 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 chunk 183 optimal weight: 1.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 134 ASN L 7 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.175550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.150779 restraints weight = 21978.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.155001 restraints weight = 11872.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.157877 restraints weight = 7745.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.159781 restraints weight = 5711.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.161026 restraints weight = 4580.316| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3685 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3685 r_free = 0.3685 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3685 r_free = 0.3685 target_work(ls_wunit_k1) = 0.161 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3685 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 16600 Z= 0.151 Angle : 0.625 8.950 22509 Z= 0.321 Chirality : 0.045 0.259 2551 Planarity : 0.005 0.116 2816 Dihedral : 4.685 32.145 2181 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.75 % Favored : 94.04 % Rotamer: Outliers : 3.73 % Allowed : 19.25 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.19), residues: 1947 helix: 1.73 (0.17), residues: 939 sheet: -0.68 (0.28), residues: 342 loop : -2.11 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 40 TYR 0.023 0.001 TYR C 19 PHE 0.023 0.002 PHE C 301 TRP 0.022 0.001 TRP B 350 HIS 0.005 0.001 HIS C 83 Details of bonding type rmsd covalent geometry : bond 0.00353 (16598) covalent geometry : angle 0.62387 (22505) SS BOND : bond 0.00673 ( 2) SS BOND : angle 2.33163 ( 4) hydrogen bonds : bond 0.04161 ( 945) hydrogen bonds : angle 4.70687 ( 2727) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 400 time to evaluate : 0.559 Fit side-chains REVERT: A 174 ILE cc_start: 0.8386 (mm) cc_final: 0.8073 (mm) REVERT: A 186 GLU cc_start: 0.6176 (mm-30) cc_final: 0.5725 (mm-30) REVERT: A 237 ARG cc_start: 0.6188 (mmm-85) cc_final: 0.5907 (mtm-85) REVERT: A 247 THR cc_start: 0.8263 (OUTLIER) cc_final: 0.7987 (m) REVERT: A 286 LYS cc_start: 0.7969 (tptt) cc_final: 0.7039 (tmtt) REVERT: A 291 MET cc_start: 0.8150 (tpt) cc_final: 0.7917 (tpt) REVERT: A 317 TYR cc_start: 0.5689 (t80) cc_final: 0.5456 (t80) REVERT: B 96 ARG cc_start: 0.8382 (ttp-110) cc_final: 0.7460 (ttm170) REVERT: B 100 GLU cc_start: 0.7211 (mt-10) cc_final: 0.6966 (mt-10) REVERT: B 154 ILE cc_start: 0.8326 (mt) cc_final: 0.8087 (mt) REVERT: B 155 ARG cc_start: 0.7364 (mmm160) cc_final: 0.6960 (tpp80) REVERT: B 163 LYS cc_start: 0.7702 (mttm) cc_final: 0.7395 (mttm) REVERT: B 186 GLU cc_start: 0.7358 (tm-30) cc_final: 0.6817 (tm-30) REVERT: B 187 LYS cc_start: 0.7622 (tttt) cc_final: 0.7247 (tttt) REVERT: B 197 GLU cc_start: 0.6795 (mm-30) cc_final: 0.6478 (mm-30) REVERT: B 245 LYS cc_start: 0.7220 (mppt) cc_final: 0.6919 (mtmm) REVERT: B 275 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7036 (mm) REVERT: B 313 MET cc_start: 0.6501 (mtp) cc_final: 0.6259 (mtp) REVERT: B 318 MET cc_start: 0.0531 (tpt) cc_final: -0.1177 (tpt) REVERT: C 225 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8583 (tt) REVERT: C 232 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8151 (mm) REVERT: C 244 GLU cc_start: 0.7633 (mp0) cc_final: 0.7400 (mp0) REVERT: C 291 MET cc_start: 0.7805 (tpp) cc_final: 0.7407 (tpp) REVERT: C 318 MET cc_start: 0.3534 (mmm) cc_final: 0.3099 (mmm) REVERT: C 327 TYR cc_start: 0.5589 (OUTLIER) cc_final: 0.4869 (t80) REVERT: D 87 LEU cc_start: 0.8476 (mt) cc_final: 0.8260 (mp) REVERT: D 98 LYS cc_start: 0.8195 (pttt) cc_final: 0.7860 (pttt) REVERT: D 121 GLU cc_start: 0.7022 (pm20) cc_final: 0.6578 (pm20) REVERT: D 163 LYS cc_start: 0.8158 (mtpp) cc_final: 0.7792 (mtmt) REVERT: D 181 TYR cc_start: 0.8597 (m-80) cc_final: 0.8187 (m-80) REVERT: D 184 LEU cc_start: 0.8723 (tt) cc_final: 0.8494 (tt) REVERT: D 318 MET cc_start: 0.5647 (ttp) cc_final: 0.4880 (ttt) REVERT: E 6 LEU cc_start: 0.7172 (pt) cc_final: 0.6898 (pt) REVERT: E 51 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.6907 (mm) REVERT: E 174 ILE cc_start: 0.8067 (mm) cc_final: 0.7799 (mm) REVERT: E 177 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8590 (mm) REVERT: E 252 ARG cc_start: 0.7285 (mtp85) cc_final: 0.6903 (ttm-80) REVERT: H 46 LYS cc_start: 0.6448 (mmmt) cc_final: 0.6014 (mmmm) REVERT: H 66 SER cc_start: 0.7102 (p) cc_final: 0.6412 (m) REVERT: H 114 TYR cc_start: 0.8795 (t80) cc_final: 0.8479 (t80) REVERT: H 117 TYR cc_start: 0.8986 (m-80) cc_final: 0.8605 (m-80) REVERT: L 2 ASP cc_start: 0.7939 (OUTLIER) cc_final: 0.7629 (t0) outliers start: 68 outliers final: 47 residues processed: 429 average time/residue: 0.1237 time to fit residues: 79.6491 Evaluate side-chains 438 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 383 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 257 HIS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 101 PHE Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 295 THR Chi-restraints excluded: chain C residue 327 TYR Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 147 PHE Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain L residue 2 ASP Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 21 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 83 optimal weight: 0.9990 chunk 186 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 111 optimal weight: 0.5980 chunk 126 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 150 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 30 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 285 ASN C 134 ASN E 212 HIS L 7 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.174564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.149610 restraints weight = 22068.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.153846 restraints weight = 11981.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.156679 restraints weight = 7840.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.158582 restraints weight = 5806.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.159960 restraints weight = 4657.084| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3675 r_free = 0.3675 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3675 r_free = 0.3675 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 16600 Z= 0.169 Angle : 0.632 8.547 22509 Z= 0.325 Chirality : 0.045 0.257 2551 Planarity : 0.005 0.117 2816 Dihedral : 4.673 32.783 2181 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.37 % Favored : 93.43 % Rotamer: Outliers : 4.06 % Allowed : 19.80 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.19), residues: 1947 helix: 1.72 (0.17), residues: 938 sheet: -0.65 (0.28), residues: 341 loop : -2.14 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 162 TYR 0.017 0.001 TYR C 19 PHE 0.021 0.002 PHE E 306 TRP 0.021 0.001 TRP B 350 HIS 0.006 0.001 HIS C 83 Details of bonding type rmsd covalent geometry : bond 0.00405 (16598) covalent geometry : angle 0.63114 (22505) SS BOND : bond 0.00496 ( 2) SS BOND : angle 2.24901 ( 4) hydrogen bonds : bond 0.04185 ( 945) hydrogen bonds : angle 4.67898 ( 2727) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 382 time to evaluate : 0.459 Fit side-chains REVERT: A 186 GLU cc_start: 0.6184 (mm-30) cc_final: 0.5725 (mm-30) REVERT: A 237 ARG cc_start: 0.6197 (mmm-85) cc_final: 0.5936 (mtm-85) REVERT: A 247 THR cc_start: 0.8282 (OUTLIER) cc_final: 0.8013 (m) REVERT: A 286 LYS cc_start: 0.7982 (tptt) cc_final: 0.7070 (tmtt) REVERT: A 291 MET cc_start: 0.8112 (tpt) cc_final: 0.7877 (tpt) REVERT: B 100 GLU cc_start: 0.7306 (mt-10) cc_final: 0.6934 (mt-10) REVERT: B 155 ARG cc_start: 0.7347 (mmm160) cc_final: 0.6907 (tpp80) REVERT: B 158 ARG cc_start: 0.8136 (ptp-170) cc_final: 0.7861 (ptp90) REVERT: B 163 LYS cc_start: 0.7732 (mttm) cc_final: 0.7429 (mttm) REVERT: B 186 GLU cc_start: 0.7327 (tm-30) cc_final: 0.6771 (tm-30) REVERT: B 187 LYS cc_start: 0.7610 (tttt) cc_final: 0.7223 (tttt) REVERT: B 197 GLU cc_start: 0.6806 (mm-30) cc_final: 0.6490 (mm-30) REVERT: B 245 LYS cc_start: 0.7207 (mppt) cc_final: 0.6905 (mtmm) REVERT: B 275 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7110 (mm) REVERT: B 313 MET cc_start: 0.6420 (mtp) cc_final: 0.6210 (mtp) REVERT: B 318 MET cc_start: 0.0557 (tpt) cc_final: -0.1186 (tpt) REVERT: C 23 TYR cc_start: 0.6717 (m-80) cc_final: 0.6342 (m-10) REVERT: C 134 ASN cc_start: 0.8401 (OUTLIER) cc_final: 0.8186 (p0) REVERT: C 190 ASP cc_start: 0.7467 (OUTLIER) cc_final: 0.7005 (m-30) REVERT: C 225 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8578 (tt) REVERT: C 232 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8227 (mm) REVERT: C 291 MET cc_start: 0.7731 (tpp) cc_final: 0.7424 (tpp) REVERT: C 318 MET cc_start: 0.3779 (mmm) cc_final: 0.3429 (mmm) REVERT: C 327 TYR cc_start: 0.5616 (OUTLIER) cc_final: 0.4865 (t80) REVERT: D 121 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.6608 (pm20) REVERT: D 163 LYS cc_start: 0.8111 (mtpp) cc_final: 0.7731 (mtmm) REVERT: D 181 TYR cc_start: 0.8606 (m-80) cc_final: 0.8233 (m-80) REVERT: D 318 MET cc_start: 0.5674 (ttp) cc_final: 0.4905 (ttt) REVERT: E 6 LEU cc_start: 0.7161 (pt) cc_final: 0.6882 (pt) REVERT: E 51 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.6939 (mm) REVERT: E 174 ILE cc_start: 0.8134 (mm) cc_final: 0.7898 (mm) REVERT: E 177 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8604 (mm) REVERT: E 252 ARG cc_start: 0.7263 (mtp85) cc_final: 0.6957 (ttm-80) REVERT: H 66 SER cc_start: 0.7162 (p) cc_final: 0.6483 (m) REVERT: H 117 TYR cc_start: 0.9024 (m-80) cc_final: 0.8610 (m-80) REVERT: L 2 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7646 (t0) outliers start: 74 outliers final: 53 residues processed: 415 average time/residue: 0.1207 time to fit residues: 75.6203 Evaluate side-chains 439 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 375 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 257 HIS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 101 PHE Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 327 TYR Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 147 PHE Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain L residue 2 ASP Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 73 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 160 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 156 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 145 optimal weight: 0.7980 chunk 179 optimal weight: 0.8980 chunk 48 optimal weight: 0.2980 chunk 137 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 134 ASN L 7 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.173541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.148581 restraints weight = 21933.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.152795 restraints weight = 11944.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.155590 restraints weight = 7848.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.157561 restraints weight = 5811.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.158862 restraints weight = 4663.756| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3665 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3665 r_free = 0.3665 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3665 r_free = 0.3665 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3665 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16600 Z= 0.176 Angle : 0.642 8.804 22509 Z= 0.331 Chirality : 0.045 0.246 2551 Planarity : 0.005 0.117 2816 Dihedral : 4.696 32.648 2181 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.16 % Favored : 93.53 % Rotamer: Outliers : 4.50 % Allowed : 19.69 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.19), residues: 1947 helix: 1.71 (0.17), residues: 938 sheet: -0.68 (0.28), residues: 335 loop : -2.12 (0.22), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 19 TYR 0.018 0.001 TYR D 23 PHE 0.024 0.002 PHE C 301 TRP 0.022 0.001 TRP B 350 HIS 0.006 0.001 HIS C 83 Details of bonding type rmsd covalent geometry : bond 0.00418 (16598) covalent geometry : angle 0.64167 (22505) SS BOND : bond 0.00444 ( 2) SS BOND : angle 2.22320 ( 4) hydrogen bonds : bond 0.04207 ( 945) hydrogen bonds : angle 4.67677 ( 2727) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 392 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 PHE cc_start: 0.6804 (t80) cc_final: 0.6217 (t80) REVERT: A 174 ILE cc_start: 0.8429 (mm) cc_final: 0.8163 (mm) REVERT: A 186 GLU cc_start: 0.6158 (mm-30) cc_final: 0.5715 (mm-30) REVERT: A 237 ARG cc_start: 0.6137 (mmm-85) cc_final: 0.5930 (mtm-85) REVERT: A 247 THR cc_start: 0.8389 (OUTLIER) cc_final: 0.8138 (m) REVERT: A 286 LYS cc_start: 0.8004 (tptt) cc_final: 0.7091 (tmtt) REVERT: B 24 ARG cc_start: 0.7912 (mmt90) cc_final: 0.7656 (mmt90) REVERT: B 96 ARG cc_start: 0.8367 (ttp-110) cc_final: 0.7357 (ttm170) REVERT: B 155 ARG cc_start: 0.7358 (mmm160) cc_final: 0.6917 (tpp80) REVERT: B 158 ARG cc_start: 0.8136 (ptp-170) cc_final: 0.7902 (ptp90) REVERT: B 163 LYS cc_start: 0.7630 (mttm) cc_final: 0.7341 (mttm) REVERT: B 186 GLU cc_start: 0.7326 (tm-30) cc_final: 0.7096 (tm-30) REVERT: B 197 GLU cc_start: 0.6817 (mm-30) cc_final: 0.6529 (mm-30) REVERT: B 245 LYS cc_start: 0.7326 (mppt) cc_final: 0.7013 (mtmm) REVERT: B 275 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7126 (mm) REVERT: B 313 MET cc_start: 0.6425 (mtp) cc_final: 0.6204 (mtp) REVERT: B 318 MET cc_start: 0.0604 (tpt) cc_final: -0.1177 (tpt) REVERT: C 23 TYR cc_start: 0.6723 (m-80) cc_final: 0.6478 (m-10) REVERT: C 26 ASP cc_start: 0.7550 (p0) cc_final: 0.7160 (p0) REVERT: C 190 ASP cc_start: 0.7440 (OUTLIER) cc_final: 0.6951 (m-30) REVERT: C 225 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8608 (tt) REVERT: C 232 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8257 (mm) REVERT: C 244 GLU cc_start: 0.7623 (mp0) cc_final: 0.7395 (mp0) REVERT: C 263 ASP cc_start: 0.7521 (m-30) cc_final: 0.7119 (m-30) REVERT: C 291 MET cc_start: 0.7790 (tpp) cc_final: 0.7528 (tpp) REVERT: C 318 MET cc_start: 0.3471 (mmm) cc_final: 0.3215 (mmm) REVERT: C 327 TYR cc_start: 0.5584 (OUTLIER) cc_final: 0.4859 (t80) REVERT: D 42 PHE cc_start: 0.7559 (t80) cc_final: 0.7322 (t80) REVERT: D 98 LYS cc_start: 0.8287 (pttt) cc_final: 0.7846 (pttt) REVERT: D 121 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6668 (pm20) REVERT: D 134 ASN cc_start: 0.7790 (OUTLIER) cc_final: 0.7461 (t0) REVERT: D 163 LYS cc_start: 0.8104 (mtpp) cc_final: 0.7725 (mtmm) REVERT: D 318 MET cc_start: 0.5669 (ttp) cc_final: 0.5179 (ttt) REVERT: E 6 LEU cc_start: 0.6988 (pt) cc_final: 0.6666 (pt) REVERT: E 51 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.6948 (mm) REVERT: E 174 ILE cc_start: 0.8158 (mm) cc_final: 0.7912 (mm) REVERT: E 177 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8562 (mm) REVERT: E 252 ARG cc_start: 0.7295 (mtp85) cc_final: 0.7001 (ttm-80) REVERT: H 66 SER cc_start: 0.7252 (p) cc_final: 0.6585 (m) REVERT: H 117 TYR cc_start: 0.9047 (m-80) cc_final: 0.8619 (m-80) REVERT: L 2 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7626 (t0) outliers start: 82 outliers final: 57 residues processed: 433 average time/residue: 0.1208 time to fit residues: 78.9191 Evaluate side-chains 457 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 389 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 257 HIS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 101 PHE Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 327 TYR Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 147 PHE Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain L residue 2 ASP Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 73 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 77 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 33 optimal weight: 0.0030 chunk 112 optimal weight: 0.0040 chunk 172 optimal weight: 0.0570 chunk 179 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 119 optimal weight: 0.6980 chunk 144 optimal weight: 0.0970 chunk 56 optimal weight: 0.0870 chunk 62 optimal weight: 0.0060 overall best weight: 0.0314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.179675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.154873 restraints weight = 21852.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.159193 restraints weight = 11775.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.162093 restraints weight = 7667.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.163916 restraints weight = 5642.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.165380 restraints weight = 4534.012| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3734 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3734 r_free = 0.3734 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3734 r_free = 0.3734 target_work(ls_wunit_k1) = 0.166 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 16600 Z= 0.132 Angle : 0.639 14.641 22509 Z= 0.323 Chirality : 0.044 0.237 2551 Planarity : 0.005 0.116 2816 Dihedral : 4.560 30.933 2181 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.24 % Favored : 94.56 % Rotamer: Outliers : 3.84 % Allowed : 20.46 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.20), residues: 1947 helix: 1.93 (0.17), residues: 938 sheet: -0.58 (0.28), residues: 346 loop : -2.06 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 54 TYR 0.018 0.001 TYR C 19 PHE 0.024 0.001 PHE E 306 TRP 0.016 0.001 TRP B 350 HIS 0.005 0.001 HIS C 83 Details of bonding type rmsd covalent geometry : bond 0.00281 (16598) covalent geometry : angle 0.63870 (22505) SS BOND : bond 0.00349 ( 2) SS BOND : angle 2.00309 ( 4) hydrogen bonds : bond 0.03809 ( 945) hydrogen bonds : angle 4.55145 ( 2727) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 392 time to evaluate : 0.646 Fit side-chains revert: symmetry clash REVERT: A 97 PRO cc_start: 0.8756 (Cg_exo) cc_final: 0.8471 (Cg_endo) REVERT: A 186 GLU cc_start: 0.6110 (mm-30) cc_final: 0.5712 (mm-30) REVERT: A 237 ARG cc_start: 0.6113 (mmm-85) cc_final: 0.5892 (mtm-85) REVERT: A 247 THR cc_start: 0.8050 (OUTLIER) cc_final: 0.7746 (m) REVERT: A 286 LYS cc_start: 0.7956 (tptt) cc_final: 0.7026 (tmtt) REVERT: B 24 ARG cc_start: 0.7863 (mmt90) cc_final: 0.7611 (mmt90) REVERT: B 96 ARG cc_start: 0.8135 (ttp-110) cc_final: 0.7119 (ttm170) REVERT: B 100 GLU cc_start: 0.7275 (mt-10) cc_final: 0.6906 (mt-10) REVERT: B 133 LYS cc_start: 0.7920 (mtmt) cc_final: 0.7493 (ttmt) REVERT: B 155 ARG cc_start: 0.7305 (mmm160) cc_final: 0.6911 (tpp80) REVERT: B 158 ARG cc_start: 0.8098 (ptp-170) cc_final: 0.7856 (ptp90) REVERT: B 186 GLU cc_start: 0.7245 (tm-30) cc_final: 0.7027 (tm-30) REVERT: B 197 GLU cc_start: 0.6748 (mm-30) cc_final: 0.6435 (mm-30) REVERT: B 245 LYS cc_start: 0.7254 (mppt) cc_final: 0.6932 (mtmm) REVERT: B 275 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7338 (mm) REVERT: B 318 MET cc_start: 0.0558 (tpt) cc_final: -0.1063 (tpt) REVERT: C 22 LYS cc_start: 0.7808 (pttm) cc_final: 0.7460 (pttp) REVERT: C 23 TYR cc_start: 0.6592 (m-80) cc_final: 0.6327 (m-10) REVERT: C 134 ASN cc_start: 0.8331 (OUTLIER) cc_final: 0.8029 (p0) REVERT: C 190 ASP cc_start: 0.7386 (OUTLIER) cc_final: 0.6921 (m-30) REVERT: C 232 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.7671 (mm) REVERT: C 244 GLU cc_start: 0.7535 (mp0) cc_final: 0.7292 (mp0) REVERT: C 318 MET cc_start: 0.3503 (mmm) cc_final: 0.3182 (mmm) REVERT: C 327 TYR cc_start: 0.5478 (OUTLIER) cc_final: 0.4734 (t80) REVERT: D 98 LYS cc_start: 0.8247 (pttt) cc_final: 0.7889 (pttp) REVERT: D 121 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6795 (pm20) REVERT: D 163 LYS cc_start: 0.8045 (mtpp) cc_final: 0.7684 (mtmm) REVERT: D 181 TYR cc_start: 0.8441 (m-80) cc_final: 0.7940 (m-80) REVERT: D 318 MET cc_start: 0.5765 (ttp) cc_final: 0.5224 (ttt) REVERT: E 6 LEU cc_start: 0.6803 (pt) cc_final: 0.6512 (pt) REVERT: E 51 LEU cc_start: 0.7160 (OUTLIER) cc_final: 0.6793 (mm) REVERT: E 174 ILE cc_start: 0.8047 (mm) cc_final: 0.7807 (mm) REVERT: E 177 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8587 (mm) REVERT: H 46 LYS cc_start: 0.6265 (mtpt) cc_final: 0.5923 (mmmm) REVERT: H 66 SER cc_start: 0.6903 (p) cc_final: 0.6220 (m) REVERT: H 117 TYR cc_start: 0.8987 (m-80) cc_final: 0.8666 (m-80) REVERT: L 56 TYR cc_start: 0.7696 (t80) cc_final: 0.6658 (t80) REVERT: L 92 SER cc_start: 0.8731 (t) cc_final: 0.8357 (t) outliers start: 70 outliers final: 50 residues processed: 426 average time/residue: 0.1344 time to fit residues: 85.7355 Evaluate side-chains 428 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 369 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 257 HIS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 142 LYS Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 101 PHE Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 133 LYS Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 327 TYR Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 147 PHE Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 73 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 150 optimal weight: 0.2980 chunk 88 optimal weight: 0.0970 chunk 100 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 71 optimal weight: 0.0870 chunk 47 optimal weight: 0.4980 chunk 77 optimal weight: 0.0170 chunk 13 optimal weight: 0.7980 chunk 131 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 overall best weight: 0.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.179783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.154806 restraints weight = 21792.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.159050 restraints weight = 11835.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.161926 restraints weight = 7742.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.163817 restraints weight = 5725.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.165186 restraints weight = 4592.889| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3728 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3728 r_free = 0.3728 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3728 r_free = 0.3728 target_work(ls_wunit_k1) = 0.165 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3728 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 16600 Z= 0.130 Angle : 0.651 12.950 22509 Z= 0.327 Chirality : 0.044 0.239 2551 Planarity : 0.005 0.117 2816 Dihedral : 4.508 30.489 2181 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.39 % Favored : 94.35 % Rotamer: Outliers : 3.46 % Allowed : 21.12 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.20), residues: 1947 helix: 1.94 (0.17), residues: 937 sheet: -0.47 (0.28), residues: 352 loop : -2.02 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 40 TYR 0.019 0.001 TYR D 23 PHE 0.022 0.001 PHE E 306 TRP 0.017 0.001 TRP B 350 HIS 0.006 0.001 HIS C 83 Details of bonding type rmsd covalent geometry : bond 0.00294 (16598) covalent geometry : angle 0.65082 (22505) SS BOND : bond 0.00412 ( 2) SS BOND : angle 2.03724 ( 4) hydrogen bonds : bond 0.03825 ( 945) hydrogen bonds : angle 4.49944 ( 2727) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 373 time to evaluate : 0.656 Fit side-chains REVERT: A 97 PRO cc_start: 0.8808 (Cg_exo) cc_final: 0.8595 (Cg_endo) REVERT: A 186 GLU cc_start: 0.6100 (mm-30) cc_final: 0.5696 (mm-30) REVERT: A 237 ARG cc_start: 0.6073 (mmm-85) cc_final: 0.5849 (mtm-85) REVERT: A 247 THR cc_start: 0.8086 (OUTLIER) cc_final: 0.7777 (m) REVERT: A 286 LYS cc_start: 0.7967 (tptt) cc_final: 0.7058 (tmtt) REVERT: A 318 MET cc_start: 0.6189 (mmm) cc_final: 0.5713 (mmt) REVERT: B 24 ARG cc_start: 0.7949 (mmt90) cc_final: 0.7693 (mmt90) REVERT: B 96 ARG cc_start: 0.8130 (ttp-110) cc_final: 0.7117 (ttm170) REVERT: B 100 GLU cc_start: 0.7295 (mt-10) cc_final: 0.6907 (mt-10) REVERT: B 133 LYS cc_start: 0.7892 (mtmt) cc_final: 0.7449 (ttmt) REVERT: B 155 ARG cc_start: 0.7292 (mmm160) cc_final: 0.6898 (tpp80) REVERT: B 158 ARG cc_start: 0.8151 (ptp-170) cc_final: 0.7916 (ptp90) REVERT: B 160 ILE cc_start: 0.7530 (OUTLIER) cc_final: 0.6968 (mt) REVERT: B 186 GLU cc_start: 0.7193 (tm-30) cc_final: 0.6663 (tm-30) REVERT: B 187 LYS cc_start: 0.7388 (tttt) cc_final: 0.6887 (tttm) REVERT: B 197 GLU cc_start: 0.6741 (mm-30) cc_final: 0.6363 (mm-30) REVERT: B 214 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8040 (tt) REVERT: B 245 LYS cc_start: 0.7240 (mppt) cc_final: 0.6916 (mtmm) REVERT: B 275 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7381 (mm) REVERT: B 318 MET cc_start: 0.0539 (tpt) cc_final: -0.1078 (tpt) REVERT: C 22 LYS cc_start: 0.7793 (pttm) cc_final: 0.7456 (pttp) REVERT: C 23 TYR cc_start: 0.6674 (m-80) cc_final: 0.6371 (m-10) REVERT: C 190 ASP cc_start: 0.7412 (OUTLIER) cc_final: 0.6963 (m-30) REVERT: C 232 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.7665 (mm) REVERT: C 244 GLU cc_start: 0.7534 (mp0) cc_final: 0.7277 (mp0) REVERT: C 291 MET cc_start: 0.7189 (tpp) cc_final: 0.6595 (mmt) REVERT: C 318 MET cc_start: 0.3477 (mmm) cc_final: 0.3147 (mmm) REVERT: C 327 TYR cc_start: 0.5476 (OUTLIER) cc_final: 0.4775 (t80) REVERT: D 98 LYS cc_start: 0.8223 (pttt) cc_final: 0.7957 (pttp) REVERT: D 121 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6727 (pm20) REVERT: D 163 LYS cc_start: 0.8053 (mtpp) cc_final: 0.7698 (mtmm) REVERT: D 237 ARG cc_start: 0.7699 (tpp80) cc_final: 0.7132 (tpp-160) REVERT: D 318 MET cc_start: 0.5652 (ttp) cc_final: 0.5134 (ttt) REVERT: E 6 LEU cc_start: 0.6819 (pt) cc_final: 0.6526 (pt) REVERT: E 177 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8580 (mm) REVERT: H 46 LYS cc_start: 0.6364 (mtpt) cc_final: 0.6018 (mmmm) REVERT: H 66 SER cc_start: 0.6775 (p) cc_final: 0.6071 (m) REVERT: H 117 TYR cc_start: 0.9042 (m-80) cc_final: 0.8644 (m-80) REVERT: L 56 TYR cc_start: 0.7701 (t80) cc_final: 0.6680 (t80) REVERT: L 92 SER cc_start: 0.8774 (t) cc_final: 0.8422 (t) outliers start: 63 outliers final: 48 residues processed: 409 average time/residue: 0.1300 time to fit residues: 80.2737 Evaluate side-chains 423 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 366 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 257 HIS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 101 PHE Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 327 TYR Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 147 PHE Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 73 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 123 optimal weight: 0.8980 chunk 146 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 145 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 184 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 5 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 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.173846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.148704 restraints weight = 21908.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.152905 restraints weight = 11973.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.155711 restraints weight = 7876.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.157663 restraints weight = 5825.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.158961 restraints weight = 4695.458| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3668 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3668 r_free = 0.3668 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3668 r_free = 0.3668 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3668 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 16600 Z= 0.193 Angle : 0.694 12.149 22509 Z= 0.353 Chirality : 0.046 0.253 2551 Planarity : 0.005 0.118 2816 Dihedral : 4.678 31.278 2181 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.57 % Favored : 93.17 % Rotamer: Outliers : 3.40 % Allowed : 21.50 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.19), residues: 1947 helix: 1.78 (0.17), residues: 931 sheet: -0.57 (0.28), residues: 338 loop : -2.03 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 24 TYR 0.030 0.002 TYR B 23 PHE 0.022 0.002 PHE E 306 TRP 0.024 0.001 TRP B 350 HIS 0.006 0.001 HIS C 83 Details of bonding type rmsd covalent geometry : bond 0.00460 (16598) covalent geometry : angle 0.69373 (22505) SS BOND : bond 0.00437 ( 2) SS BOND : angle 2.11560 ( 4) hydrogen bonds : bond 0.04257 ( 945) hydrogen bonds : angle 4.62757 ( 2727) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 401 time to evaluate : 0.625 Fit side-chains revert: symmetry clash REVERT: A 42 PHE cc_start: 0.6808 (t80) cc_final: 0.6229 (t80) REVERT: A 96 ARG cc_start: 0.8563 (ptm-80) cc_final: 0.8268 (ptm-80) REVERT: A 186 GLU cc_start: 0.6167 (mm-30) cc_final: 0.5759 (mm-30) REVERT: A 237 ARG cc_start: 0.6106 (mmm-85) cc_final: 0.5867 (mtm-85) REVERT: A 247 THR cc_start: 0.8367 (OUTLIER) cc_final: 0.8117 (m) REVERT: A 286 LYS cc_start: 0.7991 (tptt) cc_final: 0.7095 (tmtt) REVERT: A 318 MET cc_start: 0.6479 (mmm) cc_final: 0.5975 (mmm) REVERT: B 24 ARG cc_start: 0.7887 (mmt90) cc_final: 0.7625 (mmt90) REVERT: B 26 ASP cc_start: 0.6608 (t0) cc_final: 0.6262 (t0) REVERT: B 96 ARG cc_start: 0.8402 (ttp-110) cc_final: 0.7357 (ttm170) REVERT: B 155 ARG cc_start: 0.7332 (mmm160) cc_final: 0.6922 (tpp80) REVERT: B 158 ARG cc_start: 0.8176 (ptp-170) cc_final: 0.7953 (ptp-170) REVERT: B 186 GLU cc_start: 0.7264 (tm-30) cc_final: 0.6679 (tm-30) REVERT: B 187 LYS cc_start: 0.7543 (tttt) cc_final: 0.6868 (ttpt) REVERT: B 227 PRO cc_start: 0.9055 (Cg_exo) cc_final: 0.8718 (Cg_endo) REVERT: B 245 LYS cc_start: 0.7332 (mppt) cc_final: 0.7016 (mtmm) REVERT: B 275 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7480 (mm) REVERT: B 318 MET cc_start: 0.0906 (tpt) cc_final: -0.0826 (tpt) REVERT: C 23 TYR cc_start: 0.6823 (m-80) cc_final: 0.6602 (m-10) REVERT: C 124 SER cc_start: 0.8719 (p) cc_final: 0.8515 (p) REVERT: C 190 ASP cc_start: 0.7377 (OUTLIER) cc_final: 0.6908 (m-30) REVERT: C 225 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8562 (tt) REVERT: C 232 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8259 (mm) REVERT: C 263 ASP cc_start: 0.7517 (m-30) cc_final: 0.7102 (m-30) REVERT: C 291 MET cc_start: 0.6710 (tpp) cc_final: 0.5854 (mmt) REVERT: C 318 MET cc_start: 0.3543 (mmm) cc_final: 0.3202 (mmm) REVERT: C 327 TYR cc_start: 0.5644 (OUTLIER) cc_final: 0.4825 (t80) REVERT: D 121 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6736 (pm20) REVERT: D 163 LYS cc_start: 0.8077 (mtpp) cc_final: 0.7706 (mtmm) REVERT: D 318 MET cc_start: 0.5706 (ttp) cc_final: 0.5212 (ttt) REVERT: E 6 LEU cc_start: 0.6862 (pt) cc_final: 0.6550 (pt) REVERT: E 26 ASP cc_start: 0.7961 (t0) cc_final: 0.7579 (t70) REVERT: E 90 ILE cc_start: 0.8254 (mm) cc_final: 0.8016 (mm) REVERT: E 174 ILE cc_start: 0.8171 (mm) cc_final: 0.7943 (mm) REVERT: E 177 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8620 (mm) REVERT: E 204 GLU cc_start: 0.7263 (tt0) cc_final: 0.6993 (tt0) REVERT: E 252 ARG cc_start: 0.7345 (mtp85) cc_final: 0.6794 (ttm-80) REVERT: E 334 MET cc_start: 0.7134 (mmt) cc_final: 0.6832 (mmt) REVERT: H 66 SER cc_start: 0.7201 (p) cc_final: 0.6524 (m) REVERT: H 117 TYR cc_start: 0.9110 (m-80) cc_final: 0.8610 (m-80) REVERT: L 51 SER cc_start: 0.8549 (m) cc_final: 0.8320 (m) outliers start: 62 outliers final: 49 residues processed: 431 average time/residue: 0.1316 time to fit residues: 85.1156 Evaluate side-chains 452 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 395 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 112 MET Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 257 HIS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 314 ASN Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 36 ILE Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 89 ASP Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 101 PHE Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 225 ILE Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 327 TYR Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 121 GLU Chi-restraints excluded: chain D residue 147 PHE Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 302 MET Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 296 ILE Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain L residue 3 ILE Chi-restraints excluded: chain L residue 73 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 79 optimal weight: 0.3980 chunk 141 optimal weight: 5.9990 chunk 166 optimal weight: 0.5980 chunk 105 optimal weight: 0.3980 chunk 94 optimal weight: 1.9990 chunk 187 optimal weight: 0.6980 chunk 5 optimal weight: 0.0010 chunk 35 optimal weight: 1.9990 chunk 102 optimal weight: 0.0870 chunk 172 optimal weight: 0.0070 chunk 1 optimal weight: 1.9990 overall best weight: 0.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 ASN D 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.174161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.149113 restraints weight = 21774.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.153286 restraints weight = 11860.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.156112 restraints weight = 7807.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.158013 restraints weight = 5784.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.159376 restraints weight = 4649.653| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3672 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3672 r_free = 0.3672 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3672 r_free = 0.3672 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3672 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 16600 Z= 0.198 Angle : 0.863 59.200 22509 Z= 0.475 Chirality : 0.046 0.445 2551 Planarity : 0.005 0.118 2816 Dihedral : 4.741 38.259 2181 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.42 % Favored : 93.32 % Rotamer: Outliers : 3.46 % Allowed : 21.45 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.19), residues: 1947 helix: 1.78 (0.17), residues: 931 sheet: -0.57 (0.28), residues: 338 loop : -2.04 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 210 TYR 0.021 0.002 TYR B 23 PHE 0.021 0.002 PHE E 306 TRP 0.023 0.001 TRP B 350 HIS 0.006 0.001 HIS C 83 Details of bonding type rmsd covalent geometry : bond 0.00454 (16598) covalent geometry : angle 0.86225 (22505) SS BOND : bond 0.00520 ( 2) SS BOND : angle 2.29922 ( 4) hydrogen bonds : bond 0.04214 ( 945) hydrogen bonds : angle 4.62536 ( 2727) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3374.83 seconds wall clock time: 58 minutes 52.82 seconds (3532.82 seconds total)