Starting phenix.real_space_refine on Sun Aug 24 03:42:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tmq_41398/08_2025/8tmq_41398.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tmq_41398/08_2025/8tmq_41398.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tmq_41398/08_2025/8tmq_41398.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tmq_41398/08_2025/8tmq_41398.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tmq_41398/08_2025/8tmq_41398.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tmq_41398/08_2025/8tmq_41398.map" } resolution = 3.1 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 793 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 1 5.21 5 S 59 5.16 5 C 10487 2.51 5 N 2626 2.21 5 O 2963 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s 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: 16136 Number of models: 1 Model: "" Number of chains: 8 Chain: "L" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 803 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Chain: "H" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 983 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 2, 'TRANS': 125} Chain: "A" 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: "B" Number of atoms: 2935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2935 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 15, 'TRANS': 336} Chain: "C" 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: "D" Number of atoms: 2879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2879 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 15, 'TRANS': 330} 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: "A" 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: 3.27, per 1000 atoms: 0.20 Number of scatterers: 16136 At special positions: 0 Unit cell: (119.056, 147.757, 136.064, 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 1 11.99 O 2963 8.00 N 2626 7.00 C 10487 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " 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: 0.91 Conformation dependent library (CDL) restraints added in 516.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3746 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 13 sheets defined 53.0% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'H' and resid 31 through 34 Processing helix chain 'H' and resid 65 through 68 removed outlier: 3.589A pdb=" N LYS H 68 " --> pdb=" O ASP H 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 65 through 68' Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.760A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 Proline residue: A 52 - end of helix Processing helix chain 'A' and resid 69 through 80 removed outlier: 3.635A pdb=" N VAL A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 92 removed outlier: 3.515A pdb=" N LEU A 87 " --> pdb=" O HIS A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 157 Processing helix chain 'A' and resid 160 through 164 Processing helix chain 'A' and resid 165 through 201 removed outlier: 3.538A pdb=" N LEU A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU A 201 " --> pdb=" O GLU A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 238 removed outlier: 3.671A pdb=" N VAL A 208 " --> pdb=" O GLU A 204 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) Proline residue: A 227 - end of helix removed outlier: 3.996A pdb=" N ASP A 238 " --> pdb=" O SER A 234 " (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 282 removed outlier: 3.906A pdb=" N SER A 282 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 300 removed outlier: 3.557A pdb=" N ILE A 300 " --> pdb=" O ILE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 311 Processing helix chain 'A' and resid 327 through 347 removed outlier: 3.670A pdb=" N LEU A 331 " --> pdb=" O TYR A 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 54 Proline residue: B 52 - end of helix Processing helix chain 'B' and resid 69 through 81 removed outlier: 3.620A pdb=" N VAL B 73 " --> pdb=" O ARG B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'B' and resid 117 through 120 Processing helix chain 'B' and resid 147 through 157 Processing helix chain 'B' and resid 160 through 164 removed outlier: 3.568A pdb=" N LYS B 164 " --> pdb=" O ILE B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 200 removed outlier: 3.657A pdb=" N LEU B 169 " --> pdb=" O ARG B 165 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU B 198 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 238 Proline residue: B 227 - end of helix Processing helix chain 'B' and resid 247 through 312 removed outlier: 3.669A pdb=" N ASP B 270 " --> pdb=" O GLU B 266 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N SER B 273 " --> pdb=" O ARG B 269 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL B 278 " --> pdb=" O GLY B 274 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR B 279 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU B 280 " --> pdb=" O LEU B 276 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 322 through 325 Processing helix chain 'B' and resid 326 through 349 removed outlier: 3.862A pdb=" N VAL B 330 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU B 331 " --> pdb=" O TYR B 327 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N MET B 341 " --> pdb=" O ILE B 337 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS B 348 " --> pdb=" O TYR B 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 80 removed outlier: 4.370A pdb=" N VAL C 73 " --> pdb=" O ARG C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 91 removed outlier: 3.685A pdb=" N LEU C 91 " --> pdb=" O LEU C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 157 Processing helix chain 'C' and resid 166 through 202 Processing helix chain 'C' and resid 204 through 236 removed outlier: 3.952A pdb=" N VAL C 208 " --> pdb=" O GLU C 204 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLN C 209 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TRP C 226 " --> pdb=" O ARG C 222 " (cutoff:3.500A) Proline residue: C 227 - end of helix Processing helix chain 'C' and resid 247 through 312 removed outlier: 3.915A pdb=" N PHE C 251 " --> pdb=" O THR C 247 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG C 252 " --> pdb=" O VAL C 248 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL C 254 " --> pdb=" O TYR C 250 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU C 280 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN C 288 " --> pdb=" O SER C 284 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL C 293 " --> pdb=" O GLU C 289 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) Proline residue: C 303 - end of helix Processing helix chain 'C' and resid 325 through 348 Processing helix chain 'D' and resid 46 through 51 removed outlier: 4.051A pdb=" N VAL D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 80 removed outlier: 3.990A pdb=" N VAL D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 92 Processing helix chain 'D' and resid 147 through 156 Processing helix chain 'D' and resid 165 through 202 removed outlier: 3.583A pdb=" N LEU D 169 " --> pdb=" O ARG D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 235 removed outlier: 4.523A pdb=" N VAL D 208 " --> pdb=" O GLU D 204 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLN D 209 " --> pdb=" O LYS D 205 " (cutoff:3.500A) Proline residue: D 227 - end of helix Processing helix chain 'D' and resid 244 through 246 No H-bonds generated for 'chain 'D' and resid 244 through 246' Processing helix chain 'D' and resid 247 through 312 removed outlier: 3.826A pdb=" N LEU D 276 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ASP D 277 " --> pdb=" O SER D 273 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA D 298 " --> pdb=" O LEU D 294 " (cutoff:3.500A) Proline residue: D 303 - end of helix removed outlier: 3.527A pdb=" N PHE D 306 " --> pdb=" O MET D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 348 removed outlier: 3.755A pdb=" N VAL D 330 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU D 331 " --> pdb=" O TYR D 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 56 removed outlier: 3.743A pdb=" N ASP E 55 " --> pdb=" O PRO E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 81 removed outlier: 3.911A pdb=" N VAL E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 92 Processing helix chain 'E' and resid 147 through 156 Processing helix chain 'E' and resid 160 through 164 removed outlier: 4.056A pdb=" N LYS E 164 " --> pdb=" O ILE E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 202 removed outlier: 3.681A pdb=" N LEU E 169 " --> pdb=" O ARG E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 237 Proline residue: E 227 - end of helix removed outlier: 3.961A pdb=" N GLU E 230 " --> pdb=" O TRP E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 310 removed outlier: 3.990A pdb=" N LEU E 276 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASP E 277 " --> pdb=" O SER E 273 " (cutoff:3.500A) Proline residue: E 303 - end of helix Processing helix chain 'E' and resid 325 through 349 Processing sheet with id=AA1, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AA2, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.466A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 54 through 55 removed outlier: 6.466A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA5, first strand: chain 'H' and resid 61 through 63 removed outlier: 6.585A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER H 36 " --> pdb=" O SER H 102 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N CYS H 99 " --> pdb=" O TRP H 119 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N TRP H 119 " --> pdb=" O CYS H 99 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ARG H 101 " --> pdb=" O ASP H 117 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE H 107 " --> pdb=" O SER H 111 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER H 111 " --> pdb=" O ILE H 107 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 61 through 63 removed outlier: 6.585A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER H 36 " --> pdb=" O SER H 102 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 39 through 44 Processing sheet with id=AA8, first strand: chain 'A' and resid 114 through 115 removed outlier: 3.565A pdb=" N GLU A 123 " --> pdb=" O THR A 114 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 39 through 44 removed outlier: 6.648A pdb=" N THR B 60 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N MET B 138 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ILE B 62 " --> pdb=" O MET B 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 40 through 41 removed outlier: 3.581A pdb=" N TRP C 61 " --> pdb=" O MET C 32 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR C 60 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N MET C 138 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ILE C 62 " --> pdb=" O MET C 138 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLN C 140 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE C 64 " --> pdb=" O GLN C 140 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 39 through 44 removed outlier: 3.612A pdb=" N GLU D 28 " --> pdb=" O THR D 65 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 28 through 30 removed outlier: 4.385A pdb=" N GLU E 121 " --> pdb=" O ASP E 116 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASP E 116 " --> pdb=" O GLU E 121 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 32 through 34 1004 hydrogen bonds defined for protein. 2868 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.77 Time building geometry restraints manager: 1.22 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: 5074 1.34 - 1.46: 3007 1.46 - 1.58: 8313 1.58 - 1.69: 0 1.69 - 1.81: 109 Bond restraints: 16503 Sorted by residual: bond pdb=" CB ILE C 108 " pdb=" CG2 ILE C 108 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.33e+00 bond pdb=" CB MET C 291 " pdb=" CG MET C 291 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.20e+00 bond pdb=" CG LEU C 110 " pdb=" CD1 LEU C 110 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.89e+00 bond pdb=" CG MET B 291 " pdb=" SD MET B 291 " ideal model delta sigma weight residual 1.803 1.774 0.029 2.50e-02 1.60e+03 1.37e+00 bond pdb=" CA MET C 291 " pdb=" C MET C 291 " ideal model delta sigma weight residual 1.525 1.510 0.015 1.37e-02 5.33e+03 1.26e+00 ... (remaining 16498 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 21895 1.66 - 3.33: 399 3.33 - 4.99: 62 4.99 - 6.65: 19 6.65 - 8.32: 3 Bond angle restraints: 22378 Sorted by residual: angle pdb=" C LEU A 235 " pdb=" N TYR A 236 " pdb=" CA TYR A 236 " ideal model delta sigma weight residual 121.52 115.55 5.97 1.84e+00 2.95e-01 1.05e+01 angle pdb=" C VAL A 290 " pdb=" N MET A 291 " pdb=" CA MET A 291 " ideal model delta sigma weight residual 121.58 115.77 5.81 1.95e+00 2.63e-01 8.86e+00 angle pdb=" C LEU E 235 " pdb=" N TYR E 236 " pdb=" CA TYR E 236 " ideal model delta sigma weight residual 122.53 117.02 5.51 1.92e+00 2.71e-01 8.24e+00 angle pdb=" CB MET C 313 " pdb=" CG MET C 313 " pdb=" SD MET C 313 " ideal model delta sigma weight residual 112.70 121.02 -8.32 3.00e+00 1.11e-01 7.68e+00 angle pdb=" CG MET E 291 " pdb=" SD MET E 291 " pdb=" CE MET E 291 " ideal model delta sigma weight residual 100.90 94.98 5.92 2.20e+00 2.07e-01 7.24e+00 ... (remaining 22373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 8820 17.91 - 35.81: 921 35.81 - 53.72: 140 53.72 - 71.63: 25 71.63 - 89.54: 13 Dihedral angle restraints: 9919 sinusoidal: 4124 harmonic: 5795 Sorted by residual: dihedral pdb=" CA TYR A 327 " pdb=" C TYR A 327 " pdb=" N PRO A 328 " pdb=" CA PRO A 328 " ideal model delta harmonic sigma weight residual 180.00 -160.34 -19.66 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CB CYS L 24 " pdb=" SG CYS L 24 " pdb=" SG CYS L 89 " pdb=" CB CYS L 89 " ideal model delta sinusoidal sigma weight residual -86.00 -117.82 31.82 1 1.00e+01 1.00e-02 1.44e+01 dihedral pdb=" CA ILE D 300 " pdb=" C ILE D 300 " pdb=" N PHE D 301 " pdb=" CA PHE D 301 " ideal model delta harmonic sigma weight residual -180.00 -163.09 -16.91 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 9916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1839 0.043 - 0.086: 536 0.086 - 0.128: 159 0.128 - 0.171: 10 0.171 - 0.214: 1 Chirality restraints: 2545 Sorted by residual: chirality pdb=" CA MET A 291 " pdb=" N MET A 291 " pdb=" C MET A 291 " pdb=" CB MET A 291 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CB ILE C 108 " pdb=" CA ILE C 108 " pdb=" CG1 ILE C 108 " pdb=" CG2 ILE C 108 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.95e-01 chirality pdb=" CA ILE C 29 " pdb=" N ILE C 29 " pdb=" C ILE C 29 " pdb=" CB ILE C 29 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.81e-01 ... (remaining 2542 not shown) Planarity restraints: 2798 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 58 " -0.049 5.00e-02 4.00e+02 7.45e-02 8.87e+00 pdb=" N PRO A 59 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 59 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 59 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 327 " 0.039 5.00e-02 4.00e+02 5.94e-02 5.65e+00 pdb=" N PRO D 328 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO D 328 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 328 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET D 341 " 0.010 2.00e-02 2.50e+03 1.89e-02 3.59e+00 pdb=" C MET D 341 " -0.033 2.00e-02 2.50e+03 pdb=" O MET D 341 " 0.012 2.00e-02 2.50e+03 pdb=" N VAL D 342 " 0.011 2.00e-02 2.50e+03 ... (remaining 2795 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 103 2.59 - 3.17: 13988 3.17 - 3.75: 24675 3.75 - 4.32: 33431 4.32 - 4.90: 56188 Nonbonded interactions: 128385 Sorted by model distance: nonbonded pdb=" OD1 ASN B 288 " pdb=" OG1 THR C 287 " model vdw 2.017 3.040 nonbonded pdb=" NH2 ARG A 222 " pdb=" OD2 ASP E 193 " model vdw 2.203 3.120 nonbonded pdb=" OH TYR D 115 " pdb=" OE1 GLU D 191 " model vdw 2.229 3.040 nonbonded pdb=" O TYR C 255 " pdb=" OG1 THR C 258 " model vdw 2.250 3.040 nonbonded pdb=" O THR C 295 " pdb=" OG1 THR C 299 " model vdw 2.255 3.040 ... (remaining 128380 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' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 11.850 Find NCS groups from input model: 0.190 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 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 : 0.003 0.050 16505 Z= 0.133 Angle : 0.576 8.315 22382 Z= 0.310 Chirality : 0.043 0.214 2545 Planarity : 0.006 0.074 2798 Dihedral : 14.505 89.537 6167 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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: -0.09 (0.19), residues: 1940 helix: 1.07 (0.17), residues: 954 sheet: 0.02 (0.28), residues: 351 loop : -1.82 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 202 TYR 0.020 0.001 TYR A 34 PHE 0.014 0.001 PHE D 79 TRP 0.014 0.001 TRP L 36 HIS 0.002 0.000 HIS D 120 Details of bonding type rmsd covalent geometry : bond 0.00269 (16503) covalent geometry : angle 0.57592 (22378) SS BOND : bond 0.00429 ( 2) SS BOND : angle 1.13032 ( 4) hydrogen bonds : bond 0.12991 ( 981) hydrogen bonds : angle 6.68391 ( 2868) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 482 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: L 43 LYS cc_start: 0.7451 (mttm) cc_final: 0.7003 (mtmt) REVERT: H 118 TYR cc_start: 0.8826 (m-80) cc_final: 0.8406 (m-80) REVERT: A 105 TYR cc_start: 0.8391 (p90) cc_final: 0.7602 (p90) REVERT: A 226 TRP cc_start: 0.8396 (m100) cc_final: 0.8175 (m100) REVERT: A 250 TYR cc_start: 0.8080 (m-80) cc_final: 0.7858 (m-80) REVERT: B 291 MET cc_start: 0.8374 (ttm) cc_final: 0.8115 (ttt) REVERT: C 205 LYS cc_start: 0.7820 (ttpp) cc_final: 0.7605 (tttp) REVERT: D 189 ASP cc_start: 0.7857 (t0) cc_final: 0.7460 (t0) REVERT: D 204 GLU cc_start: 0.8036 (mp0) cc_final: 0.7798 (mp0) REVERT: D 246 GLU cc_start: 0.7852 (tp30) cc_final: 0.7543 (tp30) REVERT: D 284 SER cc_start: 0.8708 (t) cc_final: 0.8464 (t) REVERT: E 48 GLU cc_start: 0.7442 (mm-30) cc_final: 0.6588 (tp30) REVERT: E 341 MET cc_start: 0.5853 (mmt) cc_final: 0.5478 (mmt) outliers start: 0 outliers final: 0 residues processed: 482 average time/residue: 0.1014 time to fit residues: 76.0276 Evaluate side-chains 411 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 411 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN C 140 GLN ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.155204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.118030 restraints weight = 19645.574| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.55 r_work: 0.3058 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3054 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16505 Z= 0.227 Angle : 0.606 8.213 22382 Z= 0.322 Chirality : 0.045 0.172 2545 Planarity : 0.005 0.058 2798 Dihedral : 4.405 18.527 2165 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.87 % Allowed : 11.89 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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: 0.51 (0.19), residues: 1940 helix: 1.84 (0.16), residues: 959 sheet: -0.04 (0.27), residues: 362 loop : -1.88 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 158 TYR 0.024 0.002 TYR H 106 PHE 0.022 0.002 PHE D 306 TRP 0.007 0.001 TRP L 36 HIS 0.005 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00541 (16503) covalent geometry : angle 0.60551 (22378) SS BOND : bond 0.00296 ( 2) SS BOND : angle 1.30469 ( 4) hydrogen bonds : bond 0.05927 ( 981) hydrogen bonds : angle 4.76799 ( 2868) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 432 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: L 43 LYS cc_start: 0.7692 (mttm) cc_final: 0.7189 (mtmt) REVERT: H 118 TYR cc_start: 0.9165 (m-80) cc_final: 0.8614 (m-80) REVERT: A 152 GLU cc_start: 0.7307 (mm-30) cc_final: 0.6933 (mm-30) REVERT: A 226 TRP cc_start: 0.8331 (m100) cc_final: 0.7829 (m100) REVERT: B 1 MET cc_start: 0.6020 (tmm) cc_final: 0.5699 (mmm) REVERT: B 318 MET cc_start: 0.7531 (tpt) cc_final: 0.6672 (tpt) REVERT: C 168 TYR cc_start: 0.6790 (t80) cc_final: 0.6437 (t80) REVERT: D 134 ASN cc_start: 0.8305 (p0) cc_final: 0.8072 (p0) REVERT: D 206 GLU cc_start: 0.8179 (pm20) cc_final: 0.7577 (mp0) REVERT: D 223 LYS cc_start: 0.8184 (tttt) cc_final: 0.7973 (tttp) REVERT: D 284 SER cc_start: 0.8595 (t) cc_final: 0.8383 (t) REVERT: E 19 TYR cc_start: 0.8823 (t80) cc_final: 0.8622 (t80) REVERT: E 61 TRP cc_start: 0.9049 (t60) cc_final: 0.8728 (t60) outliers start: 34 outliers final: 29 residues processed: 445 average time/residue: 0.1024 time to fit residues: 70.9647 Evaluate side-chains 447 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 418 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 318 MET Chi-restraints excluded: chain E residue 242 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 26 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 chunk 171 optimal weight: 0.1980 chunk 134 optimal weight: 0.6980 chunk 146 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 160 optimal weight: 2.9990 chunk 22 optimal weight: 0.3980 chunk 172 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 ASN ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.157153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.119559 restraints weight = 19811.151| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.49 r_work: 0.3102 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16505 Z= 0.147 Angle : 0.541 8.771 22382 Z= 0.286 Chirality : 0.043 0.182 2545 Planarity : 0.004 0.048 2798 Dihedral : 4.270 17.796 2165 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.53 % Allowed : 15.74 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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: 0.86 (0.20), residues: 1940 helix: 2.25 (0.17), residues: 959 sheet: 0.03 (0.27), residues: 360 loop : -1.90 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 158 TYR 0.026 0.001 TYR D 34 PHE 0.022 0.001 PHE C 27 TRP 0.007 0.001 TRP H 50 HIS 0.002 0.000 HIS E 120 Details of bonding type rmsd covalent geometry : bond 0.00334 (16503) covalent geometry : angle 0.54073 (22378) SS BOND : bond 0.00383 ( 2) SS BOND : angle 1.05373 ( 4) hydrogen bonds : bond 0.05375 ( 981) hydrogen bonds : angle 4.46960 ( 2868) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 441 time to evaluate : 0.799 Fit side-chains revert: symmetry clash REVERT: L 43 LYS cc_start: 0.7640 (mttm) cc_final: 0.7109 (mtmt) REVERT: H 6 GLN cc_start: 0.8398 (tt0) cc_final: 0.8173 (mt0) REVERT: A 78 GLU cc_start: 0.6682 (OUTLIER) cc_final: 0.6298 (mp0) REVERT: A 148 ASP cc_start: 0.7984 (m-30) cc_final: 0.7734 (m-30) REVERT: A 152 GLU cc_start: 0.7283 (mm-30) cc_final: 0.6901 (mm-30) REVERT: A 344 TYR cc_start: 0.7141 (t80) cc_final: 0.6805 (t80) REVERT: B 1 MET cc_start: 0.6041 (tmm) cc_final: 0.5755 (mmm) REVERT: B 318 MET cc_start: 0.7763 (tpt) cc_final: 0.6947 (tpt) REVERT: C 74 GLN cc_start: 0.5084 (OUTLIER) cc_final: 0.4338 (mp10) REVERT: D 189 ASP cc_start: 0.7993 (t0) cc_final: 0.7539 (t0) REVERT: D 204 GLU cc_start: 0.7843 (mp0) cc_final: 0.7568 (mp0) REVERT: D 206 GLU cc_start: 0.8076 (pm20) cc_final: 0.7530 (mp0) REVERT: D 218 LEU cc_start: 0.8206 (mm) cc_final: 0.7957 (mm) REVERT: D 220 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7452 (tm-30) REVERT: D 284 SER cc_start: 0.8656 (t) cc_final: 0.8425 (t) REVERT: E 19 TYR cc_start: 0.8864 (t80) cc_final: 0.8644 (t80) REVERT: E 48 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7460 (mm-30) outliers start: 46 outliers final: 28 residues processed: 457 average time/residue: 0.1027 time to fit residues: 73.1162 Evaluate side-chains 443 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 413 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 74 GLN Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 318 MET Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 317 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 6 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 133 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.152774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.116143 restraints weight = 19885.196| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.60 r_work: 0.3019 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3038 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 16505 Z= 0.254 Angle : 0.603 9.049 22382 Z= 0.318 Chirality : 0.045 0.173 2545 Planarity : 0.005 0.044 2798 Dihedral : 4.387 19.606 2165 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.69 % Allowed : 18.27 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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: 0.72 (0.20), residues: 1940 helix: 2.14 (0.17), residues: 958 sheet: -0.01 (0.27), residues: 365 loop : -2.00 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 158 TYR 0.027 0.002 TYR D 34 PHE 0.021 0.002 PHE E 147 TRP 0.010 0.001 TRP H 50 HIS 0.004 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00614 (16503) covalent geometry : angle 0.60237 (22378) SS BOND : bond 0.00274 ( 2) SS BOND : angle 1.20953 ( 4) hydrogen bonds : bond 0.05841 ( 981) hydrogen bonds : angle 4.55721 ( 2868) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 427 time to evaluate : 0.658 Fit side-chains revert: symmetry clash REVERT: A 78 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.6501 (mp0) REVERT: A 105 TYR cc_start: 0.8586 (p90) cc_final: 0.7677 (p90) REVERT: A 148 ASP cc_start: 0.8018 (m-30) cc_final: 0.7753 (m-30) REVERT: A 152 GLU cc_start: 0.7293 (mm-30) cc_final: 0.6904 (mm-30) REVERT: A 344 TYR cc_start: 0.7203 (t80) cc_final: 0.6979 (t80) REVERT: B 1 MET cc_start: 0.6003 (tmm) cc_final: 0.5714 (mmm) REVERT: B 78 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7847 (tp30) REVERT: C 74 GLN cc_start: 0.5124 (OUTLIER) cc_final: 0.4282 (mp10) REVERT: C 168 TYR cc_start: 0.6821 (t80) cc_final: 0.6482 (t80) REVERT: D 100 GLU cc_start: 0.8073 (mp0) cc_final: 0.7166 (mt-10) REVERT: D 134 ASN cc_start: 0.8283 (p0) cc_final: 0.8060 (p0) REVERT: D 181 TYR cc_start: 0.7772 (m-10) cc_final: 0.7206 (m-80) REVERT: D 204 GLU cc_start: 0.7737 (mp0) cc_final: 0.7008 (mp0) REVERT: D 206 GLU cc_start: 0.8035 (pm20) cc_final: 0.7465 (mp0) REVERT: D 218 LEU cc_start: 0.8191 (mm) cc_final: 0.7963 (mm) REVERT: D 220 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7204 (tm-30) REVERT: D 284 SER cc_start: 0.8629 (t) cc_final: 0.8387 (t) REVERT: D 340 ILE cc_start: 0.7293 (OUTLIER) cc_final: 0.6994 (mp) REVERT: E 19 TYR cc_start: 0.8943 (t80) cc_final: 0.8658 (t80) REVERT: E 297 ILE cc_start: 0.7715 (tt) cc_final: 0.7459 (tt) outliers start: 67 outliers final: 49 residues processed: 455 average time/residue: 0.1130 time to fit residues: 80.0974 Evaluate side-chains 469 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 417 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 63 ASN Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 74 GLN Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 55 ASP Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 318 MET Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 126 GLN Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 317 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 5 optimal weight: 0.5980 chunk 156 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 187 optimal weight: 0.0970 chunk 149 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 191 optimal weight: 0.3980 chunk 142 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.156369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.119323 restraints weight = 19658.525| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.60 r_work: 0.3074 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3074 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16505 Z= 0.143 Angle : 0.543 9.117 22382 Z= 0.286 Chirality : 0.042 0.176 2545 Planarity : 0.004 0.048 2798 Dihedral : 4.271 17.798 2165 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.36 % Allowed : 19.32 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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: 0.92 (0.20), residues: 1940 helix: 2.36 (0.17), residues: 958 sheet: 0.13 (0.27), residues: 352 loop : -2.00 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 202 TYR 0.027 0.001 TYR D 34 PHE 0.021 0.001 PHE C 27 TRP 0.009 0.001 TRP H 50 HIS 0.002 0.000 HIS C 212 Details of bonding type rmsd covalent geometry : bond 0.00325 (16503) covalent geometry : angle 0.54299 (22378) SS BOND : bond 0.00298 ( 2) SS BOND : angle 1.08535 ( 4) hydrogen bonds : bond 0.05231 ( 981) hydrogen bonds : angle 4.34460 ( 2868) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 433 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.7525 (p0) cc_final: 0.7132 (p0) REVERT: A 78 GLU cc_start: 0.6651 (OUTLIER) cc_final: 0.6310 (mp0) REVERT: A 105 TYR cc_start: 0.8547 (p90) cc_final: 0.7618 (p90) REVERT: A 148 ASP cc_start: 0.7980 (m-30) cc_final: 0.7670 (m-30) REVERT: A 152 GLU cc_start: 0.7238 (mm-30) cc_final: 0.6799 (mm-30) REVERT: A 162 ARG cc_start: 0.7830 (mtp180) cc_final: 0.7448 (mtp180) REVERT: A 344 TYR cc_start: 0.7121 (t80) cc_final: 0.6915 (t80) REVERT: B 244 GLU cc_start: 0.6940 (mm-30) cc_final: 0.6165 (mt-10) REVERT: C 74 GLN cc_start: 0.5081 (OUTLIER) cc_final: 0.4298 (mp10) REVERT: C 321 LEU cc_start: 0.6464 (tp) cc_final: 0.6210 (tp) REVERT: D 100 GLU cc_start: 0.8000 (mp0) cc_final: 0.7219 (mt-10) REVERT: D 189 ASP cc_start: 0.7909 (t0) cc_final: 0.7432 (t0) REVERT: D 200 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7332 (tt) REVERT: D 204 GLU cc_start: 0.7658 (mp0) cc_final: 0.7339 (mp0) REVERT: D 206 GLU cc_start: 0.8027 (pm20) cc_final: 0.7445 (mp0) REVERT: D 218 LEU cc_start: 0.8181 (mm) cc_final: 0.7974 (mm) REVERT: D 220 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7171 (tm-30) REVERT: D 284 SER cc_start: 0.8583 (t) cc_final: 0.8328 (t) REVERT: D 286 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7946 (ttmm) REVERT: D 340 ILE cc_start: 0.7249 (OUTLIER) cc_final: 0.7019 (mp) REVERT: E 19 TYR cc_start: 0.8923 (t80) cc_final: 0.8591 (t80) outliers start: 61 outliers final: 46 residues processed: 461 average time/residue: 0.1224 time to fit residues: 87.4661 Evaluate side-chains 463 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 412 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 63 ASN Chi-restraints excluded: chain C residue 74 GLN Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 286 LYS Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 318 MET Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 126 GLN Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 317 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 6 optimal weight: 0.2980 chunk 125 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 104 optimal weight: 0.0980 chunk 170 optimal weight: 0.9980 chunk 169 optimal weight: 1.9990 chunk 168 optimal weight: 0.9980 chunk 180 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 ASN E 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.155345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.117926 restraints weight = 19689.723| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 2.58 r_work: 0.3125 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3062 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16505 Z= 0.165 Angle : 0.552 8.571 22382 Z= 0.290 Chirality : 0.042 0.208 2545 Planarity : 0.004 0.050 2798 Dihedral : 4.239 18.291 2165 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.91 % Allowed : 19.70 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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: 0.93 (0.20), residues: 1940 helix: 2.37 (0.17), residues: 958 sheet: 0.18 (0.28), residues: 352 loop : -2.01 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 165 TYR 0.028 0.001 TYR D 34 PHE 0.021 0.001 PHE C 27 TRP 0.008 0.001 TRP H 50 HIS 0.002 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00389 (16503) covalent geometry : angle 0.55235 (22378) SS BOND : bond 0.00290 ( 2) SS BOND : angle 1.09431 ( 4) hydrogen bonds : bond 0.05266 ( 981) hydrogen bonds : angle 4.33677 ( 2868) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 421 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 27 SER cc_start: 0.9203 (t) cc_final: 0.8714 (m) REVERT: A 78 GLU cc_start: 0.6631 (OUTLIER) cc_final: 0.6254 (mp0) REVERT: A 148 ASP cc_start: 0.8036 (m-30) cc_final: 0.7717 (m-30) REVERT: A 152 GLU cc_start: 0.7290 (mm-30) cc_final: 0.6839 (mm-30) REVERT: A 162 ARG cc_start: 0.7912 (mtp180) cc_final: 0.7518 (mtp180) REVERT: B 220 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7570 (mm-30) REVERT: B 244 GLU cc_start: 0.6975 (mm-30) cc_final: 0.6207 (mt-10) REVERT: B 318 MET cc_start: 0.7761 (tpt) cc_final: 0.6890 (tpt) REVERT: C 25 GLU cc_start: 0.6881 (mm-30) cc_final: 0.6605 (pp20) REVERT: C 74 GLN cc_start: 0.5124 (OUTLIER) cc_final: 0.4328 (mp10) REVERT: D 100 GLU cc_start: 0.8014 (mp0) cc_final: 0.7262 (mt-10) REVERT: D 189 ASP cc_start: 0.7964 (t0) cc_final: 0.7491 (t0) REVERT: D 200 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7370 (tt) REVERT: D 204 GLU cc_start: 0.7660 (mp0) cc_final: 0.7457 (mp0) REVERT: D 206 GLU cc_start: 0.8048 (pm20) cc_final: 0.7466 (mp0) REVERT: D 220 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7221 (tm-30) REVERT: D 284 SER cc_start: 0.8671 (t) cc_final: 0.8412 (t) REVERT: D 286 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.8006 (ttmm) REVERT: D 340 ILE cc_start: 0.7350 (OUTLIER) cc_final: 0.7122 (mp) REVERT: E 19 TYR cc_start: 0.8994 (t80) cc_final: 0.8701 (t80) outliers start: 71 outliers final: 53 residues processed: 457 average time/residue: 0.1233 time to fit residues: 87.6118 Evaluate side-chains 468 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 410 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 63 ASN Chi-restraints excluded: chain C residue 74 GLN Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 286 LYS Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 318 MET Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 126 GLN Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 317 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 173 optimal weight: 1.9990 chunk 167 optimal weight: 0.0670 chunk 128 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 156 optimal weight: 0.7980 chunk 73 optimal weight: 0.6980 chunk 93 optimal weight: 0.1980 chunk 120 optimal weight: 0.0770 chunk 69 optimal weight: 1.9990 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 288 ASN ** 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 = 0.3752 r_free = 0.3752 target = 0.157505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.121268 restraints weight = 19574.582| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.54 r_work: 0.3100 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2956 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2956 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16505 Z= 0.132 Angle : 0.538 9.374 22382 Z= 0.282 Chirality : 0.042 0.197 2545 Planarity : 0.004 0.051 2798 Dihedral : 4.174 17.441 2165 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.47 % Allowed : 20.86 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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: 1.01 (0.20), residues: 1940 helix: 2.46 (0.17), residues: 957 sheet: 0.19 (0.27), residues: 359 loop : -2.01 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 165 TYR 0.029 0.001 TYR D 34 PHE 0.020 0.001 PHE C 27 TRP 0.008 0.001 TRP H 50 HIS 0.003 0.000 HIS C 212 Details of bonding type rmsd covalent geometry : bond 0.00294 (16503) covalent geometry : angle 0.53812 (22378) SS BOND : bond 0.00352 ( 2) SS BOND : angle 0.98575 ( 4) hydrogen bonds : bond 0.04955 ( 981) hydrogen bonds : angle 4.25090 ( 2868) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 418 time to evaluate : 0.703 Fit side-chains revert: symmetry clash REVERT: L 27 SER cc_start: 0.9224 (t) cc_final: 0.8765 (m) REVERT: A 78 GLU cc_start: 0.6602 (OUTLIER) cc_final: 0.6191 (mp0) REVERT: A 152 GLU cc_start: 0.7239 (mm-30) cc_final: 0.6814 (mm-30) REVERT: A 162 ARG cc_start: 0.7935 (mtp180) cc_final: 0.7469 (mtp180) REVERT: B 220 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7628 (mm-30) REVERT: B 244 GLU cc_start: 0.7022 (mm-30) cc_final: 0.6223 (mt-10) REVERT: B 318 MET cc_start: 0.7778 (tpt) cc_final: 0.6963 (tpt) REVERT: C 25 GLU cc_start: 0.6887 (mm-30) cc_final: 0.6651 (pp20) REVERT: C 74 GLN cc_start: 0.5158 (OUTLIER) cc_final: 0.4314 (mp10) REVERT: D 100 GLU cc_start: 0.8146 (mp0) cc_final: 0.7422 (mt-10) REVERT: D 189 ASP cc_start: 0.8040 (t0) cc_final: 0.7601 (t0) REVERT: D 200 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.7165 (tt) REVERT: D 204 GLU cc_start: 0.7718 (mp0) cc_final: 0.7508 (mp0) REVERT: D 206 GLU cc_start: 0.8061 (pm20) cc_final: 0.7478 (mp0) REVERT: D 220 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7363 (tm-30) REVERT: D 284 SER cc_start: 0.8715 (t) cc_final: 0.8462 (t) REVERT: D 286 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7934 (ttmm) REVERT: D 340 ILE cc_start: 0.7333 (OUTLIER) cc_final: 0.7096 (mp) REVERT: E 19 TYR cc_start: 0.9006 (t80) cc_final: 0.8660 (t80) outliers start: 63 outliers final: 49 residues processed: 450 average time/residue: 0.1229 time to fit residues: 85.9578 Evaluate side-chains 457 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 403 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 63 ASN Chi-restraints excluded: chain C residue 74 GLN Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 286 LYS Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 318 MET Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 126 GLN Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 317 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 51 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 191 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 41 optimal weight: 0.0770 chunk 27 optimal weight: 0.6980 chunk 176 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.156771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.118633 restraints weight = 19662.579| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.48 r_work: 0.3093 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2941 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2941 r_free = 0.2941 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2941 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16505 Z= 0.149 Angle : 0.548 9.038 22382 Z= 0.287 Chirality : 0.042 0.194 2545 Planarity : 0.004 0.052 2798 Dihedral : 4.176 17.687 2165 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.80 % Allowed : 21.19 % Favored : 75.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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: 0.99 (0.20), residues: 1940 helix: 2.43 (0.17), residues: 958 sheet: 0.17 (0.27), residues: 360 loop : -2.01 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 165 TYR 0.028 0.001 TYR D 34 PHE 0.018 0.001 PHE C 27 TRP 0.008 0.001 TRP H 50 HIS 0.002 0.001 HIS C 212 Details of bonding type rmsd covalent geometry : bond 0.00347 (16503) covalent geometry : angle 0.54798 (22378) SS BOND : bond 0.00302 ( 2) SS BOND : angle 1.07701 ( 4) hydrogen bonds : bond 0.04994 ( 981) hydrogen bonds : angle 4.26490 ( 2868) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 407 time to evaluate : 0.680 Fit side-chains revert: symmetry clash REVERT: L 27 SER cc_start: 0.9217 (t) cc_final: 0.8754 (m) REVERT: A 78 GLU cc_start: 0.6612 (OUTLIER) cc_final: 0.6186 (mp0) REVERT: A 105 TYR cc_start: 0.8553 (p90) cc_final: 0.7706 (p90) REVERT: A 148 ASP cc_start: 0.7958 (m-30) cc_final: 0.7592 (m-30) REVERT: A 152 GLU cc_start: 0.7243 (mm-30) cc_final: 0.6813 (mm-30) REVERT: A 162 ARG cc_start: 0.7939 (mtp180) cc_final: 0.7502 (mtp180) REVERT: B 220 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7630 (mm-30) REVERT: B 244 GLU cc_start: 0.7023 (mm-30) cc_final: 0.6222 (mt-10) REVERT: B 291 MET cc_start: 0.8266 (mmm) cc_final: 0.8048 (mmt) REVERT: B 318 MET cc_start: 0.7841 (tpt) cc_final: 0.6987 (tpt) REVERT: C 25 GLU cc_start: 0.6890 (mm-30) cc_final: 0.6645 (pp20) REVERT: C 74 GLN cc_start: 0.5144 (OUTLIER) cc_final: 0.4307 (mp10) REVERT: D 100 GLU cc_start: 0.8124 (mp0) cc_final: 0.7403 (mt-10) REVERT: D 189 ASP cc_start: 0.8000 (t0) cc_final: 0.7563 (t0) REVERT: D 200 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.7101 (tt) REVERT: D 204 GLU cc_start: 0.7676 (mp0) cc_final: 0.7474 (mp0) REVERT: D 206 GLU cc_start: 0.8047 (pm20) cc_final: 0.7469 (mp0) REVERT: D 220 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7295 (tm-30) REVERT: D 284 SER cc_start: 0.8694 (t) cc_final: 0.8450 (t) REVERT: D 286 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7914 (ttmm) REVERT: D 340 ILE cc_start: 0.7405 (OUTLIER) cc_final: 0.7164 (mp) REVERT: E 19 TYR cc_start: 0.9038 (t80) cc_final: 0.8695 (t80) REVERT: E 297 ILE cc_start: 0.7792 (tt) cc_final: 0.7588 (tt) outliers start: 69 outliers final: 55 residues processed: 442 average time/residue: 0.1225 time to fit residues: 84.7378 Evaluate side-chains 465 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 405 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 63 ASN Chi-restraints excluded: chain C residue 74 GLN Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 286 LYS Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 318 MET Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 126 GLN Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 317 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 85 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 169 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 87 optimal weight: 0.0370 chunk 124 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 75 optimal weight: 0.7980 chunk 141 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.157177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.118929 restraints weight = 19734.120| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.49 r_work: 0.3094 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16505 Z= 0.147 Angle : 0.553 8.943 22382 Z= 0.288 Chirality : 0.042 0.188 2545 Planarity : 0.004 0.053 2798 Dihedral : 4.175 18.067 2165 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.69 % Allowed : 21.24 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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: 0.99 (0.20), residues: 1940 helix: 2.43 (0.17), residues: 958 sheet: 0.16 (0.27), residues: 360 loop : -2.00 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 165 TYR 0.028 0.001 TYR D 34 PHE 0.018 0.001 PHE C 27 TRP 0.008 0.001 TRP H 50 HIS 0.002 0.000 HIS C 212 Details of bonding type rmsd covalent geometry : bond 0.00343 (16503) covalent geometry : angle 0.55329 (22378) SS BOND : bond 0.00311 ( 2) SS BOND : angle 1.04901 ( 4) hydrogen bonds : bond 0.04957 ( 981) hydrogen bonds : angle 4.25810 ( 2868) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 408 time to evaluate : 0.683 Fit side-chains revert: symmetry clash REVERT: L 27 SER cc_start: 0.9218 (t) cc_final: 0.8758 (m) REVERT: A 78 GLU cc_start: 0.6577 (OUTLIER) cc_final: 0.6133 (mp0) REVERT: A 105 TYR cc_start: 0.8565 (p90) cc_final: 0.7718 (p90) REVERT: A 148 ASP cc_start: 0.7956 (m-30) cc_final: 0.7585 (m-30) REVERT: A 152 GLU cc_start: 0.7251 (mm-30) cc_final: 0.6818 (mm-30) REVERT: A 162 ARG cc_start: 0.7939 (mtp180) cc_final: 0.7500 (mtp180) REVERT: B 220 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7609 (mm-30) REVERT: B 244 GLU cc_start: 0.7023 (mm-30) cc_final: 0.6229 (mt-10) REVERT: B 291 MET cc_start: 0.8299 (mmm) cc_final: 0.7806 (tpt) REVERT: B 318 MET cc_start: 0.7801 (tpt) cc_final: 0.6950 (tpt) REVERT: C 25 GLU cc_start: 0.6892 (mm-30) cc_final: 0.6655 (pp20) REVERT: C 74 GLN cc_start: 0.5142 (OUTLIER) cc_final: 0.4306 (mp10) REVERT: D 100 GLU cc_start: 0.8121 (mp0) cc_final: 0.7408 (mt-10) REVERT: D 186 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7406 (mt-10) REVERT: D 189 ASP cc_start: 0.8043 (t0) cc_final: 0.7603 (t0) REVERT: D 200 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.7095 (tt) REVERT: D 204 GLU cc_start: 0.7789 (mp0) cc_final: 0.7530 (mp0) REVERT: D 206 GLU cc_start: 0.8050 (pm20) cc_final: 0.7478 (mp0) REVERT: D 220 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7266 (tm-30) REVERT: D 284 SER cc_start: 0.8690 (t) cc_final: 0.8437 (t) REVERT: D 286 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7907 (ttmm) REVERT: D 340 ILE cc_start: 0.7394 (OUTLIER) cc_final: 0.7158 (mp) REVERT: E 19 TYR cc_start: 0.9067 (t80) cc_final: 0.8669 (t80) REVERT: E 318 MET cc_start: 0.7139 (mmm) cc_final: 0.6734 (mmt) outliers start: 67 outliers final: 59 residues processed: 440 average time/residue: 0.1211 time to fit residues: 82.5832 Evaluate side-chains 468 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 404 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 63 ASN Chi-restraints excluded: chain C residue 74 GLN Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 286 LYS Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 318 MET Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 126 GLN Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 317 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 37 optimal weight: 1.9990 chunk 154 optimal weight: 0.0000 chunk 76 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 172 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 288 ASN ** 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 = 0.3738 r_free = 0.3738 target = 0.156170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.118954 restraints weight = 19762.171| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.67 r_work: 0.3071 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16505 Z= 0.167 Angle : 0.568 10.617 22382 Z= 0.295 Chirality : 0.043 0.186 2545 Planarity : 0.004 0.055 2798 Dihedral : 4.204 18.156 2165 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.52 % Allowed : 21.57 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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: 0.96 (0.20), residues: 1940 helix: 2.40 (0.17), residues: 958 sheet: 0.14 (0.27), residues: 365 loop : -2.02 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 165 TYR 0.030 0.001 TYR D 34 PHE 0.017 0.001 PHE C 27 TRP 0.008 0.001 TRP H 119 HIS 0.002 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00396 (16503) covalent geometry : angle 0.56826 (22378) SS BOND : bond 0.00280 ( 2) SS BOND : angle 1.06146 ( 4) hydrogen bonds : bond 0.05058 ( 981) hydrogen bonds : angle 4.29591 ( 2868) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 412 time to evaluate : 0.583 Fit side-chains revert: symmetry clash REVERT: L 27 SER cc_start: 0.9189 (t) cc_final: 0.8717 (m) REVERT: A 78 GLU cc_start: 0.6588 (OUTLIER) cc_final: 0.6137 (mp0) REVERT: A 105 TYR cc_start: 0.8551 (p90) cc_final: 0.7676 (p90) REVERT: A 148 ASP cc_start: 0.7994 (m-30) cc_final: 0.7637 (m-30) REVERT: A 152 GLU cc_start: 0.7242 (mm-30) cc_final: 0.6789 (mm-30) REVERT: A 162 ARG cc_start: 0.7836 (mtp180) cc_final: 0.7371 (mtp180) REVERT: B 220 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7506 (mm-30) REVERT: B 244 GLU cc_start: 0.7006 (mm-30) cc_final: 0.6217 (mt-10) REVERT: B 318 MET cc_start: 0.7720 (tpt) cc_final: 0.6887 (tpt) REVERT: C 25 GLU cc_start: 0.6850 (mm-30) cc_final: 0.6626 (pp20) REVERT: C 74 GLN cc_start: 0.5120 (OUTLIER) cc_final: 0.4318 (mp10) REVERT: D 54 ARG cc_start: 0.7333 (ptt90) cc_final: 0.6285 (ptt90) REVERT: D 100 GLU cc_start: 0.7996 (mp0) cc_final: 0.7258 (mt-10) REVERT: D 186 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7231 (mt-10) REVERT: D 189 ASP cc_start: 0.7921 (t0) cc_final: 0.7470 (t0) REVERT: D 200 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7259 (tt) REVERT: D 204 GLU cc_start: 0.7617 (mp0) cc_final: 0.7360 (mp0) REVERT: D 206 GLU cc_start: 0.8020 (pm20) cc_final: 0.7375 (mp0) REVERT: D 220 GLU cc_start: 0.7643 (tm-30) cc_final: 0.6690 (tm-30) REVERT: D 284 SER cc_start: 0.8581 (t) cc_final: 0.8322 (t) REVERT: D 340 ILE cc_start: 0.7281 (OUTLIER) cc_final: 0.7056 (mp) REVERT: E 19 TYR cc_start: 0.9062 (t80) cc_final: 0.8675 (t80) outliers start: 64 outliers final: 57 residues processed: 443 average time/residue: 0.1112 time to fit residues: 76.9016 Evaluate side-chains 470 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 409 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 95 SER Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 56 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 63 ASN Chi-restraints excluded: chain C residue 74 GLN Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 67 ILE Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 318 MET Chi-restraints excluded: chain D residue 340 ILE Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 126 GLN Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 242 LEU Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 317 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 176 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 100 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 140 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 154 optimal weight: 0.5980 chunk 147 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.156198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.119613 restraints weight = 19639.679| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.50 r_work: 0.3084 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2931 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2931 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16505 Z= 0.164 Angle : 0.572 10.478 22382 Z= 0.296 Chirality : 0.043 0.185 2545 Planarity : 0.004 0.055 2798 Dihedral : 4.215 18.339 2165 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.80 % Allowed : 21.46 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % 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: 0.96 (0.20), residues: 1940 helix: 2.40 (0.17), residues: 958 sheet: 0.12 (0.27), residues: 365 loop : -2.01 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 165 TYR 0.030 0.001 TYR D 34 PHE 0.018 0.001 PHE C 27 TRP 0.012 0.001 TRP D 350 HIS 0.002 0.001 HIS E 83 Details of bonding type rmsd covalent geometry : bond 0.00389 (16503) covalent geometry : angle 0.57170 (22378) SS BOND : bond 0.00283 ( 2) SS BOND : angle 1.05762 ( 4) hydrogen bonds : bond 0.05076 ( 981) hydrogen bonds : angle 4.30389 ( 2868) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5348.84 seconds wall clock time: 92 minutes 1.01 seconds (5521.01 seconds total)