Starting phenix.real_space_refine on Sun May 18 08:02:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tmq_41398/05_2025/8tmq_41398.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tmq_41398/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tmq_41398/05_2025/8tmq_41398.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tmq_41398/05_2025/8tmq_41398.map" model { file = "/net/cci-nas-00/data/ceres_data/8tmq_41398/05_2025/8tmq_41398.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tmq_41398/05_2025/8tmq_41398.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 9.46, per 1000 atoms: 0.59 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: 3.90 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.54 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: 4.74 Time building geometry restraints manager: 4.53 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: 2.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 34.970 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.380 ------------------------------------------------------------------------------- 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 : 9.07 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (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 TRP 0.014 0.001 TRP L 36 HIS 0.002 0.000 HIS D 120 PHE 0.014 0.001 PHE D 79 TYR 0.020 0.001 TYR A 34 ARG 0.008 0.000 ARG C 202 Details of bonding type rmsd hydrogen bonds : bond 0.12991 ( 981) hydrogen bonds : angle 6.68391 ( 2868) SS BOND : bond 0.00429 ( 2) SS BOND : angle 1.13032 ( 4) covalent geometry : bond 0.00269 (16503) covalent geometry : angle 0.57592 (22378) *********************** 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 : 1.699 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: 0.2461 time to fit residues: 180.3144 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 : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 174 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 E 95 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.152153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.107970 restraints weight = 19841.455| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.49 r_work: 0.3006 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3001 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2999 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 16505 Z= 0.304 Angle : 0.664 8.193 22382 Z= 0.352 Chirality : 0.047 0.180 2545 Planarity : 0.005 0.058 2798 Dihedral : 4.540 19.817 2165 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.26 % Allowed : 11.83 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.19), residues: 1940 helix: 1.68 (0.16), residues: 958 sheet: -0.13 (0.26), residues: 368 loop : -1.92 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 50 HIS 0.007 0.001 HIS A 257 PHE 0.024 0.002 PHE D 306 TYR 0.026 0.002 TYR H 106 ARG 0.008 0.001 ARG A 158 Details of bonding type rmsd hydrogen bonds : bond 0.06364 ( 981) hydrogen bonds : angle 4.90515 ( 2868) SS BOND : bond 0.00233 ( 2) SS BOND : angle 1.45387 ( 4) covalent geometry : bond 0.00738 (16503) covalent geometry : angle 0.66379 (22378) *********************** 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 479 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 438 time to evaluate : 1.704 Fit side-chains revert: symmetry clash REVERT: L 25 ARG cc_start: 0.8126 (ttm110) cc_final: 0.7506 (ttm110) REVERT: A 152 GLU cc_start: 0.7119 (mm-30) cc_final: 0.6783 (mm-30) REVERT: B 1 MET cc_start: 0.6040 (tmm) cc_final: 0.5716 (mmm) REVERT: C 116 ASP cc_start: 0.6483 (p0) cc_final: 0.6280 (p0) REVERT: C 168 TYR cc_start: 0.6610 (t80) cc_final: 0.6270 (t80) REVERT: D 134 ASN cc_start: 0.8303 (p0) cc_final: 0.8090 (p0) REVERT: D 181 TYR cc_start: 0.7604 (m-10) cc_final: 0.7111 (m-80) REVERT: D 206 GLU cc_start: 0.8135 (pm20) cc_final: 0.7525 (mp0) REVERT: E 19 TYR cc_start: 0.8818 (t80) cc_final: 0.8608 (t80) outliers start: 41 outliers final: 33 residues processed: 456 average time/residue: 0.2458 time to fit residues: 171.6951 Evaluate side-chains 448 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 415 time to evaluate : 1.788 ------------------------------------------------------------------------------- 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 10 SER 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 224 THR 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 103 GLU 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 90 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain D residue 318 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 119 optimal weight: 2.9990 chunk 79 optimal weight: 0.2980 chunk 118 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 175 optimal weight: 0.5980 chunk 144 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 113 optimal weight: 0.0060 chunk 96 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 overall best weight: 0.4196 ------------------------------------------------------------------------------- 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 = 0.3744 r_free = 0.3744 target = 0.156840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.120083 restraints weight = 19540.854| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.56 r_work: 0.3080 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16505 Z= 0.139 Angle : 0.547 8.482 22382 Z= 0.289 Chirality : 0.043 0.175 2545 Planarity : 0.005 0.048 2798 Dihedral : 4.328 17.853 2165 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.26 % Allowed : 16.35 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.20), residues: 1940 helix: 2.19 (0.17), residues: 959 sheet: 0.05 (0.27), residues: 354 loop : -1.95 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 50 HIS 0.002 0.000 HIS D 68 PHE 0.021 0.002 PHE C 27 TYR 0.025 0.001 TYR D 34 ARG 0.006 0.000 ARG A 158 Details of bonding type rmsd hydrogen bonds : bond 0.05477 ( 981) hydrogen bonds : angle 4.51418 ( 2868) SS BOND : bond 0.00391 ( 2) SS BOND : angle 1.06312 ( 4) covalent geometry : bond 0.00304 (16503) covalent geometry : angle 0.54637 (22378) *********************** 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 472 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 431 time to evaluate : 1.706 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 6 GLN cc_start: 0.8383 (tt0) cc_final: 0.8109 (mt0) REVERT: A 148 ASP cc_start: 0.7924 (m-30) cc_final: 0.7673 (m-30) REVERT: A 152 GLU cc_start: 0.7207 (mm-30) cc_final: 0.6777 (mm-30) REVERT: A 344 TYR cc_start: 0.7175 (t80) cc_final: 0.6860 (t80) REVERT: B 1 MET cc_start: 0.5992 (tmm) cc_final: 0.5703 (mmm) REVERT: B 318 MET cc_start: 0.7662 (tpt) cc_final: 0.6837 (tpt) REVERT: C 74 GLN cc_start: 0.5048 (OUTLIER) cc_final: 0.4270 (mp10) REVERT: D 152 GLU cc_start: 0.6134 (OUTLIER) cc_final: 0.5929 (mp0) REVERT: D 204 GLU cc_start: 0.7909 (mp0) cc_final: 0.7196 (mp0) REVERT: D 206 GLU cc_start: 0.8187 (pm20) cc_final: 0.7582 (mp0) REVERT: D 218 LEU cc_start: 0.8117 (mm) cc_final: 0.7890 (mm) REVERT: D 220 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7247 (tm-30) REVERT: E 19 TYR cc_start: 0.8818 (t80) cc_final: 0.8520 (t80) REVERT: E 48 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7370 (mm-30) outliers start: 41 outliers final: 26 residues processed: 446 average time/residue: 0.2416 time to fit residues: 165.3317 Evaluate side-chains 434 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 406 time to evaluate : 1.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain H residue 94 THR 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 122 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 291 MET Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 223 LYS Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 318 MET Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 236 TYR 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 126 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 85 optimal weight: 0.0040 chunk 22 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 182 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- 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 = 0.3725 r_free = 0.3725 target = 0.155085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.118053 restraints weight = 19589.823| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.59 r_work: 0.3054 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.1689 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= 0.173 Angle : 0.555 9.409 22382 Z= 0.293 Chirality : 0.043 0.164 2545 Planarity : 0.004 0.048 2798 Dihedral : 4.295 18.740 2165 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.25 % Allowed : 18.82 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.20), residues: 1940 helix: 2.26 (0.17), residues: 958 sheet: 0.03 (0.27), residues: 360 loop : -1.98 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 50 HIS 0.003 0.001 HIS A 257 PHE 0.021 0.001 PHE C 27 TYR 0.025 0.001 TYR D 34 ARG 0.006 0.000 ARG E 165 Details of bonding type rmsd hydrogen bonds : bond 0.05426 ( 981) hydrogen bonds : angle 4.44141 ( 2868) SS BOND : bond 0.00257 ( 2) SS BOND : angle 1.13042 ( 4) covalent geometry : bond 0.00409 (16503) covalent geometry : angle 0.55466 (22378) *********************** 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 490 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 431 time to evaluate : 2.077 Fit side-chains revert: symmetry clash REVERT: H 6 GLN cc_start: 0.8347 (tt0) cc_final: 0.8109 (mt0) REVERT: A 148 ASP cc_start: 0.7983 (m-30) cc_final: 0.7713 (m-30) REVERT: A 152 GLU cc_start: 0.7250 (mm-30) cc_final: 0.6851 (mm-30) REVERT: A 344 TYR cc_start: 0.7214 (t80) cc_final: 0.6989 (t80) REVERT: B 318 MET cc_start: 0.7682 (tpt) cc_final: 0.6853 (tpt) REVERT: C 74 GLN cc_start: 0.5105 (OUTLIER) cc_final: 0.4323 (mp10) REVERT: D 100 GLU cc_start: 0.7992 (mp0) cc_final: 0.7189 (mt-10) REVERT: D 152 GLU cc_start: 0.6132 (OUTLIER) cc_final: 0.5928 (mp0) REVERT: D 189 ASP cc_start: 0.7908 (t0) cc_final: 0.7425 (t0) REVERT: D 204 GLU cc_start: 0.7843 (mp0) cc_final: 0.7509 (mp0) REVERT: D 206 GLU cc_start: 0.7970 (pm20) cc_final: 0.7428 (mp0) REVERT: D 218 LEU cc_start: 0.8195 (mm) cc_final: 0.7979 (mm) REVERT: D 220 GLU cc_start: 0.7638 (tm-30) cc_final: 0.7165 (tm-30) REVERT: D 340 ILE cc_start: 0.7278 (OUTLIER) cc_final: 0.6981 (mp) REVERT: E 19 TYR cc_start: 0.8900 (t80) cc_final: 0.8621 (t80) outliers start: 59 outliers final: 40 residues processed: 456 average time/residue: 0.2421 time to fit residues: 170.8331 Evaluate side-chains 460 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 417 time to evaluate : 1.750 ------------------------------------------------------------------------------- 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 77 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain A residue 47 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 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 74 GLN Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 122 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 D residue 26 ASP Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 223 LYS 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 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 122 optimal weight: 1.9990 chunk 129 optimal weight: 0.0980 chunk 137 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 158 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 185 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.3707 r_free = 0.3707 target = 0.153489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.117468 restraints weight = 19906.107| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.47 r_work: 0.3050 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2899 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2899 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 16505 Z= 0.208 Angle : 0.579 9.805 22382 Z= 0.305 Chirality : 0.044 0.177 2545 Planarity : 0.005 0.050 2798 Dihedral : 4.326 18.749 2165 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 4.02 % Allowed : 19.26 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.20), residues: 1940 helix: 2.24 (0.17), residues: 958 sheet: 0.04 (0.27), residues: 365 loop : -2.01 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 50 HIS 0.003 0.001 HIS A 257 PHE 0.020 0.002 PHE C 27 TYR 0.028 0.002 TYR D 34 ARG 0.006 0.000 ARG E 165 Details of bonding type rmsd hydrogen bonds : bond 0.05591 ( 981) hydrogen bonds : angle 4.46139 ( 2868) SS BOND : bond 0.00256 ( 2) SS BOND : angle 1.16061 ( 4) covalent geometry : bond 0.00500 (16503) covalent geometry : angle 0.57872 (22378) *********************** 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 506 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 433 time to evaluate : 2.559 Fit side-chains revert: symmetry clash REVERT: L 27 SER cc_start: 0.9239 (t) cc_final: 0.8702 (m) REVERT: A 105 TYR cc_start: 0.8586 (p90) cc_final: 0.7777 (p90) REVERT: A 148 ASP cc_start: 0.8063 (m-30) cc_final: 0.7786 (m-30) REVERT: A 152 GLU cc_start: 0.7376 (mm-30) cc_final: 0.6975 (mm-30) REVERT: A 162 ARG cc_start: 0.7992 (mtp180) cc_final: 0.7790 (mtp180) REVERT: A 344 TYR cc_start: 0.7148 (t80) cc_final: 0.6942 (t80) REVERT: B 244 GLU cc_start: 0.7062 (mm-30) cc_final: 0.6259 (mt-10) REVERT: B 318 MET cc_start: 0.7848 (tpt) cc_final: 0.6997 (tpt) REVERT: C 25 GLU cc_start: 0.6865 (mm-30) cc_final: 0.6634 (pp20) REVERT: C 74 GLN cc_start: 0.5218 (OUTLIER) cc_final: 0.4351 (mp10) REVERT: D 100 GLU cc_start: 0.8223 (mp0) cc_final: 0.7379 (mt-10) REVERT: D 152 GLU cc_start: 0.6158 (OUTLIER) cc_final: 0.5951 (mp0) REVERT: D 181 TYR cc_start: 0.7815 (m-10) cc_final: 0.7280 (m-80) REVERT: D 200 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7469 (tt) REVERT: D 206 GLU cc_start: 0.8014 (pm20) cc_final: 0.7475 (mp0) REVERT: D 218 LEU cc_start: 0.8300 (mm) cc_final: 0.8090 (mm) REVERT: D 220 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7378 (tm-30) REVERT: D 340 ILE cc_start: 0.7313 (OUTLIER) cc_final: 0.7067 (mp) REVERT: E 19 TYR cc_start: 0.9012 (t80) cc_final: 0.8705 (t80) outliers start: 73 outliers final: 56 residues processed: 465 average time/residue: 0.2422 time to fit residues: 174.1004 Evaluate side-chains 484 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 424 time to evaluate : 1.677 ------------------------------------------------------------------------------- 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 77 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain A residue 47 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 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 258 THR 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 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 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 329 VAL 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 90 ILE Chi-restraints excluded: chain D residue 152 GLU 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 110 LEU 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 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 150 optimal weight: 0.9990 chunk 169 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 158 optimal weight: 0.0770 chunk 107 optimal weight: 0.7980 chunk 173 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.154359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.113703 restraints weight = 19961.359| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.22 r_work: 0.3075 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2923 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2923 r_free = 0.2923 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2923 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16505 Z= 0.175 Angle : 0.564 10.100 22382 Z= 0.296 Chirality : 0.043 0.207 2545 Planarity : 0.004 0.050 2798 Dihedral : 4.296 18.573 2165 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 4.40 % Allowed : 19.59 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.20), residues: 1940 helix: 2.31 (0.17), residues: 958 sheet: 0.12 (0.27), residues: 362 loop : -2.07 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 50 HIS 0.002 0.001 HIS A 257 PHE 0.021 0.002 PHE C 27 TYR 0.029 0.001 TYR D 34 ARG 0.006 0.000 ARG E 165 Details of bonding type rmsd hydrogen bonds : bond 0.05411 ( 981) hydrogen bonds : angle 4.39550 ( 2868) SS BOND : bond 0.00274 ( 2) SS BOND : angle 1.11466 ( 4) covalent geometry : bond 0.00414 (16503) covalent geometry : angle 0.56357 (22378) *********************** 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 512 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 432 time to evaluate : 1.957 Fit side-chains revert: symmetry clash REVERT: L 27 SER cc_start: 0.9235 (t) cc_final: 0.8741 (m) REVERT: A 105 TYR cc_start: 0.8606 (p90) cc_final: 0.7808 (p90) REVERT: A 148 ASP cc_start: 0.8065 (m-30) cc_final: 0.7764 (m-30) REVERT: A 152 GLU cc_start: 0.7392 (mm-30) cc_final: 0.6963 (mm-30) REVERT: B 244 GLU cc_start: 0.7086 (mm-30) cc_final: 0.6287 (mt-10) REVERT: B 318 MET cc_start: 0.7863 (tpt) cc_final: 0.7000 (tpt) REVERT: C 25 GLU cc_start: 0.6877 (mm-30) cc_final: 0.6610 (pp20) REVERT: C 74 GLN cc_start: 0.5215 (OUTLIER) cc_final: 0.4345 (mp10) REVERT: D 54 ARG cc_start: 0.7355 (ptt90) cc_final: 0.6237 (ptt90) REVERT: D 100 GLU cc_start: 0.8226 (mp0) cc_final: 0.7392 (mt-10) REVERT: D 152 GLU cc_start: 0.6238 (OUTLIER) cc_final: 0.6032 (mp0) REVERT: D 186 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7393 (mt-10) REVERT: D 189 ASP cc_start: 0.8035 (t0) cc_final: 0.7569 (t0) REVERT: D 204 GLU cc_start: 0.7816 (mp0) cc_final: 0.7176 (mp0) REVERT: D 206 GLU cc_start: 0.7993 (pm20) cc_final: 0.7460 (mp0) REVERT: D 218 LEU cc_start: 0.8334 (mm) cc_final: 0.8110 (mm) REVERT: D 220 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7416 (tm-30) REVERT: D 314 ASN cc_start: 0.8020 (m-40) cc_final: 0.7620 (m-40) REVERT: D 340 ILE cc_start: 0.7312 (OUTLIER) cc_final: 0.7077 (mp) REVERT: E 19 TYR cc_start: 0.9033 (t80) cc_final: 0.8697 (t80) outliers start: 80 outliers final: 60 residues processed: 472 average time/residue: 0.2385 time to fit residues: 173.7548 Evaluate side-chains 485 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 422 time to evaluate : 1.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 8 SER 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 77 THR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain A residue 47 VAL 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 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 121 GLU 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 B residue 341 MET 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 282 SER Chi-restraints excluded: chain C residue 287 THR 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 152 GLU 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 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 109 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 0.5980 chunk 135 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 chunk 118 optimal weight: 0.7980 chunk 145 optimal weight: 0.0980 chunk 34 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 188 optimal weight: 0.0470 chunk 67 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.156581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.117925 restraints weight = 19719.536| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.53 r_work: 0.3082 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 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 0.042 16505 Z= 0.135 Angle : 0.549 10.056 22382 Z= 0.287 Chirality : 0.042 0.195 2545 Planarity : 0.004 0.050 2798 Dihedral : 4.225 17.670 2165 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.63 % Allowed : 20.91 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.20), residues: 1940 helix: 2.42 (0.17), residues: 958 sheet: 0.13 (0.27), residues: 359 loop : -2.01 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 50 HIS 0.002 0.000 HIS C 212 PHE 0.020 0.001 PHE C 27 TYR 0.029 0.001 TYR D 34 ARG 0.009 0.000 ARG E 202 Details of bonding type rmsd hydrogen bonds : bond 0.05105 ( 981) hydrogen bonds : angle 4.30897 ( 2868) SS BOND : bond 0.00324 ( 2) SS BOND : angle 1.01815 ( 4) covalent geometry : bond 0.00302 (16503) covalent geometry : angle 0.54918 (22378) *********************** 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 494 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 428 time to evaluate : 1.835 Fit side-chains revert: symmetry clash REVERT: L 27 SER cc_start: 0.9192 (t) cc_final: 0.8721 (m) REVERT: A 105 TYR cc_start: 0.8516 (p90) cc_final: 0.7703 (p90) REVERT: A 148 ASP cc_start: 0.7905 (m-30) cc_final: 0.7538 (m-30) REVERT: A 152 GLU cc_start: 0.7290 (mm-30) cc_final: 0.6809 (mm-30) REVERT: B 244 GLU cc_start: 0.6969 (mm-30) cc_final: 0.6187 (mt-10) REVERT: B 318 MET cc_start: 0.7669 (tpt) cc_final: 0.6851 (tpt) REVERT: C 25 GLU cc_start: 0.6836 (mm-30) cc_final: 0.6599 (pp20) REVERT: C 74 GLN cc_start: 0.5133 (OUTLIER) cc_final: 0.4273 (mp10) REVERT: D 54 ARG cc_start: 0.7391 (ptt90) cc_final: 0.6257 (ptt90) REVERT: D 100 GLU cc_start: 0.8121 (mp0) cc_final: 0.7324 (mt-10) REVERT: D 152 GLU cc_start: 0.6153 (OUTLIER) cc_final: 0.5927 (mp0) REVERT: D 189 ASP cc_start: 0.7911 (t0) cc_final: 0.7438 (t0) REVERT: D 204 GLU cc_start: 0.7841 (mp0) cc_final: 0.7574 (mp0) REVERT: D 206 GLU cc_start: 0.7962 (pm20) cc_final: 0.7416 (mp0) REVERT: D 218 LEU cc_start: 0.8192 (mm) cc_final: 0.7976 (mm) REVERT: D 220 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7163 (tm-30) REVERT: D 314 ASN cc_start: 0.7952 (m-40) cc_final: 0.7541 (m-40) REVERT: D 340 ILE cc_start: 0.7324 (OUTLIER) cc_final: 0.7110 (mp) REVERT: E 19 TYR cc_start: 0.8992 (t80) cc_final: 0.8647 (t80) outliers start: 66 outliers final: 55 residues processed: 460 average time/residue: 0.2358 time to fit residues: 167.4002 Evaluate side-chains 473 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 415 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 8 SER Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 38 GLN 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 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 50 VAL Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 121 GLU 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 300 ILE 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 282 SER 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 143 ILE Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 277 ASP 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 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 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 43 optimal weight: 0.9980 chunk 146 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3715 r_free = 0.3715 target = 0.154001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.113395 restraints weight = 19940.201| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 2.21 r_work: 0.3069 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2926 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2918 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2918 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16505 Z= 0.193 Angle : 0.579 10.178 22382 Z= 0.303 Chirality : 0.044 0.186 2545 Planarity : 0.005 0.053 2798 Dihedral : 4.272 18.834 2165 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.69 % Allowed : 21.46 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.20), residues: 1940 helix: 2.31 (0.17), residues: 958 sheet: 0.08 (0.27), residues: 365 loop : -2.01 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 50 HIS 0.003 0.001 HIS A 257 PHE 0.022 0.002 PHE E 147 TYR 0.030 0.002 TYR D 34 ARG 0.007 0.000 ARG E 202 Details of bonding type rmsd hydrogen bonds : bond 0.05380 ( 981) hydrogen bonds : angle 4.39468 ( 2868) SS BOND : bond 0.00263 ( 2) SS BOND : angle 1.14500 ( 4) covalent geometry : bond 0.00462 (16503) covalent geometry : angle 0.57923 (22378) *********************** 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 490 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 423 time to evaluate : 1.829 Fit side-chains revert: symmetry clash REVERT: L 27 SER cc_start: 0.9227 (t) cc_final: 0.8757 (m) REVERT: A 105 TYR cc_start: 0.8612 (p90) cc_final: 0.7834 (p90) REVERT: B 244 GLU cc_start: 0.7112 (mm-30) cc_final: 0.6306 (mt-10) REVERT: B 318 MET cc_start: 0.7835 (tpt) cc_final: 0.6997 (tpt) REVERT: C 74 GLN cc_start: 0.5231 (OUTLIER) cc_final: 0.4350 (mp10) REVERT: D 54 ARG cc_start: 0.7388 (ptt90) cc_final: 0.6236 (ptt90) REVERT: D 100 GLU cc_start: 0.8236 (mp0) cc_final: 0.7478 (mt-10) REVERT: D 152 GLU cc_start: 0.6249 (OUTLIER) cc_final: 0.6026 (mp0) REVERT: D 189 ASP cc_start: 0.8056 (t0) cc_final: 0.7604 (t0) REVERT: D 204 GLU cc_start: 0.7828 (mp0) cc_final: 0.7540 (mp0) REVERT: D 206 GLU cc_start: 0.7991 (pm20) cc_final: 0.7460 (mp0) REVERT: D 218 LEU cc_start: 0.8338 (mm) cc_final: 0.8110 (mm) REVERT: D 220 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7431 (tm-30) REVERT: D 314 ASN cc_start: 0.8083 (m-40) cc_final: 0.7698 (m-40) REVERT: D 340 ILE cc_start: 0.7432 (OUTLIER) cc_final: 0.7192 (mp) REVERT: E 19 TYR cc_start: 0.9094 (t80) cc_final: 0.8728 (t80) outliers start: 67 outliers final: 61 residues processed: 456 average time/residue: 0.2378 time to fit residues: 166.9387 Evaluate side-chains 480 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 416 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 8 SER Chi-restraints excluded: chain L residue 10 SER 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 103 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 7 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 121 GLU 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 B residue 341 MET 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 287 THR 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 143 ILE Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 239 VAL 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 190 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 135 optimal weight: 2.9990 chunk 47 optimal weight: 0.4980 chunk 129 optimal weight: 0.9990 chunk 158 optimal weight: 0.6980 chunk 90 optimal weight: 0.7980 chunk 131 optimal weight: 0.7980 chunk 137 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 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 = 0.3724 r_free = 0.3724 target = 0.154810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.113397 restraints weight = 19977.457| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 2.27 r_work: 0.3078 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2924 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2924 r_free = 0.2924 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2924 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16505 Z= 0.166 Angle : 0.575 10.763 22382 Z= 0.300 Chirality : 0.043 0.188 2545 Planarity : 0.005 0.054 2798 Dihedral : 4.267 18.381 2165 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.02 % Allowed : 21.46 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.20), residues: 1940 helix: 2.34 (0.17), residues: 957 sheet: 0.09 (0.27), residues: 370 loop : -2.06 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 50 HIS 0.002 0.001 HIS E 83 PHE 0.017 0.001 PHE C 27 TYR 0.028 0.001 TYR D 34 ARG 0.007 0.000 ARG E 202 Details of bonding type rmsd hydrogen bonds : bond 0.05253 ( 981) hydrogen bonds : angle 4.36009 ( 2868) SS BOND : bond 0.00277 ( 2) SS BOND : angle 1.07272 ( 4) covalent geometry : bond 0.00390 (16503) covalent geometry : angle 0.57506 (22378) *********************** 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 491 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 418 time to evaluate : 1.911 Fit side-chains revert: symmetry clash REVERT: L 27 SER cc_start: 0.9219 (t) cc_final: 0.8752 (m) REVERT: A 105 TYR cc_start: 0.8597 (p90) cc_final: 0.7808 (p90) REVERT: A 162 ARG cc_start: 0.7900 (mtp180) cc_final: 0.7426 (ttt-90) REVERT: B 244 GLU cc_start: 0.7122 (mm-30) cc_final: 0.6315 (mt-10) REVERT: B 318 MET cc_start: 0.7788 (tpt) cc_final: 0.6919 (tpt) REVERT: C 74 GLN cc_start: 0.5217 (OUTLIER) cc_final: 0.4340 (mp10) REVERT: C 153 ARG cc_start: 0.6345 (mtp85) cc_final: 0.6056 (mtp85) REVERT: D 54 ARG cc_start: 0.7415 (ptt90) cc_final: 0.6275 (ptt90) REVERT: D 100 GLU cc_start: 0.8230 (mp0) cc_final: 0.7479 (mt-10) REVERT: D 152 GLU cc_start: 0.6236 (OUTLIER) cc_final: 0.6016 (mp0) REVERT: D 189 ASP cc_start: 0.8043 (t0) cc_final: 0.7594 (t0) REVERT: D 204 GLU cc_start: 0.7879 (mp0) cc_final: 0.7611 (mp0) REVERT: D 206 GLU cc_start: 0.7962 (pm20) cc_final: 0.7428 (mp0) REVERT: D 218 LEU cc_start: 0.8329 (mm) cc_final: 0.8101 (mm) REVERT: D 220 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7145 (tm-30) REVERT: D 340 ILE cc_start: 0.7412 (OUTLIER) cc_final: 0.7173 (mp) REVERT: E 19 TYR cc_start: 0.9083 (t80) cc_final: 0.8726 (t80) outliers start: 73 outliers final: 61 residues processed: 454 average time/residue: 0.2306 time to fit residues: 162.2622 Evaluate side-chains 479 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 415 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 8 SER Chi-restraints excluded: chain L residue 10 SER 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 103 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 112 MET Chi-restraints excluded: chain B residue 121 GLU 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 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 143 ILE Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 277 ASP 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 109 VAL Chi-restraints excluded: chain E residue 110 LEU 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 273 SER 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 21 optimal weight: 0.5980 chunk 177 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 174 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 56 optimal weight: 0.2980 chunk 153 optimal weight: 0.9980 chunk 156 optimal weight: 0.7980 chunk 168 optimal weight: 0.7980 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 = 0.3725 r_free = 0.3725 target = 0.154894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.114171 restraints weight = 19980.331| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.25 r_work: 0.3081 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2930 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2930 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16505 Z= 0.165 Angle : 0.573 10.337 22382 Z= 0.299 Chirality : 0.043 0.196 2545 Planarity : 0.004 0.055 2798 Dihedral : 4.250 18.303 2165 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.69 % Allowed : 21.90 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.20), residues: 1940 helix: 2.35 (0.17), residues: 957 sheet: 0.10 (0.27), residues: 370 loop : -2.06 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 50 HIS 0.002 0.001 HIS E 83 PHE 0.018 0.001 PHE C 27 TYR 0.030 0.001 TYR D 34 ARG 0.007 0.000 ARG E 165 Details of bonding type rmsd hydrogen bonds : bond 0.05230 ( 981) hydrogen bonds : angle 4.35493 ( 2868) SS BOND : bond 0.00291 ( 2) SS BOND : angle 1.06563 ( 4) covalent geometry : bond 0.00390 (16503) covalent geometry : angle 0.57304 (22378) ********************** 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 487 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 420 time to evaluate : 1.834 Fit side-chains revert: symmetry clash REVERT: A 105 TYR cc_start: 0.8597 (p90) cc_final: 0.7818 (p90) REVERT: A 148 ASP cc_start: 0.8173 (m-30) cc_final: 0.7785 (m-30) REVERT: A 152 GLU cc_start: 0.6766 (mt-10) cc_final: 0.5930 (mm-30) REVERT: A 162 ARG cc_start: 0.7868 (mtp180) cc_final: 0.7411 (ttt-90) REVERT: B 238 ASP cc_start: 0.6953 (m-30) cc_final: 0.6568 (m-30) REVERT: B 244 GLU cc_start: 0.7139 (mm-30) cc_final: 0.6335 (mt-10) REVERT: B 318 MET cc_start: 0.7766 (tpt) cc_final: 0.6908 (tpt) REVERT: C 74 GLN cc_start: 0.5238 (OUTLIER) cc_final: 0.4350 (mp10) REVERT: C 153 ARG cc_start: 0.6317 (mtp85) cc_final: 0.5996 (mtp85) REVERT: D 54 ARG cc_start: 0.7407 (ptt90) cc_final: 0.6657 (ptt90) REVERT: D 100 GLU cc_start: 0.8235 (mp0) cc_final: 0.7491 (mt-10) REVERT: D 152 GLU cc_start: 0.6230 (OUTLIER) cc_final: 0.6011 (mp0) REVERT: D 189 ASP cc_start: 0.8035 (t0) cc_final: 0.7585 (t0) REVERT: D 204 GLU cc_start: 0.7831 (mp0) cc_final: 0.7559 (mp0) REVERT: D 206 GLU cc_start: 0.7960 (pm20) cc_final: 0.7423 (mp0) REVERT: D 218 LEU cc_start: 0.8324 (mm) cc_final: 0.8097 (mm) REVERT: D 220 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7147 (tm-30) REVERT: D 340 ILE cc_start: 0.7413 (OUTLIER) cc_final: 0.7171 (mp) REVERT: E 19 TYR cc_start: 0.9085 (t80) cc_final: 0.8687 (t80) outliers start: 67 outliers final: 64 residues processed: 450 average time/residue: 0.2373 time to fit residues: 165.4752 Evaluate side-chains 481 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 414 time to evaluate : 1.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 8 SER Chi-restraints excluded: chain L residue 10 SER 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 103 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 112 MET Chi-restraints excluded: chain B residue 121 GLU 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 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 143 ILE Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 277 ASP 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 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 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 45 optimal weight: 0.9990 chunk 40 optimal weight: 0.2980 chunk 187 optimal weight: 0.6980 chunk 165 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 123 optimal weight: 0.0670 chunk 114 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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 = 0.3731 r_free = 0.3731 target = 0.155448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.115042 restraints weight = 19739.418| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.22 r_work: 0.3093 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2946 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16505 Z= 0.147 Angle : 0.577 10.571 22382 Z= 0.300 Chirality : 0.043 0.191 2545 Planarity : 0.004 0.054 2798 Dihedral : 4.239 18.112 2165 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.85 % Allowed : 22.01 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.20), residues: 1940 helix: 2.38 (0.17), residues: 957 sheet: 0.11 (0.27), residues: 370 loop : -2.04 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 50 HIS 0.002 0.000 HIS C 212 PHE 0.031 0.001 PHE E 147 TYR 0.030 0.001 TYR D 34 ARG 0.007 0.000 ARG E 165 Details of bonding type rmsd hydrogen bonds : bond 0.05144 ( 981) hydrogen bonds : angle 4.33868 ( 2868) SS BOND : bond 0.00285 ( 2) SS BOND : angle 1.06564 ( 4) covalent geometry : bond 0.00334 (16503) covalent geometry : angle 0.57645 (22378) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10646.95 seconds wall clock time: 184 minutes 8.25 seconds (11048.25 seconds total)