Starting phenix.real_space_refine on Sun Jun 15 00:29:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tmq_41398/06_2025/8tmq_41398.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tmq_41398/06_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_41398/06_2025/8tmq_41398.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tmq_41398/06_2025/8tmq_41398.map" model { file = "/net/cci-nas-00/data/ceres_data/8tmq_41398/06_2025/8tmq_41398.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tmq_41398/06_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-5710/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: 9.90, per 1000 atoms: 0.61 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: 4.25 Conformation dependent library (CDL) restraints added in 2.1 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: 1.58 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: 4.77 Time building geometry restraints manager: 4.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5074 1.34 - 1.46: 3007 1.46 - 1.58: 8313 1.58 - 1.69: 0 1.69 - 1.81: 109 Bond restraints: 16503 Sorted by residual: bond pdb=" CB ILE C 108 " pdb=" CG2 ILE C 108 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.33e+00 bond pdb=" CB MET C 291 " pdb=" CG MET C 291 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.20e+00 bond pdb=" CG LEU C 110 " pdb=" CD1 LEU C 110 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.89e+00 bond pdb=" CG MET B 291 " pdb=" SD MET B 291 " ideal model delta sigma weight residual 1.803 1.774 0.029 2.50e-02 1.60e+03 1.37e+00 bond pdb=" CA MET C 291 " pdb=" C MET C 291 " ideal model delta sigma weight residual 1.525 1.510 0.015 1.37e-02 5.33e+03 1.26e+00 ... (remaining 16498 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 21895 1.66 - 3.33: 399 3.33 - 4.99: 62 4.99 - 6.65: 19 6.65 - 8.32: 3 Bond angle restraints: 22378 Sorted by residual: angle pdb=" C LEU A 235 " pdb=" N TYR A 236 " pdb=" CA TYR A 236 " ideal model delta sigma weight residual 121.52 115.55 5.97 1.84e+00 2.95e-01 1.05e+01 angle pdb=" C VAL A 290 " pdb=" N MET A 291 " pdb=" CA MET A 291 " ideal model delta sigma weight residual 121.58 115.77 5.81 1.95e+00 2.63e-01 8.86e+00 angle pdb=" C LEU E 235 " pdb=" N TYR E 236 " pdb=" CA TYR E 236 " ideal model delta sigma weight residual 122.53 117.02 5.51 1.92e+00 2.71e-01 8.24e+00 angle pdb=" CB MET C 313 " pdb=" CG MET C 313 " pdb=" SD MET C 313 " ideal model delta sigma weight residual 112.70 121.02 -8.32 3.00e+00 1.11e-01 7.68e+00 angle pdb=" CG MET E 291 " pdb=" SD MET E 291 " pdb=" CE MET E 291 " ideal model delta sigma weight residual 100.90 94.98 5.92 2.20e+00 2.07e-01 7.24e+00 ... (remaining 22373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 8820 17.91 - 35.81: 921 35.81 - 53.72: 140 53.72 - 71.63: 25 71.63 - 89.54: 13 Dihedral angle restraints: 9919 sinusoidal: 4124 harmonic: 5795 Sorted by residual: dihedral pdb=" CA TYR A 327 " pdb=" C TYR A 327 " pdb=" N PRO A 328 " pdb=" CA PRO A 328 " ideal model delta harmonic sigma weight residual 180.00 -160.34 -19.66 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CB CYS L 24 " pdb=" SG CYS L 24 " pdb=" SG CYS L 89 " pdb=" CB CYS L 89 " ideal model delta sinusoidal sigma weight residual -86.00 -117.82 31.82 1 1.00e+01 1.00e-02 1.44e+01 dihedral pdb=" CA ILE D 300 " pdb=" C ILE D 300 " pdb=" N PHE D 301 " pdb=" CA PHE D 301 " ideal model delta harmonic sigma weight residual -180.00 -163.09 -16.91 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 9916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1839 0.043 - 0.086: 536 0.086 - 0.128: 159 0.128 - 0.171: 10 0.171 - 0.214: 1 Chirality restraints: 2545 Sorted by residual: chirality pdb=" CA MET A 291 " pdb=" N MET A 291 " pdb=" C MET A 291 " pdb=" CB MET A 291 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CB ILE C 108 " pdb=" CA ILE C 108 " pdb=" CG1 ILE C 108 " pdb=" CG2 ILE C 108 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.95e-01 chirality pdb=" CA ILE C 29 " pdb=" N ILE C 29 " pdb=" C ILE C 29 " pdb=" CB ILE C 29 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.81e-01 ... (remaining 2542 not shown) Planarity restraints: 2798 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 58 " -0.049 5.00e-02 4.00e+02 7.45e-02 8.87e+00 pdb=" N PRO A 59 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 59 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 59 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 327 " 0.039 5.00e-02 4.00e+02 5.94e-02 5.65e+00 pdb=" N PRO D 328 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO D 328 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 328 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET D 341 " 0.010 2.00e-02 2.50e+03 1.89e-02 3.59e+00 pdb=" C MET D 341 " -0.033 2.00e-02 2.50e+03 pdb=" O MET D 341 " 0.012 2.00e-02 2.50e+03 pdb=" N VAL D 342 " 0.011 2.00e-02 2.50e+03 ... (remaining 2795 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 103 2.59 - 3.17: 13988 3.17 - 3.75: 24675 3.75 - 4.32: 33431 4.32 - 4.90: 56188 Nonbonded interactions: 128385 Sorted by model distance: nonbonded pdb=" OD1 ASN B 288 " pdb=" OG1 THR C 287 " model vdw 2.017 3.040 nonbonded pdb=" NH2 ARG A 222 " pdb=" OD2 ASP E 193 " model vdw 2.203 3.120 nonbonded pdb=" OH TYR D 115 " pdb=" OE1 GLU D 191 " model vdw 2.229 3.040 nonbonded pdb=" O TYR C 255 " pdb=" OG1 THR C 258 " model vdw 2.250 3.040 nonbonded pdb=" O THR C 295 " pdb=" OG1 THR C 299 " model vdw 2.255 3.040 ... (remaining 128380 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 17 through 351) selection = (chain 'B' and resid 17 through 351) selection = chain 'C' selection = (chain 'D' and resid 17 through 351) selection = (chain 'E' and resid 17 through 351) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.49 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.690 Check model and map are aligned: 0.140 Set scattering table: 0.200 Process input model: 36.880 Find NCS groups from input model: 0.660 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: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.480 ------------------------------------------------------------------------------- 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 : 1.834 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: 0.2479 time to fit residues: 181.5829 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 : 1.750 ------------------------------------------------------------------------------- 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 = 40)----------------| | 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: 0.3002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 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 = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 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 : 2.154 Fit side-chains revert: symmetry clash REVERT: L 25 ARG cc_start: 0.8130 (ttm110) cc_final: 0.7511 (ttm110) REVERT: A 152 GLU cc_start: 0.7124 (mm-30) cc_final: 0.6787 (mm-30) REVERT: B 1 MET cc_start: 0.6038 (tmm) cc_final: 0.5714 (mmm) REVERT: C 116 ASP cc_start: 0.6483 (p0) cc_final: 0.6280 (p0) REVERT: C 168 TYR cc_start: 0.6615 (t80) cc_final: 0.6275 (t80) REVERT: D 134 ASN cc_start: 0.8304 (p0) cc_final: 0.8091 (p0) REVERT: D 181 TYR cc_start: 0.7608 (m-10) cc_final: 0.7114 (m-80) REVERT: D 206 GLU cc_start: 0.8136 (pm20) cc_final: 0.7526 (mp0) REVERT: E 19 TYR cc_start: 0.8819 (t80) cc_final: 0.8608 (t80) outliers start: 41 outliers final: 33 residues processed: 456 average time/residue: 0.3223 time to fit residues: 228.8860 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 : 2.265 ------------------------------------------------------------------------------- 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: 0.6980 chunk 118 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 175 optimal weight: 0.7980 chunk 144 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 113 optimal weight: 0.0030 chunk 96 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 overall best weight: 0.5590 ------------------------------------------------------------------------------- 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 = 0.3733 r_free = 0.3733 target = 0.155826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.119092 restraints weight = 19576.643| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.60 r_work: 0.3078 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3063 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 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 = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3063 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 16505 Z= 0.155 Angle : 0.555 8.576 22382 Z= 0.294 Chirality : 0.043 0.181 2545 Planarity : 0.005 0.049 2798 Dihedral : 4.357 17.962 2165 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.31 % Allowed : 16.62 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.73 (0.20), residues: 1940 helix: 2.14 (0.17), residues: 958 sheet: 0.04 (0.27), residues: 354 loop : -1.97 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 50 HIS 0.002 0.000 HIS E 83 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 0.05608 ( 981) hydrogen bonds : angle 4.56079 ( 2868) SS BOND : bond 0.00339 ( 2) SS BOND : angle 1.10561 ( 4) covalent geometry : bond 0.00356 (16503) covalent geometry : angle 0.55486 (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 468 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 426 time to evaluate : 1.965 Fit side-chains revert: symmetry clash REVERT: H 6 GLN cc_start: 0.8430 (tt0) cc_final: 0.8153 (mt0) REVERT: H 118 TYR cc_start: 0.9164 (m-80) cc_final: 0.8648 (m-80) REVERT: A 148 ASP cc_start: 0.7953 (m-30) cc_final: 0.7707 (m-30) REVERT: A 152 GLU cc_start: 0.7276 (mm-30) cc_final: 0.6896 (mm-30) REVERT: A 344 TYR cc_start: 0.7216 (t80) cc_final: 0.6907 (t80) REVERT: B 1 MET cc_start: 0.6003 (tmm) cc_final: 0.5711 (mmm) REVERT: B 334 MET cc_start: 0.7367 (mmt) cc_final: 0.7158 (mmt) REVERT: C 74 GLN cc_start: 0.5107 (OUTLIER) cc_final: 0.4319 (mp10) REVERT: D 152 GLU cc_start: 0.6216 (OUTLIER) cc_final: 0.6007 (mp0) REVERT: D 204 GLU cc_start: 0.7903 (mp0) cc_final: 0.7648 (mp0) REVERT: D 206 GLU cc_start: 0.8203 (pm20) cc_final: 0.7614 (mp0) REVERT: D 220 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7291 (tm-30) REVERT: E 19 TYR cc_start: 0.8848 (t80) cc_final: 0.8562 (t80) REVERT: E 48 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7372 (mm-30) outliers start: 42 outliers final: 27 residues processed: 442 average time/residue: 0.2454 time to fit residues: 166.9577 Evaluate side-chains 436 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 407 time to evaluate : 1.934 ------------------------------------------------------------------------------- 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 87 LEU Chi-restraints excluded: chain C residue 122 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 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: 0.9990 chunk 173 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 182 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 60 optimal weight: 0.1980 chunk 132 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 217 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.155928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.118859 restraints weight = 19545.618| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.59 r_work: 0.3070 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- 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 = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.1661 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= 0.154 Angle : 0.544 9.277 22382 Z= 0.287 Chirality : 0.042 0.177 2545 Planarity : 0.004 0.047 2798 Dihedral : 4.272 18.031 2165 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.14 % Allowed : 18.66 % Favored : 78.21 % 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: 0.87 (0.20), residues: 1940 helix: 2.30 (0.17), residues: 958 sheet: 0.10 (0.27), residues: 353 loop : -1.97 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 50 HIS 0.002 0.000 HIS E 83 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 0.05307 ( 981) hydrogen bonds : angle 4.41228 ( 2868) SS BOND : bond 0.00302 ( 2) SS BOND : angle 1.09988 ( 4) covalent geometry : bond 0.00358 (16503) covalent geometry : angle 0.54423 (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 491 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 434 time to evaluate : 1.777 Fit side-chains revert: symmetry clash REVERT: L 27 SER cc_start: 0.9197 (t) cc_final: 0.8674 (m) REVERT: H 6 GLN cc_start: 0.8342 (tt0) cc_final: 0.8104 (mt0) REVERT: H 118 TYR cc_start: 0.9151 (m-80) cc_final: 0.8634 (m-80) REVERT: A 140 GLN cc_start: 0.8583 (mt0) cc_final: 0.8376 (mt0) REVERT: A 148 ASP cc_start: 0.7974 (m-30) cc_final: 0.7694 (m-30) REVERT: A 152 GLU cc_start: 0.7254 (mm-30) cc_final: 0.6841 (mm-30) REVERT: A 162 ARG cc_start: 0.8015 (mtp180) cc_final: 0.7806 (mtp180) REVERT: A 344 TYR cc_start: 0.7231 (t80) cc_final: 0.6971 (t80) REVERT: B 318 MET cc_start: 0.7673 (tpt) cc_final: 0.6840 (tpt) REVERT: C 74 GLN cc_start: 0.5115 (OUTLIER) cc_final: 0.4327 (mp10) REVERT: D 100 GLU cc_start: 0.7989 (mp0) cc_final: 0.7188 (mt-10) REVERT: D 152 GLU cc_start: 0.6108 (OUTLIER) cc_final: 0.5902 (mp0) REVERT: D 189 ASP cc_start: 0.7920 (t0) cc_final: 0.7441 (t0) REVERT: D 204 GLU cc_start: 0.7866 (mp0) cc_final: 0.7533 (mp0) REVERT: D 206 GLU cc_start: 0.7970 (pm20) cc_final: 0.7424 (mp0) REVERT: D 218 LEU cc_start: 0.8201 (mm) cc_final: 0.7987 (mm) REVERT: D 220 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7160 (tm-30) REVERT: D 340 ILE cc_start: 0.7253 (OUTLIER) cc_final: 0.6951 (mp) REVERT: E 19 TYR cc_start: 0.8884 (t80) cc_final: 0.8601 (t80) outliers start: 57 outliers final: 41 residues processed: 459 average time/residue: 0.2410 time to fit residues: 171.1053 Evaluate side-chains 463 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 419 time to evaluate : 1.904 ------------------------------------------------------------------------------- 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 A residue 310 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 300 ILE 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 195 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 291 MET 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 273 SER 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: 0.0870 chunk 137 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 chunk 185 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.9162 ------------------------------------------------------------------------------- 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 = 0.3711 r_free = 0.3711 target = 0.153910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.116039 restraints weight = 19908.296| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.49 r_work: 0.3050 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- 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 = 0.40 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 = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2899 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16505 Z= 0.199 Angle : 0.571 9.995 22382 Z= 0.300 Chirality : 0.043 0.171 2545 Planarity : 0.005 0.050 2798 Dihedral : 4.296 18.752 2165 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.80 % Allowed : 19.37 % Favored : 76.83 % 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: 0.84 (0.20), residues: 1940 helix: 2.27 (0.17), residues: 958 sheet: 0.04 (0.27), residues: 365 loop : -2.00 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 61 HIS 0.003 0.001 HIS A 257 PHE 0.021 0.002 PHE D 301 TYR 0.027 0.002 TYR D 34 ARG 0.006 0.000 ARG E 165 Details of bonding type rmsd hydrogen bonds : bond 0.05527 ( 981) hydrogen bonds : angle 4.44056 ( 2868) SS BOND : bond 0.00258 ( 2) SS BOND : angle 1.15194 ( 4) covalent geometry : bond 0.00479 (16503) covalent geometry : angle 0.57125 (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 493 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 424 time to evaluate : 2.053 Fit side-chains revert: symmetry clash REVERT: L 27 SER cc_start: 0.9247 (t) cc_final: 0.8710 (m) REVERT: H 118 TYR cc_start: 0.9189 (m-80) cc_final: 0.8667 (m-80) REVERT: A 105 TYR cc_start: 0.8578 (p90) cc_final: 0.7770 (p90) REVERT: A 148 ASP cc_start: 0.8070 (m-30) cc_final: 0.7786 (m-30) REVERT: A 152 GLU cc_start: 0.7392 (mm-30) cc_final: 0.6992 (mm-30) REVERT: A 162 ARG cc_start: 0.8014 (mtp180) cc_final: 0.7656 (mtp180) REVERT: B 244 GLU cc_start: 0.7054 (mm-30) cc_final: 0.6256 (mt-10) REVERT: C 25 GLU cc_start: 0.6900 (mm-30) cc_final: 0.6605 (pp20) REVERT: C 74 GLN cc_start: 0.5234 (OUTLIER) cc_final: 0.4345 (mp10) REVERT: D 100 GLU cc_start: 0.8141 (mp0) cc_final: 0.7398 (mt-10) REVERT: D 152 GLU cc_start: 0.6199 (OUTLIER) cc_final: 0.5996 (mp0) REVERT: D 189 ASP cc_start: 0.8043 (t0) cc_final: 0.7579 (t0) REVERT: D 200 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7483 (tt) REVERT: D 206 GLU cc_start: 0.8015 (pm20) cc_final: 0.7470 (mp0) REVERT: D 218 LEU cc_start: 0.8338 (mm) cc_final: 0.8120 (mm) REVERT: D 220 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7397 (tm-30) REVERT: D 340 ILE cc_start: 0.7339 (OUTLIER) cc_final: 0.7101 (mp) REVERT: E 19 TYR cc_start: 0.8995 (t80) cc_final: 0.8679 (t80) outliers start: 69 outliers final: 54 residues processed: 457 average time/residue: 0.2728 time to fit residues: 191.8641 Evaluate side-chains 476 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 418 time to evaluate : 1.834 ------------------------------------------------------------------------------- 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 41 GLU Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 287 THR 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 150 optimal weight: 0.7980 chunk 169 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 158 optimal weight: 0.0980 chunk 107 optimal weight: 0.6980 chunk 173 optimal weight: 0.6980 chunk 131 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3728 r_free = 0.3728 target = 0.155363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.118681 restraints weight = 19857.908| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.62 r_work: 0.3063 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3063 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3063 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16505 Z= 0.154 Angle : 0.555 8.922 22382 Z= 0.290 Chirality : 0.042 0.203 2545 Planarity : 0.004 0.049 2798 Dihedral : 4.247 18.298 2165 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.02 % Allowed : 19.98 % 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: 0.94 (0.20), residues: 1940 helix: 2.37 (0.17), residues: 958 sheet: 0.18 (0.28), residues: 352 loop : -2.01 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 50 HIS 0.002 0.000 HIS C 212 PHE 0.020 0.001 PHE C 27 TYR 0.028 0.001 TYR D 34 ARG 0.006 0.000 ARG E 165 Details of bonding type rmsd hydrogen bonds : bond 0.05273 ( 981) hydrogen bonds : angle 4.35161 ( 2868) SS BOND : bond 0.00296 ( 2) SS BOND : angle 1.10190 ( 4) covalent geometry : bond 0.00357 (16503) covalent geometry : angle 0.55533 (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 506 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 433 time to evaluate : 2.341 Fit side-chains revert: symmetry clash REVERT: L 27 SER cc_start: 0.9202 (t) cc_final: 0.8687 (m) REVERT: H 118 TYR cc_start: 0.9146 (m-80) cc_final: 0.8647 (m-80) REVERT: A 105 TYR cc_start: 0.8549 (p90) cc_final: 0.7732 (p90) REVERT: A 148 ASP cc_start: 0.7999 (m-30) cc_final: 0.7681 (m-30) REVERT: A 152 GLU cc_start: 0.7280 (mm-30) cc_final: 0.6837 (mm-30) REVERT: A 162 ARG cc_start: 0.7884 (mtp180) cc_final: 0.7483 (mtp180) REVERT: B 244 GLU cc_start: 0.6956 (mm-30) cc_final: 0.6164 (mt-10) REVERT: B 318 MET cc_start: 0.7754 (tpt) cc_final: 0.6885 (tpt) REVERT: C 25 GLU cc_start: 0.6867 (mm-30) cc_final: 0.6587 (pp20) REVERT: C 74 GLN cc_start: 0.5134 (OUTLIER) cc_final: 0.4291 (mp10) REVERT: D 100 GLU cc_start: 0.8012 (mp0) cc_final: 0.7254 (mt-10) REVERT: D 152 GLU cc_start: 0.6162 (OUTLIER) cc_final: 0.5954 (mp0) REVERT: D 189 ASP cc_start: 0.7908 (t0) cc_final: 0.7433 (t0) REVERT: D 200 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7477 (tt) REVERT: D 206 GLU cc_start: 0.7947 (pm20) cc_final: 0.7417 (mp0) REVERT: D 218 LEU cc_start: 0.8200 (mm) cc_final: 0.7978 (mm) REVERT: D 220 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7165 (tm-30) REVERT: D 314 ASN cc_start: 0.7969 (m-40) cc_final: 0.7550 (m-40) REVERT: D 340 ILE cc_start: 0.7346 (OUTLIER) cc_final: 0.7122 (mp) REVERT: E 19 TYR cc_start: 0.8979 (t80) cc_final: 0.8608 (t80) REVERT: E 291 MET cc_start: 0.8439 (tpp) cc_final: 0.8233 (tpp) outliers start: 73 outliers final: 56 residues processed: 472 average time/residue: 0.2382 time to fit residues: 174.0567 Evaluate side-chains 478 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 418 time to evaluate : 1.750 ------------------------------------------------------------------------------- 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 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 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 73 VAL 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 50 VAL 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 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 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 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 200 LEU 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 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: 1.9990 chunk 135 optimal weight: 0.9980 chunk 170 optimal weight: 0.6980 chunk 169 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 145 optimal weight: 0.0980 chunk 34 optimal weight: 0.4980 chunk 7 optimal weight: 0.8980 chunk 188 optimal weight: 0.0010 chunk 67 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 overall best weight: 0.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 GLN C 288 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.157062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.120350 restraints weight = 19764.228| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.58 r_work: 0.3090 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3091 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3091 r_free = 0.3091 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3091 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.1917 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= 0.132 Angle : 0.545 10.496 22382 Z= 0.284 Chirality : 0.042 0.188 2545 Planarity : 0.004 0.050 2798 Dihedral : 4.176 17.700 2165 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.41 % Allowed : 21.08 % Favored : 75.51 % 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: 1.00 (0.20), residues: 1940 helix: 2.45 (0.17), residues: 957 sheet: 0.17 (0.27), residues: 359 loop : -2.00 (0.24), residues: 624 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 0.021 0.001 PHE E 147 TYR 0.030 0.001 TYR D 34 ARG 0.008 0.000 ARG E 165 Details of bonding type rmsd hydrogen bonds : bond 0.04965 ( 981) hydrogen bonds : angle 4.25851 ( 2868) SS BOND : bond 0.00348 ( 2) SS BOND : angle 1.01320 ( 4) covalent geometry : bond 0.00293 (16503) covalent geometry : angle 0.54470 (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 495 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 433 time to evaluate : 1.984 Fit side-chains revert: symmetry clash REVERT: L 27 SER cc_start: 0.9193 (t) cc_final: 0.8722 (m) REVERT: A 105 TYR cc_start: 0.8531 (p90) cc_final: 0.7668 (p90) REVERT: A 148 ASP cc_start: 0.7921 (m-30) cc_final: 0.7551 (m-30) REVERT: A 152 GLU cc_start: 0.7246 (mm-30) cc_final: 0.6783 (mm-30) REVERT: A 162 ARG cc_start: 0.7875 (mtp180) cc_final: 0.7460 (mtp180) REVERT: A 313 MET cc_start: 0.7336 (mpp) cc_final: 0.7119 (mpp) REVERT: B 244 GLU cc_start: 0.6944 (mm-30) cc_final: 0.6154 (mt-10) REVERT: B 318 MET cc_start: 0.7667 (tpt) cc_final: 0.6851 (tpt) REVERT: C 25 GLU cc_start: 0.6839 (mm-30) cc_final: 0.6598 (pp20) REVERT: C 74 GLN cc_start: 0.5112 (OUTLIER) cc_final: 0.4318 (mp10) REVERT: D 100 GLU cc_start: 0.8023 (mp0) cc_final: 0.7289 (mt-10) REVERT: D 152 GLU cc_start: 0.6137 (OUTLIER) cc_final: 0.5913 (mp0) REVERT: D 186 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7200 (mt-10) REVERT: D 189 ASP cc_start: 0.7901 (t0) cc_final: 0.7451 (t0) REVERT: D 204 GLU cc_start: 0.7666 (mp0) cc_final: 0.7108 (mp0) REVERT: D 206 GLU cc_start: 0.7946 (pm20) cc_final: 0.7401 (mp0) REVERT: D 218 LEU cc_start: 0.8184 (mm) cc_final: 0.7971 (mm) REVERT: D 220 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7164 (tm-30) REVERT: D 314 ASN cc_start: 0.7924 (m-40) cc_final: 0.7493 (m-40) REVERT: D 340 ILE cc_start: 0.7295 (OUTLIER) cc_final: 0.7078 (mp) REVERT: E 19 TYR cc_start: 0.8976 (t80) cc_final: 0.8616 (t80) outliers start: 62 outliers final: 50 residues processed: 465 average time/residue: 0.2496 time to fit residues: 178.5107 Evaluate side-chains 469 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 416 time to evaluate : 2.079 ------------------------------------------------------------------------------- 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 177 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 287 THR 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 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 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: 0.6980 chunk 118 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 52 optimal weight: 0.0970 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN E 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.155089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.116481 restraints weight = 19767.566| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.49 r_work: 0.3065 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2921 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2921 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.1999 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= 0.173 Angle : 0.566 9.292 22382 Z= 0.295 Chirality : 0.043 0.174 2545 Planarity : 0.004 0.053 2798 Dihedral : 4.214 18.317 2165 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.63 % Allowed : 21.68 % Favored : 74.68 % 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: 0.96 (0.20), residues: 1940 helix: 2.39 (0.17), residues: 957 sheet: 0.14 (0.27), residues: 365 loop : -2.00 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 50 HIS 0.002 0.001 HIS A 257 PHE 0.018 0.001 PHE C 27 TYR 0.029 0.002 TYR D 34 ARG 0.007 0.000 ARG E 165 Details of bonding type rmsd hydrogen bonds : bond 0.05190 ( 981) hydrogen bonds : angle 4.32211 ( 2868) SS BOND : bond 0.00287 ( 2) SS BOND : angle 1.08378 ( 4) covalent geometry : bond 0.00411 (16503) covalent geometry : angle 0.56579 (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 486 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 420 time to evaluate : 2.001 Fit side-chains revert: symmetry clash REVERT: L 27 SER cc_start: 0.9228 (t) cc_final: 0.8755 (m) REVERT: A 105 TYR cc_start: 0.8563 (p90) cc_final: 0.7811 (p90) REVERT: A 148 ASP cc_start: 0.8045 (m-30) cc_final: 0.7705 (m-30) REVERT: A 152 GLU cc_start: 0.7372 (mm-30) cc_final: 0.6910 (mm-30) REVERT: A 162 ARG cc_start: 0.7997 (mtp180) cc_final: 0.7549 (mtp180) REVERT: B 244 GLU cc_start: 0.7057 (mm-30) cc_final: 0.6233 (mt-10) REVERT: B 318 MET cc_start: 0.7851 (tpt) cc_final: 0.7011 (tpt) REVERT: C 74 GLN cc_start: 0.5223 (OUTLIER) cc_final: 0.4333 (mp10) REVERT: D 54 ARG cc_start: 0.7392 (ptt90) cc_final: 0.6290 (ptt90) REVERT: D 100 GLU cc_start: 0.8220 (mp0) cc_final: 0.7445 (mt-10) REVERT: D 152 GLU cc_start: 0.6128 (OUTLIER) cc_final: 0.5905 (mp0) REVERT: D 186 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7416 (mt-10) REVERT: D 189 ASP cc_start: 0.8021 (t0) cc_final: 0.7569 (t0) REVERT: D 204 GLU cc_start: 0.7795 (mp0) cc_final: 0.7207 (mp0) REVERT: D 206 GLU cc_start: 0.7968 (pm20) cc_final: 0.7433 (mp0) REVERT: D 220 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7352 (tm-30) REVERT: D 314 ASN cc_start: 0.8047 (m-40) cc_final: 0.7644 (m-40) REVERT: D 340 ILE cc_start: 0.7410 (OUTLIER) cc_final: 0.7167 (mp) REVERT: E 19 TYR cc_start: 0.9080 (t80) cc_final: 0.8689 (t80) outliers start: 66 outliers final: 55 residues processed: 457 average time/residue: 0.2494 time to fit residues: 176.9205 Evaluate side-chains 471 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 413 time to evaluate : 1.874 ------------------------------------------------------------------------------- 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 47 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 287 THR 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 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 317 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 190 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 135 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 129 optimal weight: 0.2980 chunk 158 optimal weight: 0.0020 chunk 90 optimal weight: 0.0040 chunk 131 optimal weight: 0.2980 chunk 137 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 overall best weight: 0.2400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN E 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.158615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.115563 restraints weight = 19848.047| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.50 r_work: 0.3122 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3118 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16505 Z= 0.122 Angle : 0.552 9.962 22382 Z= 0.286 Chirality : 0.042 0.197 2545 Planarity : 0.004 0.052 2798 Dihedral : 4.140 17.726 2165 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.14 % Allowed : 22.29 % Favored : 74.57 % 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: 1.07 (0.20), residues: 1940 helix: 2.49 (0.17), residues: 957 sheet: 0.28 (0.27), residues: 358 loop : -1.99 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 50 HIS 0.003 0.000 HIS C 212 PHE 0.017 0.001 PHE C 27 TYR 0.028 0.001 TYR D 34 ARG 0.007 0.000 ARG E 165 Details of bonding type rmsd hydrogen bonds : bond 0.04750 ( 981) hydrogen bonds : angle 4.20918 ( 2868) SS BOND : bond 0.00393 ( 2) SS BOND : angle 0.90873 ( 4) covalent geometry : bond 0.00262 (16503) covalent geometry : angle 0.55182 (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 466 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 409 time to evaluate : 1.763 Fit side-chains revert: symmetry clash REVERT: L 27 SER cc_start: 0.9165 (t) cc_final: 0.8690 (m) REVERT: A 30 GLU cc_start: 0.7581 (tt0) cc_final: 0.7054 (mm-30) REVERT: A 105 TYR cc_start: 0.8482 (p90) cc_final: 0.7710 (p90) REVERT: A 152 GLU cc_start: 0.7103 (mm-30) cc_final: 0.6626 (mm-30) REVERT: A 162 ARG cc_start: 0.7774 (mtp180) cc_final: 0.7341 (mtp180) REVERT: A 313 MET cc_start: 0.7226 (mpp) cc_final: 0.7010 (mpp) REVERT: B 244 GLU cc_start: 0.6922 (mm-30) cc_final: 0.6141 (mt-10) REVERT: B 318 MET cc_start: 0.7626 (tpt) cc_final: 0.6835 (tpt) REVERT: C 74 GLN cc_start: 0.5061 (OUTLIER) cc_final: 0.4278 (mp10) REVERT: D 54 ARG cc_start: 0.7320 (ptt90) cc_final: 0.6239 (ptt90) REVERT: D 100 GLU cc_start: 0.8080 (mp0) cc_final: 0.7273 (mt-10) REVERT: D 152 GLU cc_start: 0.5888 (OUTLIER) cc_final: 0.5681 (mp0) REVERT: D 189 ASP cc_start: 0.7870 (t0) cc_final: 0.7436 (t0) REVERT: D 204 GLU cc_start: 0.7718 (mp0) cc_final: 0.7188 (mp0) REVERT: D 206 GLU cc_start: 0.7839 (pm20) cc_final: 0.7309 (mp0) REVERT: D 220 GLU cc_start: 0.7575 (tm-30) cc_final: 0.6672 (tm-30) REVERT: D 340 ILE cc_start: 0.7224 (OUTLIER) cc_final: 0.7009 (mp) REVERT: E 19 TYR cc_start: 0.8967 (t80) cc_final: 0.8541 (t80) REVERT: E 32 MET cc_start: 0.8390 (mtp) cc_final: 0.8178 (ttm) outliers start: 57 outliers final: 51 residues processed: 435 average time/residue: 0.2456 time to fit residues: 165.1939 Evaluate side-chains 452 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 398 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 8 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 94 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 124 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 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 152 GLU Chi-restraints excluded: chain D residue 183 VAL Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 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 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 247 THR 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: 1.9990 chunk 177 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 174 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 153 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3726 r_free = 0.3726 target = 0.155190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.118731 restraints weight = 19894.594| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.49 r_work: 0.3074 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2921 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2921 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2104 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= 0.180 Angle : 0.584 9.628 22382 Z= 0.302 Chirality : 0.044 0.181 2545 Planarity : 0.004 0.053 2798 Dihedral : 4.199 18.402 2165 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.36 % Allowed : 22.40 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.99 (0.20), residues: 1940 helix: 2.39 (0.17), residues: 958 sheet: 0.23 (0.27), residues: 365 loop : -2.00 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 119 HIS 0.003 0.001 HIS A 257 PHE 0.019 0.001 PHE C 27 TYR 0.029 0.002 TYR D 34 ARG 0.006 0.000 ARG E 165 Details of bonding type rmsd hydrogen bonds : bond 0.05183 ( 981) hydrogen bonds : angle 4.32219 ( 2868) SS BOND : bond 0.00276 ( 2) SS BOND : angle 1.09851 ( 4) covalent geometry : bond 0.00429 (16503) covalent geometry : angle 0.58368 (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 475 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 414 time to evaluate : 1.982 Fit side-chains revert: symmetry clash REVERT: L 27 SER cc_start: 0.9220 (t) cc_final: 0.8743 (m) REVERT: A 105 TYR cc_start: 0.8571 (p90) cc_final: 0.7893 (p90) REVERT: A 148 ASP cc_start: 0.8035 (m-30) cc_final: 0.7823 (m-30) REVERT: A 162 ARG cc_start: 0.7976 (mtp180) cc_final: 0.7527 (mtp180) REVERT: B 238 ASP cc_start: 0.6919 (m-30) cc_final: 0.6513 (m-30) REVERT: B 244 GLU cc_start: 0.7106 (mm-30) cc_final: 0.6296 (mt-10) REVERT: B 318 MET cc_start: 0.7766 (tpt) cc_final: 0.6908 (tpt) REVERT: C 74 GLN cc_start: 0.5214 (OUTLIER) cc_final: 0.4320 (mp10) REVERT: C 141 GLU cc_start: 0.7337 (tp30) cc_final: 0.6832 (mm-30) REVERT: D 54 ARG cc_start: 0.7342 (ptt90) cc_final: 0.6240 (ptt90) REVERT: D 100 GLU cc_start: 0.8214 (mp0) cc_final: 0.7442 (mt-10) REVERT: D 152 GLU cc_start: 0.6060 (OUTLIER) cc_final: 0.5849 (mp0) REVERT: D 189 ASP cc_start: 0.8015 (t0) cc_final: 0.7576 (t0) REVERT: D 204 GLU cc_start: 0.7830 (mp0) cc_final: 0.7273 (mp0) REVERT: D 206 GLU cc_start: 0.7939 (pm20) cc_final: 0.7405 (mp0) REVERT: D 220 GLU cc_start: 0.7859 (tm-30) cc_final: 0.6983 (tm-30) REVERT: D 314 ASN cc_start: 0.8052 (m-40) cc_final: 0.7655 (m-40) REVERT: D 340 ILE cc_start: 0.7321 (OUTLIER) cc_final: 0.7087 (mp) REVERT: E 19 TYR cc_start: 0.9086 (t80) cc_final: 0.8652 (t80) REVERT: E 297 ILE cc_start: 0.7845 (tt) cc_final: 0.7619 (tt) outliers start: 61 outliers final: 53 residues processed: 444 average time/residue: 0.2488 time to fit residues: 171.1985 Evaluate side-chains 466 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 410 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 8 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 94 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 63 ASN Chi-restraints excluded: chain C residue 74 GLN Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 137 LEU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 282 SER Chi-restraints excluded: chain C residue 296 ILE 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 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 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: 0.0030 chunk 40 optimal weight: 4.9990 chunk 187 optimal weight: 0.7980 chunk 165 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 123 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- 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 = 0.3741 r_free = 0.3741 target = 0.156522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.118149 restraints weight = 19657.875| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.47 r_work: 0.3089 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2123 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= 0.147 Angle : 0.567 9.930 22382 Z= 0.294 Chirality : 0.043 0.192 2545 Planarity : 0.004 0.055 2798 Dihedral : 4.177 17.905 2165 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.25 % Allowed : 22.62 % 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: 1.02 (0.20), residues: 1940 helix: 2.43 (0.17), residues: 957 sheet: 0.26 (0.27), residues: 361 loop : -1.99 (0.24), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 61 HIS 0.002 0.000 HIS C 212 PHE 0.018 0.001 PHE C 27 TYR 0.029 0.001 TYR D 34 ARG 0.007 0.000 ARG E 165 Details of bonding type rmsd hydrogen bonds : bond 0.05010 ( 981) hydrogen bonds : angle 4.27357 ( 2868) SS BOND : bond 0.00287 ( 2) SS BOND : angle 1.03628 ( 4) covalent geometry : bond 0.00341 (16503) covalent geometry : angle 0.56720 (22378) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10980.44 seconds wall clock time: 191 minutes 33.03 seconds (11493.03 seconds total)