Starting phenix.real_space_refine on Sun May 18 06:43:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tmn_41395/05_2025/8tmn_41395.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tmn_41395/05_2025/8tmn_41395.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tmn_41395/05_2025/8tmn_41395.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tmn_41395/05_2025/8tmn_41395.map" model { file = "/net/cci-nas-00/data/ceres_data/8tmn_41395/05_2025/8tmn_41395.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tmn_41395/05_2025/8tmn_41395.cif" } resolution = 3.3 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= 0.015 sd= 0.037 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 3 5.21 5 S 58 5.16 5 C 10437 2.51 5 N 2613 2.21 5 O 2948 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16059 Number of models: 1 Model: "" Number of chains: 10 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: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2925 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 15, 'TRANS': 335} Chain: "C" Number of atoms: 2790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2790 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 13, 'TRANS': 319} Chain: "D" Number of atoms: 2890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2890 Classifications: {'peptide': 347} Link IDs: {'PTRANS': 15, 'TRANS': 331} Chain: "E" Number of atoms: 2860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2860 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 15, 'TRANS': 327} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.50, per 1000 atoms: 0.59 Number of scatterers: 16059 At special positions: 0 Unit cell: (125.434, 139.253, 138.19, 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 58 16.00 Mg 3 11.99 O 2948 8.00 N 2613 7.00 C 10437 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.86 Conformation dependent library (CDL) restraints added in 1.9 seconds 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3726 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 12 sheets defined 52.8% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'H' and resid 65 through 68 Processing helix chain 'H' and resid 90 through 94 removed outlier: 3.806A 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 removed outlier: 3.907A pdb=" N ASP A 55 " --> pdb=" O PRO A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 80 removed outlier: 3.571A pdb=" N VAL A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 92 Processing helix chain 'A' and resid 147 through 157 Processing helix chain 'A' and resid 160 through 165 removed outlier: 6.329A pdb=" N ARG A 165 " --> pdb=" O ARG A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 201 removed outlier: 3.696A pdb=" N LEU A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR A 171 " --> pdb=" O ASP A 167 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU A 197 " --> pdb=" O ASP A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 238 Proline residue: A 227 - end of helix removed outlier: 3.969A pdb=" N ASP A 238 " --> pdb=" O SER A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 282 removed outlier: 3.517A pdb=" N PHE A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER A 282 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 312 Proline residue: A 303 - end of helix Processing helix chain 'A' and resid 326 through 349 removed outlier: 3.559A pdb=" N VAL A 330 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR A 344 " --> pdb=" O ILE A 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 51 removed outlier: 3.864A pdb=" N VAL B 50 " --> pdb=" O ASP B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 55 removed outlier: 3.946A pdb=" N ASP B 55 " --> pdb=" O PRO B 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 52 through 55' Processing helix chain 'B' and resid 69 through 81 removed outlier: 3.655A pdb=" N VAL B 73 " --> pdb=" O ARG B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 91 Processing helix chain 'B' and resid 147 through 157 Processing helix chain 'B' and resid 160 through 164 Processing helix chain 'B' and resid 165 through 200 removed outlier: 3.563A pdb=" N LEU B 169 " --> pdb=" O ARG B 165 " (cutoff:3.500A) removed outlier: 4.173A 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 removed outlier: 3.654A pdb=" N TYR B 236 " --> pdb=" O LEU B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 311 removed outlier: 3.871A pdb=" N VAL B 290 " --> pdb=" O LYS B 286 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 325 through 348 Processing helix chain 'C' and resid 70 through 81 Processing helix chain 'C' and resid 83 through 92 Processing helix chain 'C' and resid 147 through 156 removed outlier: 3.812A pdb=" N ARG C 151 " --> pdb=" O PHE C 147 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE C 154 " --> pdb=" O VAL C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 202 removed outlier: 3.674A pdb=" N LEU C 170 " --> pdb=" O ALA C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 236 removed outlier: 3.588A pdb=" N VAL C 208 " --> pdb=" O GLU C 204 " (cutoff:3.500A) Proline residue: C 227 - end of helix Processing helix chain 'C' and resid 246 through 312 removed outlier: 4.421A pdb=" N TYR C 250 " --> pdb=" O GLU C 246 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE C 261 " --> pdb=" O HIS C 257 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA C 262 " --> pdb=" O THR C 258 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N THR C 264 " --> pdb=" O GLN C 260 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU C 266 " --> pdb=" O ALA C 262 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR C 267 " --> pdb=" O ASP C 263 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU C 280 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER C 281 " --> pdb=" O ASP C 277 " (cutoff:3.500A) Proline residue: C 303 - end of helix Processing helix chain 'C' and resid 325 through 347 removed outlier: 3.973A pdb=" N VAL C 329 " --> pdb=" O TRP C 325 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N MET C 341 " --> pdb=" O ILE C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 350 No H-bonds generated for 'chain 'C' and resid 348 through 350' Processing helix chain 'D' and resid 47 through 51 Processing helix chain 'D' and resid 70 through 81 Processing helix chain 'D' and resid 83 through 92 Processing helix chain 'D' and resid 147 through 157 removed outlier: 3.646A pdb=" N ARG D 151 " --> pdb=" O PHE D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 202 removed outlier: 3.631A pdb=" N LEU D 169 " --> pdb=" O ARG D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 238 removed outlier: 3.702A pdb=" N VAL D 208 " --> pdb=" O GLU D 204 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN D 209 " --> pdb=" O LYS D 205 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N TRP D 226 " --> pdb=" O ARG D 222 " (cutoff:3.500A) Proline residue: D 227 - end of helix removed outlier: 3.815A pdb=" N SER D 234 " --> pdb=" O GLU D 230 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU D 235 " --> pdb=" O VAL D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 311 removed outlier: 3.790A pdb=" N PHE D 251 " --> pdb=" O THR D 247 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG D 252 " --> pdb=" O VAL D 248 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP D 253 " --> pdb=" O PRO D 249 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL D 254 " --> pdb=" O TYR D 250 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ASP D 263 " --> pdb=" O ILE D 259 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N THR D 264 " --> pdb=" O GLN D 260 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP D 270 " --> pdb=" O GLU D 266 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU D 275 " --> pdb=" O ILE D 271 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP D 277 " --> pdb=" O SER D 273 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE D 297 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA D 298 " --> pdb=" O LEU D 294 " (cutoff:3.500A) Proline residue: D 303 - end of helix Processing helix chain 'D' and resid 326 through 349 removed outlier: 3.835A pdb=" N VAL D 330 " --> pdb=" O GLY D 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 56 removed outlier: 3.547A pdb=" N ASP E 55 " --> pdb=" O PRO E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 81 removed outlier: 3.713A 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 165 through 202 removed outlier: 3.660A 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: 3.643A pdb=" N GLU E 230 " --> pdb=" O TRP E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 246 No H-bonds generated for 'chain 'E' and resid 244 through 246' Processing helix chain 'E' and resid 247 through 312 removed outlier: 3.782A pdb=" N ASP E 253 " --> pdb=" O PRO E 249 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL E 254 " --> pdb=" O TYR E 250 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU E 276 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ASP E 277 " --> pdb=" O SER E 273 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA E 298 " --> pdb=" O LEU E 294 " (cutoff:3.500A) Proline residue: E 303 - end of helix Processing helix chain 'E' and resid 325 through 348 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: 6.401A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 3.625A 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: 6.401A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N TYR L 50 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 6.683A 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 14 through 15 removed outlier: 3.713A pdb=" N SER H 36 " --> pdb=" O SER H 102 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA H 52 " --> pdb=" O TRP H 39 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 14 through 15 removed outlier: 6.533A pdb=" N ARG H 101 " --> pdb=" O ASP H 117 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 39 through 44 removed outlier: 3.513A pdb=" N LYS A 98 " --> pdb=" O VAL A 109 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 39 through 44 Processing sheet with id=AA9, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AB1, first strand: chain 'C' and resid 99 through 101 removed outlier: 3.683A pdb=" N SER C 128 " --> pdb=" O PHE C 139 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 39 through 44 removed outlier: 3.867A pdb=" N PHE D 42 " --> pdb=" O VAL D 31 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL D 31 " --> pdb=" O PHE D 42 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR D 44 " --> pdb=" O ILE D 29 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ILE D 29 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL D 136 " --> pdb=" O THR D 60 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 28 through 32 removed outlier: 3.808A pdb=" N GLU E 121 " --> pdb=" O ASP E 116 " (cutoff:3.500A) 996 hydrogen bonds defined for protein. 2847 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: 4.90 Time building geometry restraints manager: 4.51 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: 5048 1.34 - 1.46: 3075 1.46 - 1.58: 8193 1.58 - 1.69: 0 1.69 - 1.81: 107 Bond restraints: 16423 Sorted by residual: bond pdb=" C LEU E 51 " pdb=" N PRO E 52 " ideal model delta sigma weight residual 1.337 1.357 -0.020 9.80e-03 1.04e+04 4.15e+00 bond pdb=" CA ARG D 202 " pdb=" CB ARG D 202 " ideal model delta sigma weight residual 1.526 1.538 -0.012 9.30e-03 1.16e+04 1.71e+00 bond pdb=" CB VAL B 254 " pdb=" CG2 VAL B 254 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.51e+00 bond pdb=" C LEU B 51 " pdb=" N PRO B 52 " ideal model delta sigma weight residual 1.334 1.358 -0.024 2.34e-02 1.83e+03 1.06e+00 bond pdb=" C ASP D 148 " pdb=" N PRO D 149 " ideal model delta sigma weight residual 1.335 1.348 -0.013 1.28e-02 6.10e+03 1.03e+00 ... (remaining 16418 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 21926 2.13 - 4.25: 291 4.25 - 6.38: 50 6.38 - 8.50: 3 8.50 - 10.63: 1 Bond angle restraints: 22271 Sorted by residual: angle pdb=" C VAL C 50 " pdb=" N LEU C 51 " pdb=" CA LEU C 51 " ideal model delta sigma weight residual 121.80 132.43 -10.63 2.44e+00 1.68e-01 1.90e+01 angle pdb=" C GLY D 326 " pdb=" N TYR D 327 " pdb=" CA TYR D 327 " ideal model delta sigma weight residual 121.80 129.86 -8.06 2.44e+00 1.68e-01 1.09e+01 angle pdb=" C LEU E 235 " pdb=" N TYR E 236 " pdb=" CA TYR E 236 " ideal model delta sigma weight residual 122.36 116.87 5.49 1.72e+00 3.38e-01 1.02e+01 angle pdb=" N GLY C 326 " pdb=" CA GLY C 326 " pdb=" C GLY C 326 " ideal model delta sigma weight residual 113.86 118.34 -4.48 1.50e+00 4.44e-01 8.93e+00 angle pdb=" N GLU A 78 " pdb=" CA GLU A 78 " pdb=" CB GLU A 78 " ideal model delta sigma weight residual 110.16 114.35 -4.19 1.48e+00 4.57e-01 8.03e+00 ... (remaining 22266 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 8761 17.92 - 35.84: 900 35.84 - 53.75: 167 53.75 - 71.67: 18 71.67 - 89.59: 22 Dihedral angle restraints: 9868 sinusoidal: 4103 harmonic: 5765 Sorted by residual: dihedral pdb=" CA HIS D 68 " pdb=" C HIS D 68 " pdb=" N ARG D 69 " pdb=" CA ARG D 69 " ideal model delta harmonic sigma weight residual 180.00 157.93 22.07 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA LEU B 321 " pdb=" C LEU B 321 " pdb=" N ARG B 322 " pdb=" CA ARG B 322 " ideal model delta harmonic sigma weight residual 180.00 -159.22 -20.78 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA PHE C 315 " pdb=" C PHE C 315 " pdb=" N GLU C 316 " pdb=" CA GLU C 316 " ideal model delta harmonic sigma weight residual -180.00 -159.78 -20.22 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 9865 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2024 0.053 - 0.106: 434 0.106 - 0.159: 70 0.159 - 0.213: 2 0.213 - 0.266: 2 Chirality restraints: 2532 Sorted by residual: chirality pdb=" CA ASP D 148 " pdb=" N ASP D 148 " pdb=" C ASP D 148 " pdb=" CB ASP D 148 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CB ILE D 130 " pdb=" CA ILE D 130 " pdb=" CG1 ILE D 130 " pdb=" CG2 ILE D 130 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA PRO D 227 " pdb=" N PRO D 227 " pdb=" C PRO D 227 " pdb=" CB PRO D 227 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.07e-01 ... (remaining 2529 not shown) Planarity restraints: 2785 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 202 " 0.058 5.00e-02 4.00e+02 8.85e-02 1.25e+01 pdb=" N PRO B 203 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO B 203 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 203 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP D 226 " -0.048 5.00e-02 4.00e+02 7.16e-02 8.21e+00 pdb=" N PRO D 227 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO D 227 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 227 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 148 " 0.042 5.00e-02 4.00e+02 6.31e-02 6.36e+00 pdb=" N PRO D 149 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO D 149 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 149 " 0.036 5.00e-02 4.00e+02 ... (remaining 2782 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 171 2.64 - 3.21: 15635 3.21 - 3.77: 25119 3.77 - 4.34: 33822 4.34 - 4.90: 54889 Nonbonded interactions: 129636 Sorted by model distance: nonbonded pdb=" O LYS C 111 " pdb=" OH TYR C 181 " model vdw 2.081 3.040 nonbonded pdb=" O VAL C 208 " pdb=" OG1 THR C 211 " model vdw 2.148 3.040 nonbonded pdb=" O TYR A 255 " pdb=" OG1 THR A 258 " model vdw 2.202 3.040 nonbonded pdb=" O TYR D 255 " pdb=" OG1 THR D 258 " model vdw 2.207 3.040 nonbonded pdb=" OD1 ASN C 33 " pdb=" OG1 THR C 58 " model vdw 2.233 3.040 ... (remaining 129631 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 19 through 351) selection = (chain 'B' and resid 19 through 351) selection = chain 'C' selection = (chain 'D' and resid 19 through 351) selection = (chain 'E' and resid 19 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: 3.870 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: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 34.940 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.070 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 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 0.041 16425 Z= 0.147 Angle : 0.625 10.629 22275 Z= 0.336 Chirality : 0.044 0.266 2532 Planarity : 0.006 0.088 2785 Dihedral : 14.945 89.588 6136 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.94 % Favored : 95.96 % Rotamer: Outliers : 0.06 % Allowed : 0.33 % Favored : 99.61 % 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: 0.01 (0.19), residues: 1930 helix: 0.82 (0.17), residues: 952 sheet: 0.57 (0.27), residues: 382 loop : -1.66 (0.24), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 350 HIS 0.004 0.001 HIS C 212 PHE 0.023 0.001 PHE E 27 TYR 0.030 0.001 TYR H 103 ARG 0.007 0.001 ARG D 96 Details of bonding type rmsd hydrogen bonds : bond 0.14164 ( 980) hydrogen bonds : angle 6.78540 ( 2847) SS BOND : bond 0.00303 ( 2) SS BOND : angle 1.12728 ( 4) covalent geometry : bond 0.00311 (16423) covalent geometry : angle 0.62518 (22271) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 461 time to evaluate : 1.864 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 102 SER cc_start: 0.8125 (p) cc_final: 0.7839 (p) REVERT: A 89 ASP cc_start: 0.7034 (m-30) cc_final: 0.6626 (m-30) REVERT: A 104 ASN cc_start: 0.7371 (m110) cc_final: 0.7153 (m110) REVERT: A 178 VAL cc_start: 0.7021 (t) cc_final: 0.5712 (p) REVERT: A 191 GLU cc_start: 0.6904 (mm-30) cc_final: 0.6664 (mm-30) REVERT: A 320 GLU cc_start: 0.5501 (pm20) cc_final: 0.4883 (tm-30) REVERT: B 85 LEU cc_start: 0.8611 (tp) cc_final: 0.8001 (tt) REVERT: B 89 ASP cc_start: 0.6900 (m-30) cc_final: 0.6565 (m-30) REVERT: B 318 MET cc_start: 0.3435 (mmt) cc_final: 0.2749 (mmt) REVERT: C 257 HIS cc_start: 0.8567 (m170) cc_final: 0.7882 (m90) REVERT: C 304 LEU cc_start: 0.8165 (mm) cc_final: 0.7858 (mm) REVERT: D 90 ILE cc_start: 0.8706 (pt) cc_final: 0.7995 (mt) REVERT: D 197 GLU cc_start: 0.8065 (pp20) cc_final: 0.7844 (pp20) REVERT: D 295 THR cc_start: 0.7565 (m) cc_final: 0.7319 (m) REVERT: E 85 LEU cc_start: 0.7379 (mm) cc_final: 0.6804 (mm) REVERT: E 89 ASP cc_start: 0.6993 (m-30) cc_final: 0.6373 (m-30) outliers start: 1 outliers final: 0 residues processed: 461 average time/residue: 0.2722 time to fit residues: 183.1419 Evaluate side-chains 395 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 395 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 161 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 77 optimal weight: 0.0770 chunk 149 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 173 optimal weight: 1.9990 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 ASN D 74 GLN ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 ASN E 209 GLN E 212 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.160137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.124661 restraints weight = 28393.354| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 3.04 r_work: 0.3280 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3272 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3271 r_free = 0.3271 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3271 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 16425 Z= 0.247 Angle : 0.697 10.730 22275 Z= 0.362 Chirality : 0.046 0.222 2532 Planarity : 0.006 0.057 2785 Dihedral : 4.844 23.256 2155 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.89 % Favored : 96.01 % Rotamer: Outliers : 2.05 % Allowed : 12.28 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.49 (0.19), residues: 1930 helix: 1.41 (0.16), residues: 965 sheet: 0.50 (0.27), residues: 364 loop : -1.59 (0.24), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 226 HIS 0.005 0.001 HIS D 68 PHE 0.024 0.002 PHE A 79 TYR 0.026 0.002 TYR H 106 ARG 0.005 0.001 ARG A 237 Details of bonding type rmsd hydrogen bonds : bond 0.05782 ( 980) hydrogen bonds : angle 5.01275 ( 2847) SS BOND : bond 0.03564 ( 2) SS BOND : angle 3.72170 ( 4) covalent geometry : bond 0.00581 (16423) covalent geometry : angle 0.69556 (22271) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 412 time to evaluate : 1.956 Fit side-chains revert: symmetry clash REVERT: H 4 GLU cc_start: 0.6866 (tp30) cc_final: 0.6603 (tp30) REVERT: H 123 THR cc_start: 0.8839 (p) cc_final: 0.8620 (p) REVERT: A 63 ASN cc_start: 0.8451 (t0) cc_final: 0.8240 (t0) REVERT: A 73 VAL cc_start: 0.8154 (p) cc_final: 0.7953 (t) REVERT: A 89 ASP cc_start: 0.7351 (m-30) cc_final: 0.6869 (m-30) REVERT: A 104 ASN cc_start: 0.7903 (m110) cc_final: 0.7654 (m110) REVERT: A 191 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7522 (mm-30) REVERT: A 197 GLU cc_start: 0.6547 (tm-30) cc_final: 0.6324 (tm-30) REVERT: A 259 ILE cc_start: 0.8739 (mp) cc_final: 0.8212 (mp) REVERT: A 263 ASP cc_start: 0.7841 (m-30) cc_final: 0.7501 (m-30) REVERT: A 277 ASP cc_start: 0.7631 (t0) cc_final: 0.6834 (t0) REVERT: B 85 LEU cc_start: 0.8839 (tp) cc_final: 0.8111 (tt) REVERT: B 89 ASP cc_start: 0.7836 (m-30) cc_final: 0.7462 (m-30) REVERT: B 212 HIS cc_start: 0.7369 (m-70) cc_final: 0.6890 (m-70) REVERT: C 200 LEU cc_start: 0.7360 (mt) cc_final: 0.6954 (mt) REVERT: C 233 SER cc_start: 0.8254 (m) cc_final: 0.8023 (p) REVERT: C 257 HIS cc_start: 0.8719 (m170) cc_final: 0.7950 (m90) REVERT: C 291 MET cc_start: 0.8220 (mmt) cc_final: 0.7715 (mmm) REVERT: D 63 ASN cc_start: 0.7666 (p0) cc_final: 0.7115 (p0) REVERT: D 90 ILE cc_start: 0.8755 (pt) cc_final: 0.8257 (mt) REVERT: D 197 GLU cc_start: 0.8504 (pp20) cc_final: 0.8218 (pp20) REVERT: D 246 GLU cc_start: 0.8642 (pt0) cc_final: 0.8410 (pp20) REVERT: E 27 PHE cc_start: 0.6834 (t80) cc_final: 0.6625 (t80) REVERT: E 85 LEU cc_start: 0.7906 (mm) cc_final: 0.7183 (mm) REVERT: E 89 ASP cc_start: 0.7316 (m-30) cc_final: 0.6715 (m-30) REVERT: E 252 ARG cc_start: 0.8102 (ttp80) cc_final: 0.7634 (ttp80) REVERT: E 256 ASP cc_start: 0.7879 (m-30) cc_final: 0.7651 (m-30) REVERT: E 318 MET cc_start: 0.3116 (mmp) cc_final: 0.2697 (mmp) outliers start: 37 outliers final: 30 residues processed: 430 average time/residue: 0.2723 time to fit residues: 173.8795 Evaluate side-chains 425 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 395 time to evaluate : 1.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain A residue 78 GLU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 126 GLN Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 285 ASN Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 302 MET Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 313 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 4 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 180 optimal weight: 5.9990 chunk 157 optimal weight: 0.9990 chunk 185 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 119 optimal weight: 0.6980 chunk 85 optimal weight: 0.4980 chunk 18 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 28 GLN L 101 GLN ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 GLN ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.163008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.121729 restraints weight = 28464.741| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.50 r_work: 0.3337 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3328 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3328 r_free = 0.3328 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3328 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16425 Z= 0.170 Angle : 0.636 10.634 22275 Z= 0.330 Chirality : 0.044 0.190 2532 Planarity : 0.005 0.051 2785 Dihedral : 4.716 22.605 2155 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.37 % Favored : 96.53 % Rotamer: Outliers : 2.65 % Allowed : 16.10 % Favored : 81.25 % 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: 0.74 (0.19), residues: 1930 helix: 1.75 (0.16), residues: 965 sheet: 0.35 (0.27), residues: 363 loop : -1.52 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 61 HIS 0.016 0.001 HIS D 68 PHE 0.014 0.001 PHE E 301 TYR 0.024 0.001 TYR A 19 ARG 0.005 0.000 ARG B 158 Details of bonding type rmsd hydrogen bonds : bond 0.05285 ( 980) hydrogen bonds : angle 4.70316 ( 2847) SS BOND : bond 0.00245 ( 2) SS BOND : angle 2.54319 ( 4) covalent geometry : bond 0.00387 (16423) covalent geometry : angle 0.63478 (22271) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 408 time to evaluate : 1.956 Fit side-chains revert: symmetry clash REVERT: H 123 THR cc_start: 0.8811 (p) cc_final: 0.8583 (p) REVERT: A 40 ARG cc_start: 0.7580 (ptm-80) cc_final: 0.7361 (ptm-80) REVERT: A 89 ASP cc_start: 0.7351 (m-30) cc_final: 0.6887 (m-30) REVERT: A 104 ASN cc_start: 0.7898 (m110) cc_final: 0.7627 (m110) REVERT: A 199 VAL cc_start: 0.7904 (t) cc_final: 0.7701 (t) REVERT: A 259 ILE cc_start: 0.8649 (mt) cc_final: 0.8341 (mp) REVERT: A 277 ASP cc_start: 0.7526 (t0) cc_final: 0.6784 (t0) REVERT: B 85 LEU cc_start: 0.8751 (tp) cc_final: 0.8045 (tt) REVERT: B 89 ASP cc_start: 0.7760 (m-30) cc_final: 0.7349 (m-30) REVERT: B 212 HIS cc_start: 0.7339 (m-70) cc_final: 0.6897 (m-70) REVERT: C 132 THR cc_start: 0.5440 (OUTLIER) cc_final: 0.5079 (p) REVERT: C 232 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7304 (tt) REVERT: C 257 HIS cc_start: 0.8690 (m170) cc_final: 0.7910 (m90) REVERT: C 291 MET cc_start: 0.8226 (mmt) cc_final: 0.7803 (mmm) REVERT: C 341 MET cc_start: 0.7713 (mpp) cc_final: 0.7440 (mtm) REVERT: D 61 TRP cc_start: 0.7493 (t60) cc_final: 0.7100 (t-100) REVERT: D 63 ASN cc_start: 0.7439 (p0) cc_final: 0.6540 (p0) REVERT: D 90 ILE cc_start: 0.8719 (pt) cc_final: 0.8445 (mt) REVERT: D 197 GLU cc_start: 0.8445 (pp20) cc_final: 0.8149 (pp20) REVERT: D 246 GLU cc_start: 0.8587 (pt0) cc_final: 0.8382 (pp20) REVERT: E 39 PHE cc_start: 0.7355 (p90) cc_final: 0.7100 (p90) REVERT: E 85 LEU cc_start: 0.7812 (mm) cc_final: 0.7266 (mm) REVERT: E 89 ASP cc_start: 0.7293 (m-30) cc_final: 0.6681 (m-30) REVERT: E 165 ARG cc_start: 0.8063 (mmp80) cc_final: 0.7819 (mmp80) REVERT: E 204 GLU cc_start: 0.6314 (OUTLIER) cc_final: 0.5000 (pm20) REVERT: E 318 MET cc_start: 0.3424 (mmp) cc_final: 0.3014 (mmp) outliers start: 48 outliers final: 32 residues processed: 431 average time/residue: 0.2746 time to fit residues: 174.2343 Evaluate side-chains 425 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 390 time to evaluate : 1.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain A residue 42 PHE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 126 GLN Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 285 ASN Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain D residue 120 HIS Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 270 ASP Chi-restraints excluded: chain E residue 283 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 27 optimal weight: 0.0070 chunk 174 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 167 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 168 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 148 optimal weight: 5.9990 chunk 104 optimal weight: 8.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 28 GLN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 GLN ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 GLN ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.163200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.121810 restraints weight = 28445.014| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.52 r_work: 0.3337 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3336 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3336 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16425 Z= 0.171 Angle : 0.630 10.598 22275 Z= 0.328 Chirality : 0.044 0.185 2532 Planarity : 0.005 0.049 2785 Dihedral : 4.693 21.856 2155 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.42 % Favored : 96.48 % Rotamer: Outliers : 3.37 % Allowed : 16.98 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.19), residues: 1930 helix: 1.80 (0.17), residues: 966 sheet: 0.31 (0.27), residues: 362 loop : -1.46 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 50 HIS 0.012 0.001 HIS D 68 PHE 0.022 0.002 PHE B 306 TYR 0.021 0.001 TYR H 106 ARG 0.005 0.000 ARG A 237 Details of bonding type rmsd hydrogen bonds : bond 0.05113 ( 980) hydrogen bonds : angle 4.59067 ( 2847) SS BOND : bond 0.00915 ( 2) SS BOND : angle 2.47202 ( 4) covalent geometry : bond 0.00393 (16423) covalent geometry : angle 0.62928 (22271) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 410 time to evaluate : 1.887 Fit side-chains REVERT: H 123 THR cc_start: 0.8821 (p) cc_final: 0.8591 (p) REVERT: A 40 ARG cc_start: 0.7628 (ptm-80) cc_final: 0.7389 (ttp-110) REVERT: A 89 ASP cc_start: 0.7347 (m-30) cc_final: 0.6860 (m-30) REVERT: A 104 ASN cc_start: 0.7829 (m110) cc_final: 0.7575 (m110) REVERT: A 173 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8041 (mt) REVERT: A 199 VAL cc_start: 0.7980 (t) cc_final: 0.7766 (t) REVERT: A 259 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8266 (mp) REVERT: A 277 ASP cc_start: 0.7607 (t0) cc_final: 0.6942 (t0) REVERT: B 85 LEU cc_start: 0.8738 (tp) cc_final: 0.8064 (tt) REVERT: B 89 ASP cc_start: 0.7755 (m-30) cc_final: 0.7343 (m-30) REVERT: B 212 HIS cc_start: 0.7358 (m-70) cc_final: 0.6942 (m-70) REVERT: C 43 LYS cc_start: 0.7850 (mtmt) cc_final: 0.7599 (mtmt) REVERT: C 250 TYR cc_start: 0.8210 (m-80) cc_final: 0.7903 (m-80) REVERT: C 257 HIS cc_start: 0.8667 (m170) cc_final: 0.7882 (m90) REVERT: C 341 MET cc_start: 0.7752 (mpp) cc_final: 0.7484 (mtm) REVERT: D 90 ILE cc_start: 0.8764 (pt) cc_final: 0.8498 (mt) REVERT: D 197 GLU cc_start: 0.8447 (pp20) cc_final: 0.8151 (pp20) REVERT: E 39 PHE cc_start: 0.7354 (p90) cc_final: 0.7083 (p90) REVERT: E 85 LEU cc_start: 0.7748 (mm) cc_final: 0.7269 (mm) REVERT: E 89 ASP cc_start: 0.7328 (m-30) cc_final: 0.6746 (m-30) REVERT: E 165 ARG cc_start: 0.8089 (mmp80) cc_final: 0.7774 (mmp80) REVERT: E 204 GLU cc_start: 0.6345 (OUTLIER) cc_final: 0.5068 (pm20) REVERT: E 291 MET cc_start: 0.8102 (mmt) cc_final: 0.7643 (mmt) REVERT: E 318 MET cc_start: 0.3490 (mmp) cc_final: 0.3228 (mmp) outliers start: 61 outliers final: 43 residues processed: 442 average time/residue: 0.2716 time to fit residues: 178.5916 Evaluate side-chains 443 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 397 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 126 GLN Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 285 ASN Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain D residue 120 HIS Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 270 ASP Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 313 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 82 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 133 optimal weight: 7.9990 chunk 25 optimal weight: 0.0570 chunk 158 optimal weight: 0.3980 chunk 107 optimal weight: 2.9990 chunk 12 optimal weight: 0.1980 chunk 110 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 28 GLN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 GLN ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN ** D 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.164843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.129753 restraints weight = 28932.156| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.76 r_work: 0.3363 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3329 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3329 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16425 Z= 0.157 Angle : 0.618 10.583 22275 Z= 0.324 Chirality : 0.044 0.179 2532 Planarity : 0.005 0.050 2785 Dihedral : 4.655 22.393 2155 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.21 % Favored : 96.68 % Rotamer: Outliers : 3.82 % Allowed : 18.31 % Favored : 77.88 % 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: 1930 helix: 1.85 (0.17), residues: 966 sheet: 0.39 (0.27), residues: 360 loop : -1.45 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 61 HIS 0.011 0.001 HIS D 68 PHE 0.020 0.001 PHE E 27 TYR 0.025 0.001 TYR A 19 ARG 0.005 0.000 ARG E 54 Details of bonding type rmsd hydrogen bonds : bond 0.04921 ( 980) hydrogen bonds : angle 4.50177 ( 2847) SS BOND : bond 0.00023 ( 2) SS BOND : angle 2.17270 ( 4) covalent geometry : bond 0.00356 (16423) covalent geometry : angle 0.61740 (22271) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 405 time to evaluate : 1.830 Fit side-chains REVERT: H 123 THR cc_start: 0.8854 (p) cc_final: 0.8624 (p) REVERT: A 89 ASP cc_start: 0.7264 (m-30) cc_final: 0.6746 (m-30) REVERT: A 104 ASN cc_start: 0.7803 (m110) cc_final: 0.7577 (m110) REVERT: A 173 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8062 (mt) REVERT: A 199 VAL cc_start: 0.8010 (t) cc_final: 0.7744 (t) REVERT: A 259 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8291 (mp) REVERT: A 277 ASP cc_start: 0.7616 (t0) cc_final: 0.6958 (t0) REVERT: B 85 LEU cc_start: 0.8760 (tp) cc_final: 0.8087 (tt) REVERT: B 89 ASP cc_start: 0.7747 (m-30) cc_final: 0.7339 (m-30) REVERT: B 212 HIS cc_start: 0.7370 (m-70) cc_final: 0.6891 (m-70) REVERT: C 209 GLN cc_start: 0.8163 (tm-30) cc_final: 0.7830 (tm-30) REVERT: C 213 GLN cc_start: 0.8140 (pt0) cc_final: 0.7881 (pt0) REVERT: C 232 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7319 (tt) REVERT: C 250 TYR cc_start: 0.8257 (m-80) cc_final: 0.7960 (m-80) REVERT: C 257 HIS cc_start: 0.8697 (m170) cc_final: 0.8000 (m90) REVERT: D 23 TYR cc_start: 0.8112 (m-80) cc_final: 0.7887 (m-10) REVERT: D 32 MET cc_start: 0.7319 (ptp) cc_final: 0.7026 (mtm) REVERT: D 90 ILE cc_start: 0.8799 (pt) cc_final: 0.8520 (mt) REVERT: D 143 ILE cc_start: 0.8016 (OUTLIER) cc_final: 0.7786 (mt) REVERT: D 197 GLU cc_start: 0.8376 (pp20) cc_final: 0.8079 (pp20) REVERT: E 39 PHE cc_start: 0.7348 (p90) cc_final: 0.7114 (p90) REVERT: E 85 LEU cc_start: 0.7613 (mm) cc_final: 0.7125 (mm) REVERT: E 89 ASP cc_start: 0.7106 (m-30) cc_final: 0.6508 (m-30) REVERT: E 132 THR cc_start: 0.7028 (OUTLIER) cc_final: 0.6776 (t) REVERT: E 204 GLU cc_start: 0.6360 (OUTLIER) cc_final: 0.5093 (pm20) REVERT: E 318 MET cc_start: 0.3694 (mmp) cc_final: 0.3481 (mmp) outliers start: 69 outliers final: 48 residues processed: 444 average time/residue: 0.2704 time to fit residues: 177.6618 Evaluate side-chains 444 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 390 time to evaluate : 2.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 126 GLN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 285 ASN Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 270 ASP Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 284 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 105 optimal weight: 4.9990 chunk 115 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 chunk 101 optimal weight: 10.0000 chunk 174 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 145 optimal weight: 0.7980 chunk 112 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 28 GLN ** L 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 GLN B 74 GLN ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.162039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.126606 restraints weight = 28658.414| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.88 r_work: 0.3317 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3284 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3284 r_free = 0.3284 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3284 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 16425 Z= 0.234 Angle : 0.665 10.628 22275 Z= 0.348 Chirality : 0.046 0.231 2532 Planarity : 0.005 0.050 2785 Dihedral : 4.792 21.975 2155 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.94 % Favored : 95.96 % Rotamer: Outliers : 4.54 % Allowed : 18.53 % Favored : 76.94 % 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: 0.68 (0.19), residues: 1930 helix: 1.69 (0.16), residues: 963 sheet: 0.34 (0.27), residues: 366 loop : -1.54 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 50 HIS 0.006 0.001 HIS C 212 PHE 0.021 0.002 PHE E 27 TYR 0.030 0.002 TYR H 106 ARG 0.006 0.001 ARG B 54 Details of bonding type rmsd hydrogen bonds : bond 0.05268 ( 980) hydrogen bonds : angle 4.62066 ( 2847) SS BOND : bond 0.00210 ( 2) SS BOND : angle 2.55047 ( 4) covalent geometry : bond 0.00559 (16423) covalent geometry : angle 0.66386 (22271) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 393 time to evaluate : 1.777 Fit side-chains revert: symmetry clash REVERT: A 40 ARG cc_start: 0.7450 (ttp-110) cc_final: 0.7117 (ptm-80) REVERT: A 89 ASP cc_start: 0.7400 (m-30) cc_final: 0.6976 (m-30) REVERT: A 104 ASN cc_start: 0.7886 (m110) cc_final: 0.7669 (m110) REVERT: A 173 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8040 (mt) REVERT: A 199 VAL cc_start: 0.8084 (t) cc_final: 0.7862 (t) REVERT: A 259 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8362 (mp) REVERT: A 277 ASP cc_start: 0.7841 (t0) cc_final: 0.7152 (t0) REVERT: B 85 LEU cc_start: 0.8809 (tp) cc_final: 0.8123 (tt) REVERT: B 89 ASP cc_start: 0.7763 (m-30) cc_final: 0.7369 (m-30) REVERT: B 212 HIS cc_start: 0.7416 (m-70) cc_final: 0.6929 (m-70) REVERT: C 209 GLN cc_start: 0.8115 (tm-30) cc_final: 0.7791 (tm-30) REVERT: C 213 GLN cc_start: 0.8105 (pt0) cc_final: 0.7643 (pt0) REVERT: C 232 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7303 (tt) REVERT: C 250 TYR cc_start: 0.8282 (m-80) cc_final: 0.8010 (m-80) REVERT: C 257 HIS cc_start: 0.8637 (m170) cc_final: 0.7877 (m90) REVERT: C 278 VAL cc_start: 0.8805 (OUTLIER) cc_final: 0.8403 (m) REVERT: C 291 MET cc_start: 0.7873 (mmm) cc_final: 0.7614 (mmm) REVERT: C 341 MET cc_start: 0.7411 (mtm) cc_final: 0.6690 (mpp) REVERT: D 32 MET cc_start: 0.7191 (ptp) cc_final: 0.6937 (mtm) REVERT: D 90 ILE cc_start: 0.8844 (pt) cc_final: 0.8584 (mt) REVERT: D 143 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7838 (mt) REVERT: D 197 GLU cc_start: 0.8447 (pp20) cc_final: 0.8150 (pp20) REVERT: E 39 PHE cc_start: 0.7398 (p90) cc_final: 0.7090 (p90) REVERT: E 85 LEU cc_start: 0.7726 (mm) cc_final: 0.7228 (mm) REVERT: E 89 ASP cc_start: 0.7365 (m-30) cc_final: 0.6777 (m-30) REVERT: E 132 THR cc_start: 0.7169 (OUTLIER) cc_final: 0.6921 (t) REVERT: E 204 GLU cc_start: 0.6416 (OUTLIER) cc_final: 0.5224 (pm20) REVERT: E 318 MET cc_start: 0.3539 (mmp) cc_final: 0.3326 (mmp) outliers start: 82 outliers final: 62 residues processed: 441 average time/residue: 0.2787 time to fit residues: 181.9850 Evaluate side-chains 446 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 377 time to evaluate : 1.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain A residue 42 PHE Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 126 GLN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 285 ASN Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 120 HIS Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain E residue 212 HIS Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 313 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 60 optimal weight: 0.1980 chunk 93 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 115 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 GLN B 74 GLN ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.163553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.128721 restraints weight = 28592.155| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.83 r_work: 0.3353 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3325 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3325 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16425 Z= 0.159 Angle : 0.645 10.702 22275 Z= 0.332 Chirality : 0.044 0.221 2532 Planarity : 0.005 0.054 2785 Dihedral : 4.706 21.241 2155 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.47 % Favored : 96.42 % Rotamer: Outliers : 3.76 % Allowed : 20.58 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.19), residues: 1930 helix: 1.80 (0.17), residues: 964 sheet: 0.32 (0.27), residues: 370 loop : -1.52 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 226 HIS 0.009 0.001 HIS D 68 PHE 0.019 0.001 PHE E 27 TYR 0.028 0.001 TYR A 19 ARG 0.005 0.000 ARG A 237 Details of bonding type rmsd hydrogen bonds : bond 0.04927 ( 980) hydrogen bonds : angle 4.50427 ( 2847) SS BOND : bond 0.00069 ( 2) SS BOND : angle 2.01951 ( 4) covalent geometry : bond 0.00365 (16423) covalent geometry : angle 0.64441 (22271) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 389 time to evaluate : 1.751 Fit side-chains revert: symmetry clash REVERT: A 40 ARG cc_start: 0.7344 (ttp-110) cc_final: 0.7068 (ptm-80) REVERT: A 63 ASN cc_start: 0.8494 (t0) cc_final: 0.8201 (t0) REVERT: A 89 ASP cc_start: 0.7305 (m-30) cc_final: 0.6841 (m-30) REVERT: A 104 ASN cc_start: 0.7876 (m110) cc_final: 0.7668 (m110) REVERT: A 173 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8041 (mt) REVERT: A 199 VAL cc_start: 0.8078 (t) cc_final: 0.7840 (t) REVERT: A 259 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8263 (mp) REVERT: A 277 ASP cc_start: 0.7739 (t0) cc_final: 0.7098 (t0) REVERT: B 85 LEU cc_start: 0.8760 (tp) cc_final: 0.8072 (tt) REVERT: B 89 ASP cc_start: 0.7735 (m-30) cc_final: 0.7317 (m-30) REVERT: B 212 HIS cc_start: 0.7375 (m-70) cc_final: 0.6904 (m-70) REVERT: C 43 LYS cc_start: 0.8027 (mptt) cc_final: 0.7827 (mptt) REVERT: C 209 GLN cc_start: 0.8022 (tm-30) cc_final: 0.7583 (tm-30) REVERT: C 213 GLN cc_start: 0.8035 (pt0) cc_final: 0.7502 (pt0) REVERT: C 232 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7522 (tt) REVERT: C 250 TYR cc_start: 0.8290 (m-80) cc_final: 0.8032 (m-80) REVERT: C 257 HIS cc_start: 0.8659 (m170) cc_final: 0.7981 (m90) REVERT: C 278 VAL cc_start: 0.8828 (OUTLIER) cc_final: 0.8339 (m) REVERT: C 341 MET cc_start: 0.7411 (mtm) cc_final: 0.6643 (mpp) REVERT: D 32 MET cc_start: 0.7190 (ptp) cc_final: 0.6951 (mtm) REVERT: D 90 ILE cc_start: 0.8754 (pt) cc_final: 0.8453 (mt) REVERT: D 143 ILE cc_start: 0.8065 (OUTLIER) cc_final: 0.7836 (mt) REVERT: D 197 GLU cc_start: 0.8409 (pp20) cc_final: 0.8109 (pp20) REVERT: E 39 PHE cc_start: 0.7385 (p90) cc_final: 0.7055 (p90) REVERT: E 85 LEU cc_start: 0.7625 (mm) cc_final: 0.7128 (mm) REVERT: E 89 ASP cc_start: 0.7340 (m-30) cc_final: 0.6770 (m-30) REVERT: E 132 THR cc_start: 0.7103 (OUTLIER) cc_final: 0.6860 (t) REVERT: E 204 GLU cc_start: 0.6393 (OUTLIER) cc_final: 0.5154 (pm20) outliers start: 68 outliers final: 52 residues processed: 431 average time/residue: 0.2640 time to fit residues: 168.5338 Evaluate side-chains 433 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 374 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 126 GLN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 285 ASN Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 120 HIS Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain E residue 212 HIS Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 313 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 69 optimal weight: 0.9990 chunk 155 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 139 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 GLN B 74 GLN ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 257 HIS ** E 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.162951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.127820 restraints weight = 28493.972| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.78 r_work: 0.3326 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3297 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3297 r_free = 0.3297 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3297 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 16425 Z= 0.229 Angle : 0.689 10.618 22275 Z= 0.357 Chirality : 0.046 0.230 2532 Planarity : 0.005 0.051 2785 Dihedral : 4.809 21.555 2155 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.78 % Favored : 96.11 % Rotamer: Outliers : 4.37 % Allowed : 20.85 % Favored : 74.78 % 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: 0.58 (0.19), residues: 1930 helix: 1.64 (0.16), residues: 963 sheet: 0.22 (0.27), residues: 371 loop : -1.61 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 50 HIS 0.007 0.001 HIS D 68 PHE 0.019 0.002 PHE E 27 TYR 0.029 0.002 TYR H 106 ARG 0.010 0.001 ARG B 54 Details of bonding type rmsd hydrogen bonds : bond 0.05192 ( 980) hydrogen bonds : angle 4.63422 ( 2847) SS BOND : bond 0.00187 ( 2) SS BOND : angle 2.45074 ( 4) covalent geometry : bond 0.00547 (16423) covalent geometry : angle 0.68853 (22271) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 377 time to evaluate : 1.846 Fit side-chains revert: symmetry clash REVERT: A 40 ARG cc_start: 0.7399 (ttp-110) cc_final: 0.7071 (ptm-80) REVERT: A 63 ASN cc_start: 0.8485 (t0) cc_final: 0.8215 (t0) REVERT: A 89 ASP cc_start: 0.7369 (m-30) cc_final: 0.6910 (m-30) REVERT: A 104 ASN cc_start: 0.7876 (m110) cc_final: 0.7665 (m110) REVERT: A 173 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8034 (mt) REVERT: A 199 VAL cc_start: 0.8098 (t) cc_final: 0.7854 (t) REVERT: A 259 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8340 (mp) REVERT: A 277 ASP cc_start: 0.7863 (t0) cc_final: 0.7215 (t0) REVERT: A 320 GLU cc_start: 0.5763 (pm20) cc_final: 0.4854 (tm-30) REVERT: B 85 LEU cc_start: 0.8782 (tp) cc_final: 0.8093 (tt) REVERT: B 89 ASP cc_start: 0.7774 (m-30) cc_final: 0.7371 (m-30) REVERT: B 212 HIS cc_start: 0.7430 (m-70) cc_final: 0.6955 (m-70) REVERT: C 43 LYS cc_start: 0.8103 (mptt) cc_final: 0.7826 (mptt) REVERT: C 209 GLN cc_start: 0.8022 (tm-30) cc_final: 0.7550 (tm-30) REVERT: C 213 GLN cc_start: 0.8066 (pt0) cc_final: 0.7495 (pt0) REVERT: C 232 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7569 (tt) REVERT: C 250 TYR cc_start: 0.8400 (m-80) cc_final: 0.8138 (m-80) REVERT: C 257 HIS cc_start: 0.8643 (m170) cc_final: 0.7899 (m90) REVERT: C 278 VAL cc_start: 0.8846 (OUTLIER) cc_final: 0.8347 (m) REVERT: C 291 MET cc_start: 0.7854 (mmm) cc_final: 0.7636 (mmm) REVERT: C 341 MET cc_start: 0.7519 (mtm) cc_final: 0.6920 (mpp) REVERT: D 90 ILE cc_start: 0.8817 (pt) cc_final: 0.8543 (mt) REVERT: D 143 ILE cc_start: 0.8046 (OUTLIER) cc_final: 0.7829 (mt) REVERT: D 155 ARG cc_start: 0.8661 (mpp80) cc_final: 0.8376 (mtm-85) REVERT: D 186 GLU cc_start: 0.8641 (tt0) cc_final: 0.8215 (tp30) REVERT: D 197 GLU cc_start: 0.8401 (pp20) cc_final: 0.8114 (pp20) REVERT: D 291 MET cc_start: 0.8159 (mmm) cc_final: 0.7793 (mmt) REVERT: E 39 PHE cc_start: 0.7436 (p90) cc_final: 0.7101 (p90) REVERT: E 85 LEU cc_start: 0.7738 (mm) cc_final: 0.7226 (mm) REVERT: E 89 ASP cc_start: 0.7347 (m-30) cc_final: 0.6757 (m-30) REVERT: E 109 VAL cc_start: 0.8640 (OUTLIER) cc_final: 0.8414 (p) REVERT: E 204 GLU cc_start: 0.6453 (OUTLIER) cc_final: 0.5244 (pm20) REVERT: E 318 MET cc_start: 0.3090 (mmp) cc_final: 0.2795 (mmp) outliers start: 79 outliers final: 62 residues processed: 425 average time/residue: 0.2748 time to fit residues: 170.6467 Evaluate side-chains 443 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 374 time to evaluate : 1.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 82 GLU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 126 GLN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 285 ASN Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 234 SER Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 300 ILE Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain E residue 212 HIS Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 313 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 28 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 22 optimal weight: 0.0020 chunk 163 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 126 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 chunk 81 optimal weight: 0.4980 chunk 138 optimal weight: 0.6980 chunk 69 optimal weight: 0.0870 overall best weight: 0.3566 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 GLN B 74 GLN C 126 GLN E 209 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.164080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.128837 restraints weight = 28607.979| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.76 r_work: 0.3359 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3362 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3362 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16425 Z= 0.144 Angle : 0.660 10.537 22275 Z= 0.339 Chirality : 0.044 0.202 2532 Planarity : 0.005 0.069 2785 Dihedral : 4.692 20.655 2155 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.37 % Favored : 96.53 % Rotamer: Outliers : 3.26 % Allowed : 22.29 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.19), residues: 1930 helix: 1.86 (0.17), residues: 959 sheet: 0.19 (0.27), residues: 360 loop : -1.52 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 226 HIS 0.006 0.001 HIS D 68 PHE 0.018 0.001 PHE A 39 TYR 0.028 0.001 TYR A 19 ARG 0.009 0.000 ARG B 54 Details of bonding type rmsd hydrogen bonds : bond 0.04784 ( 980) hydrogen bonds : angle 4.49195 ( 2847) SS BOND : bond 0.00037 ( 2) SS BOND : angle 1.80057 ( 4) covalent geometry : bond 0.00323 (16423) covalent geometry : angle 0.65919 (22271) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 401 time to evaluate : 1.744 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ASN cc_start: 0.8508 (t0) cc_final: 0.8237 (t0) REVERT: A 89 ASP cc_start: 0.7266 (m-30) cc_final: 0.6766 (m-30) REVERT: A 104 ASN cc_start: 0.7883 (m110) cc_final: 0.7679 (m110) REVERT: A 173 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8056 (mt) REVERT: A 199 VAL cc_start: 0.8053 (t) cc_final: 0.7803 (t) REVERT: A 259 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8229 (mp) REVERT: A 277 ASP cc_start: 0.7836 (t0) cc_final: 0.7224 (t0) REVERT: A 320 GLU cc_start: 0.5709 (pm20) cc_final: 0.4776 (tm-30) REVERT: B 85 LEU cc_start: 0.8754 (tp) cc_final: 0.8077 (tt) REVERT: B 89 ASP cc_start: 0.7761 (m-30) cc_final: 0.7342 (m-30) REVERT: B 212 HIS cc_start: 0.7375 (m-70) cc_final: 0.6937 (m-70) REVERT: B 341 MET cc_start: 0.6020 (OUTLIER) cc_final: 0.5701 (ptt) REVERT: C 126 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.8011 (mt0) REVERT: C 209 GLN cc_start: 0.8066 (tm-30) cc_final: 0.7574 (tm-30) REVERT: C 213 GLN cc_start: 0.8115 (pt0) cc_final: 0.7591 (pt0) REVERT: C 232 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7514 (tt) REVERT: C 250 TYR cc_start: 0.8368 (m-80) cc_final: 0.8134 (m-80) REVERT: C 257 HIS cc_start: 0.8661 (m170) cc_final: 0.7909 (m90) REVERT: D 90 ILE cc_start: 0.8744 (pt) cc_final: 0.8476 (mt) REVERT: D 155 ARG cc_start: 0.8661 (mpp80) cc_final: 0.8390 (mtm-85) REVERT: D 197 GLU cc_start: 0.8423 (pp20) cc_final: 0.8098 (pp20) REVERT: D 257 HIS cc_start: 0.7466 (m90) cc_final: 0.7138 (m90) REVERT: E 39 PHE cc_start: 0.7443 (p90) cc_final: 0.7100 (p90) REVERT: E 85 LEU cc_start: 0.7665 (mm) cc_final: 0.7125 (mm) REVERT: E 89 ASP cc_start: 0.7340 (m-30) cc_final: 0.6766 (m-30) REVERT: E 165 ARG cc_start: 0.8093 (mmp80) cc_final: 0.7830 (mmp80) REVERT: E 204 GLU cc_start: 0.6359 (OUTLIER) cc_final: 0.5167 (pm20) REVERT: E 318 MET cc_start: 0.3351 (mmp) cc_final: 0.3048 (mmp) outliers start: 59 outliers final: 47 residues processed: 432 average time/residue: 0.2686 time to fit residues: 172.2449 Evaluate side-chains 439 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 386 time to evaluate : 1.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 126 GLN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 285 ASN Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 126 GLN Chi-restraints excluded: chain C residue 128 SER Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 120 HIS Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain E residue 284 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 85 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 147 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 GLN B 74 GLN C 126 GLN ** D 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.162862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.128200 restraints weight = 28886.406| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.83 r_work: 0.3327 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3331 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.64 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 16425 Z= 0.222 Angle : 0.703 10.614 22275 Z= 0.362 Chirality : 0.046 0.200 2532 Planarity : 0.005 0.067 2785 Dihedral : 4.798 21.295 2155 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.58 % Favored : 96.32 % Rotamer: Outliers : 3.43 % Allowed : 22.35 % Favored : 74.23 % 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: 0.60 (0.19), residues: 1930 helix: 1.69 (0.16), residues: 959 sheet: 0.18 (0.27), residues: 369 loop : -1.60 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 226 HIS 0.007 0.001 HIS D 68 PHE 0.015 0.002 PHE A 39 TYR 0.029 0.002 TYR H 106 ARG 0.009 0.001 ARG B 54 Details of bonding type rmsd hydrogen bonds : bond 0.05063 ( 980) hydrogen bonds : angle 4.61828 ( 2847) SS BOND : bond 0.00145 ( 2) SS BOND : angle 2.34827 ( 4) covalent geometry : bond 0.00531 (16423) covalent geometry : angle 0.70262 (22271) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3860 Ramachandran restraints generated. 1930 Oldfield, 0 Emsley, 1930 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 378 time to evaluate : 1.896 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ASN cc_start: 0.8481 (t0) cc_final: 0.8232 (t0) REVERT: A 89 ASP cc_start: 0.7377 (m-30) cc_final: 0.6942 (m-30) REVERT: A 104 ASN cc_start: 0.7886 (m110) cc_final: 0.7669 (m110) REVERT: A 173 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8062 (mt) REVERT: A 199 VAL cc_start: 0.8024 (t) cc_final: 0.7772 (t) REVERT: A 259 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8362 (mp) REVERT: A 277 ASP cc_start: 0.7903 (t0) cc_final: 0.7278 (t0) REVERT: A 320 GLU cc_start: 0.5765 (pm20) cc_final: 0.4930 (tm-30) REVERT: B 58 THR cc_start: 0.8401 (m) cc_final: 0.8177 (t) REVERT: B 85 LEU cc_start: 0.8809 (tp) cc_final: 0.8129 (tt) REVERT: B 89 ASP cc_start: 0.7768 (m-30) cc_final: 0.7376 (m-30) REVERT: B 212 HIS cc_start: 0.7399 (m-70) cc_final: 0.6963 (m-70) REVERT: B 341 MET cc_start: 0.6051 (OUTLIER) cc_final: 0.5709 (ptt) REVERT: C 209 GLN cc_start: 0.8005 (tm-30) cc_final: 0.7421 (tm-30) REVERT: C 213 GLN cc_start: 0.8046 (pt0) cc_final: 0.7434 (pt0) REVERT: C 232 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7514 (tt) REVERT: C 250 TYR cc_start: 0.8466 (m-80) cc_final: 0.8210 (m-80) REVERT: C 257 HIS cc_start: 0.8679 (m170) cc_final: 0.7964 (m90) REVERT: C 341 MET cc_start: 0.7276 (mtm) cc_final: 0.6400 (mpp) REVERT: D 90 ILE cc_start: 0.8819 (pt) cc_final: 0.8525 (mt) REVERT: D 155 ARG cc_start: 0.8701 (mpp80) cc_final: 0.8422 (mtm-85) REVERT: D 162 ARG cc_start: 0.8404 (mmm160) cc_final: 0.8039 (mmm160) REVERT: D 186 GLU cc_start: 0.8704 (tt0) cc_final: 0.8255 (tp30) REVERT: D 197 GLU cc_start: 0.8407 (pp20) cc_final: 0.8108 (pp20) REVERT: D 257 HIS cc_start: 0.7484 (m90) cc_final: 0.7229 (m-70) REVERT: E 39 PHE cc_start: 0.7480 (p90) cc_final: 0.7147 (p90) REVERT: E 85 LEU cc_start: 0.7709 (mm) cc_final: 0.7183 (mm) REVERT: E 89 ASP cc_start: 0.7371 (m-30) cc_final: 0.6812 (m-30) REVERT: E 204 GLU cc_start: 0.6437 (OUTLIER) cc_final: 0.5235 (pm20) REVERT: E 318 MET cc_start: 0.3365 (mmp) cc_final: 0.3102 (mmp) outliers start: 62 outliers final: 51 residues processed: 411 average time/residue: 0.2819 time to fit residues: 170.4336 Evaluate side-chains 427 residues out of total 1808 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 371 time to evaluate : 2.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 117 ASP Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain A residue 42 PHE Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 126 GLN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 285 ASN Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 341 MET Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 58 THR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 313 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 127 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 chunk 181 optimal weight: 0.8980 chunk 156 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 177 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 165 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 GLN B 74 GLN ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.163192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.127693 restraints weight = 28637.596| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.72 r_work: 0.3340 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3343 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3343 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16425 Z= 0.188 Angle : 0.687 11.023 22275 Z= 0.352 Chirality : 0.045 0.196 2532 Planarity : 0.005 0.065 2785 Dihedral : 4.784 21.248 2155 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.32 % Favored : 96.58 % Rotamer: Outliers : 3.76 % Allowed : 22.12 % Favored : 74.12 % 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: 0.62 (0.19), residues: 1930 helix: 1.72 (0.16), residues: 960 sheet: 0.20 (0.27), residues: 368 loop : -1.61 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 226 HIS 0.006 0.001 HIS D 68 PHE 0.016 0.001 PHE A 39 TYR 0.029 0.002 TYR A 19 ARG 0.009 0.001 ARG B 54 Details of bonding type rmsd hydrogen bonds : bond 0.04960 ( 980) hydrogen bonds : angle 4.58978 ( 2847) SS BOND : bond 0.00104 ( 2) SS BOND : angle 2.18222 ( 4) covalent geometry : bond 0.00444 (16423) covalent geometry : angle 0.68616 (22271) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9018.51 seconds wall clock time: 157 minutes 2.03 seconds (9422.03 seconds total)