Starting phenix.real_space_refine on Sat Jul 26 14:50:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xoj_38531/07_2025/8xoj_38531.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xoj_38531/07_2025/8xoj_38531.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xoj_38531/07_2025/8xoj_38531.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xoj_38531/07_2025/8xoj_38531.map" model { file = "/net/cci-nas-00/data/ceres_data/8xoj_38531/07_2025/8xoj_38531.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xoj_38531/07_2025/8xoj_38531.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.007 sd= 0.109 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 5585 2.51 5 N 1531 2.21 5 O 1615 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 8785 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1864 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2573 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1736 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 9, 'TRANS': 218} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 435 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "R" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2177 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 7, 'TRANS': 258} Chain breaks: 3 Time building chain proxies: 5.20, per 1000 atoms: 0.59 Number of scatterers: 8785 At special positions: 0 Unit cell: (91.035, 121.023, 128.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1615 8.00 N 1531 7.00 C 5585 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.39 Conformation dependent library (CDL) restraints added in 960.4 milliseconds 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 12 sheets defined 41.4% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 15 through 38 removed outlier: 3.789A pdb=" N ALA A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 233 through 237 removed outlier: 3.517A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.950A pdb=" N ARG A 283 " --> pdb=" O ARG A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.464A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.564A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.075A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 220 through 224 Processing helix chain 'G' and resid 7 through 25 removed outlier: 4.169A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 removed outlier: 3.508A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'R' and resid 51 through 87 removed outlier: 4.273A pdb=" N PHE R 70 " --> pdb=" O THR R 66 " (cutoff:3.500A) Proline residue: R 71 - end of helix Processing helix chain 'R' and resid 88 through 91 Processing helix chain 'R' and resid 92 through 116 removed outlier: 3.617A pdb=" N TYR R 97 " --> pdb=" O ILE R 93 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE R 114 " --> pdb=" O ALA R 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 117 through 123 removed outlier: 5.806A pdb=" N HIS R 120 " --> pdb=" O PHE R 117 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU R 121 " --> pdb=" O ASN R 118 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR R 123 " --> pdb=" O HIS R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 161 Processing helix chain 'R' and resid 170 through 200 Proline residue: R 192 - end of helix Processing helix chain 'R' and resid 211 through 223 Processing helix chain 'R' and resid 223 through 248 removed outlier: 3.744A pdb=" N HIS R 247 " --> pdb=" O ARG R 243 " (cutoff:3.500A) Processing helix chain 'R' and resid 254 through 285 removed outlier: 3.541A pdb=" N VAL R 265 " --> pdb=" O ILE R 261 " (cutoff:3.500A) Proline residue: R 274 - end of helix Processing helix chain 'R' and resid 302 through 325 removed outlier: 3.608A pdb=" N HIS R 307 " --> pdb=" O PRO R 303 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN R 316 " --> pdb=" O ALA R 312 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER R 317 " --> pdb=" O ALA R 313 " (cutoff:3.500A) Proline residue: R 321 - end of helix Processing helix chain 'R' and resid 328 through 342 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 4.422A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 9.305A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.711A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.629A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.778A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.681A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.563A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.634A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.691A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.539A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.547A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) 467 hydrogen bonds defined for protein. 1320 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.41 Time building geometry restraints manager: 2.78 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: 2865 1.34 - 1.46: 1546 1.46 - 1.57: 4474 1.57 - 1.69: 0 1.69 - 1.81: 79 Bond restraints: 8964 Sorted by residual: bond pdb=" CA ASN A 292 " pdb=" CB ASN A 292 " ideal model delta sigma weight residual 1.528 1.563 -0.035 1.61e-02 3.86e+03 4.82e+00 bond pdb=" N THR G 6 " pdb=" CA THR G 6 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.90e-02 2.77e+03 3.51e+00 bond pdb=" N GLU B 3 " pdb=" CA GLU B 3 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 bond pdb=" N VAL E 2 " pdb=" CA VAL E 2 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.78e+00 bond pdb=" N GLU A 15 " pdb=" CA GLU A 15 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.78e+00 ... (remaining 8959 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 11618 1.24 - 2.47: 438 2.47 - 3.71: 56 3.71 - 4.94: 18 4.94 - 6.18: 6 Bond angle restraints: 12136 Sorted by residual: angle pdb=" N MET E 192 " pdb=" CA MET E 192 " pdb=" CB MET E 192 " ideal model delta sigma weight residual 114.17 109.08 5.09 1.14e+00 7.69e-01 1.99e+01 angle pdb=" N TYR B 105 " pdb=" CA TYR B 105 " pdb=" C TYR B 105 " ideal model delta sigma weight residual 108.34 102.16 6.18 1.64e+00 3.72e-01 1.42e+01 angle pdb=" C SER R 325 " pdb=" N PHE R 326 " pdb=" CA PHE R 326 " ideal model delta sigma weight residual 122.65 117.24 5.41 1.60e+00 3.91e-01 1.15e+01 angle pdb=" N ASN A 292 " pdb=" CA ASN A 292 " pdb=" C ASN A 292 " ideal model delta sigma weight residual 110.53 114.89 -4.36 1.29e+00 6.01e-01 1.14e+01 angle pdb=" N ASP B 290 " pdb=" CA ASP B 290 " pdb=" CB ASP B 290 " ideal model delta sigma weight residual 110.39 116.09 -5.70 1.75e+00 3.27e-01 1.06e+01 ... (remaining 12131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4748 17.95 - 35.90: 442 35.90 - 53.84: 97 53.84 - 71.79: 19 71.79 - 89.74: 11 Dihedral angle restraints: 5317 sinusoidal: 2076 harmonic: 3241 Sorted by residual: dihedral pdb=" CA HIS R 302 " pdb=" C HIS R 302 " pdb=" N PRO R 303 " pdb=" CA PRO R 303 " ideal model delta harmonic sigma weight residual -180.00 -160.99 -19.01 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA ARG E 191 " pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta harmonic sigma weight residual 180.00 161.45 18.55 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 163.53 16.47 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 5314 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1025 0.039 - 0.077: 249 0.077 - 0.116: 81 0.116 - 0.155: 21 0.155 - 0.193: 1 Chirality restraints: 1377 Sorted by residual: chirality pdb=" CA TYR B 105 " pdb=" N TYR B 105 " pdb=" C TYR B 105 " pdb=" CB TYR B 105 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.33e-01 chirality pdb=" CA ASN B 340 " pdb=" N ASN B 340 " pdb=" C ASN B 340 " pdb=" CB ASN B 340 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.49e-01 chirality pdb=" CA LEU A 291 " pdb=" N LEU A 291 " pdb=" C LEU A 291 " pdb=" CB LEU A 291 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 5.09e-01 ... (remaining 1374 not shown) Planarity restraints: 1542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 13 " -0.211 9.50e-02 1.11e+02 9.45e-02 5.61e+00 pdb=" NE ARG G 13 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG G 13 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG G 13 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG G 13 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL E 147 " 0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO E 148 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO E 148 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 148 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 62 " 0.119 9.50e-02 1.11e+02 5.35e-02 1.97e+00 pdb=" NE ARG G 62 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG G 62 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG G 62 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG G 62 " 0.002 2.00e-02 2.50e+03 ... (remaining 1539 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2812 2.83 - 3.35: 8448 3.35 - 3.86: 14235 3.86 - 4.38: 16883 4.38 - 4.90: 29921 Nonbonded interactions: 72299 Sorted by model distance: nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.311 3.040 nonbonded pdb=" O ASN A 239 " pdb=" OD1 ASP A 240 " model vdw 2.326 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.329 3.040 nonbonded pdb=" OD2 ASP B 170 " pdb=" OG1 THR B 173 " model vdw 2.335 3.040 nonbonded pdb=" O THR B 34 " pdb=" NZ LYS B 301 " model vdw 2.352 3.120 ... (remaining 72294 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=1.00 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: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 22.460 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 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 0.036 8964 Z= 0.151 Angle : 0.564 6.178 12136 Z= 0.332 Chirality : 0.040 0.193 1377 Planarity : 0.004 0.094 1542 Dihedral : 15.110 89.740 3217 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.32 % Allowed : 11.58 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.26), residues: 1093 helix: 1.74 (0.25), residues: 403 sheet: 0.28 (0.31), residues: 278 loop : 0.33 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 216 HIS 0.003 0.001 HIS R 197 PHE 0.010 0.001 PHE R 193 TYR 0.010 0.001 TYR E 103 ARG 0.013 0.001 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.17138 ( 467) hydrogen bonds : angle 6.80430 ( 1320) covalent geometry : bond 0.00299 ( 8964) covalent geometry : angle 0.56403 (12136) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 170 time to evaluate : 0.970 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8435 (mmtp) cc_final: 0.7784 (mttt) REVERT: A 25 MET cc_start: 0.8322 (mmm) cc_final: 0.8120 (mtp) REVERT: B 33 ILE cc_start: 0.8517 (mm) cc_final: 0.8304 (mt) REVERT: B 209 LYS cc_start: 0.9223 (mttm) cc_final: 0.8879 (mttm) REVERT: E 82 GLN cc_start: 0.7929 (tp40) cc_final: 0.7545 (tp40) REVERT: E 93 MET cc_start: 0.8391 (ttp) cc_final: 0.8154 (ttm) REVERT: E 202 ARG cc_start: 0.8067 (mtm110) cc_final: 0.7866 (mtm110) REVERT: G 29 LYS cc_start: 0.8693 (mmtm) cc_final: 0.8259 (ttpp) REVERT: G 38 MET cc_start: 0.7677 (mtm) cc_final: 0.7399 (mtp) REVERT: R 59 LEU cc_start: 0.8973 (tp) cc_final: 0.8507 (mp) REVERT: R 302 HIS cc_start: 0.5649 (m90) cc_final: 0.5359 (m-70) outliers start: 3 outliers final: 2 residues processed: 173 average time/residue: 0.2486 time to fit residues: 56.9131 Evaluate side-chains 152 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 150 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain G residue 17 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 1.9990 chunk 81 optimal weight: 0.0870 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 43 optimal weight: 0.0980 chunk 84 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.8362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN B 259 GLN R 282 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.162572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.119284 restraints weight = 10481.930| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.56 r_work: 0.3134 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8964 Z= 0.129 Angle : 0.543 5.775 12136 Z= 0.292 Chirality : 0.042 0.165 1377 Planarity : 0.004 0.049 1542 Dihedral : 5.051 58.336 1217 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.47 % Allowed : 12.42 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.25), residues: 1093 helix: 2.06 (0.25), residues: 407 sheet: 0.70 (0.32), residues: 264 loop : 0.24 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 169 HIS 0.003 0.001 HIS R 197 PHE 0.016 0.001 PHE R 136 TYR 0.013 0.001 TYR E 190 ARG 0.005 0.000 ARG E 67 Details of bonding type rmsd hydrogen bonds : bond 0.04349 ( 467) hydrogen bonds : angle 4.89620 ( 1320) covalent geometry : bond 0.00283 ( 8964) covalent geometry : angle 0.54260 (12136) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 163 time to evaluate : 0.962 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8262 (mmtp) cc_final: 0.7603 (mttt) REVERT: A 25 MET cc_start: 0.8458 (mmm) cc_final: 0.8187 (mtp) REVERT: A 232 ARG cc_start: 0.8134 (ttp-110) cc_final: 0.7822 (ttp-170) REVERT: A 294 GLN cc_start: 0.7957 (mm-40) cc_final: 0.7694 (mm-40) REVERT: A 299 GLU cc_start: 0.8494 (pt0) cc_final: 0.8282 (pt0) REVERT: A 333 ARG cc_start: 0.8688 (ptp-170) cc_final: 0.8432 (mtm110) REVERT: B 197 ARG cc_start: 0.8311 (mtp-110) cc_final: 0.8080 (mtp-110) REVERT: B 213 VAL cc_start: 0.8487 (m) cc_final: 0.8264 (t) REVERT: E 82 GLN cc_start: 0.7940 (tp40) cc_final: 0.7396 (tp-100) REVERT: E 164 SER cc_start: 0.8661 (t) cc_final: 0.8374 (p) REVERT: E 183 GLN cc_start: 0.7087 (mp10) cc_final: 0.6647 (mp10) REVERT: E 202 ARG cc_start: 0.7583 (mtm110) cc_final: 0.7291 (mtm110) REVERT: G 17 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.7985 (tp30) REVERT: G 21 MET cc_start: 0.8877 (mmm) cc_final: 0.8119 (mmm) REVERT: R 59 LEU cc_start: 0.8671 (tp) cc_final: 0.8179 (mp) REVERT: R 302 HIS cc_start: 0.5459 (m90) cc_final: 0.5256 (m-70) outliers start: 14 outliers final: 7 residues processed: 170 average time/residue: 0.2427 time to fit residues: 55.1686 Evaluate side-chains 160 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 152 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain R residue 163 MET Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 270 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 16 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 104 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 chunk 79 optimal weight: 9.9990 chunk 29 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 GLN A 371 ASN R 197 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.162470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.119103 restraints weight = 10615.431| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.53 r_work: 0.3127 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8964 Z= 0.132 Angle : 0.514 6.133 12136 Z= 0.274 Chirality : 0.042 0.195 1377 Planarity : 0.004 0.045 1542 Dihedral : 4.937 59.754 1217 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.21 % Allowed : 13.68 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.25), residues: 1093 helix: 2.15 (0.25), residues: 405 sheet: 0.66 (0.31), residues: 267 loop : 0.20 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.003 0.001 HIS A 357 PHE 0.012 0.001 PHE R 193 TYR 0.013 0.001 TYR E 190 ARG 0.006 0.000 ARG E 67 Details of bonding type rmsd hydrogen bonds : bond 0.03937 ( 467) hydrogen bonds : angle 4.56339 ( 1320) covalent geometry : bond 0.00300 ( 8964) covalent geometry : angle 0.51395 (12136) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 0.980 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8265 (mmtp) cc_final: 0.7649 (mttt) REVERT: A 25 MET cc_start: 0.8319 (mmm) cc_final: 0.8084 (mtp) REVERT: A 333 ARG cc_start: 0.8636 (ptp-170) cc_final: 0.8397 (mtm110) REVERT: B 234 PHE cc_start: 0.9258 (OUTLIER) cc_final: 0.8916 (m-80) REVERT: B 258 ASP cc_start: 0.8815 (t0) cc_final: 0.8462 (t0) REVERT: E 43 LYS cc_start: 0.8173 (ptpt) cc_final: 0.7565 (ptpp) REVERT: E 164 SER cc_start: 0.8607 (t) cc_final: 0.8294 (p) REVERT: E 202 ARG cc_start: 0.7775 (mtm110) cc_final: 0.7426 (mtm110) REVERT: G 17 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8024 (tp30) REVERT: G 21 MET cc_start: 0.8789 (mmm) cc_final: 0.8152 (mmm) REVERT: R 59 LEU cc_start: 0.8596 (tp) cc_final: 0.8128 (mp) REVERT: R 119 LEU cc_start: 0.7796 (mp) cc_final: 0.7138 (tt) outliers start: 21 outliers final: 13 residues processed: 173 average time/residue: 0.2412 time to fit residues: 55.7786 Evaluate side-chains 165 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 270 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 4 optimal weight: 10.0000 chunk 88 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 63 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.161807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.119097 restraints weight = 10599.428| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.55 r_work: 0.3123 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8964 Z= 0.134 Angle : 0.507 5.503 12136 Z= 0.272 Chirality : 0.042 0.248 1377 Planarity : 0.003 0.043 1542 Dihedral : 4.858 56.767 1217 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.32 % Allowed : 15.47 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.25), residues: 1093 helix: 2.16 (0.25), residues: 405 sheet: 0.52 (0.31), residues: 269 loop : 0.15 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS A 357 PHE 0.014 0.001 PHE R 193 TYR 0.012 0.001 TYR E 190 ARG 0.005 0.000 ARG A 280 Details of bonding type rmsd hydrogen bonds : bond 0.03773 ( 467) hydrogen bonds : angle 4.49433 ( 1320) covalent geometry : bond 0.00307 ( 8964) covalent geometry : angle 0.50727 (12136) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8220 (mmtp) cc_final: 0.7638 (mttt) REVERT: A 333 ARG cc_start: 0.8670 (ptp-170) cc_final: 0.8396 (mtm110) REVERT: A 385 GLN cc_start: 0.7887 (tp40) cc_final: 0.7608 (tp40) REVERT: B 31 SER cc_start: 0.8851 (OUTLIER) cc_final: 0.8649 (p) REVERT: B 68 ARG cc_start: 0.9279 (OUTLIER) cc_final: 0.9043 (ttt180) REVERT: B 197 ARG cc_start: 0.8341 (mtp-110) cc_final: 0.8041 (mtp-110) REVERT: B 214 ARG cc_start: 0.8228 (mtt-85) cc_final: 0.7926 (mtt-85) REVERT: B 234 PHE cc_start: 0.9258 (OUTLIER) cc_final: 0.8856 (m-80) REVERT: B 258 ASP cc_start: 0.8793 (t0) cc_final: 0.8478 (t0) REVERT: E 43 LYS cc_start: 0.8199 (ptpt) cc_final: 0.7611 (ptpp) REVERT: E 164 SER cc_start: 0.8583 (t) cc_final: 0.8277 (p) REVERT: E 202 ARG cc_start: 0.7755 (mtm110) cc_final: 0.7345 (mtm110) REVERT: G 17 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8036 (tp30) REVERT: G 21 MET cc_start: 0.8811 (mmm) cc_final: 0.8278 (mmm) REVERT: G 46 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8227 (mmmm) REVERT: R 119 LEU cc_start: 0.7832 (mp) cc_final: 0.7195 (tt) outliers start: 22 outliers final: 12 residues processed: 168 average time/residue: 0.2311 time to fit residues: 52.2644 Evaluate side-chains 162 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 270 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 32 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 24 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.163008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.119997 restraints weight = 10540.112| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.49 r_work: 0.3144 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8964 Z= 0.114 Angle : 0.489 6.278 12136 Z= 0.262 Chirality : 0.041 0.174 1377 Planarity : 0.003 0.040 1542 Dihedral : 4.661 55.887 1217 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.74 % Allowed : 15.37 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.25), residues: 1093 helix: 2.31 (0.25), residues: 404 sheet: 0.48 (0.30), residues: 270 loop : 0.16 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.003 0.001 HIS A 357 PHE 0.013 0.001 PHE R 193 TYR 0.012 0.001 TYR E 190 ARG 0.003 0.000 ARG E 67 Details of bonding type rmsd hydrogen bonds : bond 0.03545 ( 467) hydrogen bonds : angle 4.34945 ( 1320) covalent geometry : bond 0.00255 ( 8964) covalent geometry : angle 0.48879 (12136) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8271 (mmtp) cc_final: 0.7672 (mttt) REVERT: A 333 ARG cc_start: 0.8673 (ptp-170) cc_final: 0.8401 (mtm110) REVERT: A 385 GLN cc_start: 0.8059 (tp40) cc_final: 0.7813 (tp40) REVERT: B 68 ARG cc_start: 0.9314 (OUTLIER) cc_final: 0.9043 (ttt180) REVERT: B 197 ARG cc_start: 0.8380 (mtp-110) cc_final: 0.7812 (mtp-110) REVERT: B 214 ARG cc_start: 0.8446 (mtt-85) cc_final: 0.7850 (mtt-85) REVERT: B 226 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7646 (mm-30) REVERT: B 234 PHE cc_start: 0.9340 (OUTLIER) cc_final: 0.8937 (m-80) REVERT: B 251 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.8194 (mpt180) REVERT: B 258 ASP cc_start: 0.8827 (t0) cc_final: 0.8533 (t0) REVERT: B 264 TYR cc_start: 0.9092 (m-80) cc_final: 0.8806 (m-80) REVERT: E 43 LYS cc_start: 0.8142 (ptpt) cc_final: 0.7510 (ptpp) REVERT: E 164 SER cc_start: 0.8572 (t) cc_final: 0.8258 (p) REVERT: E 202 ARG cc_start: 0.7650 (mtm110) cc_final: 0.7227 (mtm110) REVERT: G 38 MET cc_start: 0.7658 (mtm) cc_final: 0.7262 (mtp) REVERT: G 46 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8247 (mmmm) REVERT: R 119 LEU cc_start: 0.7807 (mp) cc_final: 0.7187 (tt) REVERT: R 163 MET cc_start: 0.8846 (mtm) cc_final: 0.8630 (mtm) REVERT: R 246 ARG cc_start: 0.7819 (ttm-80) cc_final: 0.7590 (ttm170) outliers start: 26 outliers final: 13 residues processed: 174 average time/residue: 0.2493 time to fit residues: 57.3708 Evaluate side-chains 163 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 270 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 47 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.159605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.116758 restraints weight = 10608.267| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.56 r_work: 0.3085 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 8964 Z= 0.192 Angle : 0.545 5.492 12136 Z= 0.291 Chirality : 0.043 0.182 1377 Planarity : 0.004 0.039 1542 Dihedral : 4.461 56.084 1214 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.26 % Allowed : 15.16 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.25), residues: 1093 helix: 2.20 (0.25), residues: 403 sheet: 0.36 (0.30), residues: 271 loop : 0.04 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 169 HIS 0.003 0.001 HIS R 307 PHE 0.015 0.002 PHE R 193 TYR 0.012 0.001 TYR E 103 ARG 0.008 0.000 ARG A 280 Details of bonding type rmsd hydrogen bonds : bond 0.03978 ( 467) hydrogen bonds : angle 4.48566 ( 1320) covalent geometry : bond 0.00455 ( 8964) covalent geometry : angle 0.54534 (12136) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 149 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8107 (mmtp) cc_final: 0.7513 (mttt) REVERT: A 385 GLN cc_start: 0.7918 (tp40) cc_final: 0.7646 (tp40) REVERT: B 68 ARG cc_start: 0.9289 (OUTLIER) cc_final: 0.9065 (ttt180) REVERT: B 226 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7509 (mm-30) REVERT: B 234 PHE cc_start: 0.9256 (OUTLIER) cc_final: 0.8829 (m-80) REVERT: B 251 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.7729 (mpt180) REVERT: B 258 ASP cc_start: 0.8827 (t0) cc_final: 0.8586 (t70) REVERT: E 43 LYS cc_start: 0.8213 (ptpt) cc_final: 0.7901 (ptpp) REVERT: E 164 SER cc_start: 0.8580 (t) cc_final: 0.8265 (p) REVERT: E 202 ARG cc_start: 0.7787 (mtm110) cc_final: 0.7344 (mtm110) REVERT: G 38 MET cc_start: 0.7619 (mtm) cc_final: 0.7226 (mtp) REVERT: G 46 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8212 (mmmm) REVERT: R 119 LEU cc_start: 0.7886 (mp) cc_final: 0.7278 (tt) REVERT: R 163 MET cc_start: 0.8826 (mtm) cc_final: 0.8608 (mtm) REVERT: R 246 ARG cc_start: 0.7756 (ttm-80) cc_final: 0.7516 (ttm170) outliers start: 31 outliers final: 16 residues processed: 168 average time/residue: 0.2592 time to fit residues: 57.4350 Evaluate side-chains 161 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 254 ARG Chi-restraints excluded: chain R residue 270 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.162345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.120121 restraints weight = 10635.076| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.56 r_work: 0.3132 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8964 Z= 0.115 Angle : 0.494 5.730 12136 Z= 0.264 Chirality : 0.041 0.168 1377 Planarity : 0.003 0.038 1542 Dihedral : 4.302 56.071 1214 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.05 % Allowed : 16.42 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.25), residues: 1093 helix: 2.37 (0.25), residues: 404 sheet: 0.31 (0.30), residues: 272 loop : 0.03 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.002 0.001 HIS A 357 PHE 0.013 0.001 PHE R 193 TYR 0.012 0.001 TYR E 190 ARG 0.008 0.000 ARG G 62 Details of bonding type rmsd hydrogen bonds : bond 0.03509 ( 467) hydrogen bonds : angle 4.35401 ( 1320) covalent geometry : bond 0.00257 ( 8964) covalent geometry : angle 0.49369 (12136) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8142 (mmtp) cc_final: 0.7549 (mttt) REVERT: A 385 GLN cc_start: 0.7970 (tp40) cc_final: 0.7665 (tp40) REVERT: B 68 ARG cc_start: 0.9285 (OUTLIER) cc_final: 0.9033 (ttt180) REVERT: B 226 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7603 (mm-30) REVERT: B 234 PHE cc_start: 0.9323 (OUTLIER) cc_final: 0.8937 (m-80) REVERT: B 251 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.8074 (mpt180) REVERT: B 258 ASP cc_start: 0.8781 (t0) cc_final: 0.8533 (t0) REVERT: B 336 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8616 (tp) REVERT: E 43 LYS cc_start: 0.8160 (ptpt) cc_final: 0.7787 (ptpp) REVERT: E 164 SER cc_start: 0.8561 (t) cc_final: 0.8243 (p) REVERT: E 202 ARG cc_start: 0.7623 (mtm110) cc_final: 0.7124 (mtm110) REVERT: G 38 MET cc_start: 0.7567 (mtm) cc_final: 0.7181 (mtp) REVERT: R 119 LEU cc_start: 0.7706 (mp) cc_final: 0.7091 (tt) REVERT: R 246 ARG cc_start: 0.7714 (ttm-80) cc_final: 0.7484 (ttm170) outliers start: 29 outliers final: 17 residues processed: 173 average time/residue: 0.2588 time to fit residues: 58.6905 Evaluate side-chains 170 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 133 MET Chi-restraints excluded: chain R residue 167 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 55 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 20 optimal weight: 0.6980 chunk 102 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 21 optimal weight: 0.7980 chunk 52 optimal weight: 8.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN R 197 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.162447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.120226 restraints weight = 10698.319| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.56 r_work: 0.3134 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8964 Z= 0.117 Angle : 0.503 5.391 12136 Z= 0.270 Chirality : 0.042 0.251 1377 Planarity : 0.003 0.038 1542 Dihedral : 4.245 56.024 1214 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.16 % Allowed : 16.32 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.25), residues: 1093 helix: 2.38 (0.25), residues: 404 sheet: 0.33 (0.30), residues: 272 loop : 0.03 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS A 357 PHE 0.023 0.001 PHE R 168 TYR 0.011 0.001 TYR E 190 ARG 0.007 0.000 ARG G 62 Details of bonding type rmsd hydrogen bonds : bond 0.03497 ( 467) hydrogen bonds : angle 4.29205 ( 1320) covalent geometry : bond 0.00261 ( 8964) covalent geometry : angle 0.50289 (12136) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8104 (mmtp) cc_final: 0.7515 (mttt) REVERT: A 385 GLN cc_start: 0.8003 (tp40) cc_final: 0.7729 (tp40) REVERT: B 38 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.8146 (m-30) REVERT: B 46 ARG cc_start: 0.8402 (mtp-110) cc_final: 0.8137 (mtp-110) REVERT: B 68 ARG cc_start: 0.9288 (OUTLIER) cc_final: 0.9040 (ttt180) REVERT: B 234 PHE cc_start: 0.9329 (OUTLIER) cc_final: 0.8927 (m-80) REVERT: B 251 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.8194 (mpt180) REVERT: B 258 ASP cc_start: 0.8669 (t0) cc_final: 0.8437 (t0) REVERT: E 43 LYS cc_start: 0.8143 (ptpt) cc_final: 0.7778 (ptpp) REVERT: E 164 SER cc_start: 0.8592 (t) cc_final: 0.8279 (p) REVERT: E 202 ARG cc_start: 0.7636 (mtm110) cc_final: 0.7140 (mtm110) REVERT: G 38 MET cc_start: 0.7490 (mtm) cc_final: 0.7115 (mtp) REVERT: R 119 LEU cc_start: 0.7600 (mp) cc_final: 0.7086 (tt) REVERT: R 246 ARG cc_start: 0.7743 (ttm-80) cc_final: 0.7541 (ttm170) outliers start: 30 outliers final: 20 residues processed: 170 average time/residue: 0.2492 time to fit residues: 56.1564 Evaluate side-chains 167 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 3 GLU Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 133 MET Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 270 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 89 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 85 optimal weight: 0.8980 chunk 86 optimal weight: 0.2980 chunk 77 optimal weight: 2.9990 chunk 25 optimal weight: 0.0870 chunk 90 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 97 optimal weight: 7.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.163630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.121439 restraints weight = 10639.244| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.50 r_work: 0.3158 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8964 Z= 0.104 Angle : 0.491 6.471 12136 Z= 0.264 Chirality : 0.041 0.220 1377 Planarity : 0.003 0.038 1542 Dihedral : 4.164 56.102 1214 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.42 % Allowed : 17.47 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.25), residues: 1093 helix: 2.56 (0.25), residues: 398 sheet: 0.38 (0.30), residues: 270 loop : 0.06 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS A 357 PHE 0.017 0.001 PHE R 168 TYR 0.010 0.001 TYR E 190 ARG 0.006 0.000 ARG G 62 Details of bonding type rmsd hydrogen bonds : bond 0.03357 ( 467) hydrogen bonds : angle 4.22420 ( 1320) covalent geometry : bond 0.00226 ( 8964) covalent geometry : angle 0.49133 (12136) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8244 (mmtp) cc_final: 0.7680 (mttt) REVERT: A 385 GLN cc_start: 0.8125 (tp40) cc_final: 0.7860 (tp40) REVERT: B 38 ASP cc_start: 0.8511 (OUTLIER) cc_final: 0.8152 (m-30) REVERT: B 68 ARG cc_start: 0.9309 (OUTLIER) cc_final: 0.9057 (ttt180) REVERT: B 234 PHE cc_start: 0.9344 (OUTLIER) cc_final: 0.8945 (m-80) REVERT: E 43 LYS cc_start: 0.8175 (ptpt) cc_final: 0.7817 (pttt) REVERT: E 164 SER cc_start: 0.8570 (t) cc_final: 0.8236 (p) REVERT: E 202 ARG cc_start: 0.7702 (mtm110) cc_final: 0.7204 (mtm110) REVERT: R 119 LEU cc_start: 0.7643 (mp) cc_final: 0.7103 (tt) outliers start: 23 outliers final: 18 residues processed: 164 average time/residue: 0.2490 time to fit residues: 54.7388 Evaluate side-chains 167 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 270 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 1 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.159992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.117385 restraints weight = 10654.340| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.50 r_work: 0.3103 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8964 Z= 0.178 Angle : 0.549 6.235 12136 Z= 0.295 Chirality : 0.043 0.231 1377 Planarity : 0.004 0.038 1542 Dihedral : 4.362 56.018 1214 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.95 % Allowed : 16.74 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.25), residues: 1093 helix: 2.31 (0.25), residues: 404 sheet: 0.21 (0.30), residues: 273 loop : -0.04 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS G 44 PHE 0.016 0.002 PHE R 193 TYR 0.012 0.001 TYR E 103 ARG 0.006 0.000 ARG G 62 Details of bonding type rmsd hydrogen bonds : bond 0.03846 ( 467) hydrogen bonds : angle 4.41243 ( 1320) covalent geometry : bond 0.00424 ( 8964) covalent geometry : angle 0.54896 (12136) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8151 (mmtp) cc_final: 0.7524 (mttt) REVERT: B 46 ARG cc_start: 0.8399 (mtp-110) cc_final: 0.8117 (mtp-110) REVERT: B 68 ARG cc_start: 0.9292 (OUTLIER) cc_final: 0.9071 (ttt180) REVERT: B 234 PHE cc_start: 0.9315 (OUTLIER) cc_final: 0.8868 (m-80) REVERT: B 251 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7977 (mpt180) REVERT: E 43 LYS cc_start: 0.8163 (ptpt) cc_final: 0.7514 (ptpp) REVERT: E 164 SER cc_start: 0.8586 (t) cc_final: 0.8298 (p) REVERT: E 202 ARG cc_start: 0.7652 (mtm110) cc_final: 0.7193 (mtm110) REVERT: G 38 MET cc_start: 0.7600 (mtm) cc_final: 0.7255 (mtp) outliers start: 28 outliers final: 21 residues processed: 162 average time/residue: 0.2441 time to fit residues: 52.8597 Evaluate side-chains 166 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 142 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 383 ILE Chi-restraints excluded: chain A residue 391 TYR Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 133 MET Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 282 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 42 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 16 optimal weight: 0.6980 chunk 20 optimal weight: 0.0370 chunk 95 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 overall best weight: 0.9464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.161933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.119147 restraints weight = 10623.070| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.49 r_work: 0.3132 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8964 Z= 0.124 Angle : 0.516 6.226 12136 Z= 0.280 Chirality : 0.042 0.214 1377 Planarity : 0.003 0.037 1542 Dihedral : 4.273 56.007 1214 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.63 % Allowed : 17.05 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.25), residues: 1093 helix: 2.51 (0.25), residues: 398 sheet: 0.20 (0.30), residues: 273 loop : 0.02 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS A 357 PHE 0.014 0.001 PHE R 193 TYR 0.011 0.001 TYR E 190 ARG 0.006 0.000 ARG G 62 Details of bonding type rmsd hydrogen bonds : bond 0.03531 ( 467) hydrogen bonds : angle 4.30945 ( 1320) covalent geometry : bond 0.00281 ( 8964) covalent geometry : angle 0.51625 (12136) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5582.99 seconds wall clock time: 95 minutes 55.46 seconds (5755.46 seconds total)