Starting phenix.real_space_refine on Fri Aug 22 23:55:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xoj_38531/08_2025/8xoj_38531.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xoj_38531/08_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_38531/08_2025/8xoj_38531.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xoj_38531/08_2025/8xoj_38531.map" model { file = "/net/cci-nas-00/data/ceres_data/8xoj_38531/08_2025/8xoj_38531.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xoj_38531/08_2025/8xoj_38531.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.007 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'ASP:plan': 1, 'ARG:plan': 1, 'GLU: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: 1.78, per 1000 atoms: 0.20 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: 0.75 Conformation dependent library (CDL) restraints added in 349.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.33 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: 1.25 Time building geometry restraints manager: 0.99 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: 0.450 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: 0.090 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.220 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.950 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (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 ARG 0.013 0.001 ARG B 197 TYR 0.010 0.001 TYR E 103 PHE 0.010 0.001 PHE R 193 TRP 0.014 0.001 TRP R 216 HIS 0.003 0.001 HIS R 197 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 8964) covalent geometry : angle 0.56403 (12136) hydrogen bonds : bond 0.17138 ( 467) hydrogen bonds : angle 6.80430 ( 1320) *********************** 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 : 0.271 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: 0.0930 time to fit residues: 21.4942 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 : 0.210 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 197 HIS R 282 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.159764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.116748 restraints weight = 10673.033| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.57 r_work: 0.3087 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1201 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 : 0.589 6.887 12136 Z= 0.315 Chirality : 0.044 0.184 1377 Planarity : 0.004 0.050 1542 Dihedral : 5.200 57.019 1217 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.00 % Allowed : 13.05 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.25), residues: 1093 helix: 1.90 (0.25), residues: 406 sheet: 0.60 (0.32), residues: 259 loop : 0.10 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 67 TYR 0.014 0.001 TYR E 103 PHE 0.017 0.002 PHE R 326 TRP 0.020 0.002 TRP B 169 HIS 0.004 0.001 HIS R 282 Details of bonding type rmsd covalent geometry : bond 0.00453 ( 8964) covalent geometry : angle 0.58898 (12136) hydrogen bonds : bond 0.04600 ( 467) hydrogen bonds : angle 4.95660 ( 1320) *********************** 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 178 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 232 ARG cc_start: 0.8199 (ttp-110) cc_final: 0.7927 (ttp-170) REVERT: A 333 ARG cc_start: 0.8673 (ptp-170) cc_final: 0.8426 (mtm110) REVERT: B 197 ARG cc_start: 0.8367 (mtp-110) cc_final: 0.8098 (mtp-110) REVERT: E 82 GLN cc_start: 0.8038 (tp40) cc_final: 0.7533 (tp-100) REVERT: E 183 GLN cc_start: 0.7270 (mp10) cc_final: 0.6807 (mp10) REVERT: E 202 ARG cc_start: 0.7737 (mtm110) cc_final: 0.7484 (mtm110) REVERT: G 17 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8010 (tp30) REVERT: G 21 MET cc_start: 0.8908 (mmm) cc_final: 0.8166 (mmm) REVERT: R 59 LEU cc_start: 0.8729 (tp) cc_final: 0.8223 (mp) REVERT: R 302 HIS cc_start: 0.5592 (m90) cc_final: 0.5388 (m-70) outliers start: 19 outliers final: 9 residues processed: 169 average time/residue: 0.0985 time to fit residues: 22.3370 Evaluate side-chains 156 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 146 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 275 SER 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 189 ILE Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain R residue 163 MET 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 22 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 77 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 67 optimal weight: 0.2980 chunk 59 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 102 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 E 171 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.160818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.117222 restraints weight = 10563.169| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.52 r_work: 0.3100 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8964 Z= 0.154 Angle : 0.536 6.416 12136 Z= 0.286 Chirality : 0.042 0.193 1377 Planarity : 0.004 0.047 1542 Dihedral : 5.056 57.178 1217 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.21 % Allowed : 14.95 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.25), residues: 1093 helix: 2.00 (0.25), residues: 407 sheet: 0.53 (0.31), residues: 267 loop : 0.09 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 67 TYR 0.013 0.001 TYR E 190 PHE 0.012 0.001 PHE R 193 TRP 0.017 0.001 TRP B 169 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 8964) covalent geometry : angle 0.53607 (12136) hydrogen bonds : bond 0.04115 ( 467) hydrogen bonds : angle 4.65839 ( 1320) *********************** 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 184 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8154 (mmtp) cc_final: 0.7516 (mttt) REVERT: A 216 LYS cc_start: 0.8704 (mtmt) cc_final: 0.8485 (mtmm) REVERT: A 333 ARG cc_start: 0.8659 (ptp-170) cc_final: 0.8406 (mtm110) REVERT: B 68 ARG cc_start: 0.9280 (OUTLIER) cc_final: 0.9035 (ttt180) REVERT: B 234 PHE cc_start: 0.9261 (OUTLIER) cc_final: 0.8932 (m-80) REVERT: B 258 ASP cc_start: 0.8851 (t0) cc_final: 0.8506 (t0) REVERT: E 164 SER cc_start: 0.8629 (t) cc_final: 0.8305 (p) REVERT: E 171 ASN cc_start: 0.8545 (OUTLIER) cc_final: 0.8332 (m110) REVERT: E 202 ARG cc_start: 0.7819 (mtm110) cc_final: 0.7479 (mtm110) REVERT: G 17 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8001 (tp30) REVERT: G 21 MET cc_start: 0.8836 (mmm) cc_final: 0.8221 (mmm) REVERT: R 59 LEU cc_start: 0.8596 (tp) cc_final: 0.8134 (mp) REVERT: R 119 LEU cc_start: 0.7799 (mp) cc_final: 0.7145 (tt) outliers start: 21 outliers final: 13 residues processed: 175 average time/residue: 0.0993 time to fit residues: 23.0728 Evaluate side-chains 167 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU 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 234 PHE Chi-restraints excluded: chain B residue 249 THR 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 171 ASN Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 152 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 1 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 75 optimal weight: 0.0470 chunk 78 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 overall best weight: 3.8086 ------------------------------------------------------------------------------- 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** A 227 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 = 0.3812 r_free = 0.3812 target = 0.155974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.113218 restraints weight = 10907.796| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.78 r_work: 0.3008 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 8964 Z= 0.337 Angle : 0.659 6.458 12136 Z= 0.352 Chirality : 0.048 0.215 1377 Planarity : 0.005 0.048 1542 Dihedral : 5.343 55.595 1217 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.21 % Allowed : 14.32 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.25), residues: 1093 helix: 1.65 (0.25), residues: 407 sheet: 0.25 (0.31), residues: 266 loop : -0.02 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 280 TYR 0.015 0.002 TYR E 103 PHE 0.023 0.002 PHE R 326 TRP 0.018 0.002 TRP B 99 HIS 0.005 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00809 ( 8964) covalent geometry : angle 0.65931 (12136) hydrogen bonds : bond 0.04895 ( 467) hydrogen bonds : angle 4.89110 ( 1320) *********************** 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 191 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 151 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 216 LYS cc_start: 0.8655 (mtmt) cc_final: 0.8402 (mtmm) REVERT: A 333 ARG cc_start: 0.8736 (ptp-170) cc_final: 0.8420 (mtm110) REVERT: B 31 SER cc_start: 0.8717 (OUTLIER) cc_final: 0.8513 (p) REVERT: B 68 ARG cc_start: 0.9243 (OUTLIER) cc_final: 0.9032 (ttt180) REVERT: B 197 ARG cc_start: 0.8363 (mtp-110) cc_final: 0.8154 (mtp-110) REVERT: B 234 PHE cc_start: 0.9231 (OUTLIER) cc_final: 0.8789 (m-80) REVERT: B 251 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7324 (mpt180) REVERT: B 258 ASP cc_start: 0.8885 (t0) cc_final: 0.8463 (t0) REVERT: E 202 ARG cc_start: 0.7786 (mtm110) cc_final: 0.7463 (mtm110) REVERT: G 38 MET cc_start: 0.7673 (mtm) cc_final: 0.7158 (mtm) REVERT: G 42 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7636 (mm-30) REVERT: R 59 LEU cc_start: 0.8538 (tp) cc_final: 0.8103 (mp) REVERT: R 119 LEU cc_start: 0.7823 (mp) cc_final: 0.7188 (tt) REVERT: R 284 LEU cc_start: 0.7156 (mt) cc_final: 0.6953 (mp) REVERT: R 327 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8010 (mp) outliers start: 40 outliers final: 24 residues processed: 178 average time/residue: 0.1010 time to fit residues: 23.6295 Evaluate side-chains 172 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 270 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 81 ILE Chi-restraints excluded: chain B residue 189 SER 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 270 ILE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 152 SER Chi-restraints excluded: chain R residue 163 MET Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 171 LYS Chi-restraints excluded: chain R residue 270 VAL Chi-restraints excluded: chain R residue 327 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 67 optimal weight: 8.9990 chunk 27 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 E 171 ASN R 197 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.160985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.118416 restraints weight = 10652.670| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.58 r_work: 0.3105 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1918 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= 0.118 Angle : 0.508 6.244 12136 Z= 0.272 Chirality : 0.041 0.175 1377 Planarity : 0.004 0.042 1542 Dihedral : 5.036 59.564 1217 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.95 % Allowed : 16.21 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.25), residues: 1093 helix: 2.07 (0.25), residues: 405 sheet: 0.35 (0.32), residues: 250 loop : -0.10 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 62 TYR 0.013 0.001 TYR E 190 PHE 0.011 0.001 PHE R 193 TRP 0.019 0.001 TRP B 169 HIS 0.002 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 8964) covalent geometry : angle 0.50845 (12136) hydrogen bonds : bond 0.03748 ( 467) hydrogen bonds : angle 4.52176 ( 1320) *********************** 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 190 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7978 (mmtp) cc_final: 0.7316 (mttt) REVERT: A 216 LYS cc_start: 0.8656 (mtmt) cc_final: 0.8421 (mtmm) REVERT: A 333 ARG cc_start: 0.8705 (ptp-170) cc_final: 0.8414 (mtm110) REVERT: B 197 ARG cc_start: 0.8259 (mtp-110) cc_final: 0.8057 (mtp-110) REVERT: B 234 PHE cc_start: 0.9213 (OUTLIER) cc_final: 0.8839 (m-80) REVERT: B 251 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7662 (mpt180) REVERT: B 258 ASP cc_start: 0.8770 (t0) cc_final: 0.8515 (t0) REVERT: E 164 SER cc_start: 0.8611 (t) cc_final: 0.8323 (p) REVERT: E 171 ASN cc_start: 0.8659 (m-40) cc_final: 0.8395 (m-40) REVERT: E 202 ARG cc_start: 0.7718 (mtm110) cc_final: 0.7252 (mtm110) REVERT: R 59 LEU cc_start: 0.8545 (tp) cc_final: 0.8117 (mp) REVERT: R 119 LEU cc_start: 0.7814 (mp) cc_final: 0.7197 (tt) REVERT: R 284 LEU cc_start: 0.7159 (mt) cc_final: 0.6930 (mp) outliers start: 28 outliers final: 16 residues processed: 182 average time/residue: 0.0929 time to fit residues: 22.7397 Evaluate side-chains 173 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 248 VAL 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 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 251 ARG 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 G residue 17 GLU Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 133 MET Chi-restraints excluded: chain R residue 152 SER Chi-restraints excluded: chain R residue 167 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 75 optimal weight: 8.9990 chunk 104 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 60 optimal weight: 0.0060 chunk 32 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 overall best weight: 0.9398 ------------------------------------------------------------------------------- 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 = 0.3873 r_free = 0.3873 target = 0.161105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.118723 restraints weight = 10652.178| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.61 r_work: 0.3109 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2074 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= 0.123 Angle : 0.507 6.251 12136 Z= 0.271 Chirality : 0.042 0.278 1377 Planarity : 0.003 0.039 1542 Dihedral : 4.821 56.358 1217 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.74 % Allowed : 16.95 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.25), residues: 1093 helix: 2.20 (0.25), residues: 404 sheet: 0.39 (0.31), residues: 255 loop : -0.01 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 62 TYR 0.012 0.001 TYR E 190 PHE 0.013 0.001 PHE R 193 TRP 0.016 0.001 TRP B 169 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 8964) covalent geometry : angle 0.50653 (12136) hydrogen bonds : bond 0.03660 ( 467) hydrogen bonds : angle 4.41198 ( 1320) *********************** 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 187 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7988 (mmtp) cc_final: 0.7352 (mttt) REVERT: A 216 LYS cc_start: 0.8652 (mtmt) cc_final: 0.8413 (mtmm) REVERT: A 280 ARG cc_start: 0.8173 (ttp-110) cc_final: 0.7897 (ttp80) REVERT: B 68 ARG cc_start: 0.9232 (OUTLIER) cc_final: 0.9008 (ttt180) REVERT: B 234 PHE cc_start: 0.9191 (OUTLIER) cc_final: 0.8807 (m-80) REVERT: B 251 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7943 (mpt180) REVERT: B 258 ASP cc_start: 0.8770 (t0) cc_final: 0.8513 (t0) REVERT: E 164 SER cc_start: 0.8593 (t) cc_final: 0.8284 (p) REVERT: E 171 ASN cc_start: 0.8643 (m-40) cc_final: 0.8400 (m-40) REVERT: E 202 ARG cc_start: 0.7725 (mtm110) cc_final: 0.7093 (mtm110) REVERT: G 17 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8082 (tp30) REVERT: G 21 MET cc_start: 0.8740 (mmp) cc_final: 0.8022 (mmm) REVERT: G 38 MET cc_start: 0.7517 (mtm) cc_final: 0.7123 (mtp) REVERT: R 119 LEU cc_start: 0.7771 (mp) cc_final: 0.7257 (tt) outliers start: 26 outliers final: 17 residues processed: 181 average time/residue: 0.0928 time to fit residues: 22.3877 Evaluate side-chains 171 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 248 VAL 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 68 ARG Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 251 ARG 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 G residue 17 GLU Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 152 SER Chi-restraints excluded: chain R residue 167 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 93 optimal weight: 0.1980 chunk 96 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 chunk 46 optimal weight: 0.1980 chunk 4 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 52 optimal weight: 8.9990 chunk 45 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.163338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.120574 restraints weight = 10682.680| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.55 r_work: 0.3144 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8964 Z= 0.100 Angle : 0.487 6.357 12136 Z= 0.259 Chirality : 0.041 0.206 1377 Planarity : 0.003 0.038 1542 Dihedral : 4.548 55.825 1217 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.25), residues: 1093 helix: 2.40 (0.25), residues: 404 sheet: 0.31 (0.30), residues: 271 loop : -0.04 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 62 TYR 0.011 0.001 TYR E 190 PHE 0.012 0.001 PHE R 193 TRP 0.017 0.001 TRP B 169 HIS 0.002 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 8964) covalent geometry : angle 0.48673 (12136) hydrogen bonds : bond 0.03381 ( 467) hydrogen bonds : angle 4.27250 ( 1320) *********************** 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 185 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8114 (mmtp) cc_final: 0.7544 (mttt) REVERT: A 216 LYS cc_start: 0.8673 (mtmt) cc_final: 0.8453 (mtmm) REVERT: A 368 ASP cc_start: 0.6625 (m-30) cc_final: 0.6383 (m-30) REVERT: B 68 ARG cc_start: 0.9255 (OUTLIER) cc_final: 0.9035 (ttt180) REVERT: B 234 PHE cc_start: 0.9233 (OUTLIER) cc_final: 0.8845 (m-80) REVERT: B 251 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.8084 (mpt180) REVERT: E 164 SER cc_start: 0.8532 (t) cc_final: 0.8174 (p) REVERT: E 171 ASN cc_start: 0.8646 (m-40) cc_final: 0.8425 (m-40) REVERT: E 202 ARG cc_start: 0.7785 (mtm110) cc_final: 0.7197 (mtm110) REVERT: G 38 MET cc_start: 0.7434 (mtm) cc_final: 0.7073 (mtp) REVERT: R 119 LEU cc_start: 0.7678 (mp) cc_final: 0.7169 (tt) outliers start: 28 outliers final: 19 residues processed: 180 average time/residue: 0.0938 time to fit residues: 22.5955 Evaluate side-chains 162 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 248 VAL 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 68 ARG Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 189 SER 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 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 152 SER 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 87 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 94 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 45 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 0.1980 chunk 86 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 78 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3891 r_free = 0.3891 target = 0.162865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.121163 restraints weight = 10525.935| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.59 r_work: 0.3124 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8964 Z= 0.109 Angle : 0.498 5.753 12136 Z= 0.266 Chirality : 0.041 0.183 1377 Planarity : 0.003 0.038 1542 Dihedral : 4.191 55.885 1214 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.63 % Allowed : 16.84 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.25), residues: 1093 helix: 2.53 (0.25), residues: 398 sheet: 0.40 (0.30), residues: 269 loop : 0.02 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 280 TYR 0.011 0.001 TYR E 190 PHE 0.013 0.001 PHE R 193 TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 8964) covalent geometry : angle 0.49820 (12136) hydrogen bonds : bond 0.03401 ( 467) hydrogen bonds : angle 4.24266 ( 1320) *********************** 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 167 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8161 (mmtp) cc_final: 0.7612 (mttt) REVERT: A 216 LYS cc_start: 0.8710 (mtmt) cc_final: 0.8506 (mtmm) REVERT: A 368 ASP cc_start: 0.6462 (m-30) cc_final: 0.6257 (m-30) REVERT: B 68 ARG cc_start: 0.9273 (OUTLIER) cc_final: 0.9053 (ttt180) REVERT: B 234 PHE cc_start: 0.9244 (OUTLIER) cc_final: 0.8843 (m-80) REVERT: E 145 SER cc_start: 0.7945 (m) cc_final: 0.7662 (p) REVERT: E 164 SER cc_start: 0.8556 (t) cc_final: 0.8213 (p) REVERT: E 171 ASN cc_start: 0.8657 (m-40) cc_final: 0.8445 (m-40) REVERT: E 202 ARG cc_start: 0.7798 (mtm110) cc_final: 0.7210 (mtm110) REVERT: G 38 MET cc_start: 0.7473 (mtm) cc_final: 0.7116 (mtp) REVERT: R 119 LEU cc_start: 0.7705 (mp) cc_final: 0.7181 (tt) outliers start: 25 outliers final: 16 residues processed: 162 average time/residue: 0.0798 time to fit residues: 17.7388 Evaluate side-chains 157 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU 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 68 ARG Chi-restraints excluded: chain B residue 71 VAL 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 336 LEU Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 152 SER Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 282 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 81 optimal weight: 0.4980 chunk 91 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 16 optimal weight: 0.2980 chunk 50 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3896 r_free = 0.3896 target = 0.163169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.120512 restraints weight = 10547.530| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.52 r_work: 0.3148 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8964 Z= 0.109 Angle : 0.506 6.021 12136 Z= 0.269 Chirality : 0.041 0.168 1377 Planarity : 0.003 0.038 1542 Dihedral : 4.172 55.834 1214 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.53 % Allowed : 17.16 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.25), residues: 1093 helix: 2.57 (0.25), residues: 398 sheet: 0.28 (0.30), residues: 271 loop : 0.08 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 280 TYR 0.010 0.001 TYR E 190 PHE 0.013 0.001 PHE R 193 TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 8964) covalent geometry : angle 0.50564 (12136) hydrogen bonds : bond 0.03374 ( 467) hydrogen bonds : angle 4.21321 ( 1320) *********************** 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 167 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8116 (mmtp) cc_final: 0.7526 (mttt) REVERT: A 216 LYS cc_start: 0.8649 (mtmt) cc_final: 0.8416 (mtmm) REVERT: A 368 ASP cc_start: 0.6370 (m-30) cc_final: 0.6134 (m-30) REVERT: B 46 ARG cc_start: 0.8435 (mtp-110) cc_final: 0.8143 (mtp-110) REVERT: B 68 ARG cc_start: 0.9276 (OUTLIER) cc_final: 0.9050 (ttt180) REVERT: B 234 PHE cc_start: 0.9283 (OUTLIER) cc_final: 0.8847 (m-80) REVERT: E 145 SER cc_start: 0.7964 (m) cc_final: 0.7708 (p) REVERT: E 164 SER cc_start: 0.8608 (t) cc_final: 0.8292 (p) REVERT: E 171 ASN cc_start: 0.8624 (m-40) cc_final: 0.8420 (m-40) REVERT: E 202 ARG cc_start: 0.7593 (mtm110) cc_final: 0.6965 (mtm110) REVERT: R 119 LEU cc_start: 0.7597 (mp) cc_final: 0.7076 (tt) outliers start: 24 outliers final: 17 residues processed: 161 average time/residue: 0.0862 time to fit residues: 18.7362 Evaluate side-chains 158 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 248 VAL 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 68 ARG Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 189 SER 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 336 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 152 SER Chi-restraints excluded: chain R residue 167 LEU 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 3 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 13 optimal weight: 0.0980 chunk 50 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3897 r_free = 0.3897 target = 0.163261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.120831 restraints weight = 10572.790| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.51 r_work: 0.3152 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 8964 Z= 0.111 Angle : 0.509 6.534 12136 Z= 0.272 Chirality : 0.041 0.170 1377 Planarity : 0.003 0.038 1542 Dihedral : 4.157 56.064 1214 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.42 % Allowed : 17.26 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.25), residues: 1093 helix: 2.53 (0.25), residues: 398 sheet: 0.28 (0.30), residues: 271 loop : 0.10 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 280 TYR 0.010 0.001 TYR E 190 PHE 0.014 0.001 PHE R 193 TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 8964) covalent geometry : angle 0.50912 (12136) hydrogen bonds : bond 0.03378 ( 467) hydrogen bonds : angle 4.21138 ( 1320) ********************** 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 165 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8120 (mmtp) cc_final: 0.7535 (mttt) REVERT: A 216 LYS cc_start: 0.8643 (mtmt) cc_final: 0.8410 (mtmm) REVERT: A 368 ASP cc_start: 0.6446 (m-30) cc_final: 0.6203 (m-30) REVERT: B 46 ARG cc_start: 0.8430 (mtp-110) cc_final: 0.8140 (mtp-110) REVERT: B 68 ARG cc_start: 0.9284 (OUTLIER) cc_final: 0.9058 (ttt180) REVERT: B 234 PHE cc_start: 0.9283 (OUTLIER) cc_final: 0.8850 (m-80) REVERT: E 145 SER cc_start: 0.7953 (m) cc_final: 0.7697 (p) REVERT: E 164 SER cc_start: 0.8593 (t) cc_final: 0.8282 (p) REVERT: E 171 ASN cc_start: 0.8637 (m-40) cc_final: 0.8435 (m-40) REVERT: E 202 ARG cc_start: 0.7614 (mtm110) cc_final: 0.6997 (mtm110) REVERT: G 38 MET cc_start: 0.7525 (mtm) cc_final: 0.6836 (mtm) REVERT: G 42 GLU cc_start: 0.8491 (pt0) cc_final: 0.8120 (mp0) outliers start: 23 outliers final: 20 residues processed: 159 average time/residue: 0.0927 time to fit residues: 19.7702 Evaluate side-chains 162 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 SER Chi-restraints excluded: chain A residue 211 LYS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 LEU 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 68 ARG Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 189 SER 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 336 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 152 SER Chi-restraints excluded: chain R residue 167 LEU 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 107 optimal weight: 0.7980 chunk 64 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 101 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 74 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3895 r_free = 0.3895 target = 0.163152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.120680 restraints weight = 10472.704| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.47 r_work: 0.3150 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8964 Z= 0.114 Angle : 0.510 6.396 12136 Z= 0.271 Chirality : 0.041 0.170 1377 Planarity : 0.003 0.038 1542 Dihedral : 4.155 56.146 1214 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.63 % Allowed : 17.26 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.25), residues: 1093 helix: 2.55 (0.25), residues: 398 sheet: 0.24 (0.30), residues: 272 loop : 0.10 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 280 TYR 0.010 0.001 TYR E 190 PHE 0.014 0.001 PHE R 193 TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 8964) covalent geometry : angle 0.51025 (12136) hydrogen bonds : bond 0.03391 ( 467) hydrogen bonds : angle 4.19260 ( 1320) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2179.95 seconds wall clock time: 37 minutes 53.08 seconds (2273.08 seconds total)