Starting phenix.real_space_refine on Wed Jan 15 18:11:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xoj_38531/01_2025/8xoj_38531.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xoj_38531/01_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_38531/01_2025/8xoj_38531.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xoj_38531/01_2025/8xoj_38531.map" model { file = "/net/cci-nas-00/data/ceres_data/8xoj_38531/01_2025/8xoj_38531.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xoj_38531/01_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-5571/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: 4.81, per 1000 atoms: 0.55 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: 2.16 Conformation dependent library (CDL) restraints added in 999.1 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: 0.94 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: 2.57 Time building geometry restraints manager: 2.47 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: 0.650 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.580 Find NCS groups from input model: 0.130 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.650 ------------------------------------------------------------------------------- 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= 0.198 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 *********************** 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 : 0.894 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: 0.2513 time to fit residues: 57.5295 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 : 1.041 ------------------------------------------------------------------------------- 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 = 10481.928| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.56 r_work: 0.3134 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 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= 0.183 Angle : 0.543 5.776 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 *********************** 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 : 0.953 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8263 (mmtp) cc_final: 0.7604 (mttt) REVERT: A 25 MET cc_start: 0.8461 (mmm) cc_final: 0.8190 (mtp) REVERT: A 232 ARG cc_start: 0.8128 (ttp-110) cc_final: 0.7815 (ttp-170) REVERT: A 294 GLN cc_start: 0.7957 (mm-40) cc_final: 0.7694 (mm-40) REVERT: A 299 GLU cc_start: 0.8493 (pt0) cc_final: 0.8280 (pt0) REVERT: A 333 ARG cc_start: 0.8687 (ptp-170) cc_final: 0.8435 (mtm110) REVERT: B 197 ARG cc_start: 0.8315 (mtp-110) cc_final: 0.8085 (mtp-110) REVERT: B 213 VAL cc_start: 0.8483 (m) cc_final: 0.8262 (t) REVERT: E 82 GLN cc_start: 0.7944 (tp40) cc_final: 0.7403 (tp-100) REVERT: E 164 SER cc_start: 0.8661 (t) cc_final: 0.8374 (p) REVERT: E 183 GLN cc_start: 0.7097 (mp10) cc_final: 0.6657 (mp10) REVERT: E 202 ARG cc_start: 0.7588 (mtm110) cc_final: 0.7296 (mtm110) REVERT: G 17 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.7988 (tp30) REVERT: G 21 MET cc_start: 0.8879 (mmm) cc_final: 0.8123 (mmm) REVERT: R 59 LEU cc_start: 0.8678 (tp) cc_final: 0.8184 (mp) REVERT: R 302 HIS cc_start: 0.5461 (m90) cc_final: 0.5260 (m-70) outliers start: 14 outliers final: 7 residues processed: 170 average time/residue: 0.2469 time to fit residues: 55.5836 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 : 0.912 ------------------------------------------------------------------------------- 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: 5.9990 chunk 12 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 104 optimal weight: 8.9990 chunk 8 optimal weight: 0.7980 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: 1.2782 ------------------------------------------------------------------------------- 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 A 371 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 = 0.3879 r_free = 0.3879 target = 0.161674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.118870 restraints weight = 10627.214| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.55 r_work: 0.3116 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1517 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= 0.216 Angle : 0.523 6.065 12136 Z= 0.280 Chirality : 0.042 0.170 1377 Planarity : 0.004 0.046 1542 Dihedral : 4.976 59.433 1217 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.21 % Allowed : 13.89 % Favored : 83.89 % 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: 1.49 (0.25), residues: 1093 helix: 2.12 (0.25), residues: 405 sheet: 0.66 (0.31), residues: 267 loop : 0.19 (0.30), residues: 421 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 0.012 0.001 PHE R 193 TYR 0.013 0.001 TYR E 190 ARG 0.006 0.000 ARG E 67 *********************** 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 182 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 1.004 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8270 (mmtp) cc_final: 0.7652 (mttt) REVERT: A 25 MET cc_start: 0.8345 (mmm) cc_final: 0.8117 (mtp) REVERT: A 333 ARG cc_start: 0.8638 (ptp-170) cc_final: 0.8398 (mtm110) REVERT: B 234 PHE cc_start: 0.9256 (OUTLIER) cc_final: 0.8905 (m-80) REVERT: B 258 ASP cc_start: 0.8822 (t0) cc_final: 0.8458 (t0) REVERT: E 43 LYS cc_start: 0.8167 (ptpt) cc_final: 0.7560 (ptpp) REVERT: E 164 SER cc_start: 0.8616 (t) cc_final: 0.8280 (p) REVERT: E 202 ARG cc_start: 0.7777 (mtm110) cc_final: 0.7433 (mtm110) REVERT: G 17 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8027 (tp30) REVERT: G 21 MET cc_start: 0.8780 (mmm) cc_final: 0.8149 (mmm) REVERT: R 59 LEU cc_start: 0.8730 (tp) cc_final: 0.8217 (mp) REVERT: R 119 LEU cc_start: 0.7790 (mp) cc_final: 0.7130 (tt) outliers start: 21 outliers final: 14 residues processed: 174 average time/residue: 0.2498 time to fit residues: 57.5246 Evaluate side-chains 166 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 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 41 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 2 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 76 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.3877 r_free = 0.3877 target = 0.161491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.118822 restraints weight = 10579.305| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.53 r_work: 0.3119 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1773 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= 0.197 Angle : 0.506 5.329 12136 Z= 0.271 Chirality : 0.042 0.168 1377 Planarity : 0.003 0.044 1542 Dihedral : 4.882 57.647 1217 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.11 % Allowed : 15.89 % Favored : 82.00 % 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: 1.45 (0.25), residues: 1093 helix: 2.19 (0.25), residues: 405 sheet: 0.51 (0.31), residues: 269 loop : 0.14 (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 0.013 0.001 PHE R 193 TYR 0.013 0.001 TYR E 190 ARG 0.005 0.000 ARG A 280 *********************** 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 173 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 1.069 Fit side-chains revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8218 (mmtp) cc_final: 0.7632 (mttt) REVERT: A 333 ARG cc_start: 0.8669 (ptp-170) cc_final: 0.8397 (mtm110) REVERT: B 68 ARG cc_start: 0.9279 (OUTLIER) cc_final: 0.9040 (ttt180) REVERT: B 197 ARG cc_start: 0.8329 (mtp-110) cc_final: 0.8120 (mtp-110) REVERT: B 234 PHE cc_start: 0.9253 (OUTLIER) cc_final: 0.8852 (m-80) REVERT: B 258 ASP cc_start: 0.8795 (t0) cc_final: 0.8472 (t0) REVERT: E 43 LYS cc_start: 0.8166 (ptpt) cc_final: 0.7560 (ptpp) REVERT: E 164 SER cc_start: 0.8581 (t) cc_final: 0.8278 (p) REVERT: E 202 ARG cc_start: 0.7767 (mtm110) cc_final: 0.7367 (mtm110) REVERT: G 17 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8079 (tp30) REVERT: G 21 MET cc_start: 0.8817 (mmm) cc_final: 0.8203 (mmm) REVERT: R 119 LEU cc_start: 0.7822 (mp) cc_final: 0.7176 (tt) outliers start: 20 outliers final: 11 residues processed: 166 average time/residue: 0.2427 time to fit residues: 53.5249 Evaluate side-chains 160 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 32 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 24 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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** E 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.162291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.112967 restraints weight = 10533.388| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.49 r_work: 0.3137 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1971 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= 0.178 Angle : 0.495 6.653 12136 Z= 0.265 Chirality : 0.041 0.251 1377 Planarity : 0.003 0.041 1542 Dihedral : 4.713 55.867 1217 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.74 % Allowed : 15.58 % Favored : 81.68 % 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: 1.47 (0.25), residues: 1093 helix: 2.25 (0.25), residues: 404 sheet: 0.47 (0.30), residues: 270 loop : 0.15 (0.30), residues: 419 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 0.013 0.001 PHE R 193 TYR 0.012 0.001 TYR E 190 ARG 0.004 0.000 ARG E 67 *********************** 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 181 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8122 (mmtp) cc_final: 0.7499 (mttt) REVERT: A 333 ARG cc_start: 0.8701 (ptp-170) cc_final: 0.8409 (mtm110) REVERT: A 368 ASP cc_start: 0.6613 (m-30) cc_final: 0.6404 (m-30) REVERT: A 385 GLN cc_start: 0.7934 (tp40) cc_final: 0.7692 (tp40) REVERT: B 68 ARG cc_start: 0.9279 (OUTLIER) cc_final: 0.9018 (ttt180) REVERT: B 197 ARG cc_start: 0.8291 (mtp-110) cc_final: 0.7973 (mtp-110) REVERT: B 226 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7620 (mm-30) REVERT: B 234 PHE cc_start: 0.9306 (OUTLIER) cc_final: 0.8891 (m-80) REVERT: B 258 ASP cc_start: 0.8785 (t0) cc_final: 0.8467 (t0) REVERT: B 264 TYR cc_start: 0.9101 (m-80) cc_final: 0.8769 (m-80) REVERT: E 43 LYS cc_start: 0.8106 (ptpt) cc_final: 0.7505 (ptpp) REVERT: E 164 SER cc_start: 0.8600 (t) cc_final: 0.8322 (p) REVERT: E 202 ARG cc_start: 0.7546 (mtm110) cc_final: 0.7088 (mtm110) REVERT: G 38 MET cc_start: 0.7611 (mtm) cc_final: 0.7223 (mtp) REVERT: R 119 LEU cc_start: 0.7740 (mp) cc_final: 0.7132 (tt) outliers start: 26 outliers final: 15 residues processed: 171 average time/residue: 0.2451 time to fit residues: 55.5568 Evaluate side-chains 164 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 1.068 ------------------------------------------------------------------------------- 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 358 ILE 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 68 ARG Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 47 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.3860 r_free = 0.3860 target = 0.160038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.117849 restraints weight = 10595.229| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.59 r_work: 0.3091 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8964 Z= 0.274 Angle : 0.537 5.702 12136 Z= 0.286 Chirality : 0.043 0.203 1377 Planarity : 0.004 0.039 1542 Dihedral : 4.436 56.024 1214 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.16 % Allowed : 15.37 % 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 (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: 1.33 (0.25), residues: 1093 helix: 2.20 (0.25), residues: 404 sheet: 0.35 (0.30), residues: 271 loop : 0.04 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 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 0.007 0.000 ARG A 280 *********************** 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: 30 poor density : 150 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.7975 (mmtp) cc_final: 0.7350 (mttt) REVERT: A 368 ASP cc_start: 0.6766 (m-30) cc_final: 0.6444 (m-30) REVERT: A 385 GLN cc_start: 0.7848 (tp40) cc_final: 0.7349 (tp40) REVERT: B 68 ARG cc_start: 0.9251 (OUTLIER) cc_final: 0.9036 (ttt180) REVERT: B 226 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7528 (mm-30) REVERT: B 234 PHE cc_start: 0.9214 (OUTLIER) cc_final: 0.8828 (m-80) REVERT: B 251 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7643 (mpt180) REVERT: B 258 ASP cc_start: 0.8780 (t0) cc_final: 0.8532 (t70) REVERT: E 43 LYS cc_start: 0.8186 (ptpt) cc_final: 0.7840 (ptpp) REVERT: E 164 SER cc_start: 0.8590 (t) cc_final: 0.8296 (p) REVERT: E 202 ARG cc_start: 0.7709 (mtm110) cc_final: 0.7268 (mtm110) REVERT: G 38 MET cc_start: 0.7550 (mtm) cc_final: 0.7159 (mtp) REVERT: R 119 LEU cc_start: 0.7838 (mp) cc_final: 0.7237 (tt) REVERT: R 246 ARG cc_start: 0.7749 (ttm-80) cc_final: 0.7512 (ttm170) outliers start: 30 outliers final: 17 residues processed: 170 average time/residue: 0.2570 time to fit residues: 57.5297 Evaluate side-chains 165 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 1.025 ------------------------------------------------------------------------------- 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 249 THR 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 99 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 chunk 58 optimal weight: 0.8980 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** B 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.163276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.120573 restraints weight = 10614.779| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.52 r_work: 0.3146 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2200 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= 0.150 Angle : 0.486 5.446 12136 Z= 0.260 Chirality : 0.041 0.165 1377 Planarity : 0.003 0.041 1542 Dihedral : 4.254 56.014 1214 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.84 % Allowed : 16.11 % Favored : 81.05 % 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: 2.39 (0.25), residues: 404 sheet: 0.33 (0.30), residues: 272 loop : 0.02 (0.30), 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 0.011 0.001 TYR E 190 ARG 0.007 0.000 ARG G 62 *********************** 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: 27 poor density : 158 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8241 (mmtp) cc_final: 0.7666 (mttt) REVERT: A 368 ASP cc_start: 0.6525 (m-30) cc_final: 0.6287 (m-30) REVERT: A 385 GLN cc_start: 0.8055 (tp40) cc_final: 0.7829 (tp40) REVERT: B 68 ARG cc_start: 0.9329 (OUTLIER) cc_final: 0.9053 (ttt180) REVERT: B 226 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7598 (mm-30) REVERT: B 234 PHE cc_start: 0.9362 (OUTLIER) cc_final: 0.8973 (m-80) REVERT: B 251 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.8192 (mpt180) REVERT: B 258 ASP cc_start: 0.8805 (t0) cc_final: 0.8568 (t0) REVERT: B 264 TYR cc_start: 0.9080 (m-80) cc_final: 0.8771 (m-80) REVERT: B 336 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8588 (tp) REVERT: E 43 LYS cc_start: 0.8174 (ptpt) cc_final: 0.7793 (ptpp) REVERT: E 164 SER cc_start: 0.8545 (t) cc_final: 0.8216 (p) REVERT: E 202 ARG cc_start: 0.7660 (mtm110) cc_final: 0.7171 (mtm110) REVERT: G 38 MET cc_start: 0.7615 (mtm) cc_final: 0.7226 (mtp) REVERT: R 119 LEU cc_start: 0.7713 (mp) cc_final: 0.7091 (tt) REVERT: R 246 ARG cc_start: 0.7708 (ttm-80) cc_final: 0.7496 (ttm170) outliers start: 27 outliers final: 14 residues processed: 177 average time/residue: 0.2481 time to fit residues: 58.0517 Evaluate side-chains 168 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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 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 167 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 55 optimal weight: 10.0000 chunk 95 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 chunk 76 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 4 optimal weight: 8.9990 chunk 21 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 ** 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 = 0.3889 r_free = 0.3889 target = 0.162590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.120568 restraints weight = 10699.160| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.60 r_work: 0.3136 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2306 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= 0.172 Angle : 0.507 5.487 12136 Z= 0.272 Chirality : 0.041 0.169 1377 Planarity : 0.003 0.038 1542 Dihedral : 4.218 56.103 1214 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.42 % Allowed : 16.63 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.46 (0.25), residues: 1093 helix: 2.41 (0.25), residues: 404 sheet: 0.35 (0.30), residues: 272 loop : 0.02 (0.30), residues: 417 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 0.011 0.001 TYR E 190 ARG 0.007 0.000 ARG G 62 *********************** 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 174 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8005 (mmtp) cc_final: 0.7412 (mttt) REVERT: A 368 ASP cc_start: 0.6667 (m-30) cc_final: 0.6397 (m-30) REVERT: A 385 GLN cc_start: 0.7832 (tp40) cc_final: 0.7553 (tp40) REVERT: B 38 ASP cc_start: 0.8412 (OUTLIER) cc_final: 0.8045 (m-30) REVERT: B 68 ARG cc_start: 0.9236 (OUTLIER) cc_final: 0.9029 (ttt180) REVERT: B 234 PHE cc_start: 0.9219 (OUTLIER) cc_final: 0.8814 (m-80) REVERT: B 251 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.8023 (mpt180) REVERT: B 258 ASP cc_start: 0.8618 (t0) cc_final: 0.8386 (t0) REVERT: E 43 LYS cc_start: 0.8193 (ptpt) cc_final: 0.7570 (ptpp) REVERT: E 164 SER cc_start: 0.8533 (t) cc_final: 0.8208 (p) REVERT: E 202 ARG cc_start: 0.7725 (mtm110) cc_final: 0.7241 (mtm110) REVERT: G 38 MET cc_start: 0.7422 (mtm) cc_final: 0.7047 (mtp) REVERT: R 119 LEU cc_start: 0.7755 (mp) cc_final: 0.7145 (tt) outliers start: 23 outliers final: 13 residues processed: 166 average time/residue: 0.2465 time to fit residues: 54.2067 Evaluate side-chains 159 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 0.972 ------------------------------------------------------------------------------- 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 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 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 R residue 99 ILE Chi-restraints excluded: chain R residue 167 LEU 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: 1.9990 chunk 75 optimal weight: 20.0000 chunk 85 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 97 optimal weight: 6.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3883 r_free = 0.3883 target = 0.162100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.119711 restraints weight = 10651.756| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.52 r_work: 0.3132 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8964 Z= 0.195 Angle : 0.511 6.551 12136 Z= 0.274 Chirality : 0.042 0.255 1377 Planarity : 0.003 0.038 1542 Dihedral : 4.232 56.185 1214 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.32 % Allowed : 17.26 % Favored : 80.42 % 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: 1.39 (0.25), residues: 1093 helix: 2.38 (0.25), residues: 404 sheet: 0.27 (0.30), residues: 273 loop : 0.01 (0.30), residues: 416 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 0.011 0.001 TYR E 190 ARG 0.006 0.000 ARG G 62 *********************** 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 174 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8123 (mmtp) cc_final: 0.7541 (mttt) REVERT: A 385 GLN cc_start: 0.8044 (tp40) cc_final: 0.7778 (tp40) REVERT: B 38 ASP cc_start: 0.8516 (OUTLIER) cc_final: 0.8144 (m-30) REVERT: B 46 ARG cc_start: 0.8411 (mtp-110) cc_final: 0.8142 (mtp-110) REVERT: B 68 ARG cc_start: 0.9297 (OUTLIER) cc_final: 0.9039 (ttt180) REVERT: B 234 PHE cc_start: 0.9331 (OUTLIER) cc_final: 0.8930 (m-80) REVERT: B 251 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.8077 (mpt180) REVERT: B 258 ASP cc_start: 0.8755 (t0) cc_final: 0.8504 (t0) REVERT: E 43 LYS cc_start: 0.8141 (ptpt) cc_final: 0.7775 (ptpp) REVERT: E 164 SER cc_start: 0.8603 (t) cc_final: 0.8303 (p) REVERT: E 202 ARG cc_start: 0.7650 (mtm110) cc_final: 0.6991 (mtm110) REVERT: G 38 MET cc_start: 0.7511 (mtm) cc_final: 0.7139 (mtp) REVERT: R 119 LEU cc_start: 0.7571 (mp) cc_final: 0.7044 (tt) outliers start: 22 outliers final: 15 residues processed: 166 average time/residue: 0.2537 time to fit residues: 55.5373 Evaluate side-chains 169 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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 391 TYR Chi-restraints excluded: chain B residue 3 GLU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 1 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 = 0.3867 r_free = 0.3867 target = 0.160522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.117592 restraints weight = 10662.366| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.53 r_work: 0.3105 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8964 Z= 0.253 Angle : 0.542 6.203 12136 Z= 0.291 Chirality : 0.043 0.254 1377 Planarity : 0.004 0.039 1542 Dihedral : 4.324 56.089 1214 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.42 % Allowed : 16.95 % Favored : 80.63 % 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: 1.29 (0.25), residues: 1093 helix: 2.31 (0.25), residues: 404 sheet: 0.19 (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 ********************** 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 169 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 LYS cc_start: 0.8141 (mmtp) cc_final: 0.7511 (mttt) REVERT: B 46 ARG cc_start: 0.8418 (mtp-110) cc_final: 0.8140 (mtp-110) REVERT: B 68 ARG cc_start: 0.9295 (OUTLIER) cc_final: 0.9050 (ttt180) REVERT: B 234 PHE cc_start: 0.9338 (OUTLIER) cc_final: 0.8895 (m-80) REVERT: B 251 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7907 (mpt180) REVERT: E 43 LYS cc_start: 0.8144 (ptpt) cc_final: 0.7494 (ptpp) REVERT: E 164 SER cc_start: 0.8595 (t) cc_final: 0.8316 (p) REVERT: E 202 ARG cc_start: 0.7633 (mtm110) cc_final: 0.7114 (mtm110) REVERT: G 38 MET cc_start: 0.7531 (mtm) cc_final: 0.7156 (mtp) REVERT: R 119 LEU cc_start: 0.7610 (mp) cc_final: 0.7080 (tt) outliers start: 23 outliers final: 16 residues processed: 161 average time/residue: 0.2617 time to fit residues: 55.5304 Evaluate side-chains 160 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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 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 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 318 LEU Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain R residue 99 ILE Chi-restraints excluded: chain R residue 167 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 42 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 20 optimal weight: 0.0020 chunk 95 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.7994 ------------------------------------------------------------------------------- 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 = 0.3863 r_free = 0.3863 target = 0.160082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.117216 restraints weight = 10683.849| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.52 r_work: 0.3093 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8964 Z= 0.278 Angle : 0.551 6.315 12136 Z= 0.298 Chirality : 0.044 0.253 1377 Planarity : 0.004 0.039 1542 Dihedral : 4.384 55.811 1214 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.21 % Allowed : 17.47 % 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: 2.38 (0.25), residues: 398 sheet: 0.14 (0.31), residues: 260 loop : -0.01 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS E 35 PHE 0.049 0.002 PHE R 168 TYR 0.012 0.001 TYR E 103 ARG 0.006 0.000 ARG G 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5166.18 seconds wall clock time: 92 minutes 30.69 seconds (5550.69 seconds total)