Starting phenix.real_space_refine on Wed Sep 17 15:03:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m0r_63561/09_2025/9m0r_63561.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m0r_63561/09_2025/9m0r_63561.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9m0r_63561/09_2025/9m0r_63561.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m0r_63561/09_2025/9m0r_63561.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9m0r_63561/09_2025/9m0r_63561.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m0r_63561/09_2025/9m0r_63561.map" } resolution = 2.47 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= -0.000 sd= 0.012 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 68 5.16 5 C 5742 2.51 5 N 1548 2.21 5 O 1662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9020 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 2631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2631 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 5, 'TRANS': 337} Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 438 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "L" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 68 Classifications: {'peptide': 8} Link IDs: {'PTRANS': 2, 'TRANS': 5} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1811 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 225} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "R" Number of atoms: 2313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2313 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 279} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "S" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1758 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Time building chain proxies: 2.26, per 1000 atoms: 0.25 Number of scatterers: 9020 At special positions: 0 Unit cell: (89.06, 120.45, 132.86, 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 68 16.00 O 1662 8.00 N 1548 7.00 C 5742 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 351 " - pdb=" SG CYS R 144 " distance=2.03 Simple disulfide: pdb=" SG CYS R 116 " - pdb=" SG CYS R 203 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 367.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2176 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 16 sheets defined 36.7% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'B' and resid 1 through 25 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 8 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.441A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 3.675A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.905A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 Processing helix chain 'A' and resid 327 through 351 removed outlier: 4.246A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 70 Processing helix chain 'R' and resid 76 through 105 removed outlier: 4.701A pdb=" N MET R 97 " --> pdb=" O GLY R 93 " (cutoff:3.500A) Proline residue: R 98 - end of helix removed outlier: 3.733A pdb=" N ASN R 104 " --> pdb=" O THR R 100 " (cutoff:3.500A) Processing helix chain 'R' and resid 113 through 147 removed outlier: 3.834A pdb=" N LYS R 117 " --> pdb=" O ASN R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 154 through 172 Processing helix chain 'R' and resid 173 through 178 Processing helix chain 'R' and resid 210 through 226 removed outlier: 4.031A pdb=" N ARG R 214 " --> pdb=" O LYS R 210 " (cutoff:3.500A) Processing helix chain 'R' and resid 226 through 244 Processing helix chain 'R' and resid 265 through 282 removed outlier: 3.522A pdb=" N VAL R 269 " --> pdb=" O ARG R 265 " (cutoff:3.500A) Processing helix chain 'R' and resid 283 through 296 removed outlier: 3.779A pdb=" N TRP R 287 " --> pdb=" O TRP R 283 " (cutoff:3.500A) Processing helix chain 'R' and resid 299 through 309 Processing helix chain 'R' and resid 309 through 329 removed outlier: 3.644A pdb=" N PHE R 313 " --> pdb=" O TYR R 309 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN R 321 " --> pdb=" O LEU R 317 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N SER R 322 " --> pdb=" O ALA R 318 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER R 323 " --> pdb=" O PHE R 319 " (cutoff:3.500A) Proline residue: R 326 - end of helix Processing helix chain 'R' and resid 334 through 339 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'B' and resid 45 through 51 removed outlier: 5.573A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 60 through 63 removed outlier: 3.560A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.835A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.470A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.755A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.638A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.657A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.662A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 31 through 33 Processing sheet with id=AB1, first strand: chain 'R' and resid 180 through 181 removed outlier: 3.750A pdb=" N THR R 181 " --> pdb=" O TRP R 204 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TRP R 204 " --> pdb=" O THR R 181 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'R' and resid 184 through 185 Processing sheet with id=AB3, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.780A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 10 through 12 removed outlier: 4.329A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB7, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.431A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) 470 hydrogen bonds defined for protein. 1302 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: 1.82 Time building geometry restraints manager: 1.26 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: 2902 1.34 - 1.46: 1706 1.46 - 1.57: 4503 1.57 - 1.69: 0 1.69 - 1.81: 101 Bond restraints: 9212 Sorted by residual: bond pdb=" N ASP B 254 " pdb=" CA ASP B 254 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.19e-02 7.06e+03 6.71e+00 bond pdb=" N PHE L 8 " pdb=" CA PHE L 8 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.32e+00 bond pdb=" C ALA R 300 " pdb=" N PRO R 301 " ideal model delta sigma weight residual 1.335 1.352 -0.017 1.30e-02 5.92e+03 1.65e+00 bond pdb=" CA VAL L 1 " pdb=" C VAL L 1 " ideal model delta sigma weight residual 1.525 1.550 -0.025 2.10e-02 2.27e+03 1.38e+00 bond pdb=" CB GLU A 297 " pdb=" CG GLU A 297 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.05e+00 ... (remaining 9207 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 12319 2.08 - 4.15: 134 4.15 - 6.23: 27 6.23 - 8.31: 4 8.31 - 10.38: 2 Bond angle restraints: 12486 Sorted by residual: angle pdb=" CA ASP B 254 " pdb=" CB ASP B 254 " pdb=" CG ASP B 254 " ideal model delta sigma weight residual 112.60 117.36 -4.76 1.00e+00 1.00e+00 2.26e+01 angle pdb=" C TYR S 235 " pdb=" N PRO S 236 " pdb=" CA PRO S 236 " ideal model delta sigma weight residual 119.84 114.99 4.85 1.25e+00 6.40e-01 1.51e+01 angle pdb=" C ARG R 241 " pdb=" N LYS R 242 " pdb=" CA LYS R 242 " ideal model delta sigma weight residual 120.31 115.31 5.00 1.52e+00 4.33e-01 1.08e+01 angle pdb=" N TYR S 235 " pdb=" CA TYR S 235 " pdb=" C TYR S 235 " ideal model delta sigma weight residual 109.81 116.91 -7.10 2.21e+00 2.05e-01 1.03e+01 angle pdb=" CA TYR S 235 " pdb=" CB TYR S 235 " pdb=" CG TYR S 235 " ideal model delta sigma weight residual 113.90 108.12 5.78 1.80e+00 3.09e-01 1.03e+01 ... (remaining 12481 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.00: 4650 17.00 - 34.01: 604 34.01 - 51.01: 164 51.01 - 68.01: 34 68.01 - 85.02: 11 Dihedral angle restraints: 5463 sinusoidal: 2096 harmonic: 3367 Sorted by residual: dihedral pdb=" CB CYS R 116 " pdb=" SG CYS R 116 " pdb=" SG CYS R 203 " pdb=" CB CYS R 203 " ideal model delta sinusoidal sigma weight residual 93.00 161.82 -68.82 1 1.00e+01 1.00e-02 6.13e+01 dihedral pdb=" CB CYS A 351 " pdb=" SG CYS A 351 " pdb=" SG CYS R 144 " pdb=" CB CYS R 144 " ideal model delta sinusoidal sigma weight residual -86.00 -140.53 54.53 1 1.00e+01 1.00e-02 4.03e+01 dihedral pdb=" CA ARG S 191 " pdb=" C ARG S 191 " pdb=" N MET S 192 " pdb=" CA MET S 192 " ideal model delta harmonic sigma weight residual 180.00 161.83 18.17 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 5460 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1283 0.071 - 0.142: 137 0.142 - 0.213: 1 0.213 - 0.284: 1 0.284 - 0.355: 1 Chirality restraints: 1423 Sorted by residual: chirality pdb=" CG LEU R 52 " pdb=" CB LEU R 52 " pdb=" CD1 LEU R 52 " pdb=" CD2 LEU R 52 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.14e+00 chirality pdb=" CA TYR S 235 " pdb=" N TYR S 235 " pdb=" C TYR S 235 " pdb=" CB TYR S 235 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA MET R 97 " pdb=" N MET R 97 " pdb=" C MET R 97 " pdb=" CB MET R 97 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.94e-01 ... (remaining 1420 not shown) Planarity restraints: 1576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR S 235 " 0.032 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO S 236 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO S 236 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO S 236 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE R 311 " -0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO R 312 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO R 312 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO R 312 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR R 198 " 0.021 5.00e-02 4.00e+02 3.23e-02 1.66e+00 pdb=" N PRO R 199 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO R 199 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO R 199 " 0.018 5.00e-02 4.00e+02 ... (remaining 1573 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 4936 3.00 - 3.48: 9216 3.48 - 3.95: 15077 3.95 - 4.43: 18070 4.43 - 4.90: 28636 Nonbonded interactions: 75935 Sorted by model distance: nonbonded pdb=" N GLU A 297 " pdb=" OE1 GLU A 297 " model vdw 2.528 3.120 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.537 3.040 nonbonded pdb=" N ASP A 315 " pdb=" OD1 ASP A 315 " model vdw 2.539 3.120 nonbonded pdb=" O THR G 52 " pdb=" OG1 THR G 52 " model vdw 2.547 3.040 nonbonded pdb=" N TYR S 102 " pdb=" O TYR S 102 " model vdw 2.594 2.496 ... (remaining 75930 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: 4.630 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: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.760 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:9.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 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 : 0.004 0.106 9216 Z= 0.205 Angle : 0.589 10.383 12492 Z= 0.312 Chirality : 0.043 0.355 1423 Planarity : 0.004 0.048 1576 Dihedral : 16.767 85.018 3278 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.57 % Allowed : 24.30 % Favored : 73.12 % 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: 0.40 (0.26), residues: 1142 helix: 1.75 (0.27), residues: 398 sheet: 0.03 (0.29), residues: 302 loop : -0.89 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 19 TYR 0.022 0.001 TYR S 235 PHE 0.012 0.001 PHE R 95 TRP 0.021 0.001 TRP R 287 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 9212) covalent geometry : angle 0.58729 (12486) SS BOND : bond 0.00141 ( 3) SS BOND : angle 2.08309 ( 6) hydrogen bonds : bond 0.15036 ( 463) hydrogen bonds : angle 7.19340 ( 1302) Misc. bond : bond 0.10607 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 169 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 45 MET cc_start: 0.5867 (ttm) cc_final: 0.5619 (ttm) REVERT: R 61 ASN cc_start: 0.7118 (m-40) cc_final: 0.6833 (m110) REVERT: R 165 ILE cc_start: 0.7979 (OUTLIER) cc_final: 0.7583 (pp) REVERT: R 184 ARG cc_start: 0.7285 (mpp-170) cc_final: 0.6912 (mmp80) REVERT: R 303 LEU cc_start: 0.7251 (OUTLIER) cc_final: 0.6707 (mt) REVERT: S 235 TYR cc_start: 0.6563 (OUTLIER) cc_final: 0.6304 (t80) outliers start: 25 outliers final: 13 residues processed: 188 average time/residue: 0.6246 time to fit residues: 124.7283 Evaluate side-chains 176 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 144 CYS Chi-restraints excluded: chain R residue 145 ILE Chi-restraints excluded: chain R residue 165 ILE Chi-restraints excluded: chain R residue 178 VAL Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 303 LEU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 30.0000 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 237 ASN A 188 HIS ** R 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 186 GLN S 194 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.146103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.088531 restraints weight = 12522.097| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.64 r_work: 0.2976 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9216 Z= 0.151 Angle : 0.560 8.501 12492 Z= 0.297 Chirality : 0.043 0.252 1423 Planarity : 0.004 0.047 1576 Dihedral : 5.812 57.495 1275 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.94 % Allowed : 25.03 % Favored : 70.03 % 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: 0.57 (0.26), residues: 1142 helix: 1.93 (0.27), residues: 398 sheet: 0.21 (0.29), residues: 293 loop : -0.91 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 19 TYR 0.021 0.001 TYR S 235 PHE 0.010 0.001 PHE R 95 TRP 0.018 0.002 TRP B 82 HIS 0.003 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 9212) covalent geometry : angle 0.55909 (12486) SS BOND : bond 0.00247 ( 3) SS BOND : angle 1.71875 ( 6) hydrogen bonds : bond 0.03924 ( 463) hydrogen bonds : angle 5.37915 ( 1302) Misc. bond : bond 0.00003 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 161 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 217 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.7383 (pmt) REVERT: G 62 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.6321 (ptp-170) REVERT: A 287 TYR cc_start: 0.7680 (m-80) cc_final: 0.7337 (m-80) REVERT: R 61 ASN cc_start: 0.7167 (m-40) cc_final: 0.6779 (m110) REVERT: R 125 MET cc_start: 0.7192 (tpt) cc_final: 0.6797 (tpp) REVERT: R 190 MET cc_start: 0.2576 (mtm) cc_final: 0.1552 (mmp) REVERT: R 225 TYR cc_start: 0.8099 (t80) cc_final: 0.7896 (t80) REVERT: S 235 TYR cc_start: 0.7094 (OUTLIER) cc_final: 0.6409 (t80) outliers start: 48 outliers final: 12 residues processed: 186 average time/residue: 0.5822 time to fit residues: 115.1405 Evaluate side-chains 171 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 144 CYS Chi-restraints excluded: chain R residue 178 VAL Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 63 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 72 optimal weight: 6.9990 chunk 39 optimal weight: 0.2980 chunk 10 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN A 188 HIS R 79 ASN S 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.147115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.089871 restraints weight = 12604.942| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.67 r_work: 0.2999 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9216 Z= 0.120 Angle : 0.538 8.761 12492 Z= 0.282 Chirality : 0.042 0.305 1423 Planarity : 0.004 0.048 1576 Dihedral : 5.356 57.183 1263 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.63 % Allowed : 25.85 % Favored : 69.52 % 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: 0.60 (0.25), residues: 1142 helix: 2.00 (0.27), residues: 397 sheet: 0.22 (0.30), residues: 279 loop : -0.89 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 19 TYR 0.018 0.001 TYR S 235 PHE 0.012 0.001 PHE R 95 TRP 0.017 0.001 TRP B 82 HIS 0.002 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 9212) covalent geometry : angle 0.53764 (12486) SS BOND : bond 0.00248 ( 3) SS BOND : angle 1.45915 ( 6) hydrogen bonds : bond 0.03514 ( 463) hydrogen bonds : angle 5.08224 ( 1302) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 163 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 62 ARG cc_start: 0.7348 (OUTLIER) cc_final: 0.6296 (ptp-170) REVERT: A 276 GLU cc_start: 0.8797 (tp30) cc_final: 0.8593 (tp30) REVERT: A 287 TYR cc_start: 0.7727 (m-80) cc_final: 0.7425 (m-80) REVERT: R 45 MET cc_start: 0.5738 (ttm) cc_final: 0.5457 (ptp) REVERT: R 61 ASN cc_start: 0.7165 (m-40) cc_final: 0.6792 (m110) REVERT: R 80 MET cc_start: 0.7473 (ttt) cc_final: 0.7171 (ttt) REVERT: R 97 MET cc_start: 0.7382 (pmm) cc_final: 0.7109 (pmm) REVERT: R 125 MET cc_start: 0.7207 (tpt) cc_final: 0.6805 (tpp) REVERT: R 128 SER cc_start: 0.8368 (m) cc_final: 0.8143 (p) REVERT: R 165 ILE cc_start: 0.7379 (OUTLIER) cc_final: 0.6915 (pp) REVERT: R 184 ARG cc_start: 0.7995 (mpp-170) cc_final: 0.7226 (mmp80) REVERT: R 190 MET cc_start: 0.2789 (mtm) cc_final: 0.1539 (mmp) REVERT: R 212 MET cc_start: 0.5800 (mmt) cc_final: 0.5386 (mtt) REVERT: S 235 TYR cc_start: 0.6798 (OUTLIER) cc_final: 0.6146 (t80) outliers start: 45 outliers final: 14 residues processed: 191 average time/residue: 0.5698 time to fit residues: 115.9356 Evaluate side-chains 169 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain R residue 53 ILE Chi-restraints excluded: chain R residue 144 CYS Chi-restraints excluded: chain R residue 165 ILE Chi-restraints excluded: chain R residue 178 VAL Chi-restraints excluded: chain R residue 180 LEU Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 78 optimal weight: 20.0000 chunk 75 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 89 optimal weight: 0.0770 chunk 42 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 overall best weight: 1.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 237 ASN A 188 HIS R 223 HIS S 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.144467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.086710 restraints weight = 12716.481| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.67 r_work: 0.2945 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 9216 Z= 0.198 Angle : 0.575 7.924 12492 Z= 0.304 Chirality : 0.044 0.280 1423 Planarity : 0.004 0.049 1576 Dihedral : 5.312 55.804 1260 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 6.80 % Allowed : 24.41 % Favored : 68.80 % 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: 0.45 (0.25), residues: 1142 helix: 1.91 (0.27), residues: 399 sheet: 0.09 (0.30), residues: 286 loop : -1.01 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 19 TYR 0.023 0.001 TYR S 235 PHE 0.012 0.001 PHE B 235 TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 9212) covalent geometry : angle 0.57400 (12486) SS BOND : bond 0.00377 ( 3) SS BOND : angle 1.70246 ( 6) hydrogen bonds : bond 0.03835 ( 463) hydrogen bonds : angle 5.12763 ( 1302) Misc. bond : bond 0.00013 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 154 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: G 62 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.6276 (ptp-170) REVERT: A 195 HIS cc_start: 0.8069 (m-70) cc_final: 0.7644 (m-70) REVERT: A 242 ARG cc_start: 0.7202 (ttm170) cc_final: 0.6819 (ttp-110) REVERT: A 276 GLU cc_start: 0.8814 (tp30) cc_final: 0.8586 (tp30) REVERT: A 287 TYR cc_start: 0.7797 (m-80) cc_final: 0.7404 (m-80) REVERT: R 61 ASN cc_start: 0.7201 (m-40) cc_final: 0.6821 (m110) REVERT: R 125 MET cc_start: 0.7234 (tpt) cc_final: 0.6827 (tpp) REVERT: R 128 SER cc_start: 0.8355 (m) cc_final: 0.7356 (p) REVERT: R 132 PHE cc_start: 0.8085 (m-10) cc_final: 0.7561 (m-80) REVERT: R 165 ILE cc_start: 0.7452 (OUTLIER) cc_final: 0.6893 (pp) REVERT: R 184 ARG cc_start: 0.7993 (mpp-170) cc_final: 0.7271 (mmp80) REVERT: R 190 MET cc_start: 0.2760 (mtm) cc_final: 0.1560 (mmp) REVERT: R 212 MET cc_start: 0.5870 (mmt) cc_final: 0.5517 (mtt) REVERT: R 303 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.6808 (mt) REVERT: R 311 PHE cc_start: 0.7350 (OUTLIER) cc_final: 0.7044 (t80) REVERT: S 235 TYR cc_start: 0.7220 (OUTLIER) cc_final: 0.6584 (t80) outliers start: 66 outliers final: 22 residues processed: 197 average time/residue: 0.6052 time to fit residues: 126.7691 Evaluate side-chains 175 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 144 CYS Chi-restraints excluded: chain R residue 165 ILE Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 178 VAL Chi-restraints excluded: chain R residue 180 LEU Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 210 LYS Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 303 LEU Chi-restraints excluded: chain R residue 311 PHE Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 56 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 220 GLN A 188 HIS R 79 ASN R 321 ASN S 186 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.146151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.088850 restraints weight = 12612.486| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.66 r_work: 0.2984 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9216 Z= 0.137 Angle : 0.545 7.594 12492 Z= 0.287 Chirality : 0.042 0.238 1423 Planarity : 0.004 0.046 1576 Dihedral : 5.186 56.608 1260 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 6.18 % Allowed : 24.72 % Favored : 69.10 % 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: 0.44 (0.25), residues: 1142 helix: 1.88 (0.27), residues: 403 sheet: 0.13 (0.30), residues: 271 loop : -1.01 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 19 TYR 0.019 0.001 TYR S 235 PHE 0.013 0.001 PHE R 95 TRP 0.031 0.002 TRP R 109 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 9212) covalent geometry : angle 0.54413 (12486) SS BOND : bond 0.00462 ( 3) SS BOND : angle 1.53785 ( 6) hydrogen bonds : bond 0.03468 ( 463) hydrogen bonds : angle 4.99113 ( 1302) Misc. bond : bond 0.00004 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 153 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 217 MET cc_start: 0.7650 (OUTLIER) cc_final: 0.6995 (pmt) REVERT: G 62 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.6203 (ptp-170) REVERT: A 195 HIS cc_start: 0.8087 (m-70) cc_final: 0.7627 (m-70) REVERT: A 242 ARG cc_start: 0.7160 (ttm170) cc_final: 0.6804 (ttp-110) REVERT: A 276 GLU cc_start: 0.8836 (tp30) cc_final: 0.8608 (tp30) REVERT: A 287 TYR cc_start: 0.7781 (m-80) cc_final: 0.7575 (m-80) REVERT: R 125 MET cc_start: 0.7208 (tpt) cc_final: 0.6800 (tpp) REVERT: R 128 SER cc_start: 0.8392 (m) cc_final: 0.8163 (p) REVERT: R 165 ILE cc_start: 0.7455 (OUTLIER) cc_final: 0.6969 (pp) REVERT: R 180 LEU cc_start: 0.7160 (OUTLIER) cc_final: 0.6699 (tm) REVERT: R 184 ARG cc_start: 0.8035 (mpp-170) cc_final: 0.7332 (mmp80) REVERT: R 190 MET cc_start: 0.2876 (mtm) cc_final: 0.1730 (mmp) REVERT: R 212 MET cc_start: 0.5970 (mmt) cc_final: 0.5594 (mtt) REVERT: R 225 TYR cc_start: 0.7967 (t80) cc_final: 0.7710 (t80) REVERT: R 303 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.6827 (mp) REVERT: S 235 TYR cc_start: 0.6830 (OUTLIER) cc_final: 0.6179 (t80) outliers start: 60 outliers final: 23 residues processed: 191 average time/residue: 0.5915 time to fit residues: 120.4300 Evaluate side-chains 176 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 147 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 144 CYS Chi-restraints excluded: chain R residue 165 ILE Chi-restraints excluded: chain R residue 178 VAL Chi-restraints excluded: chain R residue 180 LEU Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 210 LYS Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 303 LEU Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 96 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 61 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 220 GLN B 237 ASN A 188 HIS R 79 ASN S 186 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.147227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.089575 restraints weight = 12574.007| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.67 r_work: 0.2995 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9216 Z= 0.127 Angle : 0.547 8.092 12492 Z= 0.285 Chirality : 0.041 0.222 1423 Planarity : 0.004 0.051 1576 Dihedral : 5.125 55.907 1260 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 5.87 % Allowed : 25.75 % Favored : 68.38 % 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: 0.40 (0.25), residues: 1142 helix: 1.89 (0.27), residues: 403 sheet: -0.11 (0.29), residues: 287 loop : -0.94 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 19 TYR 0.017 0.001 TYR S 235 PHE 0.015 0.001 PHE R 95 TRP 0.016 0.001 TRP B 82 HIS 0.002 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 9212) covalent geometry : angle 0.54585 (12486) SS BOND : bond 0.00255 ( 3) SS BOND : angle 1.47116 ( 6) hydrogen bonds : bond 0.03365 ( 463) hydrogen bonds : angle 4.91655 ( 1302) Misc. bond : bond 0.00007 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 159 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 217 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.7043 (pmt) REVERT: G 62 ARG cc_start: 0.7337 (OUTLIER) cc_final: 0.6190 (ptp-170) REVERT: A 186 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8249 (tm-30) REVERT: A 195 HIS cc_start: 0.8140 (m-70) cc_final: 0.7663 (m-70) REVERT: A 287 TYR cc_start: 0.7711 (m-80) cc_final: 0.7406 (m-80) REVERT: R 61 ASN cc_start: 0.7200 (m-40) cc_final: 0.6852 (m110) REVERT: R 80 MET cc_start: 0.7366 (ttt) cc_final: 0.7014 (ttt) REVERT: R 125 MET cc_start: 0.7222 (tpt) cc_final: 0.6804 (tpp) REVERT: R 128 SER cc_start: 0.8379 (m) cc_final: 0.8158 (p) REVERT: R 165 ILE cc_start: 0.7460 (OUTLIER) cc_final: 0.6955 (pp) REVERT: R 180 LEU cc_start: 0.7162 (OUTLIER) cc_final: 0.6438 (tm) REVERT: R 184 ARG cc_start: 0.8086 (mpp-170) cc_final: 0.7393 (mmp80) REVERT: R 190 MET cc_start: 0.3040 (mtm) cc_final: 0.1734 (mmp) REVERT: R 212 MET cc_start: 0.6044 (mmt) cc_final: 0.5657 (mtt) REVERT: R 303 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.6850 (mp) REVERT: R 311 PHE cc_start: 0.7354 (OUTLIER) cc_final: 0.7072 (t80) REVERT: S 235 TYR cc_start: 0.6788 (OUTLIER) cc_final: 0.6177 (t80) outliers start: 57 outliers final: 24 residues processed: 196 average time/residue: 0.5941 time to fit residues: 123.8575 Evaluate side-chains 179 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain R residue 53 ILE Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 144 CYS Chi-restraints excluded: chain R residue 165 ILE Chi-restraints excluded: chain R residue 178 VAL Chi-restraints excluded: chain R residue 180 LEU Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 303 LEU Chi-restraints excluded: chain R residue 311 PHE Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 20 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 32 optimal weight: 0.0000 chunk 15 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 220 GLN A 188 HIS R 79 ASN S 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.147986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.090698 restraints weight = 12618.829| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.66 r_work: 0.3014 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9216 Z= 0.118 Angle : 0.550 8.075 12492 Z= 0.286 Chirality : 0.041 0.209 1423 Planarity : 0.004 0.049 1576 Dihedral : 5.063 58.371 1260 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 5.56 % Allowed : 26.36 % Favored : 68.07 % 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: 0.42 (0.25), residues: 1142 helix: 1.91 (0.27), residues: 400 sheet: -0.08 (0.29), residues: 287 loop : -0.93 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 19 TYR 0.016 0.001 TYR S 235 PHE 0.014 0.001 PHE R 95 TRP 0.016 0.001 TRP B 82 HIS 0.002 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 9212) covalent geometry : angle 0.54906 (12486) SS BOND : bond 0.00451 ( 3) SS BOND : angle 1.62686 ( 6) hydrogen bonds : bond 0.03322 ( 463) hydrogen bonds : angle 4.86447 ( 1302) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 156 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 62 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.6204 (ptp-170) REVERT: A 186 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8196 (tm-30) REVERT: A 195 HIS cc_start: 0.8141 (m-70) cc_final: 0.7648 (m-70) REVERT: A 242 ARG cc_start: 0.7169 (ttm170) cc_final: 0.6906 (ttp-110) REVERT: A 287 TYR cc_start: 0.7730 (m-80) cc_final: 0.7371 (m-80) REVERT: R 61 ASN cc_start: 0.7109 (m-40) cc_final: 0.6451 (m110) REVERT: R 80 MET cc_start: 0.7284 (ttt) cc_final: 0.6928 (ttt) REVERT: R 125 MET cc_start: 0.7187 (tpt) cc_final: 0.6771 (tpp) REVERT: R 128 SER cc_start: 0.8384 (m) cc_final: 0.8153 (p) REVERT: R 180 LEU cc_start: 0.7134 (OUTLIER) cc_final: 0.6458 (tm) REVERT: R 184 ARG cc_start: 0.8148 (mpp-170) cc_final: 0.7462 (mmp80) REVERT: R 190 MET cc_start: 0.3176 (mtm) cc_final: 0.1584 (mmp) REVERT: R 212 MET cc_start: 0.6021 (mmt) cc_final: 0.5632 (mtt) REVERT: R 225 TYR cc_start: 0.7959 (t80) cc_final: 0.7704 (t80) REVERT: R 303 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.6866 (mp) REVERT: S 235 TYR cc_start: 0.6640 (OUTLIER) cc_final: 0.6051 (t80) outliers start: 54 outliers final: 31 residues processed: 192 average time/residue: 0.5568 time to fit residues: 114.1518 Evaluate side-chains 186 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 151 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain R residue 53 ILE Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 144 CYS Chi-restraints excluded: chain R residue 145 ILE Chi-restraints excluded: chain R residue 165 ILE Chi-restraints excluded: chain R residue 178 VAL Chi-restraints excluded: chain R residue 180 LEU Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 303 LEU Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 49 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 220 GLN B 237 ASN A 188 HIS R 79 ASN S 186 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.147693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.090425 restraints weight = 12541.921| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.65 r_work: 0.3008 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9216 Z= 0.128 Angle : 0.559 8.265 12492 Z= 0.290 Chirality : 0.042 0.212 1423 Planarity : 0.004 0.052 1576 Dihedral : 5.056 59.776 1260 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 5.15 % Allowed : 27.19 % Favored : 67.66 % 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: 0.42 (0.25), residues: 1142 helix: 1.82 (0.27), residues: 404 sheet: 0.09 (0.29), residues: 277 loop : -0.97 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 19 TYR 0.015 0.001 TYR S 235 PHE 0.016 0.001 PHE R 81 TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 9212) covalent geometry : angle 0.55768 (12486) SS BOND : bond 0.00157 ( 3) SS BOND : angle 1.75330 ( 6) hydrogen bonds : bond 0.03351 ( 463) hydrogen bonds : angle 4.85281 ( 1302) Misc. bond : bond 0.00008 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 155 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 62 ARG cc_start: 0.7330 (OUTLIER) cc_final: 0.6179 (ptp-170) REVERT: A 186 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8204 (tm-30) REVERT: A 195 HIS cc_start: 0.8147 (m-70) cc_final: 0.7628 (m-70) REVERT: A 287 TYR cc_start: 0.7731 (m-80) cc_final: 0.7385 (m-80) REVERT: R 80 MET cc_start: 0.7337 (ttt) cc_final: 0.6914 (ttt) REVERT: R 125 MET cc_start: 0.7203 (tpt) cc_final: 0.6779 (tpp) REVERT: R 128 SER cc_start: 0.8398 (m) cc_final: 0.7515 (p) REVERT: R 132 PHE cc_start: 0.8065 (m-10) cc_final: 0.7362 (m-80) REVERT: R 190 MET cc_start: 0.3239 (mtm) cc_final: 0.1714 (mmp) REVERT: R 212 MET cc_start: 0.5997 (mmt) cc_final: 0.5619 (mtt) REVERT: R 303 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.6857 (mp) REVERT: S 235 TYR cc_start: 0.6651 (OUTLIER) cc_final: 0.6118 (t80) outliers start: 50 outliers final: 31 residues processed: 190 average time/residue: 0.6130 time to fit residues: 123.9261 Evaluate side-chains 183 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 149 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain R residue 53 ILE Chi-restraints excluded: chain R residue 144 CYS Chi-restraints excluded: chain R residue 145 ILE Chi-restraints excluded: chain R residue 178 VAL Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 303 LEU Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 9 optimal weight: 0.0980 chunk 83 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 43 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 220 GLN A 188 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.147433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.089918 restraints weight = 12552.460| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.65 r_work: 0.3001 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9216 Z= 0.137 Angle : 0.581 13.246 12492 Z= 0.297 Chirality : 0.042 0.223 1423 Planarity : 0.004 0.050 1576 Dihedral : 5.060 57.921 1260 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 4.53 % Allowed : 27.60 % Favored : 67.87 % 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: 0.39 (0.25), residues: 1142 helix: 1.86 (0.27), residues: 399 sheet: 0.04 (0.30), residues: 277 loop : -1.00 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 19 TYR 0.016 0.001 TYR S 235 PHE 0.016 0.001 PHE R 95 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 9212) covalent geometry : angle 0.58027 (12486) SS BOND : bond 0.00152 ( 3) SS BOND : angle 1.68906 ( 6) hydrogen bonds : bond 0.03407 ( 463) hydrogen bonds : angle 4.87487 ( 1302) Misc. bond : bond 0.00007 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 152 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 217 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7130 (pmt) REVERT: G 62 ARG cc_start: 0.7341 (OUTLIER) cc_final: 0.6192 (ptp-170) REVERT: A 186 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8214 (tm-30) REVERT: A 195 HIS cc_start: 0.8150 (m-70) cc_final: 0.7634 (m-70) REVERT: A 287 TYR cc_start: 0.7727 (m-80) cc_final: 0.7431 (m-80) REVERT: R 125 MET cc_start: 0.7200 (tpt) cc_final: 0.6737 (tpp) REVERT: R 128 SER cc_start: 0.8387 (m) cc_final: 0.8178 (p) REVERT: R 180 LEU cc_start: 0.7040 (mm) cc_final: 0.6511 (mt) REVERT: R 184 ARG cc_start: 0.8171 (mpp-170) cc_final: 0.7427 (mmp80) REVERT: R 190 MET cc_start: 0.3166 (mtm) cc_final: 0.1625 (mmp) REVERT: R 212 MET cc_start: 0.5966 (mmt) cc_final: 0.5591 (mtt) REVERT: R 225 TYR cc_start: 0.7966 (t80) cc_final: 0.7681 (t80) REVERT: R 303 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.6825 (mt) REVERT: R 311 PHE cc_start: 0.7347 (OUTLIER) cc_final: 0.7076 (t80) REVERT: S 235 TYR cc_start: 0.6659 (OUTLIER) cc_final: 0.6116 (t80) outliers start: 44 outliers final: 30 residues processed: 181 average time/residue: 0.6399 time to fit residues: 123.0642 Evaluate side-chains 181 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 146 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 53 ILE Chi-restraints excluded: chain R residue 144 CYS Chi-restraints excluded: chain R residue 145 ILE Chi-restraints excluded: chain R residue 178 VAL Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 303 LEU Chi-restraints excluded: chain R residue 311 PHE Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 0.9980 chunk 14 optimal weight: 0.4980 chunk 110 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 chunk 74 optimal weight: 0.2980 chunk 44 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 220 GLN B 237 ASN A 188 HIS R 195 ASN S 186 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.148526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.091159 restraints weight = 12477.231| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.66 r_work: 0.3019 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9216 Z= 0.116 Angle : 0.574 12.102 12492 Z= 0.294 Chirality : 0.042 0.196 1423 Planarity : 0.004 0.051 1576 Dihedral : 4.652 53.584 1258 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 4.33 % Allowed : 28.32 % Favored : 67.35 % 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: 0.39 (0.25), residues: 1142 helix: 1.87 (0.27), residues: 399 sheet: 0.05 (0.29), residues: 277 loop : -1.03 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 19 TYR 0.013 0.001 TYR S 235 PHE 0.013 0.001 PHE R 81 TRP 0.016 0.001 TRP B 82 HIS 0.002 0.000 HIS R 187 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 9212) covalent geometry : angle 0.57318 (12486) SS BOND : bond 0.00153 ( 3) SS BOND : angle 1.52938 ( 6) hydrogen bonds : bond 0.03270 ( 463) hydrogen bonds : angle 4.79926 ( 1302) Misc. bond : bond 0.00006 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 162 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 217 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.7184 (pmt) REVERT: G 62 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.6203 (ptp-170) REVERT: A 186 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8187 (tm-30) REVERT: A 195 HIS cc_start: 0.8105 (m-70) cc_final: 0.7589 (m-70) REVERT: A 242 ARG cc_start: 0.7128 (ttm170) cc_final: 0.6871 (ttp-110) REVERT: A 256 ASN cc_start: 0.8662 (t0) cc_final: 0.7953 (t0) REVERT: A 287 TYR cc_start: 0.7713 (m-80) cc_final: 0.7446 (m-80) REVERT: A 309 ASP cc_start: 0.8477 (m-30) cc_final: 0.8265 (m-30) REVERT: R 125 MET cc_start: 0.7150 (tpt) cc_final: 0.6731 (tpp) REVERT: R 180 LEU cc_start: 0.7143 (mm) cc_final: 0.6354 (tm) REVERT: R 190 MET cc_start: 0.2980 (mtm) cc_final: 0.1492 (mmp) REVERT: R 205 GLU cc_start: 0.8170 (mp0) cc_final: 0.7937 (mp0) REVERT: R 212 MET cc_start: 0.5890 (mmt) cc_final: 0.5066 (mpt) REVERT: R 225 TYR cc_start: 0.7943 (t80) cc_final: 0.7699 (t80) REVERT: R 337 ARG cc_start: 0.6811 (OUTLIER) cc_final: 0.6507 (ttt90) REVERT: S 235 TYR cc_start: 0.6454 (OUTLIER) cc_final: 0.5966 (t80) outliers start: 42 outliers final: 28 residues processed: 193 average time/residue: 0.5751 time to fit residues: 117.9859 Evaluate side-chains 186 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 154 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 62 ARG Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 206 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain R residue 52 LEU Chi-restraints excluded: chain R residue 53 ILE Chi-restraints excluded: chain R residue 144 CYS Chi-restraints excluded: chain R residue 145 ILE Chi-restraints excluded: chain R residue 178 VAL Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 337 ARG Chi-restraints excluded: chain S residue 19 LYS Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 150 THR Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 226 VAL Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 107 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 100 optimal weight: 0.0470 chunk 94 optimal weight: 0.9980 chunk 101 optimal weight: 0.1980 chunk 8 optimal weight: 0.5980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 220 GLN A 188 HIS S 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.148814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.091662 restraints weight = 12391.982| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.66 r_work: 0.3028 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9216 Z= 0.115 Angle : 0.573 12.310 12492 Z= 0.292 Chirality : 0.042 0.192 1423 Planarity : 0.004 0.052 1576 Dihedral : 4.618 52.790 1258 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.71 % Allowed : 29.15 % Favored : 67.15 % 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: 0.39 (0.25), residues: 1142 helix: 1.89 (0.27), residues: 399 sheet: 0.07 (0.30), residues: 272 loop : -1.05 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 19 TYR 0.013 0.001 TYR S 235 PHE 0.012 0.001 PHE R 81 TRP 0.017 0.001 TRP R 109 HIS 0.002 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 9212) covalent geometry : angle 0.57232 (12486) SS BOND : bond 0.00171 ( 3) SS BOND : angle 1.57797 ( 6) hydrogen bonds : bond 0.03258 ( 463) hydrogen bonds : angle 4.79280 ( 1302) Misc. bond : bond 0.00006 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5468.87 seconds wall clock time: 93 minutes 42.29 seconds (5622.29 seconds total)