Starting phenix.real_space_refine on Sat Oct 11 21:21:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iru_35686/10_2025/8iru_35686_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iru_35686/10_2025/8iru_35686.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8iru_35686/10_2025/8iru_35686_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iru_35686/10_2025/8iru_35686_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8iru_35686/10_2025/8iru_35686.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iru_35686/10_2025/8iru_35686.map" } resolution = 3.2 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= 0.004 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: 5 Type Number sf(0) Gaussians S 59 5.16 5 C 5788 2.51 5 N 1522 2.21 5 O 1637 1.98 5 H 8649 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 79 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17655 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3771 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 5094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 5094 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "E" Number of atoms: 3492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3492 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "G" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 887 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "R" Number of atoms: 4137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 4137 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 14, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "R" Number of atoms: 274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 274 Unusual residues: {'CLR': 9, 'R5F': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Time building chain proxies: 3.36, per 1000 atoms: 0.19 Number of scatterers: 17655 At special positions: 0 Unit cell: (112.32, 132.84, 110.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 59 16.00 O 1637 8.00 N 1522 7.00 C 5788 6.00 H 8649 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 108 " - pdb=" SG CYS R 185 " distance=2.03 Simple disulfide: pdb=" SG CYS R 372 " - pdb=" SG CYS R 375 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 501.1 milliseconds Enol-peptide restraints added in 1.4 microseconds 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2094 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 13 sheets defined 39.8% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.981A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 55 removed outlier: 4.563A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 218 removed outlier: 3.834A pdb=" N ASP A 217 " --> pdb=" O CYS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 246 through 250 removed outlier: 3.865A pdb=" N ARG A 250 " --> pdb=" O ARG A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 270 Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 298 through 320 removed outlier: 3.799A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'B' and resid 5 through 25 removed outlier: 3.827A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.977A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.543A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 224 Processing helix chain 'G' and resid 10 through 24 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'R' and resid 33 through 62 Processing helix chain 'R' and resid 63 through 66 Processing helix chain 'R' and resid 69 through 87 removed outlier: 4.278A pdb=" N ILE R 73 " --> pdb=" O THR R 69 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 97 Processing helix chain 'R' and resid 104 through 139 removed outlier: 3.553A pdb=" N VAL R 137 " --> pdb=" O ARG R 133 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 144 removed outlier: 3.515A pdb=" N ASN R 144 " --> pdb=" O PRO R 140 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 172 Proline residue: R 169 - end of helix Processing helix chain 'R' and resid 173 through 177 removed outlier: 3.801A pdb=" N VAL R 177 " --> pdb=" O LEU R 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 189 through 201 Processing helix chain 'R' and resid 203 through 226 Processing helix chain 'R' and resid 343 through 372 removed outlier: 3.758A pdb=" N LEU R 348 " --> pdb=" O ALA R 344 " (cutoff:3.500A) Proline residue: R 349 - end of helix Proline residue: R 361 - end of helix removed outlier: 3.588A pdb=" N ALA R 370 " --> pdb=" O HIS R 366 " (cutoff:3.500A) Processing helix chain 'R' and resid 378 through 403 removed outlier: 3.788A pdb=" N ASN R 392 " --> pdb=" O LEU R 388 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N SER R 393 " --> pdb=" O GLY R 389 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA R 394 " --> pdb=" O TYR R 390 " (cutoff:3.500A) Proline residue: R 397 - end of helix removed outlier: 4.514A pdb=" N PHE R 403 " --> pdb=" O ILE R 399 " (cutoff:3.500A) Processing helix chain 'R' and resid 404 through 412 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 6.209A pdb=" N HIS A 34 " --> pdb=" O HIS A 197 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N PHE A 199 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N VAL A 201 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N LEU A 38 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.701A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL B 327 " --> pdb=" O TRP B 339 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.540A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.709A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.658A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.524A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.697A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.549A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.764A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.361A pdb=" N VAL E 147 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.361A pdb=" N VAL E 147 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR E 238 " --> pdb=" O GLN E 231 " (cutoff:3.500A) 452 hydrogen bonds defined for protein. 1263 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.27 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 8623 1.12 - 1.30: 1531 1.30 - 1.47: 3451 1.47 - 1.65: 4173 1.65 - 1.82: 84 Bond restraints: 17862 Sorted by residual: bond pdb=" NH2 ARG R 346 " pdb="HH21 ARG R 346 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CE1 PHE A 312 " pdb=" HE1 PHE A 312 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" CD2 PHE R 363 " pdb=" HD2 PHE R 363 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N ALA A 32 " pdb=" H ALA A 32 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" NE ARG A 205 " pdb=" HE ARG A 205 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 ... (remaining 17857 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 27570 2.74 - 5.47: 3519 5.47 - 8.21: 933 8.21 - 10.95: 25 10.95 - 13.69: 24 Bond angle restraints: 32071 Sorted by residual: angle pdb=" CA PHE E 68 " pdb=" CB PHE E 68 " pdb=" CG PHE E 68 " ideal model delta sigma weight residual 113.80 119.78 -5.98 1.00e+00 1.00e+00 3.58e+01 angle pdb=" CA ASP A 335 " pdb=" CB ASP A 335 " pdb=" CG ASP A 335 " ideal model delta sigma weight residual 112.60 118.58 -5.98 1.00e+00 1.00e+00 3.58e+01 angle pdb=" CA ASN A 43 " pdb=" CB ASN A 43 " pdb=" CG ASN A 43 " ideal model delta sigma weight residual 112.60 118.10 -5.50 1.00e+00 1.00e+00 3.02e+01 angle pdb=" N ILE A 275 " pdb=" CA ILE A 275 " pdb=" C ILE A 275 " ideal model delta sigma weight residual 110.36 116.01 -5.65 1.05e+00 9.07e-01 2.90e+01 angle pdb=" C ASN B 119 " pdb=" N ILE B 120 " pdb=" CA ILE B 120 " ideal model delta sigma weight residual 120.63 127.48 -6.85 1.33e+00 5.65e-01 2.65e+01 ... (remaining 32066 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 8137 17.92 - 35.84: 467 35.84 - 53.77: 145 53.77 - 71.69: 138 71.69 - 89.61: 11 Dihedral angle restraints: 8898 sinusoidal: 5068 harmonic: 3830 Sorted by residual: dihedral pdb=" CA LEU B 190 " pdb=" C LEU B 190 " pdb=" N SER B 191 " pdb=" CA SER B 191 " ideal model delta harmonic sigma weight residual 180.00 150.45 29.55 0 5.00e+00 4.00e-02 3.49e+01 dihedral pdb=" CA LEU B 284 " pdb=" C LEU B 284 " pdb=" N LEU B 285 " pdb=" CA LEU B 285 " ideal model delta harmonic sigma weight residual 180.00 150.82 29.18 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA TYR B 289 " pdb=" C TYR B 289 " pdb=" N ASP B 290 " pdb=" CA ASP B 290 " ideal model delta harmonic sigma weight residual 180.00 150.94 29.06 0 5.00e+00 4.00e-02 3.38e+01 ... (remaining 8895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 1032 0.104 - 0.208: 360 0.208 - 0.312: 44 0.312 - 0.416: 6 0.416 - 0.521: 1 Chirality restraints: 1443 Sorted by residual: chirality pdb=" CA TYR B 59 " pdb=" N TYR B 59 " pdb=" C TYR B 59 " pdb=" CB TYR B 59 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.77e+00 chirality pdb=" CA PHE R 202 " pdb=" N PHE R 202 " pdb=" C PHE R 202 " pdb=" CB PHE R 202 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.18e+00 chirality pdb=" CA SER B 334 " pdb=" N SER B 334 " pdb=" C SER B 334 " pdb=" CB SER B 334 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.88e+00 ... (remaining 1440 not shown) Planarity restraints: 2625 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 47 " 0.011 2.00e-02 2.50e+03 9.62e-02 3.70e+02 pdb=" CG TRP E 47 " -0.092 2.00e-02 2.50e+03 pdb=" CD1 TRP E 47 " -0.057 2.00e-02 2.50e+03 pdb=" CD2 TRP E 47 " -0.078 2.00e-02 2.50e+03 pdb=" NE1 TRP E 47 " -0.029 2.00e-02 2.50e+03 pdb=" CE2 TRP E 47 " -0.089 2.00e-02 2.50e+03 pdb=" CE3 TRP E 47 " -0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 47 " -0.078 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 47 " 0.027 2.00e-02 2.50e+03 pdb=" CH2 TRP E 47 " -0.030 2.00e-02 2.50e+03 pdb=" HD1 TRP E 47 " 0.032 2.00e-02 2.50e+03 pdb=" HE1 TRP E 47 " 0.291 2.00e-02 2.50e+03 pdb=" HE3 TRP E 47 " 0.048 2.00e-02 2.50e+03 pdb=" HZ2 TRP E 47 " -0.078 2.00e-02 2.50e+03 pdb=" HZ3 TRP E 47 " 0.138 2.00e-02 2.50e+03 pdb=" HH2 TRP E 47 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " -0.257 2.00e-02 2.50e+03 1.06e-01 3.34e+02 pdb=" CG TYR B 59 " 0.102 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " 0.085 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " 0.114 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " 0.067 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " 0.043 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " 0.014 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " -0.150 2.00e-02 2.50e+03 pdb=" HD1 TYR B 59 " -0.009 2.00e-02 2.50e+03 pdb=" HD2 TYR B 59 " 0.055 2.00e-02 2.50e+03 pdb=" HE1 TYR B 59 " 0.007 2.00e-02 2.50e+03 pdb=" HE2 TYR B 59 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 222 " 0.158 2.00e-02 2.50e+03 9.05e-02 3.28e+02 pdb=" CG TRP R 222 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP R 222 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP R 222 " -0.019 2.00e-02 2.50e+03 pdb=" NE1 TRP R 222 " -0.050 2.00e-02 2.50e+03 pdb=" CE2 TRP R 222 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP R 222 " -0.062 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 222 " 0.056 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 222 " -0.042 2.00e-02 2.50e+03 pdb=" CH2 TRP R 222 " 0.039 2.00e-02 2.50e+03 pdb=" HD1 TRP R 222 " 0.035 2.00e-02 2.50e+03 pdb=" HE1 TRP R 222 " -0.231 2.00e-02 2.50e+03 pdb=" HE3 TRP R 222 " -0.098 2.00e-02 2.50e+03 pdb=" HZ2 TRP R 222 " 0.119 2.00e-02 2.50e+03 pdb=" HZ3 TRP R 222 " -0.065 2.00e-02 2.50e+03 pdb=" HH2 TRP R 222 " 0.089 2.00e-02 2.50e+03 ... (remaining 2622 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 1130 2.18 - 2.78: 31276 2.78 - 3.39: 50402 3.39 - 3.99: 68016 3.99 - 4.60: 98479 Nonbonded interactions: 249303 Sorted by model distance: nonbonded pdb=" HG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 1.572 2.450 nonbonded pdb=" HG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 1.581 2.450 nonbonded pdb=" HH TYR A 327 " pdb=" OD2 ASP A 348 " model vdw 1.581 2.450 nonbonded pdb=" OD1 ASP R 80 " pdb=" HG SER R 393 " model vdw 1.592 2.450 nonbonded pdb=" OE1 GLU A 14 " pdb=" HG SER E 52 " model vdw 1.593 2.450 ... (remaining 249298 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.480 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: 0.110 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.570 Find NCS groups from input model: 0.070 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 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 : 0.012 0.080 9217 Z= 0.734 Angle : 1.767 10.996 12556 Z= 1.174 Chirality : 0.100 0.521 1443 Planarity : 0.019 0.300 1549 Dihedral : 12.589 89.609 3813 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 0.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.48 % Peptide Plane: Cis-proline : 2.56 % 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: -0.54 (0.23), residues: 1107 helix: -0.68 (0.23), residues: 382 sheet: 0.53 (0.31), residues: 257 loop : -0.41 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 232 TYR 0.241 0.024 TYR B 59 PHE 0.076 0.014 PHE R 362 TRP 0.093 0.022 TRP R 222 HIS 0.021 0.004 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.01221 ( 9213) covalent geometry : angle 1.76692 (12548) SS BOND : bond 0.00411 ( 4) SS BOND : angle 1.83877 ( 8) hydrogen bonds : bond 0.15149 ( 449) hydrogen bonds : angle 7.26712 ( 1263) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 333 is missing expected H atoms. Skipping. Evaluate side-chains 273 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 LYS cc_start: 0.8432 (mtpp) cc_final: 0.8207 (mttm) REVERT: A 345 ASP cc_start: 0.8063 (m-30) cc_final: 0.7772 (m-30) REVERT: A 357 ASP cc_start: 0.8083 (m-30) cc_final: 0.7399 (m-30) REVERT: B 188 MET cc_start: 0.8786 (mmm) cc_final: 0.8539 (mmm) REVERT: B 219 ARG cc_start: 0.7879 (ttm-80) cc_final: 0.7408 (mtt-85) REVERT: B 279 SER cc_start: 0.8591 (p) cc_final: 0.8323 (p) REVERT: G 18 GLN cc_start: 0.8260 (tp40) cc_final: 0.8021 (tp40) REVERT: G 31 SER cc_start: 0.9041 (t) cc_final: 0.8794 (p) REVERT: R 115 ASP cc_start: 0.8368 (t70) cc_final: 0.7984 (t70) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.2803 time to fit residues: 98.9436 Evaluate side-chains 175 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN B 75 GLN B 88 ASN B 237 ASN E 171 ASN R 33 GLN R 175 ASN R 396 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.110233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.084080 restraints weight = 47665.836| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.93 r_work: 0.3044 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9217 Z= 0.164 Angle : 0.627 7.567 12556 Z= 0.343 Chirality : 0.042 0.153 1443 Planarity : 0.005 0.043 1549 Dihedral : 7.470 57.992 1831 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.53 % Allowed : 7.62 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.35 (0.24), residues: 1107 helix: 0.87 (0.25), residues: 400 sheet: 0.26 (0.30), residues: 277 loop : -0.24 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG R 63 TYR 0.020 0.002 TYR B 105 PHE 0.017 0.002 PHE R 362 TRP 0.016 0.002 TRP R 222 HIS 0.005 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 9213) covalent geometry : angle 0.62700 (12548) SS BOND : bond 0.00337 ( 4) SS BOND : angle 0.76564 ( 8) hydrogen bonds : bond 0.04798 ( 449) hydrogen bonds : angle 5.26676 ( 1263) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 333 is missing expected H atoms. Skipping. Evaluate side-chains 206 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 201 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 TYR cc_start: 0.7564 (m-80) cc_final: 0.7320 (m-80) REVERT: B 35 ASN cc_start: 0.8444 (m-40) cc_final: 0.8240 (m110) REVERT: B 118 ASP cc_start: 0.7982 (t0) cc_final: 0.7711 (p0) REVERT: B 188 MET cc_start: 0.8872 (mmm) cc_final: 0.8659 (mmm) REVERT: B 219 ARG cc_start: 0.8486 (ttm-80) cc_final: 0.8138 (mtt-85) REVERT: E 3 GLN cc_start: 0.8005 (mp10) cc_final: 0.7765 (mp10) REVERT: E 218 ARG cc_start: 0.8217 (ptp-110) cc_final: 0.7815 (mtm110) REVERT: G 18 GLN cc_start: 0.8681 (tp40) cc_final: 0.8093 (tp-100) REVERT: G 31 SER cc_start: 0.9475 (t) cc_final: 0.8826 (m) REVERT: R 393 SER cc_start: 0.9388 (m) cc_final: 0.8661 (m) outliers start: 5 outliers final: 2 residues processed: 204 average time/residue: 0.2299 time to fit residues: 63.4996 Evaluate side-chains 174 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 172 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain R residue 395 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 13 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 66 optimal weight: 0.0070 chunk 36 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 overall best weight: 2.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN B 293 ASN R 392 ASN R 396 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.107322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.081039 restraints weight = 48349.315| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.95 r_work: 0.2994 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9217 Z= 0.213 Angle : 0.588 7.672 12556 Z= 0.322 Chirality : 0.041 0.148 1443 Planarity : 0.004 0.048 1549 Dihedral : 6.733 59.407 1831 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.16 % Allowed : 10.26 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.49 (0.25), residues: 1107 helix: 1.35 (0.26), residues: 394 sheet: -0.24 (0.31), residues: 269 loop : -0.09 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 15 TYR 0.020 0.002 TYR B 105 PHE 0.013 0.002 PHE B 253 TRP 0.012 0.001 TRP A 211 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 9213) covalent geometry : angle 0.58824 (12548) SS BOND : bond 0.00323 ( 4) SS BOND : angle 0.72556 ( 8) hydrogen bonds : bond 0.04259 ( 449) hydrogen bonds : angle 4.95623 ( 1263) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 333 is missing expected H atoms. Skipping. Evaluate side-chains 191 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 180 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 SER cc_start: 0.8859 (t) cc_final: 0.8144 (p) REVERT: B 118 ASP cc_start: 0.8082 (t0) cc_final: 0.7574 (p0) REVERT: B 120 ILE cc_start: 0.9120 (mt) cc_final: 0.8897 (mp) REVERT: B 219 ARG cc_start: 0.8663 (ttm-80) cc_final: 0.8256 (mtt-85) REVERT: E 3 GLN cc_start: 0.8043 (mp10) cc_final: 0.7764 (mp10) REVERT: E 220 GLU cc_start: 0.7459 (mp0) cc_final: 0.6989 (mp0) REVERT: G 18 GLN cc_start: 0.8646 (tp40) cc_final: 0.8425 (tp40) REVERT: G 31 SER cc_start: 0.9501 (t) cc_final: 0.8843 (m) REVERT: G 36 ASP cc_start: 0.8826 (m-30) cc_final: 0.8456 (m-30) outliers start: 11 outliers final: 9 residues processed: 185 average time/residue: 0.2230 time to fit residues: 56.8248 Evaluate side-chains 172 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 163 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 197 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 79 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.105882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.079604 restraints weight = 48606.575| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.96 r_work: 0.2972 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9217 Z= 0.246 Angle : 0.591 7.627 12556 Z= 0.322 Chirality : 0.042 0.143 1443 Planarity : 0.004 0.057 1549 Dihedral : 6.687 57.429 1831 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.69 % Allowed : 11.96 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.56 (0.25), residues: 1107 helix: 1.51 (0.26), residues: 388 sheet: -0.29 (0.31), residues: 272 loop : -0.08 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 15 TYR 0.018 0.002 TYR B 105 PHE 0.022 0.002 PHE E 68 TRP 0.011 0.001 TRP A 211 HIS 0.006 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00539 ( 9213) covalent geometry : angle 0.59119 (12548) SS BOND : bond 0.00338 ( 4) SS BOND : angle 0.73144 ( 8) hydrogen bonds : bond 0.04098 ( 449) hydrogen bonds : angle 4.89852 ( 1263) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 333 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 166 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 SER cc_start: 0.8882 (t) cc_final: 0.8246 (p) REVERT: A 357 ASP cc_start: 0.8621 (m-30) cc_final: 0.8261 (m-30) REVERT: B 118 ASP cc_start: 0.8112 (t0) cc_final: 0.7559 (p0) REVERT: B 188 MET cc_start: 0.8876 (mmm) cc_final: 0.8497 (mmm) REVERT: B 217 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8307 (ptt) REVERT: B 340 ASN cc_start: 0.7264 (OUTLIER) cc_final: 0.6771 (m110) REVERT: E 3 GLN cc_start: 0.8039 (mp10) cc_final: 0.7773 (mp10) REVERT: G 18 GLN cc_start: 0.8460 (tp40) cc_final: 0.7832 (tp-100) REVERT: G 31 SER cc_start: 0.9495 (t) cc_final: 0.8984 (p) REVERT: G 36 ASP cc_start: 0.8944 (m-30) cc_final: 0.8544 (m-30) outliers start: 16 outliers final: 11 residues processed: 175 average time/residue: 0.2100 time to fit residues: 51.5795 Evaluate side-chains 169 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain R residue 80 ASP Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 197 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.105971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.079900 restraints weight = 48546.099| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.92 r_work: 0.2975 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.4740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9217 Z= 0.221 Angle : 0.569 7.387 12556 Z= 0.310 Chirality : 0.041 0.146 1443 Planarity : 0.004 0.053 1549 Dihedral : 6.610 59.599 1831 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.48 % Allowed : 13.65 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.53 (0.25), residues: 1107 helix: 1.48 (0.26), residues: 393 sheet: -0.30 (0.31), residues: 270 loop : -0.11 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 15 TYR 0.017 0.001 TYR B 105 PHE 0.013 0.002 PHE E 68 TRP 0.012 0.001 TRP B 339 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00482 ( 9213) covalent geometry : angle 0.56881 (12548) SS BOND : bond 0.00313 ( 4) SS BOND : angle 0.61085 ( 8) hydrogen bonds : bond 0.03942 ( 449) hydrogen bonds : angle 4.79262 ( 1263) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 333 is missing expected H atoms. Skipping. Evaluate side-chains 181 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 167 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 SER cc_start: 0.8890 (t) cc_final: 0.8253 (p) REVERT: A 310 ASP cc_start: 0.8436 (m-30) cc_final: 0.8119 (m-30) REVERT: B 118 ASP cc_start: 0.8104 (t0) cc_final: 0.7545 (p0) REVERT: B 188 MET cc_start: 0.8854 (mmm) cc_final: 0.8506 (mmm) REVERT: B 217 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8280 (ptt) REVERT: E 3 GLN cc_start: 0.8056 (mp10) cc_final: 0.7780 (mp10) REVERT: G 18 GLN cc_start: 0.8533 (tp40) cc_final: 0.7876 (tp-100) REVERT: G 31 SER cc_start: 0.9502 (t) cc_final: 0.9006 (p) REVERT: G 36 ASP cc_start: 0.8951 (m-30) cc_final: 0.8547 (m-30) REVERT: R 80 ASP cc_start: 0.8052 (OUTLIER) cc_final: 0.7741 (t70) outliers start: 14 outliers final: 9 residues processed: 176 average time/residue: 0.2179 time to fit residues: 54.0030 Evaluate side-chains 166 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 155 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 80 ASP Chi-restraints excluded: chain R residue 130 SER Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 203 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 61 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 chunk 109 optimal weight: 0.6980 chunk 14 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 19 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.108547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.082660 restraints weight = 48055.631| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.94 r_work: 0.3025 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9217 Z= 0.124 Angle : 0.513 6.294 12556 Z= 0.275 Chirality : 0.040 0.155 1443 Planarity : 0.004 0.037 1549 Dihedral : 6.075 54.928 1831 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.95 % Allowed : 13.76 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.78 (0.25), residues: 1107 helix: 1.72 (0.26), residues: 395 sheet: -0.22 (0.31), residues: 269 loop : 0.04 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 314 TYR 0.013 0.001 TYR B 105 PHE 0.012 0.001 PHE E 68 TRP 0.008 0.001 TRP A 211 HIS 0.005 0.001 HIS R 366 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 9213) covalent geometry : angle 0.51298 (12548) SS BOND : bond 0.00275 ( 4) SS BOND : angle 0.41928 ( 8) hydrogen bonds : bond 0.03500 ( 449) hydrogen bonds : angle 4.52811 ( 1263) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 333 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 173 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 SER cc_start: 0.8855 (t) cc_final: 0.8212 (p) REVERT: B 12 GLU cc_start: 0.9252 (tp30) cc_final: 0.9039 (mt-10) REVERT: B 118 ASP cc_start: 0.8102 (t0) cc_final: 0.7483 (p0) REVERT: B 120 ILE cc_start: 0.9075 (mt) cc_final: 0.8870 (mp) REVERT: B 188 MET cc_start: 0.8730 (mmm) cc_final: 0.8348 (mmm) REVERT: E 3 GLN cc_start: 0.8058 (mp10) cc_final: 0.7776 (mp10) REVERT: G 18 GLN cc_start: 0.8408 (tp40) cc_final: 0.7667 (tp-100) REVERT: G 22 GLU cc_start: 0.8250 (tp30) cc_final: 0.7945 (tp30) REVERT: G 31 SER cc_start: 0.9487 (t) cc_final: 0.9005 (p) REVERT: G 36 ASP cc_start: 0.8946 (m-30) cc_final: 0.8576 (m-30) REVERT: R 390 TYR cc_start: 0.8686 (m-80) cc_final: 0.8393 (m-10) outliers start: 9 outliers final: 9 residues processed: 179 average time/residue: 0.1970 time to fit residues: 49.7398 Evaluate side-chains 170 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 161 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 80 ASP Chi-restraints excluded: chain R residue 163 SER Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 203 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.107191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.081087 restraints weight = 48557.068| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.94 r_work: 0.2995 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.5057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9217 Z= 0.180 Angle : 0.531 6.780 12556 Z= 0.287 Chirality : 0.040 0.144 1443 Planarity : 0.004 0.035 1549 Dihedral : 6.057 53.835 1831 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.48 % Allowed : 13.23 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.80 (0.25), residues: 1107 helix: 1.83 (0.26), residues: 390 sheet: -0.27 (0.32), residues: 259 loop : -0.01 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 72 TYR 0.015 0.001 TYR B 105 PHE 0.033 0.001 PHE E 68 TRP 0.010 0.001 TRP A 211 HIS 0.005 0.001 HIS R 366 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 9213) covalent geometry : angle 0.53059 (12548) SS BOND : bond 0.00258 ( 4) SS BOND : angle 0.53263 ( 8) hydrogen bonds : bond 0.03584 ( 449) hydrogen bonds : angle 4.55556 ( 1263) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 333 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 SER cc_start: 0.8768 (t) cc_final: 0.8100 (p) REVERT: B 118 ASP cc_start: 0.8101 (t0) cc_final: 0.7462 (p0) REVERT: B 120 ILE cc_start: 0.9059 (mt) cc_final: 0.8847 (mp) REVERT: B 188 MET cc_start: 0.8802 (mmm) cc_final: 0.8403 (mmm) REVERT: B 217 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8319 (ptt) REVERT: B 340 ASN cc_start: 0.7560 (OUTLIER) cc_final: 0.7356 (m-40) REVERT: E 3 GLN cc_start: 0.8048 (mp10) cc_final: 0.7769 (mp10) REVERT: G 18 GLN cc_start: 0.8490 (tp40) cc_final: 0.7962 (tp40) REVERT: G 31 SER cc_start: 0.9499 (t) cc_final: 0.9012 (p) REVERT: G 36 ASP cc_start: 0.8937 (m-30) cc_final: 0.8581 (m-30) REVERT: R 80 ASP cc_start: 0.7902 (OUTLIER) cc_final: 0.7542 (t70) outliers start: 14 outliers final: 10 residues processed: 173 average time/residue: 0.2090 time to fit residues: 50.5992 Evaluate side-chains 172 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 159 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain R residue 80 ASP Chi-restraints excluded: chain R residue 163 SER Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 203 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 6 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 104 optimal weight: 0.1980 chunk 108 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.109208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.083433 restraints weight = 47963.457| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.93 r_work: 0.3043 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.5163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9217 Z= 0.101 Angle : 0.501 6.027 12556 Z= 0.266 Chirality : 0.040 0.164 1443 Planarity : 0.004 0.034 1549 Dihedral : 5.890 53.456 1831 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.38 % Allowed : 13.54 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.93 (0.25), residues: 1107 helix: 2.00 (0.27), residues: 390 sheet: -0.21 (0.32), residues: 254 loop : 0.02 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 72 TYR 0.012 0.001 TYR E 190 PHE 0.026 0.001 PHE E 68 TRP 0.017 0.001 TRP B 339 HIS 0.005 0.001 HIS R 366 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 9213) covalent geometry : angle 0.50064 (12548) SS BOND : bond 0.00218 ( 4) SS BOND : angle 0.32073 ( 8) hydrogen bonds : bond 0.03331 ( 449) hydrogen bonds : angle 4.40706 ( 1263) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 333 is missing expected H atoms. Skipping. Evaluate side-chains 185 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 172 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 SER cc_start: 0.8824 (t) cc_final: 0.8165 (p) REVERT: B 188 MET cc_start: 0.8703 (mmm) cc_final: 0.8300 (mmm) REVERT: E 3 GLN cc_start: 0.8032 (mp10) cc_final: 0.7771 (mp10) REVERT: G 18 GLN cc_start: 0.8338 (tp40) cc_final: 0.7793 (tp40) REVERT: G 22 GLU cc_start: 0.8325 (tp30) cc_final: 0.8091 (tp30) REVERT: G 31 SER cc_start: 0.9480 (t) cc_final: 0.9001 (p) REVERT: G 36 ASP cc_start: 0.8901 (m-30) cc_final: 0.8547 (m-30) REVERT: R 80 ASP cc_start: 0.7978 (OUTLIER) cc_final: 0.7546 (t70) REVERT: R 112 MET cc_start: 0.8150 (mmp) cc_final: 0.7884 (tpp) outliers start: 13 outliers final: 11 residues processed: 180 average time/residue: 0.2000 time to fit residues: 50.5079 Evaluate side-chains 173 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 161 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 80 ASP Chi-restraints excluded: chain R residue 163 SER Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 203 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 90 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 79 optimal weight: 8.9990 chunk 106 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 25 optimal weight: 0.2980 chunk 64 optimal weight: 8.9990 chunk 108 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.109286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.083624 restraints weight = 47963.612| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.92 r_work: 0.3045 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.5258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9217 Z= 0.114 Angle : 0.506 7.818 12556 Z= 0.268 Chirality : 0.039 0.146 1443 Planarity : 0.003 0.035 1549 Dihedral : 5.698 52.394 1831 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.69 % Allowed : 13.76 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.99 (0.25), residues: 1107 helix: 2.14 (0.27), residues: 389 sheet: -0.20 (0.32), residues: 254 loop : -0.03 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 72 TYR 0.012 0.001 TYR E 190 PHE 0.022 0.001 PHE E 68 TRP 0.007 0.001 TRP A 211 HIS 0.004 0.001 HIS R 366 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 9213) covalent geometry : angle 0.50577 (12548) SS BOND : bond 0.00219 ( 4) SS BOND : angle 0.39586 ( 8) hydrogen bonds : bond 0.03302 ( 449) hydrogen bonds : angle 4.33417 ( 1263) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 333 is missing expected H atoms. Skipping. Evaluate side-chains 184 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 168 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 SER cc_start: 0.8831 (t) cc_final: 0.8177 (p) REVERT: B 118 ASP cc_start: 0.8105 (t0) cc_final: 0.7453 (p0) REVERT: B 188 MET cc_start: 0.8675 (mmm) cc_final: 0.8237 (mmm) REVERT: E 3 GLN cc_start: 0.8078 (mp10) cc_final: 0.7791 (mp10) REVERT: G 18 GLN cc_start: 0.8409 (tp40) cc_final: 0.7857 (tp40) REVERT: G 22 GLU cc_start: 0.8314 (tp30) cc_final: 0.8082 (tp30) REVERT: G 31 SER cc_start: 0.9486 (t) cc_final: 0.9010 (p) REVERT: G 36 ASP cc_start: 0.8905 (m-30) cc_final: 0.8563 (m-30) REVERT: R 80 ASP cc_start: 0.7973 (OUTLIER) cc_final: 0.7565 (t70) REVERT: R 112 MET cc_start: 0.8203 (mmp) cc_final: 0.7885 (tpp) REVERT: R 139 VAL cc_start: 0.8853 (t) cc_final: 0.8647 (m) outliers start: 16 outliers final: 11 residues processed: 178 average time/residue: 0.2051 time to fit residues: 51.6558 Evaluate side-chains 176 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 164 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 80 ASP Chi-restraints excluded: chain R residue 163 SER Chi-restraints excluded: chain R residue 193 VAL Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 203 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 66 optimal weight: 0.5980 chunk 59 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 16 optimal weight: 0.0670 chunk 70 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 ASN ** R 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.110401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.084908 restraints weight = 47736.469| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.92 r_work: 0.3070 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.5386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9217 Z= 0.100 Angle : 0.493 6.304 12556 Z= 0.262 Chirality : 0.039 0.146 1443 Planarity : 0.003 0.033 1549 Dihedral : 5.536 51.466 1831 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.38 % Allowed : 13.86 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.26), residues: 1107 helix: 2.27 (0.27), residues: 389 sheet: -0.21 (0.32), residues: 249 loop : -0.05 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 134 TYR 0.010 0.001 TYR E 190 PHE 0.019 0.001 PHE E 68 TRP 0.008 0.001 TRP B 169 HIS 0.005 0.001 HIS R 366 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 9213) covalent geometry : angle 0.49352 (12548) SS BOND : bond 0.00229 ( 4) SS BOND : angle 0.37306 ( 8) hydrogen bonds : bond 0.03163 ( 449) hydrogen bonds : angle 4.24505 ( 1263) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 333 is missing expected H atoms. Skipping. Evaluate side-chains 189 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 176 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 SER cc_start: 0.8837 (t) cc_final: 0.8180 (p) REVERT: B 59 TYR cc_start: 0.8217 (OUTLIER) cc_final: 0.7998 (m-80) REVERT: B 118 ASP cc_start: 0.8130 (t0) cc_final: 0.7537 (p0) REVERT: B 188 MET cc_start: 0.8636 (mmm) cc_final: 0.8393 (mmm) REVERT: E 3 GLN cc_start: 0.8114 (mp10) cc_final: 0.7833 (mp10) REVERT: G 18 GLN cc_start: 0.8381 (tp40) cc_final: 0.7817 (tp40) REVERT: G 22 GLU cc_start: 0.8291 (tp30) cc_final: 0.8074 (tp30) REVERT: G 31 SER cc_start: 0.9485 (t) cc_final: 0.9015 (p) REVERT: G 36 ASP cc_start: 0.8897 (m-30) cc_final: 0.8559 (m-30) REVERT: R 80 ASP cc_start: 0.7913 (OUTLIER) cc_final: 0.7524 (t70) REVERT: R 112 MET cc_start: 0.8197 (mmp) cc_final: 0.7880 (tpp) REVERT: R 139 VAL cc_start: 0.8768 (t) cc_final: 0.8560 (m) outliers start: 13 outliers final: 8 residues processed: 184 average time/residue: 0.2084 time to fit residues: 53.8752 Evaluate side-chains 179 residues out of total 948 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 169 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 TYR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 80 ASP Chi-restraints excluded: chain R residue 163 SER Chi-restraints excluded: chain R residue 203 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 69 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.110128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.084600 restraints weight = 47957.009| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.92 r_work: 0.3066 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.5467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9217 Z= 0.110 Angle : 0.496 5.452 12556 Z= 0.264 Chirality : 0.039 0.145 1443 Planarity : 0.003 0.034 1549 Dihedral : 5.439 50.291 1831 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.16 % Allowed : 14.29 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.26), residues: 1107 helix: 2.30 (0.27), residues: 389 sheet: -0.18 (0.32), residues: 249 loop : -0.04 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 134 TYR 0.012 0.001 TYR E 190 PHE 0.018 0.001 PHE E 68 TRP 0.007 0.001 TRP B 169 HIS 0.006 0.001 HIS R 366 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 9213) covalent geometry : angle 0.49599 (12548) SS BOND : bond 0.00215 ( 4) SS BOND : angle 0.41398 ( 8) hydrogen bonds : bond 0.03173 ( 449) hydrogen bonds : angle 4.22067 ( 1263) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4169.87 seconds wall clock time: 71 minutes 31.27 seconds (4291.27 seconds total)