Starting phenix.real_space_refine on Thu Aug 6 10:11:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ee9_47952/08_2026/9ee9_47952.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ee9_47952/08_2026/9ee9_47952.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ee9_47952/08_2026/9ee9_47952.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ee9_47952/08_2026/9ee9_47952.map" model { file = "/net/cci-nas-00/data/ceres_data/9ee9_47952/08_2026/9ee9_47952.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ee9_47952/08_2026/9ee9_47952.cif" } resolution = 3.16 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= 0.011 sd= 0.273 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 48 5.16 5 C 4853 2.51 5 N 1318 2.21 5 O 1387 1.98 5 H 7140 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14746 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 4130 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} Chain breaks: 2 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'HIS:plan': 2, 'GLU:plan': 3, 'GLN:plan1': 3, 'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 53 Chain: "B" Number of atoms: 4724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 4724 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 4, 'GLN:plan1': 6, 'ARG:plan': 7, 'GLU:plan': 4, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 93 Chain: "C" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 594 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "D" Number of atoms: 3440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3440 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 136 Unresolved non-hydrogen angles: 160 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 6, 'GLU:plan': 7, 'ASP:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 87 Chain: "E" Number of atoms: 1839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1839 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'ADN%rna2p': 1} Classifications: {'undetermined': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 1.97, per 1000 atoms: 0.13 Number of scatterers: 14746 At special positions: 0 Unit cell: (71.81, 102.705, 131.93, 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 48 16.00 O 1387 8.00 N 1318 7.00 C 4853 6.00 H 7140 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 99 " - pdb=" SG CYS E 107 " 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=0, symmetry=0 Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 304.8 milliseconds 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1916 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 10 sheets defined 43.9% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 8 through 33 removed outlier: 3.553A pdb=" N VAL A 12 " --> pdb=" O VAL A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 69 removed outlier: 3.993A pdb=" N PHE A 44 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL A 45 " --> pdb=" O THR A 41 " (cutoff:3.500A) Proline residue: A 61 - end of helix removed outlier: 3.669A pdb=" N ILE A 64 " --> pdb=" O ILE A 60 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLY A 69 " --> pdb=" O THR A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 75 Processing helix chain 'A' and resid 77 through 108 removed outlier: 4.124A pdb=" N ALA A 81 " --> pdb=" O CYS A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 116 removed outlier: 4.303A pdb=" N ASN A 113 " --> pdb=" O PRO A 109 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N GLY A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 137 Processing helix chain 'A' and resid 138 through 142 Processing helix chain 'A' and resid 168 through 172 Processing helix chain 'A' and resid 173 through 180 removed outlier: 3.621A pdb=" N MET A 177 " --> pdb=" O PRO A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 187 Processing helix chain 'A' and resid 187 through 212 removed outlier: 3.969A pdb=" N MET A 211 " --> pdb=" O GLN A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 259 removed outlier: 3.850A pdb=" N GLU A 228 " --> pdb=" O THR A 224 " (cutoff:3.500A) Proline residue: A 248 - end of helix Processing helix chain 'A' and resid 266 through 289 removed outlier: 3.565A pdb=" N MET A 270 " --> pdb=" O PRO A 266 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N SER A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL A 282 " --> pdb=" O HIS A 278 " (cutoff:3.500A) Proline residue: A 285 - end of helix Processing helix chain 'A' and resid 292 through 307 removed outlier: 3.583A pdb=" N ARG A 300 " --> pdb=" O ARG A 296 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS A 301 " --> pdb=" O GLN A 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'C' and resid 12 through 24 removed outlier: 3.724A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'D' and resid 12 through 40 removed outlier: 3.934A pdb=" N GLU D 16 " --> pdb=" O GLN D 12 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS D 32 " --> pdb=" O LYS D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 56 removed outlier: 3.970A pdb=" N ILE D 56 " --> pdb=" O LYS D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 239 removed outlier: 3.609A pdb=" N ASN D 239 " --> pdb=" O GLN D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 269 removed outlier: 4.190A pdb=" N GLN D 257 " --> pdb=" O TYR D 253 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLU D 258 " --> pdb=" O ASN D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 294 Processing helix chain 'D' and resid 297 through 301 Processing helix chain 'D' and resid 302 through 308 Processing helix chain 'D' and resid 321 through 342 removed outlier: 3.986A pdb=" N ILE D 338 " --> pdb=" O GLU D 334 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER D 339 " --> pdb=" O PHE D 335 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N SER D 342 " --> pdb=" O ILE D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 380 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.640A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 77 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.640A pdb=" N THR E 91 " --> pdb=" O PRO E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.871A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.553A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N CYS B 114 " --> pdb=" O SER B 122 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.482A 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 148 removed outlier: 6.786A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.129A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.866A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.318A 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: 6.643A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 208 through 214 removed outlier: 3.686A pdb=" N PHE D 212 " --> pdb=" O PHE D 219 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ARG D 42 " --> pdb=" O ALA D 243 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N ILE D 245 " --> pdb=" O ARG D 42 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU D 44 " --> pdb=" O ILE D 245 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N VAL D 247 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU D 46 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N ASP D 249 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE D 244 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N PHE D 280 " --> pdb=" O ILE D 244 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N PHE D 246 " --> pdb=" O PHE D 280 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ASN D 282 " --> pdb=" O PHE D 246 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL D 248 " --> pdb=" O ASN D 282 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 8 removed outlier: 3.755A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET E 83 " --> pdb=" O LEU E 18 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU E 79 " --> pdb=" O CYS E 22 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 58 through 60 removed outlier: 4.095A pdb=" N SER E 59 " --> pdb=" O ASP E 50 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP E 50 " --> pdb=" O SER E 59 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASP E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N MET E 34 " --> pdb=" O ASP E 50 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N VAL E 124 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR E 94 " --> pdb=" O THR E 122 " (cutoff:3.500A) 398 hydrogen bonds defined for protein. 1101 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.72 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7117 1.03 - 1.23: 59 1.23 - 1.43: 3288 1.43 - 1.62: 4378 1.62 - 1.82: 66 Bond restraints: 14908 Sorted by residual: bond pdb=" N GLN C 11 " pdb=" CA GLN C 11 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.10e+00 bond pdb=" N GLU D 10 " pdb=" CA GLU D 10 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 bond pdb=" N ASP B 5 " pdb=" CA ASP B 5 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.01e+00 bond pdb=" N GLN E 1 " pdb=" CA GLN E 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 bond pdb=" N GLN C 11 " pdb=" H GLN C 11 " ideal model delta sigma weight residual 0.860 0.892 -0.032 2.00e-02 2.50e+03 2.53e+00 ... (remaining 14903 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.41: 26721 10.41 - 20.82: 1 20.82 - 31.23: 0 31.23 - 41.63: 0 41.63 - 52.04: 2 Bond angle restraints: 26724 Sorted by residual: angle pdb=" C ILE A 287 " pdb=" N TYR A 288 " pdb=" H TYR A 288 " ideal model delta sigma weight residual 124.71 72.67 52.04 3.00e+00 1.11e-01 3.01e+02 angle pdb=" CA TYR A 288 " pdb=" N TYR A 288 " pdb=" H TYR A 288 " ideal model delta sigma weight residual 114.41 62.57 51.84 3.00e+00 1.11e-01 2.99e+02 angle pdb=" C ILE A 287 " pdb=" N TYR A 288 " pdb=" CA TYR A 288 " ideal model delta sigma weight residual 120.88 135.24 -14.36 1.62e+00 3.81e-01 7.85e+01 angle pdb=" N ILE D 207 " pdb=" CA ILE D 207 " pdb=" C ILE D 207 " ideal model delta sigma weight residual 111.62 108.94 2.68 7.90e-01 1.60e+00 1.15e+01 angle pdb=" C ARG E 98 " pdb=" N CYS E 99 " pdb=" CA CYS E 99 " ideal model delta sigma weight residual 121.48 115.44 6.04 2.04e+00 2.40e-01 8.77e+00 ... (remaining 26719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 6245 17.30 - 34.60: 663 34.60 - 51.90: 170 51.90 - 69.21: 47 69.21 - 86.51: 18 Dihedral angle restraints: 7143 sinusoidal: 3632 harmonic: 3511 Sorted by residual: dihedral pdb=" CB CYS E 99 " pdb=" SG CYS E 99 " pdb=" SG CYS E 107 " pdb=" CB CYS E 107 " ideal model delta sinusoidal sigma weight residual -86.00 -35.72 -50.28 1 1.00e+01 1.00e-02 3.46e+01 dihedral pdb=" CA CYS E 99 " pdb=" C CYS E 99 " pdb=" N PRO E 100 " pdb=" CA PRO E 100 " ideal model delta harmonic sigma weight residual -180.00 -160.27 -19.73 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA GLY A 56 " pdb=" C GLY A 56 " pdb=" N VAL A 57 " pdb=" CA VAL A 57 " ideal model delta harmonic sigma weight residual -180.00 -160.31 -19.69 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 7140 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 866 0.035 - 0.070: 260 0.070 - 0.104: 66 0.104 - 0.139: 44 0.139 - 0.174: 1 Chirality restraints: 1237 Sorted by residual: chirality pdb=" CG LEU D 260 " pdb=" CB LEU D 260 " pdb=" CD1 LEU D 260 " pdb=" CD2 LEU D 260 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.58e-01 chirality pdb=" CA ILE B 123 " pdb=" N ILE B 123 " pdb=" C ILE B 123 " pdb=" CB ILE B 123 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA ILE B 229 " pdb=" N ILE B 229 " pdb=" C ILE B 229 " pdb=" CB ILE B 229 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.27e-01 ... (remaining 1234 not shown) Planarity restraints: 2332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 56 " -0.010 2.00e-02 2.50e+03 2.04e-02 4.18e+00 pdb=" C GLY A 56 " 0.035 2.00e-02 2.50e+03 pdb=" O GLY A 56 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL A 57 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.023 5.00e-02 4.00e+02 3.45e-02 1.91e+00 pdb=" N PRO B 236 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 183 " 0.006 2.00e-02 2.50e+03 1.30e-02 1.69e+00 pdb=" C PHE A 183 " -0.023 2.00e-02 2.50e+03 pdb=" O PHE A 183 " 0.008 2.00e-02 2.50e+03 pdb=" N ALA A 184 " 0.008 2.00e-02 2.50e+03 ... (remaining 2329 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.14: 489 2.14 - 2.75: 26310 2.75 - 3.37: 40774 3.37 - 3.98: 50303 3.98 - 4.60: 78164 Nonbonded interactions: 196040 Sorted by model distance: nonbonded pdb=" H TYR A 288 " pdb=" HA TYR A 288 " model vdw 1.524 1.816 nonbonded pdb=" O ASP B 170 " pdb=" H GLY B 174 " model vdw 1.549 2.450 nonbonded pdb=" OE1 GLU E 89 " pdb=" H GLU E 89 " model vdw 1.554 2.450 nonbonded pdb=" O TYR E 32 " pdb="HH22 ARG E 72 " model vdw 1.573 2.450 nonbonded pdb=" OD1 ASP D 321 " pdb=" H ARG D 323 " model vdw 1.588 2.450 ... (remaining 196035 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: 2.230 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: 0.070 Extract box with map and model: 0.180 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 12.240 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7771 Z= 0.125 Angle : 0.560 14.357 10598 Z= 0.306 Chirality : 0.040 0.174 1237 Planarity : 0.003 0.035 1350 Dihedral : 16.957 86.508 2631 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.58 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 33.24 % Favored : 66.76 % 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 are not related in a simple way. whole: 0.59 (0.29), residues: 1004 helix: 2.29 (0.27), residues: 394 sheet: -0.66 (0.38), residues: 207 loop : -0.94 (0.33), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 38 TYR 0.012 0.001 TYR E 117 PHE 0.009 0.001 PHE A 183 TRP 0.008 0.001 TRP A 246 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 ( 7768) covalent geometry : angle 0.55922 / 0.31 (10592) SS BOND : bond 0.00609 / 0.37 ( 3) SS BOND : angle 1.56907 / 0.82 ( 6) hydrogen bonds : bond 0.16558 / 10.76 ( 398) hydrogen bonds : angle 6.12550 / 4.51 ( 1101) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 6 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue THR 256 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue LYS 290 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 357 is missing expected H atoms. Skipping. Residue MET 376 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 111 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Evaluate side-chains 167 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.348 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: B 61 MET cc_start: 0.8784 (ppp) cc_final: 0.8282 (ppp) REVERT: D 342 SER cc_start: 0.9033 (p) cc_final: 0.8825 (t) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.1495 time to fit residues: 34.1414 Evaluate side-chains 148 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 220 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.105514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.093828 restraints weight = 74656.900| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 4.33 r_work: 0.3561 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7771 Z= 0.131 Angle : 0.568 14.055 10598 Z= 0.311 Chirality : 0.040 0.163 1237 Planarity : 0.004 0.045 1350 Dihedral : 7.647 71.809 1116 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.68 % Favored : 95.22 % Rotamer: Outliers : 2.41 % Allowed : 31.64 % Favored : 65.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.29), residues: 1004 helix: 2.58 (0.27), residues: 378 sheet: -0.65 (0.37), residues: 217 loop : -0.81 (0.33), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 307 TYR 0.008 0.001 TYR E 95 PHE 0.022 0.001 PHE D 212 TRP 0.009 0.001 TRP A 246 HIS 0.006 0.001 HIS D 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 ( 7768) covalent geometry : angle 0.56804 / 0.31 (10592) SS BOND : bond 0.00603 / 0.36 ( 3) SS BOND : angle 1.08797 / 0.57 ( 6) hydrogen bonds : bond 0.04800 / 3.26 ( 398) hydrogen bonds : angle 5.04522 / 3.69 ( 1101) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 6 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue THR 256 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue LYS 290 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 357 is missing expected H atoms. Skipping. Residue MET 376 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 111 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Evaluate side-chains 171 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 153 time to evaluate : 0.344 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: A 62 PHE cc_start: 0.8291 (m-10) cc_final: 0.8086 (m-80) REVERT: B 61 MET cc_start: 0.8879 (ppp) cc_final: 0.8317 (ppp) REVERT: D 348 TYR cc_start: 0.7964 (m-80) cc_final: 0.7649 (m-80) outliers start: 18 outliers final: 11 residues processed: 163 average time/residue: 0.1497 time to fit residues: 34.5735 Evaluate side-chains 155 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 TRP Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 266 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 63 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 15 optimal weight: 0.4980 chunk 50 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 23 optimal weight: 0.1980 chunk 35 optimal weight: 0.9980 chunk 60 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.105942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.094561 restraints weight = 74428.665| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 4.33 r_work: 0.3568 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7771 Z= 0.110 Angle : 0.544 13.927 10598 Z= 0.295 Chirality : 0.039 0.146 1237 Planarity : 0.003 0.029 1350 Dihedral : 7.493 70.775 1116 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.38 % Favored : 95.52 % Rotamer: Outliers : 2.01 % Allowed : 31.23 % Favored : 66.76 % 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 are not related in a simple way. whole: 0.79 (0.29), residues: 1004 helix: 2.60 (0.27), residues: 378 sheet: -0.61 (0.37), residues: 217 loop : -0.82 (0.33), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 307 TYR 0.007 0.001 TYR E 95 PHE 0.024 0.001 PHE D 212 TRP 0.009 0.001 TRP A 246 HIS 0.011 0.001 HIS D 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 ( 7768) covalent geometry : angle 0.54418 / 0.29 (10592) SS BOND : bond 0.00538 / 0.32 ( 3) SS BOND : angle 0.92676 / 0.48 ( 6) hydrogen bonds : bond 0.04093 / 2.81 ( 398) hydrogen bonds : angle 4.78645 / 3.49 ( 1101) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 6 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue THR 256 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue LYS 290 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 357 is missing expected H atoms. Skipping. Residue MET 376 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 111 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Evaluate side-chains 171 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 0.283 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: B 61 MET cc_start: 0.8820 (ppp) cc_final: 0.8272 (ppp) REVERT: D 334 GLU cc_start: 0.9370 (tp30) cc_final: 0.9114 (tp30) REVERT: D 348 TYR cc_start: 0.7980 (m-80) cc_final: 0.7656 (m-80) outliers start: 15 outliers final: 14 residues processed: 166 average time/residue: 0.1537 time to fit residues: 36.3038 Evaluate side-chains 164 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 TRP Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain E residue 99 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 38 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 80 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.104677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.093486 restraints weight = 74870.826| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 4.26 r_work: 0.3545 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7771 Z= 0.157 Angle : 0.554 13.861 10598 Z= 0.304 Chirality : 0.039 0.140 1237 Planarity : 0.004 0.029 1350 Dihedral : 7.483 69.654 1116 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.58 % Favored : 94.32 % Rotamer: Outliers : 2.41 % Allowed : 30.83 % Favored : 66.76 % 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 are not related in a simple way. whole: 0.71 (0.28), residues: 1004 helix: 2.48 (0.27), residues: 381 sheet: -0.64 (0.36), residues: 219 loop : -0.83 (0.33), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 307 TYR 0.007 0.001 TYR D 329 PHE 0.017 0.001 PHE D 212 TRP 0.011 0.001 TRP B 339 HIS 0.011 0.001 HIS D 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.16 ( 7768) covalent geometry : angle 0.55388 / 0.30 (10592) SS BOND : bond 0.00890 / 0.55 ( 3) SS BOND : angle 1.08389 / 0.55 ( 6) hydrogen bonds : bond 0.04016 / 2.74 ( 398) hydrogen bonds : angle 4.76632 / 3.49 ( 1101) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 6 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue THR 256 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue LYS 290 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 357 is missing expected H atoms. Skipping. Residue MET 376 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 111 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.427 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: B 61 MET cc_start: 0.8874 (ppp) cc_final: 0.8263 (ppp) REVERT: D 348 TYR cc_start: 0.8036 (m-80) cc_final: 0.7710 (m-80) outliers start: 18 outliers final: 16 residues processed: 151 average time/residue: 0.1718 time to fit residues: 36.3608 Evaluate side-chains 148 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 TRP Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 380 GLN Chi-restraints excluded: chain E residue 99 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 11 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 4 optimal weight: 0.7980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 GLN A 89 GLN D 257 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.104681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.093443 restraints weight = 75365.714| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 4.30 r_work: 0.3547 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7771 Z= 0.144 Angle : 0.547 13.901 10598 Z= 0.300 Chirality : 0.039 0.140 1237 Planarity : 0.004 0.042 1350 Dihedral : 7.399 68.584 1116 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.58 % Favored : 94.32 % Rotamer: Outliers : 2.95 % Allowed : 30.16 % Favored : 66.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.28), residues: 1004 helix: 2.43 (0.27), residues: 380 sheet: -0.63 (0.36), residues: 221 loop : -0.90 (0.33), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 96 TYR 0.007 0.001 TYR C 40 PHE 0.016 0.001 PHE A 62 TRP 0.011 0.001 TRP B 339 HIS 0.008 0.001 HIS D 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 7768) covalent geometry : angle 0.54664 / 0.30 (10592) SS BOND : bond 0.00826 / 0.51 ( 3) SS BOND : angle 1.01249 / 0.52 ( 6) hydrogen bonds : bond 0.03919 / 2.68 ( 398) hydrogen bonds : angle 4.65811 / 3.40 ( 1101) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 6 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue THR 256 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue LYS 290 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 357 is missing expected H atoms. Skipping. Residue MET 376 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 111 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Evaluate side-chains 158 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.347 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: D 348 TYR cc_start: 0.8022 (m-80) cc_final: 0.7680 (m-80) outliers start: 22 outliers final: 19 residues processed: 153 average time/residue: 0.1550 time to fit residues: 34.2660 Evaluate side-chains 154 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 TRP Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 298 ILE Chi-restraints excluded: chain D residue 380 GLN Chi-restraints excluded: chain E residue 99 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 45 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 GLN A 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.105095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.093703 restraints weight = 73781.285| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 4.35 r_work: 0.3557 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7771 Z= 0.113 Angle : 0.540 14.063 10598 Z= 0.292 Chirality : 0.040 0.203 1237 Planarity : 0.003 0.038 1350 Dihedral : 7.294 68.747 1116 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.98 % Favored : 94.92 % Rotamer: Outliers : 2.55 % Allowed : 30.70 % Favored : 66.76 % 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 are not related in a simple way. whole: 0.75 (0.28), residues: 1004 helix: 2.52 (0.27), residues: 380 sheet: -0.58 (0.36), residues: 215 loop : -0.84 (0.33), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 307 TYR 0.007 0.001 TYR D 308 PHE 0.014 0.001 PHE A 62 TRP 0.010 0.001 TRP B 339 HIS 0.008 0.001 HIS D 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 7768) covalent geometry : angle 0.53952 / 0.29 (10592) SS BOND : bond 0.00677 / 0.41 ( 3) SS BOND : angle 0.93519 / 0.48 ( 6) hydrogen bonds : bond 0.03740 / 2.56 ( 398) hydrogen bonds : angle 4.53595 / 3.32 ( 1101) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 6 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue THR 256 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue LYS 290 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 357 is missing expected H atoms. Skipping. Residue MET 376 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 111 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.353 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: D 348 TYR cc_start: 0.8013 (m-80) cc_final: 0.7675 (m-80) REVERT: E 73 ASP cc_start: 0.9034 (t70) cc_final: 0.8746 (t0) outliers start: 19 outliers final: 18 residues processed: 151 average time/residue: 0.1306 time to fit residues: 28.5144 Evaluate side-chains 155 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 TRP Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 380 GLN Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 99 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 80 optimal weight: 0.3980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 GLN A 89 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.105728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.094419 restraints weight = 73764.202| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 4.30 r_work: 0.3567 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7771 Z= 0.105 Angle : 0.531 14.131 10598 Z= 0.285 Chirality : 0.040 0.176 1237 Planarity : 0.003 0.037 1350 Dihedral : 7.212 69.055 1116 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.88 % Favored : 95.02 % Rotamer: Outliers : 2.55 % Allowed : 30.16 % Favored : 67.29 % 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 are not related in a simple way. whole: 0.88 (0.29), residues: 1004 helix: 2.67 (0.27), residues: 380 sheet: -0.57 (0.36), residues: 221 loop : -0.77 (0.33), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 270 TYR 0.007 0.001 TYR C 40 PHE 0.015 0.001 PHE A 62 TRP 0.010 0.001 TRP B 297 HIS 0.007 0.001 HIS D 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 ( 7768) covalent geometry : angle 0.53087 / 0.29 (10592) SS BOND : bond 0.00629 / 0.38 ( 3) SS BOND : angle 0.91080 / 0.46 ( 6) hydrogen bonds : bond 0.03605 / 2.47 ( 398) hydrogen bonds : angle 4.44476 / 3.25 ( 1101) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 6 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue THR 256 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue LYS 290 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 357 is missing expected H atoms. Skipping. Residue MET 376 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 111 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Evaluate side-chains 156 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.419 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: D 348 TYR cc_start: 0.7938 (m-80) cc_final: 0.7573 (m-80) REVERT: E 73 ASP cc_start: 0.9019 (t70) cc_final: 0.8745 (t0) outliers start: 19 outliers final: 14 residues processed: 150 average time/residue: 0.1437 time to fit residues: 31.3282 Evaluate side-chains 150 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 TRP Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 99 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 37 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 53 optimal weight: 0.0040 chunk 70 optimal weight: 1.9990 overall best weight: 0.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 GLN ** E 82 GLN ** 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 = 0.3847 r_free = 0.3847 target = 0.104559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.092878 restraints weight = 74771.008| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 4.33 r_work: 0.3565 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7771 Z= 0.109 Angle : 0.540 14.150 10598 Z= 0.289 Chirality : 0.040 0.177 1237 Planarity : 0.003 0.038 1350 Dihedral : 7.171 69.155 1116 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.88 % Favored : 95.02 % Rotamer: Outliers : 2.68 % Allowed : 29.62 % Favored : 67.69 % 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 are not related in a simple way. whole: 0.90 (0.29), residues: 1004 helix: 2.71 (0.27), residues: 378 sheet: -0.63 (0.35), residues: 223 loop : -0.71 (0.33), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 307 TYR 0.007 0.001 TYR C 40 PHE 0.014 0.001 PHE D 212 TRP 0.010 0.001 TRP B 339 HIS 0.007 0.001 HIS D 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 7768) covalent geometry : angle 0.53947 / 0.29 (10592) SS BOND : bond 0.00639 / 0.39 ( 3) SS BOND : angle 0.88096 / 0.45 ( 6) hydrogen bonds : bond 0.03564 / 2.43 ( 398) hydrogen bonds : angle 4.40054 / 3.22 ( 1101) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 6 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue THR 256 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue LYS 290 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 357 is missing expected H atoms. Skipping. Residue MET 376 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 111 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.402 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: A 176 TYR cc_start: 0.7459 (OUTLIER) cc_final: 0.5647 (t80) REVERT: B 325 MET cc_start: 0.7819 (tpp) cc_final: 0.7465 (tpp) REVERT: D 348 TYR cc_start: 0.7956 (m-80) cc_final: 0.7600 (m-80) REVERT: E 73 ASP cc_start: 0.9033 (t70) cc_final: 0.8754 (t0) outliers start: 20 outliers final: 18 residues processed: 151 average time/residue: 0.1438 time to fit residues: 30.8166 Evaluate side-chains 154 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 TRP Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 99 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 20 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 80 optimal weight: 0.1980 chunk 40 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.104442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.092741 restraints weight = 75278.292| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 4.31 r_work: 0.3554 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7771 Z= 0.125 Angle : 0.551 13.573 10598 Z= 0.295 Chirality : 0.040 0.172 1237 Planarity : 0.003 0.038 1350 Dihedral : 7.159 68.799 1116 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.38 % Favored : 94.52 % Rotamer: Outliers : 2.41 % Allowed : 30.43 % Favored : 67.16 % 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 are not related in a simple way. whole: 0.88 (0.28), residues: 1004 helix: 2.66 (0.27), residues: 378 sheet: -0.66 (0.35), residues: 229 loop : -0.67 (0.33), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 307 TYR 0.008 0.001 TYR C 40 PHE 0.014 0.001 PHE A 62 TRP 0.010 0.001 TRP B 339 HIS 0.008 0.001 HIS D 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 7768) covalent geometry : angle 0.55056 / 0.29 (10592) SS BOND : bond 0.00707 / 0.43 ( 3) SS BOND : angle 0.91929 / 0.47 ( 6) hydrogen bonds : bond 0.03548 / 2.43 ( 398) hydrogen bonds : angle 4.41350 / 3.22 ( 1101) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 6 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue THR 256 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue LYS 290 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 357 is missing expected H atoms. Skipping. Residue MET 376 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 111 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Evaluate side-chains 151 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.412 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: A 176 TYR cc_start: 0.7489 (OUTLIER) cc_final: 0.5646 (t80) REVERT: D 348 TYR cc_start: 0.7981 (m-80) cc_final: 0.7606 (m-80) REVERT: E 73 ASP cc_start: 0.9040 (t70) cc_final: 0.8766 (t0) outliers start: 18 outliers final: 17 residues processed: 146 average time/residue: 0.1516 time to fit residues: 31.2562 Evaluate side-chains 150 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 TRP Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 99 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 22 optimal weight: 0.7980 chunk 44 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 66 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.102550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.091091 restraints weight = 75552.110| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 4.30 r_work: 0.3529 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7771 Z= 0.175 Angle : 0.576 13.388 10598 Z= 0.313 Chirality : 0.040 0.168 1237 Planarity : 0.004 0.037 1350 Dihedral : 7.227 67.467 1116 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.18 % Favored : 93.73 % Rotamer: Outliers : 2.55 % Allowed : 30.16 % Favored : 67.29 % 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 are not related in a simple way. whole: 0.67 (0.28), residues: 1004 helix: 2.44 (0.27), residues: 381 sheet: -0.79 (0.35), residues: 233 loop : -0.74 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 270 TYR 0.008 0.001 TYR A 179 PHE 0.016 0.001 PHE A 62 TRP 0.012 0.001 TRP B 339 HIS 0.008 0.001 HIS D 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.18 ( 7768) covalent geometry : angle 0.57554 / 0.31 (10592) SS BOND : bond 0.00912 / 0.56 ( 3) SS BOND : angle 1.01453 / 0.52 ( 6) hydrogen bonds : bond 0.03822 / 2.60 ( 398) hydrogen bonds : angle 4.56164 / 3.34 ( 1101) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 6 is missing expected H atoms. Skipping. Residue SER 90 is missing expected H atoms. Skipping. Residue LYS 209 is missing expected H atoms. Skipping. Residue MET 211 is missing expected H atoms. Skipping. Residue LYS 233 is missing expected H atoms. Skipping. Residue THR 256 is missing expected H atoms. Skipping. Residue ILE 292 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue LYS 15 is missing expected H atoms. Skipping. Residue ILE 18 is missing expected H atoms. Skipping. Residue LYS 23 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Residue SER 245 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 15 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue ILE 25 is missing expected H atoms. Skipping. Residue LYS 29 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue LYS 46 is missing expected H atoms. Skipping. Residue THR 52 is missing expected H atoms. Skipping. Residue VAL 54 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue ILE 26 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LYS 264 is missing expected H atoms. Skipping. Residue LYS 290 is missing expected H atoms. Skipping. Residue LYS 295 is missing expected H atoms. Skipping. Residue LYS 297 is missing expected H atoms. Skipping. Residue VAL 357 is missing expected H atoms. Skipping. Residue MET 376 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue THR 111 is missing expected H atoms. Skipping. Residue SER 112 is missing expected H atoms. Skipping. Residue THR 113 is missing expected H atoms. Skipping. Residue THR 114 is missing expected H atoms. Skipping. Evaluate side-chains 147 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.343 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 176 TYR cc_start: 0.7563 (OUTLIER) cc_final: 0.5728 (t80) REVERT: A 177 MET cc_start: 0.7874 (tpt) cc_final: 0.7627 (tpt) REVERT: B 61 MET cc_start: 0.8859 (ppp) cc_final: 0.8462 (ppp) REVERT: D 348 TYR cc_start: 0.8058 (m-80) cc_final: 0.7715 (m-80) outliers start: 19 outliers final: 17 residues processed: 141 average time/residue: 0.1533 time to fit residues: 30.9768 Evaluate side-chains 144 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 TRP Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 99 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 7 optimal weight: 4.9990 chunk 50 optimal weight: 0.3980 chunk 37 optimal weight: 3.9990 chunk 81 optimal weight: 0.0980 chunk 25 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 99 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 GLN A 89 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.105427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.093712 restraints weight = 74431.021| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 4.32 r_work: 0.3565 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7771 Z= 0.104 Angle : 0.548 13.687 10598 Z= 0.292 Chirality : 0.040 0.156 1237 Planarity : 0.003 0.038 1350 Dihedral : 7.136 68.928 1116 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.18 % Favored : 95.72 % Rotamer: Outliers : 2.41 % Allowed : 30.16 % Favored : 67.43 % 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 are not related in a simple way. whole: 0.95 (0.29), residues: 1004 helix: 2.69 (0.27), residues: 379 sheet: -0.61 (0.36), residues: 224 loop : -0.63 (0.34), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 270 TYR 0.009 0.001 TYR C 40 PHE 0.016 0.001 PHE A 62 TRP 0.010 0.001 TRP B 297 HIS 0.007 0.001 HIS D 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 ( 7768) covalent geometry : angle 0.54822 / 0.29 (10592) SS BOND : bond 0.00616 / 0.37 ( 3) SS BOND : angle 0.81680 / 0.42 ( 6) hydrogen bonds : bond 0.03520 / 2.41 ( 398) hydrogen bonds : angle 4.37532 / 3.19 ( 1101) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2983.36 seconds wall clock time: 51 minutes 23.97 seconds (3083.97 seconds total)