Starting phenix.real_space_refine on Fri Jun 13 06:18:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ee9_47952/06_2025/9ee9_47952.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ee9_47952/06_2025/9ee9_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_47952/06_2025/9ee9_47952.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ee9_47952/06_2025/9ee9_47952.map" model { file = "/net/cci-nas-00/data/ceres_data/9ee9_47952/06_2025/9ee9_47952.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ee9_47952/06_2025/9ee9_47952.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 3, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, '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: {'GLN:plan1': 6, 'GLU:plan': 4, 'ARG:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 4} 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: {'GLU:plan': 5, 'ARG:plan': 2, '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, 'GLU:plan': 7, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 6} 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: 7.49, per 1000 atoms: 0.51 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: 3.73 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.21 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: 5.55 Time building geometry restraints manager: 4.55 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: 6243 17.30 - 34.60: 663 34.60 - 51.90: 170 51.90 - 69.21: 49 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 - 0.047: 1012 0.047 - 0.093: 159 0.093 - 0.140: 63 0.140 - 0.187: 2 0.187 - 0.233: 1 Chirality restraints: 1237 Sorted by residual: chirality pdb=" C2' ADN A 400 " pdb=" C1' ADN A 400 " pdb=" C3' ADN A 400 " pdb=" O2' ADN A 400 " both_signs ideal model delta sigma weight residual False -2.75 -2.52 -0.23 2.00e-01 2.50e+01 1.36e+00 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=" C3' ADN A 400 " pdb=" C2' ADN A 400 " pdb=" C4' ADN A 400 " pdb=" O3' ADN A 400 " both_signs ideal model delta sigma weight residual False -2.56 -2.73 0.17 2.00e-01 2.50e+01 7.30e-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: 2.360 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: 0.250 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 33.980 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.050 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 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= 0.128 Angle : 0.566 14.357 10598 Z= 0.307 Chirality : 0.041 0.233 1237 Planarity : 0.003 0.035 1350 Dihedral : 17.058 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.008 0.001 TRP A 246 HIS 0.005 0.001 HIS B 54 PHE 0.009 0.001 PHE A 183 TYR 0.012 0.001 TYR E 117 ARG 0.003 0.000 ARG D 38 Details of bonding type rmsd hydrogen bonds : bond 0.16558 ( 398) hydrogen bonds : angle 6.12550 ( 1101) SS BOND : bond 0.00609 ( 3) SS BOND : angle 1.56907 ( 6) covalent geometry : bond 0.00258 ( 7768) covalent geometry : angle 0.56485 (10592) *********************** 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 : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 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: 0.3865 time to fit residues: 87.4773 Evaluate side-chains 149 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 220 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.104138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.093021 restraints weight = 74938.973| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 4.25 r_work: 0.3541 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7771 Z= 0.180 Angle : 0.595 13.940 10598 Z= 0.326 Chirality : 0.040 0.162 1237 Planarity : 0.004 0.054 1350 Dihedral : 6.650 54.665 1116 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.68 % Favored : 94.22 % Rotamer: Outliers : 3.08 % Allowed : 31.90 % Favored : 65.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.29), residues: 1004 helix: 2.40 (0.27), residues: 379 sheet: -0.67 (0.37), residues: 217 loop : -0.92 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 246 HIS 0.005 0.001 HIS D 220 PHE 0.021 0.001 PHE D 212 TYR 0.008 0.001 TYR E 95 ARG 0.003 0.000 ARG D 307 Details of bonding type rmsd hydrogen bonds : bond 0.04656 ( 398) hydrogen bonds : angle 5.14508 ( 1101) SS BOND : bond 0.00828 ( 3) SS BOND : angle 1.15787 ( 6) covalent geometry : bond 0.00378 ( 7768) covalent geometry : angle 0.59426 (10592) *********************** 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 172 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 1.212 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: B 61 MET cc_start: 0.8899 (ppp) cc_final: 0.8334 (ppp) REVERT: D 348 TYR cc_start: 0.8029 (m-80) cc_final: 0.7715 (m-80) outliers start: 23 outliers final: 14 residues processed: 163 average time/residue: 0.3733 time to fit residues: 84.4844 Evaluate side-chains 153 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 1.095 ------------------------------------------------------------------------------- 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 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 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 260 LEU Chi-restraints excluded: chain D residue 298 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 22 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.103856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.092373 restraints weight = 75641.119| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 4.24 r_work: 0.3537 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7771 Z= 0.168 Angle : 0.576 13.896 10598 Z= 0.314 Chirality : 0.039 0.143 1237 Planarity : 0.004 0.032 1350 Dihedral : 5.592 55.235 1116 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.98 % Favored : 93.92 % Rotamer: Outliers : 3.08 % Allowed : 31.64 % Favored : 65.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.28), residues: 1004 helix: 2.27 (0.27), residues: 380 sheet: -0.62 (0.37), residues: 217 loop : -0.95 (0.33), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 339 HIS 0.010 0.001 HIS D 220 PHE 0.022 0.001 PHE D 212 TYR 0.007 0.001 TYR B 111 ARG 0.004 0.000 ARG D 307 Details of bonding type rmsd hydrogen bonds : bond 0.04430 ( 398) hydrogen bonds : angle 4.99360 ( 1101) SS BOND : bond 0.00710 ( 3) SS BOND : angle 1.12728 ( 6) covalent geometry : bond 0.00360 ( 7768) covalent geometry : angle 0.57524 (10592) *********************** 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 166 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 1.067 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: 0.8845 (ppp) cc_final: 0.8272 (ppp) REVERT: D 348 TYR cc_start: 0.8033 (m-80) cc_final: 0.7727 (m-80) REVERT: E 34 MET cc_start: 0.7619 (mmm) cc_final: 0.6710 (mmm) outliers start: 23 outliers final: 20 residues processed: 158 average time/residue: 0.3690 time to fit residues: 80.8370 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 : 1.173 ------------------------------------------------------------------------------- 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 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 84 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 237 ASN 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 298 ILE Chi-restraints excluded: chain D residue 380 GLN Chi-restraints excluded: chain E residue 87 LYS 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 30 optimal weight: 1.9990 chunk 8 optimal weight: 0.0870 chunk 61 optimal weight: 10.0000 chunk 1 optimal weight: 0.5980 chunk 27 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 63 optimal weight: 0.0570 chunk 87 optimal weight: 4.9990 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.106208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.094955 restraints weight = 74989.678| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 4.28 r_work: 0.3571 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7771 Z= 0.102 Angle : 0.543 13.958 10598 Z= 0.291 Chirality : 0.039 0.152 1237 Planarity : 0.003 0.031 1350 Dihedral : 5.075 54.575 1116 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.18 % Favored : 95.72 % Rotamer: Outliers : 1.88 % Allowed : 30.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.29), residues: 1004 helix: 2.59 (0.27), residues: 380 sheet: -0.53 (0.37), residues: 211 loop : -0.86 (0.33), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 297 HIS 0.013 0.002 HIS D 220 PHE 0.020 0.001 PHE D 212 TYR 0.007 0.001 TYR D 37 ARG 0.006 0.000 ARG D 307 Details of bonding type rmsd hydrogen bonds : bond 0.03893 ( 398) hydrogen bonds : angle 4.63681 ( 1101) SS BOND : bond 0.00591 ( 3) SS BOND : angle 0.87036 ( 6) covalent geometry : bond 0.00223 ( 7768) covalent geometry : angle 0.54227 (10592) *********************** 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 171 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 157 time to evaluate : 1.078 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: B 61 MET cc_start: 0.8749 (ppp) cc_final: 0.8248 (ppp) REVERT: D 348 TYR cc_start: 0.7927 (m-80) cc_final: 0.7609 (m-80) outliers start: 14 outliers final: 12 residues processed: 166 average time/residue: 0.4047 time to fit residues: 93.6467 Evaluate side-chains 153 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 29 TRP 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 234 PHE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 31 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 30 optimal weight: 0.4980 chunk 77 optimal weight: 0.0870 chunk 2 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.105921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.094647 restraints weight = 75413.072| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 4.29 r_work: 0.3571 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7771 Z= 0.104 Angle : 0.534 14.021 10598 Z= 0.286 Chirality : 0.039 0.142 1237 Planarity : 0.003 0.038 1350 Dihedral : 4.933 53.351 1116 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.78 % Favored : 95.12 % Rotamer: Outliers : 2.14 % Allowed : 31.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.29), residues: 1004 helix: 2.64 (0.28), residues: 380 sheet: -0.53 (0.36), residues: 215 loop : -0.84 (0.33), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.007 0.001 HIS D 220 PHE 0.015 0.001 PHE D 212 TYR 0.007 0.001 TYR D 37 ARG 0.006 0.000 ARG D 307 Details of bonding type rmsd hydrogen bonds : bond 0.03710 ( 398) hydrogen bonds : angle 4.51438 ( 1101) SS BOND : bond 0.00625 ( 3) SS BOND : angle 0.88465 ( 6) covalent geometry : bond 0.00230 ( 7768) covalent geometry : angle 0.53358 (10592) *********************** 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 159 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 1.037 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: 0.8800 (ppp) cc_final: 0.8232 (ppp) REVERT: D 348 TYR cc_start: 0.7902 (m-80) cc_final: 0.7560 (m-80) REVERT: E 73 ASP cc_start: 0.9010 (t70) cc_final: 0.8779 (t70) outliers start: 16 outliers final: 14 residues processed: 154 average time/residue: 0.3487 time to fit residues: 75.1482 Evaluate side-chains 153 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 1.203 ------------------------------------------------------------------------------- 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 198 LEU Chi-restraints excluded: chain B residue 234 PHE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 90 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 21 optimal weight: 0.4980 chunk 39 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN D 257 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.104073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.092941 restraints weight = 76009.103| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 4.28 r_work: 0.3538 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7771 Z= 0.177 Angle : 0.568 13.991 10598 Z= 0.310 Chirality : 0.040 0.172 1237 Planarity : 0.004 0.048 1350 Dihedral : 5.022 52.148 1116 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.78 % Favored : 94.12 % Rotamer: Outliers : 2.55 % Allowed : 30.97 % Favored : 66.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.28), residues: 1004 helix: 2.43 (0.27), residues: 380 sheet: -0.63 (0.36), residues: 221 loop : -0.95 (0.33), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.007 0.001 HIS D 220 PHE 0.015 0.001 PHE A 62 TYR 0.008 0.001 TYR D 381 ARG 0.008 0.000 ARG D 307 Details of bonding type rmsd hydrogen bonds : bond 0.03904 ( 398) hydrogen bonds : angle 4.66753 ( 1101) SS BOND : bond 0.00900 ( 3) SS BOND : angle 1.09216 ( 6) covalent geometry : bond 0.00376 ( 7768) covalent geometry : angle 0.56779 (10592) *********************** 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 150 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 1.345 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: 0.8021 (m-80) cc_final: 0.7688 (m-80) outliers start: 19 outliers final: 19 residues processed: 142 average time/residue: 0.3733 time to fit residues: 76.6403 Evaluate side-chains 150 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 1.072 ------------------------------------------------------------------------------- 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 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 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 336 LEU 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 298 ILE 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 29 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 27 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.104985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.093248 restraints weight = 74830.310| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 4.34 r_work: 0.3563 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2146 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= 0.104 Angle : 0.537 14.067 10598 Z= 0.288 Chirality : 0.040 0.180 1237 Planarity : 0.003 0.034 1350 Dihedral : 4.804 49.330 1116 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.48 % Favored : 95.42 % Rotamer: Outliers : 2.28 % Allowed : 30.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.29), residues: 1004 helix: 2.58 (0.27), residues: 379 sheet: -0.63 (0.36), residues: 223 loop : -0.84 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.008 0.001 HIS D 220 PHE 0.017 0.001 PHE A 62 TYR 0.007 0.001 TYR D 308 ARG 0.006 0.000 ARG D 307 Details of bonding type rmsd hydrogen bonds : bond 0.03685 ( 398) hydrogen bonds : angle 4.48976 ( 1101) SS BOND : bond 0.00659 ( 3) SS BOND : angle 0.90706 ( 6) covalent geometry : bond 0.00229 ( 7768) covalent geometry : angle 0.53623 (10592) *********************** 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 158 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 1.688 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: E 73 ASP cc_start: 0.9004 (t70) cc_final: 0.8797 (t70) outliers start: 17 outliers final: 14 residues processed: 152 average time/residue: 0.3678 time to fit residues: 80.2991 Evaluate side-chains 151 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 TRP 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 86 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 0.4980 chunk 21 optimal weight: 0.5980 chunk 92 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 39 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3848 r_free = 0.3848 target = 0.105392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.093564 restraints weight = 75797.252| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 4.35 r_work: 0.3555 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2272 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= 0.116 Angle : 0.541 14.146 10598 Z= 0.291 Chirality : 0.040 0.175 1237 Planarity : 0.003 0.035 1350 Dihedral : 4.698 47.536 1116 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.08 % Favored : 94.82 % Rotamer: Outliers : 2.95 % Allowed : 30.56 % Favored : 66.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.29), residues: 1004 helix: 2.59 (0.27), residues: 380 sheet: -0.62 (0.35), residues: 223 loop : -0.78 (0.33), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 339 HIS 0.008 0.001 HIS D 220 PHE 0.016 0.001 PHE A 62 TYR 0.008 0.001 TYR C 40 ARG 0.006 0.000 ARG D 307 Details of bonding type rmsd hydrogen bonds : bond 0.03630 ( 398) hydrogen bonds : angle 4.45152 ( 1101) SS BOND : bond 0.00687 ( 3) SS BOND : angle 0.93819 ( 6) covalent geometry : bond 0.00258 ( 7768) covalent geometry : angle 0.54073 (10592) *********************** 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: 22 poor density : 135 time to evaluate : 1.216 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: A 176 TYR cc_start: 0.7486 (OUTLIER) cc_final: 0.5665 (t80) REVERT: B 325 MET cc_start: 0.7880 (tpp) cc_final: 0.7668 (tpp) REVERT: E 73 ASP cc_start: 0.9006 (t70) cc_final: 0.8786 (t70) outliers start: 22 outliers final: 18 residues processed: 151 average time/residue: 0.3679 time to fit residues: 78.1635 Evaluate side-chains 152 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 TRP 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 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain D residue 218 ASN Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 57 SER 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 32 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 72 optimal weight: 0.4980 chunk 34 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 99 optimal weight: 0.4980 chunk 94 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3831 r_free = 0.3831 target = 0.103865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.092255 restraints weight = 76426.682| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 4.34 r_work: 0.3541 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7771 Z= 0.147 Angle : 0.559 14.136 10598 Z= 0.301 Chirality : 0.040 0.168 1237 Planarity : 0.004 0.035 1350 Dihedral : 4.715 46.679 1116 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.78 % Favored : 94.12 % Rotamer: Outliers : 2.95 % Allowed : 30.83 % Favored : 66.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.28), residues: 1004 helix: 2.53 (0.27), residues: 379 sheet: -0.69 (0.35), residues: 229 loop : -0.78 (0.33), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 339 HIS 0.008 0.001 HIS D 220 PHE 0.015 0.001 PHE A 62 TYR 0.008 0.001 TYR E 94 ARG 0.005 0.000 ARG D 270 Details of bonding type rmsd hydrogen bonds : bond 0.03715 ( 398) hydrogen bonds : angle 4.52845 ( 1101) SS BOND : bond 0.00801 ( 3) SS BOND : angle 0.99751 ( 6) covalent geometry : bond 0.00321 ( 7768) covalent geometry : angle 0.55855 (10592) *********************** 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 155 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 1.180 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: A 176 TYR cc_start: 0.7526 (OUTLIER) cc_final: 0.5680 (t80) outliers start: 22 outliers final: 20 residues processed: 149 average time/residue: 0.3404 time to fit residues: 72.2777 Evaluate side-chains 153 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 TRP 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 198 LEU 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 336 LEU 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 57 SER 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 18 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3847 r_free = 0.3847 target = 0.105201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.093851 restraints weight = 75717.731| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 4.36 r_work: 0.3555 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7771 Z= 0.115 Angle : 0.554 14.184 10598 Z= 0.296 Chirality : 0.040 0.170 1237 Planarity : 0.003 0.036 1350 Dihedral : 4.600 44.465 1116 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.88 % Favored : 95.02 % Rotamer: Outliers : 2.82 % Allowed : 30.70 % Favored : 66.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.29), residues: 1004 helix: 2.62 (0.27), residues: 379 sheet: -0.63 (0.35), residues: 224 loop : -0.72 (0.33), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.008 0.001 HIS D 220 PHE 0.015 0.001 PHE A 62 TYR 0.010 0.001 TYR E 94 ARG 0.008 0.000 ARG D 307 Details of bonding type rmsd hydrogen bonds : bond 0.03612 ( 398) hydrogen bonds : angle 4.41170 ( 1101) SS BOND : bond 0.00725 ( 3) SS BOND : angle 0.87807 ( 6) covalent geometry : bond 0.00257 ( 7768) covalent geometry : angle 0.55425 (10592) ********************** 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 157 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 TYR cc_start: 0.7546 (OUTLIER) cc_final: 0.5682 (t80) REVERT: B 325 MET cc_start: 0.7878 (tpp) cc_final: 0.7630 (tpp) REVERT: E 46 GLU cc_start: 0.8346 (pm20) cc_final: 0.8111 (pm20) outliers start: 21 outliers final: 20 residues processed: 152 average time/residue: 0.4791 time to fit residues: 106.9832 Evaluate side-chains 153 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 TRP 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 168 LEU Chi-restraints excluded: chain B residue 198 LEU 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 336 LEU 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 57 SER 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 35 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 88 optimal weight: 8.9990 chunk 56 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3827 r_free = 0.3827 target = 0.103810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.092628 restraints weight = 76603.975| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 4.33 r_work: 0.3533 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7771 Z= 0.170 Angle : 0.578 14.114 10598 Z= 0.313 Chirality : 0.040 0.161 1237 Planarity : 0.004 0.034 1350 Dihedral : 4.713 45.019 1116 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.47 % Favored : 93.43 % Rotamer: Outliers : 2.82 % Allowed : 31.50 % Favored : 65.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.28), residues: 1004 helix: 2.44 (0.27), residues: 379 sheet: -0.73 (0.35), residues: 231 loop : -0.76 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.008 0.001 HIS D 220 PHE 0.017 0.001 PHE A 62 TYR 0.008 0.001 TYR D 329 ARG 0.005 0.000 ARG D 270 Details of bonding type rmsd hydrogen bonds : bond 0.03811 ( 398) hydrogen bonds : angle 4.57220 ( 1101) SS BOND : bond 0.00888 ( 3) SS BOND : angle 1.02229 ( 6) covalent geometry : bond 0.00367 ( 7768) covalent geometry : angle 0.57810 (10592) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7035.95 seconds wall clock time: 122 minutes 37.45 seconds (7357.45 seconds total)