Starting phenix.real_space_refine on Fri May 16 18:31:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ee9_47952/05_2025/9ee9_47952.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ee9_47952/05_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_47952/05_2025/9ee9_47952.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ee9_47952/05_2025/9ee9_47952.map" model { file = "/net/cci-nas-00/data/ceres_data/9ee9_47952/05_2025/9ee9_47952.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ee9_47952/05_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-5687/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: 7.11, per 1000 atoms: 0.48 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: 3.59 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: 1.20 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: 5.48 Time building geometry restraints manager: 4.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 7117 1.03 - 1.23: 59 1.23 - 1.43: 3288 1.43 - 1.62: 4378 1.62 - 1.82: 66 Bond restraints: 14908 Sorted by residual: bond pdb=" N GLN C 11 " pdb=" CA GLN C 11 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.10e+00 bond pdb=" N GLU D 10 " pdb=" CA GLU D 10 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 bond pdb=" N ASP B 5 " pdb=" CA ASP B 5 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.01e+00 bond pdb=" N GLN E 1 " pdb=" CA GLN E 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 bond pdb=" N GLN C 11 " pdb=" H GLN C 11 " ideal model delta sigma weight residual 0.860 0.892 -0.032 2.00e-02 2.50e+03 2.53e+00 ... (remaining 14903 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.41: 26721 10.41 - 20.82: 1 20.82 - 31.23: 0 31.23 - 41.63: 0 41.63 - 52.04: 2 Bond angle restraints: 26724 Sorted by residual: angle pdb=" C ILE A 287 " pdb=" N TYR A 288 " pdb=" H TYR A 288 " ideal model delta sigma weight residual 124.71 72.67 52.04 3.00e+00 1.11e-01 3.01e+02 angle pdb=" CA TYR A 288 " pdb=" N TYR A 288 " pdb=" H TYR A 288 " ideal model delta sigma weight residual 114.41 62.57 51.84 3.00e+00 1.11e-01 2.99e+02 angle pdb=" C ILE A 287 " pdb=" N TYR A 288 " pdb=" CA TYR A 288 " ideal model delta sigma weight residual 120.88 135.24 -14.36 1.62e+00 3.81e-01 7.85e+01 angle pdb=" N ILE D 207 " pdb=" CA ILE D 207 " pdb=" C ILE D 207 " ideal model delta sigma weight residual 111.62 108.94 2.68 7.90e-01 1.60e+00 1.15e+01 angle pdb=" C ARG E 98 " pdb=" N CYS E 99 " pdb=" CA CYS E 99 " ideal model delta sigma weight residual 121.48 115.44 6.04 2.04e+00 2.40e-01 8.77e+00 ... (remaining 26719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 6245 17.30 - 34.60: 663 34.60 - 51.90: 170 51.90 - 69.21: 47 69.21 - 86.51: 18 Dihedral angle restraints: 7143 sinusoidal: 3632 harmonic: 3511 Sorted by residual: dihedral pdb=" CB CYS E 99 " pdb=" SG CYS E 99 " pdb=" SG CYS E 107 " pdb=" CB CYS E 107 " ideal model delta sinusoidal sigma weight residual -86.00 -35.72 -50.28 1 1.00e+01 1.00e-02 3.46e+01 dihedral pdb=" CA CYS E 99 " pdb=" C CYS E 99 " pdb=" N PRO E 100 " pdb=" CA PRO E 100 " ideal model delta harmonic sigma weight residual -180.00 -160.27 -19.73 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA GLY A 56 " pdb=" C GLY A 56 " pdb=" N VAL A 57 " pdb=" CA VAL A 57 " ideal model delta harmonic sigma weight residual -180.00 -160.31 -19.69 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 7140 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 866 0.035 - 0.070: 260 0.070 - 0.104: 66 0.104 - 0.139: 44 0.139 - 0.174: 1 Chirality restraints: 1237 Sorted by residual: chirality pdb=" CG LEU D 260 " pdb=" CB LEU D 260 " pdb=" CD1 LEU D 260 " pdb=" CD2 LEU D 260 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.58e-01 chirality pdb=" CA ILE B 123 " pdb=" N ILE B 123 " pdb=" C ILE B 123 " pdb=" CB ILE B 123 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA ILE B 229 " pdb=" N ILE B 229 " pdb=" C ILE B 229 " pdb=" CB ILE B 229 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.27e-01 ... (remaining 1234 not shown) Planarity restraints: 2332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 56 " -0.010 2.00e-02 2.50e+03 2.04e-02 4.18e+00 pdb=" C GLY A 56 " 0.035 2.00e-02 2.50e+03 pdb=" O GLY A 56 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL A 57 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.023 5.00e-02 4.00e+02 3.45e-02 1.91e+00 pdb=" N PRO B 236 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 183 " 0.006 2.00e-02 2.50e+03 1.30e-02 1.69e+00 pdb=" C PHE A 183 " -0.023 2.00e-02 2.50e+03 pdb=" O PHE A 183 " 0.008 2.00e-02 2.50e+03 pdb=" N ALA A 184 " 0.008 2.00e-02 2.50e+03 ... (remaining 2329 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.14: 489 2.14 - 2.75: 26310 2.75 - 3.37: 40774 3.37 - 3.98: 50303 3.98 - 4.60: 78164 Nonbonded interactions: 196040 Sorted by model distance: nonbonded pdb=" H TYR A 288 " pdb=" HA TYR A 288 " model vdw 1.524 1.816 nonbonded pdb=" O ASP B 170 " pdb=" H GLY B 174 " model vdw 1.549 2.450 nonbonded pdb=" OE1 GLU E 89 " pdb=" H GLU E 89 " model vdw 1.554 2.450 nonbonded pdb=" O TYR E 32 " pdb="HH22 ARG E 72 " model vdw 1.573 2.450 nonbonded pdb=" OD1 ASP D 321 " pdb=" H ARG D 323 " model vdw 1.588 2.450 ... (remaining 196035 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.900 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: 0.270 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 33.110 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.040 ------------------------------------------------------------------------------- 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= 0.125 Angle : 0.560 14.357 10598 Z= 0.306 Chirality : 0.040 0.174 1237 Planarity : 0.003 0.035 1350 Dihedral : 16.957 86.508 2631 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.58 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 33.24 % Favored : 66.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 0.00252 ( 7768) covalent geometry : angle 0.55922 (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 : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.3887 time to fit residues: 87.5381 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 : 1.132 ------------------------------------------------------------------------------- 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 = 0.104183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.093137 restraints weight = 75198.978| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 4.23 r_work: 0.3542 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7771 Z= 0.180 Angle : 0.589 13.969 10598 Z= 0.325 Chirality : 0.040 0.160 1237 Planarity : 0.004 0.053 1350 Dihedral : 7.691 71.116 1116 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.68 % Favored : 94.22 % Rotamer: Outliers : 3.08 % Allowed : 32.04 % Favored : 64.88 % 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: 2.41 (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 38 Details of bonding type rmsd hydrogen bonds : bond 0.04763 ( 398) hydrogen bonds : angle 5.15262 ( 1101) SS BOND : bond 0.00822 ( 3) SS BOND : angle 1.18067 ( 6) covalent geometry : bond 0.00377 ( 7768) covalent geometry : angle 0.58820 (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 : 1.092 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: 0.8846 (ppp) cc_final: 0.8304 (ppp) REVERT: D 348 TYR cc_start: 0.8005 (m-80) cc_final: 0.7694 (m-80) outliers start: 23 outliers final: 14 residues processed: 162 average time/residue: 0.3698 time to fit residues: 82.8621 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 : 1.078 ------------------------------------------------------------------------------- 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 D residue 260 LEU Chi-restraints excluded: chain D residue 266 ILE 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: 0.2980 chunk 62 optimal weight: 9.9990 chunk 98 optimal weight: 0.1980 chunk 2 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3852 r_free = 0.3852 target = 0.105765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.094029 restraints weight = 73763.219| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 4.28 r_work: 0.3568 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7771 Z= 0.109 Angle : 0.548 13.876 10598 Z= 0.296 Chirality : 0.039 0.148 1237 Planarity : 0.003 0.029 1350 Dihedral : 7.466 70.206 1116 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.28 % Favored : 95.62 % Rotamer: Outliers : 1.88 % Allowed : 31.77 % Favored : 66.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.78 (0.29), residues: 1004 helix: 2.58 (0.27), residues: 379 sheet: -0.57 (0.37), residues: 216 loop : -0.85 (0.33), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 246 HIS 0.010 0.001 HIS D 220 PHE 0.024 0.001 PHE D 212 TYR 0.007 0.001 TYR D 37 ARG 0.005 0.000 ARG D 307 Details of bonding type rmsd hydrogen bonds : bond 0.04082 ( 398) hydrogen bonds : angle 4.76830 ( 1101) SS BOND : bond 0.00651 ( 3) SS BOND : angle 0.93786 ( 6) covalent geometry : bond 0.00240 ( 7768) covalent geometry : angle 0.54818 (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 169 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 155 time to evaluate : 1.083 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: 0.8813 (ppp) cc_final: 0.8272 (ppp) REVERT: D 334 GLU cc_start: 0.9360 (tp30) cc_final: 0.9128 (tp30) REVERT: D 348 TYR cc_start: 0.7972 (m-80) cc_final: 0.7649 (m-80) outliers start: 14 outliers final: 12 residues processed: 164 average time/residue: 0.3603 time to fit residues: 81.8876 Evaluate side-chains 160 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 1.202 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 30 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 80 optimal weight: 0.4980 chunk 73 optimal weight: 2.9990 chunk 81 optimal weight: 0.0030 chunk 63 optimal weight: 0.3980 chunk 87 optimal weight: 3.9990 overall best weight: 0.4790 ------------------------------------------------------------------------------- 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 = 0.3864 r_free = 0.3864 target = 0.106379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.095061 restraints weight = 74230.294| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 4.29 r_work: 0.3574 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1674 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= 0.102 Angle : 0.533 14.050 10598 Z= 0.288 Chirality : 0.039 0.146 1237 Planarity : 0.003 0.031 1350 Dihedral : 7.388 70.303 1116 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.48 % Favored : 95.42 % Rotamer: Outliers : 1.88 % Allowed : 30.97 % Favored : 67.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.65 (0.28), residues: 380 sheet: -0.61 (0.36), residues: 221 loop : -0.85 (0.33), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 297 HIS 0.013 0.001 HIS D 220 PHE 0.019 0.001 PHE D 212 TYR 0.006 0.001 TYR D 37 ARG 0.007 0.000 ARG D 307 Details of bonding type rmsd hydrogen bonds : bond 0.03782 ( 398) hydrogen bonds : angle 4.59508 ( 1101) SS BOND : bond 0.00571 ( 3) SS BOND : angle 0.86732 ( 6) covalent geometry : bond 0.00223 ( 7768) covalent geometry : angle 0.53310 (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 169 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 155 time to evaluate : 1.110 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: 0.8746 (ppp) cc_final: 0.8218 (ppp) REVERT: D 348 TYR cc_start: 0.7917 (m-80) cc_final: 0.7583 (m-80) REVERT: E 73 ASP cc_start: 0.9013 (t70) cc_final: 0.8761 (t70) outliers start: 14 outliers final: 13 residues processed: 165 average time/residue: 0.3939 time to fit residues: 89.6623 Evaluate side-chains 155 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 1.139 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 31 optimal weight: 0.6980 chunk 59 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.3847 r_free = 0.3847 target = 0.105487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.094203 restraints weight = 75287.292| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 4.29 r_work: 0.3561 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7771 Z= 0.132 Angle : 0.541 13.924 10598 Z= 0.295 Chirality : 0.039 0.139 1237 Planarity : 0.004 0.046 1350 Dihedral : 7.365 69.509 1116 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.18 % Favored : 94.72 % Rotamer: Outliers : 2.14 % Allowed : 31.23 % Favored : 66.62 % 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 (0.29), residues: 1004 helix: 2.60 (0.27), residues: 380 sheet: -0.65 (0.35), residues: 221 loop : -0.89 (0.33), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.006 0.001 HIS B 54 PHE 0.016 0.001 PHE D 212 TYR 0.010 0.001 TYR D 381 ARG 0.008 0.000 ARG D 307 Details of bonding type rmsd hydrogen bonds : bond 0.03789 ( 398) hydrogen bonds : angle 4.57119 ( 1101) SS BOND : bond 0.00756 ( 3) SS BOND : angle 1.00971 ( 6) covalent geometry : bond 0.00284 ( 7768) covalent geometry : angle 0.54111 (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 154 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 1.109 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: 0.8808 (ppp) cc_final: 0.8228 (ppp) REVERT: D 220 HIS cc_start: 0.7940 (t70) cc_final: 0.7127 (t70) REVERT: D 348 TYR cc_start: 0.7933 (m-80) cc_final: 0.7582 (m-80) REVERT: E 73 ASP cc_start: 0.9025 (t70) cc_final: 0.8792 (t70) outliers start: 16 outliers final: 15 residues processed: 149 average time/residue: 0.3458 time to fit residues: 71.9774 Evaluate side-chains 153 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 TRP Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 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 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: 4.9990 chunk 28 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 34 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 220 HIS ** 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 = 0.3826 r_free = 0.3826 target = 0.103877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.092595 restraints weight = 75618.259| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 4.28 r_work: 0.3531 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7771 Z= 0.197 Angle : 0.580 13.968 10598 Z= 0.319 Chirality : 0.040 0.180 1237 Planarity : 0.004 0.044 1350 Dihedral : 7.413 67.879 1116 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.37 % Favored : 93.53 % Rotamer: Outliers : 3.35 % Allowed : 30.56 % Favored : 66.09 % 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: 0.49 (0.28), residues: 1004 helix: 2.30 (0.27), residues: 380 sheet: -0.75 (0.36), residues: 223 loop : -0.95 (0.33), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.013 0.002 HIS D 220 PHE 0.016 0.001 PHE A 62 TYR 0.009 0.001 TYR D 329 ARG 0.009 0.001 ARG D 307 Details of bonding type rmsd hydrogen bonds : bond 0.04008 ( 398) hydrogen bonds : angle 4.75095 ( 1101) SS BOND : bond 0.00974 ( 3) SS BOND : angle 1.13866 ( 6) covalent geometry : bond 0.00419 ( 7768) covalent geometry : angle 0.57947 (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 159 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 1.123 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: D 348 TYR cc_start: 0.8024 (m-80) cc_final: 0.7699 (m-80) outliers start: 25 outliers final: 23 residues processed: 147 average time/residue: 0.3706 time to fit residues: 76.3091 Evaluate side-chains 157 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU 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 79 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 200 VAL 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 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 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: 0.9980 chunk 4 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 27 optimal weight: 9.9990 chunk 30 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 220 HIS ** 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 = 0.3830 r_free = 0.3830 target = 0.104251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.092535 restraints weight = 75983.708| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 4.31 r_work: 0.3536 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2150 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= 0.156 Angle : 0.560 14.005 10598 Z= 0.306 Chirality : 0.040 0.175 1237 Planarity : 0.004 0.036 1350 Dihedral : 7.348 67.234 1116 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.08 % Favored : 93.82 % Rotamer: Outliers : 3.49 % Allowed : 30.16 % Favored : 66.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.55 (0.28), residues: 1004 helix: 2.35 (0.27), residues: 380 sheet: -0.68 (0.36), residues: 217 loop : -0.95 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 339 HIS 0.005 0.001 HIS B 54 PHE 0.017 0.001 PHE A 62 TYR 0.007 0.001 TYR C 40 ARG 0.003 0.000 ARG D 307 Details of bonding type rmsd hydrogen bonds : bond 0.03938 ( 398) hydrogen bonds : angle 4.66860 ( 1101) SS BOND : bond 0.00859 ( 3) SS BOND : angle 1.06710 ( 6) covalent geometry : bond 0.00336 ( 7768) covalent geometry : angle 0.55914 (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 161 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 1.084 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: 0.7536 (OUTLIER) cc_final: 0.5764 (t80) outliers start: 26 outliers final: 23 residues processed: 148 average time/residue: 0.3471 time to fit residues: 71.5002 Evaluate side-chains 156 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 29 TRP Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain 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 200 VAL 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 339 TRP Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 218 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 39 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 220 HIS ** 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 = 0.3841 r_free = 0.3841 target = 0.104830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.093593 restraints weight = 75663.290| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 4.30 r_work: 0.3548 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7771 Z= 0.119 Angle : 0.551 14.121 10598 Z= 0.297 Chirality : 0.040 0.180 1237 Planarity : 0.003 0.039 1350 Dihedral : 7.253 67.524 1116 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.28 % Favored : 94.62 % Rotamer: Outliers : 2.68 % Allowed : 31.10 % 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: 0.70 (0.29), residues: 1004 helix: 2.50 (0.27), residues: 380 sheet: -0.65 (0.36), residues: 221 loop : -0.86 (0.33), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.005 0.001 HIS B 54 PHE 0.017 0.001 PHE A 62 TYR 0.008 0.001 TYR C 40 ARG 0.005 0.000 ARG D 307 Details of bonding type rmsd hydrogen bonds : bond 0.03796 ( 398) hydrogen bonds : angle 4.53397 ( 1101) SS BOND : bond 0.00709 ( 3) SS BOND : angle 0.96109 ( 6) covalent geometry : bond 0.00261 ( 7768) covalent geometry : angle 0.55048 (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: 20 poor density : 137 time to evaluate : 1.093 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: 0.7508 (OUTLIER) cc_final: 0.5723 (t80) REVERT: E 73 ASP cc_start: 0.9023 (t70) cc_final: 0.8799 (t70) outliers start: 20 outliers final: 18 residues processed: 149 average time/residue: 0.3506 time to fit residues: 73.5865 Evaluate side-chains 154 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 29 TRP Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 32 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 94 optimal weight: 0.0870 chunk 86 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.105038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.093804 restraints weight = 75403.644| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 4.30 r_work: 0.3551 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7771 Z= 0.118 Angle : 0.550 14.173 10598 Z= 0.296 Chirality : 0.040 0.174 1237 Planarity : 0.003 0.039 1350 Dihedral : 7.207 67.857 1116 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.68 % Favored : 94.22 % Rotamer: Outliers : 2.82 % Allowed : 30.97 % 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: 0.75 (0.29), residues: 1004 helix: 2.55 (0.27), residues: 379 sheet: -0.64 (0.36), residues: 221 loop : -0.81 (0.34), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 339 HIS 0.005 0.001 HIS B 54 PHE 0.016 0.001 PHE A 62 TYR 0.008 0.001 TYR C 40 ARG 0.005 0.000 ARG D 307 Details of bonding type rmsd hydrogen bonds : bond 0.03697 ( 398) hydrogen bonds : angle 4.50782 ( 1101) SS BOND : bond 0.00704 ( 3) SS BOND : angle 0.94707 ( 6) covalent geometry : bond 0.00261 ( 7768) covalent geometry : angle 0.54938 (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 158 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 1.105 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: 0.7524 (OUTLIER) cc_final: 0.5717 (t80) REVERT: B 325 MET cc_start: 0.7863 (tpp) cc_final: 0.7599 (tpp) REVERT: E 73 ASP cc_start: 0.9007 (t70) cc_final: 0.8781 (t70) outliers start: 21 outliers final: 20 residues processed: 151 average time/residue: 0.3697 time to fit residues: 77.6364 Evaluate side-chains 156 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 29 TRP Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 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 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 18 optimal weight: 6.9990 chunk 77 optimal weight: 0.0000 chunk 50 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.105232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.093983 restraints weight = 75664.357| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 4.31 r_work: 0.3552 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7771 Z= 0.118 Angle : 0.555 14.219 10598 Z= 0.298 Chirality : 0.040 0.167 1237 Planarity : 0.003 0.038 1350 Dihedral : 7.175 68.068 1116 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.08 % Favored : 94.82 % 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: 0.81 (0.29), residues: 1004 helix: 2.57 (0.27), residues: 380 sheet: -0.66 (0.35), residues: 221 loop : -0.73 (0.34), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 339 HIS 0.005 0.001 HIS B 54 PHE 0.016 0.001 PHE A 62 TYR 0.008 0.001 TYR C 40 ARG 0.003 0.000 ARG D 307 Details of bonding type rmsd hydrogen bonds : bond 0.03632 ( 398) hydrogen bonds : angle 4.46837 ( 1101) SS BOND : bond 0.00703 ( 3) SS BOND : angle 0.90014 ( 6) covalent geometry : bond 0.00261 ( 7768) covalent geometry : angle 0.55441 (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 156 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 TYR cc_start: 0.7535 (OUTLIER) cc_final: 0.5692 (t80) REVERT: B 325 MET cc_start: 0.7848 (tpp) cc_final: 0.7550 (tpp) REVERT: E 73 ASP cc_start: 0.9028 (t70) cc_final: 0.8799 (t70) outliers start: 21 outliers final: 20 residues processed: 150 average time/residue: 0.3869 time to fit residues: 81.8256 Evaluate side-chains 155 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 29 TRP Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 176 TYR Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 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 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: 3.9990 chunk 19 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 62 optimal weight: 8.9990 chunk 57 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 56 optimal weight: 0.6980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 220 HIS ** 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 = 0.3823 r_free = 0.3823 target = 0.103771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.092239 restraints weight = 75648.963| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 4.29 r_work: 0.3529 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7771 Z= 0.178 Angle : 0.575 14.166 10598 Z= 0.314 Chirality : 0.040 0.170 1237 Planarity : 0.004 0.037 1350 Dihedral : 7.254 66.923 1116 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.18 % Favored : 93.73 % Rotamer: Outliers : 2.95 % Allowed : 31.64 % Favored : 65.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.28), residues: 1004 helix: 2.38 (0.27), residues: 379 sheet: -0.86 (0.35), residues: 231 loop : -0.82 (0.33), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.006 0.001 HIS B 142 PHE 0.015 0.001 PHE A 62 TYR 0.008 0.001 TYR E 94 ARG 0.004 0.000 ARG D 307 Details of bonding type rmsd hydrogen bonds : bond 0.03893 ( 398) hydrogen bonds : angle 4.63878 ( 1101) SS BOND : bond 0.00892 ( 3) SS BOND : angle 1.03759 ( 6) covalent geometry : bond 0.00383 ( 7768) covalent geometry : angle 0.57460 (10592) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6403.96 seconds wall clock time: 110 minutes 47.44 seconds (6647.44 seconds total)