Starting phenix.real_space_refine on Sun Apr 5 03:49:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ppy_71778/04_2026/9ppy_71778_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ppy_71778/04_2026/9ppy_71778.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ppy_71778/04_2026/9ppy_71778.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ppy_71778/04_2026/9ppy_71778.map" model { file = "/net/cci-nas-00/data/ceres_data/9ppy_71778/04_2026/9ppy_71778_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ppy_71778/04_2026/9ppy_71778_neut.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 5072 2.51 5 N 1335 2.21 5 O 1418 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7879 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 1930 Classifications: {'peptide': 277} Incomplete info: {'truncation_to_alanine': 67} Link IDs: {'PTRANS': 12, 'TRANS': 264} Chain breaks: 2 Unresolved non-hydrogen bonds: 247 Unresolved non-hydrogen angles: 304 Unresolved non-hydrogen dihedrals: 207 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'PHE:plan': 5, 'ASP:plan': 9, 'GLU:plan': 4, 'ARG:plan': 10, 'GLN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 136 Chain: "B" Number of atoms: 1493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1493 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 2, 'TRANS': 196} Chain breaks: 3 Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 10, 'ASP:plan': 6, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 76 Chain: "C" Number of atoms: 2440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2440 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 174 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 5, 'GLN:plan1': 5, 'ARG:plan': 9, 'GLU:plan': 5, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 109 Chain: "D" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 284 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 2, 'TRANS': 41} Chain breaks: 1 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "E" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1692 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ASP:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 54 Chain: "F" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Classifications: {'peptide': 3} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 2} Chain: "F" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 20 Classifications: {'peptide': 2} Modifications used: {'COO': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 1} Time building chain proxies: 1.54, per 1000 atoms: 0.20 Number of scatterers: 7879 At special positions: 0 Unit cell: (84.48, 122.32, 123.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1418 8.00 N 1335 7.00 C 5072 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 198 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " 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 Links applied TRANS " DPN F 4 " - " GLY F 3 " Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 247.9 milliseconds 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTY F 1 " pdb=" CB DPN F 4 " Number of C-beta restraints generated: 2042 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 14 sheets defined 38.1% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 47 through 75 removed outlier: 3.915A pdb=" N ALA A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR A 53 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA A 54 " --> pdb=" O ILE A 50 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 70 " --> pdb=" O GLY A 66 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N MET A 71 " --> pdb=" O ASN A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 100 Processing helix chain 'A' and resid 101 through 112 removed outlier: 3.510A pdb=" N GLN A 105 " --> pdb=" O THR A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 152 removed outlier: 4.064A pdb=" N ALA A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 158 Processing helix chain 'A' and resid 161 through 186 removed outlier: 3.788A pdb=" N VAL A 179 " --> pdb=" O LEU A 175 " (cutoff:3.500A) Proline residue: A 182 - end of helix Processing helix chain 'A' and resid 205 through 222 removed outlier: 3.966A pdb=" N TRP A 209 " --> pdb=" O PRO A 205 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR A 211 " --> pdb=" O TRP A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 244 removed outlier: 3.609A pdb=" N ARG A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER A 242 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 287 Proline residue: A 276 - end of helix Processing helix chain 'A' and resid 293 through 319 removed outlier: 3.963A pdb=" N VAL A 297 " --> pdb=" O ASP A 293 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASN A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N SER A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Proline residue: A 315 - end of helix Processing helix chain 'A' and resid 322 through 327 Processing helix chain 'B' and resid 6 through 32 removed outlier: 3.582A pdb=" N ALA B 11 " --> pdb=" O ALA B 7 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 216 removed outlier: 4.397A pdb=" N ILE B 212 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N HIS B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE B 215 " --> pdb=" O ILE B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 231 removed outlier: 4.115A pdb=" N ASP B 231 " --> pdb=" O SER B 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 228 through 231' Processing helix chain 'B' and resid 241 through 255 Processing helix chain 'B' and resid 256 through 260 removed outlier: 4.110A pdb=" N THR B 260 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 279 removed outlier: 3.586A pdb=" N GLU B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 286 Processing helix chain 'B' and resid 298 through 310 removed outlier: 3.845A pdb=" N LEU B 310 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 351 removed outlier: 3.889A pdb=" N VAL B 335 " --> pdb=" O ASN B 331 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP B 341 " --> pdb=" O ASP B 337 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL B 342 " --> pdb=" O ALA B 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 26 removed outlier: 4.154A pdb=" N GLU C 10 " --> pdb=" O GLN C 6 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA C 11 " --> pdb=" O LEU C 7 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN C 13 " --> pdb=" O GLN C 9 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG C 19 " --> pdb=" O LYS C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'D' and resid 13 through 24 Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.105A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.830A pdb=" N ASP E 90 " --> pdb=" O ARG E 87 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'A' and resid 187 through 192 Processing sheet with id=AA2, first strand: chain 'B' and resid 185 through 190 removed outlier: 3.575A pdb=" N PHE B 189 " --> pdb=" O PHE B 196 " (cutoff:3.500A) removed outlier: 8.991A pdb=" N ALA B 220 " --> pdb=" O GLU B 33 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LYS B 35 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N ILE B 222 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU B 37 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N CYS B 224 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LEU B 39 " --> pdb=" O CYS B 224 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N ALA B 226 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE B 221 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ASN B 269 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL B 225 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.482A pdb=" N THR C 47 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ASN C 340 " --> pdb=" O THR C 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.514A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.849A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 151 removed outlier: 4.116A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 189 through 192 removed outlier: 3.594A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.596A pdb=" N SER C 245 " --> pdb=" O THR C 249 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN C 259 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 276 through 278 removed outlier: 3.735A pdb=" N CYS C 294 " --> pdb=" O LEU C 308 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.740A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.522A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AB5, first strand: chain 'E' and resid 135 through 136 removed outlier: 6.375A pdb=" N VAL E 135 " --> pdb=" O GLU E 234 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) 418 hydrogen bonds defined for protein. 1194 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.24 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1256 1.31 - 1.44: 2222 1.44 - 1.56: 4487 1.56 - 1.69: 0 1.69 - 1.82: 79 Bond restraints: 8044 Sorted by residual: bond pdb=" C GLY F 2 " pdb=" N GLY F 3 " ideal model delta sigma weight residual 1.329 1.456 -0.127 1.40e-02 5.10e+03 8.28e+01 bond pdb=" C DPN F 4 " pdb=" N MET F 5 " ideal model delta sigma weight residual 1.329 1.455 -0.126 1.40e-02 5.10e+03 8.07e+01 bond pdb=" C DTY F 1 " pdb=" N GLY F 2 " ideal model delta sigma weight residual 1.329 1.454 -0.125 1.40e-02 5.10e+03 7.92e+01 bond pdb=" C GLY F 2 " pdb=" O GLY F 2 " ideal model delta sigma weight residual 1.231 1.182 0.049 2.00e-02 2.50e+03 6.03e+00 bond pdb=" C DPN F 4 " pdb=" O DPN F 4 " ideal model delta sigma weight residual 1.231 1.184 0.047 2.00e-02 2.50e+03 5.57e+00 ... (remaining 8039 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 10879 2.09 - 4.19: 79 4.19 - 6.28: 18 6.28 - 8.37: 3 8.37 - 10.46: 2 Bond angle restraints: 10981 Sorted by residual: angle pdb=" CG MET F 5 " pdb=" SD MET F 5 " pdb=" CE MET F 5 " ideal model delta sigma weight residual 100.90 109.20 -8.30 2.20e+00 2.07e-01 1.42e+01 angle pdb=" CA LEU B 353 " pdb=" CB LEU B 353 " pdb=" CG LEU B 353 " ideal model delta sigma weight residual 116.30 126.76 -10.46 3.50e+00 8.16e-02 8.94e+00 angle pdb=" CA LEU B 283 " pdb=" CB LEU B 283 " pdb=" CG LEU B 283 " ideal model delta sigma weight residual 116.30 126.36 -10.06 3.50e+00 8.16e-02 8.27e+00 angle pdb=" CA CYS A 328 " pdb=" CB CYS A 328 " pdb=" SG CYS A 328 " ideal model delta sigma weight residual 114.40 120.29 -5.89 2.30e+00 1.89e-01 6.57e+00 angle pdb=" CA THR C 87 " pdb=" CB THR C 87 " pdb=" CG2 THR C 87 " ideal model delta sigma weight residual 110.50 114.46 -3.96 1.70e+00 3.46e-01 5.42e+00 ... (remaining 10976 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 4087 17.89 - 35.79: 436 35.79 - 53.68: 105 53.68 - 71.58: 27 71.58 - 89.47: 6 Dihedral angle restraints: 4661 sinusoidal: 1499 harmonic: 3162 Sorted by residual: dihedral pdb=" CB CYS E 147 " pdb=" SG CYS E 147 " pdb=" SG CYS E 217 " pdb=" CB CYS E 217 " ideal model delta sinusoidal sigma weight residual 93.00 168.56 -75.56 1 1.00e+01 1.00e-02 7.21e+01 dihedral pdb=" CA PHE C 151 " pdb=" C PHE C 151 " pdb=" N LEU C 152 " pdb=" CA LEU C 152 " ideal model delta harmonic sigma weight residual 180.00 162.81 17.19 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CB GLU E 222 " pdb=" CG GLU E 222 " pdb=" CD GLU E 222 " pdb=" OE1 GLU E 222 " ideal model delta sinusoidal sigma weight residual 0.00 -89.47 89.47 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 4658 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 820 0.031 - 0.063: 334 0.063 - 0.094: 81 0.094 - 0.125: 72 0.125 - 0.157: 5 Chirality restraints: 1312 Sorted by residual: chirality pdb=" CB VAL A 272 " pdb=" CA VAL A 272 " pdb=" CG1 VAL A 272 " pdb=" CG2 VAL A 272 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.12e-01 chirality pdb=" CA DPN F 4 " pdb=" N DPN F 4 " pdb=" C DPN F 4 " pdb=" CB DPN F 4 " both_signs ideal model delta sigma weight residual False -2.51 -2.36 -0.15 2.00e-01 2.50e+01 5.32e-01 chirality pdb=" CA ILE E 177 " pdb=" N ILE E 177 " pdb=" C ILE E 177 " pdb=" CB ILE E 177 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 1309 not shown) Planarity restraints: 1383 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 161 " -0.034 5.00e-02 4.00e+02 5.18e-02 4.29e+00 pdb=" N PRO A 162 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 162 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 162 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR C 87 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.12e+00 pdb=" C THR C 87 " 0.035 2.00e-02 2.50e+03 pdb=" O THR C 87 " -0.013 2.00e-02 2.50e+03 pdb=" N ASN C 88 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE C 235 " -0.028 5.00e-02 4.00e+02 4.30e-02 2.96e+00 pdb=" N PRO C 236 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " -0.024 5.00e-02 4.00e+02 ... (remaining 1380 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1044 2.76 - 3.29: 7268 3.29 - 3.83: 13448 3.83 - 4.36: 15332 4.36 - 4.90: 27734 Nonbonded interactions: 64826 Sorted by model distance: nonbonded pdb=" OG SER C 245 " pdb=" OD1 ASP C 247 " model vdw 2.219 3.040 nonbonded pdb=" O SER E 106 " pdb=" OG SER E 106 " model vdw 2.297 3.040 nonbonded pdb=" ND2 ASN C 230 " pdb=" OD1 ASP C 246 " model vdw 2.312 3.120 nonbonded pdb=" OG1 THR C 274 " pdb=" O VAL C 315 " model vdw 2.315 3.040 nonbonded pdb=" O ILE C 58 " pdb=" OG SER C 316 " model vdw 2.328 3.040 ... (remaining 64821 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: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 7.990 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3484 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.127 8047 Z= 0.241 Angle : 0.543 10.463 10988 Z= 0.279 Chirality : 0.042 0.157 1312 Planarity : 0.004 0.052 1382 Dihedral : 16.491 89.469 2610 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.82 % Allowed : 30.70 % Favored : 68.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.26), residues: 1064 helix: 0.19 (0.25), residues: 372 sheet: 0.63 (0.34), residues: 273 loop : -0.64 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 219 TYR 0.018 0.001 TYR E 178 PHE 0.014 0.001 PHE E 68 TRP 0.010 0.001 TRP C 211 HIS 0.004 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 8044) covalent geometry : angle 0.54161 (10981) SS BOND : bond 0.00129 ( 2) SS BOND : angle 1.36250 ( 4) hydrogen bonds : bond 0.21294 ( 418) hydrogen bonds : angle 7.36163 ( 1194) link_TRANS : bond 0.12574 ( 1) link_TRANS : angle 2.17648 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 109 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 113 average time/residue: 0.0730 time to fit residues: 12.0079 Evaluate side-chains 92 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 0.0670 chunk 97 optimal weight: 0.0470 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.0370 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.1980 overall best weight: 0.1894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 HIS ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.131355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.115456 restraints weight = 11975.328| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.67 r_work: 0.3337 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4306 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 8047 Z= 0.132 Angle : 0.536 9.801 10988 Z= 0.284 Chirality : 0.041 0.150 1312 Planarity : 0.004 0.047 1382 Dihedral : 4.402 42.071 1157 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.09 % Allowed : 26.19 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.26), residues: 1064 helix: 1.40 (0.26), residues: 378 sheet: 0.79 (0.32), residues: 264 loop : -0.70 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 18 TYR 0.015 0.001 TYR E 178 PHE 0.013 0.001 PHE E 68 TRP 0.019 0.002 TRP C 339 HIS 0.004 0.001 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 8044) covalent geometry : angle 0.53485 (10981) SS BOND : bond 0.00436 ( 2) SS BOND : angle 2.00585 ( 4) hydrogen bonds : bond 0.04092 ( 418) hydrogen bonds : angle 4.89562 ( 1194) link_TRANS : bond 0.00194 ( 1) link_TRANS : angle 0.96826 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 0.251 Fit side-chains REVERT: B 249 LEU cc_start: 0.6273 (OUTLIER) cc_final: 0.5962 (tt) outliers start: 30 outliers final: 3 residues processed: 127 average time/residue: 0.0657 time to fit residues: 12.1264 Evaluate side-chains 99 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 95 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 234 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 13 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 54 optimal weight: 0.0170 chunk 69 optimal weight: 0.0970 chunk 22 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 73 optimal weight: 0.3980 chunk 78 optimal weight: 2.9990 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 152 HIS B 322 HIS B 331 ASN ** C 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.144782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.129209 restraints weight = 12375.160| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.75 r_work: 0.3508 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6531 moved from start: 0.7405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.147 8047 Z= 0.223 Angle : 0.784 13.372 10988 Z= 0.407 Chirality : 0.048 0.261 1312 Planarity : 0.005 0.049 1382 Dihedral : 5.145 33.984 1157 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 6.14 % Allowed : 25.92 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.26), residues: 1064 helix: 1.27 (0.27), residues: 375 sheet: 0.28 (0.29), residues: 287 loop : -0.75 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 68 TYR 0.023 0.003 TYR C 85 PHE 0.039 0.004 PHE D 61 TRP 0.021 0.003 TRP C 339 HIS 0.008 0.002 HIS A 152 Details of bonding type rmsd covalent geometry : bond 0.00492 ( 8044) covalent geometry : angle 0.78285 (10981) SS BOND : bond 0.03328 ( 2) SS BOND : angle 2.08487 ( 4) hydrogen bonds : bond 0.04937 ( 418) hydrogen bonds : angle 5.04864 ( 1194) link_TRANS : bond 0.00101 ( 1) link_TRANS : angle 1.53882 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 172 time to evaluate : 0.291 Fit side-chains REVERT: A 102 LEU cc_start: 0.6226 (OUTLIER) cc_final: 0.5899 (mt) REVERT: B 189 PHE cc_start: 0.7953 (p90) cc_final: 0.7752 (p90) REVERT: B 340 THR cc_start: 0.6828 (m) cc_final: 0.6533 (m) REVERT: C 76 ASP cc_start: 0.7375 (p0) cc_final: 0.6637 (p0) REVERT: C 228 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.7240 (p0) REVERT: C 234 PHE cc_start: 0.8049 (OUTLIER) cc_final: 0.7827 (t80) REVERT: C 290 ASP cc_start: 0.6792 (OUTLIER) cc_final: 0.6516 (m-30) REVERT: C 292 PHE cc_start: 0.7521 (m-10) cc_final: 0.7148 (m-10) REVERT: C 313 ASN cc_start: 0.8335 (t0) cc_final: 0.7630 (t0) REVERT: C 338 ILE cc_start: 0.7597 (OUTLIER) cc_final: 0.7394 (mt) REVERT: E 60 TYR cc_start: 0.7828 (m-80) cc_final: 0.7619 (m-80) outliers start: 45 outliers final: 12 residues processed: 198 average time/residue: 0.0828 time to fit residues: 22.5075 Evaluate side-chains 160 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 204 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 40 optimal weight: 0.0020 chunk 23 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 78 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 99 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN A 131 ASN B 213 HIS B 269 ASN C 88 ASN D 18 GLN D 44 HIS E 159 ASN E 167 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.132280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.114752 restraints weight = 11889.235| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.74 r_work: 0.3336 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 1.0380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8047 Z= 0.184 Angle : 0.693 8.276 10988 Z= 0.358 Chirality : 0.047 0.177 1312 Planarity : 0.005 0.052 1382 Dihedral : 4.690 39.708 1156 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.14 % Allowed : 23.87 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.26), residues: 1064 helix: 1.74 (0.27), residues: 375 sheet: 0.36 (0.30), residues: 293 loop : -0.54 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 219 TYR 0.024 0.002 TYR C 85 PHE 0.026 0.002 PHE C 241 TRP 0.017 0.002 TRP C 169 HIS 0.006 0.002 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 8044) covalent geometry : angle 0.68991 (10981) SS BOND : bond 0.00861 ( 2) SS BOND : angle 3.58043 ( 4) hydrogen bonds : bond 0.04144 ( 418) hydrogen bonds : angle 4.82910 ( 1194) link_TRANS : bond 0.00192 ( 1) link_TRANS : angle 0.79364 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 190 time to evaluate : 0.251 Fit side-chains REVERT: A 184 MET cc_start: 0.4822 (tpt) cc_final: 0.4314 (tpt) REVERT: C 49 ARG cc_start: 0.8335 (tpp-160) cc_final: 0.8000 (mpt180) REVERT: C 52 ARG cc_start: 0.7950 (ptp90) cc_final: 0.7563 (mtt-85) REVERT: C 65 THR cc_start: 0.8210 (m) cc_final: 0.7970 (m) REVERT: E 130 GLN cc_start: 0.7960 (mt0) cc_final: 0.7661 (mt0) outliers start: 23 outliers final: 9 residues processed: 207 average time/residue: 0.0785 time to fit residues: 22.4843 Evaluate side-chains 185 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 176 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 204 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 1.9990 chunk 63 optimal weight: 0.0980 chunk 9 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 94 optimal weight: 0.3980 chunk 3 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 82 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN B 269 ASN C 110 ASN C 125 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.127482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.109725 restraints weight = 11816.663| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.76 r_work: 0.3259 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 1.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8047 Z= 0.141 Angle : 0.577 10.025 10988 Z= 0.295 Chirality : 0.043 0.142 1312 Planarity : 0.004 0.050 1382 Dihedral : 4.363 42.483 1156 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.86 % Allowed : 24.97 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.26), residues: 1064 helix: 2.13 (0.28), residues: 371 sheet: 0.43 (0.30), residues: 275 loop : -0.57 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 219 TYR 0.020 0.001 TYR E 178 PHE 0.015 0.002 PHE B 191 TRP 0.019 0.002 TRP B 211 HIS 0.008 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8044) covalent geometry : angle 0.57665 (10981) SS BOND : bond 0.00244 ( 2) SS BOND : angle 0.54490 ( 4) hydrogen bonds : bond 0.03665 ( 418) hydrogen bonds : angle 4.39727 ( 1194) link_TRANS : bond 0.00193 ( 1) link_TRANS : angle 0.89684 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 195 time to evaluate : 0.270 Fit side-chains REVERT: B 247 MET cc_start: 0.8255 (ttm) cc_final: 0.7880 (ttm) REVERT: C 49 ARG cc_start: 0.8476 (tpp-160) cc_final: 0.8114 (mmt-90) REVERT: E 71 SER cc_start: 0.8400 (m) cc_final: 0.8097 (p) REVERT: E 95 TYR cc_start: 0.8526 (m-80) cc_final: 0.7881 (m-80) outliers start: 21 outliers final: 12 residues processed: 206 average time/residue: 0.0831 time to fit residues: 23.3852 Evaluate side-chains 197 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 185 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 187 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 66 optimal weight: 0.0470 chunk 85 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 GLN E 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.121270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.103760 restraints weight = 11719.252| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.75 r_work: 0.3162 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 1.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8047 Z= 0.171 Angle : 0.591 7.996 10988 Z= 0.308 Chirality : 0.044 0.221 1312 Planarity : 0.004 0.052 1382 Dihedral : 4.468 45.498 1156 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.68 % Allowed : 24.42 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.26), residues: 1064 helix: 2.09 (0.28), residues: 377 sheet: 0.35 (0.29), residues: 290 loop : -0.38 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 219 TYR 0.025 0.002 TYR E 178 PHE 0.015 0.002 PHE C 151 TRP 0.018 0.002 TRP C 169 HIS 0.004 0.001 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 8044) covalent geometry : angle 0.59045 (10981) SS BOND : bond 0.00094 ( 2) SS BOND : angle 0.48735 ( 4) hydrogen bonds : bond 0.03917 ( 418) hydrogen bonds : angle 4.47169 ( 1194) link_TRANS : bond 0.00156 ( 1) link_TRANS : angle 0.89527 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 206 time to evaluate : 0.311 Fit side-chains REVERT: A 264 LEU cc_start: 0.8667 (mt) cc_final: 0.8340 (mt) REVERT: A 317 LEU cc_start: 0.7758 (mt) cc_final: 0.7554 (mt) REVERT: B 314 LYS cc_start: 0.8375 (ptpp) cc_final: 0.8137 (ptpp) REVERT: C 48 ARG cc_start: 0.8380 (mmt180) cc_final: 0.8179 (mmt-90) REVERT: C 234 PHE cc_start: 0.8946 (OUTLIER) cc_final: 0.8638 (m-80) REVERT: C 258 ASP cc_start: 0.7670 (t0) cc_final: 0.7129 (t0) REVERT: C 304 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7638 (ttm-80) REVERT: E 71 SER cc_start: 0.8515 (OUTLIER) cc_final: 0.8240 (p) REVERT: E 95 TYR cc_start: 0.8555 (m-80) cc_final: 0.7797 (m-80) outliers start: 27 outliers final: 19 residues processed: 216 average time/residue: 0.0850 time to fit residues: 25.1857 Evaluate side-chains 225 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 203 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 304 ARG Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 207 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 74 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 45 optimal weight: 0.0370 chunk 99 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 50 optimal weight: 2.9990 overall best weight: 0.8862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 GLN B 333 GLN C 176 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.115672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.099046 restraints weight = 11829.053| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.71 r_work: 0.3111 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 1.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 8047 Z= 0.206 Angle : 0.603 8.737 10988 Z= 0.316 Chirality : 0.045 0.203 1312 Planarity : 0.004 0.052 1382 Dihedral : 4.573 50.056 1156 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 4.23 % Allowed : 24.28 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.26), residues: 1064 helix: 1.95 (0.27), residues: 373 sheet: 0.32 (0.30), residues: 284 loop : -0.52 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 304 TYR 0.027 0.002 TYR E 178 PHE 0.016 0.002 PHE C 151 TRP 0.014 0.002 TRP C 169 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00490 ( 8044) covalent geometry : angle 0.60242 (10981) SS BOND : bond 0.00360 ( 2) SS BOND : angle 0.56648 ( 4) hydrogen bonds : bond 0.04208 ( 418) hydrogen bonds : angle 4.56212 ( 1194) link_TRANS : bond 0.00029 ( 1) link_TRANS : angle 0.92990 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 203 time to evaluate : 0.296 Fit side-chains REVERT: A 136 ILE cc_start: 0.8151 (mm) cc_final: 0.7788 (mt) REVERT: A 230 THR cc_start: 0.8476 (m) cc_final: 0.8083 (m) REVERT: A 264 LEU cc_start: 0.8402 (mt) cc_final: 0.8166 (mt) REVERT: A 280 PHE cc_start: 0.8621 (t80) cc_final: 0.8393 (t80) REVERT: A 317 LEU cc_start: 0.7942 (mt) cc_final: 0.7727 (mt) REVERT: B 209 LYS cc_start: 0.8347 (ptmt) cc_final: 0.8098 (ptmt) REVERT: B 314 LYS cc_start: 0.8463 (ptpp) cc_final: 0.8166 (ptpp) REVERT: B 339 VAL cc_start: 0.8188 (p) cc_final: 0.7931 (m) REVERT: C 219 ARG cc_start: 0.8179 (mtt-85) cc_final: 0.7895 (mtt-85) REVERT: C 258 ASP cc_start: 0.7804 (t0) cc_final: 0.7290 (t0) REVERT: C 262 MET cc_start: 0.8442 (tpp) cc_final: 0.7986 (tpp) REVERT: D 38 MET cc_start: 0.7936 (ttp) cc_final: 0.7676 (ttm) REVERT: E 95 TYR cc_start: 0.8557 (m-80) cc_final: 0.7756 (m-80) outliers start: 31 outliers final: 23 residues processed: 216 average time/residue: 0.0876 time to fit residues: 25.6719 Evaluate side-chains 217 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 194 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain F residue 5 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 74 optimal weight: 0.5980 chunk 83 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 0.0770 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN C 295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.117843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.101324 restraints weight = 11718.674| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.71 r_work: 0.3109 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 1.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8047 Z= 0.153 Angle : 0.557 8.826 10988 Z= 0.288 Chirality : 0.043 0.180 1312 Planarity : 0.004 0.052 1382 Dihedral : 4.407 50.633 1156 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.55 % Allowed : 26.19 % Favored : 70.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.26), residues: 1064 helix: 2.02 (0.28), residues: 376 sheet: 0.41 (0.30), residues: 283 loop : -0.58 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 219 TYR 0.020 0.001 TYR E 178 PHE 0.016 0.002 PHE C 151 TRP 0.016 0.002 TRP C 169 HIS 0.003 0.001 HIS C 62 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 8044) covalent geometry : angle 0.55703 (10981) SS BOND : bond 0.00125 ( 2) SS BOND : angle 0.48600 ( 4) hydrogen bonds : bond 0.03682 ( 418) hydrogen bonds : angle 4.46039 ( 1194) link_TRANS : bond 0.00125 ( 1) link_TRANS : angle 0.89492 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 187 time to evaluate : 0.313 Fit side-chains REVERT: A 230 THR cc_start: 0.8466 (OUTLIER) cc_final: 0.8179 (m) REVERT: A 264 LEU cc_start: 0.8441 (mt) cc_final: 0.8212 (mt) REVERT: A 280 PHE cc_start: 0.8550 (t80) cc_final: 0.8291 (t80) REVERT: B 209 LYS cc_start: 0.8303 (ptmt) cc_final: 0.8085 (ptmt) REVERT: B 314 LYS cc_start: 0.8460 (ptpp) cc_final: 0.8149 (ptpp) REVERT: C 219 ARG cc_start: 0.8167 (mtt-85) cc_final: 0.7893 (mtt-85) REVERT: C 234 PHE cc_start: 0.8940 (OUTLIER) cc_final: 0.8576 (m-80) REVERT: C 258 ASP cc_start: 0.7796 (t0) cc_final: 0.7271 (t0) REVERT: D 38 MET cc_start: 0.7858 (ttp) cc_final: 0.7607 (ttm) REVERT: E 95 TYR cc_start: 0.8555 (m-80) cc_final: 0.7729 (m-80) outliers start: 26 outliers final: 22 residues processed: 195 average time/residue: 0.0953 time to fit residues: 24.6493 Evaluate side-chains 207 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain F residue 5 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 83 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 96 optimal weight: 0.0070 chunk 12 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 ASN ** B 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.115940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.099762 restraints weight = 11623.189| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.67 r_work: 0.3096 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 1.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8047 Z= 0.163 Angle : 0.569 9.485 10988 Z= 0.293 Chirality : 0.044 0.184 1312 Planarity : 0.004 0.052 1382 Dihedral : 4.450 52.044 1156 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.41 % Allowed : 26.60 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.26), residues: 1064 helix: 1.99 (0.28), residues: 376 sheet: 0.42 (0.30), residues: 283 loop : -0.66 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 304 TYR 0.025 0.002 TYR E 178 PHE 0.024 0.002 PHE A 104 TRP 0.015 0.002 TRP C 169 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 8044) covalent geometry : angle 0.56835 (10981) SS BOND : bond 0.00158 ( 2) SS BOND : angle 0.54158 ( 4) hydrogen bonds : bond 0.03767 ( 418) hydrogen bonds : angle 4.46234 ( 1194) link_TRANS : bond 0.00132 ( 1) link_TRANS : angle 0.99727 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 188 time to evaluate : 0.275 Fit side-chains REVERT: A 116 PHE cc_start: 0.7388 (m-10) cc_final: 0.7175 (m-80) REVERT: A 184 MET cc_start: 0.6813 (tpt) cc_final: 0.6560 (tpt) REVERT: A 230 THR cc_start: 0.8457 (m) cc_final: 0.8165 (m) REVERT: A 264 LEU cc_start: 0.8343 (mt) cc_final: 0.8115 (mt) REVERT: A 280 PHE cc_start: 0.8556 (t80) cc_final: 0.8234 (t80) REVERT: B 209 LYS cc_start: 0.8286 (ptmt) cc_final: 0.8068 (ptmt) REVERT: B 247 MET cc_start: 0.8613 (ttm) cc_final: 0.8300 (mtt) REVERT: B 314 LYS cc_start: 0.8478 (ptpp) cc_final: 0.8149 (ptpp) REVERT: C 219 ARG cc_start: 0.8164 (mtt-85) cc_final: 0.7903 (mtt-85) REVERT: C 258 ASP cc_start: 0.7815 (t0) cc_final: 0.7294 (t0) REVERT: D 38 MET cc_start: 0.7888 (ttp) cc_final: 0.7639 (ttm) REVERT: E 95 TYR cc_start: 0.8568 (m-80) cc_final: 0.7811 (m-80) outliers start: 25 outliers final: 24 residues processed: 196 average time/residue: 0.0911 time to fit residues: 24.0667 Evaluate side-chains 205 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 181 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain F residue 5 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 15 optimal weight: 0.9990 chunk 80 optimal weight: 0.3980 chunk 26 optimal weight: 0.0870 chunk 17 optimal weight: 0.7980 chunk 13 optimal weight: 0.3980 chunk 50 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 96 optimal weight: 0.0050 chunk 102 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.3372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 ASN B 331 ASN C 110 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.116991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.101440 restraints weight = 11910.971| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.67 r_work: 0.3113 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 1.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8047 Z= 0.111 Angle : 0.526 9.536 10988 Z= 0.271 Chirality : 0.042 0.164 1312 Planarity : 0.004 0.051 1382 Dihedral : 4.257 50.741 1156 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.00 % Allowed : 25.78 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.26), residues: 1064 helix: 2.22 (0.28), residues: 371 sheet: 0.51 (0.30), residues: 285 loop : -0.57 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 219 TYR 0.016 0.001 TYR E 178 PHE 0.012 0.001 PHE C 199 TRP 0.015 0.001 TRP C 169 HIS 0.003 0.001 HIS C 183 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 8044) covalent geometry : angle 0.52561 (10981) SS BOND : bond 0.00055 ( 2) SS BOND : angle 0.33833 ( 4) hydrogen bonds : bond 0.03270 ( 418) hydrogen bonds : angle 4.30455 ( 1194) link_TRANS : bond 0.00174 ( 1) link_TRANS : angle 0.93346 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 174 time to evaluate : 0.293 Fit side-chains REVERT: A 184 MET cc_start: 0.6853 (tpt) cc_final: 0.6582 (tpt) REVERT: A 230 THR cc_start: 0.8405 (m) cc_final: 0.8003 (m) REVERT: A 236 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.8067 (ttp) REVERT: A 262 MET cc_start: 0.8048 (tpp) cc_final: 0.7710 (tpp) REVERT: A 264 LEU cc_start: 0.8403 (mt) cc_final: 0.8148 (mt) REVERT: A 280 PHE cc_start: 0.8550 (t80) cc_final: 0.8169 (t80) REVERT: B 247 MET cc_start: 0.8568 (ttm) cc_final: 0.8251 (mtt) REVERT: B 314 LYS cc_start: 0.8513 (ptpp) cc_final: 0.8197 (ptpp) REVERT: C 258 ASP cc_start: 0.7747 (t0) cc_final: 0.7198 (t0) REVERT: D 38 MET cc_start: 0.7802 (ttp) cc_final: 0.7590 (ttm) outliers start: 22 outliers final: 16 residues processed: 183 average time/residue: 0.0941 time to fit residues: 23.0641 Evaluate side-chains 192 residues out of total 930 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 175 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 236 MET Chi-restraints excluded: chain B residue 8 GLU Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 254 CYS Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 339 TRP Chi-restraints excluded: chain D residue 41 CYS Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain F residue 5 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 15 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 94 optimal weight: 0.3980 chunk 66 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 ASN C 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.116027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.099443 restraints weight = 11736.956| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 1.73 r_work: 0.3089 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 1.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8047 Z= 0.156 Angle : 0.568 10.116 10988 Z= 0.292 Chirality : 0.043 0.181 1312 Planarity : 0.004 0.052 1382 Dihedral : 4.386 52.405 1156 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.86 % Allowed : 26.06 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.26), residues: 1064 helix: 2.05 (0.28), residues: 376 sheet: 0.51 (0.30), residues: 283 loop : -0.63 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 48 TYR 0.025 0.001 TYR E 178 PHE 0.016 0.002 PHE E 80 TRP 0.015 0.002 TRP C 169 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 8044) covalent geometry : angle 0.56770 (10981) SS BOND : bond 0.00167 ( 2) SS BOND : angle 0.49884 ( 4) hydrogen bonds : bond 0.03682 ( 418) hydrogen bonds : angle 4.36341 ( 1194) link_TRANS : bond 0.00129 ( 1) link_TRANS : angle 1.00247 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2194.70 seconds wall clock time: 38 minutes 18.80 seconds (2298.80 seconds total)