Starting phenix.real_space_refine on Fri Oct 23 15:35:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xh2_66864/10_2026/9xh2_66864.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xh2_66864/10_2026/9xh2_66864.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9xh2_66864/10_2026/9xh2_66864.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xh2_66864/10_2026/9xh2_66864.map" model { file = "/net/cci-nas-00/data/ceres_data/9xh2_66864/10_2026/9xh2_66864.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xh2_66864/10_2026/9xh2_66864.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.026 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 P 2 5.49 5 S 68 5.16 5 C 6487 2.51 5 N 1726 2.21 5 O 1878 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10161 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2892 Classifications: {'peptide': 352} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 340} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2595 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 427 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1767 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2365 Classifications: {'peptide': 290} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 279} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 59 Classifications: {'peptide': 7} Link IDs: {'PTRANS': 1, 'TRANS': 5} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.26, per 1000 atoms: 0.22 Number of scatterers: 10161 At special positions: 0 Unit cell: (102.818, 124.196, 135.394, 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 68 16.00 P 2 15.00 O 1878 8.00 N 1726 7.00 C 6487 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " distance=2.04 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 263 " distance=2.03 Simple disulfide: pdb=" SG CYS R 104 " - pdb=" SG CYS R 173 " 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: 0.96 Conformation dependent library (CDL) restraints added in 405.0 milliseconds 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2414 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 14 sheets defined 42.4% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 5 through 36 removed outlier: 3.846A pdb=" N ALA A 10 " --> pdb=" O ALA A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 63 Processing helix chain 'A' and resid 68 through 73 Processing helix chain 'A' and resid 75 through 97 removed outlier: 3.879A pdb=" N ASP A 95 " --> pdb=" O ILE A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 115 removed outlier: 3.845A pdb=" N ALA A 108 " --> pdb=" O GLU A 104 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU A 115 " --> pdb=" O GLN A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 121 Processing helix chain 'A' and resid 125 through 138 Processing helix chain 'A' and resid 138 through 147 Processing helix chain 'A' and resid 148 through 151 removed outlier: 3.501A pdb=" N TYR A 151 " --> pdb=" O ARG A 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 148 through 151' Processing helix chain 'A' and resid 156 through 162 Processing helix chain 'A' and resid 163 through 169 removed outlier: 3.571A pdb=" N VAL A 167 " --> pdb=" O ASP A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 181 Processing helix chain 'A' and resid 212 through 221 removed outlier: 4.631A pdb=" N ILE A 217 " --> pdb=" O ARG A 214 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N HIS A 218 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 237 removed outlier: 4.268A pdb=" N ASP A 236 " --> pdb=" O SER A 233 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN A 237 " --> pdb=" O GLU A 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 233 through 237' Processing helix chain 'A' and resid 246 through 261 Processing helix chain 'A' and resid 262 through 265 removed outlier: 3.596A pdb=" N GLN A 265 " --> pdb=" O PRO A 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 262 through 265' Processing helix chain 'A' and resid 275 through 283 Processing helix chain 'A' and resid 287 through 291 Processing helix chain 'A' and resid 301 through 315 removed outlier: 3.505A pdb=" N ALA A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 352 removed outlier: 3.854A pdb=" N ASP A 346 " --> pdb=" O ALA A 342 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR A 347 " --> pdb=" O ALA A 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.502A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 23 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.641A pdb=" N THR D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 60 Proline residue: R 34 - end of helix removed outlier: 3.642A pdb=" N ILE R 49 " --> pdb=" O LEU R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 96 removed outlier: 3.655A pdb=" N VAL R 70 " --> pdb=" O CYS R 66 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU R 86 " --> pdb=" O PHE R 82 " (cutoff:3.500A) Proline residue: R 87 - end of helix Processing helix chain 'R' and resid 100 through 135 Processing helix chain 'R' and resid 140 through 160 Processing helix chain 'R' and resid 161 through 163 No H-bonds generated for 'chain 'R' and resid 161 through 163' Processing helix chain 'R' and resid 182 through 218 removed outlier: 4.304A pdb=" N ILE R 186 " --> pdb=" O VAL R 182 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ILE R 199 " --> pdb=" O GLY R 195 " (cutoff:3.500A) Proline residue: R 200 - end of helix removed outlier: 3.566A pdb=" N SER R 218 " --> pdb=" O ILE R 214 " (cutoff:3.500A) Processing helix chain 'R' and resid 222 through 256 Proline residue: R 243 - end of helix Processing helix chain 'R' and resid 262 through 281 Processing helix chain 'R' and resid 282 through 292 Proline residue: R 288 - end of helix removed outlier: 3.670A pdb=" N TYR R 291 " --> pdb=" O ASN R 287 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL R 292 " --> pdb=" O PRO R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 295 through 310 Processing helix chain 'L' and resid 2 through 6 Processing sheet with id=AA1, first strand: chain 'A' and resid 190 through 196 removed outlier: 9.034A pdb=" N SER A 225 " --> pdb=" O GLU A 39 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LYS A 41 " --> pdb=" O SER A 225 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N MET A 227 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU A 43 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N LEU A 229 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU A 45 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N ALA A 231 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE A 226 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N PHE A 272 " --> pdb=" O ILE A 226 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N PHE A 228 " --> pdb=" O PHE A 272 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ASN A 274 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL A 230 " --> pdb=" O ASN A 274 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.728A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.884A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.927A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.694A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.971A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.698A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.827A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'D' and resid 11 through 12 removed outlier: 5.865A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 11 through 12 removed outlier: 4.200A pdb=" N PHE D 110 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'D' and resid 134 through 136 removed outlier: 6.156A pdb=" N VAL D 135 " --> pdb=" O GLU D 234 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU D 162 " --> pdb=" O TYR D 178 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N TYR D 178 " --> pdb=" O LEU D 162 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N TRP D 164 " --> pdb=" O LEU D 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 134 through 136 removed outlier: 6.156A pdb=" N VAL D 135 " --> pdb=" O GLU D 234 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N THR D 226 " --> pdb=" O GLN D 219 " (cutoff:3.500A) 512 hydrogen bonds defined for protein. 1443 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: 1.49 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3276 1.34 - 1.46: 2562 1.46 - 1.58: 4448 1.58 - 1.70: 3 1.70 - 1.82: 99 Bond restraints: 10388 Sorted by residual: bond pdb=" C ILE R 160 " pdb=" N PRO R 161 " ideal model delta sigma weight residual 1.337 1.353 -0.016 9.80e-03 1.04e+04 2.82e+00 bond pdb=" C5 GDP A 401 " pdb=" C4 GDP A 401 " ideal model delta sigma weight residual 1.490 1.465 0.025 2.00e-02 2.50e+03 1.55e+00 bond pdb=" C GLY D 66 " pdb=" N ARG D 67 " ideal model delta sigma weight residual 1.332 1.316 0.016 1.40e-02 5.10e+03 1.35e+00 bond pdb=" CB ASN R 171 " pdb=" CG ASN R 171 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.23e+00 bond pdb=" C3 CLR R 401 " pdb=" O1 CLR R 401 " ideal model delta sigma weight residual 1.413 1.392 0.021 2.00e-02 2.50e+03 1.12e+00 ... (remaining 10383 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 13837 1.67 - 3.35: 223 3.35 - 5.02: 33 5.02 - 6.70: 7 6.70 - 8.37: 2 Bond angle restraints: 14102 Sorted by residual: angle pdb=" C CYS A 2 " pdb=" N THR A 3 " pdb=" CA THR A 3 " ideal model delta sigma weight residual 122.08 127.09 -5.01 1.47e+00 4.63e-01 1.16e+01 angle pdb=" CA GLU R 124 " pdb=" CB GLU R 124 " pdb=" CG GLU R 124 " ideal model delta sigma weight residual 114.10 120.02 -5.92 2.00e+00 2.50e-01 8.75e+00 angle pdb=" CB MET R 164 " pdb=" CG MET R 164 " pdb=" SD MET R 164 " ideal model delta sigma weight residual 112.70 121.07 -8.37 3.00e+00 1.11e-01 7.79e+00 angle pdb=" CA MET R 164 " pdb=" CB MET R 164 " pdb=" CG MET R 164 " ideal model delta sigma weight residual 114.10 119.61 -5.51 2.00e+00 2.50e-01 7.60e+00 angle pdb=" N ASN R 171 " pdb=" CA ASN R 171 " pdb=" C ASN R 171 " ideal model delta sigma weight residual 113.72 109.96 3.76 1.52e+00 4.33e-01 6.13e+00 ... (remaining 14097 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.61: 5612 20.61 - 41.22: 480 41.22 - 61.83: 111 61.83 - 82.44: 18 82.44 - 103.05: 4 Dihedral angle restraints: 6225 sinusoidal: 2484 harmonic: 3741 Sorted by residual: dihedral pdb=" C5' GDP A 401 " pdb=" O5' GDP A 401 " pdb=" PA GDP A 401 " pdb=" O3A GDP A 401 " ideal model delta sinusoidal sigma weight residual 179.98 76.93 103.05 1 2.00e+01 2.50e-03 2.94e+01 dihedral pdb=" CA GLN B 75 " pdb=" C GLN B 75 " pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta harmonic sigma weight residual 180.00 157.59 22.41 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CG ARG B 19 " pdb=" CD ARG B 19 " pdb=" NE ARG B 19 " pdb=" CZ ARG B 19 " ideal model delta sinusoidal sigma weight residual 90.00 41.12 48.88 2 1.50e+01 4.44e-03 1.21e+01 ... (remaining 6222 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1390 0.064 - 0.128: 196 0.128 - 0.193: 5 0.193 - 0.257: 2 0.257 - 0.321: 1 Chirality restraints: 1594 Sorted by residual: chirality pdb=" C14 CLR R 401 " pdb=" C13 CLR R 401 " pdb=" C15 CLR R 401 " pdb=" C8 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.64 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" C17 CLR R 401 " pdb=" C13 CLR R 401 " pdb=" C16 CLR R 401 " pdb=" C20 CLR R 401 " both_signs ideal model delta sigma weight residual False 2.55 2.78 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" C9 CLR R 401 " pdb=" C10 CLR R 401 " pdb=" C11 CLR R 401 " pdb=" C8 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.45 -2.65 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 1591 not shown) Planarity restraints: 1778 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.031 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO B 236 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 54 " 0.029 5.00e-02 4.00e+02 4.43e-02 3.14e+00 pdb=" N PRO C 55 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 55 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 55 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE R 160 " -0.026 5.00e-02 4.00e+02 3.87e-02 2.40e+00 pdb=" N PRO R 161 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO R 161 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO R 161 " -0.022 5.00e-02 4.00e+02 ... (remaining 1775 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 4820 2.98 - 3.46: 9632 3.46 - 3.94: 16399 3.94 - 4.42: 19402 4.42 - 4.90: 31654 Nonbonded interactions: 81907 Sorted by model distance: nonbonded pdb=" O GLU R 124 " pdb=" OE1 GLU R 124 " model vdw 2.500 3.040 nonbonded pdb=" O3' GDP A 401 " pdb=" O2' GDP A 401 " model vdw 2.505 2.432 nonbonded pdb=" O THR C 52 " pdb=" OG1 THR C 52 " model vdw 2.540 3.040 nonbonded pdb=" C THR D 129 " pdb=" OG1 THR D 129 " model vdw 2.594 2.616 nonbonded pdb=" N TYR D 102 " pdb=" O TYR D 102 " model vdw 2.597 2.496 ... (remaining 81902 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: 2.460 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: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.520 Find NCS groups from input model: 0.060 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:6.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 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 0.038 10392 Z= 0.126 Angle : 0.551 8.372 14110 Z= 0.294 Chirality : 0.043 0.321 1594 Planarity : 0.004 0.047 1778 Dihedral : 16.356 103.047 3799 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.54 % Allowed : 19.35 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.21 (0.24), residues: 1263 helix: 2.51 (0.24), residues: 473 sheet: 0.59 (0.29), residues: 280 loop : -0.75 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 19 TYR 0.011 0.001 TYR D 95 PHE 0.018 0.001 PHE R 111 TRP 0.012 0.001 TRP B 339 HIS 0.003 0.001 HIS R 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.13 (10388) covalent geometry : angle 0.54994 / 0.29 (14102) SS BOND : bond 0.00724 / 0.43 ( 4) SS BOND : angle 1.28181 / 0.64 ( 8) hydrogen bonds : bond 0.14203 / 9.31 ( 505) hydrogen bonds : angle 5.17480 / 3.69 ( 1443) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 145 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 77 LYS cc_start: 0.7343 (ttpp) cc_final: 0.6981 (ttpt) REVERT: A 92 ARG cc_start: 0.7442 (ttp80) cc_final: 0.7064 (ttp80) REVERT: A 152 GLN cc_start: 0.8269 (mt0) cc_final: 0.8010 (mt0) REVERT: A 165 ASP cc_start: 0.7674 (m-30) cc_final: 0.7291 (m-30) REVERT: A 245 GLU cc_start: 0.5988 (OUTLIER) cc_final: 0.5104 (tp30) REVERT: A 247 ARG cc_start: 0.7645 (mtp180) cc_final: 0.7249 (mmt90) REVERT: A 354 LYS cc_start: 0.7679 (mttp) cc_final: 0.6939 (mtmm) REVERT: B 23 LYS cc_start: 0.7558 (tppt) cc_final: 0.7212 (tptp) REVERT: B 146 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8279 (tp) REVERT: B 175 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7377 (mp10) REVERT: B 188 MET cc_start: 0.8782 (mmm) cc_final: 0.8446 (mmm) REVERT: B 234 PHE cc_start: 0.9388 (OUTLIER) cc_final: 0.9012 (m-80) REVERT: C 32 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7518 (ttmt) REVERT: C 47 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7746 (pt0) REVERT: D 87 ARG cc_start: 0.7155 (mtm-85) cc_final: 0.6874 (mtt180) REVERT: D 142 SER cc_start: 0.7619 (m) cc_final: 0.7103 (t) REVERT: R 90 MET cc_start: 0.5712 (mtp) cc_final: 0.5444 (mtp) REVERT: R 244 TYR cc_start: 0.7726 (t80) cc_final: 0.7472 (t80) outliers start: 39 outliers final: 29 residues processed: 172 average time/residue: 0.5963 time to fit residues: 109.7506 Evaluate side-chains 178 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain R residue 23 CYS Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 96 HIS Chi-restraints excluded: chain R residue 136 MET Chi-restraints excluded: chain R residue 178 ASP Chi-restraints excluded: chain R residue 279 LEU Chi-restraints excluded: chain L residue 1 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [108, 49, 97, 113, 53, 5, 33, 123, 65, 62, 51] chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.0470 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 197 GLN A 350 GLN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.182475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.142402 restraints weight = 10606.517| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 1.61 r_work: 0.3472 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.0497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10392 Z= 0.111 Angle : 0.498 6.198 14110 Z= 0.267 Chirality : 0.041 0.154 1594 Planarity : 0.004 0.046 1778 Dihedral : 8.410 102.540 1544 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 4.18 % Allowed : 18.71 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.45 (0.24), residues: 1263 helix: 2.73 (0.24), residues: 477 sheet: 0.80 (0.29), residues: 276 loop : -0.71 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 19 TYR 0.011 0.001 TYR D 178 PHE 0.017 0.001 PHE R 111 TRP 0.012 0.001 TRP B 169 HIS 0.002 0.001 HIS A 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.11 (10388) covalent geometry : angle 0.49709 / 0.27 (14102) SS BOND : bond 0.00624 / 0.37 ( 4) SS BOND : angle 1.24701 / 0.64 ( 8) hydrogen bonds : bond 0.04803 / 3.27 ( 505) hydrogen bonds : angle 4.17894 / 3.03 ( 1443) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 150 time to evaluate : 0.384 Fit side-chains REVERT: A 92 ARG cc_start: 0.7422 (ttp80) cc_final: 0.7138 (ttp80) REVERT: A 152 GLN cc_start: 0.8135 (mt0) cc_final: 0.7886 (mt0) REVERT: A 247 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.7003 (mmm160) REVERT: A 354 LYS cc_start: 0.7875 (mttp) cc_final: 0.7341 (mtmt) REVERT: B 23 LYS cc_start: 0.7768 (tppt) cc_final: 0.7534 (tptp) REVERT: B 175 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.7680 (mp10) REVERT: B 188 MET cc_start: 0.8953 (mmm) cc_final: 0.8632 (mmm) REVERT: B 234 PHE cc_start: 0.9450 (OUTLIER) cc_final: 0.9126 (m-80) REVERT: D 87 ARG cc_start: 0.7484 (mtm-85) cc_final: 0.7227 (mtt180) REVERT: D 142 SER cc_start: 0.7885 (m) cc_final: 0.7461 (t) REVERT: R 90 MET cc_start: 0.5630 (mtp) cc_final: 0.5346 (mtp) REVERT: R 244 TYR cc_start: 0.7404 (t80) cc_final: 0.7179 (t80) outliers start: 46 outliers final: 19 residues processed: 181 average time/residue: 0.6118 time to fit residues: 118.1400 Evaluate side-chains 168 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 183 LEU Chi-restraints excluded: chain R residue 217 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [115, 52, 37, 24, 104, 71, 84, 34, 44, 81, 77] chunk 115 optimal weight: 5.9990 chunk 52 optimal weight: 0.0070 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 104 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 ASN A 197 GLN B 142 HIS ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN D 182 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.181126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.136082 restraints weight = 10638.849| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.59 r_work: 0.3443 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.0608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10392 Z= 0.122 Angle : 0.518 7.133 14110 Z= 0.276 Chirality : 0.042 0.142 1594 Planarity : 0.004 0.047 1778 Dihedral : 7.338 102.651 1503 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 5.18 % Allowed : 18.62 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.45 (0.24), residues: 1263 helix: 2.85 (0.24), residues: 476 sheet: 0.68 (0.29), residues: 281 loop : -0.76 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 19 TYR 0.011 0.001 TYR D 95 PHE 0.017 0.001 PHE R 111 TRP 0.012 0.001 TRP B 339 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (10388) covalent geometry : angle 0.51691 / 0.28 (14102) SS BOND : bond 0.00717 / 0.42 ( 4) SS BOND : angle 1.34576 / 0.66 ( 8) hydrogen bonds : bond 0.04918 / 3.35 ( 505) hydrogen bonds : angle 4.11435 / 3.00 ( 1443) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 147 time to evaluate : 0.321 Fit side-chains REVERT: A 77 LYS cc_start: 0.7187 (ttpp) cc_final: 0.6831 (ttpt) REVERT: A 92 ARG cc_start: 0.7455 (ttp80) cc_final: 0.7190 (ttp80) REVERT: A 97 LEU cc_start: 0.5623 (OUTLIER) cc_final: 0.5314 (pp) REVERT: A 152 GLN cc_start: 0.8205 (mt0) cc_final: 0.7951 (mt0) REVERT: A 245 GLU cc_start: 0.5926 (OUTLIER) cc_final: 0.5099 (tp30) REVERT: A 247 ARG cc_start: 0.7550 (OUTLIER) cc_final: 0.7102 (mmt90) REVERT: A 354 LYS cc_start: 0.7902 (mttp) cc_final: 0.7257 (mtmt) REVERT: B 23 LYS cc_start: 0.7778 (tppt) cc_final: 0.7571 (tptp) REVERT: B 175 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.7728 (mp10) REVERT: B 188 MET cc_start: 0.9040 (mmm) cc_final: 0.8686 (mmm) REVERT: B 195 ASP cc_start: 0.6738 (OUTLIER) cc_final: 0.6280 (p0) REVERT: B 234 PHE cc_start: 0.9453 (OUTLIER) cc_final: 0.9150 (m-80) REVERT: D 142 SER cc_start: 0.7869 (m) cc_final: 0.7435 (t) REVERT: R 90 MET cc_start: 0.5600 (mtp) cc_final: 0.5322 (mtp) REVERT: R 244 TYR cc_start: 0.7420 (t80) cc_final: 0.7182 (t80) outliers start: 57 outliers final: 27 residues processed: 182 average time/residue: 0.5803 time to fit residues: 112.7695 Evaluate side-chains 178 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 136 MET Chi-restraints excluded: chain R residue 178 ASP Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 252 THR Chi-restraints excluded: chain R residue 279 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [40, 28, 122, 23, 82, 19, 123, 83, 109, 53, 24] chunk 40 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 23 optimal weight: 0.1980 chunk 82 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 123 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 109 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 197 GLN A 265 GLN B 142 HIS ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.183669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.139490 restraints weight = 10760.952| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.56 r_work: 0.3476 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.0718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10392 Z= 0.108 Angle : 0.489 6.258 14110 Z= 0.261 Chirality : 0.041 0.141 1594 Planarity : 0.004 0.046 1778 Dihedral : 7.253 102.286 1502 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 5.00 % Allowed : 19.07 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.52 (0.24), residues: 1263 helix: 2.90 (0.24), residues: 477 sheet: 0.78 (0.29), residues: 277 loop : -0.76 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 19 TYR 0.010 0.001 TYR D 95 PHE 0.017 0.001 PHE R 111 TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 (10388) covalent geometry : angle 0.48818 / 0.26 (14102) SS BOND : bond 0.00595 / 0.35 ( 4) SS BOND : angle 1.11021 / 0.55 ( 8) hydrogen bonds : bond 0.04484 / 3.04 ( 505) hydrogen bonds : angle 4.01017 / 2.92 ( 1443) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 147 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 97 LEU cc_start: 0.5654 (OUTLIER) cc_final: 0.5385 (pp) REVERT: A 107 LYS cc_start: 0.7093 (mttp) cc_final: 0.6828 (mmmm) REVERT: A 152 GLN cc_start: 0.8187 (mt0) cc_final: 0.7942 (mt0) REVERT: A 245 GLU cc_start: 0.5904 (OUTLIER) cc_final: 0.5048 (tp30) REVERT: A 247 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.7097 (mmt90) REVERT: A 354 LYS cc_start: 0.7917 (mttp) cc_final: 0.7297 (mtmt) REVERT: B 23 LYS cc_start: 0.7767 (tppt) cc_final: 0.7563 (tptp) REVERT: B 175 GLN cc_start: 0.8547 (OUTLIER) cc_final: 0.7790 (mp10) REVERT: B 188 MET cc_start: 0.8990 (mmm) cc_final: 0.8649 (mmm) REVERT: B 226 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8424 (mm-30) REVERT: B 234 PHE cc_start: 0.9433 (OUTLIER) cc_final: 0.9111 (m-80) REVERT: D 142 SER cc_start: 0.7824 (m) cc_final: 0.7391 (t) REVERT: R 90 MET cc_start: 0.5726 (mtp) cc_final: 0.5429 (mtp) REVERT: R 244 TYR cc_start: 0.7475 (t80) cc_final: 0.7256 (t80) outliers start: 55 outliers final: 29 residues processed: 180 average time/residue: 0.5607 time to fit residues: 108.1532 Evaluate side-chains 180 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 145 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 96 HIS Chi-restraints excluded: chain R residue 136 MET Chi-restraints excluded: chain R residue 178 ASP Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 252 THR Chi-restraints excluded: chain R residue 279 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [22, 83, 67, 106, 100, 75, 109, 30, 77, 24, 120] chunk 22 optimal weight: 4.9990 chunk 83 optimal weight: 0.5980 chunk 67 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 chunk 75 optimal weight: 6.9990 chunk 109 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 77 optimal weight: 0.0170 chunk 24 optimal weight: 0.7980 chunk 120 optimal weight: 9.9990 overall best weight: 1.4820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 142 HIS ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.180666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.136301 restraints weight = 10624.916| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.54 r_work: 0.3436 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.0769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10392 Z= 0.152 Angle : 0.563 8.912 14110 Z= 0.299 Chirality : 0.043 0.143 1594 Planarity : 0.004 0.047 1778 Dihedral : 7.033 102.694 1499 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 5.36 % Allowed : 18.89 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.37 (0.24), residues: 1263 helix: 2.82 (0.24), residues: 476 sheet: 0.64 (0.29), residues: 281 loop : -0.86 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 19 TYR 0.013 0.002 TYR D 103 PHE 0.019 0.002 PHE R 111 TRP 0.015 0.002 TRP B 339 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (10388) covalent geometry : angle 0.56198 / 0.30 (14102) SS BOND : bond 0.00934 / 0.55 ( 4) SS BOND : angle 1.71366 / 0.84 ( 8) hydrogen bonds : bond 0.05406 / 3.68 ( 505) hydrogen bonds : angle 4.18347 / 3.04 ( 1443) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 148 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 97 LEU cc_start: 0.5821 (OUTLIER) cc_final: 0.5496 (pp) REVERT: A 152 GLN cc_start: 0.8203 (mt0) cc_final: 0.7979 (mt0) REVERT: A 245 GLU cc_start: 0.5893 (OUTLIER) cc_final: 0.5035 (tp30) REVERT: A 247 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.7135 (mmm160) REVERT: B 23 LYS cc_start: 0.7837 (tppt) cc_final: 0.7604 (tptp) REVERT: B 175 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.7822 (mp10) REVERT: B 188 MET cc_start: 0.9021 (mmm) cc_final: 0.8683 (mmm) REVERT: B 195 ASP cc_start: 0.6699 (OUTLIER) cc_final: 0.6214 (p0) REVERT: B 226 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8425 (mm-30) REVERT: B 234 PHE cc_start: 0.9449 (OUTLIER) cc_final: 0.9158 (m-80) REVERT: D 19 LYS cc_start: 0.7936 (ttpp) cc_final: 0.7500 (tttt) REVERT: D 142 SER cc_start: 0.7856 (m) cc_final: 0.7409 (t) REVERT: R 90 MET cc_start: 0.5649 (mtp) cc_final: 0.5373 (mtp) outliers start: 59 outliers final: 34 residues processed: 187 average time/residue: 0.5711 time to fit residues: 114.4163 Evaluate side-chains 184 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 143 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 96 HIS Chi-restraints excluded: chain R residue 178 ASP Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 252 THR Chi-restraints excluded: chain R residue 306 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [27, 75, 25, 122, 29, 46, 81, 45, 13, 22, 24] chunk 27 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 142 HIS ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.181173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.136470 restraints weight = 10708.963| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.57 r_work: 0.3447 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.0801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10392 Z= 0.143 Angle : 0.555 8.827 14110 Z= 0.295 Chirality : 0.043 0.142 1594 Planarity : 0.004 0.048 1778 Dihedral : 7.058 102.890 1499 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.72 % Allowed : 20.07 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.35 (0.24), residues: 1263 helix: 2.78 (0.24), residues: 476 sheet: 0.67 (0.29), residues: 281 loop : -0.86 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 19 TYR 0.013 0.001 TYR D 103 PHE 0.019 0.002 PHE R 111 TRP 0.013 0.002 TRP B 339 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (10388) covalent geometry : angle 0.55444 / 0.29 (14102) SS BOND : bond 0.01016 / 0.59 ( 4) SS BOND : angle 1.37326 / 0.62 ( 8) hydrogen bonds : bond 0.05289 / 3.59 ( 505) hydrogen bonds : angle 4.17491 / 3.04 ( 1443) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 143 time to evaluate : 0.309 Fit side-chains REVERT: A 97 LEU cc_start: 0.5711 (OUTLIER) cc_final: 0.5374 (pp) REVERT: A 152 GLN cc_start: 0.8199 (mt0) cc_final: 0.7959 (mt0) REVERT: A 245 GLU cc_start: 0.5843 (OUTLIER) cc_final: 0.4989 (tp30) REVERT: A 247 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.7017 (mmm160) REVERT: A 354 LYS cc_start: 0.7914 (mttp) cc_final: 0.7237 (mtmt) REVERT: B 23 LYS cc_start: 0.7763 (tppt) cc_final: 0.7511 (tptp) REVERT: B 55 LEU cc_start: 0.8008 (mt) cc_final: 0.7801 (mt) REVERT: B 175 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.7741 (mp10) REVERT: B 188 MET cc_start: 0.9011 (mmm) cc_final: 0.8680 (mmm) REVERT: B 195 ASP cc_start: 0.6629 (OUTLIER) cc_final: 0.6158 (p0) REVERT: B 226 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8353 (mm-30) REVERT: B 234 PHE cc_start: 0.9438 (OUTLIER) cc_final: 0.9135 (m-80) REVERT: D 19 LYS cc_start: 0.7989 (ttpp) cc_final: 0.7532 (tttt) REVERT: D 142 SER cc_start: 0.7825 (m) cc_final: 0.7384 (t) REVERT: R 90 MET cc_start: 0.5601 (mtp) cc_final: 0.5326 (mtp) outliers start: 52 outliers final: 34 residues processed: 177 average time/residue: 0.5906 time to fit residues: 111.7014 Evaluate side-chains 184 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 143 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 113 GLN Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain R residue 23 CYS Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 136 MET Chi-restraints excluded: chain R residue 178 ASP Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 252 THR Chi-restraints excluded: chain R residue 306 LEU Chi-restraints excluded: chain L residue 1 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [20, 90, 1, 39, 48, 83, 62, 17, 22, 7, 67] chunk 20 optimal weight: 0.0170 chunk 90 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 39 optimal weight: 0.1980 chunk 48 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 17 optimal weight: 0.4980 chunk 22 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.184844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.141135 restraints weight = 10669.320| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.55 r_work: 0.3491 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.0868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10392 Z= 0.100 Angle : 0.476 6.943 14110 Z= 0.253 Chirality : 0.041 0.142 1594 Planarity : 0.004 0.047 1778 Dihedral : 6.742 101.282 1499 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.18 % Allowed : 20.89 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.58 (0.24), residues: 1263 helix: 2.95 (0.24), residues: 477 sheet: 0.82 (0.29), residues: 278 loop : -0.74 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 19 TYR 0.009 0.001 TYR D 178 PHE 0.017 0.001 PHE R 111 TRP 0.014 0.001 TRP B 169 HIS 0.002 0.001 HIS R 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.10 (10388) covalent geometry : angle 0.47634 / 0.25 (14102) SS BOND : bond 0.00554 / 0.32 ( 4) SS BOND : angle 0.66773 / 0.30 ( 8) hydrogen bonds : bond 0.04112 / 2.79 ( 505) hydrogen bonds : angle 3.92708 / 2.86 ( 1443) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 148 time to evaluate : 0.736 Fit side-chains revert: symmetry clash REVERT: A 77 LYS cc_start: 0.7163 (ttpp) cc_final: 0.6805 (ttpt) REVERT: A 97 LEU cc_start: 0.5522 (OUTLIER) cc_final: 0.5278 (pp) REVERT: A 107 LYS cc_start: 0.7082 (mttp) cc_final: 0.6816 (mmmm) REVERT: A 152 GLN cc_start: 0.8177 (mt0) cc_final: 0.7938 (mt0) REVERT: A 245 GLU cc_start: 0.5797 (OUTLIER) cc_final: 0.4949 (tp30) REVERT: A 247 ARG cc_start: 0.7483 (OUTLIER) cc_final: 0.7095 (mmm-85) REVERT: A 260 THR cc_start: 0.7464 (m) cc_final: 0.7248 (m) REVERT: A 280 GLU cc_start: 0.7501 (mt-10) cc_final: 0.7289 (mt-10) REVERT: A 354 LYS cc_start: 0.7863 (mttp) cc_final: 0.7310 (mtmt) REVERT: B 23 LYS cc_start: 0.7727 (tppt) cc_final: 0.7498 (tptp) REVERT: B 175 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.7810 (mp10) REVERT: B 188 MET cc_start: 0.8983 (mmm) cc_final: 0.8665 (mmm) REVERT: B 195 ASP cc_start: 0.6665 (OUTLIER) cc_final: 0.6208 (p0) REVERT: B 226 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8376 (mm-30) REVERT: B 234 PHE cc_start: 0.9411 (OUTLIER) cc_final: 0.9129 (m-80) REVERT: C 32 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7515 (ttmt) REVERT: D 62 ASP cc_start: 0.8391 (OUTLIER) cc_final: 0.8128 (m-30) REVERT: D 76 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7240 (mttt) REVERT: D 142 SER cc_start: 0.7826 (m) cc_final: 0.7406 (t) REVERT: R 90 MET cc_start: 0.5652 (mtp) cc_final: 0.5373 (mtp) outliers start: 46 outliers final: 21 residues processed: 177 average time/residue: 0.5931 time to fit residues: 112.3227 Evaluate side-chains 176 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain R residue 23 CYS Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 96 HIS Chi-restraints excluded: chain R residue 136 MET Chi-restraints excluded: chain R residue 178 ASP Chi-restraints excluded: chain R residue 252 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [15, 115, 99, 24, 37, 82, 4, 70, 73, 80, 48] chunk 15 optimal weight: 0.0060 chunk 115 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 37 optimal weight: 0.0770 chunk 82 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 overall best weight: 0.7956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 350 GLN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.183551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.139444 restraints weight = 10674.689| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.55 r_work: 0.3473 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.0865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10392 Z= 0.111 Angle : 0.503 6.315 14110 Z= 0.267 Chirality : 0.041 0.140 1594 Planarity : 0.004 0.046 1778 Dihedral : 6.786 100.933 1499 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.18 % Allowed : 21.16 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.58 (0.24), residues: 1263 helix: 2.98 (0.24), residues: 477 sheet: 0.76 (0.29), residues: 280 loop : -0.73 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 19 TYR 0.011 0.001 TYR D 95 PHE 0.017 0.001 PHE R 111 TRP 0.012 0.001 TRP B 339 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (10388) covalent geometry : angle 0.50299 / 0.27 (14102) SS BOND : bond 0.00754 / 0.44 ( 4) SS BOND : angle 1.07712 / 0.48 ( 8) hydrogen bonds : bond 0.04482 / 3.04 ( 505) hydrogen bonds : angle 3.96779 / 2.89 ( 1443) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 145 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 77 LYS cc_start: 0.7149 (ttpp) cc_final: 0.6816 (ttpt) REVERT: A 97 LEU cc_start: 0.5541 (OUTLIER) cc_final: 0.5295 (pp) REVERT: A 107 LYS cc_start: 0.7093 (mttp) cc_final: 0.6828 (mmmm) REVERT: A 152 GLN cc_start: 0.8197 (mt0) cc_final: 0.7957 (mt0) REVERT: A 245 GLU cc_start: 0.5806 (OUTLIER) cc_final: 0.4956 (tp30) REVERT: A 247 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.7139 (mmm-85) REVERT: A 280 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7254 (mt-10) REVERT: A 354 LYS cc_start: 0.7853 (mttp) cc_final: 0.7299 (mtmt) REVERT: B 23 LYS cc_start: 0.7706 (tppt) cc_final: 0.7480 (tptp) REVERT: B 175 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.7822 (mp10) REVERT: B 188 MET cc_start: 0.9002 (mmm) cc_final: 0.8662 (mmm) REVERT: B 195 ASP cc_start: 0.6700 (OUTLIER) cc_final: 0.6244 (p0) REVERT: B 234 PHE cc_start: 0.9422 (OUTLIER) cc_final: 0.9115 (m-80) REVERT: C 32 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7560 (ttmt) REVERT: C 47 GLU cc_start: 0.7828 (pt0) cc_final: 0.7589 (pt0) REVERT: D 62 ASP cc_start: 0.8365 (OUTLIER) cc_final: 0.8120 (m-30) REVERT: D 76 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7235 (mttt) REVERT: D 142 SER cc_start: 0.7830 (m) cc_final: 0.7415 (t) REVERT: R 90 MET cc_start: 0.5643 (mtp) cc_final: 0.5367 (mtp) outliers start: 46 outliers final: 25 residues processed: 173 average time/residue: 0.6087 time to fit residues: 112.5266 Evaluate side-chains 177 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 143 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 32 LYS Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain R residue 23 CYS Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 96 HIS Chi-restraints excluded: chain R residue 136 MET Chi-restraints excluded: chain R residue 178 ASP Chi-restraints excluded: chain R residue 252 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [112, 73, 0, 27, 97, 23, 24, 103, 96, 120, 119] chunk 112 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 120 optimal weight: 5.9990 chunk 119 optimal weight: 0.0270 overall best weight: 1.1644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 350 GLN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.181822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.137674 restraints weight = 10618.370| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.54 r_work: 0.3451 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.0868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10392 Z= 0.132 Angle : 0.540 7.646 14110 Z= 0.285 Chirality : 0.042 0.140 1594 Planarity : 0.004 0.046 1778 Dihedral : 6.927 102.101 1499 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.45 % Allowed : 20.89 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.50 (0.24), residues: 1263 helix: 2.94 (0.24), residues: 476 sheet: 0.70 (0.29), residues: 281 loop : -0.79 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 19 TYR 0.012 0.001 TYR D 95 PHE 0.018 0.001 PHE R 111 TRP 0.014 0.001 TRP B 339 HIS 0.005 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (10388) covalent geometry : angle 0.53884 / 0.28 (14102) SS BOND : bond 0.00917 / 0.54 ( 4) SS BOND : angle 1.32588 / 0.60 ( 8) hydrogen bonds : bond 0.05003 / 3.40 ( 505) hydrogen bonds : angle 4.06411 / 2.96 ( 1443) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 141 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 97 LEU cc_start: 0.5648 (OUTLIER) cc_final: 0.5354 (pp) REVERT: A 107 LYS cc_start: 0.7105 (mttp) cc_final: 0.6837 (mmmm) REVERT: A 152 GLN cc_start: 0.8225 (mt0) cc_final: 0.7991 (mt0) REVERT: A 245 GLU cc_start: 0.5835 (OUTLIER) cc_final: 0.4990 (tp30) REVERT: A 247 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.7150 (mmm-85) REVERT: A 280 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7326 (mt-10) REVERT: A 354 LYS cc_start: 0.7812 (mttp) cc_final: 0.7271 (mtmt) REVERT: B 23 LYS cc_start: 0.7750 (tppt) cc_final: 0.7518 (tptp) REVERT: B 175 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.7839 (mp10) REVERT: B 188 MET cc_start: 0.9027 (mmm) cc_final: 0.8663 (mmm) REVERT: B 195 ASP cc_start: 0.6673 (OUTLIER) cc_final: 0.6199 (p0) REVERT: B 234 PHE cc_start: 0.9433 (OUTLIER) cc_final: 0.9133 (m-80) REVERT: C 47 GLU cc_start: 0.7904 (pt0) cc_final: 0.7701 (pt0) REVERT: D 19 LYS cc_start: 0.7945 (ttpp) cc_final: 0.7505 (tttt) REVERT: D 76 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7227 (mttt) REVERT: D 142 SER cc_start: 0.7820 (m) cc_final: 0.7407 (t) REVERT: R 90 MET cc_start: 0.5651 (mtp) cc_final: 0.5375 (mtp) outliers start: 49 outliers final: 31 residues processed: 173 average time/residue: 0.5958 time to fit residues: 110.0946 Evaluate side-chains 179 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 141 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain R residue 23 CYS Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 96 HIS Chi-restraints excluded: chain R residue 136 MET Chi-restraints excluded: chain R residue 174 MET Chi-restraints excluded: chain R residue 178 ASP Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 252 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [6, 123, 25, 62, 7, 40, 30, 99, 119, 71, 41] chunk 6 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 25 optimal weight: 0.0970 chunk 62 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.182129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.137846 restraints weight = 10542.778| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 1.55 r_work: 0.3478 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.0896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10392 Z= 0.106 Angle : 0.499 9.714 14110 Z= 0.263 Chirality : 0.041 0.140 1594 Planarity : 0.004 0.047 1778 Dihedral : 6.788 101.713 1499 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.63 % Allowed : 21.80 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.58 (0.24), residues: 1263 helix: 2.98 (0.24), residues: 477 sheet: 0.76 (0.29), residues: 280 loop : -0.72 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 19 TYR 0.010 0.001 TYR D 95 PHE 0.017 0.001 PHE R 111 TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 (10388) covalent geometry : angle 0.49855 / 0.26 (14102) SS BOND : bond 0.00647 / 0.38 ( 4) SS BOND : angle 0.85626 / 0.39 ( 8) hydrogen bonds : bond 0.04351 / 2.95 ( 505) hydrogen bonds : angle 3.92861 / 2.86 ( 1443) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 146 time to evaluate : 0.284 Fit side-chains REVERT: A 77 LYS cc_start: 0.7164 (ttpp) cc_final: 0.6853 (ttpp) REVERT: A 97 LEU cc_start: 0.5547 (OUTLIER) cc_final: 0.5301 (pp) REVERT: A 107 LYS cc_start: 0.7088 (mttp) cc_final: 0.6822 (mmmm) REVERT: A 152 GLN cc_start: 0.8192 (mt0) cc_final: 0.7958 (mt0) REVERT: A 245 GLU cc_start: 0.5765 (OUTLIER) cc_final: 0.4942 (tp30) REVERT: A 247 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.7123 (mmm-85) REVERT: A 280 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7265 (mt-10) REVERT: A 354 LYS cc_start: 0.7839 (mttp) cc_final: 0.7291 (mtmt) REVERT: B 23 LYS cc_start: 0.7725 (tppt) cc_final: 0.7504 (tptp) REVERT: B 175 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.7892 (mp10) REVERT: B 188 MET cc_start: 0.8987 (mmm) cc_final: 0.8644 (mmm) REVERT: B 195 ASP cc_start: 0.6668 (OUTLIER) cc_final: 0.6207 (p0) REVERT: B 234 PHE cc_start: 0.9415 (OUTLIER) cc_final: 0.9087 (m-80) REVERT: C 47 GLU cc_start: 0.7827 (pt0) cc_final: 0.7579 (pt0) REVERT: D 19 LYS cc_start: 0.7948 (ttpp) cc_final: 0.7537 (tttt) REVERT: D 62 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.8061 (m-30) REVERT: D 76 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7242 (mttt) REVERT: D 142 SER cc_start: 0.7808 (m) cc_final: 0.7406 (t) REVERT: R 90 MET cc_start: 0.5666 (mtp) cc_final: 0.5391 (mtp) outliers start: 40 outliers final: 29 residues processed: 171 average time/residue: 0.5992 time to fit residues: 109.5357 Evaluate side-chains 181 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 144 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 SER Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 122 SER Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 245 GLU Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain R residue 23 CYS Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 28 VAL Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 136 MET Chi-restraints excluded: chain R residue 174 MET Chi-restraints excluded: chain R residue 178 ASP Chi-restraints excluded: chain R residue 252 THR Chi-restraints excluded: chain R residue 279 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: [32, 96, 116, 123, 12, 75, 81, 8, 29, 1, 79] chunk 32 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 chunk 123 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 81 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 350 GLN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.182465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.137892 restraints weight = 10667.040| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.57 r_work: 0.3465 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.0892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10392 Z= 0.127 Angle : 0.538 9.677 14110 Z= 0.283 Chirality : 0.042 0.140 1594 Planarity : 0.004 0.048 1778 Dihedral : 6.886 101.737 1499 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.63 % Allowed : 21.71 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.50 (0.24), residues: 1263 helix: 2.92 (0.24), residues: 477 sheet: 0.68 (0.29), residues: 281 loop : -0.76 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 19 TYR 0.011 0.001 TYR D 95 PHE 0.018 0.001 PHE R 111 TRP 0.013 0.001 TRP B 339 HIS 0.015 0.001 HIS R 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (10388) covalent geometry : angle 0.53725 / 0.28 (14102) SS BOND : bond 0.00866 / 0.51 ( 4) SS BOND : angle 1.24989 / 0.57 ( 8) hydrogen bonds : bond 0.04829 / 3.28 ( 505) hydrogen bonds : angle 4.04541 / 2.94 ( 1443) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4522.54 seconds wall clock time: 77 minutes 34.45 seconds (4654.45 seconds total)