Starting phenix.real_space_refine on Sat Aug 23 04:48:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xx6_38747/08_2025/8xx6_38747.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xx6_38747/08_2025/8xx6_38747.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xx6_38747/08_2025/8xx6_38747.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xx6_38747/08_2025/8xx6_38747.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xx6_38747/08_2025/8xx6_38747.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xx6_38747/08_2025/8xx6_38747.map" } resolution = 2.99 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 6293 2.51 5 N 1671 2.21 5 O 1824 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9854 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2421 Classifications: {'peptide': 303} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 291} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 575 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 68} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 500 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 60} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1689 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2529 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "G" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 375 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "S" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1765 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Time building chain proxies: 1.81, per 1000 atoms: 0.18 Number of scatterers: 9854 At special positions: 0 Unit cell: (88.1875, 123.463, 158.738, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 1824 8.00 N 1671 7.00 C 6293 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS R 39 " - pdb=" SG CYS R 286 " distance=2.03 Simple disulfide: pdb=" SG CYS R 119 " - pdb=" SG CYS R 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 7 " - pdb=" SG CYS D 34 " distance=2.03 Simple disulfide: pdb=" SG CYS D 9 " - pdb=" SG CYS D 50 " distance=2.03 Simple disulfide: pdb=" SG CYS E 5 " - pdb=" SG CYS E 32 " distance=2.03 Simple disulfide: pdb=" SG CYS E 7 " - pdb=" SG CYS E 48 " distance=2.03 Simple disulfide: pdb=" SG CYS B 103 " - pdb=" SG CYS B 114 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.59 Conformation dependent library (CDL) restraints added in 313.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2400 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 16 sheets defined 35.8% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'R' and resid 45 through 76 removed outlier: 4.414A pdb=" N SER R 76 " --> pdb=" O VAL R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 111 Proline residue: R 102 - end of helix Processing helix chain 'R' and resid 115 through 149 Processing helix chain 'R' and resid 154 through 160 removed outlier: 3.877A pdb=" N TYR R 160 " --> pdb=" O GLN R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 177 Processing helix chain 'R' and resid 177 through 183 removed outlier: 3.541A pdb=" N LEU R 181 " --> pdb=" O ALA R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 212 Processing helix chain 'R' and resid 212 through 218 Processing helix chain 'R' and resid 220 through 241 removed outlier: 3.588A pdb=" N LYS R 240 " --> pdb=" O ARG R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 279 Proline residue: R 266 - end of helix Processing helix chain 'R' and resid 285 through 304 Processing helix chain 'R' and resid 305 through 315 Proline residue: R 311 - end of helix Processing helix chain 'R' and resid 318 through 329 Processing helix chain 'D' and resid 18 through 20 No H-bonds generated for 'chain 'D' and resid 18 through 20' Processing helix chain 'D' and resid 55 through 71 removed outlier: 3.815A pdb=" N GLN D 59 " --> pdb=" O GLU D 55 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG D 60 " --> pdb=" O ASN D 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 18 No H-bonds generated for 'chain 'E' and resid 16 through 18' Processing helix chain 'E' and resid 53 through 68 Processing helix chain 'A' and resid 6 through 30 Processing helix chain 'A' and resid 208 through 217 removed outlier: 4.787A pdb=" N ILE A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N HIS A 214 " --> pdb=" O LYS A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 256 Processing helix chain 'A' and resid 271 through 282 removed outlier: 4.113A pdb=" N LYS A 280 " --> pdb=" O GLY A 276 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 6 through 26 removed outlier: 3.706A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 12 through 24 removed outlier: 3.607A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.646A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.016A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.809A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 184 through 187 Processing sheet with id=AA2, first strand: chain 'D' and resid 48 through 51 removed outlier: 4.363A pdb=" N ILE D 39 " --> pdb=" O LEU D 51 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU D 24 " --> pdb=" O LYS D 42 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE E 37 " --> pdb=" O LEU E 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 186 through 188 Processing sheet with id=AA4, first strand: chain 'A' and resid 186 through 188 removed outlier: 9.585A pdb=" N ALA A 221 " --> pdb=" O ASP A 33 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N LYS A 35 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ILE A 223 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU A 37 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N CYS A 225 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU A 39 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N ASP A 227 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 52 removed outlier: 4.401A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.964A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 103 removed outlier: 4.210A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 153 removed outlier: 4.599A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.566A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.407A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.395A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.721A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY S 44 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 128 through 130 removed outlier: 3.510A pdb=" N ALA S 199 " --> pdb=" O SER S 196 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.167A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE S 177 " --> pdb=" O TRP S 164 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.167A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR S 226 " --> pdb=" O GLN S 219 " (cutoff:3.500A) 483 hydrogen bonds defined for protein. 1359 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: 1.26 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1678 1.32 - 1.45: 2668 1.45 - 1.57: 5624 1.57 - 1.70: 0 1.70 - 1.82: 89 Bond restraints: 10059 Sorted by residual: bond pdb=" C ASN B 88 " pdb=" O ASN B 88 " ideal model delta sigma weight residual 1.234 1.198 0.036 1.22e-02 6.72e+03 8.94e+00 bond pdb=" CB CYS B 103 " pdb=" SG CYS B 103 " ideal model delta sigma weight residual 1.808 1.764 0.044 3.30e-02 9.18e+02 1.80e+00 bond pdb=" CA LEU R 99 " pdb=" C LEU R 99 " ideal model delta sigma weight residual 1.522 1.506 0.017 1.36e-02 5.41e+03 1.48e+00 bond pdb=" C ASN B 88 " pdb=" N LYS B 89 " ideal model delta sigma weight residual 1.331 1.314 0.017 1.43e-02 4.89e+03 1.38e+00 bond pdb=" CA ARG B 197 " pdb=" CB ARG B 197 " ideal model delta sigma weight residual 1.537 1.521 0.016 1.41e-02 5.03e+03 1.22e+00 ... (remaining 10054 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 13187 1.09 - 2.17: 387 2.17 - 3.26: 66 3.26 - 4.35: 14 4.35 - 5.43: 7 Bond angle restraints: 13661 Sorted by residual: angle pdb=" C ALA B 309 " pdb=" CA ALA B 309 " pdb=" CB ALA B 309 " ideal model delta sigma weight residual 115.89 110.46 5.43 1.32e+00 5.74e-01 1.69e+01 angle pdb=" CA ASN B 88 " pdb=" C ASN B 88 " pdb=" O ASN B 88 " ideal model delta sigma weight residual 121.16 117.13 4.03 1.13e+00 7.83e-01 1.27e+01 angle pdb=" C ASN B 88 " pdb=" CA ASN B 88 " pdb=" CB ASN B 88 " ideal model delta sigma weight residual 109.37 114.43 -5.06 1.83e+00 2.99e-01 7.63e+00 angle pdb=" C TYR S 178 " pdb=" N ARG S 179 " pdb=" CA ARG S 179 " ideal model delta sigma weight residual 121.90 118.93 2.97 1.26e+00 6.30e-01 5.56e+00 angle pdb=" N ASN B 88 " pdb=" CA ASN B 88 " pdb=" C ASN B 88 " ideal model delta sigma weight residual 109.95 106.33 3.62 1.59e+00 3.96e-01 5.18e+00 ... (remaining 13656 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 5488 17.77 - 35.54: 424 35.54 - 53.31: 60 53.31 - 71.08: 17 71.08 - 88.85: 5 Dihedral angle restraints: 5994 sinusoidal: 2282 harmonic: 3712 Sorted by residual: dihedral pdb=" CB CYS E 5 " pdb=" SG CYS E 5 " pdb=" SG CYS E 32 " pdb=" CB CYS E 32 " ideal model delta sinusoidal sigma weight residual -86.00 -141.86 55.86 1 1.00e+01 1.00e-02 4.21e+01 dihedral pdb=" CB CYS S 147 " pdb=" SG CYS S 147 " pdb=" SG CYS S 217 " pdb=" CB CYS S 217 " ideal model delta sinusoidal sigma weight residual 93.00 140.07 -47.07 1 1.00e+01 1.00e-02 3.06e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 162.33 17.67 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 5991 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1074 0.033 - 0.066: 348 0.066 - 0.100: 103 0.100 - 0.133: 57 0.133 - 0.166: 3 Chirality restraints: 1585 Sorted by residual: chirality pdb=" CA TYR S 178 " pdb=" N TYR S 178 " pdb=" C TYR S 178 " pdb=" CB TYR S 178 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.90e-01 chirality pdb=" CA ILE S 177 " pdb=" N ILE S 177 " pdb=" C ILE S 177 " pdb=" CB ILE S 177 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.47e-01 chirality pdb=" CB ILE A 55 " pdb=" CA ILE A 55 " pdb=" CG1 ILE A 55 " pdb=" CG2 ILE A 55 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.72e-01 ... (remaining 1582 not shown) Planarity restraints: 1729 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL G 54 " 0.026 5.00e-02 4.00e+02 4.01e-02 2.57e+00 pdb=" N PRO G 55 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO G 55 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 55 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.025 5.00e-02 4.00e+02 3.77e-02 2.27e+00 pdb=" N PRO B 236 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 87 " 0.007 2.00e-02 2.50e+03 1.36e-02 1.84e+00 pdb=" C THR B 87 " -0.023 2.00e-02 2.50e+03 pdb=" O THR B 87 " 0.009 2.00e-02 2.50e+03 pdb=" N ASN B 88 " 0.008 2.00e-02 2.50e+03 ... (remaining 1726 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1512 2.76 - 3.30: 9229 3.30 - 3.83: 15847 3.83 - 4.37: 18525 4.37 - 4.90: 33252 Nonbonded interactions: 78365 Sorted by model distance: nonbonded pdb=" O GLY R 201 " pdb=" OG1 THR R 204 " model vdw 2.229 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.230 3.040 nonbonded pdb=" OG1 THR B 165 " pdb=" O PHE B 180 " model vdw 2.259 3.040 nonbonded pdb=" O PHE S 29 " pdb=" NH2 ARG S 72 " model vdw 2.262 3.120 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.282 3.040 ... (remaining 78360 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 Found NCS groups: ncs_group { reference = (chain 'D' and (resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 19 or (resid 20 and (name N or name \ CA or name C or name O or name CB )) or resid 21 through 53 or (resid 54 throug \ h 55 and (name N or name CA or name C or name O or name CB )) or resid 56 throug \ h 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or re \ sid 65 through 70 or (resid 71 and (name N or name CA or name C or name O or nam \ e CB )))) selection = (chain 'E' and (resid 5 through 52 or (resid 53 and (name N or name CA or name C \ or name O or name CB )) or resid 54 through 69)) } 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: 0.810 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: 0.020 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.080 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 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 : 0.002 0.044 10068 Z= 0.118 Angle : 0.468 5.434 13679 Z= 0.271 Chirality : 0.040 0.166 1585 Planarity : 0.003 0.040 1729 Dihedral : 12.904 88.847 3567 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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 aren not related in a simple way. whole: 0.68 (0.24), residues: 1260 helix: 2.20 (0.25), residues: 410 sheet: -0.11 (0.28), residues: 333 loop : -0.54 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 72 TYR 0.016 0.001 TYR S 178 PHE 0.014 0.001 PHE B 234 TRP 0.015 0.001 TRP B 211 HIS 0.002 0.001 HIS S 220 Details of bonding type rmsd covalent geometry : bond 0.00218 (10059) covalent geometry : angle 0.46572 (13661) SS BOND : bond 0.00256 ( 9) SS BOND : angle 1.40099 ( 18) hydrogen bonds : bond 0.20912 ( 477) hydrogen bonds : angle 6.50163 ( 1359) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 337 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: R 95 LEU cc_start: 0.8216 (tp) cc_final: 0.7974 (pp) REVERT: R 203 ASN cc_start: 0.7541 (t0) cc_final: 0.7208 (t0) REVERT: R 214 LEU cc_start: 0.8733 (mt) cc_final: 0.8388 (mt) REVERT: R 262 LEU cc_start: 0.8771 (tp) cc_final: 0.8505 (tm) REVERT: R 291 HIS cc_start: 0.7796 (m170) cc_final: 0.7260 (m170) REVERT: A 273 ASP cc_start: 0.7464 (p0) cc_final: 0.7098 (t0) REVERT: A 354 TYR cc_start: 0.6857 (t80) cc_final: 0.6560 (t80) REVERT: B 13 GLN cc_start: 0.8386 (pp30) cc_final: 0.8018 (pp30) REVERT: B 213 VAL cc_start: 0.8843 (p) cc_final: 0.8584 (t) REVERT: S 69 THR cc_start: 0.8144 (t) cc_final: 0.7795 (m) outliers start: 0 outliers final: 1 residues processed: 337 average time/residue: 0.4612 time to fit residues: 167.2904 Evaluate side-chains 210 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 209 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 36 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.0370 chunk 33 optimal weight: 0.0030 chunk 123 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 overall best weight: 0.7270 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 47 ASN R 150 HIS ** R 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 ASN A 43 ASN A 256 ASN B 88 ASN B 91 HIS B 230 ASN B 259 GLN G 18 GLN S 174 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.133746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.097077 restraints weight = 17893.097| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.87 r_work: 0.3153 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 10068 Z= 0.138 Angle : 0.637 12.375 13679 Z= 0.330 Chirality : 0.045 0.189 1585 Planarity : 0.005 0.082 1729 Dihedral : 4.034 33.616 1376 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.06 % Allowed : 15.09 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: 0.74 (0.24), residues: 1260 helix: 2.22 (0.25), residues: 421 sheet: 0.06 (0.28), residues: 342 loop : -0.66 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 96 TYR 0.021 0.001 TYR S 178 PHE 0.016 0.001 PHE S 108 TRP 0.014 0.001 TRP B 339 HIS 0.003 0.001 HIS S 220 Details of bonding type rmsd covalent geometry : bond 0.00313 (10059) covalent geometry : angle 0.62408 (13661) SS BOND : bond 0.01011 ( 9) SS BOND : angle 3.53817 ( 18) hydrogen bonds : bond 0.04577 ( 477) hydrogen bonds : angle 4.83042 ( 1359) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 220 time to evaluate : 0.320 Fit side-chains REVERT: R 61 LEU cc_start: 0.8989 (mt) cc_final: 0.8615 (mp) REVERT: R 112 TRP cc_start: 0.7898 (t-100) cc_final: 0.7605 (t-100) REVERT: R 128 VAL cc_start: 0.8982 (p) cc_final: 0.8647 (m) REVERT: R 211 LEU cc_start: 0.8923 (mt) cc_final: 0.8595 (mp) REVERT: R 214 LEU cc_start: 0.8774 (mt) cc_final: 0.8562 (mt) REVERT: R 240 LYS cc_start: 0.8549 (ttpp) cc_final: 0.8294 (mtmm) REVERT: R 291 HIS cc_start: 0.8006 (m170) cc_final: 0.7519 (m170) REVERT: R 313 ILE cc_start: 0.9301 (tt) cc_final: 0.8818 (pt) REVERT: D 27 VAL cc_start: 0.8900 (t) cc_final: 0.8630 (m) REVERT: A 231 TYR cc_start: 0.8040 (m-80) cc_final: 0.7646 (m-80) REVERT: A 273 ASP cc_start: 0.7346 (p0) cc_final: 0.7018 (t0) REVERT: A 277 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.8070 (mp0) REVERT: A 307 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.7252 (mp10) REVERT: B 12 GLU cc_start: 0.8968 (tp30) cc_final: 0.8668 (pp20) REVERT: B 32 GLN cc_start: 0.8737 (tt0) cc_final: 0.8458 (pt0) REVERT: B 213 VAL cc_start: 0.8901 (p) cc_final: 0.8650 (t) REVERT: G 50 LEU cc_start: 0.8791 (mt) cc_final: 0.8510 (mt) REVERT: S 69 THR cc_start: 0.8551 (t) cc_final: 0.8156 (m) REVERT: S 168 ARG cc_start: 0.8785 (mtt90) cc_final: 0.8533 (mtt90) REVERT: S 171 GLN cc_start: 0.7951 (mp10) cc_final: 0.7647 (mp10) REVERT: S 211 ASP cc_start: 0.8345 (m-30) cc_final: 0.7779 (m-30) outliers start: 43 outliers final: 11 residues processed: 244 average time/residue: 0.4857 time to fit residues: 127.0825 Evaluate side-chains 206 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 193 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 221 ILE Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 301 ILE Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 184 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 93 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 46 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 89 optimal weight: 0.0470 chunk 4 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 overall best weight: 1.5482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 43 ASN B 16 ASN B 259 GLN S 130 GLN S 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.131148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.093537 restraints weight = 18075.723| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.73 r_work: 0.3092 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 10068 Z= 0.173 Angle : 0.669 19.671 13679 Z= 0.340 Chirality : 0.044 0.217 1585 Planarity : 0.004 0.060 1729 Dihedral : 4.276 29.433 1374 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.96 % Allowed : 18.40 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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 aren not related in a simple way. whole: 0.69 (0.24), residues: 1260 helix: 2.12 (0.25), residues: 427 sheet: 0.06 (0.28), residues: 335 loop : -0.69 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 96 TYR 0.027 0.002 TYR S 178 PHE 0.015 0.001 PHE S 108 TRP 0.011 0.001 TRP B 82 HIS 0.005 0.001 HIS S 220 Details of bonding type rmsd covalent geometry : bond 0.00405 (10059) covalent geometry : angle 0.66079 (13661) SS BOND : bond 0.00906 ( 9) SS BOND : angle 3.01227 ( 18) hydrogen bonds : bond 0.04384 ( 477) hydrogen bonds : angle 4.67209 ( 1359) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 200 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: R 83 THR cc_start: 0.8733 (OUTLIER) cc_final: 0.8472 (t) REVERT: R 90 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8315 (tt) REVERT: R 214 LEU cc_start: 0.8840 (mt) cc_final: 0.8602 (mt) REVERT: R 258 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8622 (mm) REVERT: R 287 GLU cc_start: 0.8395 (pm20) cc_final: 0.7955 (pm20) REVERT: R 291 HIS cc_start: 0.8022 (m170) cc_final: 0.7578 (m170) REVERT: R 321 PHE cc_start: 0.7850 (t80) cc_final: 0.7596 (t80) REVERT: D 20 LYS cc_start: 0.8749 (pttm) cc_final: 0.8538 (pptt) REVERT: D 27 VAL cc_start: 0.8938 (t) cc_final: 0.8486 (p) REVERT: A 273 ASP cc_start: 0.7502 (p0) cc_final: 0.7039 (t0) REVERT: A 277 GLU cc_start: 0.8321 (mp0) cc_final: 0.8074 (mp0) REVERT: A 307 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7198 (mp10) REVERT: B 10 GLU cc_start: 0.8144 (tp30) cc_final: 0.7704 (tp30) REVERT: B 12 GLU cc_start: 0.8968 (tp30) cc_final: 0.8701 (pp20) REVERT: B 32 GLN cc_start: 0.8767 (tt0) cc_final: 0.8520 (pt0) REVERT: B 213 VAL cc_start: 0.8958 (p) cc_final: 0.8749 (t) REVERT: G 50 LEU cc_start: 0.8906 (mt) cc_final: 0.8653 (mt) REVERT: S 69 THR cc_start: 0.8545 (t) cc_final: 0.8153 (m) REVERT: S 73 ASP cc_start: 0.7346 (t0) cc_final: 0.6459 (t70) REVERT: S 171 GLN cc_start: 0.8078 (mp10) cc_final: 0.7682 (mp10) REVERT: S 183 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8937 (mp) REVERT: S 211 ASP cc_start: 0.8357 (m-30) cc_final: 0.7942 (m-30) outliers start: 42 outliers final: 19 residues processed: 227 average time/residue: 0.6342 time to fit residues: 153.4620 Evaluate side-chains 206 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 182 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 221 ILE Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 202 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 121 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 51 optimal weight: 0.4980 chunk 67 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 242 HIS R 283 GLN A 43 ASN ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN B 16 ASN B 259 GLN S 174 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.127222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.087269 restraints weight = 18077.044| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.48 r_work: 0.3027 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.093 10068 Z= 0.324 Angle : 0.759 16.744 13679 Z= 0.395 Chirality : 0.049 0.334 1585 Planarity : 0.005 0.051 1729 Dihedral : 4.973 33.745 1374 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 5.94 % Allowed : 17.45 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: 0.30 (0.23), residues: 1260 helix: 1.85 (0.25), residues: 427 sheet: -0.19 (0.27), residues: 336 loop : -0.93 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 313 TYR 0.032 0.002 TYR B 105 PHE 0.016 0.002 PHE B 234 TRP 0.015 0.002 TRP S 47 HIS 0.009 0.002 HIS S 220 Details of bonding type rmsd covalent geometry : bond 0.00765 (10059) covalent geometry : angle 0.75227 (13661) SS BOND : bond 0.00950 ( 9) SS BOND : angle 2.92079 ( 18) hydrogen bonds : bond 0.05112 ( 477) hydrogen bonds : angle 4.87617 ( 1359) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 187 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: R 185 ARG cc_start: 0.7499 (ptm-80) cc_final: 0.7278 (ptp90) REVERT: R 258 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8794 (mm) REVERT: R 321 PHE cc_start: 0.8141 (t80) cc_final: 0.7916 (t80) REVERT: D 27 VAL cc_start: 0.9040 (t) cc_final: 0.8734 (m) REVERT: E 40 LYS cc_start: 0.8014 (mttt) cc_final: 0.6929 (mppt) REVERT: A 243 ARG cc_start: 0.8656 (mmm-85) cc_final: 0.8334 (mtm180) REVERT: A 273 ASP cc_start: 0.7791 (p0) cc_final: 0.7148 (OUTLIER) REVERT: A 277 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8254 (mp0) REVERT: A 307 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.7454 (mp10) REVERT: B 10 GLU cc_start: 0.8208 (tp30) cc_final: 0.7801 (tp30) REVERT: B 12 GLU cc_start: 0.9047 (tp30) cc_final: 0.8709 (pp20) REVERT: B 32 GLN cc_start: 0.8815 (tt0) cc_final: 0.8516 (pt0) REVERT: B 211 TRP cc_start: 0.8396 (OUTLIER) cc_final: 0.7577 (m-90) REVERT: G 50 LEU cc_start: 0.9112 (mt) cc_final: 0.8873 (mt) REVERT: S 69 THR cc_start: 0.8670 (t) cc_final: 0.8293 (m) REVERT: S 171 GLN cc_start: 0.8420 (mp10) cc_final: 0.8003 (mp10) REVERT: S 211 ASP cc_start: 0.8395 (m-30) cc_final: 0.7923 (m-30) outliers start: 63 outliers final: 23 residues processed: 229 average time/residue: 0.6438 time to fit residues: 157.3994 Evaluate side-chains 195 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 296 LEU Chi-restraints excluded: chain R residue 325 LEU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 202 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 59 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 2 optimal weight: 0.1980 chunk 103 optimal weight: 0.6980 chunk 117 optimal weight: 0.7980 chunk 32 optimal weight: 20.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 242 HIS B 16 ASN B 259 GLN S 174 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.130516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.091755 restraints weight = 18145.431| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.52 r_work: 0.3107 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10068 Z= 0.130 Angle : 0.674 22.246 13679 Z= 0.345 Chirality : 0.045 0.264 1585 Planarity : 0.004 0.053 1729 Dihedral : 4.437 33.040 1374 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.06 % Allowed : 21.13 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: 0.50 (0.24), residues: 1260 helix: 2.03 (0.25), residues: 427 sheet: 0.01 (0.27), residues: 325 loop : -0.91 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 96 TYR 0.020 0.001 TYR S 178 PHE 0.011 0.001 PHE B 234 TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS D 33 Details of bonding type rmsd covalent geometry : bond 0.00296 (10059) covalent geometry : angle 0.65930 (13661) SS BOND : bond 0.00631 ( 9) SS BOND : angle 3.97194 ( 18) hydrogen bonds : bond 0.03975 ( 477) hydrogen bonds : angle 4.55957 ( 1359) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 180 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 83 THR cc_start: 0.8760 (OUTLIER) cc_final: 0.8524 (t) REVERT: R 262 LEU cc_start: 0.8960 (tm) cc_final: 0.8747 (tt) REVERT: R 287 GLU cc_start: 0.8374 (pm20) cc_final: 0.7900 (pm20) REVERT: R 291 HIS cc_start: 0.7949 (m-70) cc_final: 0.7462 (m170) REVERT: R 321 PHE cc_start: 0.7892 (OUTLIER) cc_final: 0.7428 (t80) REVERT: D 27 VAL cc_start: 0.8999 (t) cc_final: 0.8576 (p) REVERT: E 40 LYS cc_start: 0.8014 (mttt) cc_final: 0.6931 (mppt) REVERT: A 243 ARG cc_start: 0.8660 (mmm-85) cc_final: 0.8340 (mtt180) REVERT: A 273 ASP cc_start: 0.7809 (p0) cc_final: 0.7582 (p0) REVERT: A 307 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.7639 (mp10) REVERT: B 12 GLU cc_start: 0.9076 (tp30) cc_final: 0.8731 (pp20) REVERT: B 32 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8534 (pt0) REVERT: G 50 LEU cc_start: 0.9093 (mt) cc_final: 0.8802 (mt) REVERT: S 69 THR cc_start: 0.8663 (t) cc_final: 0.8279 (m) REVERT: S 87 ARG cc_start: 0.8404 (mtt-85) cc_final: 0.8178 (mtt-85) REVERT: S 171 GLN cc_start: 0.8359 (mp10) cc_final: 0.7793 (mp10) REVERT: S 211 ASP cc_start: 0.8299 (m-30) cc_final: 0.7829 (m-30) outliers start: 43 outliers final: 17 residues processed: 206 average time/residue: 0.6657 time to fit residues: 146.0473 Evaluate side-chains 189 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 221 ILE Chi-restraints excluded: chain R residue 243 MET Chi-restraints excluded: chain R residue 321 PHE Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 202 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 85 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 242 HIS B 16 ASN B 75 GLN B 259 GLN S 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.126993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.087327 restraints weight = 18288.012| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 2.53 r_work: 0.3007 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 10068 Z= 0.237 Angle : 0.765 27.998 13679 Z= 0.390 Chirality : 0.048 0.377 1585 Planarity : 0.005 0.049 1729 Dihedral : 4.715 30.712 1374 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.06 % Allowed : 21.70 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: 0.35 (0.23), residues: 1260 helix: 1.90 (0.25), residues: 427 sheet: -0.06 (0.27), residues: 320 loop : -0.97 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 313 TYR 0.023 0.002 TYR S 178 PHE 0.016 0.002 PHE B 234 TRP 0.012 0.002 TRP B 82 HIS 0.005 0.001 HIS S 220 Details of bonding type rmsd covalent geometry : bond 0.00556 (10059) covalent geometry : angle 0.74900 (13661) SS BOND : bond 0.01268 ( 9) SS BOND : angle 4.32529 ( 18) hydrogen bonds : bond 0.04605 ( 477) hydrogen bonds : angle 4.65602 ( 1359) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 174 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 83 THR cc_start: 0.8763 (OUTLIER) cc_final: 0.8530 (t) REVERT: R 258 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8757 (mm) REVERT: R 262 LEU cc_start: 0.8967 (tm) cc_final: 0.8756 (tt) REVERT: R 321 PHE cc_start: 0.7776 (t80) cc_final: 0.7469 (t80) REVERT: D 27 VAL cc_start: 0.8978 (t) cc_final: 0.8578 (p) REVERT: E 40 LYS cc_start: 0.7925 (mttt) cc_final: 0.6892 (mppt) REVERT: A 243 ARG cc_start: 0.8629 (mmm-85) cc_final: 0.8251 (mtt180) REVERT: A 273 ASP cc_start: 0.7867 (p0) cc_final: 0.7662 (p0) REVERT: A 307 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.7544 (mp10) REVERT: B 10 GLU cc_start: 0.8189 (tp30) cc_final: 0.7787 (tp30) REVERT: B 12 GLU cc_start: 0.9095 (tp30) cc_final: 0.8734 (pp20) REVERT: B 32 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.8465 (pt0) REVERT: B 43 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8710 (mp) REVERT: G 50 LEU cc_start: 0.9142 (mt) cc_final: 0.8885 (mt) REVERT: S 69 THR cc_start: 0.8709 (t) cc_final: 0.8346 (m) REVERT: S 171 GLN cc_start: 0.8385 (mp10) cc_final: 0.7890 (mp10) outliers start: 43 outliers final: 22 residues processed: 200 average time/residue: 0.6808 time to fit residues: 144.7697 Evaluate side-chains 190 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 95 LEU Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 279 THR Chi-restraints excluded: chain R residue 325 LEU Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 202 LEU Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 114 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 chunk 87 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 242 HIS A 194 ASN B 16 ASN B 259 GLN S 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.129783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.092203 restraints weight = 18270.921| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.53 r_work: 0.3065 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10068 Z= 0.128 Angle : 0.705 24.447 13679 Z= 0.355 Chirality : 0.044 0.286 1585 Planarity : 0.004 0.045 1729 Dihedral : 4.379 29.292 1374 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.58 % Allowed : 22.17 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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 aren not related in a simple way. whole: 0.51 (0.24), residues: 1260 helix: 2.06 (0.26), residues: 428 sheet: 0.04 (0.27), residues: 321 loop : -0.95 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 313 TYR 0.017 0.001 TYR S 178 PHE 0.028 0.001 PHE R 316 TRP 0.010 0.001 TRP B 82 HIS 0.002 0.001 HIS R 291 Details of bonding type rmsd covalent geometry : bond 0.00289 (10059) covalent geometry : angle 0.68724 (13661) SS BOND : bond 0.00848 ( 9) SS BOND : angle 4.35831 ( 18) hydrogen bonds : bond 0.03872 ( 477) hydrogen bonds : angle 4.44451 ( 1359) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 174 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 70 MET cc_start: 0.7957 (mtt) cc_final: 0.7416 (mtm) REVERT: R 83 THR cc_start: 0.8617 (OUTLIER) cc_final: 0.8376 (t) REVERT: R 262 LEU cc_start: 0.8913 (tm) cc_final: 0.8704 (tt) REVERT: R 321 PHE cc_start: 0.7747 (t80) cc_final: 0.7466 (t80) REVERT: D 27 VAL cc_start: 0.8897 (t) cc_final: 0.8482 (p) REVERT: E 40 LYS cc_start: 0.7957 (mttt) cc_final: 0.6940 (mppt) REVERT: A 243 ARG cc_start: 0.8503 (mmm-85) cc_final: 0.8145 (mtt180) REVERT: A 273 ASP cc_start: 0.7690 (p0) cc_final: 0.7449 (p0) REVERT: A 303 TYR cc_start: 0.8614 (t80) cc_final: 0.8101 (t80) REVERT: A 307 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.7626 (mp10) REVERT: B 12 GLU cc_start: 0.9051 (tp30) cc_final: 0.8716 (pp20) REVERT: B 32 GLN cc_start: 0.8712 (tt0) cc_final: 0.8488 (pt0) REVERT: G 50 LEU cc_start: 0.9068 (mt) cc_final: 0.8817 (mt) REVERT: S 13 GLN cc_start: 0.8687 (tp40) cc_final: 0.8393 (mm110) REVERT: S 69 THR cc_start: 0.8511 (t) cc_final: 0.8114 (m) REVERT: S 171 GLN cc_start: 0.8171 (mp10) cc_final: 0.7614 (mp10) outliers start: 38 outliers final: 18 residues processed: 198 average time/residue: 0.6662 time to fit residues: 140.4323 Evaluate side-chains 190 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 202 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 25 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 112 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 45 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 86 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 242 HIS A 194 ASN B 16 ASN B 75 GLN B 259 GLN S 174 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.130321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.092813 restraints weight = 18002.827| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.81 r_work: 0.3088 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.4328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10068 Z= 0.144 Angle : 0.733 23.768 13679 Z= 0.364 Chirality : 0.045 0.300 1585 Planarity : 0.004 0.049 1729 Dihedral : 4.372 28.348 1374 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.68 % Allowed : 22.36 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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 aren not related in a simple way. whole: 0.58 (0.24), residues: 1260 helix: 2.06 (0.25), residues: 427 sheet: 0.15 (0.27), residues: 327 loop : -0.90 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 313 TYR 0.018 0.001 TYR S 178 PHE 0.011 0.001 PHE B 234 TRP 0.011 0.001 TRP S 47 HIS 0.003 0.001 HIS S 220 Details of bonding type rmsd covalent geometry : bond 0.00335 (10059) covalent geometry : angle 0.71544 (13661) SS BOND : bond 0.00854 ( 9) SS BOND : angle 4.40841 ( 18) hydrogen bonds : bond 0.03935 ( 477) hydrogen bonds : angle 4.45647 ( 1359) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 172 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 83 THR cc_start: 0.8695 (OUTLIER) cc_final: 0.8436 (t) REVERT: R 185 ARG cc_start: 0.6856 (ptp90) cc_final: 0.6563 (ptm-80) REVERT: R 262 LEU cc_start: 0.8894 (tm) cc_final: 0.8691 (tt) REVERT: R 321 PHE cc_start: 0.7768 (t80) cc_final: 0.7440 (t80) REVERT: D 27 VAL cc_start: 0.8914 (t) cc_final: 0.8495 (p) REVERT: E 40 LYS cc_start: 0.7973 (mttt) cc_final: 0.6901 (mppt) REVERT: A 243 ARG cc_start: 0.8514 (mmm-85) cc_final: 0.8175 (mtt180) REVERT: B 12 GLU cc_start: 0.9031 (tp30) cc_final: 0.8714 (pp20) REVERT: B 32 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.8509 (pt0) REVERT: G 50 LEU cc_start: 0.9093 (mt) cc_final: 0.8866 (mt) REVERT: S 13 GLN cc_start: 0.8686 (tp40) cc_final: 0.8409 (mm110) REVERT: S 69 THR cc_start: 0.8523 (t) cc_final: 0.8132 (m) REVERT: S 171 GLN cc_start: 0.8147 (mp10) cc_final: 0.7613 (mp10) outliers start: 39 outliers final: 22 residues processed: 195 average time/residue: 0.6652 time to fit residues: 138.2640 Evaluate side-chains 189 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain R residue 221 ILE Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 202 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 57 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 41 optimal weight: 20.0000 chunk 86 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 118 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 242 HIS A 194 ASN B 16 ASN B 259 GLN S 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.128870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.090613 restraints weight = 18000.022| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.94 r_work: 0.3034 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10068 Z= 0.181 Angle : 0.772 24.735 13679 Z= 0.385 Chirality : 0.046 0.317 1585 Planarity : 0.004 0.051 1729 Dihedral : 4.480 28.552 1374 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.68 % Allowed : 22.26 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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 aren not related in a simple way. whole: 0.56 (0.24), residues: 1260 helix: 2.08 (0.25), residues: 421 sheet: 0.16 (0.27), residues: 325 loop : -0.93 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 313 TYR 0.020 0.002 TYR S 178 PHE 0.027 0.001 PHE R 316 TRP 0.011 0.001 TRP R 104 HIS 0.004 0.001 HIS S 220 Details of bonding type rmsd covalent geometry : bond 0.00426 (10059) covalent geometry : angle 0.75549 (13661) SS BOND : bond 0.00968 ( 9) SS BOND : angle 4.47445 ( 18) hydrogen bonds : bond 0.04149 ( 477) hydrogen bonds : angle 4.51556 ( 1359) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 172 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: R 83 THR cc_start: 0.8669 (OUTLIER) cc_final: 0.8411 (t) REVERT: R 185 ARG cc_start: 0.6844 (ptp90) cc_final: 0.6542 (ptm-80) REVERT: R 262 LEU cc_start: 0.8866 (tm) cc_final: 0.8659 (tt) REVERT: R 280 GLN cc_start: 0.8759 (mm-40) cc_final: 0.8542 (mp10) REVERT: R 321 PHE cc_start: 0.7703 (t80) cc_final: 0.7400 (t80) REVERT: R 323 HIS cc_start: 0.7614 (OUTLIER) cc_final: 0.7027 (p-80) REVERT: D 27 VAL cc_start: 0.8975 (t) cc_final: 0.8562 (p) REVERT: E 40 LYS cc_start: 0.8027 (mttt) cc_final: 0.6967 (mppt) REVERT: A 243 ARG cc_start: 0.8611 (mmm-85) cc_final: 0.8368 (mtm180) REVERT: A 303 TYR cc_start: 0.8569 (t80) cc_final: 0.8322 (t80) REVERT: B 10 GLU cc_start: 0.7984 (tp30) cc_final: 0.7408 (tp30) REVERT: B 12 GLU cc_start: 0.9042 (tp30) cc_final: 0.8716 (pp20) REVERT: B 13 GLN cc_start: 0.8342 (pp30) cc_final: 0.7523 (pp30) REVERT: B 32 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8484 (pt0) REVERT: G 50 LEU cc_start: 0.9105 (mt) cc_final: 0.8879 (mt) REVERT: S 69 THR cc_start: 0.8569 (t) cc_final: 0.8183 (m) REVERT: S 171 GLN cc_start: 0.8199 (mp10) cc_final: 0.7740 (mp10) outliers start: 39 outliers final: 24 residues processed: 193 average time/residue: 0.6411 time to fit residues: 131.5180 Evaluate side-chains 194 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 167 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain R residue 221 ILE Chi-restraints excluded: chain R residue 279 THR Chi-restraints excluded: chain R residue 323 HIS Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 202 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 216 GLN R 242 HIS A 194 ASN B 16 ASN B 75 GLN B 259 GLN S 174 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.129840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.091877 restraints weight = 17884.373| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.53 r_work: 0.3086 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10068 Z= 0.163 Angle : 0.778 24.022 13679 Z= 0.386 Chirality : 0.045 0.304 1585 Planarity : 0.004 0.071 1729 Dihedral : 4.465 27.768 1374 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.21 % Allowed : 23.02 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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 aren not related in a simple way. whole: 0.59 (0.23), residues: 1260 helix: 2.09 (0.25), residues: 419 sheet: 0.19 (0.27), residues: 325 loop : -0.89 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 96 TYR 0.018 0.001 TYR S 178 PHE 0.011 0.001 PHE B 234 TRP 0.012 0.001 TRP R 104 HIS 0.003 0.001 HIS S 220 Details of bonding type rmsd covalent geometry : bond 0.00385 (10059) covalent geometry : angle 0.76164 (13661) SS BOND : bond 0.00888 ( 9) SS BOND : angle 4.44604 ( 18) hydrogen bonds : bond 0.04031 ( 477) hydrogen bonds : angle 4.50931 ( 1359) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 173 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: R 83 THR cc_start: 0.8712 (OUTLIER) cc_final: 0.8440 (t) REVERT: R 185 ARG cc_start: 0.7011 (ptp90) cc_final: 0.6692 (ptm-80) REVERT: R 280 GLN cc_start: 0.8758 (mm-40) cc_final: 0.8500 (mp10) REVERT: R 321 PHE cc_start: 0.7746 (t80) cc_final: 0.7432 (t80) REVERT: R 323 HIS cc_start: 0.7651 (OUTLIER) cc_final: 0.7070 (p-80) REVERT: D 27 VAL cc_start: 0.8990 (t) cc_final: 0.8576 (p) REVERT: E 40 LYS cc_start: 0.8024 (mttt) cc_final: 0.6951 (mppt) REVERT: A 243 ARG cc_start: 0.8699 (mmm-85) cc_final: 0.8489 (mtm180) REVERT: A 303 TYR cc_start: 0.8559 (t80) cc_final: 0.8285 (t80) REVERT: B 10 GLU cc_start: 0.7987 (tp30) cc_final: 0.7555 (tp30) REVERT: B 12 GLU cc_start: 0.9106 (tp30) cc_final: 0.8729 (pp20) REVERT: B 32 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8533 (pt0) REVERT: S 62 ASP cc_start: 0.8383 (t70) cc_final: 0.8175 (t70) REVERT: S 69 THR cc_start: 0.8663 (t) cc_final: 0.8287 (m) REVERT: S 87 ARG cc_start: 0.8509 (mtt-85) cc_final: 0.8299 (mtt-85) REVERT: S 171 GLN cc_start: 0.8270 (mp10) cc_final: 0.7828 (mp10) outliers start: 34 outliers final: 23 residues processed: 194 average time/residue: 0.6782 time to fit residues: 139.9812 Evaluate side-chains 192 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain R residue 221 ILE Chi-restraints excluded: chain R residue 279 THR Chi-restraints excluded: chain R residue 323 HIS Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 202 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 121 optimal weight: 4.9990 chunk 112 optimal weight: 0.3980 chunk 38 optimal weight: 10.0000 chunk 81 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 98 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 242 HIS A 194 ASN B 16 ASN B 259 GLN S 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.131331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.093884 restraints weight = 17986.215| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.87 r_work: 0.3105 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10068 Z= 0.137 Angle : 0.755 21.971 13679 Z= 0.374 Chirality : 0.045 0.280 1585 Planarity : 0.004 0.064 1729 Dihedral : 4.344 26.849 1374 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.83 % Allowed : 23.49 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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 aren not related in a simple way. whole: 0.57 (0.23), residues: 1260 helix: 1.96 (0.25), residues: 425 sheet: 0.27 (0.27), residues: 319 loop : -0.90 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 96 TYR 0.017 0.001 TYR S 178 PHE 0.028 0.001 PHE R 316 TRP 0.014 0.001 TRP R 104 HIS 0.003 0.001 HIS R 291 Details of bonding type rmsd covalent geometry : bond 0.00316 (10059) covalent geometry : angle 0.73906 (13661) SS BOND : bond 0.00722 ( 9) SS BOND : angle 4.36084 ( 18) hydrogen bonds : bond 0.03826 ( 477) hydrogen bonds : angle 4.47463 ( 1359) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4220.26 seconds wall clock time: 72 minutes 39.69 seconds (4359.69 seconds total)