Starting phenix.real_space_refine on Wed Apr 30 18:32:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xx6_38747/04_2025/8xx6_38747.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xx6_38747/04_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8xx6_38747/04_2025/8xx6_38747.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xx6_38747/04_2025/8xx6_38747.map" model { file = "/net/cci-nas-00/data/ceres_data/8xx6_38747/04_2025/8xx6_38747.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xx6_38747/04_2025/8xx6_38747.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: {'GLU:plan': 1, 'ARG:plan': 2} 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: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP: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, 'GLU:plan': 1, 'ARG: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: 5.69, per 1000 atoms: 0.58 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: 2.41 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.09 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: 2.95 Time building geometry restraints manager: 2.84 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: 1.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 23.980 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.670 ------------------------------------------------------------------------------- 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 : 4.30 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.24), 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 TRP 0.015 0.001 TRP B 211 HIS 0.002 0.001 HIS S 220 PHE 0.014 0.001 PHE B 234 TYR 0.016 0.001 TYR S 178 ARG 0.002 0.000 ARG S 72 Details of bonding type rmsd hydrogen bonds : bond 0.20912 ( 477) hydrogen bonds : angle 6.50163 ( 1359) SS BOND : bond 0.00256 ( 9) SS BOND : angle 1.40099 ( 18) covalent geometry : bond 0.00218 (10059) covalent geometry : angle 0.46572 (13661) *********************** 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 : 1.031 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: 1.1218 time to fit residues: 405.9794 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 : 1.155 ------------------------------------------------------------------------------- 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 105 optimal weight: 4.9990 chunk 94 optimal weight: 8.9990 chunk 52 optimal weight: 0.0170 chunk 32 optimal weight: 20.0000 chunk 63 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 97 optimal weight: 6.9990 chunk 37 optimal weight: 0.5980 chunk 59 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 113 optimal weight: 0.4980 overall best weight: 0.5218 ------------------------------------------------------------------------------- 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 = 0.3876 r_free = 0.3876 target = 0.134450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.097999 restraints weight = 17729.297| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.94 r_work: 0.3164 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 10068 Z= 0.132 Angle : 0.632 12.708 13679 Z= 0.327 Chirality : 0.044 0.185 1585 Planarity : 0.005 0.082 1729 Dihedral : 3.993 32.717 1376 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.96 % Allowed : 15.28 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.24), residues: 1260 helix: 2.22 (0.25), residues: 421 sheet: 0.01 (0.28), residues: 332 loop : -0.62 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 339 HIS 0.003 0.001 HIS S 220 PHE 0.014 0.001 PHE S 108 TYR 0.020 0.001 TYR S 178 ARG 0.010 0.001 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.04526 ( 477) hydrogen bonds : angle 4.81173 ( 1359) SS BOND : bond 0.00372 ( 9) SS BOND : angle 3.18789 ( 18) covalent geometry : bond 0.00295 (10059) covalent geometry : angle 0.62208 (13661) *********************** 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 264 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 222 time to evaluate : 1.120 Fit side-chains REVERT: R 61 LEU cc_start: 0.9032 (mt) cc_final: 0.8671 (mp) REVERT: R 94 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7772 (t70) REVERT: R 112 TRP cc_start: 0.7854 (t-100) cc_final: 0.7533 (t-100) REVERT: R 128 VAL cc_start: 0.8963 (p) cc_final: 0.8627 (m) REVERT: R 211 LEU cc_start: 0.8884 (mt) cc_final: 0.8552 (mp) REVERT: R 240 LYS cc_start: 0.8535 (ttpp) cc_final: 0.8290 (mtmm) REVERT: R 291 HIS cc_start: 0.8003 (m170) cc_final: 0.7510 (m170) REVERT: R 313 ILE cc_start: 0.9301 (tt) cc_final: 0.8846 (pt) REVERT: D 27 VAL cc_start: 0.8891 (t) cc_final: 0.8617 (m) REVERT: A 231 TYR cc_start: 0.8041 (m-80) cc_final: 0.7658 (m-80) REVERT: A 273 ASP cc_start: 0.7331 (p0) cc_final: 0.6974 (t0) REVERT: A 277 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.8097 (mp0) REVERT: A 307 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7258 (mp10) REVERT: B 12 GLU cc_start: 0.8962 (tp30) cc_final: 0.8667 (pp20) REVERT: B 32 GLN cc_start: 0.8737 (tt0) cc_final: 0.8481 (pt0) REVERT: B 213 VAL cc_start: 0.8899 (p) cc_final: 0.8643 (t) REVERT: G 47 GLU cc_start: 0.8289 (mp0) cc_final: 0.8033 (mp0) REVERT: S 69 THR cc_start: 0.8535 (t) cc_final: 0.8121 (m) REVERT: S 168 ARG cc_start: 0.8800 (mtt90) cc_final: 0.8549 (mtt90) REVERT: S 171 GLN cc_start: 0.7911 (mp10) cc_final: 0.7630 (mp10) REVERT: S 211 ASP cc_start: 0.8372 (m-30) cc_final: 0.7788 (m-30) outliers start: 42 outliers final: 10 residues processed: 244 average time/residue: 1.1835 time to fit residues: 309.6010 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 : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 141 SER 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 100 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 41 optimal weight: 0.0170 chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 chunk 103 optimal weight: 0.1980 chunk 92 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.0422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 283 GLN ** R 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 43 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 = 0.3853 r_free = 0.3853 target = 0.132832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.094803 restraints weight = 18049.094| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.77 r_work: 0.3128 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 10068 Z= 0.142 Angle : 0.643 18.573 13679 Z= 0.325 Chirality : 0.044 0.203 1585 Planarity : 0.004 0.060 1729 Dihedral : 4.130 28.882 1374 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.87 % Allowed : 18.21 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.24), residues: 1260 helix: 2.18 (0.25), residues: 427 sheet: 0.11 (0.28), residues: 342 loop : -0.78 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.004 0.001 HIS S 220 PHE 0.015 0.001 PHE S 108 TYR 0.025 0.001 TYR S 178 ARG 0.008 0.001 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.04142 ( 477) hydrogen bonds : angle 4.58485 ( 1359) SS BOND : bond 0.00872 ( 9) SS BOND : angle 3.09404 ( 18) covalent geometry : bond 0.00330 (10059) covalent geometry : angle 0.63342 (13661) *********************** 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 239 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 198 time to evaluate : 1.117 Fit side-chains REVERT: R 83 THR cc_start: 0.8717 (OUTLIER) cc_final: 0.8461 (t) REVERT: R 258 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8648 (mm) REVERT: R 283 GLN cc_start: 0.5961 (OUTLIER) cc_final: 0.5586 (pp30) REVERT: R 287 GLU cc_start: 0.8368 (pm20) cc_final: 0.8002 (pm20) REVERT: R 291 HIS cc_start: 0.7998 (m170) cc_final: 0.7528 (m170) REVERT: R 321 PHE cc_start: 0.7826 (t80) cc_final: 0.7625 (t80) REVERT: D 20 LYS cc_start: 0.8704 (pttm) cc_final: 0.8494 (pptt) REVERT: D 27 VAL cc_start: 0.8898 (t) cc_final: 0.8437 (p) REVERT: A 273 ASP cc_start: 0.7402 (p0) cc_final: 0.6987 (t0) REVERT: A 277 GLU cc_start: 0.8321 (mp0) cc_final: 0.8078 (mp0) REVERT: A 307 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7375 (mp10) REVERT: B 12 GLU cc_start: 0.8936 (tp30) cc_final: 0.8694 (pp20) REVERT: B 32 GLN cc_start: 0.8739 (tt0) cc_final: 0.8527 (pt0) REVERT: B 213 VAL cc_start: 0.8920 (p) cc_final: 0.8705 (t) REVERT: G 47 GLU cc_start: 0.8232 (mp0) cc_final: 0.7977 (mp0) REVERT: G 50 LEU cc_start: 0.8809 (mt) cc_final: 0.8540 (mt) REVERT: S 69 THR cc_start: 0.8518 (t) cc_final: 0.8138 (m) REVERT: S 73 ASP cc_start: 0.7214 (t0) cc_final: 0.6748 (t70) REVERT: S 171 GLN cc_start: 0.8036 (mp10) cc_final: 0.7691 (mp10) REVERT: S 183 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8931 (mp) REVERT: S 211 ASP cc_start: 0.8323 (m-30) cc_final: 0.7879 (m-30) outliers start: 41 outliers final: 15 residues processed: 224 average time/residue: 1.3194 time to fit residues: 316.4111 Evaluate side-chains 200 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 1.156 ------------------------------------------------------------------------------- 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 221 ILE Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 283 GLN 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 112 VAL Chi-restraints excluded: chain B residue 148 CYS 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 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 65 optimal weight: 2.9990 chunk 115 optimal weight: 30.0000 chunk 33 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 50 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 283 GLN A 43 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 = 0.3832 r_free = 0.3832 target = 0.131250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.092784 restraints weight = 17928.692| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.46 r_work: 0.3122 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 10068 Z= 0.157 Angle : 0.648 18.203 13679 Z= 0.331 Chirality : 0.044 0.262 1585 Planarity : 0.004 0.049 1729 Dihedral : 4.276 34.531 1374 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.15 % Allowed : 18.77 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.24), residues: 1260 helix: 2.14 (0.25), residues: 427 sheet: 0.04 (0.27), residues: 341 loop : -0.71 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 112 HIS 0.004 0.001 HIS S 220 PHE 0.011 0.001 PHE B 234 TYR 0.026 0.002 TYR S 178 ARG 0.008 0.001 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.04063 ( 477) hydrogen bonds : angle 4.47609 ( 1359) SS BOND : bond 0.00814 ( 9) SS BOND : angle 2.85534 ( 18) covalent geometry : bond 0.00367 (10059) covalent geometry : angle 0.64000 (13661) *********************** 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 236 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 192 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 83 THR cc_start: 0.8749 (OUTLIER) cc_final: 0.8511 (t) REVERT: R 90 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8342 (tt) REVERT: R 258 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8717 (mm) REVERT: R 287 GLU cc_start: 0.8526 (pm20) cc_final: 0.8092 (pm20) REVERT: R 291 HIS cc_start: 0.8076 (m170) cc_final: 0.7572 (m170) REVERT: R 321 PHE cc_start: 0.7916 (t80) cc_final: 0.7644 (t80) REVERT: D 27 VAL cc_start: 0.8999 (t) cc_final: 0.8544 (p) REVERT: A 243 ARG cc_start: 0.8631 (mmm-85) cc_final: 0.8268 (mtt180) REVERT: A 273 ASP cc_start: 0.7684 (p0) cc_final: 0.7220 (t0) REVERT: A 277 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8286 (mp0) REVERT: A 307 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.7628 (mp10) REVERT: B 10 GLU cc_start: 0.8132 (tp30) cc_final: 0.7586 (tp30) REVERT: B 12 GLU cc_start: 0.9009 (tp30) cc_final: 0.8697 (pp20) REVERT: B 13 GLN cc_start: 0.8375 (pp30) cc_final: 0.7917 (pp30) REVERT: B 32 GLN cc_start: 0.8758 (tt0) cc_final: 0.8538 (pt0) REVERT: B 45 MET cc_start: 0.8584 (mtt) cc_final: 0.7972 (mtt) REVERT: G 47 GLU cc_start: 0.8392 (mp0) cc_final: 0.8162 (mp0) REVERT: G 50 LEU cc_start: 0.8910 (mt) cc_final: 0.8644 (mt) REVERT: S 69 THR cc_start: 0.8646 (t) cc_final: 0.8260 (m) REVERT: S 171 GLN cc_start: 0.8259 (mp10) cc_final: 0.7780 (mp10) REVERT: S 211 ASP cc_start: 0.8331 (m-30) cc_final: 0.7860 (m-30) outliers start: 44 outliers final: 22 residues processed: 222 average time/residue: 1.4003 time to fit residues: 332.4639 Evaluate side-chains 203 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 176 time to evaluate : 1.581 ------------------------------------------------------------------------------- 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 190 SER Chi-restraints excluded: chain R residue 221 ILE Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 296 LEU Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 277 GLU 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 41 CYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 40 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 0 optimal weight: 40.0000 chunk 87 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 66 ASN R 242 HIS R 283 GLN A 346 ASN B 16 ASN B 259 GLN S 130 GLN S 174 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.127639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.088366 restraints weight = 17842.923| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.46 r_work: 0.3041 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 10068 Z= 0.271 Angle : 0.716 12.777 13679 Z= 0.371 Chirality : 0.048 0.316 1585 Planarity : 0.005 0.057 1729 Dihedral : 4.752 32.848 1374 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 5.19 % Allowed : 19.43 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.23), residues: 1260 helix: 1.89 (0.25), residues: 427 sheet: -0.07 (0.27), residues: 336 loop : -0.88 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 112 HIS 0.007 0.002 HIS S 220 PHE 0.014 0.002 PHE B 234 TYR 0.029 0.002 TYR S 178 ARG 0.014 0.001 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.04738 ( 477) hydrogen bonds : angle 4.70406 ( 1359) SS BOND : bond 0.01070 ( 9) SS BOND : angle 2.77467 ( 18) covalent geometry : bond 0.00641 (10059) covalent geometry : angle 0.70968 (13661) *********************** 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 237 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 182 time to evaluate : 1.094 Fit side-chains revert: symmetry clash REVERT: R 50 PHE cc_start: 0.8130 (m-80) cc_final: 0.7925 (m-80) REVERT: R 83 THR cc_start: 0.8794 (OUTLIER) cc_final: 0.8546 (t) REVERT: R 185 ARG cc_start: 0.7482 (ptm-80) cc_final: 0.7261 (ptp90) REVERT: R 258 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8783 (mm) REVERT: R 321 PHE cc_start: 0.8041 (t80) cc_final: 0.7802 (t80) REVERT: D 27 VAL cc_start: 0.9040 (t) cc_final: 0.8613 (p) REVERT: E 40 LYS cc_start: 0.7990 (mttt) cc_final: 0.6924 (mppt) REVERT: A 243 ARG cc_start: 0.8663 (mmm-85) cc_final: 0.8300 (mtt180) REVERT: A 273 ASP cc_start: 0.7737 (p0) cc_final: 0.7096 (t0) REVERT: A 277 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8233 (mp0) REVERT: A 307 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.7539 (mp10) REVERT: B 10 GLU cc_start: 0.8135 (tp30) cc_final: 0.7814 (tp30) REVERT: B 12 GLU cc_start: 0.9090 (tp30) cc_final: 0.8732 (pp20) REVERT: B 32 GLN cc_start: 0.8788 (tt0) cc_final: 0.8507 (pt0) REVERT: B 44 GLN cc_start: 0.8175 (mm-40) cc_final: 0.7877 (tp-100) REVERT: B 45 MET cc_start: 0.8563 (mtt) cc_final: 0.8184 (mtt) REVERT: G 47 GLU cc_start: 0.8489 (mp0) cc_final: 0.8233 (mp0) REVERT: G 50 LEU cc_start: 0.9104 (mt) cc_final: 0.8874 (mt) REVERT: S 13 GLN cc_start: 0.8858 (tp40) cc_final: 0.8632 (mm110) REVERT: S 69 THR cc_start: 0.8686 (t) cc_final: 0.8301 (m) REVERT: S 171 GLN cc_start: 0.8371 (mp10) cc_final: 0.7922 (mp10) REVERT: S 211 ASP cc_start: 0.8319 (m-30) cc_final: 0.7917 (m-30) outliers start: 55 outliers final: 24 residues processed: 217 average time/residue: 1.2353 time to fit residues: 287.0146 Evaluate side-chains 202 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 174 time to evaluate : 1.037 ------------------------------------------------------------------------------- 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 221 ILE 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 301 ILE Chi-restraints excluded: chain R residue 325 LEU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 218 ASP 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 14 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 91 optimal weight: 0.3980 chunk 45 optimal weight: 4.9990 chunk 115 optimal weight: 30.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3813 r_free = 0.3813 target = 0.129958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.090691 restraints weight = 17961.371| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.52 r_work: 0.3086 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10068 Z= 0.153 Angle : 0.656 14.366 13679 Z= 0.336 Chirality : 0.045 0.286 1585 Planarity : 0.004 0.047 1729 Dihedral : 4.439 30.792 1374 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.49 % Allowed : 22.17 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.24), residues: 1260 helix: 2.02 (0.25), residues: 427 sheet: -0.01 (0.27), residues: 337 loop : -0.85 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 112 HIS 0.003 0.001 HIS S 220 PHE 0.011 0.001 PHE B 234 TYR 0.021 0.001 TYR S 178 ARG 0.011 0.001 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.04057 ( 477) hydrogen bonds : angle 4.54048 ( 1359) SS BOND : bond 0.00844 ( 9) SS BOND : angle 2.90225 ( 18) covalent geometry : bond 0.00356 (10059) covalent geometry : angle 0.64770 (13661) *********************** 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 218 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 181 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 83 THR cc_start: 0.8744 (OUTLIER) cc_final: 0.8482 (t) REVERT: R 321 PHE cc_start: 0.7924 (t80) cc_final: 0.7683 (t80) REVERT: D 27 VAL cc_start: 0.8995 (t) cc_final: 0.8579 (p) REVERT: E 40 LYS cc_start: 0.8006 (mttt) cc_final: 0.6946 (mppt) REVERT: A 243 ARG cc_start: 0.8643 (mmm-85) cc_final: 0.8257 (mtt180) REVERT: A 273 ASP cc_start: 0.7798 (p0) cc_final: 0.7576 (p0) REVERT: A 307 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.7750 (mp10) REVERT: B 10 GLU cc_start: 0.8200 (tp30) cc_final: 0.7715 (tp30) REVERT: B 12 GLU cc_start: 0.9112 (tp30) cc_final: 0.8725 (pp20) REVERT: B 32 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8521 (pt0) REVERT: B 43 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8731 (mp) REVERT: B 44 GLN cc_start: 0.8120 (mm-40) cc_final: 0.7915 (tm-30) REVERT: B 96 ARG cc_start: 0.8447 (mtp-110) cc_final: 0.8230 (ttm110) REVERT: G 47 GLU cc_start: 0.8483 (mp0) cc_final: 0.8278 (mp0) REVERT: G 48 ASP cc_start: 0.8199 (t0) cc_final: 0.7967 (t0) REVERT: G 50 LEU cc_start: 0.9055 (mt) cc_final: 0.8807 (mt) REVERT: S 13 GLN cc_start: 0.8847 (tp40) cc_final: 0.8631 (mm110) REVERT: S 69 THR cc_start: 0.8660 (t) cc_final: 0.8279 (m) REVERT: S 87 ARG cc_start: 0.8440 (mtt-85) cc_final: 0.8222 (mtt-85) REVERT: S 171 GLN cc_start: 0.8312 (mp10) cc_final: 0.7752 (mp10) REVERT: S 211 ASP cc_start: 0.8281 (m-30) cc_final: 0.7843 (m-30) outliers start: 37 outliers final: 16 residues processed: 206 average time/residue: 1.3359 time to fit residues: 294.0130 Evaluate side-chains 189 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 1.024 ------------------------------------------------------------------------------- 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 301 ILE 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 32 GLN Chi-restraints excluded: chain B residue 43 ILE 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 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 202 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 107 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 95 optimal weight: 0.0370 chunk 7 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.0064 ------------------------------------------------------------------------------- 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 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 = 0.3823 r_free = 0.3823 target = 0.130601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.091684 restraints weight = 18150.213| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.52 r_work: 0.3103 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10068 Z= 0.138 Angle : 0.656 16.608 13679 Z= 0.334 Chirality : 0.044 0.274 1585 Planarity : 0.004 0.047 1729 Dihedral : 4.319 28.042 1374 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.49 % Allowed : 21.89 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.24), residues: 1260 helix: 2.16 (0.25), residues: 426 sheet: 0.11 (0.27), residues: 328 loop : -0.83 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 112 HIS 0.003 0.001 HIS S 220 PHE 0.012 0.001 PHE B 234 TYR 0.020 0.001 TYR S 178 ARG 0.013 0.001 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.03827 ( 477) hydrogen bonds : angle 4.45531 ( 1359) SS BOND : bond 0.00814 ( 9) SS BOND : angle 3.25932 ( 18) covalent geometry : bond 0.00318 (10059) covalent geometry : angle 0.64615 (13661) *********************** 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 214 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 177 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 83 THR cc_start: 0.8734 (OUTLIER) cc_final: 0.8493 (t) REVERT: R 321 PHE cc_start: 0.8037 (t80) cc_final: 0.7822 (t80) REVERT: D 27 VAL cc_start: 0.8967 (t) cc_final: 0.8533 (p) REVERT: E 40 LYS cc_start: 0.7990 (mttt) cc_final: 0.6956 (mppt) REVERT: A 243 ARG cc_start: 0.8643 (mmm-85) cc_final: 0.8279 (mtt180) REVERT: A 273 ASP cc_start: 0.7743 (p0) cc_final: 0.7237 (p0) REVERT: B 10 GLU cc_start: 0.8037 (tp30) cc_final: 0.7488 (tp30) REVERT: B 12 GLU cc_start: 0.9100 (tp30) cc_final: 0.8727 (pp20) REVERT: B 13 GLN cc_start: 0.8470 (pp30) cc_final: 0.7791 (pp30) REVERT: B 32 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8541 (pt0) REVERT: G 47 GLU cc_start: 0.8496 (mp0) cc_final: 0.8287 (mp0) REVERT: G 50 LEU cc_start: 0.9044 (mt) cc_final: 0.8805 (mt) REVERT: S 13 GLN cc_start: 0.8736 (tp40) cc_final: 0.8509 (mm110) REVERT: S 69 THR cc_start: 0.8674 (t) cc_final: 0.8292 (m) REVERT: S 87 ARG cc_start: 0.8460 (mtt-85) cc_final: 0.8191 (mtt-85) REVERT: S 171 GLN cc_start: 0.8270 (mp10) cc_final: 0.7699 (mp10) outliers start: 37 outliers final: 19 residues processed: 199 average time/residue: 1.3098 time to fit residues: 279.7913 Evaluate side-chains 191 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 170 time to evaluate : 1.190 ------------------------------------------------------------------------------- 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 221 ILE Chi-restraints excluded: chain D residue 42 LYS Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 61 MET 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 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 202 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 30 optimal weight: 0.3980 chunk 98 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 123 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3823 r_free = 0.3823 target = 0.130624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.092842 restraints weight = 18071.392| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.59 r_work: 0.3099 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10068 Z= 0.141 Angle : 0.685 18.280 13679 Z= 0.343 Chirality : 0.044 0.258 1585 Planarity : 0.004 0.048 1729 Dihedral : 4.280 26.228 1374 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.30 % Allowed : 22.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.24), residues: 1260 helix: 2.19 (0.25), residues: 426 sheet: 0.15 (0.27), residues: 328 loop : -0.87 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 63 HIS 0.004 0.001 HIS B 62 PHE 0.012 0.001 PHE B 234 TYR 0.021 0.001 TYR S 178 ARG 0.014 0.001 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.03810 ( 477) hydrogen bonds : angle 4.43461 ( 1359) SS BOND : bond 0.00909 ( 9) SS BOND : angle 3.55691 ( 18) covalent geometry : bond 0.00328 (10059) covalent geometry : angle 0.67332 (13661) *********************** 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 209 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 174 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 83 THR cc_start: 0.8739 (OUTLIER) cc_final: 0.8496 (t) REVERT: R 321 PHE cc_start: 0.8048 (t80) cc_final: 0.7794 (t80) REVERT: D 27 VAL cc_start: 0.8970 (t) cc_final: 0.8549 (p) REVERT: E 40 LYS cc_start: 0.7964 (mttt) cc_final: 0.6942 (mppt) REVERT: A 243 ARG cc_start: 0.8632 (mmm-85) cc_final: 0.8269 (mtt180) REVERT: A 303 TYR cc_start: 0.8571 (t80) cc_final: 0.8315 (t80) REVERT: B 10 GLU cc_start: 0.8056 (tp30) cc_final: 0.7624 (tp30) REVERT: B 12 GLU cc_start: 0.9111 (tp30) cc_final: 0.8725 (pp20) REVERT: B 13 GLN cc_start: 0.8475 (pp30) cc_final: 0.8043 (pp30) REVERT: B 32 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8525 (pt0) REVERT: G 47 GLU cc_start: 0.8499 (mp0) cc_final: 0.8282 (mp0) REVERT: G 48 ASP cc_start: 0.8155 (t0) cc_final: 0.7915 (t0) REVERT: G 50 LEU cc_start: 0.9031 (mt) cc_final: 0.8785 (mt) REVERT: S 13 GLN cc_start: 0.8756 (tp40) cc_final: 0.8543 (mm110) REVERT: S 69 THR cc_start: 0.8676 (t) cc_final: 0.8298 (m) REVERT: S 171 GLN cc_start: 0.8242 (mp10) cc_final: 0.7669 (mp10) outliers start: 35 outliers final: 25 residues processed: 193 average time/residue: 1.3118 time to fit residues: 270.6773 Evaluate side-chains 195 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 168 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 92 LEU 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 221 ILE Chi-restraints excluded: chain R residue 279 THR 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 292 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 61 MET 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 91 THR 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 92 optimal weight: 3.9990 chunk 12 optimal weight: 0.0770 chunk 8 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 41 optimal weight: 30.0000 chunk 104 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 overall best weight: 2.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 216 GLN R 242 HIS A 194 ASN B 16 ASN 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 = 0.3788 r_free = 0.3788 target = 0.128020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.088285 restraints weight = 18131.404| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.54 r_work: 0.3043 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 10068 Z= 0.244 Angle : 0.782 21.952 13679 Z= 0.395 Chirality : 0.048 0.298 1585 Planarity : 0.005 0.054 1729 Dihedral : 4.651 29.606 1374 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.87 % Allowed : 22.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.23), residues: 1260 helix: 1.98 (0.25), residues: 426 sheet: -0.05 (0.27), residues: 328 loop : -0.91 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 104 HIS 0.006 0.001 HIS B 62 PHE 0.014 0.002 PHE B 234 TYR 0.026 0.002 TYR S 178 ARG 0.015 0.001 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.04484 ( 477) hydrogen bonds : angle 4.64735 ( 1359) SS BOND : bond 0.01133 ( 9) SS BOND : angle 4.19269 ( 18) covalent geometry : bond 0.00578 (10059) covalent geometry : angle 0.76721 (13661) *********************** 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 212 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 171 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 83 THR cc_start: 0.8786 (OUTLIER) cc_final: 0.8532 (t) REVERT: R 321 PHE cc_start: 0.8042 (t80) cc_final: 0.7830 (t80) REVERT: D 27 VAL cc_start: 0.9044 (t) cc_final: 0.8628 (p) REVERT: E 40 LYS cc_start: 0.8027 (mttt) cc_final: 0.7021 (mppt) REVERT: A 243 ARG cc_start: 0.8641 (mmm-85) cc_final: 0.8307 (mtt180) REVERT: B 10 GLU cc_start: 0.8138 (tp30) cc_final: 0.7634 (tp30) REVERT: B 12 GLU cc_start: 0.9097 (tp30) cc_final: 0.8719 (pp20) REVERT: B 13 GLN cc_start: 0.8476 (pp30) cc_final: 0.7996 (pp30) REVERT: B 32 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8469 (pt0) REVERT: B 43 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8730 (mp) REVERT: G 47 GLU cc_start: 0.8529 (mp0) cc_final: 0.8322 (mp0) REVERT: S 13 GLN cc_start: 0.8819 (tp40) cc_final: 0.8582 (mm110) REVERT: S 69 THR cc_start: 0.8712 (t) cc_final: 0.8331 (m) REVERT: S 171 GLN cc_start: 0.8411 (mp10) cc_final: 0.7923 (mp10) outliers start: 41 outliers final: 29 residues processed: 193 average time/residue: 1.3384 time to fit residues: 275.9629 Evaluate side-chains 199 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 70 MET Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 92 LEU 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 243 MET Chi-restraints excluded: chain R residue 279 THR Chi-restraints excluded: chain R residue 301 ILE Chi-restraints excluded: chain R residue 323 HIS Chi-restraints excluded: chain R residue 325 LEU 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 277 GLU 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 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 202 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 52 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 216 GLN R 242 HIS A 194 ASN B 16 ASN 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 = 0.3814 r_free = 0.3814 target = 0.129957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.090758 restraints weight = 18051.630| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.52 r_work: 0.3090 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 10068 Z= 0.155 Angle : 0.733 21.661 13679 Z= 0.367 Chirality : 0.045 0.232 1585 Planarity : 0.005 0.062 1729 Dihedral : 4.464 26.388 1374 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.49 % Allowed : 22.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.23), residues: 1260 helix: 2.07 (0.25), residues: 426 sheet: 0.04 (0.27), residues: 326 loop : -0.94 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 47 HIS 0.003 0.001 HIS S 220 PHE 0.012 0.001 PHE B 234 TYR 0.021 0.001 TYR S 178 ARG 0.016 0.001 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.04002 ( 477) hydrogen bonds : angle 4.53875 ( 1359) SS BOND : bond 0.00797 ( 9) SS BOND : angle 4.00065 ( 18) covalent geometry : bond 0.00365 (10059) covalent geometry : angle 0.71912 (13661) ********************** 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: 37 poor density : 170 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 83 THR cc_start: 0.8728 (OUTLIER) cc_final: 0.8469 (t) REVERT: R 280 GLN cc_start: 0.8807 (mm-40) cc_final: 0.8525 (mp10) REVERT: D 27 VAL cc_start: 0.9011 (t) cc_final: 0.8601 (p) REVERT: E 40 LYS cc_start: 0.8020 (mttt) cc_final: 0.6957 (mppt) REVERT: A 303 TYR cc_start: 0.8551 (t80) cc_final: 0.8297 (t80) REVERT: B 10 GLU cc_start: 0.8040 (tp30) cc_final: 0.7610 (tp30) REVERT: B 12 GLU cc_start: 0.9107 (tp30) cc_final: 0.8726 (pp20) REVERT: B 13 GLN cc_start: 0.8464 (pp30) cc_final: 0.8065 (pp30) REVERT: B 32 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8470 (pt0) REVERT: G 47 GLU cc_start: 0.8520 (mp0) cc_final: 0.8317 (mp0) REVERT: S 13 GLN cc_start: 0.8789 (tp40) cc_final: 0.8562 (mm110) REVERT: S 69 THR cc_start: 0.8686 (t) cc_final: 0.8298 (m) REVERT: S 87 ARG cc_start: 0.8491 (mtt-85) cc_final: 0.8279 (mtt-85) REVERT: S 171 GLN cc_start: 0.8291 (mp10) cc_final: 0.7801 (mp10) outliers start: 37 outliers final: 25 residues processed: 193 average time/residue: 1.2447 time to fit residues: 257.5353 Evaluate side-chains 192 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 70 MET Chi-restraints excluded: chain R residue 71 LEU 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 279 THR Chi-restraints excluded: chain R residue 325 LEU Chi-restraints excluded: chain D residue 42 LYS 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 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 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 202 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 70 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 E 57 GLN 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 = 0.3826 r_free = 0.3826 target = 0.130701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.092693 restraints weight = 17891.361| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.60 r_work: 0.3096 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 10068 Z= 0.143 Angle : 0.726 21.212 13679 Z= 0.363 Chirality : 0.044 0.200 1585 Planarity : 0.005 0.057 1729 Dihedral : 4.387 30.415 1374 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.74 % Allowed : 23.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.23), residues: 1260 helix: 2.01 (0.25), residues: 426 sheet: 0.11 (0.27), residues: 325 loop : -0.92 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 104 HIS 0.003 0.001 HIS R 323 PHE 0.011 0.001 PHE B 234 TYR 0.019 0.001 TYR S 178 ARG 0.015 0.001 ARG A 313 Details of bonding type rmsd hydrogen bonds : bond 0.03834 ( 477) hydrogen bonds : angle 4.50257 ( 1359) SS BOND : bond 0.00637 ( 9) SS BOND : angle 3.90652 ( 18) covalent geometry : bond 0.00338 (10059) covalent geometry : angle 0.71220 (13661) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9345.16 seconds wall clock time: 163 minutes 28.08 seconds (9808.08 seconds total)