Starting phenix.real_space_refine on Tue May 13 02:16:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xxh_38749/05_2025/8xxh_38749.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xxh_38749/05_2025/8xxh_38749.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xxh_38749/05_2025/8xxh_38749.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xxh_38749/05_2025/8xxh_38749.map" model { file = "/net/cci-nas-00/data/ceres_data/8xxh_38749/05_2025/8xxh_38749.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xxh_38749/05_2025/8xxh_38749.cif" } resolution = 2.8 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 70 5.16 5 C 6148 2.51 5 N 1641 2.21 5 O 1787 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 9646 Number of models: 1 Model: "" Number of chains: 7 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 Chain: "R" Number of atoms: 2367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2367 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 288} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 496 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 63} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 425 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 55} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 7.03, per 1000 atoms: 0.73 Number of scatterers: 9646 At special positions: 0 Unit cell: (88.1875, 122.425, 151.475, 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 70 16.00 O 1787 8.00 N 1641 7.00 C 6148 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 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 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 9 " - pdb=" SG CYS D 35 " distance=2.03 Simple disulfide: pdb=" SG CYS D 11 " - pdb=" SG CYS D 51 " distance=2.03 Simple disulfide: pdb=" SG CYS E 9 " - pdb=" SG CYS E 35 " distance=2.03 Simple disulfide: pdb=" SG CYS E 11 " - pdb=" SG CYS E 51 " 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: 2.42 Conformation dependent library (CDL) restraints added in 1.2 seconds 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2368 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 16 sheets defined 35.7% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... 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: 5.193A 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: 3.705A 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: 3.645A 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 helix chain 'R' and resid 44 through 76 removed outlier: 3.601A pdb=" N PHE R 50 " --> pdb=" O ILE R 46 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL R 52 " --> pdb=" O LYS R 48 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE R 53 " --> pdb=" O TYR R 49 " (cutoff:3.500A) removed outlier: 4.409A 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 153 through 160 removed outlier: 3.833A pdb=" N THR R 156 " --> pdb=" O ARG R 153 " (cutoff:3.500A) removed outlier: 3.622A 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: 3.588A 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 240 removed outlier: 3.662A 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 330 removed outlier: 3.848A pdb=" N ALA R 330 " --> pdb=" O LEU R 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 21 No H-bonds generated for 'chain 'D' and resid 19 through 21' Processing helix chain 'D' and resid 56 through 69 removed outlier: 3.808A pdb=" N LYS D 60 " --> pdb=" O SER D 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 68 removed outlier: 3.915A pdb=" N LYS E 60 " --> pdb=" O SER E 56 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 188 Processing sheet with id=AA2, 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: 7.202A pdb=" N LYS A 35 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N ILE A 223 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.151A 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: 7.154A 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=AA3, 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=AA4, 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: 6.178A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, 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: 6.408A 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=AA6, 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: 5.174A 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: 3.536A 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=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.567A 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: 7.100A 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=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.406A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.269A 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: 6.531A 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=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.394A 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: 6.970A 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: 6.816A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, 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: 4.734A 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=AB3, first strand: chain 'S' and resid 128 through 130 removed outlier: 3.511A pdb=" N ALA S 199 " --> pdb=" O SER S 196 " (cutoff:3.500A) Processing sheet with id=AB4, 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: 6.278A 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=AB5, 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) Processing sheet with id=AB6, first strand: chain 'R' and resid 184 through 187 Processing sheet with id=AB7, first strand: chain 'D' and resid 49 through 52 removed outlier: 4.240A pdb=" N VAL D 40 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR E 43 " --> pdb=" O GLN E 24 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N VAL E 26 " --> pdb=" O ILE E 41 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE E 41 " --> pdb=" O VAL E 26 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL E 28 " --> pdb=" O GLU E 39 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLU E 39 " --> pdb=" O VAL E 28 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL E 40 " --> pdb=" O LEU E 52 " (cutoff:3.500A) 470 hydrogen bonds defined for protein. 1323 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: 2.92 Time building geometry restraints manager: 2.79 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: 1639 1.32 - 1.45: 2572 1.45 - 1.57: 5528 1.57 - 1.70: 0 1.70 - 1.82: 97 Bond restraints: 9836 Sorted by residual: bond pdb=" C ASN B 88 " pdb=" O ASN B 88 " ideal model delta sigma weight residual 1.234 1.197 0.037 1.22e-02 6.72e+03 9.29e+00 bond pdb=" N GLN E 13 " pdb=" CA GLN E 13 " ideal model delta sigma weight residual 1.455 1.482 -0.026 1.25e-02 6.40e+03 4.39e+00 bond pdb=" C GLN E 13 " pdb=" O GLN E 13 " ideal model delta sigma weight residual 1.235 1.253 -0.018 1.22e-02 6.72e+03 2.22e+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 1.81e+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 ... (remaining 9831 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 12879 1.08 - 2.16: 394 2.16 - 3.24: 61 3.24 - 4.32: 22 4.32 - 5.40: 6 Bond angle restraints: 13362 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 115.89 110.49 5.40 1.32e+00 5.74e-01 1.67e+01 angle pdb=" CA ASN B 88 " pdb=" C ASN B 88 " pdb=" O ASN B 88 " ideal model delta sigma weight residual 121.16 117.11 4.05 1.13e+00 7.83e-01 1.28e+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 121.90 118.91 2.99 1.26e+00 6.30e-01 5.64e+00 angle pdb=" N ASN B 88 " pdb=" CA ASN B 88 " pdb=" C ASN B 88 " ideal model delta sigma weight residual 109.95 106.31 3.64 1.59e+00 3.96e-01 5.24e+00 ... (remaining 13357 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 5411 17.97 - 35.95: 389 35.95 - 53.92: 55 53.92 - 71.90: 13 71.90 - 89.87: 5 Dihedral angle restraints: 5873 sinusoidal: 2209 harmonic: 3664 Sorted by residual: 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 93.00 140.05 -47.05 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 180.00 162.34 17.66 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CB GLU B 172 " pdb=" CG GLU B 172 " pdb=" CD GLU B 172 " pdb=" OE1 GLU B 172 " ideal model delta sinusoidal sigma weight residual 0.00 86.50 -86.50 1 3.00e+01 1.11e-03 1.00e+01 ... (remaining 5870 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1052 0.034 - 0.067: 361 0.067 - 0.101: 96 0.101 - 0.134: 58 0.134 - 0.168: 3 Chirality restraints: 1570 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 7.02e-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 2.60 -0.16 2.00e-01 2.50e+01 6.78e-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 5.67e-01 ... (remaining 1567 not shown) Planarity restraints: 1689 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL G 54 " -0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO G 55 " 0.070 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 3.79e-02 2.30e+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 1.35e-02 1.83e+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 1686 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1495 2.76 - 3.30: 9053 3.30 - 3.83: 15483 3.83 - 4.37: 18294 4.37 - 4.90: 32767 Nonbonded interactions: 77092 Sorted by model distance: 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 nonbonded pdb=" OD1 ASN A 270 " pdb=" OG1 THR A 324 " model vdw 2.317 3.040 ... (remaining 77087 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 9 through 11 or (resid 12 through 13 and (name N or name C \ A or name C or name O or name CB )) or resid 14 through 36 or (resid 37 and (nam \ e N or name CA or name C or name O or name CB )) or resid 38 through 68)) selection = (chain 'E' and (resid 9 through 63 or (resid 64 through 65 and (name N or name C \ A or name C or name O or name CB )) or resid 66 through 67 or (resid 68 and (nam \ e N or name CA or name C or name O or name CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.780 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9845 Z= 0.140 Angle : 0.483 5.399 13380 Z= 0.279 Chirality : 0.040 0.168 1570 Planarity : 0.003 0.040 1689 Dihedral : 12.741 89.870 3478 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.50 (0.24), residues: 1246 helix: 1.69 (0.26), residues: 407 sheet: -0.02 (0.28), residues: 343 loop : -0.46 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.007 0.001 HIS R 150 PHE 0.014 0.001 PHE B 234 TYR 0.016 0.001 TYR S 178 ARG 0.003 0.000 ARG R 159 Details of bonding type rmsd hydrogen bonds : bond 0.20772 ( 464) hydrogen bonds : angle 6.65477 ( 1323) SS BOND : bond 0.00302 ( 9) SS BOND : angle 1.51783 ( 18) covalent geometry : bond 0.00274 ( 9836) covalent geometry : angle 0.48004 (13362) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 1.124 Fit side-chains revert: symmetry clash REVERT: A 243 ARG cc_start: 0.8021 (mtt180) cc_final: 0.7586 (tpp80) REVERT: A 244 MET cc_start: 0.8541 (tpp) cc_final: 0.8161 (tpp) REVERT: B 16 ASN cc_start: 0.8103 (m-40) cc_final: 0.7896 (m-40) REVERT: B 138 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7981 (mt-10) REVERT: B 221 THR cc_start: 0.8859 (t) cc_final: 0.8638 (m) REVERT: G 38 MET cc_start: 0.8376 (ttm) cc_final: 0.8158 (ttp) REVERT: G 52 THR cc_start: 0.7504 (p) cc_final: 0.7275 (t) REVERT: S 132 THR cc_start: 0.8256 (t) cc_final: 0.8045 (p) REVERT: R 112 TRP cc_start: 0.6078 (t-100) cc_final: 0.5732 (t-100) REVERT: R 272 LEU cc_start: 0.8131 (tp) cc_final: 0.7885 (tt) outliers start: 0 outliers final: 1 residues processed: 301 average time/residue: 1.1217 time to fit residues: 362.5035 Evaluate side-chains 158 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 295 ASN A 333 GLN B 88 ASN B 119 ASN B 266 HIS B 340 ASN S 130 GLN R 242 HIS R 319 GLN D 10 GLN D 48 GLN E 24 GLN E 48 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.139906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.091309 restraints weight = 16807.387| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.39 r_work: 0.3067 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 9845 Z= 0.231 Angle : 0.718 17.931 13380 Z= 0.371 Chirality : 0.047 0.254 1570 Planarity : 0.005 0.047 1689 Dihedral : 4.878 73.103 1353 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.05 % Allowed : 15.93 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.83 (0.24), residues: 1246 helix: 2.16 (0.25), residues: 408 sheet: 0.22 (0.28), residues: 323 loop : -0.50 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 112 HIS 0.008 0.002 HIS B 62 PHE 0.024 0.002 PHE S 108 TYR 0.039 0.002 TYR B 105 ARG 0.007 0.001 ARG S 148 Details of bonding type rmsd hydrogen bonds : bond 0.05043 ( 464) hydrogen bonds : angle 4.87974 ( 1323) SS BOND : bond 0.01023 ( 9) SS BOND : angle 3.61974 ( 18) covalent geometry : bond 0.00546 ( 9836) covalent geometry : angle 0.70626 (13362) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 166 time to evaluate : 1.168 Fit side-chains REVERT: A 280 LYS cc_start: 0.8232 (mmpt) cc_final: 0.7796 (ptpt) REVERT: A 354 TYR cc_start: 0.6887 (t80) cc_final: 0.6670 (t80) REVERT: B 52 ARG cc_start: 0.9086 (OUTLIER) cc_final: 0.7864 (ptp90) REVERT: B 98 SER cc_start: 0.9191 (OUTLIER) cc_final: 0.8864 (t) REVERT: B 175 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7447 (mp-120) REVERT: B 269 ILE cc_start: 0.8372 (mm) cc_final: 0.8076 (mm) REVERT: G 28 ILE cc_start: 0.9085 (pt) cc_final: 0.8857 (pp) REVERT: G 58 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7661 (mp0) REVERT: S 1 ASP cc_start: 0.7699 (p0) cc_final: 0.7389 (p0) REVERT: S 34 MET cc_start: 0.9293 (OUTLIER) cc_final: 0.9015 (mmt) REVERT: S 87 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.8107 (mtt-85) REVERT: S 190 ARG cc_start: 0.8529 (ptt-90) cc_final: 0.8223 (ptt-90) REVERT: S 211 ASP cc_start: 0.8698 (m-30) cc_final: 0.8448 (m-30) REVERT: R 49 TYR cc_start: 0.7387 (OUTLIER) cc_final: 0.6972 (t80) REVERT: R 139 CYS cc_start: 0.8393 (m) cc_final: 0.8193 (m) REVERT: R 272 LEU cc_start: 0.8548 (tp) cc_final: 0.8257 (tt) REVERT: R 329 LEU cc_start: 0.5986 (pp) cc_final: 0.5340 (tt) outliers start: 42 outliers final: 14 residues processed: 188 average time/residue: 1.1893 time to fit residues: 239.7208 Evaluate side-chains 163 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 58 GLU Chi-restraints excluded: chain S residue 34 MET Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 204 ILE Chi-restraints excluded: chain R residue 49 TYR Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 53 ILE Chi-restraints excluded: chain R residue 92 LEU Chi-restraints excluded: chain R residue 132 SER Chi-restraints excluded: chain R residue 222 VAL Chi-restraints excluded: chain R residue 281 VAL Chi-restraints excluded: chain D residue 5 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 119 optimal weight: 30.0000 chunk 84 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 63 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 GLN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.140296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.092518 restraints weight = 16939.359| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.34 r_work: 0.3076 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 9845 Z= 0.159 Angle : 0.649 18.206 13380 Z= 0.330 Chirality : 0.045 0.292 1570 Planarity : 0.004 0.049 1689 Dihedral : 4.181 20.394 1351 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.86 % Allowed : 17.57 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.24), residues: 1246 helix: 2.12 (0.26), residues: 408 sheet: 0.27 (0.28), residues: 326 loop : -0.59 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.004 0.001 HIS B 62 PHE 0.017 0.002 PHE R 59 TYR 0.026 0.001 TYR S 178 ARG 0.009 0.001 ARG S 148 Details of bonding type rmsd hydrogen bonds : bond 0.04386 ( 464) hydrogen bonds : angle 4.60095 ( 1323) SS BOND : bond 0.00684 ( 9) SS BOND : angle 2.84241 ( 18) covalent geometry : bond 0.00371 ( 9836) covalent geometry : angle 0.64110 (13362) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 157 time to evaluate : 1.069 Fit side-chains revert: symmetry clash REVERT: A 250 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8786 (tt) REVERT: A 280 LYS cc_start: 0.8201 (mmpt) cc_final: 0.7904 (ptpt) REVERT: A 354 TYR cc_start: 0.6966 (t80) cc_final: 0.6704 (t80) REVERT: B 10 GLU cc_start: 0.8808 (tp30) cc_final: 0.8588 (tp30) REVERT: B 52 ARG cc_start: 0.9034 (OUTLIER) cc_final: 0.7752 (ptp90) REVERT: B 175 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7372 (mp-120) REVERT: B 269 ILE cc_start: 0.8360 (mm) cc_final: 0.8126 (mm) REVERT: B 335 PHE cc_start: 0.8965 (m-80) cc_final: 0.8703 (m-80) REVERT: S 34 MET cc_start: 0.9326 (OUTLIER) cc_final: 0.8986 (mmt) REVERT: S 87 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8110 (mtt-85) REVERT: S 211 ASP cc_start: 0.8734 (m-30) cc_final: 0.8471 (m-30) REVERT: R 49 TYR cc_start: 0.7352 (OUTLIER) cc_final: 0.6940 (t80) REVERT: R 53 ILE cc_start: 0.7445 (OUTLIER) cc_final: 0.7195 (pp) REVERT: R 70 MET cc_start: 0.7129 (mtm) cc_final: 0.6825 (mtm) REVERT: R 272 LEU cc_start: 0.8530 (tp) cc_final: 0.8220 (tt) outliers start: 40 outliers final: 16 residues processed: 180 average time/residue: 1.0961 time to fit residues: 212.0401 Evaluate side-chains 166 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 34 MET Chi-restraints excluded: chain S residue 76 LYS Chi-restraints excluded: chain S residue 87 ARG Chi-restraints excluded: chain S residue 204 ILE Chi-restraints excluded: chain R residue 49 TYR Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 53 ILE Chi-restraints excluded: chain R residue 130 PHE Chi-restraints excluded: chain R residue 132 SER Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 222 VAL Chi-restraints excluded: chain D residue 5 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 1 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 114 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 31 optimal weight: 8.9990 chunk 104 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 54 optimal weight: 8.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN B 75 GLN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.141052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.092803 restraints weight = 16783.057| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.36 r_work: 0.3091 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9845 Z= 0.130 Angle : 0.626 18.704 13380 Z= 0.318 Chirality : 0.044 0.247 1570 Planarity : 0.004 0.049 1689 Dihedral : 4.057 18.866 1351 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.15 % Allowed : 17.18 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.84 (0.24), residues: 1246 helix: 2.06 (0.26), residues: 412 sheet: 0.46 (0.28), residues: 314 loop : -0.58 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 339 HIS 0.003 0.001 HIS S 220 PHE 0.013 0.001 PHE R 59 TYR 0.025 0.001 TYR S 178 ARG 0.008 0.000 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.03951 ( 464) hydrogen bonds : angle 4.44840 ( 1323) SS BOND : bond 0.00518 ( 9) SS BOND : angle 2.85946 ( 18) covalent geometry : bond 0.00296 ( 9836) covalent geometry : angle 0.61799 (13362) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 156 time to evaluate : 1.173 Fit side-chains revert: symmetry clash REVERT: A 280 LYS cc_start: 0.8245 (mmpt) cc_final: 0.7974 (ptpt) REVERT: A 307 GLN cc_start: 0.9041 (mm-40) cc_final: 0.8787 (mm110) REVERT: B 10 GLU cc_start: 0.8785 (tp30) cc_final: 0.8494 (tp30) REVERT: B 14 LEU cc_start: 0.8999 (mm) cc_final: 0.8761 (mm) REVERT: B 52 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.7712 (ptp90) REVERT: B 175 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7417 (mp-120) REVERT: B 260 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.8715 (tt0) REVERT: B 269 ILE cc_start: 0.8341 (mm) cc_final: 0.8114 (mm) REVERT: B 335 PHE cc_start: 0.8989 (m-80) cc_final: 0.8716 (m-80) REVERT: S 211 ASP cc_start: 0.8750 (m-30) cc_final: 0.8477 (m-30) REVERT: S 232 LYS cc_start: 0.8978 (tttm) cc_final: 0.8768 (tttt) REVERT: R 53 ILE cc_start: 0.7482 (OUTLIER) cc_final: 0.7221 (pp) REVERT: R 63 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8123 (pp) REVERT: R 272 LEU cc_start: 0.8529 (tp) cc_final: 0.8190 (tt) REVERT: D 8 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7207 (mtt90) REVERT: E 66 MET cc_start: 0.6780 (OUTLIER) cc_final: 0.6279 (mpt) outliers start: 43 outliers final: 16 residues processed: 182 average time/residue: 1.1900 time to fit residues: 232.1988 Evaluate side-chains 162 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 52 ARG 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 175 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain S residue 76 LYS Chi-restraints excluded: chain S residue 204 ILE Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 53 ILE Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 132 SER Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain D residue 8 ARG Chi-restraints excluded: chain E residue 66 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 113 optimal weight: 30.0000 chunk 89 optimal weight: 1.9990 chunk 121 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 chunk 2 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 53 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.139542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.090928 restraints weight = 16795.280| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.37 r_work: 0.3051 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 9845 Z= 0.171 Angle : 0.654 20.496 13380 Z= 0.334 Chirality : 0.045 0.249 1570 Planarity : 0.004 0.050 1689 Dihedral : 4.174 22.372 1351 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.15 % Allowed : 18.34 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.90 (0.24), residues: 1246 helix: 2.14 (0.26), residues: 412 sheet: 0.44 (0.28), residues: 314 loop : -0.54 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 112 HIS 0.004 0.001 HIS B 62 PHE 0.015 0.002 PHE R 164 TYR 0.028 0.001 TYR S 178 ARG 0.010 0.001 ARG S 148 Details of bonding type rmsd hydrogen bonds : bond 0.04178 ( 464) hydrogen bonds : angle 4.43628 ( 1323) SS BOND : bond 0.00756 ( 9) SS BOND : angle 2.68064 ( 18) covalent geometry : bond 0.00402 ( 9836) covalent geometry : angle 0.64745 (13362) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 146 time to evaluate : 1.139 Fit side-chains revert: symmetry clash REVERT: A 280 LYS cc_start: 0.8298 (mmpt) cc_final: 0.8027 (ptpt) REVERT: A 354 TYR cc_start: 0.7042 (t80) cc_final: 0.6724 (t80) REVERT: B 10 GLU cc_start: 0.8771 (tp30) cc_final: 0.8412 (tp30) REVERT: B 52 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.7799 (ptp90) REVERT: B 175 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7455 (mp-120) REVERT: B 260 GLU cc_start: 0.9060 (OUTLIER) cc_final: 0.8815 (tt0) REVERT: B 269 ILE cc_start: 0.8339 (mm) cc_final: 0.8102 (mm) REVERT: B 335 PHE cc_start: 0.8986 (m-80) cc_final: 0.8704 (m-80) REVERT: S 34 MET cc_start: 0.9321 (OUTLIER) cc_final: 0.8933 (mmt) REVERT: S 90 ASP cc_start: 0.9028 (m-30) cc_final: 0.8797 (m-30) REVERT: S 211 ASP cc_start: 0.8823 (m-30) cc_final: 0.8519 (m-30) REVERT: R 63 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8150 (pp) REVERT: R 132 SER cc_start: 0.8741 (OUTLIER) cc_final: 0.8497 (t) REVERT: R 272 LEU cc_start: 0.8563 (tp) cc_final: 0.8221 (tt) REVERT: D 8 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7097 (mtt90) REVERT: E 66 MET cc_start: 0.6841 (OUTLIER) cc_final: 0.6418 (mpt) outliers start: 43 outliers final: 21 residues processed: 171 average time/residue: 1.1568 time to fit residues: 212.2317 Evaluate side-chains 166 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 34 MET Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 133 SER Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 53 ILE Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 132 SER Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 222 VAL Chi-restraints excluded: chain R residue 279 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 8 ARG Chi-restraints excluded: chain E residue 66 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 109 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 72 optimal weight: 0.0670 chunk 57 optimal weight: 0.0870 chunk 85 optimal weight: 0.9980 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN R 242 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.141721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.093610 restraints weight = 16802.171| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.39 r_work: 0.3104 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9845 Z= 0.116 Angle : 0.627 19.933 13380 Z= 0.314 Chirality : 0.043 0.200 1570 Planarity : 0.004 0.049 1689 Dihedral : 3.972 17.615 1351 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.28 % Allowed : 19.79 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.98 (0.24), residues: 1246 helix: 2.25 (0.26), residues: 412 sheet: 0.49 (0.28), residues: 314 loop : -0.54 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 339 HIS 0.002 0.000 HIS R 242 PHE 0.019 0.001 PHE R 183 TYR 0.024 0.001 TYR S 178 ARG 0.010 0.000 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.03586 ( 464) hydrogen bonds : angle 4.33057 ( 1323) SS BOND : bond 0.00406 ( 9) SS BOND : angle 3.23614 ( 18) covalent geometry : bond 0.00261 ( 9836) covalent geometry : angle 0.61595 (13362) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 LYS cc_start: 0.8301 (mmpt) cc_final: 0.8050 (ptpt) REVERT: A 305 GLN cc_start: 0.8503 (tm-30) cc_final: 0.8265 (tt0) REVERT: A 307 GLN cc_start: 0.8979 (mm-40) cc_final: 0.8730 (mm110) REVERT: B 175 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7333 (mp-120) REVERT: B 228 ASP cc_start: 0.8728 (p0) cc_final: 0.8505 (p0) REVERT: B 260 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8717 (tt0) REVERT: B 269 ILE cc_start: 0.8337 (mm) cc_final: 0.8103 (mm) REVERT: B 335 PHE cc_start: 0.8938 (m-80) cc_final: 0.8681 (m-80) REVERT: S 34 MET cc_start: 0.9236 (mmm) cc_final: 0.8876 (mmt) REVERT: S 211 ASP cc_start: 0.8835 (m-30) cc_final: 0.8543 (m-30) REVERT: R 53 ILE cc_start: 0.7580 (OUTLIER) cc_final: 0.7321 (pp) REVERT: R 63 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8118 (pp) REVERT: R 132 SER cc_start: 0.8833 (OUTLIER) cc_final: 0.8215 (p) REVERT: R 245 GLN cc_start: 0.7644 (OUTLIER) cc_final: 0.7257 (mp-120) REVERT: R 272 LEU cc_start: 0.8526 (tp) cc_final: 0.8179 (tt) REVERT: D 8 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7045 (mtt90) outliers start: 34 outliers final: 17 residues processed: 168 average time/residue: 1.1939 time to fit residues: 215.0338 Evaluate side-chains 164 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 260 GLU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 133 SER Chi-restraints excluded: chain S residue 204 ILE Chi-restraints excluded: chain R residue 53 ILE Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 132 SER Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 222 VAL Chi-restraints excluded: chain R residue 245 GLN Chi-restraints excluded: chain R residue 301 ILE Chi-restraints excluded: chain D residue 8 ARG Chi-restraints excluded: chain D residue 20 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 56 optimal weight: 0.9980 chunk 57 optimal weight: 0.0980 chunk 95 optimal weight: 0.9980 chunk 50 optimal weight: 0.0070 chunk 14 optimal weight: 6.9990 chunk 66 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN A 333 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.142489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.094728 restraints weight = 17037.768| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.40 r_work: 0.3128 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9845 Z= 0.111 Angle : 0.601 18.641 13380 Z= 0.304 Chirality : 0.042 0.194 1570 Planarity : 0.004 0.049 1689 Dihedral : 3.823 17.100 1351 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.70 % Allowed : 20.56 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.05 (0.24), residues: 1246 helix: 2.24 (0.26), residues: 412 sheet: 0.62 (0.28), residues: 312 loop : -0.50 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 112 HIS 0.002 0.000 HIS S 35 PHE 0.026 0.001 PHE R 183 TYR 0.023 0.001 TYR S 178 ARG 0.012 0.000 ARG S 148 Details of bonding type rmsd hydrogen bonds : bond 0.03446 ( 464) hydrogen bonds : angle 4.26418 ( 1323) SS BOND : bond 0.00583 ( 9) SS BOND : angle 2.74577 ( 18) covalent geometry : bond 0.00251 ( 9836) covalent geometry : angle 0.59300 (13362) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 1.204 Fit side-chains revert: symmetry clash REVERT: A 280 LYS cc_start: 0.8300 (mmpt) cc_final: 0.8061 (ptpt) REVERT: A 307 GLN cc_start: 0.8946 (mm-40) cc_final: 0.8640 (mm110) REVERT: B 10 GLU cc_start: 0.8680 (tp30) cc_final: 0.8370 (tp30) REVERT: B 52 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.8740 (ptp-170) REVERT: B 228 ASP cc_start: 0.8691 (p0) cc_final: 0.8448 (p0) REVERT: B 269 ILE cc_start: 0.8311 (mm) cc_final: 0.8074 (mm) REVERT: G 42 GLU cc_start: 0.8868 (tp30) cc_final: 0.8620 (tm-30) REVERT: S 34 MET cc_start: 0.9164 (mmm) cc_final: 0.8921 (mmt) REVERT: S 211 ASP cc_start: 0.8780 (m-30) cc_final: 0.8513 (m-30) REVERT: R 63 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8076 (pp) REVERT: R 245 GLN cc_start: 0.7560 (OUTLIER) cc_final: 0.7274 (mp-120) REVERT: R 272 LEU cc_start: 0.8481 (tp) cc_final: 0.8132 (tt) REVERT: D 8 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.6809 (mtt90) outliers start: 28 outliers final: 14 residues processed: 173 average time/residue: 1.1949 time to fit residues: 221.5196 Evaluate side-chains 162 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 133 SER Chi-restraints excluded: chain S residue 204 ILE Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 222 VAL Chi-restraints excluded: chain R residue 245 GLN Chi-restraints excluded: chain D residue 8 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 116 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 118 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 113 optimal weight: 30.0000 chunk 105 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN B 75 GLN R 242 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.137304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.088078 restraints weight = 16837.482| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.37 r_work: 0.3000 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.4572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.096 9845 Z= 0.283 Angle : 0.765 23.442 13380 Z= 0.391 Chirality : 0.049 0.300 1570 Planarity : 0.005 0.061 1689 Dihedral : 4.516 25.828 1351 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.76 % Allowed : 20.37 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.88 (0.24), residues: 1246 helix: 2.09 (0.26), residues: 412 sheet: 0.44 (0.28), residues: 321 loop : -0.54 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 211 HIS 0.006 0.002 HIS S 220 PHE 0.028 0.002 PHE R 130 TYR 0.032 0.002 TYR S 178 ARG 0.013 0.001 ARG S 148 Details of bonding type rmsd hydrogen bonds : bond 0.04772 ( 464) hydrogen bonds : angle 4.58178 ( 1323) SS BOND : bond 0.01114 ( 9) SS BOND : angle 3.28739 ( 18) covalent geometry : bond 0.00669 ( 9836) covalent geometry : angle 0.75545 (13362) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 147 time to evaluate : 1.106 Fit side-chains REVERT: A 354 TYR cc_start: 0.7236 (t80) cc_final: 0.6769 (t80) REVERT: B 52 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.7872 (ptp90) REVERT: B 98 SER cc_start: 0.9285 (OUTLIER) cc_final: 0.8969 (t) REVERT: B 175 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7360 (mp-120) REVERT: B 269 ILE cc_start: 0.8332 (mm) cc_final: 0.8060 (mm) REVERT: B 325 MET cc_start: 0.9151 (tpp) cc_final: 0.8936 (mmt) REVERT: B 335 PHE cc_start: 0.9045 (m-80) cc_final: 0.8798 (m-80) REVERT: S 211 ASP cc_start: 0.8857 (m-30) cc_final: 0.8532 (m-30) REVERT: R 63 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8151 (pp) REVERT: R 245 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.7210 (mt0) REVERT: R 272 LEU cc_start: 0.8628 (tp) cc_final: 0.8357 (tt) REVERT: D 8 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.6849 (mtt90) outliers start: 39 outliers final: 16 residues processed: 171 average time/residue: 1.1567 time to fit residues: 212.2201 Evaluate side-chains 162 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 204 ILE Chi-restraints excluded: chain R residue 53 ILE Chi-restraints excluded: chain R residue 60 LEU Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 174 LEU Chi-restraints excluded: chain R residue 222 VAL Chi-restraints excluded: chain R residue 245 GLN Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 8 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 0.8980 chunk 57 optimal weight: 0.0070 chunk 113 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 86 optimal weight: 0.4980 chunk 109 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 70 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.140995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.092887 restraints weight = 16753.611| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.36 r_work: 0.3095 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 9845 Z= 0.130 Angle : 0.691 20.302 13380 Z= 0.346 Chirality : 0.044 0.233 1570 Planarity : 0.004 0.053 1689 Dihedral : 4.261 23.625 1351 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.61 % Allowed : 21.81 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.01 (0.24), residues: 1246 helix: 2.21 (0.26), residues: 412 sheet: 0.57 (0.28), residues: 312 loop : -0.50 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 47 HIS 0.003 0.001 HIS D 34 PHE 0.031 0.001 PHE R 130 TYR 0.026 0.001 TYR S 178 ARG 0.014 0.001 ARG S 148 Details of bonding type rmsd hydrogen bonds : bond 0.03702 ( 464) hydrogen bonds : angle 4.46346 ( 1323) SS BOND : bond 0.00581 ( 9) SS BOND : angle 3.76573 ( 18) covalent geometry : bond 0.00300 ( 9836) covalent geometry : angle 0.67727 (13362) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 1.047 Fit side-chains REVERT: B 52 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8738 (ptp-170) REVERT: B 269 ILE cc_start: 0.8294 (mm) cc_final: 0.8033 (mm) REVERT: B 325 MET cc_start: 0.9027 (tpp) cc_final: 0.8803 (mmt) REVERT: B 335 PHE cc_start: 0.8924 (m-80) cc_final: 0.8630 (m-80) REVERT: S 34 MET cc_start: 0.9255 (mmm) cc_final: 0.8890 (mmt) REVERT: S 211 ASP cc_start: 0.8830 (m-30) cc_final: 0.8565 (m-30) REVERT: R 63 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8148 (pp) REVERT: R 272 LEU cc_start: 0.8536 (tp) cc_final: 0.8209 (tt) REVERT: D 8 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7240 (mtt90) outliers start: 27 outliers final: 11 residues processed: 165 average time/residue: 1.1587 time to fit residues: 205.2976 Evaluate side-chains 158 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 204 ILE Chi-restraints excluded: chain R residue 52 VAL Chi-restraints excluded: chain R residue 53 ILE Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 222 VAL Chi-restraints excluded: chain D residue 8 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 5 optimal weight: 0.0000 chunk 39 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 115 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.141268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.093090 restraints weight = 16872.419| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.37 r_work: 0.3092 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.4651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 9845 Z= 0.133 Angle : 0.663 14.851 13380 Z= 0.335 Chirality : 0.045 0.253 1570 Planarity : 0.004 0.053 1689 Dihedral : 4.131 28.360 1351 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.83 % Allowed : 22.68 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.00 (0.24), residues: 1246 helix: 2.16 (0.26), residues: 412 sheet: 0.54 (0.28), residues: 314 loop : -0.45 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 47 HIS 0.002 0.000 HIS S 220 PHE 0.030 0.001 PHE R 130 TYR 0.026 0.001 TYR S 178 ARG 0.013 0.001 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.03694 ( 464) hydrogen bonds : angle 4.41700 ( 1323) SS BOND : bond 0.00422 ( 9) SS BOND : angle 2.57336 ( 18) covalent geometry : bond 0.00316 ( 9836) covalent geometry : angle 0.65669 (13362) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 1.056 Fit side-chains revert: symmetry clash REVERT: A 280 LYS cc_start: 0.8315 (mmmt) cc_final: 0.8032 (ptpt) REVERT: A 307 GLN cc_start: 0.8984 (mm-40) cc_final: 0.8699 (mm110) REVERT: B 52 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8771 (ptp-170) REVERT: B 228 ASP cc_start: 0.8763 (p0) cc_final: 0.8478 (p0) REVERT: B 269 ILE cc_start: 0.8244 (mm) cc_final: 0.7987 (mm) REVERT: S 211 ASP cc_start: 0.8773 (m-30) cc_final: 0.8508 (m-30) REVERT: S 232 LYS cc_start: 0.9004 (tttp) cc_final: 0.8587 (tttm) REVERT: R 63 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8149 (pp) REVERT: R 272 LEU cc_start: 0.8568 (tp) cc_final: 0.8231 (tt) REVERT: D 8 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7729 (mtt90) outliers start: 19 outliers final: 14 residues processed: 161 average time/residue: 1.1699 time to fit residues: 201.7582 Evaluate side-chains 161 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 204 ILE Chi-restraints excluded: chain R residue 53 ILE Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 178 LEU Chi-restraints excluded: chain R residue 222 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 8 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 122 optimal weight: 9.9990 chunk 51 optimal weight: 0.4980 chunk 38 optimal weight: 6.9990 chunk 111 optimal weight: 7.9990 chunk 120 optimal weight: 30.0000 chunk 107 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 26 optimal weight: 0.2980 chunk 35 optimal weight: 4.9990 chunk 115 optimal weight: 20.0000 chunk 93 optimal weight: 1.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN A 333 GLN B 75 GLN G 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.138168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.089285 restraints weight = 16868.973| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.36 r_work: 0.3019 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.4781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 9845 Z= 0.233 Angle : 0.779 23.088 13380 Z= 0.395 Chirality : 0.048 0.263 1570 Planarity : 0.005 0.056 1689 Dihedral : 4.541 27.427 1351 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.22 % Allowed : 21.91 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 0.86 (0.24), residues: 1246 helix: 2.01 (0.26), residues: 412 sheet: 0.43 (0.28), residues: 321 loop : -0.48 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 169 HIS 0.005 0.001 HIS B 62 PHE 0.027 0.002 PHE R 130 TYR 0.031 0.002 TYR S 178 ARG 0.014 0.001 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.04502 ( 464) hydrogen bonds : angle 4.64343 ( 1323) SS BOND : bond 0.01034 ( 9) SS BOND : angle 4.54825 ( 18) covalent geometry : bond 0.00550 ( 9836) covalent geometry : angle 0.76157 (13362) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9549.65 seconds wall clock time: 164 minutes 32.99 seconds (9872.99 seconds total)