Starting phenix.real_space_refine on Fri Feb 14 05:01:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xx6_38747/02_2025/8xx6_38747.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xx6_38747/02_2025/8xx6_38747.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xx6_38747/02_2025/8xx6_38747.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xx6_38747/02_2025/8xx6_38747.map" model { file = "/net/cci-nas-00/data/ceres_data/8xx6_38747/02_2025/8xx6_38747.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xx6_38747/02_2025/8xx6_38747.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 6293 2.51 5 N 1671 2.21 5 O 1824 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9854 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2421 Classifications: {'peptide': 303} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 291} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 575 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 68} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 500 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 60} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1689 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2529 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "G" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 375 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "S" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1765 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Time building chain proxies: 5.58, per 1000 atoms: 0.57 Number of scatterers: 9854 At special positions: 0 Unit cell: (88.1875, 123.463, 158.738, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 1824 8.00 N 1671 7.00 C 6293 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS R 39 " - pdb=" SG CYS R 286 " distance=2.03 Simple disulfide: pdb=" SG CYS R 119 " - pdb=" SG CYS R 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 7 " - pdb=" SG CYS D 34 " distance=2.03 Simple disulfide: pdb=" SG CYS D 9 " - pdb=" SG CYS D 50 " distance=2.03 Simple disulfide: pdb=" SG CYS E 5 " - pdb=" SG CYS E 32 " distance=2.03 Simple disulfide: pdb=" SG CYS E 7 " - pdb=" SG CYS E 48 " distance=2.03 Simple disulfide: pdb=" SG CYS B 103 " - pdb=" SG CYS B 114 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.53 Conformation dependent library (CDL) restraints added in 1.3 seconds 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2400 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 16 sheets defined 35.8% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'R' and resid 45 through 76 removed outlier: 4.414A pdb=" N SER R 76 " --> pdb=" O VAL R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 111 Proline residue: R 102 - end of helix Processing helix chain 'R' and resid 115 through 149 Processing helix chain 'R' and resid 154 through 160 removed outlier: 3.877A pdb=" N TYR R 160 " --> pdb=" O GLN R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 177 Processing helix chain 'R' and resid 177 through 183 removed outlier: 3.541A pdb=" N LEU R 181 " --> pdb=" O ALA R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 212 Processing helix chain 'R' and resid 212 through 218 Processing helix chain 'R' and resid 220 through 241 removed outlier: 3.588A pdb=" N LYS R 240 " --> pdb=" O ARG R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 279 Proline residue: R 266 - end of helix Processing helix chain 'R' and resid 285 through 304 Processing helix chain 'R' and resid 305 through 315 Proline residue: R 311 - end of helix Processing helix chain 'R' and resid 318 through 329 Processing helix chain 'D' and resid 18 through 20 No H-bonds generated for 'chain 'D' and resid 18 through 20' Processing helix chain 'D' and resid 55 through 71 removed outlier: 3.815A pdb=" N GLN D 59 " --> pdb=" O GLU D 55 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG D 60 " --> pdb=" O ASN D 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 18 No H-bonds generated for 'chain 'E' and resid 16 through 18' Processing helix chain 'E' and resid 53 through 68 Processing helix chain 'A' and resid 6 through 30 Processing helix chain 'A' and resid 208 through 217 removed outlier: 4.787A pdb=" N ILE A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N HIS A 214 " --> pdb=" O LYS A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 256 Processing helix chain 'A' and resid 271 through 282 removed outlier: 4.113A pdb=" N LYS A 280 " --> pdb=" O GLY A 276 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 6 through 26 removed outlier: 3.706A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 12 through 24 removed outlier: 3.607A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.646A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.016A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.809A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 184 through 187 Processing sheet with id=AA2, first strand: chain 'D' and resid 48 through 51 removed outlier: 4.363A pdb=" N ILE D 39 " --> pdb=" O LEU D 51 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU D 24 " --> pdb=" O LYS D 42 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE E 37 " --> pdb=" O LEU E 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 186 through 188 Processing sheet with id=AA4, first strand: chain 'A' and resid 186 through 188 removed outlier: 9.585A pdb=" N ALA A 221 " --> pdb=" O ASP A 33 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N LYS A 35 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ILE A 223 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU A 37 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N CYS A 225 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU A 39 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N ASP A 227 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 52 removed outlier: 4.401A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.964A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 103 removed outlier: 4.210A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 153 removed outlier: 4.599A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.566A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.407A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.395A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.721A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY S 44 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 128 through 130 removed outlier: 3.510A pdb=" N ALA S 199 " --> pdb=" O SER S 196 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.167A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE S 177 " --> pdb=" O TRP S 164 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.167A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR S 226 " --> pdb=" O GLN S 219 " (cutoff:3.500A) 483 hydrogen bonds defined for protein. 1359 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.14 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1678 1.32 - 1.45: 2668 1.45 - 1.57: 5624 1.57 - 1.70: 0 1.70 - 1.82: 89 Bond restraints: 10059 Sorted by residual: bond pdb=" C ASN B 88 " pdb=" O ASN B 88 " ideal model delta sigma weight residual 1.234 1.198 0.036 1.22e-02 6.72e+03 8.94e+00 bond pdb=" CB CYS B 103 " pdb=" SG CYS B 103 " ideal model delta sigma weight residual 1.808 1.764 0.044 3.30e-02 9.18e+02 1.80e+00 bond pdb=" CA LEU R 99 " pdb=" C LEU R 99 " ideal model delta sigma weight residual 1.522 1.506 0.017 1.36e-02 5.41e+03 1.48e+00 bond pdb=" C ASN B 88 " pdb=" N LYS B 89 " ideal model delta sigma weight residual 1.331 1.314 0.017 1.43e-02 4.89e+03 1.38e+00 bond pdb=" CA ARG B 197 " pdb=" CB ARG B 197 " ideal model delta sigma weight residual 1.537 1.521 0.016 1.41e-02 5.03e+03 1.22e+00 ... (remaining 10054 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 13187 1.09 - 2.17: 387 2.17 - 3.26: 66 3.26 - 4.35: 14 4.35 - 5.43: 7 Bond angle restraints: 13661 Sorted by residual: angle pdb=" C ALA B 309 " pdb=" CA ALA B 309 " pdb=" CB ALA B 309 " ideal model delta sigma weight residual 115.89 110.46 5.43 1.32e+00 5.74e-01 1.69e+01 angle pdb=" CA ASN B 88 " pdb=" C ASN B 88 " pdb=" O ASN B 88 " ideal model delta sigma weight residual 121.16 117.13 4.03 1.13e+00 7.83e-01 1.27e+01 angle pdb=" C ASN B 88 " pdb=" CA ASN B 88 " pdb=" CB ASN B 88 " ideal model delta sigma weight residual 109.37 114.43 -5.06 1.83e+00 2.99e-01 7.63e+00 angle pdb=" C TYR S 178 " pdb=" N ARG S 179 " pdb=" CA ARG S 179 " ideal model delta sigma weight residual 121.90 118.93 2.97 1.26e+00 6.30e-01 5.56e+00 angle pdb=" N ASN B 88 " pdb=" CA ASN B 88 " pdb=" C ASN B 88 " ideal model delta sigma weight residual 109.95 106.33 3.62 1.59e+00 3.96e-01 5.18e+00 ... (remaining 13656 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 5488 17.77 - 35.54: 424 35.54 - 53.31: 60 53.31 - 71.08: 17 71.08 - 88.85: 5 Dihedral angle restraints: 5994 sinusoidal: 2282 harmonic: 3712 Sorted by residual: dihedral pdb=" CB CYS E 5 " pdb=" SG CYS E 5 " pdb=" SG CYS E 32 " pdb=" CB CYS E 32 " ideal model delta sinusoidal sigma weight residual -86.00 -141.86 55.86 1 1.00e+01 1.00e-02 4.21e+01 dihedral pdb=" CB CYS S 147 " pdb=" SG CYS S 147 " pdb=" SG CYS S 217 " pdb=" CB CYS S 217 " ideal model delta sinusoidal sigma weight residual 93.00 140.07 -47.07 1 1.00e+01 1.00e-02 3.06e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 162.33 17.67 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 5991 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1074 0.033 - 0.066: 348 0.066 - 0.100: 103 0.100 - 0.133: 57 0.133 - 0.166: 3 Chirality restraints: 1585 Sorted by residual: chirality pdb=" CA TYR S 178 " pdb=" N TYR S 178 " pdb=" C TYR S 178 " pdb=" CB TYR S 178 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.90e-01 chirality pdb=" CA ILE S 177 " pdb=" N ILE S 177 " pdb=" C ILE S 177 " pdb=" CB ILE S 177 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.47e-01 chirality pdb=" CB ILE A 55 " pdb=" CA ILE A 55 " pdb=" CG1 ILE A 55 " pdb=" CG2 ILE A 55 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.72e-01 ... (remaining 1582 not shown) Planarity restraints: 1729 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL G 54 " 0.026 5.00e-02 4.00e+02 4.01e-02 2.57e+00 pdb=" N PRO G 55 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO G 55 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 55 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.025 5.00e-02 4.00e+02 3.77e-02 2.27e+00 pdb=" N PRO B 236 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 87 " 0.007 2.00e-02 2.50e+03 1.36e-02 1.84e+00 pdb=" C THR B 87 " -0.023 2.00e-02 2.50e+03 pdb=" O THR B 87 " 0.009 2.00e-02 2.50e+03 pdb=" N ASN B 88 " 0.008 2.00e-02 2.50e+03 ... (remaining 1726 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1512 2.76 - 3.30: 9229 3.30 - 3.83: 15847 3.83 - 4.37: 18525 4.37 - 4.90: 33252 Nonbonded interactions: 78365 Sorted by model distance: nonbonded pdb=" O GLY R 201 " pdb=" OG1 THR R 204 " model vdw 2.229 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.230 3.040 nonbonded pdb=" OG1 THR B 165 " pdb=" O PHE B 180 " model vdw 2.259 3.040 nonbonded pdb=" O PHE S 29 " pdb=" NH2 ARG S 72 " model vdw 2.262 3.120 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR S 163 " model vdw 2.282 3.040 ... (remaining 78360 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and (resid 7 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 19 or (resid 20 and (name N or name \ CA or name C or name O or name CB )) or resid 21 through 53 or (resid 54 throug \ h 55 and (name N or name CA or name C or name O or name CB )) or resid 56 throug \ h 63 or (resid 64 and (name N or name CA or name C or name O or name CB )) or re \ sid 65 through 70 or (resid 71 and (name N or name CA or name C or name O or nam \ e CB )))) selection = (chain 'E' and (resid 5 through 52 or (resid 53 and (name N or name CA or name C \ or name O or name CB )) or resid 54 through 69)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 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: 24.830 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:15.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 10059 Z= 0.140 Angle : 0.466 5.434 13661 Z= 0.270 Chirality : 0.040 0.166 1585 Planarity : 0.003 0.040 1729 Dihedral : 12.904 88.847 3567 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.24), residues: 1260 helix: 2.20 (0.25), residues: 410 sheet: -0.11 (0.28), residues: 333 loop : -0.54 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.002 0.001 HIS S 220 PHE 0.014 0.001 PHE B 234 TYR 0.016 0.001 TYR S 178 ARG 0.002 0.000 ARG S 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 337 time to evaluate : 1.116 Fit side-chains revert: symmetry clash REVERT: R 95 LEU cc_start: 0.8216 (tp) cc_final: 0.7974 (pp) REVERT: R 203 ASN cc_start: 0.7541 (t0) cc_final: 0.7208 (t0) REVERT: R 214 LEU cc_start: 0.8733 (mt) cc_final: 0.8388 (mt) REVERT: R 262 LEU cc_start: 0.8771 (tp) cc_final: 0.8505 (tm) REVERT: R 291 HIS cc_start: 0.7796 (m170) cc_final: 0.7260 (m170) REVERT: A 273 ASP cc_start: 0.7464 (p0) cc_final: 0.7098 (t0) REVERT: A 354 TYR cc_start: 0.6857 (t80) cc_final: 0.6560 (t80) REVERT: B 13 GLN cc_start: 0.8386 (pp30) cc_final: 0.8018 (pp30) REVERT: B 213 VAL cc_start: 0.8843 (p) cc_final: 0.8584 (t) REVERT: S 69 THR cc_start: 0.8144 (t) cc_final: 0.7795 (m) outliers start: 0 outliers final: 1 residues processed: 337 average time/residue: 1.1701 time to fit residues: 423.1557 Evaluate side-chains 210 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 209 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 36 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 4.9990 chunk 94 optimal weight: 8.9990 chunk 52 optimal weight: 0.0170 chunk 32 optimal weight: 20.0000 chunk 63 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 97 optimal weight: 6.9990 chunk 37 optimal weight: 0.5980 chunk 59 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 113 optimal weight: 0.4980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 47 ASN R 150 HIS ** R 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 ASN A 43 ASN A 256 ASN B 88 ASN B 91 HIS B 230 ASN B 259 GLN G 18 GLN S 174 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.134450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.098000 restraints weight = 17729.294| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.94 r_work: 0.3165 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 10059 Z= 0.186 Angle : 0.622 12.709 13661 Z= 0.323 Chirality : 0.044 0.185 1585 Planarity : 0.005 0.082 1729 Dihedral : 3.993 32.717 1376 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.96 % Allowed : 15.28 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.24), residues: 1260 helix: 2.22 (0.25), residues: 421 sheet: 0.01 (0.28), residues: 332 loop : -0.62 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 339 HIS 0.003 0.001 HIS S 220 PHE 0.014 0.001 PHE S 108 TYR 0.020 0.001 TYR S 178 ARG 0.010 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 222 time to evaluate : 1.085 Fit side-chains REVERT: R 61 LEU cc_start: 0.9031 (mt) cc_final: 0.8671 (mp) REVERT: R 94 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7765 (t70) REVERT: R 112 TRP cc_start: 0.7851 (t-100) cc_final: 0.7534 (t-100) REVERT: R 128 VAL cc_start: 0.8969 (p) cc_final: 0.8633 (m) REVERT: R 211 LEU cc_start: 0.8884 (mt) cc_final: 0.8554 (mp) REVERT: R 240 LYS cc_start: 0.8530 (ttpp) cc_final: 0.8289 (mtmm) REVERT: R 291 HIS cc_start: 0.8005 (m170) cc_final: 0.7515 (m170) REVERT: R 313 ILE cc_start: 0.9299 (tt) cc_final: 0.8847 (pt) REVERT: D 27 VAL cc_start: 0.8899 (t) cc_final: 0.8622 (m) REVERT: A 231 TYR cc_start: 0.8036 (m-80) cc_final: 0.7654 (m-80) REVERT: A 273 ASP cc_start: 0.7337 (p0) cc_final: 0.6973 (t0) REVERT: A 277 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.8074 (mp0) REVERT: A 307 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.7258 (mp10) REVERT: B 12 GLU cc_start: 0.8957 (tp30) cc_final: 0.8667 (pp20) REVERT: B 32 GLN cc_start: 0.8740 (tt0) cc_final: 0.8482 (pt0) REVERT: B 213 VAL cc_start: 0.8899 (p) cc_final: 0.8644 (t) REVERT: G 47 GLU cc_start: 0.8292 (mp0) cc_final: 0.8036 (mp0) REVERT: S 69 THR cc_start: 0.8535 (t) cc_final: 0.8122 (m) REVERT: S 168 ARG cc_start: 0.8802 (mtt90) cc_final: 0.8551 (mtt90) REVERT: S 171 GLN cc_start: 0.7913 (mp10) cc_final: 0.7632 (mp10) REVERT: S 211 ASP cc_start: 0.8373 (m-30) cc_final: 0.7791 (m-30) outliers start: 42 outliers final: 10 residues processed: 244 average time/residue: 1.2332 time to fit residues: 322.4866 Evaluate side-chains 206 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 193 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 301 ILE Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 184 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 100 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 41 optimal weight: 0.0060 chunk 29 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 109 optimal weight: 10.0000 chunk 103 optimal weight: 0.0020 chunk 92 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 overall best weight: 0.5806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 283 GLN ** R 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 43 ASN B 16 ASN B 259 GLN S 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.134105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.097080 restraints weight = 18048.534| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.80 r_work: 0.3159 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10059 Z= 0.175 Angle : 0.618 17.268 13661 Z= 0.312 Chirality : 0.043 0.183 1585 Planarity : 0.004 0.060 1729 Dihedral : 4.036 29.682 1374 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.58 % Allowed : 18.40 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.24), residues: 1260 helix: 2.19 (0.25), residues: 427 sheet: 0.09 (0.28), residues: 328 loop : -0.77 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.003 0.001 HIS S 220 PHE 0.013 0.001 PHE S 108 TYR 0.022 0.001 TYR S 178 ARG 0.008 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 199 time to evaluate : 1.145 Fit side-chains revert: symmetry clash REVERT: R 83 THR cc_start: 0.8722 (OUTLIER) cc_final: 0.8465 (t) REVERT: R 94 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7589 (t70) REVERT: R 258 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8614 (mm) REVERT: R 287 GLU cc_start: 0.8388 (pm20) cc_final: 0.8036 (pm20) REVERT: R 291 HIS cc_start: 0.8012 (m170) cc_final: 0.7529 (m170) REVERT: R 321 PHE cc_start: 0.7821 (t80) cc_final: 0.7610 (t80) REVERT: D 27 VAL cc_start: 0.8901 (t) cc_final: 0.8440 (p) REVERT: A 43 ASN cc_start: 0.8136 (OUTLIER) cc_final: 0.7892 (m-40) REVERT: A 243 ARG cc_start: 0.8636 (mmm-85) cc_final: 0.8054 (mtt180) REVERT: A 273 ASP cc_start: 0.7384 (p0) cc_final: 0.6951 (t0) REVERT: A 277 GLU cc_start: 0.8322 (mp0) cc_final: 0.8076 (mp0) REVERT: A 303 TYR cc_start: 0.8676 (t80) cc_final: 0.7893 (t80) REVERT: A 307 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7255 (mp10) REVERT: B 12 GLU cc_start: 0.8934 (tp30) cc_final: 0.8684 (pp20) REVERT: B 32 GLN cc_start: 0.8737 (tt0) cc_final: 0.8536 (pt0) REVERT: B 213 VAL cc_start: 0.8911 (p) cc_final: 0.8692 (t) REVERT: G 47 GLU cc_start: 0.8304 (mp0) cc_final: 0.8081 (mp0) REVERT: G 50 LEU cc_start: 0.8731 (mt) cc_final: 0.8481 (mt) REVERT: S 11 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8142 (tt) REVERT: S 69 THR cc_start: 0.8488 (t) cc_final: 0.8104 (m) REVERT: S 73 ASP cc_start: 0.7152 (t0) cc_final: 0.6740 (t70) REVERT: S 171 GLN cc_start: 0.7974 (mp10) cc_final: 0.7647 (mp10) REVERT: S 183 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8938 (mp) REVERT: S 211 ASP cc_start: 0.8327 (m-30) cc_final: 0.7864 (m-30) outliers start: 38 outliers final: 12 residues processed: 223 average time/residue: 1.2559 time to fit residues: 300.0343 Evaluate side-chains 204 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 185 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 221 ILE Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 202 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 65 optimal weight: 9.9990 chunk 115 optimal weight: 30.0000 chunk 33 optimal weight: 20.0000 chunk 75 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 41 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 54 ASN B 16 ASN B 259 GLN S 130 GLN S 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.130492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.091786 restraints weight = 17895.224| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.47 r_work: 0.3104 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 10059 Z= 0.276 Angle : 0.656 18.087 13661 Z= 0.338 Chirality : 0.045 0.300 1585 Planarity : 0.004 0.048 1729 Dihedral : 4.318 31.000 1374 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.15 % Allowed : 18.96 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.24), residues: 1260 helix: 2.13 (0.25), residues: 427 sheet: -0.03 (0.27), residues: 335 loop : -0.67 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 112 HIS 0.005 0.001 HIS S 220 PHE 0.013 0.001 PHE S 108 TYR 0.028 0.002 TYR S 178 ARG 0.008 0.001 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 194 time to evaluate : 1.050 Fit side-chains REVERT: R 50 PHE cc_start: 0.8167 (m-80) cc_final: 0.7939 (m-80) REVERT: R 83 THR cc_start: 0.8749 (OUTLIER) cc_final: 0.8508 (t) REVERT: R 258 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8735 (mm) REVERT: R 287 GLU cc_start: 0.8491 (pm20) cc_final: 0.8153 (pm20) REVERT: R 291 HIS cc_start: 0.8071 (m170) cc_final: 0.7568 (m170) REVERT: R 321 PHE cc_start: 0.7958 (t80) cc_final: 0.7664 (t80) REVERT: D 27 VAL cc_start: 0.9043 (t) cc_final: 0.8581 (p) REVERT: A 273 ASP cc_start: 0.7673 (p0) cc_final: 0.7238 (t0) REVERT: A 277 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8253 (mp0) REVERT: A 307 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7299 (mp10) REVERT: B 10 GLU cc_start: 0.8182 (tp30) cc_final: 0.7697 (tp30) REVERT: B 12 GLU cc_start: 0.8986 (tp30) cc_final: 0.8705 (pp20) REVERT: B 13 GLN cc_start: 0.8691 (pp30) cc_final: 0.8436 (pp30) REVERT: B 32 GLN cc_start: 0.8756 (tt0) cc_final: 0.8512 (pt0) REVERT: B 268 ASN cc_start: 0.8053 (t160) cc_final: 0.7829 (t0) REVERT: G 47 GLU cc_start: 0.8404 (mp0) cc_final: 0.8172 (mp0) REVERT: G 50 LEU cc_start: 0.8931 (mt) cc_final: 0.8650 (mt) REVERT: S 69 THR cc_start: 0.8647 (t) cc_final: 0.8270 (m) REVERT: S 171 GLN cc_start: 0.8289 (mp10) cc_final: 0.7817 (mp10) REVERT: S 183 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.8967 (mp) REVERT: S 211 ASP cc_start: 0.8387 (m-30) cc_final: 0.7926 (m-30) outliers start: 44 outliers final: 22 residues processed: 222 average time/residue: 1.2997 time to fit residues: 308.8072 Evaluate side-chains 206 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 179 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 190 SER Chi-restraints excluded: chain R residue 221 ILE Chi-restraints excluded: chain R residue 243 MET Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 296 LEU Chi-restraints excluded: chain D residue 36 ASN Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 202 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 40 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 0 optimal weight: 40.0000 chunk 87 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 66 ASN R 242 HIS B 16 ASN B 259 GLN B 268 ASN S 174 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.130850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.092753 restraints weight = 17860.321| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.63 r_work: 0.3089 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10059 Z= 0.236 Angle : 0.628 12.691 13661 Z= 0.324 Chirality : 0.044 0.262 1585 Planarity : 0.004 0.045 1729 Dihedral : 4.329 31.532 1374 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.43 % Allowed : 20.19 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.24), residues: 1260 helix: 2.06 (0.25), residues: 427 sheet: 0.12 (0.27), residues: 336 loop : -0.80 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 112 HIS 0.004 0.001 HIS S 220 PHE 0.011 0.001 PHE B 234 TYR 0.025 0.001 TYR S 178 ARG 0.009 0.001 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 185 time to evaluate : 1.164 Fit side-chains REVERT: R 50 PHE cc_start: 0.8143 (m-80) cc_final: 0.7941 (m-80) REVERT: R 83 THR cc_start: 0.8702 (OUTLIER) cc_final: 0.8461 (t) REVERT: R 90 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8280 (tt) REVERT: R 185 ARG cc_start: 0.7254 (ptm-80) cc_final: 0.7051 (ptp90) REVERT: R 262 LEU cc_start: 0.8904 (tm) cc_final: 0.8690 (tt) REVERT: R 287 GLU cc_start: 0.8533 (pm20) cc_final: 0.8198 (pm20) REVERT: R 291 HIS cc_start: 0.8010 (m170) cc_final: 0.7521 (m170) REVERT: R 321 PHE cc_start: 0.7900 (t80) cc_final: 0.7645 (t80) REVERT: D 27 VAL cc_start: 0.8934 (t) cc_final: 0.8502 (p) REVERT: A 243 ARG cc_start: 0.8678 (mmm-85) cc_final: 0.8186 (mtt180) REVERT: A 273 ASP cc_start: 0.7681 (p0) cc_final: 0.7031 (t0) REVERT: A 277 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8036 (mp0) REVERT: A 307 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.7557 (mp10) REVERT: B 12 GLU cc_start: 0.9030 (tp30) cc_final: 0.8716 (pp20) REVERT: B 32 GLN cc_start: 0.8738 (tt0) cc_final: 0.8533 (pt0) REVERT: B 44 GLN cc_start: 0.8018 (mm-40) cc_final: 0.7762 (tp-100) REVERT: G 50 LEU cc_start: 0.8936 (mt) cc_final: 0.8689 (mt) REVERT: S 69 THR cc_start: 0.8490 (t) cc_final: 0.8102 (m) REVERT: S 171 GLN cc_start: 0.8212 (mp10) cc_final: 0.7709 (mp10) REVERT: S 211 ASP cc_start: 0.8303 (m-30) cc_final: 0.7860 (m-30) outliers start: 47 outliers final: 21 residues processed: 215 average time/residue: 1.2004 time to fit residues: 276.9388 Evaluate side-chains 197 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 172 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 221 ILE Chi-restraints excluded: chain R residue 296 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 202 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 14 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 115 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 242 HIS A 194 ASN A 346 ASN B 16 ASN B 75 GLN B 259 GLN S 174 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.125426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.085138 restraints weight = 18065.618| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.50 r_work: 0.2975 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.087 10059 Z= 0.585 Angle : 0.800 16.461 13661 Z= 0.417 Chirality : 0.052 0.379 1585 Planarity : 0.005 0.052 1729 Dihedral : 5.072 31.076 1374 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.72 % Allowed : 20.75 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.23), residues: 1260 helix: 1.57 (0.25), residues: 427 sheet: -0.18 (0.27), residues: 336 loop : -1.06 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP S 47 HIS 0.008 0.002 HIS S 220 PHE 0.018 0.002 PHE B 234 TYR 0.031 0.003 TYR S 178 ARG 0.009 0.001 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 176 time to evaluate : 1.141 Fit side-chains REVERT: R 90 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8327 (tt) REVERT: R 185 ARG cc_start: 0.7455 (ptm-80) cc_final: 0.7241 (ptm-80) REVERT: R 258 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8801 (mm) REVERT: R 262 LEU cc_start: 0.9019 (tm) cc_final: 0.8818 (tt) REVERT: R 321 PHE cc_start: 0.8117 (t80) cc_final: 0.7816 (t80) REVERT: D 27 VAL cc_start: 0.9034 (t) cc_final: 0.8717 (m) REVERT: E 40 LYS cc_start: 0.7999 (mttt) cc_final: 0.6976 (mppt) REVERT: A 243 ARG cc_start: 0.8802 (mmm-85) cc_final: 0.8447 (mtt180) REVERT: A 273 ASP cc_start: 0.7909 (p0) cc_final: 0.7688 (p0) REVERT: A 307 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.7431 (mp10) REVERT: B 10 GLU cc_start: 0.8184 (tp30) cc_final: 0.7824 (tp30) REVERT: B 12 GLU cc_start: 0.9080 (tp30) cc_final: 0.8689 (pp20) REVERT: B 32 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8493 (pt0) REVERT: B 44 GLN cc_start: 0.8210 (mm-40) cc_final: 0.7981 (tm-30) REVERT: B 212 ASP cc_start: 0.8791 (t70) cc_final: 0.8541 (t0) REVERT: S 13 GLN cc_start: 0.8950 (tp40) cc_final: 0.8662 (mm110) REVERT: S 69 THR cc_start: 0.8685 (t) cc_final: 0.8304 (m) REVERT: S 87 ARG cc_start: 0.8337 (mtt-85) cc_final: 0.8132 (mtt-85) REVERT: S 171 GLN cc_start: 0.8447 (mp10) cc_final: 0.7916 (mp10) outliers start: 50 outliers final: 27 residues processed: 212 average time/residue: 1.2627 time to fit residues: 286.1067 Evaluate side-chains 196 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 157 GLN Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 189 SER Chi-restraints excluded: chain R residue 221 ILE Chi-restraints excluded: chain R residue 237 THR Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 296 LEU Chi-restraints excluded: chain R residue 301 ILE Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 202 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 107 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 95 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 29 optimal weight: 9.9990 chunk 54 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 242 HIS A 194 ASN B 16 ASN B 259 GLN S 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.129697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.090801 restraints weight = 18129.174| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.50 r_work: 0.3088 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10059 Z= 0.220 Angle : 0.660 17.382 13661 Z= 0.340 Chirality : 0.045 0.242 1585 Planarity : 0.004 0.047 1729 Dihedral : 4.551 28.270 1374 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.49 % Allowed : 22.26 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.40 (0.23), residues: 1260 helix: 1.91 (0.25), residues: 425 sheet: -0.03 (0.26), residues: 337 loop : -0.95 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS S 220 PHE 0.011 0.001 PHE B 234 TYR 0.018 0.001 TYR S 178 ARG 0.013 0.001 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 176 time to evaluate : 1.034 Fit side-chains revert: symmetry clash REVERT: R 83 THR cc_start: 0.8747 (OUTLIER) cc_final: 0.8483 (t) REVERT: R 185 ARG cc_start: 0.7306 (ptm-80) cc_final: 0.7093 (ptp90) REVERT: R 262 LEU cc_start: 0.8969 (tm) cc_final: 0.8752 (tt) REVERT: R 321 PHE cc_start: 0.8028 (t80) cc_final: 0.7774 (t80) REVERT: D 27 VAL cc_start: 0.8980 (t) cc_final: 0.8566 (p) REVERT: E 40 LYS cc_start: 0.8038 (mttt) cc_final: 0.7002 (mppt) REVERT: A 243 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8524 (mtt180) REVERT: A 273 ASP cc_start: 0.7821 (p0) cc_final: 0.7610 (p0) REVERT: A 307 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.7698 (mp10) REVERT: B 12 GLU cc_start: 0.9096 (tp30) cc_final: 0.8732 (pp20) REVERT: B 32 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8453 (pt0) REVERT: B 44 GLN cc_start: 0.8051 (mm-40) cc_final: 0.7840 (tm-30) REVERT: S 13 GLN cc_start: 0.8871 (tp40) cc_final: 0.8626 (mm110) REVERT: S 69 THR cc_start: 0.8629 (t) cc_final: 0.8231 (m) REVERT: S 87 ARG cc_start: 0.8348 (mtt-85) cc_final: 0.8105 (mtt-85) REVERT: S 171 GLN cc_start: 0.8395 (mp10) cc_final: 0.7915 (mp10) outliers start: 37 outliers final: 21 residues processed: 198 average time/residue: 1.3956 time to fit residues: 295.7038 Evaluate side-chains 192 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 83 THR Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 221 ILE Chi-restraints excluded: chain R residue 301 ILE Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 286 ILE Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 202 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 30 optimal weight: 0.0010 chunk 98 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 chunk 60 optimal weight: 0.0670 chunk 118 optimal weight: 0.1980 chunk 104 optimal weight: 6.9990 chunk 123 optimal weight: 0.9980 chunk 93 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 120 optimal weight: 0.3980 chunk 70 optimal weight: 0.9990 overall best weight: 0.3324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 242 HIS A 194 ASN B 16 ASN B 75 GLN B 259 GLN S 174 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.131378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.093838 restraints weight = 18131.412| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.87 r_work: 0.3099 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10059 Z= 0.179 Angle : 0.662 18.019 13661 Z= 0.335 Chirality : 0.044 0.234 1585 Planarity : 0.004 0.050 1729 Dihedral : 4.286 26.811 1374 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.74 % Allowed : 23.49 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.23), residues: 1260 helix: 2.10 (0.25), residues: 421 sheet: 0.15 (0.27), residues: 324 loop : -0.94 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 112 HIS 0.002 0.001 HIS A 196 PHE 0.009 0.001 PHE B 234 TYR 0.017 0.001 TYR S 178 ARG 0.014 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 178 time to evaluate : 1.097 Fit side-chains revert: symmetry clash REVERT: R 83 THR cc_start: 0.8602 (p) cc_final: 0.8335 (t) REVERT: R 185 ARG cc_start: 0.7097 (ptm-80) cc_final: 0.6881 (ptp90) REVERT: R 200 MET cc_start: 0.6920 (mtm) cc_final: 0.6467 (mtm) REVERT: R 262 LEU cc_start: 0.8937 (tm) cc_final: 0.8733 (tt) REVERT: R 321 PHE cc_start: 0.8022 (t80) cc_final: 0.7622 (t80) REVERT: D 27 VAL cc_start: 0.8867 (t) cc_final: 0.8443 (p) REVERT: E 40 LYS cc_start: 0.7938 (mttt) cc_final: 0.6949 (mppt) REVERT: A 243 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8408 (mtt180) REVERT: A 273 ASP cc_start: 0.7625 (p0) cc_final: 0.7404 (p0) REVERT: A 303 TYR cc_start: 0.8583 (t80) cc_final: 0.8319 (t80) REVERT: B 12 GLU cc_start: 0.9046 (tp30) cc_final: 0.8706 (pp20) REVERT: B 44 GLN cc_start: 0.7906 (mm-40) cc_final: 0.7696 (tm-30) REVERT: B 210 LEU cc_start: 0.8761 (tp) cc_final: 0.8515 (tp) REVERT: S 13 GLN cc_start: 0.8654 (tp40) cc_final: 0.8331 (mm110) REVERT: S 69 THR cc_start: 0.8524 (t) cc_final: 0.8117 (m) REVERT: S 87 ARG cc_start: 0.8308 (mtt-85) cc_final: 0.8045 (mtt-85) REVERT: S 171 GLN cc_start: 0.8191 (mp10) cc_final: 0.7612 (mp10) outliers start: 29 outliers final: 15 residues processed: 198 average time/residue: 1.3010 time to fit residues: 274.9576 Evaluate side-chains 184 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 168 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain R residue 221 ILE Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 202 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 92 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 101 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 41 optimal weight: 20.0000 chunk 104 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 80 optimal weight: 6.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 216 GLN R 242 HIS B 16 ASN B 259 GLN S 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.128111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.088687 restraints weight = 18193.203| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.51 r_work: 0.3054 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.4444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 10059 Z= 0.368 Angle : 0.762 21.893 13661 Z= 0.384 Chirality : 0.047 0.275 1585 Planarity : 0.004 0.049 1729 Dihedral : 4.629 28.954 1374 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.64 % Allowed : 24.06 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.23), residues: 1260 helix: 1.96 (0.25), residues: 424 sheet: 0.01 (0.27), residues: 331 loop : -0.95 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 82 HIS 0.006 0.001 HIS S 220 PHE 0.015 0.002 PHE B 234 TYR 0.024 0.002 TYR S 178 ARG 0.016 0.001 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 1.132 Fit side-chains revert: symmetry clash REVERT: R 83 THR cc_start: 0.8744 (p) cc_final: 0.8488 (t) REVERT: R 200 MET cc_start: 0.7110 (mtm) cc_final: 0.6659 (mtm) REVERT: R 321 PHE cc_start: 0.7947 (t80) cc_final: 0.7625 (t80) REVERT: D 27 VAL cc_start: 0.9029 (t) cc_final: 0.8624 (p) REVERT: E 40 LYS cc_start: 0.8035 (mttt) cc_final: 0.7018 (mppt) REVERT: A 243 ARG cc_start: 0.8764 (mmm-85) cc_final: 0.8519 (mtt180) REVERT: A 273 ASP cc_start: 0.7850 (p0) cc_final: 0.7629 (p0) REVERT: B 10 GLU cc_start: 0.7999 (tp30) cc_final: 0.7415 (tp30) REVERT: B 12 GLU cc_start: 0.9096 (tp30) cc_final: 0.8712 (pp20) REVERT: B 13 GLN cc_start: 0.8364 (pp30) cc_final: 0.7515 (pp30) REVERT: B 45 MET cc_start: 0.8559 (mtt) cc_final: 0.8130 (mtt) REVERT: B 101 MET cc_start: 0.8833 (mtm) cc_final: 0.8212 (ptp) REVERT: S 13 GLN cc_start: 0.8890 (tp40) cc_final: 0.8654 (mm110) REVERT: S 69 THR cc_start: 0.8690 (t) cc_final: 0.8302 (m) REVERT: S 171 GLN cc_start: 0.8399 (mp10) cc_final: 0.7911 (mp10) outliers start: 28 outliers final: 19 residues processed: 188 average time/residue: 1.3604 time to fit residues: 272.6877 Evaluate side-chains 185 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 70 MET Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain R residue 221 ILE Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 202 LEU Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 52 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 23 optimal weight: 0.0050 chunk 72 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 94 optimal weight: 0.0770 chunk 120 optimal weight: 0.5980 overall best weight: 0.5354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 216 GLN R 242 HIS A 194 ASN B 16 ASN B 259 GLN S 174 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.131771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.094920 restraints weight = 18032.592| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.45 r_work: 0.3134 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10059 Z= 0.192 Angle : 0.697 19.495 13661 Z= 0.348 Chirality : 0.044 0.192 1585 Planarity : 0.004 0.054 1729 Dihedral : 4.283 25.580 1374 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.79 % Allowed : 24.91 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.24), residues: 1260 helix: 2.11 (0.26), residues: 419 sheet: 0.21 (0.27), residues: 325 loop : -0.94 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 112 HIS 0.003 0.001 HIS R 291 PHE 0.032 0.001 PHE R 316 TYR 0.015 0.001 TYR S 178 ARG 0.014 0.001 ARG A 313 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 83 THR cc_start: 0.8671 (p) cc_final: 0.8400 (t) REVERT: R 200 MET cc_start: 0.6987 (mtm) cc_final: 0.6507 (mtm) REVERT: R 321 PHE cc_start: 0.7927 (t80) cc_final: 0.7630 (t80) REVERT: D 27 VAL cc_start: 0.8980 (t) cc_final: 0.8551 (p) REVERT: E 40 LYS cc_start: 0.7980 (mttt) cc_final: 0.6917 (mppt) REVERT: A 243 ARG cc_start: 0.8743 (mmm-85) cc_final: 0.8468 (mtt180) REVERT: A 273 ASP cc_start: 0.7721 (p0) cc_final: 0.7491 (p0) REVERT: S 69 THR cc_start: 0.8625 (t) cc_final: 0.8239 (m) REVERT: S 87 ARG cc_start: 0.8479 (mtt-85) cc_final: 0.8272 (mtt-85) REVERT: S 171 GLN cc_start: 0.8234 (mp10) cc_final: 0.7661 (mp10) outliers start: 19 outliers final: 12 residues processed: 187 average time/residue: 1.3416 time to fit residues: 267.5870 Evaluate side-chains 177 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 165 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 141 SER Chi-restraints excluded: chain R residue 192 VAL Chi-restraints excluded: chain R residue 221 ILE Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain S residue 143 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 70 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 23 optimal weight: 0.0060 chunk 58 optimal weight: 2.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 216 GLN R 242 HIS A 194 ASN B 16 ASN B 259 GLN S 174 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.131023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.092504 restraints weight = 17953.240| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.46 r_work: 0.3110 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.4505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10059 Z= 0.206 Angle : 0.726 20.073 13661 Z= 0.357 Chirality : 0.044 0.187 1585 Planarity : 0.004 0.068 1729 Dihedral : 4.253 25.457 1374 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.79 % Allowed : 25.28 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.24), residues: 1260 helix: 2.09 (0.26), residues: 419 sheet: 0.26 (0.27), residues: 325 loop : -0.90 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 104 HIS 0.004 0.001 HIS R 291 PHE 0.010 0.001 PHE B 234 TYR 0.023 0.001 TYR A 303 ARG 0.016 0.001 ARG A 313 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8549.48 seconds wall clock time: 151 minutes 22.18 seconds (9082.18 seconds total)