Starting phenix.real_space_refine on Sun May 3 01:12:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xhh_66874/05_2026/9xhh_66874.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xhh_66874/05_2026/9xhh_66874.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xhh_66874/05_2026/9xhh_66874.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xhh_66874/05_2026/9xhh_66874.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xhh_66874/05_2026/9xhh_66874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xhh_66874/05_2026/9xhh_66874.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 6055 2.51 5 N 1606 2.21 5 O 1732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9463 Number of models: 1 Model: "" Number of chains: 7 Chain: "L" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 532 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 61} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "R" Number of atoms: 2430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2430 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 297} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2576 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ASP:plan': 3, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 383 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1756 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "D" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1758 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.44, per 1000 atoms: 0.26 Number of scatterers: 9463 At special positions: 0 Unit cell: (88.875, 118.5, 156.025, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 70 16.00 O 1732 8.00 N 1606 7.00 C 6055 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS L 8 " - pdb=" SG CYS L 34 " distance=2.03 Simple disulfide: pdb=" SG CYS L 9 " - pdb=" SG CYS L 50 " distance=2.03 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 298 " distance=2.03 Simple disulfide: pdb=" SG CYS R 129 " - pdb=" SG CYS R 210 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 368.1 milliseconds 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2282 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 14 sheets defined 38.7% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'L' and resid 18 through 22 removed outlier: 4.006A pdb=" N ILE L 21 " --> pdb=" O PRO L 18 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL L 22 " --> pdb=" O GLY L 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 18 through 22' Processing helix chain 'L' and resid 29 through 33 Processing helix chain 'L' and resid 55 through 68 Processing helix chain 'R' and resid 50 through 86 Proline residue: R 62 - end of helix removed outlier: 4.083A pdb=" N LEU R 73 " --> pdb=" O CYS R 69 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE R 86 " --> pdb=" O THR R 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 120 Proline residue: R 112 - end of helix Processing helix chain 'R' and resid 125 through 159 removed outlier: 3.617A pdb=" N LEU R 148 " --> pdb=" O MET R 144 " (cutoff:3.500A) Processing helix chain 'R' and resid 160 through 167 Processing helix chain 'R' and resid 167 through 190 removed outlier: 3.696A pdb=" N LEU R 172 " --> pdb=" O ARG R 168 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU R 173 " --> pdb=" O ALA R 169 " (cutoff:3.500A) Processing helix chain 'R' and resid 190 through 196 Processing helix chain 'R' and resid 216 through 232 removed outlier: 3.910A pdb=" N PHE R 220 " --> pdb=" O HIS R 216 " (cutoff:3.500A) Processing helix chain 'R' and resid 232 through 251 Processing helix chain 'R' and resid 257 through 275 removed outlier: 3.814A pdb=" N ALA R 267 " --> pdb=" O LYS R 263 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL R 271 " --> pdb=" O ALA R 267 " (cutoff:3.500A) Processing helix chain 'R' and resid 276 through 291 Processing helix chain 'R' and resid 297 through 327 removed outlier: 4.845A pdb=" N CYS R 319 " --> pdb=" O ALA R 315 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N CYS R 320 " --> pdb=" O CYS R 316 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 330 through 342 Processing helix chain 'B' and resid 6 through 25 Processing helix chain 'B' and resid 28 through 32 Processing helix chain 'C' and resid 12 through 24 removed outlier: 3.703A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.583A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 55 removed outlier: 3.506A pdb=" N ILE A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.534A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TRP A 211 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.684A pdb=" N ASN A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 282 through 286 removed outlier: 4.192A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.724A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 53 through 56 removed outlier: 3.899A pdb=" N GLY D 56 " --> pdb=" O SER D 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 53 through 56' Processing helix chain 'D' and resid 87 through 91 removed outlier: 4.096A pdb=" N THR D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 25 through 28 Processing sheet with id=AA2, first strand: chain 'R' and resid 197 through 200 Processing sheet with id=AA3, first strand: chain 'B' and resid 49 through 51 Processing sheet with id=AA4, first strand: chain 'B' and resid 57 through 62 removed outlier: 3.526A pdb=" N ALA B 59 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS B 77 " --> pdb=" O SER B 73 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ASP B 82 " --> pdb=" O LYS B 88 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N LYS B 88 " --> pdb=" O ASP B 82 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 99 through 104 removed outlier: 6.968A pdb=" N GLY B 114 " --> pdb=" O MET B 100 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N CYS B 102 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ALA B 112 " --> pdb=" O CYS B 102 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N TYR B 104 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N TYR B 110 " --> pdb=" O TYR B 104 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N CYS B 120 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLU B 137 " --> pdb=" O CYS B 120 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE B 122 " --> pdb=" O SER B 135 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 145 through 150 removed outlier: 3.512A pdb=" N CYS B 147 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR B 164 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ASP B 169 " --> pdb=" O GLN B 175 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLN B 175 " --> pdb=" O ASP B 169 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 186 through 191 removed outlier: 7.120A pdb=" N GLY B 201 " --> pdb=" O MET B 187 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LEU B 189 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL B 199 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N LEU B 191 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N LEU B 197 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN B 219 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASP B 211 " --> pdb=" O CYS B 217 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N CYS B 217 " --> pdb=" O ASP B 211 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 228 through 233 removed outlier: 6.721A pdb=" N GLY B 243 " --> pdb=" O ASN B 229 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ILE B 231 " --> pdb=" O ALA B 241 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ALA B 241 " --> pdb=" O ILE B 231 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N PHE B 233 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ALA B 239 " --> pdb=" O PHE B 233 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N MET B 261 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ASP B 253 " --> pdb=" O GLU B 259 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLU B 259 " --> pdb=" O ASP B 253 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 272 through 277 removed outlier: 3.627A pdb=" N SER B 274 " --> pdb=" O GLY B 287 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ASP B 297 " --> pdb=" O ARG B 303 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG B 303 " --> pdb=" O ASP B 297 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.163A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 18 through 23 Processing sheet with id=AB3, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.576A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N PHE D 110 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 129 through 130 Processing sheet with id=AB5, first strand: chain 'D' and resid 134 through 136 removed outlier: 6.696A pdb=" N TRP D 164 " --> pdb=" O LEU D 176 " (cutoff:3.500A) 473 hydrogen bonds defined for protein. 1320 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.32 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3023 1.34 - 1.46: 2369 1.46 - 1.58: 4169 1.58 - 1.70: 0 1.70 - 1.82: 98 Bond restraints: 9659 Sorted by residual: bond pdb=" CA GLY B 329 " pdb=" C GLY B 329 " ideal model delta sigma weight residual 1.520 1.508 0.012 7.30e-03 1.88e+04 2.55e+00 bond pdb=" C ASP D 74 " pdb=" N PRO D 75 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.36e-02 5.41e+03 1.66e+00 bond pdb=" CG1 ILE R 158 " pdb=" CD1 ILE R 158 " ideal model delta sigma weight residual 1.513 1.466 0.047 3.90e-02 6.57e+02 1.46e+00 bond pdb=" C3 CLR R 601 " pdb=" O1 CLR R 601 " ideal model delta sigma weight residual 1.413 1.389 0.024 2.00e-02 2.50e+03 1.42e+00 bond pdb=" C17 CLR R 601 " pdb=" C20 CLR R 601 " ideal model delta sigma weight residual 1.535 1.558 -0.023 2.00e-02 2.50e+03 1.30e+00 ... (remaining 9654 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 12783 1.78 - 3.56: 251 3.56 - 5.33: 38 5.33 - 7.11: 19 7.11 - 8.89: 5 Bond angle restraints: 13096 Sorted by residual: angle pdb=" C THR L 43 " pdb=" N LEU L 44 " pdb=" CA LEU L 44 " ideal model delta sigma weight residual 120.38 124.94 -4.56 1.37e+00 5.33e-01 1.11e+01 angle pdb=" CG1 ILE R 230 " pdb=" CB ILE R 230 " pdb=" CG2 ILE R 230 " ideal model delta sigma weight residual 110.70 101.97 8.73 3.00e+00 1.11e-01 8.47e+00 angle pdb=" C ASP R 40 " pdb=" N TYR R 41 " pdb=" CA TYR R 41 " ideal model delta sigma weight residual 121.54 126.97 -5.43 1.91e+00 2.74e-01 8.08e+00 angle pdb=" C ILE C 25 " pdb=" N ASP C 26 " pdb=" CA ASP C 26 " ideal model delta sigma weight residual 122.82 126.59 -3.77 1.42e+00 4.96e-01 7.05e+00 angle pdb=" CA TYR R 41 " pdb=" CB TYR R 41 " pdb=" CG TYR R 41 " ideal model delta sigma weight residual 113.90 118.62 -4.72 1.80e+00 3.09e-01 6.87e+00 ... (remaining 13091 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 5199 17.61 - 35.21: 494 35.21 - 52.82: 76 52.82 - 70.43: 14 70.43 - 88.04: 5 Dihedral angle restraints: 5788 sinusoidal: 2254 harmonic: 3534 Sorted by residual: dihedral pdb=" CB CYS R 129 " pdb=" SG CYS R 129 " pdb=" SG CYS R 210 " pdb=" CB CYS R 210 " ideal model delta sinusoidal sigma weight residual -86.00 -174.04 88.04 1 1.00e+01 1.00e-02 9.27e+01 dihedral pdb=" CA TRP B 81 " pdb=" C TRP B 81 " pdb=" N ASP B 82 " pdb=" CA ASP B 82 " ideal model delta harmonic sigma weight residual 180.00 159.11 20.89 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA TYR D 101 " pdb=" C TYR D 101 " pdb=" N TYR D 102 " pdb=" CA TYR D 102 " ideal model delta harmonic sigma weight residual 180.00 159.69 20.31 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 5785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1301 0.067 - 0.133: 195 0.133 - 0.200: 9 0.200 - 0.266: 4 0.266 - 0.333: 2 Chirality restraints: 1511 Sorted by residual: chirality pdb=" C14 CLR R 601 " pdb=" C13 CLR R 601 " pdb=" C15 CLR R 601 " pdb=" C8 CLR R 601 " both_signs ideal model delta sigma weight residual False -2.32 -2.65 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" C9 CLR R 601 " pdb=" C10 CLR R 601 " pdb=" C11 CLR R 601 " pdb=" C8 CLR R 601 " both_signs ideal model delta sigma weight residual False -2.45 -2.72 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C17 CLR R 601 " pdb=" C13 CLR R 601 " pdb=" C16 CLR R 601 " pdb=" C20 CLR R 601 " both_signs ideal model delta sigma weight residual False 2.55 2.82 -0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 1508 not shown) Planarity restraints: 1641 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 74 " 0.036 5.00e-02 4.00e+02 5.44e-02 4.74e+00 pdb=" N PRO D 75 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 234 " -0.032 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO B 235 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 235 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 235 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 266 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.43e+00 pdb=" C ILE R 266 " 0.032 2.00e-02 2.50e+03 pdb=" O ILE R 266 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA R 267 " -0.011 2.00e-02 2.50e+03 ... (remaining 1638 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 440 2.72 - 3.27: 9454 3.27 - 3.81: 16223 3.81 - 4.36: 19557 4.36 - 4.90: 33595 Nonbonded interactions: 79269 Sorted by model distance: nonbonded pdb=" OG SER B 160 " pdb=" OD1 ASP B 162 " model vdw 2.176 3.040 nonbonded pdb=" OH TYR R 136 " pdb=" OH TYR R 312 " model vdw 2.229 3.040 nonbonded pdb=" O ILE B 57 " pdb=" OG SER B 315 " model vdw 2.239 3.040 nonbonded pdb=" OG1 THR B 273 " pdb=" O VAL B 314 " model vdw 2.246 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR D 163 " model vdw 2.247 3.040 ... (remaining 79264 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 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: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.030 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 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 : 0.004 0.047 9665 Z= 0.182 Angle : 0.666 8.891 13108 Z= 0.342 Chirality : 0.048 0.333 1511 Planarity : 0.005 0.054 1641 Dihedral : 13.636 87.578 3488 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.24), residues: 1198 helix: 0.42 (0.25), residues: 421 sheet: -0.83 (0.28), residues: 309 loop : -0.96 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 318 TYR 0.019 0.002 TYR R 41 PHE 0.014 0.002 PHE B 198 TRP 0.019 0.002 TRP R 59 HIS 0.004 0.001 HIS L 26 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 9659) covalent geometry : angle 0.66416 (13096) SS BOND : bond 0.00432 ( 6) SS BOND : angle 1.64765 ( 12) hydrogen bonds : bond 0.12607 ( 473) hydrogen bonds : angle 6.40326 ( 1320) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 13 LEU cc_start: 0.9091 (tp) cc_final: 0.8882 (tp) REVERT: B 60 MET cc_start: 0.8853 (ppp) cc_final: 0.8349 (ppp) REVERT: B 129 GLU cc_start: 0.8401 (mt-10) cc_final: 0.7686 (mp0) REVERT: B 302 ASP cc_start: 0.7794 (m-30) cc_final: 0.7244 (p0) REVERT: B 311 ASP cc_start: 0.7579 (t0) cc_final: 0.7248 (t0) REVERT: C 22 GLU cc_start: 0.8482 (tm-30) cc_final: 0.8182 (tm-30) REVERT: A 22 ASN cc_start: 0.8402 (m110) cc_final: 0.7957 (m110) REVERT: A 24 ARG cc_start: 0.7268 (ttp-110) cc_final: 0.6649 (ttp-110) REVERT: A 26 ASP cc_start: 0.8311 (m-30) cc_final: 0.8061 (m-30) REVERT: A 188 HIS cc_start: 0.7730 (m90) cc_final: 0.7473 (t70) REVERT: A 313 ARG cc_start: 0.6218 (ttt-90) cc_final: 0.5953 (ttt-90) REVERT: A 314 LYS cc_start: 0.6793 (mptt) cc_final: 0.5918 (tptm) REVERT: D 168 ARG cc_start: 0.7639 (mtm-85) cc_final: 0.7331 (mtm-85) REVERT: D 222 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7484 (mm-30) outliers start: 0 outliers final: 1 residues processed: 229 average time/residue: 0.5722 time to fit residues: 140.0294 Evaluate side-chains 170 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 169 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.0270 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 overall best weight: 2.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 165 HIS R 200 GLN R 335 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 HIS B 229 ASN B 265 HIS ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN A 304 GLN A 306 GLN A 331 ASN A 346 ASN D 130 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.179346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.146219 restraints weight = 13044.271| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 2.50 r_work: 0.3751 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3622 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 9665 Z= 0.275 Angle : 0.718 10.199 13108 Z= 0.368 Chirality : 0.046 0.159 1511 Planarity : 0.005 0.047 1641 Dihedral : 5.565 59.330 1381 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.12 % Allowed : 16.09 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.24), residues: 1198 helix: 0.76 (0.26), residues: 420 sheet: -1.01 (0.29), residues: 294 loop : -0.79 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 205 TYR 0.032 0.002 TYR D 178 PHE 0.016 0.002 PHE A 354 TRP 0.026 0.002 TRP B 168 HIS 0.006 0.001 HIS B 90 Details of bonding type rmsd covalent geometry : bond 0.00640 ( 9659) covalent geometry : angle 0.71648 (13096) SS BOND : bond 0.00333 ( 6) SS BOND : angle 1.63908 ( 12) hydrogen bonds : bond 0.05298 ( 473) hydrogen bonds : angle 5.57693 ( 1320) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 180 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 45 GLU cc_start: 0.5185 (pm20) cc_final: 0.4937 (pm20) REVERT: B 41 ARG cc_start: 0.7728 (ttp-110) cc_final: 0.7267 (tmm-80) REVERT: B 302 ASP cc_start: 0.7961 (m-30) cc_final: 0.7597 (p0) REVERT: B 311 ASP cc_start: 0.7608 (t0) cc_final: 0.7293 (t0) REVERT: C 18 GLN cc_start: 0.9050 (tp40) cc_final: 0.8833 (tp-100) REVERT: C 19 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8220 (mm) REVERT: C 22 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8155 (tm-30) REVERT: C 38 MET cc_start: 0.6602 (OUTLIER) cc_final: 0.6395 (mtm) REVERT: A 22 ASN cc_start: 0.8479 (m110) cc_final: 0.7987 (m110) REVERT: A 24 ARG cc_start: 0.7299 (ttp-110) cc_final: 0.6724 (ttp-110) REVERT: A 26 ASP cc_start: 0.8334 (m-30) cc_final: 0.8065 (m-30) REVERT: A 188 HIS cc_start: 0.7874 (m90) cc_final: 0.7623 (t-90) REVERT: A 247 MET cc_start: 0.8355 (ttt) cc_final: 0.8089 (ttp) REVERT: A 295 THR cc_start: 0.7597 (m) cc_final: 0.7261 (p) REVERT: A 314 LYS cc_start: 0.6830 (mptt) cc_final: 0.5837 (tptm) outliers start: 42 outliers final: 22 residues processed: 198 average time/residue: 0.5674 time to fit residues: 120.3431 Evaluate side-chains 191 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 92 MET Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 187 THR Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 320 CYS Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 160 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 25 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 39 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 21 optimal weight: 0.0980 chunk 11 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS A 255 ASN D 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.184902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.149176 restraints weight = 12903.530| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 2.46 r_work: 0.3807 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3677 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9665 Z= 0.139 Angle : 0.616 9.693 13108 Z= 0.313 Chirality : 0.042 0.134 1511 Planarity : 0.004 0.043 1641 Dihedral : 5.342 58.423 1381 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.04 % Allowed : 19.33 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.25), residues: 1198 helix: 1.15 (0.26), residues: 414 sheet: -0.82 (0.28), residues: 305 loop : -0.71 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 205 TYR 0.029 0.002 TYR D 178 PHE 0.011 0.001 PHE R 113 TRP 0.022 0.002 TRP L 57 HIS 0.003 0.001 HIS L 26 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 9659) covalent geometry : angle 0.61539 (13096) SS BOND : bond 0.00319 ( 6) SS BOND : angle 1.20502 ( 12) hydrogen bonds : bond 0.04337 ( 473) hydrogen bonds : angle 5.18462 ( 1320) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 186 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 45 GLU cc_start: 0.5145 (pm20) cc_final: 0.4878 (pm20) REVERT: R 94 ASP cc_start: 0.7789 (m-30) cc_final: 0.7516 (m-30) REVERT: R 199 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8308 (mp) REVERT: R 297 THR cc_start: 0.8644 (t) cc_final: 0.8091 (p) REVERT: B 41 ARG cc_start: 0.7746 (ttp-110) cc_final: 0.7160 (tmm-80) REVERT: B 302 ASP cc_start: 0.7963 (m-30) cc_final: 0.7427 (p0) REVERT: B 311 ASP cc_start: 0.7530 (t0) cc_final: 0.7234 (t0) REVERT: C 18 GLN cc_start: 0.9035 (tp40) cc_final: 0.8748 (tp-100) REVERT: C 22 GLU cc_start: 0.8477 (tm-30) cc_final: 0.8118 (tm-30) REVERT: C 38 MET cc_start: 0.6363 (mtm) cc_final: 0.6120 (mtm) REVERT: C 58 GLU cc_start: 0.7518 (pt0) cc_final: 0.7208 (pm20) REVERT: A 22 ASN cc_start: 0.8469 (m110) cc_final: 0.8204 (m110) REVERT: A 24 ARG cc_start: 0.7247 (ttp-110) cc_final: 0.6644 (ttp-110) REVERT: A 295 THR cc_start: 0.7513 (m) cc_final: 0.7182 (p) REVERT: A 314 LYS cc_start: 0.6815 (mptt) cc_final: 0.5897 (tptm) REVERT: D 222 GLU cc_start: 0.7644 (mm-30) cc_final: 0.7383 (mm-30) outliers start: 31 outliers final: 13 residues processed: 201 average time/residue: 0.5540 time to fit residues: 119.2553 Evaluate side-chains 183 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 169 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 320 CYS Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 208 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 27 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 34 optimal weight: 0.5980 chunk 5 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 127 HIS R 200 GLN R 224 GLN R 335 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN A 269 ASN D 113 GLN ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.177750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.142984 restraints weight = 13061.939| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 2.40 r_work: 0.3714 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3584 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 9665 Z= 0.267 Angle : 0.712 12.324 13108 Z= 0.362 Chirality : 0.046 0.155 1511 Planarity : 0.004 0.050 1641 Dihedral : 5.579 58.911 1381 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.61 % Allowed : 20.22 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.25), residues: 1198 helix: 0.97 (0.26), residues: 418 sheet: -1.14 (0.28), residues: 301 loop : -0.74 (0.30), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 205 TYR 0.028 0.002 TYR D 178 PHE 0.014 0.002 PHE D 27 TRP 0.046 0.002 TRP L 57 HIS 0.005 0.001 HIS B 90 Details of bonding type rmsd covalent geometry : bond 0.00625 ( 9659) covalent geometry : angle 0.71071 (13096) SS BOND : bond 0.00343 ( 6) SS BOND : angle 1.56668 ( 12) hydrogen bonds : bond 0.05035 ( 473) hydrogen bonds : angle 5.44951 ( 1320) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 169 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 60 ARG cc_start: 0.9249 (ttp80) cc_final: 0.8351 (ttp80) REVERT: B 41 ARG cc_start: 0.7872 (ttp-110) cc_final: 0.7286 (tmm-80) REVERT: B 302 ASP cc_start: 0.8058 (m-30) cc_final: 0.7644 (p0) REVERT: B 311 ASP cc_start: 0.7507 (t0) cc_final: 0.7207 (t0) REVERT: C 18 GLN cc_start: 0.9048 (tp40) cc_final: 0.8774 (tp-100) REVERT: C 22 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8094 (tm-30) REVERT: C 38 MET cc_start: 0.6533 (mtm) cc_final: 0.6258 (mtm) REVERT: C 58 GLU cc_start: 0.7609 (pt0) cc_final: 0.7233 (pm20) REVERT: A 22 ASN cc_start: 0.8444 (m110) cc_final: 0.7966 (m110) REVERT: A 24 ARG cc_start: 0.7298 (ttp-110) cc_final: 0.6713 (ttp-110) REVERT: A 26 ASP cc_start: 0.8331 (m-30) cc_final: 0.8091 (m-30) REVERT: A 295 THR cc_start: 0.7620 (OUTLIER) cc_final: 0.7258 (t) REVERT: A 313 ARG cc_start: 0.6254 (ttt-90) cc_final: 0.6007 (ttt-90) REVERT: A 314 LYS cc_start: 0.6850 (mptt) cc_final: 0.5794 (tptm) REVERT: A 331 ASN cc_start: 0.8345 (OUTLIER) cc_final: 0.7824 (m-40) REVERT: D 222 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7416 (mm-30) outliers start: 47 outliers final: 30 residues processed: 190 average time/residue: 0.5637 time to fit residues: 114.7718 Evaluate side-chains 195 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 163 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 273 ILE Chi-restraints excluded: chain R residue 320 CYS Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 160 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 36 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN A 269 ASN ** D 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.180528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.146417 restraints weight = 13077.919| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 2.61 r_work: 0.3737 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9665 Z= 0.182 Angle : 0.666 13.102 13108 Z= 0.335 Chirality : 0.044 0.313 1511 Planarity : 0.004 0.054 1641 Dihedral : 5.513 59.873 1381 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 4.71 % Allowed : 22.57 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.24), residues: 1198 helix: 1.11 (0.26), residues: 413 sheet: -1.04 (0.28), residues: 287 loop : -0.80 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG L 60 TYR 0.024 0.002 TYR D 178 PHE 0.012 0.001 PHE R 113 TRP 0.040 0.002 TRP L 57 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 9659) covalent geometry : angle 0.66509 (13096) SS BOND : bond 0.00308 ( 6) SS BOND : angle 1.26775 ( 12) hydrogen bonds : bond 0.04642 ( 473) hydrogen bonds : angle 5.28684 ( 1320) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 173 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 57 TRP cc_start: 0.8531 (p90) cc_final: 0.8317 (p90) REVERT: R 45 GLU cc_start: 0.5279 (pm20) cc_final: 0.5005 (pm20) REVERT: B 41 ARG cc_start: 0.7852 (ttp-110) cc_final: 0.7222 (tmm-80) REVERT: B 302 ASP cc_start: 0.8023 (m-30) cc_final: 0.7603 (p0) REVERT: B 311 ASP cc_start: 0.7445 (t0) cc_final: 0.7191 (t0) REVERT: C 22 GLU cc_start: 0.8487 (tm-30) cc_final: 0.8034 (tm-30) REVERT: C 58 GLU cc_start: 0.7552 (pt0) cc_final: 0.7178 (pm20) REVERT: A 22 ASN cc_start: 0.8441 (m110) cc_final: 0.7935 (m110) REVERT: A 24 ARG cc_start: 0.7266 (ttp-110) cc_final: 0.6652 (ttp-110) REVERT: A 26 ASP cc_start: 0.8325 (m-30) cc_final: 0.8070 (m-30) REVERT: A 254 CYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7273 (t) REVERT: A 295 THR cc_start: 0.7577 (m) cc_final: 0.7208 (t) REVERT: A 314 LYS cc_start: 0.6831 (mptt) cc_final: 0.5789 (tptm) REVERT: A 331 ASN cc_start: 0.8278 (OUTLIER) cc_final: 0.7761 (m-40) REVERT: D 222 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7446 (mm-30) outliers start: 48 outliers final: 30 residues processed: 197 average time/residue: 0.5375 time to fit residues: 113.5579 Evaluate side-chains 193 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 17 ILE Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 320 CYS Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 208 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 71 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 chunk 68 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 118 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN ** B 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN D 113 GLN D 130 GLN ** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.181828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.148737 restraints weight = 12927.190| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 2.52 r_work: 0.3768 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3639 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9665 Z= 0.146 Angle : 0.661 13.505 13108 Z= 0.330 Chirality : 0.043 0.286 1511 Planarity : 0.004 0.064 1641 Dihedral : 5.390 58.899 1381 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.22 % Allowed : 24.14 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.24), residues: 1198 helix: 1.13 (0.26), residues: 419 sheet: -0.95 (0.29), residues: 283 loop : -0.76 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 205 TYR 0.022 0.002 TYR D 178 PHE 0.012 0.001 PHE R 113 TRP 0.028 0.002 TRP L 57 HIS 0.003 0.001 HIS L 26 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 9659) covalent geometry : angle 0.66009 (13096) SS BOND : bond 0.00297 ( 6) SS BOND : angle 1.06675 ( 12) hydrogen bonds : bond 0.04265 ( 473) hydrogen bonds : angle 5.18277 ( 1320) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 172 time to evaluate : 0.368 Fit side-chains revert: symmetry clash REVERT: L 57 TRP cc_start: 0.8656 (p90) cc_final: 0.8388 (p90) REVERT: R 45 GLU cc_start: 0.5155 (pm20) cc_final: 0.4924 (pm20) REVERT: R 94 ASP cc_start: 0.7908 (m-30) cc_final: 0.7611 (m-30) REVERT: B 41 ARG cc_start: 0.7824 (ttp-110) cc_final: 0.7229 (tmm-80) REVERT: B 302 ASP cc_start: 0.7946 (m-30) cc_final: 0.7476 (p0) REVERT: B 311 ASP cc_start: 0.7423 (t0) cc_final: 0.7115 (t0) REVERT: C 22 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8082 (tm-30) REVERT: C 58 GLU cc_start: 0.7515 (pt0) cc_final: 0.7148 (pm20) REVERT: A 22 ASN cc_start: 0.8427 (m110) cc_final: 0.7934 (m110) REVERT: A 24 ARG cc_start: 0.7325 (ttp-110) cc_final: 0.6622 (ttp-110) REVERT: A 26 ASP cc_start: 0.8354 (m-30) cc_final: 0.8113 (m-30) REVERT: A 295 THR cc_start: 0.7525 (OUTLIER) cc_final: 0.7135 (t) REVERT: A 313 ARG cc_start: 0.6270 (ttt-90) cc_final: 0.5957 (ttt-90) REVERT: A 314 LYS cc_start: 0.6783 (mptt) cc_final: 0.5773 (tptm) REVERT: A 331 ASN cc_start: 0.8197 (OUTLIER) cc_final: 0.7706 (m-40) REVERT: D 128 MET cc_start: 0.4864 (OUTLIER) cc_final: 0.3356 (mtm) REVERT: D 130 GLN cc_start: 0.3912 (OUTLIER) cc_final: 0.3530 (mm-40) REVERT: D 148 ARG cc_start: 0.6322 (pmm150) cc_final: 0.6005 (pmm150) REVERT: D 222 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7450 (mm-30) outliers start: 43 outliers final: 18 residues processed: 193 average time/residue: 0.5585 time to fit residues: 115.7799 Evaluate side-chains 184 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain R residue 67 ILE Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 320 CYS Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 128 MET Chi-restraints excluded: chain D residue 130 GLN Chi-restraints excluded: chain D residue 160 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 76 optimal weight: 0.4980 chunk 37 optimal weight: 9.9990 chunk 115 optimal weight: 0.9990 chunk 90 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 59 optimal weight: 0.2980 chunk 74 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 200 GLN R 224 GLN R 335 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 GLN B 118 ASN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN D 130 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.183669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.150337 restraints weight = 13007.457| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 2.63 r_work: 0.3787 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3657 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9665 Z= 0.141 Angle : 0.668 12.728 13108 Z= 0.332 Chirality : 0.043 0.152 1511 Planarity : 0.004 0.043 1641 Dihedral : 5.330 58.491 1381 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.12 % Allowed : 25.32 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.25), residues: 1198 helix: 1.17 (0.26), residues: 419 sheet: -0.93 (0.28), residues: 309 loop : -0.64 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 60 TYR 0.021 0.002 TYR D 178 PHE 0.012 0.001 PHE R 113 TRP 0.024 0.002 TRP L 57 HIS 0.003 0.001 HIS L 26 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 9659) covalent geometry : angle 0.66733 (13096) SS BOND : bond 0.00313 ( 6) SS BOND : angle 1.41049 ( 12) hydrogen bonds : bond 0.04092 ( 473) hydrogen bonds : angle 5.13343 ( 1320) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 176 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 57 TRP cc_start: 0.8727 (p90) cc_final: 0.8427 (p90) REVERT: R 45 GLU cc_start: 0.5059 (pm20) cc_final: 0.4745 (pm20) REVERT: R 94 ASP cc_start: 0.7890 (m-30) cc_final: 0.7569 (m-30) REVERT: R 117 SER cc_start: 0.7678 (OUTLIER) cc_final: 0.7298 (p) REVERT: B 41 ARG cc_start: 0.7838 (ttp-110) cc_final: 0.7234 (tmm-80) REVERT: B 197 LEU cc_start: 0.8856 (mt) cc_final: 0.8360 (mm) REVERT: B 302 ASP cc_start: 0.7944 (m-30) cc_final: 0.7466 (p0) REVERT: B 311 ASP cc_start: 0.7457 (t0) cc_final: 0.7135 (t0) REVERT: C 22 GLU cc_start: 0.8560 (tm-30) cc_final: 0.8073 (tm-30) REVERT: C 58 GLU cc_start: 0.7480 (pt0) cc_final: 0.7096 (pm20) REVERT: A 22 ASN cc_start: 0.8428 (m110) cc_final: 0.7901 (m110) REVERT: A 24 ARG cc_start: 0.7322 (ttp-110) cc_final: 0.6618 (ttp-110) REVERT: A 26 ASP cc_start: 0.8297 (m-30) cc_final: 0.8033 (m-30) REVERT: A 254 CYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7608 (m) REVERT: A 295 THR cc_start: 0.7497 (OUTLIER) cc_final: 0.7105 (t) REVERT: A 313 ARG cc_start: 0.6280 (ttt-90) cc_final: 0.5986 (ttt-90) REVERT: A 314 LYS cc_start: 0.6747 (mptt) cc_final: 0.5798 (tptm) REVERT: A 331 ASN cc_start: 0.8247 (OUTLIER) cc_final: 0.7729 (m-40) REVERT: D 128 MET cc_start: 0.4864 (OUTLIER) cc_final: 0.3224 (mtm) REVERT: D 148 ARG cc_start: 0.6296 (pmm150) cc_final: 0.6037 (pmm150) REVERT: D 222 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7452 (mm-30) outliers start: 42 outliers final: 21 residues processed: 199 average time/residue: 0.5606 time to fit residues: 119.7387 Evaluate side-chains 194 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 320 CYS Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 128 MET Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 208 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 70 optimal weight: 9.9990 chunk 93 optimal weight: 0.0980 chunk 84 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 97 optimal weight: 0.0000 chunk 80 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 109 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 overall best weight: 1.2190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 GLN ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN ** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.181412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.148500 restraints weight = 12834.703| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 2.48 r_work: 0.3763 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3634 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9665 Z= 0.177 Angle : 0.711 13.037 13108 Z= 0.354 Chirality : 0.044 0.176 1511 Planarity : 0.004 0.078 1641 Dihedral : 5.344 58.199 1379 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 4.42 % Allowed : 25.22 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.25), residues: 1198 helix: 1.10 (0.26), residues: 419 sheet: -0.98 (0.29), residues: 294 loop : -0.72 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 205 TYR 0.020 0.002 TYR D 178 PHE 0.011 0.001 PHE B 198 TRP 0.023 0.002 TRP L 57 HIS 0.003 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 9659) covalent geometry : angle 0.71020 (13096) SS BOND : bond 0.00305 ( 6) SS BOND : angle 1.23769 ( 12) hydrogen bonds : bond 0.04376 ( 473) hydrogen bonds : angle 5.22263 ( 1320) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 169 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: L 57 TRP cc_start: 0.8770 (p90) cc_final: 0.8423 (p90) REVERT: L 60 ARG cc_start: 0.9151 (ttp80) cc_final: 0.8627 (ttp80) REVERT: R 45 GLU cc_start: 0.4990 (pm20) cc_final: 0.4686 (pm20) REVERT: R 94 ASP cc_start: 0.7890 (m-30) cc_final: 0.7511 (m-30) REVERT: R 117 SER cc_start: 0.7680 (OUTLIER) cc_final: 0.7299 (p) REVERT: B 41 ARG cc_start: 0.7832 (ttp-110) cc_final: 0.7217 (tmm-80) REVERT: B 197 LEU cc_start: 0.8889 (mt) cc_final: 0.8375 (mm) REVERT: B 302 ASP cc_start: 0.7948 (m-30) cc_final: 0.7497 (p0) REVERT: B 311 ASP cc_start: 0.7439 (t0) cc_final: 0.7117 (t0) REVERT: C 22 GLU cc_start: 0.8573 (tm-30) cc_final: 0.8057 (tm-30) REVERT: C 58 GLU cc_start: 0.7398 (pt0) cc_final: 0.6983 (pm20) REVERT: A 22 ASN cc_start: 0.8465 (m110) cc_final: 0.7960 (m110) REVERT: A 24 ARG cc_start: 0.7327 (ttp-110) cc_final: 0.6646 (ttp-110) REVERT: A 26 ASP cc_start: 0.8296 (m-30) cc_final: 0.8038 (m-30) REVERT: A 254 CYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7730 (m) REVERT: A 295 THR cc_start: 0.7478 (OUTLIER) cc_final: 0.7088 (t) REVERT: A 314 LYS cc_start: 0.6784 (mptt) cc_final: 0.5817 (tptm) REVERT: A 331 ASN cc_start: 0.8280 (OUTLIER) cc_final: 0.7538 (m-40) REVERT: D 128 MET cc_start: 0.4949 (OUTLIER) cc_final: 0.3483 (mtm) REVERT: D 148 ARG cc_start: 0.6477 (pmm150) cc_final: 0.6195 (pmm150) REVERT: D 222 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7489 (mm-30) outliers start: 45 outliers final: 24 residues processed: 193 average time/residue: 0.5424 time to fit residues: 112.4237 Evaluate side-chains 187 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain R residue 117 SER Chi-restraints excluded: chain R residue 136 TYR Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 191 ILE Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 320 CYS Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 128 MET Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 208 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 80 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 30 optimal weight: 0.6980 chunk 113 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 224 GLN R 335 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN D 113 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.181558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.148679 restraints weight = 12926.413| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 2.53 r_work: 0.3766 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3635 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9665 Z= 0.178 Angle : 0.736 13.957 13108 Z= 0.363 Chirality : 0.044 0.167 1511 Planarity : 0.004 0.042 1641 Dihedral : 5.338 58.524 1379 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.53 % Allowed : 26.01 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.25), residues: 1198 helix: 1.03 (0.26), residues: 419 sheet: -0.93 (0.28), residues: 307 loop : -0.73 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG R 209 TYR 0.020 0.002 TYR D 178 PHE 0.012 0.001 PHE A 354 TRP 0.022 0.002 TRP L 57 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00418 ( 9659) covalent geometry : angle 0.73588 (13096) SS BOND : bond 0.00321 ( 6) SS BOND : angle 1.22428 ( 12) hydrogen bonds : bond 0.04403 ( 473) hydrogen bonds : angle 5.24419 ( 1320) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 168 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 57 TRP cc_start: 0.8724 (p90) cc_final: 0.8334 (p90) REVERT: L 65 LEU cc_start: 0.9153 (tm) cc_final: 0.8829 (pp) REVERT: R 45 GLU cc_start: 0.5038 (pm20) cc_final: 0.4714 (pm20) REVERT: R 94 ASP cc_start: 0.7912 (m-30) cc_final: 0.7612 (m-30) REVERT: R 117 SER cc_start: 0.7708 (t) cc_final: 0.7322 (p) REVERT: R 201 ARG cc_start: 0.7071 (mpt180) cc_final: 0.6754 (mpt180) REVERT: B 41 ARG cc_start: 0.7819 (ttp-110) cc_final: 0.7211 (tmm-80) REVERT: B 197 LEU cc_start: 0.8890 (mt) cc_final: 0.8409 (mm) REVERT: B 302 ASP cc_start: 0.7950 (m-30) cc_final: 0.7500 (p0) REVERT: B 311 ASP cc_start: 0.7471 (t0) cc_final: 0.7145 (t0) REVERT: C 15 LEU cc_start: 0.8090 (tt) cc_final: 0.7670 (mp) REVERT: C 22 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8039 (tm-30) REVERT: C 58 GLU cc_start: 0.7339 (pt0) cc_final: 0.6946 (pm20) REVERT: A 9 ASP cc_start: 0.7766 (m-30) cc_final: 0.7540 (m-30) REVERT: A 22 ASN cc_start: 0.8449 (m110) cc_final: 0.7958 (m110) REVERT: A 24 ARG cc_start: 0.7327 (ttp-110) cc_final: 0.6641 (ttp-110) REVERT: A 26 ASP cc_start: 0.8305 (m-30) cc_final: 0.8073 (m-30) REVERT: A 247 MET cc_start: 0.8268 (ttt) cc_final: 0.8061 (ttp) REVERT: A 254 CYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7843 (m) REVERT: A 295 THR cc_start: 0.7443 (OUTLIER) cc_final: 0.7059 (t) REVERT: A 314 LYS cc_start: 0.6759 (mptt) cc_final: 0.5780 (tptm) REVERT: A 331 ASN cc_start: 0.8286 (OUTLIER) cc_final: 0.7528 (m-40) REVERT: D 148 ARG cc_start: 0.6524 (pmm150) cc_final: 0.6283 (pmm150) REVERT: D 222 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7587 (mm-30) outliers start: 36 outliers final: 23 residues processed: 187 average time/residue: 0.5365 time to fit residues: 107.7567 Evaluate side-chains 188 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 199 LEU Chi-restraints excluded: chain R residue 319 CYS Chi-restraints excluded: chain R residue 320 CYS Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 208 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 69 optimal weight: 6.9990 chunk 117 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 61 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 GLN A 255 ASN A 331 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.184276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.148966 restraints weight = 12999.771| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 2.38 r_work: 0.3795 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3669 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9665 Z= 0.155 Angle : 0.755 13.761 13108 Z= 0.368 Chirality : 0.044 0.173 1511 Planarity : 0.004 0.084 1641 Dihedral : 5.319 58.550 1379 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.14 % Allowed : 26.59 % Favored : 70.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.25), residues: 1198 helix: 1.03 (0.25), residues: 419 sheet: -0.96 (0.28), residues: 313 loop : -0.67 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 205 TYR 0.017 0.002 TYR D 50 PHE 0.012 0.001 PHE A 354 TRP 0.022 0.002 TRP L 57 HIS 0.004 0.001 HIS L 26 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 9659) covalent geometry : angle 0.75470 (13096) SS BOND : bond 0.00312 ( 6) SS BOND : angle 1.07365 ( 12) hydrogen bonds : bond 0.04243 ( 473) hydrogen bonds : angle 5.18653 ( 1320) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2396 Ramachandran restraints generated. 1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 57 TRP cc_start: 0.8665 (p90) cc_final: 0.8228 (p90) REVERT: R 45 GLU cc_start: 0.5043 (pm20) cc_final: 0.4674 (pm20) REVERT: R 94 ASP cc_start: 0.7879 (m-30) cc_final: 0.7578 (m-30) REVERT: R 117 SER cc_start: 0.7672 (t) cc_final: 0.7288 (p) REVERT: B 41 ARG cc_start: 0.7851 (ttp-110) cc_final: 0.7349 (mmp-170) REVERT: B 197 LEU cc_start: 0.8882 (mt) cc_final: 0.8390 (mm) REVERT: B 302 ASP cc_start: 0.7915 (m-30) cc_final: 0.7495 (p0) REVERT: B 311 ASP cc_start: 0.7510 (t0) cc_final: 0.7191 (t0) REVERT: C 15 LEU cc_start: 0.8097 (tt) cc_final: 0.7480 (mp) REVERT: C 22 GLU cc_start: 0.8536 (tm-30) cc_final: 0.7972 (tm-30) REVERT: C 58 GLU cc_start: 0.7283 (pt0) cc_final: 0.6909 (pm20) REVERT: A 22 ASN cc_start: 0.8436 (m110) cc_final: 0.7911 (m110) REVERT: A 24 ARG cc_start: 0.7326 (ttp-110) cc_final: 0.6651 (ttp-110) REVERT: A 26 ASP cc_start: 0.8296 (m-30) cc_final: 0.8033 (m-30) REVERT: A 247 MET cc_start: 0.8273 (ttt) cc_final: 0.8055 (ttp) REVERT: A 254 CYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7850 (m) REVERT: A 295 THR cc_start: 0.7460 (OUTLIER) cc_final: 0.7087 (t) REVERT: A 314 LYS cc_start: 0.6659 (mptt) cc_final: 0.5766 (tptm) REVERT: A 331 ASN cc_start: 0.8238 (OUTLIER) cc_final: 0.7348 (m-40) REVERT: D 128 MET cc_start: 0.4897 (OUTLIER) cc_final: 0.3436 (mtm) REVERT: D 148 ARG cc_start: 0.6486 (pmm150) cc_final: 0.6253 (pmm150) REVERT: D 222 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7536 (mm-30) outliers start: 32 outliers final: 21 residues processed: 186 average time/residue: 0.5429 time to fit residues: 108.4625 Evaluate side-chains 188 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 163 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 36 VAL Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 319 CYS Chi-restraints excluded: chain R residue 320 CYS Chi-restraints excluded: chain R residue 321 VAL Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 274 SER Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 128 MET Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 208 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 90 optimal weight: 10.0000 chunk 13 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 106 optimal weight: 0.4980 chunk 31 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 88 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 224 GLN R 335 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN A 331 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.183912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.149999 restraints weight = 12764.787| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 2.37 r_work: 0.3787 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 9665 Z= 0.149 Angle : 0.745 14.848 13108 Z= 0.364 Chirality : 0.044 0.373 1511 Planarity : 0.004 0.042 1641 Dihedral : 5.282 58.358 1379 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.94 % Allowed : 26.99 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.25), residues: 1198 helix: 1.18 (0.26), residues: 413 sheet: -0.98 (0.28), residues: 317 loop : -0.67 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG L 60 TYR 0.017 0.002 TYR D 178 PHE 0.011 0.001 PHE R 113 TRP 0.024 0.002 TRP L 57 HIS 0.004 0.001 HIS L 26 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 9659) covalent geometry : angle 0.74423 (13096) SS BOND : bond 0.00315 ( 6) SS BOND : angle 1.00709 ( 12) hydrogen bonds : bond 0.04134 ( 473) hydrogen bonds : angle 5.13946 ( 1320) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4347.09 seconds wall clock time: 74 minutes 52.62 seconds (4492.62 seconds total)