Starting phenix.real_space_refine on Wed Aug 5 06:37:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pa2_71430/08_2026/9pa2_71430.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pa2_71430/08_2026/9pa2_71430.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pa2_71430/08_2026/9pa2_71430.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pa2_71430/08_2026/9pa2_71430.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pa2_71430/08_2026/9pa2_71430.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pa2_71430/08_2026/9pa2_71430.map" } resolution = 2.86 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= 0.029 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 69 5.16 5 C 5517 2.51 5 N 1462 2.21 5 O 1625 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8673 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2123 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 10, 'TRANS': 273} Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PHE:plan': 3, 'TYR:plan': 3, 'ARG:plan': 5, 'GLN:plan1': 1, 'TRP:plan': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 97 Chain: "A" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1775 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 224} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 1, 'GLU:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 2562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2562 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 2, 'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 33 Chain: "C" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 423 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1772 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'1PC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.79, per 1000 atoms: 0.21 Number of scatterers: 8673 At special positions: 0 Unit cell: (86.94, 119.232, 123.372, 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 69 16.00 O 1625 8.00 N 1462 7.00 C 5517 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 142 " - pdb=" SG CYS R 219 " distance=2.03 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 230 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.59 Conformation dependent library (CDL) restraints added in 383.2 milliseconds 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2136 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 13 sheets defined 38.9% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'R' and resid 67 through 98 Processing helix chain 'R' and resid 103 through 133 Proline residue: R 124 - end of helix Processing helix chain 'R' and resid 138 through 173 Processing helix chain 'R' and resid 173 through 181 removed outlier: 4.151A pdb=" N ASP R 179 " --> pdb=" O VAL R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 182 through 207 Proline residue: R 203 - end of helix Processing helix chain 'R' and resid 228 through 264 Proline residue: R 246 - end of helix Processing helix chain 'R' and resid 270 through 308 Proline residue: R 297 - end of helix Processing helix chain 'R' and resid 313 through 341 Proline residue: R 335 - end of helix removed outlier: 4.101A pdb=" N LEU R 341 " --> pdb=" O LEU R 337 " (cutoff:3.500A) Processing helix chain 'R' and resid 342 through 350 Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.933A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 54 removed outlier: 4.038A pdb=" N THR A 48 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.436A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.317A 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 243 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.585A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 278 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 4.019A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 327 through 351 removed outlier: 3.518A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.540A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 24 removed outlier: 3.538A 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 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.863A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.030A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 268 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.934A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.736A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.135A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.129A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 6.437A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.670A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.423A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.532A pdb=" N THR E 78 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER E 71 " --> pdb=" O PHE E 80 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.855A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 11 through 12 removed outlier: 4.318A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 147 through 149 removed outlier: 3.528A pdb=" N GLU E 247 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU E 175 " --> pdb=" O TYR E 191 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N TYR E 191 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TRP E 177 " --> pdb=" O LEU E 189 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 156 through 161 removed outlier: 3.560A pdb=" N ALA E 212 " --> pdb=" O SER E 209 " (cutoff:3.500A) 476 hydrogen bonds defined for protein. 1350 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: 1.42 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2795 1.35 - 1.46: 2153 1.46 - 1.58: 3803 1.58 - 1.70: 0 1.70 - 1.82: 99 Bond restraints: 8850 Sorted by residual: bond pdb=" CG 1PC R 401 " pdb=" NM 1PC R 401 " ideal model delta sigma weight residual 1.461 1.566 -0.105 2.00e-02 2.50e+03 2.76e+01 bond pdb=" CR 1PC R 401 " pdb=" NM 1PC R 401 " ideal model delta sigma weight residual 1.450 1.504 -0.054 2.00e-02 2.50e+03 7.21e+00 bond pdb=" CN 1PC R 401 " pdb=" NM 1PC R 401 " ideal model delta sigma weight residual 1.450 1.490 -0.040 2.00e-02 2.50e+03 3.96e+00 bond pdb=" CB VAL R 145 " pdb=" CG1 VAL R 145 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.85e+00 bond pdb=" C THR R 296 " pdb=" N PRO R 297 " ideal model delta sigma weight residual 1.335 1.356 -0.021 1.36e-02 5.41e+03 2.39e+00 ... (remaining 8845 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 11853 2.34 - 4.67: 123 4.67 - 7.01: 37 7.01 - 9.34: 9 9.34 - 11.68: 5 Bond angle restraints: 12027 Sorted by residual: angle pdb=" CA ARG A 32 " pdb=" CB ARG A 32 " pdb=" CG ARG A 32 " ideal model delta sigma weight residual 114.10 122.06 -7.96 2.00e+00 2.50e-01 1.58e+01 angle pdb=" CB MET R 245 " pdb=" CG MET R 245 " pdb=" SD MET R 245 " ideal model delta sigma weight residual 112.70 124.22 -11.52 3.00e+00 1.11e-01 1.47e+01 angle pdb=" CA LYS E 43 " pdb=" CB LYS E 43 " pdb=" CG LYS E 43 " ideal model delta sigma weight residual 114.10 121.45 -7.35 2.00e+00 2.50e-01 1.35e+01 angle pdb=" C ASP B 195 " pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta sigma weight residual 121.54 128.09 -6.55 1.91e+00 2.74e-01 1.17e+01 angle pdb=" CB ILE R 188 " pdb=" CG1 ILE R 188 " pdb=" CD1 ILE R 188 " ideal model delta sigma weight residual 113.80 120.95 -7.15 2.10e+00 2.27e-01 1.16e+01 ... (remaining 12022 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.69: 4614 22.69 - 45.38: 511 45.38 - 68.07: 95 68.07 - 90.76: 11 90.76 - 113.45: 4 Dihedral angle restraints: 5235 sinusoidal: 1930 harmonic: 3305 Sorted by residual: dihedral pdb=" CH 1PC R 401 " pdb=" CI 1PC R 401 " pdb=" CJ 1PC R 401 " pdb=" CK 1PC R 401 " ideal model delta sinusoidal sigma weight residual -52.72 60.73 -113.45 1 3.00e+01 1.11e-03 1.49e+01 dihedral pdb=" CG 1PC R 401 " pdb=" CH 1PC R 401 " pdb=" CI 1PC R 401 " pdb=" CJ 1PC R 401 " ideal model delta sinusoidal sigma weight residual 58.08 -55.08 113.16 1 3.00e+01 1.11e-03 1.49e+01 dihedral pdb=" CI 1PC R 401 " pdb=" CJ 1PC R 401 " pdb=" CK 1PC R 401 " pdb=" CL 1PC R 401 " ideal model delta sinusoidal sigma weight residual 52.66 -57.35 110.01 1 3.00e+01 1.11e-03 1.43e+01 ... (remaining 5232 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1042 0.045 - 0.090: 275 0.090 - 0.136: 78 0.136 - 0.181: 5 0.181 - 0.226: 2 Chirality restraints: 1402 Sorted by residual: chirality pdb=" CA TYR E 236 " pdb=" N TYR E 236 " pdb=" C TYR E 236 " pdb=" CB TYR E 236 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA THR R 296 " pdb=" N THR R 296 " pdb=" C THR R 296 " pdb=" CB THR R 296 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.92e-01 chirality pdb=" CB VAL R 145 " pdb=" CA VAL R 145 " pdb=" CG1 VAL R 145 " pdb=" CG2 VAL R 145 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.16 2.00e-01 2.50e+01 6.78e-01 ... (remaining 1399 not shown) Planarity restraints: 1516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 320 " 0.017 2.00e-02 2.50e+03 1.81e-02 8.23e+00 pdb=" CG TRP R 320 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP R 320 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP R 320 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP R 320 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP R 320 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 320 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 320 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 320 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP R 320 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 211 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.08e+00 pdb=" C THR E 211 " -0.049 2.00e-02 2.50e+03 pdb=" O THR E 211 " 0.018 2.00e-02 2.50e+03 pdb=" N ALA E 212 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 196 " 0.014 2.00e-02 2.50e+03 2.75e-02 7.59e+00 pdb=" C THR B 196 " -0.048 2.00e-02 2.50e+03 pdb=" O THR B 196 " 0.018 2.00e-02 2.50e+03 pdb=" N ARG B 197 " 0.016 2.00e-02 2.50e+03 ... (remaining 1513 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 363 2.72 - 3.26: 8202 3.26 - 3.81: 14795 3.81 - 4.35: 18206 4.35 - 4.90: 31452 Nonbonded interactions: 73018 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.170 3.040 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 176 " model vdw 2.258 3.040 nonbonded pdb=" O HIS B 54 " pdb=" OG SER B 334 " model vdw 2.258 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.272 3.040 nonbonded pdb=" O ALA R 115 " pdb=" ND2 ASN R 152 " model vdw 2.273 3.120 ... (remaining 73013 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: 2.040 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: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 8.470 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 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 0.105 8852 Z= 0.169 Angle : 0.713 11.679 12031 Z= 0.355 Chirality : 0.044 0.226 1402 Planarity : 0.005 0.060 1516 Dihedral : 18.866 113.452 3093 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 6.54 % Allowed : 33.77 % Favored : 59.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.08 (0.25), residues: 1124 helix: 0.89 (0.24), residues: 405 sheet: -0.24 (0.31), residues: 289 loop : -0.71 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 256 TYR 0.025 0.001 TYR R 168 PHE 0.025 0.001 PHE R 125 TRP 0.049 0.002 TRP R 320 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 ( 8850) covalent geometry : angle 0.71284 / 0.35 (12027) SS BOND : bond 0.00193 / 0.09 ( 2) SS BOND : angle 0.77502 / 0.38 ( 4) hydrogen bonds : bond 0.17932 / 12.30 ( 471) hydrogen bonds : angle 6.73695 / 4.98 ( 1350) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 126 time to evaluate : 0.266 Fit side-chains REVERT: R 76 LEU cc_start: 0.6637 (pp) cc_final: 0.6350 (pp) REVERT: R 221 LEU cc_start: 0.6695 (mm) cc_final: 0.6250 (pt) REVERT: A 198 MET cc_start: 0.7351 (ttm) cc_final: 0.7071 (mmm) outliers start: 60 outliers final: 56 residues processed: 184 average time/residue: 0.3714 time to fit residues: 74.1608 Evaluate side-chains 177 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 121 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 142 CYS Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 224 SER Chi-restraints excluded: chain R residue 237 CYS Chi-restraints excluded: chain R residue 268 SER Chi-restraints excluded: chain R residue 281 THR Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 293 VAL Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 313 THR Chi-restraints excluded: chain R residue 331 SER Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 23 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain E residue 214 THR Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 236 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 0.0970 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.0870 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 0.0970 overall best weight: 0.6556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 111 ASN ** R 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.186455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.133653 restraints weight = 9924.104| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.74 r_work: 0.3462 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8852 Z= 0.125 Angle : 0.538 8.044 12031 Z= 0.278 Chirality : 0.041 0.198 1402 Planarity : 0.004 0.058 1516 Dihedral : 9.695 113.839 1307 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 7.63 % Allowed : 28.54 % Favored : 63.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.47 (0.25), residues: 1124 helix: 1.72 (0.25), residues: 410 sheet: -0.09 (0.31), residues: 273 loop : -0.71 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 256 TYR 0.013 0.001 TYR E 236 PHE 0.015 0.001 PHE B 253 TRP 0.019 0.002 TRP B 169 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 8850) covalent geometry : angle 0.53764 / 0.28 (12027) SS BOND : bond 0.00349 / 0.17 ( 2) SS BOND : angle 0.80653 / 0.37 ( 4) hydrogen bonds : bond 0.04170 / 2.72 ( 471) hydrogen bonds : angle 4.78527 / 3.55 ( 1350) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 132 time to evaluate : 0.219 Fit side-chains REVERT: R 76 LEU cc_start: 0.6830 (pp) cc_final: 0.6512 (pp) REVERT: R 145 VAL cc_start: 0.5214 (OUTLIER) cc_final: 0.4944 (p) REVERT: R 345 PHE cc_start: 0.5425 (OUTLIER) cc_final: 0.3706 (t80) REVERT: B 10 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.7061 (mm-30) REVERT: C 42 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6550 (mp0) REVERT: E 89 GLU cc_start: 0.8045 (pm20) cc_final: 0.7831 (pm20) REVERT: E 224 ASP cc_start: 0.8058 (m-30) cc_final: 0.7807 (m-30) outliers start: 70 outliers final: 29 residues processed: 187 average time/residue: 0.3859 time to fit residues: 77.8724 Evaluate side-chains 154 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 142 CYS Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain R residue 148 ILE Chi-restraints excluded: chain R residue 237 CYS Chi-restraints excluded: chain R residue 283 MET Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 335 PHE Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 236 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 42 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 83 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 92 optimal weight: 0.3980 chunk 15 optimal weight: 9.9990 chunk 18 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 330 ASN A 306 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.183722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.130053 restraints weight = 9777.562| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 1.73 r_work: 0.3403 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8852 Z= 0.167 Angle : 0.576 8.179 12031 Z= 0.295 Chirality : 0.043 0.255 1402 Planarity : 0.004 0.046 1516 Dihedral : 8.197 109.163 1264 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 6.97 % Allowed : 29.30 % Favored : 63.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.25), residues: 1124 helix: 1.91 (0.25), residues: 410 sheet: -0.35 (0.29), residues: 285 loop : -0.58 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 208 TYR 0.020 0.001 TYR E 236 PHE 0.013 0.001 PHE R 125 TRP 0.023 0.002 TRP R 320 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.17 ( 8850) covalent geometry : angle 0.57551 / 0.29 (12027) SS BOND : bond 0.00314 / 0.15 ( 2) SS BOND : angle 0.81664 / 0.38 ( 4) hydrogen bonds : bond 0.04286 / 2.79 ( 471) hydrogen bonds : angle 4.79268 / 3.54 ( 1350) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 122 time to evaluate : 0.265 Fit side-chains REVERT: R 76 LEU cc_start: 0.6735 (pp) cc_final: 0.6491 (pp) REVERT: R 145 VAL cc_start: 0.5330 (OUTLIER) cc_final: 0.5050 (p) REVERT: R 221 LEU cc_start: 0.6637 (OUTLIER) cc_final: 0.6235 (pt) REVERT: R 345 PHE cc_start: 0.5577 (OUTLIER) cc_final: 0.3890 (t80) REVERT: A 33 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6412 (mt-10) REVERT: C 15 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7723 (tt) REVERT: C 42 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6479 (mp0) REVERT: E 224 ASP cc_start: 0.8153 (m-30) cc_final: 0.7896 (m-30) outliers start: 64 outliers final: 38 residues processed: 169 average time/residue: 0.3731 time to fit residues: 67.9683 Evaluate side-chains 157 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 113 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 SER Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 142 CYS Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 237 CYS Chi-restraints excluded: chain R residue 283 MET Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 344 ASN Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 236 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 50.0000 chunk 30 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 78 optimal weight: 0.2980 chunk 48 optimal weight: 0.7980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN A 346 ASN C 24 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.182780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.134403 restraints weight = 9998.480| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.83 r_work: 0.3409 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8852 Z= 0.177 Angle : 0.573 8.090 12031 Z= 0.294 Chirality : 0.043 0.263 1402 Planarity : 0.004 0.045 1516 Dihedral : 7.628 79.523 1264 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.56 % Favored : 96.35 % Rotamer: Outliers : 8.17 % Allowed : 27.67 % Favored : 64.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.57 (0.25), residues: 1124 helix: 2.00 (0.25), residues: 408 sheet: -0.40 (0.29), residues: 285 loop : -0.57 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 256 TYR 0.020 0.001 TYR E 236 PHE 0.014 0.001 PHE R 125 TRP 0.023 0.002 TRP R 320 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 ( 8850) covalent geometry : angle 0.57291 / 0.29 (12027) SS BOND : bond 0.00294 / 0.14 ( 2) SS BOND : angle 0.85892 / 0.41 ( 4) hydrogen bonds : bond 0.04164 / 2.70 ( 471) hydrogen bonds : angle 4.76610 / 3.52 ( 1350) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 122 time to evaluate : 0.346 Fit side-chains REVERT: R 145 VAL cc_start: 0.5263 (OUTLIER) cc_final: 0.4981 (p) REVERT: R 195 ILE cc_start: 0.6241 (OUTLIER) cc_final: 0.5767 (mp) REVERT: R 221 LEU cc_start: 0.6641 (OUTLIER) cc_final: 0.6117 (pt) REVERT: R 345 PHE cc_start: 0.5582 (OUTLIER) cc_final: 0.3785 (t80) REVERT: A 33 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6448 (mt-10) REVERT: B 12 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6501 (mp0) REVERT: B 215 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7311 (mm-30) REVERT: C 42 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6421 (mp0) REVERT: E 89 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7902 (pm20) REVERT: E 224 ASP cc_start: 0.8153 (m-30) cc_final: 0.7907 (m-30) outliers start: 75 outliers final: 40 residues processed: 178 average time/residue: 0.3727 time to fit residues: 71.9246 Evaluate side-chains 166 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 117 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 SER Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 142 CYS Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 238 VAL Chi-restraints excluded: chain R residue 251 THR Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 283 MET Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 236 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 18 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 86 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 330 ASN A 306 GLN B 266 HIS C 24 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.180679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.133082 restraints weight = 9880.456| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.91 r_work: 0.3372 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8852 Z= 0.230 Angle : 0.632 9.562 12031 Z= 0.323 Chirality : 0.045 0.318 1402 Planarity : 0.004 0.046 1516 Dihedral : 7.736 81.339 1263 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.91 % Favored : 96.00 % Rotamer: Outliers : 8.17 % Allowed : 28.43 % Favored : 63.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.50 (0.25), residues: 1124 helix: 1.93 (0.25), residues: 408 sheet: -0.43 (0.29), residues: 287 loop : -0.61 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 72 TYR 0.024 0.002 TYR E 236 PHE 0.029 0.002 PHE E 68 TRP 0.025 0.002 TRP R 320 HIS 0.006 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.23 ( 8850) covalent geometry : angle 0.63140 / 0.32 (12027) SS BOND : bond 0.00287 / 0.14 ( 2) SS BOND : angle 0.89732 / 0.43 ( 4) hydrogen bonds : bond 0.04438 / 2.87 ( 471) hydrogen bonds : angle 4.90279 / 3.62 ( 1350) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 127 time to evaluate : 0.211 Fit side-chains REVERT: R 76 LEU cc_start: 0.7024 (pp) cc_final: 0.6685 (pp) REVERT: R 145 VAL cc_start: 0.5290 (OUTLIER) cc_final: 0.5009 (p) REVERT: R 195 ILE cc_start: 0.6233 (OUTLIER) cc_final: 0.5788 (mp) REVERT: R 221 LEU cc_start: 0.6723 (OUTLIER) cc_final: 0.6054 (pp) REVERT: R 345 PHE cc_start: 0.5667 (OUTLIER) cc_final: 0.3953 (t80) REVERT: A 32 ARG cc_start: 0.7281 (tpp80) cc_final: 0.7076 (tpp80) REVERT: B 12 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6462 (mp0) REVERT: B 197 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.7080 (mmp-170) REVERT: B 215 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7272 (mm-30) REVERT: C 42 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6491 (mp0) REVERT: E 224 ASP cc_start: 0.8188 (m-30) cc_final: 0.7920 (m-30) outliers start: 75 outliers final: 39 residues processed: 181 average time/residue: 0.3751 time to fit residues: 73.3720 Evaluate side-chains 169 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 122 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 SER Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 142 CYS Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain R residue 148 ILE Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 238 VAL Chi-restraints excluded: chain R residue 251 THR Chi-restraints excluded: chain R residue 264 VAL Chi-restraints excluded: chain R residue 283 MET Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 236 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 36 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 chunk 53 optimal weight: 0.0570 chunk 26 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 105 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 193 ASN ** R 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.185273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.132472 restraints weight = 9796.034| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.73 r_work: 0.3442 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8852 Z= 0.114 Angle : 0.525 8.274 12031 Z= 0.271 Chirality : 0.041 0.222 1402 Planarity : 0.004 0.042 1516 Dihedral : 7.172 82.957 1263 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.20 % Favored : 96.71 % Rotamer: Outliers : 5.66 % Allowed : 30.83 % Favored : 63.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.70 (0.25), residues: 1124 helix: 2.18 (0.25), residues: 407 sheet: -0.33 (0.30), residues: 275 loop : -0.60 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 208 TYR 0.016 0.001 TYR E 236 PHE 0.022 0.001 PHE E 68 TRP 0.028 0.002 TRP R 320 HIS 0.002 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 ( 8850) covalent geometry : angle 0.52480 / 0.27 (12027) SS BOND : bond 0.00236 / 0.11 ( 2) SS BOND : angle 0.80246 / 0.39 ( 4) hydrogen bonds : bond 0.03755 / 2.44 ( 471) hydrogen bonds : angle 4.58654 / 3.37 ( 1350) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 128 time to evaluate : 0.241 Fit side-chains REVERT: R 76 LEU cc_start: 0.7010 (pp) cc_final: 0.6690 (pp) REVERT: R 145 VAL cc_start: 0.5241 (OUTLIER) cc_final: 0.4970 (p) REVERT: R 195 ILE cc_start: 0.6216 (OUTLIER) cc_final: 0.5728 (mp) REVERT: R 221 LEU cc_start: 0.6825 (OUTLIER) cc_final: 0.6280 (pt) REVERT: R 276 ASN cc_start: 0.6238 (m110) cc_final: 0.5971 (m110) REVERT: R 345 PHE cc_start: 0.5637 (OUTLIER) cc_final: 0.3901 (t80) REVERT: C 14 LYS cc_start: 0.7165 (OUTLIER) cc_final: 0.6604 (pptt) REVERT: C 15 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7769 (tt) REVERT: C 42 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6360 (mp0) REVERT: E 224 ASP cc_start: 0.8112 (m-30) cc_final: 0.7867 (m-30) outliers start: 52 outliers final: 24 residues processed: 163 average time/residue: 0.3872 time to fit residues: 68.0762 Evaluate side-chains 152 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 123 LEU Chi-restraints excluded: chain R residue 142 CYS Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain R residue 148 ILE Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 283 MET Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 236 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 33 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 101 optimal weight: 0.0040 chunk 80 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.184789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.131631 restraints weight = 9950.373| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.75 r_work: 0.3421 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8852 Z= 0.127 Angle : 0.551 8.304 12031 Z= 0.280 Chirality : 0.042 0.217 1402 Planarity : 0.004 0.047 1516 Dihedral : 6.874 83.565 1253 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.29 % Favored : 96.62 % Rotamer: Outliers : 5.56 % Allowed : 30.94 % Favored : 63.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.25), residues: 1124 helix: 2.22 (0.25), residues: 408 sheet: -0.37 (0.30), residues: 279 loop : -0.50 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 208 TYR 0.015 0.001 TYR E 236 PHE 0.023 0.001 PHE E 68 TRP 0.023 0.001 TRP R 320 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 ( 8850) covalent geometry : angle 0.55045 / 0.28 (12027) SS BOND : bond 0.00226 / 0.11 ( 2) SS BOND : angle 0.74203 / 0.35 ( 4) hydrogen bonds : bond 0.03793 / 2.48 ( 471) hydrogen bonds : angle 4.55407 / 3.34 ( 1350) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 126 time to evaluate : 0.231 Fit side-chains REVERT: R 76 LEU cc_start: 0.6883 (pp) cc_final: 0.6561 (pp) REVERT: R 145 VAL cc_start: 0.5272 (OUTLIER) cc_final: 0.5002 (p) REVERT: R 195 ILE cc_start: 0.6236 (OUTLIER) cc_final: 0.5757 (mp) REVERT: R 221 LEU cc_start: 0.6734 (OUTLIER) cc_final: 0.6222 (pt) REVERT: R 276 ASN cc_start: 0.6339 (m110) cc_final: 0.6038 (m110) REVERT: R 345 PHE cc_start: 0.5644 (OUTLIER) cc_final: 0.3857 (t80) REVERT: A 33 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6254 (mt-10) REVERT: C 15 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7758 (tt) REVERT: C 42 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.6452 (mp0) outliers start: 51 outliers final: 29 residues processed: 164 average time/residue: 0.3850 time to fit residues: 67.9336 Evaluate side-chains 157 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 121 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 SER Chi-restraints excluded: chain R residue 142 CYS Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain R residue 148 ILE Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 283 MET Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 236 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 58 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 15 optimal weight: 0.0370 chunk 99 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 42 optimal weight: 0.0040 overall best weight: 0.8074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.184855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.142213 restraints weight = 9839.891| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.30 r_work: 0.3406 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8852 Z= 0.130 Angle : 0.552 8.398 12031 Z= 0.283 Chirality : 0.042 0.220 1402 Planarity : 0.004 0.044 1516 Dihedral : 6.848 83.129 1253 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.29 % Favored : 96.62 % Rotamer: Outliers : 5.34 % Allowed : 31.37 % Favored : 63.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.77 (0.25), residues: 1124 helix: 2.24 (0.25), residues: 407 sheet: -0.39 (0.30), residues: 281 loop : -0.47 (0.31), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 208 TYR 0.016 0.001 TYR E 236 PHE 0.016 0.001 PHE E 68 TRP 0.020 0.001 TRP R 320 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 8850) covalent geometry : angle 0.55239 / 0.28 (12027) SS BOND : bond 0.00241 / 0.12 ( 2) SS BOND : angle 0.75766 / 0.36 ( 4) hydrogen bonds : bond 0.03786 / 2.47 ( 471) hydrogen bonds : angle 4.55333 / 3.34 ( 1350) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 122 time to evaluate : 0.335 Fit side-chains REVERT: R 76 LEU cc_start: 0.6820 (pp) cc_final: 0.6534 (pp) REVERT: R 145 VAL cc_start: 0.5238 (OUTLIER) cc_final: 0.4977 (p) REVERT: R 195 ILE cc_start: 0.6187 (OUTLIER) cc_final: 0.5708 (mp) REVERT: R 221 LEU cc_start: 0.6942 (OUTLIER) cc_final: 0.6338 (pt) REVERT: R 276 ASN cc_start: 0.6331 (m110) cc_final: 0.6010 (m110) REVERT: R 345 PHE cc_start: 0.5664 (OUTLIER) cc_final: 0.3933 (t80) REVERT: A 33 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6208 (mt-10) REVERT: C 14 LYS cc_start: 0.7223 (OUTLIER) cc_final: 0.6645 (pptt) REVERT: C 15 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7762 (tt) REVERT: C 42 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.6508 (mp0) outliers start: 49 outliers final: 29 residues processed: 159 average time/residue: 0.3958 time to fit residues: 67.6919 Evaluate side-chains 158 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 121 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 SER Chi-restraints excluded: chain R residue 142 CYS Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain R residue 148 ILE Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 283 MET Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 236 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 64 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 15 optimal weight: 30.0000 chunk 97 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 3 optimal weight: 0.0060 chunk 28 optimal weight: 3.9990 overall best weight: 1.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.181974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.128722 restraints weight = 9834.864| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.71 r_work: 0.3385 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8852 Z= 0.191 Angle : 0.610 8.291 12031 Z= 0.311 Chirality : 0.044 0.269 1402 Planarity : 0.004 0.045 1516 Dihedral : 7.008 81.808 1253 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.91 % Favored : 96.00 % Rotamer: Outliers : 4.58 % Allowed : 32.03 % Favored : 63.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.66 (0.25), residues: 1124 helix: 2.08 (0.25), residues: 407 sheet: -0.39 (0.29), residues: 286 loop : -0.49 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 208 TYR 0.020 0.001 TYR E 236 PHE 0.022 0.001 PHE E 68 TRP 0.018 0.002 TRP R 320 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 ( 8850) covalent geometry : angle 0.61020 / 0.31 (12027) SS BOND : bond 0.00276 / 0.13 ( 2) SS BOND : angle 0.84843 / 0.39 ( 4) hydrogen bonds : bond 0.04117 / 2.67 ( 471) hydrogen bonds : angle 4.75230 / 3.49 ( 1350) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 121 time to evaluate : 0.317 Fit side-chains REVERT: R 76 LEU cc_start: 0.6897 (pp) cc_final: 0.6622 (pp) REVERT: R 123 LEU cc_start: 0.7707 (pp) cc_final: 0.7421 (pt) REVERT: R 145 VAL cc_start: 0.5321 (OUTLIER) cc_final: 0.5048 (p) REVERT: R 195 ILE cc_start: 0.6298 (OUTLIER) cc_final: 0.5813 (mp) REVERT: R 221 LEU cc_start: 0.6892 (OUTLIER) cc_final: 0.6286 (pt) REVERT: R 276 ASN cc_start: 0.6323 (m110) cc_final: 0.6016 (m110) REVERT: A 33 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6214 (mt-10) REVERT: C 14 LYS cc_start: 0.7163 (OUTLIER) cc_final: 0.6590 (pptt) REVERT: C 15 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7744 (tt) REVERT: C 42 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6442 (mp0) outliers start: 42 outliers final: 27 residues processed: 153 average time/residue: 0.4075 time to fit residues: 67.3080 Evaluate side-chains 153 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 119 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 SER Chi-restraints excluded: chain R residue 142 CYS Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain R residue 148 ILE Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 283 MET Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 236 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 45 optimal weight: 0.9990 chunk 43 optimal weight: 0.4980 chunk 39 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 38 optimal weight: 0.0770 chunk 101 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 58 optimal weight: 0.0870 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 330 ASN C 24 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.184482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.142302 restraints weight = 9854.471| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.29 r_work: 0.3407 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8852 Z= 0.128 Angle : 0.556 7.891 12031 Z= 0.285 Chirality : 0.042 0.223 1402 Planarity : 0.004 0.043 1516 Dihedral : 6.864 82.650 1253 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.20 % Favored : 96.71 % Rotamer: Outliers : 4.36 % Allowed : 32.68 % Favored : 62.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.72 (0.25), residues: 1124 helix: 2.19 (0.25), residues: 406 sheet: -0.39 (0.29), residues: 281 loop : -0.50 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 256 TYR 0.016 0.001 TYR E 236 PHE 0.015 0.001 PHE E 68 TRP 0.030 0.002 TRP R 320 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 8850) covalent geometry : angle 0.55624 / 0.29 (12027) SS BOND : bond 0.00235 / 0.11 ( 2) SS BOND : angle 0.77498 / 0.36 ( 4) hydrogen bonds : bond 0.03800 / 2.48 ( 471) hydrogen bonds : angle 4.59069 / 3.36 ( 1350) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 124 time to evaluate : 0.225 Fit side-chains REVERT: R 76 LEU cc_start: 0.6897 (pp) cc_final: 0.6632 (pp) REVERT: R 145 VAL cc_start: 0.5273 (OUTLIER) cc_final: 0.5009 (p) REVERT: R 195 ILE cc_start: 0.6203 (OUTLIER) cc_final: 0.5721 (mp) REVERT: R 221 LEU cc_start: 0.6978 (OUTLIER) cc_final: 0.6393 (pt) REVERT: R 276 ASN cc_start: 0.6301 (m110) cc_final: 0.5982 (m110) REVERT: A 33 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.6151 (mt-10) REVERT: B 18 ILE cc_start: 0.7320 (pt) cc_final: 0.7058 (pt) REVERT: C 14 LYS cc_start: 0.7217 (OUTLIER) cc_final: 0.6650 (pptt) REVERT: C 15 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7742 (tt) REVERT: C 42 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.6490 (mp0) outliers start: 40 outliers final: 29 residues processed: 153 average time/residue: 0.4400 time to fit residues: 72.4492 Evaluate side-chains 156 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 120 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 SER Chi-restraints excluded: chain R residue 142 CYS Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain R residue 148 ILE Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 283 MET Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 345 PHE Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 309 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 236 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 93 optimal weight: 0.0170 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 110 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 44 optimal weight: 5.9990 overall best weight: 0.9220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** R 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 330 ASN C 24 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.183814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.141421 restraints weight = 9763.188| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.21 r_work: 0.3396 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8852 Z= 0.143 Angle : 0.581 7.937 12031 Z= 0.297 Chirality : 0.042 0.224 1402 Planarity : 0.004 0.046 1516 Dihedral : 6.684 59.212 1253 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.38 % Favored : 96.53 % Rotamer: Outliers : 4.79 % Allowed : 32.46 % Favored : 62.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.70 (0.25), residues: 1124 helix: 2.13 (0.25), residues: 406 sheet: -0.35 (0.29), residues: 283 loop : -0.50 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 256 TYR 0.016 0.001 TYR E 236 PHE 0.017 0.001 PHE E 68 TRP 0.036 0.002 TRP R 320 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 8850) covalent geometry : angle 0.58085 / 0.30 (12027) SS BOND : bond 0.00323 / 0.15 ( 2) SS BOND : angle 0.89076 / 0.41 ( 4) hydrogen bonds : bond 0.03873 / 2.54 ( 471) hydrogen bonds : angle 4.64185 / 3.41 ( 1350) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3010.25 seconds wall clock time: 52 minutes 0.00 seconds (3120.00 seconds total)