Starting phenix.real_space_refine on Wed Mar 4 03:53:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y67_33636/03_2026/7y67_33636_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y67_33636/03_2026/7y67_33636.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7y67_33636/03_2026/7y67_33636_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y67_33636/03_2026/7y67_33636_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y67_33636/03_2026/7y67_33636.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y67_33636/03_2026/7y67_33636.map" } resolution = 2.8 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= 0.002 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2047 atoms to isotropic. 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 59 5.16 5 C 5675 2.51 5 N 1514 2.21 5 O 1641 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8889 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1803 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2611 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "D" Number of atoms: 2197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2197 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 11, 'TRANS': 266} Chain breaks: 1 Chain: "S" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1777 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Chain: "L" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 53 Classifications: {'peptide': 5} Link IDs: {'PTRANS': 1, 'TRANS': 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'MEA:plan-2': 1, 'ZAL:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "L" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Classifications: {'peptide': 1} Modifications used: {'COO': 1, 'PEPT-D': 1} Time building chain proxies: 2.22, per 1000 atoms: 0.25 Number of scatterers: 8889 At special positions: 0 Unit cell: (95.2, 123.25, 132.6, 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 59 16.00 O 1641 8.00 N 1514 7.00 C 5675 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS D 109 " - pdb=" SG CYS D 188 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.62 Conformation dependent library (CDL) restraints added in 318.1 milliseconds 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB ZAL L 4 " Input residue name is d-peptide pdb=" CB DAR L 6 " Number of C-beta restraints generated: 2120 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 13 sheets defined 37.7% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 6 through 30 removed outlier: 3.734A pdb=" N LYS A 10 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 215 removed outlier: 4.488A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 278 removed outlier: 3.857A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 4.165A 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 330 through 351 removed outlier: 3.605A pdb=" N PHE A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 25 removed outlier: 3.736A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 7 through 23 Processing helix chain 'C' and resid 29 through 45 removed outlier: 3.653A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 55 through 59 removed outlier: 3.562A pdb=" N ASN C 59 " --> pdb=" O ALA C 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 65 removed outlier: 3.650A pdb=" N ILE D 38 " --> pdb=" O ARG D 34 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU D 39 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU D 65 " --> pdb=" O VAL D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 88 removed outlier: 3.784A pdb=" N PHE D 75 " --> pdb=" O ASN D 71 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN D 77 " --> pdb=" O ILE D 73 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU D 78 " --> pdb=" O TRP D 74 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA D 88 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 98 removed outlier: 3.795A pdb=" N LEU D 92 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN D 98 " --> pdb=" O THR D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 110 Processing helix chain 'D' and resid 117 through 139 removed outlier: 3.749A pdb=" N TYR D 121 " --> pdb=" O LEU D 117 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N SER D 123 " --> pdb=" O ASN D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 147 removed outlier: 3.778A pdb=" N CYS D 144 " --> pdb=" O LYS D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 174 removed outlier: 3.679A pdb=" N ALA D 153 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA D 164 " --> pdb=" O ALA D 160 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU D 165 " --> pdb=" O TRP D 161 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU D 166 " --> pdb=" O GLY D 162 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU D 167 " --> pdb=" O LEU D 163 " (cutoff:3.500A) Proline residue: D 170 - end of helix Processing helix chain 'D' and resid 196 through 231 Proline residue: D 214 - end of helix Processing helix chain 'D' and resid 238 through 268 removed outlier: 3.503A pdb=" N LYS D 242 " --> pdb=" O THR D 238 " (cutoff:3.500A) Proline residue: D 257 - end of helix removed outlier: 3.591A pdb=" N MET D 264 " --> pdb=" O VAL D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 288 removed outlier: 4.560A pdb=" N SER D 283 " --> pdb=" O LYS D 279 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 303 removed outlier: 3.946A pdb=" N CYS D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) Proline residue: D 297 - end of helix removed outlier: 3.933A pdb=" N TYR D 300 " --> pdb=" O ASN D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 314 Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.565A pdb=" N SER S 31 " --> pdb=" O ALA S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 65 removed outlier: 3.520A pdb=" N LYS S 65 " --> pdb=" O ASP S 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 62 through 65' Processing helix chain 'S' and resid 220 through 224 removed outlier: 4.137A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.655A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.282A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.875A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.573A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.875A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.897A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.958A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 7.243A 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: 3.551A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 175 through 178 removed outlier: 4.568A pdb=" N VAL D 190 " --> pdb=" O LYS L 2 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS L 2 " --> pdb=" O VAL D 190 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12 removed outlier: 6.834A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 148 removed outlier: 6.072A pdb=" N VAL S 147 " --> pdb=" O GLU S 246 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 155 through 160 414 hydrogen bonds defined for protein. 1176 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: 1.39 Time building geometry restraints manager: 0.91 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: 2858 1.35 - 1.47: 2244 1.47 - 1.58: 3891 1.58 - 1.70: 1 1.70 - 1.82: 83 Bond restraints: 9077 Sorted by residual: bond pdb=" C MEA L 1 " pdb=" N LYS L 2 " ideal model delta sigma weight residual 1.329 1.390 -0.061 1.40e-02 5.10e+03 1.92e+01 bond pdb=" N ARG A 208 " pdb=" CA ARG A 208 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.30e-02 5.92e+03 7.66e+00 bond pdb=" CB PRO S 75 " pdb=" CG PRO S 75 " ideal model delta sigma weight residual 1.492 1.597 -0.105 5.00e-02 4.00e+02 4.39e+00 bond pdb=" CE1 HIS D 100 " pdb=" NE2 HIS D 100 " ideal model delta sigma weight residual 1.321 1.338 -0.017 1.00e-02 1.00e+04 2.81e+00 bond pdb=" N LYS D 279 " pdb=" CA LYS D 279 " ideal model delta sigma weight residual 1.458 1.479 -0.021 1.30e-02 5.92e+03 2.60e+00 ... (remaining 9072 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.86: 12279 4.86 - 9.73: 17 9.73 - 14.59: 0 14.59 - 19.46: 0 19.46 - 24.32: 3 Bond angle restraints: 12299 Sorted by residual: angle pdb=" O MEA L 1 " pdb=" C MEA L 1 " pdb=" N LYS L 2 " ideal model delta sigma weight residual 123.00 99.93 23.07 1.60e+00 3.91e-01 2.08e+02 angle pdb=" CA MEA L 1 " pdb=" C MEA L 1 " pdb=" N LYS L 2 " ideal model delta sigma weight residual 116.20 140.52 -24.32 2.00e+00 2.50e-01 1.48e+02 angle pdb=" C MEA L 1 " pdb=" N LYS L 2 " pdb=" CA LYS L 2 " ideal model delta sigma weight residual 121.70 142.91 -21.21 1.80e+00 3.09e-01 1.39e+02 angle pdb=" CA PRO S 75 " pdb=" N PRO S 75 " pdb=" CD PRO S 75 " ideal model delta sigma weight residual 112.00 104.63 7.37 1.40e+00 5.10e-01 2.77e+01 angle pdb=" N LYS D 279 " pdb=" CA LYS D 279 " pdb=" C LYS D 279 " ideal model delta sigma weight residual 112.23 106.24 5.99 1.26e+00 6.30e-01 2.26e+01 ... (remaining 12294 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.34: 5130 25.34 - 50.67: 218 50.67 - 76.01: 14 76.01 - 101.35: 5 101.35 - 126.68: 1 Dihedral angle restraints: 5368 sinusoidal: 2086 harmonic: 3282 Sorted by residual: dihedral pdb=" CD DAR L 6 " pdb=" NE DAR L 6 " pdb=" CZ DAR L 6 " pdb=" NH1 DAR L 6 " ideal model delta sinusoidal sigma weight residual 0.00 -126.68 126.68 1 1.00e+01 1.00e-02 1.53e+02 dihedral pdb=" CA ZAL L 4 " pdb=" C ZAL L 4 " pdb=" N TRP L 5 " pdb=" CA TRP L 5 " ideal model delta harmonic sigma weight residual 180.00 -151.08 -28.92 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA TRP B 297 " pdb=" C TRP B 297 " pdb=" N ASP B 298 " pdb=" CA ASP B 298 " ideal model delta harmonic sigma weight residual 180.00 163.00 17.00 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 5365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 853 0.030 - 0.059: 338 0.059 - 0.089: 128 0.089 - 0.119: 67 0.119 - 0.148: 16 Chirality restraints: 1402 Sorted by residual: chirality pdb=" CA HIS D 100 " pdb=" N HIS D 100 " pdb=" C HIS D 100 " pdb=" CB HIS D 100 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.50e-01 chirality pdb=" CA ILE A 265 " pdb=" N ILE A 265 " pdb=" C ILE A 265 " pdb=" CB ILE A 265 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.66e-01 chirality pdb=" C1 ZAL L 4 " pdb=" CB ZAL L 4 " pdb=" C2 ZAL L 4 " pdb=" C6 ZAL L 4 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.13 2.00e-01 2.50e+01 4.45e-01 ... (remaining 1399 not shown) Planarity restraints: 1548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD DAR L 6 " -0.905 9.50e-02 1.11e+02 4.06e-01 9.95e+01 pdb=" NE DAR L 6 " 0.052 2.00e-02 2.50e+03 pdb=" CZ DAR L 6 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 DAR L 6 " -0.024 2.00e-02 2.50e+03 pdb=" NH2 DAR L 6 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " 0.078 5.00e-02 4.00e+02 1.14e-01 2.09e+01 pdb=" N PRO S 75 " -0.198 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MEA L 1 " -0.022 2.00e-02 2.50e+03 3.50e-02 1.22e+01 pdb=" C MEA L 1 " 0.060 2.00e-02 2.50e+03 pdb=" O MEA L 1 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS L 2 " -0.021 2.00e-02 2.50e+03 ... (remaining 1545 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 2 2.04 - 2.76: 1178 2.76 - 3.47: 11769 3.47 - 4.19: 19275 4.19 - 4.90: 35114 Nonbonded interactions: 67338 Sorted by model distance: nonbonded pdb=" C TRP L 5 " pdb=" N DAR L 6 " model vdw 1.329 3.350 nonbonded pdb=" O THR A 327 " pdb=" OD1 ASP A 328 " model vdw 1.877 3.040 nonbonded pdb=" O ZAL L 4 " pdb=" O TRP L 5 " model vdw 2.214 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.227 3.040 nonbonded pdb=" O TRP L 5 " pdb=" N DAR L 6 " model vdw 2.248 3.120 ... (remaining 67333 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 9.550 Find NCS groups from input model: 0.040 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:6.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 9079 Z= 0.143 Angle : 0.692 24.323 12303 Z= 0.388 Chirality : 0.042 0.148 1402 Planarity : 0.011 0.406 1548 Dihedral : 13.096 126.683 3242 Min Nonbonded Distance : 1.329 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.10 % Allowed : 0.21 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.25), residues: 1114 helix: 2.03 (0.28), residues: 367 sheet: 0.71 (0.31), residues: 296 loop : -1.25 (0.25), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 200 TYR 0.018 0.001 TYR D 300 PHE 0.017 0.001 PHE S 177 TRP 0.011 0.001 TRP L 5 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 9077) covalent geometry : angle 0.69141 (12299) SS BOND : bond 0.00789 ( 2) SS BOND : angle 1.28820 ( 4) hydrogen bonds : bond 0.12174 ( 414) hydrogen bonds : angle 4.81840 ( 1176) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 213 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 23 LEU cc_start: 0.7670 (tp) cc_final: 0.7431 (tp) REVERT: A 25 GLU cc_start: 0.6857 (tm-30) cc_final: 0.6417 (tm-30) REVERT: A 26 ASP cc_start: 0.6825 (m-30) cc_final: 0.6336 (m-30) REVERT: A 33 GLU cc_start: 0.6946 (mm-30) cc_final: 0.6639 (mm-30) REVERT: A 197 LYS cc_start: 0.7350 (tppt) cc_final: 0.6909 (tptp) REVERT: A 248 LYS cc_start: 0.7453 (ttpp) cc_final: 0.7105 (mtpp) REVERT: A 252 SER cc_start: 0.7869 (m) cc_final: 0.7645 (m) REVERT: A 261 ASP cc_start: 0.6431 (t0) cc_final: 0.6159 (t0) REVERT: B 212 ASP cc_start: 0.7003 (t70) cc_final: 0.6750 (t0) REVERT: B 217 MET cc_start: 0.6469 (ppp) cc_final: 0.6085 (ppp) REVERT: B 237 ASN cc_start: 0.7553 (t0) cc_final: 0.7343 (t0) REVERT: B 331 SER cc_start: 0.8069 (p) cc_final: 0.7802 (p) REVERT: D 282 ASP cc_start: 0.7911 (t70) cc_final: 0.7541 (t70) REVERT: S 21 SER cc_start: 0.8323 (m) cc_final: 0.8028 (p) REVERT: S 119 VAL cc_start: 0.8728 (t) cc_final: 0.8411 (p) REVERT: S 193 SER cc_start: 0.7595 (m) cc_final: 0.7336 (t) outliers start: 1 outliers final: 0 residues processed: 214 average time/residue: 0.5375 time to fit residues: 122.6637 Evaluate side-chains 173 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 125 ASN B 340 ASN C 59 ASN S 35 HIS S 186 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.131665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.110172 restraints weight = 13253.866| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.00 r_work: 0.3364 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9079 Z= 0.144 Angle : 0.564 6.585 12303 Z= 0.295 Chirality : 0.042 0.134 1402 Planarity : 0.004 0.063 1548 Dihedral : 6.730 176.418 1235 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.87 % Allowed : 12.47 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.25), residues: 1114 helix: 1.94 (0.27), residues: 382 sheet: 0.69 (0.31), residues: 292 loop : -1.32 (0.25), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 68 TYR 0.015 0.001 TYR S 190 PHE 0.018 0.002 PHE B 234 TRP 0.010 0.001 TRP S 47 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 9077) covalent geometry : angle 0.56354 (12299) SS BOND : bond 0.01024 ( 2) SS BOND : angle 1.89812 ( 4) hydrogen bonds : bond 0.05234 ( 414) hydrogen bonds : angle 4.48767 ( 1176) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 184 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: A 23 LEU cc_start: 0.8058 (tp) cc_final: 0.7835 (tp) REVERT: A 25 GLU cc_start: 0.7788 (tm-30) cc_final: 0.7306 (tm-30) REVERT: A 26 ASP cc_start: 0.7697 (m-30) cc_final: 0.7321 (m-30) REVERT: A 248 LYS cc_start: 0.7966 (ttpp) cc_final: 0.7605 (mtpp) REVERT: A 261 ASP cc_start: 0.7332 (t0) cc_final: 0.7050 (t0) REVERT: B 187 VAL cc_start: 0.8710 (OUTLIER) cc_final: 0.8354 (t) REVERT: B 212 ASP cc_start: 0.7577 (t70) cc_final: 0.7278 (t70) REVERT: B 217 MET cc_start: 0.7755 (ppp) cc_final: 0.7227 (ppp) REVERT: B 228 ASP cc_start: 0.7802 (m-30) cc_final: 0.7555 (p0) REVERT: B 254 ASP cc_start: 0.7687 (t70) cc_final: 0.7329 (t0) REVERT: B 303 ASP cc_start: 0.7594 (m-30) cc_final: 0.7393 (m-30) REVERT: D 263 ILE cc_start: 0.8160 (tp) cc_final: 0.7943 (tp) REVERT: D 282 ASP cc_start: 0.8339 (t70) cc_final: 0.7998 (t70) REVERT: S 21 SER cc_start: 0.8550 (m) cc_final: 0.8264 (p) REVERT: S 119 VAL cc_start: 0.8834 (t) cc_final: 0.8531 (p) REVERT: S 154 SER cc_start: 0.8515 (p) cc_final: 0.8277 (m) REVERT: S 192 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.8070 (ttp) outliers start: 18 outliers final: 8 residues processed: 196 average time/residue: 0.5364 time to fit residues: 112.2621 Evaluate side-chains 184 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 174 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 74 optimal weight: 0.0970 chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 102 optimal weight: 0.5980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 HIS B 75 GLN B 125 ASN B 237 ASN C 44 HIS C 59 ASN D 145 GLN S 142 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.131439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.109618 restraints weight = 12951.936| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.00 r_work: 0.3351 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9079 Z= 0.126 Angle : 0.531 8.079 12303 Z= 0.280 Chirality : 0.041 0.131 1402 Planarity : 0.004 0.053 1548 Dihedral : 6.639 179.286 1235 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.81 % Allowed : 14.45 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.25), residues: 1114 helix: 2.06 (0.27), residues: 382 sheet: 0.63 (0.31), residues: 289 loop : -1.39 (0.25), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG S 98 TYR 0.012 0.001 TYR S 190 PHE 0.016 0.001 PHE A 189 TRP 0.010 0.001 TRP S 47 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 9077) covalent geometry : angle 0.53024 (12299) SS BOND : bond 0.00910 ( 2) SS BOND : angle 1.74362 ( 4) hydrogen bonds : bond 0.04972 ( 414) hydrogen bonds : angle 4.39923 ( 1176) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 182 time to evaluate : 0.339 Fit side-chains REVERT: A 25 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7221 (tm-30) REVERT: A 197 LYS cc_start: 0.8142 (tppt) cc_final: 0.7809 (mmmt) REVERT: A 229 ASP cc_start: 0.7735 (m-30) cc_final: 0.7484 (t0) REVERT: A 240 MET cc_start: 0.6505 (mmp) cc_final: 0.5963 (mmp) REVERT: A 248 LYS cc_start: 0.7840 (ttpp) cc_final: 0.7570 (mtpp) REVERT: A 261 ASP cc_start: 0.7327 (t0) cc_final: 0.7030 (t0) REVERT: A 277 LYS cc_start: 0.8126 (mtpt) cc_final: 0.7876 (ttmt) REVERT: A 304 GLN cc_start: 0.8309 (tm-30) cc_final: 0.7999 (tt0) REVERT: B 187 VAL cc_start: 0.8646 (OUTLIER) cc_final: 0.8286 (t) REVERT: B 212 ASP cc_start: 0.7617 (t70) cc_final: 0.7286 (t70) REVERT: B 217 MET cc_start: 0.7759 (ppp) cc_final: 0.7235 (ppp) REVERT: B 228 ASP cc_start: 0.7813 (m-30) cc_final: 0.7524 (p0) REVERT: B 254 ASP cc_start: 0.7721 (t70) cc_final: 0.7287 (t0) REVERT: B 303 ASP cc_start: 0.7690 (m-30) cc_final: 0.7473 (m-30) REVERT: D 82 ASP cc_start: 0.7232 (OUTLIER) cc_final: 0.6911 (t70) REVERT: D 236 ARG cc_start: 0.8494 (ttp-110) cc_final: 0.8257 (ttp-110) REVERT: D 282 ASP cc_start: 0.8383 (t70) cc_final: 0.8014 (t70) REVERT: S 21 SER cc_start: 0.8577 (m) cc_final: 0.8267 (p) REVERT: S 119 VAL cc_start: 0.8870 (t) cc_final: 0.8524 (p) REVERT: S 154 SER cc_start: 0.8493 (p) cc_final: 0.8247 (m) REVERT: S 192 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.8132 (ttp) outliers start: 27 outliers final: 11 residues processed: 197 average time/residue: 0.5426 time to fit residues: 113.9715 Evaluate side-chains 190 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 176 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 265 MET Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 192 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 61 optimal weight: 0.2980 chunk 7 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 87 optimal weight: 0.0870 chunk 79 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 ASN B 75 GLN B 268 ASN C 59 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.131939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.110110 restraints weight = 13192.753| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.02 r_work: 0.3363 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9079 Z= 0.107 Angle : 0.497 8.575 12303 Z= 0.260 Chirality : 0.041 0.132 1402 Planarity : 0.003 0.047 1548 Dihedral : 6.528 179.069 1235 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.39 % Allowed : 17.67 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.25), residues: 1114 helix: 2.17 (0.27), residues: 382 sheet: 0.59 (0.31), residues: 290 loop : -1.34 (0.25), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 98 TYR 0.014 0.001 TYR S 190 PHE 0.014 0.001 PHE A 189 TRP 0.010 0.001 TRP S 176 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 9077) covalent geometry : angle 0.49614 (12299) SS BOND : bond 0.00805 ( 2) SS BOND : angle 1.52194 ( 4) hydrogen bonds : bond 0.04538 ( 414) hydrogen bonds : angle 4.30175 ( 1176) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 0.353 Fit side-chains REVERT: A 25 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7384 (tm-30) REVERT: A 197 LYS cc_start: 0.8142 (tppt) cc_final: 0.7880 (tppp) REVERT: A 229 ASP cc_start: 0.7691 (m-30) cc_final: 0.7372 (t0) REVERT: A 240 MET cc_start: 0.6523 (mmp) cc_final: 0.5975 (mmp) REVERT: A 248 LYS cc_start: 0.7843 (ttpp) cc_final: 0.7599 (mtpp) REVERT: A 261 ASP cc_start: 0.7321 (t0) cc_final: 0.7009 (t0) REVERT: A 277 LYS cc_start: 0.8126 (mtpt) cc_final: 0.7898 (ttmt) REVERT: A 304 GLN cc_start: 0.8309 (tm-30) cc_final: 0.8032 (tt0) REVERT: B 187 VAL cc_start: 0.8647 (OUTLIER) cc_final: 0.8291 (t) REVERT: B 212 ASP cc_start: 0.7623 (t70) cc_final: 0.7313 (t70) REVERT: B 217 MET cc_start: 0.7799 (ppp) cc_final: 0.7303 (ppp) REVERT: B 228 ASP cc_start: 0.7820 (m-30) cc_final: 0.7619 (p0) REVERT: B 254 ASP cc_start: 0.7727 (t70) cc_final: 0.7288 (t0) REVERT: B 303 ASP cc_start: 0.7682 (m-30) cc_final: 0.7472 (m-30) REVERT: D 82 ASP cc_start: 0.7244 (OUTLIER) cc_final: 0.6927 (t70) REVERT: D 236 ARG cc_start: 0.8511 (ttp-110) cc_final: 0.8268 (ttp-110) REVERT: D 263 ILE cc_start: 0.8146 (tp) cc_final: 0.7910 (tp) REVERT: D 282 ASP cc_start: 0.8393 (t70) cc_final: 0.8172 (t70) REVERT: S 21 SER cc_start: 0.8611 (m) cc_final: 0.8316 (p) REVERT: S 119 VAL cc_start: 0.8864 (t) cc_final: 0.8521 (p) REVERT: S 154 SER cc_start: 0.8467 (p) cc_final: 0.8233 (m) REVERT: S 192 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.8134 (ttp) REVERT: S 199 VAL cc_start: 0.8622 (m) cc_final: 0.8415 (t) outliers start: 23 outliers final: 12 residues processed: 197 average time/residue: 0.5187 time to fit residues: 109.2818 Evaluate side-chains 194 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 179 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 192 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 103 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN C 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.129466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.107523 restraints weight = 13076.342| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.03 r_work: 0.3308 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9079 Z= 0.166 Angle : 0.560 10.149 12303 Z= 0.295 Chirality : 0.042 0.133 1402 Planarity : 0.004 0.037 1548 Dihedral : 6.659 179.497 1235 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.33 % Allowed : 18.92 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.25), residues: 1114 helix: 2.18 (0.26), residues: 376 sheet: 0.58 (0.31), residues: 295 loop : -1.42 (0.25), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 98 TYR 0.013 0.002 TYR S 228 PHE 0.016 0.002 PHE A 189 TRP 0.011 0.001 TRP S 47 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 9077) covalent geometry : angle 0.55899 (12299) SS BOND : bond 0.01200 ( 2) SS BOND : angle 2.29629 ( 4) hydrogen bonds : bond 0.05693 ( 414) hydrogen bonds : angle 4.49174 ( 1176) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 185 time to evaluate : 0.291 Fit side-chains REVERT: A 25 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7520 (tm-30) REVERT: A 229 ASP cc_start: 0.7732 (m-30) cc_final: 0.7377 (t0) REVERT: A 240 MET cc_start: 0.6574 (mmp) cc_final: 0.6078 (mmp) REVERT: A 248 LYS cc_start: 0.7833 (ttpp) cc_final: 0.7602 (mtpp) REVERT: A 261 ASP cc_start: 0.7394 (t0) cc_final: 0.7095 (t0) REVERT: A 304 GLN cc_start: 0.8304 (tm-30) cc_final: 0.7986 (tt0) REVERT: B 187 VAL cc_start: 0.8659 (OUTLIER) cc_final: 0.8308 (t) REVERT: B 212 ASP cc_start: 0.7622 (t70) cc_final: 0.7309 (t70) REVERT: B 217 MET cc_start: 0.7753 (ppp) cc_final: 0.7197 (ppp) REVERT: B 228 ASP cc_start: 0.7878 (m-30) cc_final: 0.7578 (p0) REVERT: B 254 ASP cc_start: 0.7787 (t70) cc_final: 0.7280 (t0) REVERT: B 303 ASP cc_start: 0.7794 (m-30) cc_final: 0.7570 (m-30) REVERT: D 82 ASP cc_start: 0.7270 (OUTLIER) cc_final: 0.6934 (t70) REVERT: D 136 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8247 (tp) REVERT: D 236 ARG cc_start: 0.8490 (ttp-110) cc_final: 0.8205 (ttp-110) REVERT: D 263 ILE cc_start: 0.8115 (tp) cc_final: 0.7892 (tp) REVERT: S 21 SER cc_start: 0.8582 (m) cc_final: 0.8272 (p) REVERT: S 119 VAL cc_start: 0.8842 (t) cc_final: 0.8495 (p) REVERT: S 154 SER cc_start: 0.8479 (p) cc_final: 0.8252 (m) REVERT: S 192 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.8214 (ttp) outliers start: 32 outliers final: 16 residues processed: 199 average time/residue: 0.5544 time to fit residues: 117.6725 Evaluate side-chains 202 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 182 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 45 LEU Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 224 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 46 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 87 optimal weight: 0.4980 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN C 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.130421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.108585 restraints weight = 13033.365| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.03 r_work: 0.3324 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9079 Z= 0.133 Angle : 0.534 12.694 12303 Z= 0.279 Chirality : 0.042 0.134 1402 Planarity : 0.004 0.036 1548 Dihedral : 6.598 179.673 1235 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.22 % Allowed : 20.27 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.25), residues: 1114 helix: 2.30 (0.27), residues: 376 sheet: 0.64 (0.31), residues: 293 loop : -1.43 (0.25), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 98 TYR 0.012 0.001 TYR S 190 PHE 0.015 0.001 PHE A 189 TRP 0.012 0.001 TRP S 47 HIS 0.004 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 9077) covalent geometry : angle 0.53280 (12299) SS BOND : bond 0.00996 ( 2) SS BOND : angle 1.87989 ( 4) hydrogen bonds : bond 0.05100 ( 414) hydrogen bonds : angle 4.41826 ( 1176) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 187 time to evaluate : 0.423 Fit side-chains REVERT: A 240 MET cc_start: 0.6579 (mmp) cc_final: 0.6098 (mmp) REVERT: A 248 LYS cc_start: 0.7801 (ttpp) cc_final: 0.7583 (mtpp) REVERT: A 261 ASP cc_start: 0.7408 (t0) cc_final: 0.7112 (t0) REVERT: A 280 LYS cc_start: 0.7584 (mppt) cc_final: 0.7293 (mppt) REVERT: A 304 GLN cc_start: 0.8305 (tm-30) cc_final: 0.7985 (tt0) REVERT: B 187 VAL cc_start: 0.8656 (OUTLIER) cc_final: 0.8307 (t) REVERT: B 212 ASP cc_start: 0.7617 (t70) cc_final: 0.7321 (t70) REVERT: B 217 MET cc_start: 0.7789 (ppp) cc_final: 0.7199 (ppp) REVERT: B 228 ASP cc_start: 0.7869 (m-30) cc_final: 0.7627 (p0) REVERT: B 254 ASP cc_start: 0.7798 (t70) cc_final: 0.7305 (t0) REVERT: B 303 ASP cc_start: 0.7750 (m-30) cc_final: 0.7519 (m-30) REVERT: D 82 ASP cc_start: 0.7293 (OUTLIER) cc_final: 0.6964 (t70) REVERT: D 136 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8257 (tp) REVERT: D 236 ARG cc_start: 0.8475 (ttp-110) cc_final: 0.8176 (ttp-110) REVERT: D 263 ILE cc_start: 0.8101 (tp) cc_final: 0.7880 (tp) REVERT: D 282 ASP cc_start: 0.8475 (t0) cc_final: 0.8214 (t70) REVERT: S 21 SER cc_start: 0.8623 (m) cc_final: 0.8327 (p) REVERT: S 119 VAL cc_start: 0.8859 (t) cc_final: 0.8504 (p) REVERT: S 154 SER cc_start: 0.8460 (p) cc_final: 0.8216 (m) REVERT: S 192 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8217 (ttp) outliers start: 31 outliers final: 19 residues processed: 201 average time/residue: 0.5577 time to fit residues: 119.4419 Evaluate side-chains 208 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 185 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 224 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 36 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 53 optimal weight: 0.1980 chunk 49 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 61 optimal weight: 0.1980 chunk 91 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 75 GLN B 340 ASN C 59 ASN S 35 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.131738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.109926 restraints weight = 13245.726| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.05 r_work: 0.3345 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9079 Z= 0.108 Angle : 0.504 12.900 12303 Z= 0.262 Chirality : 0.041 0.135 1402 Planarity : 0.003 0.034 1548 Dihedral : 6.465 178.490 1235 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.81 % Allowed : 21.52 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.25), residues: 1114 helix: 2.40 (0.27), residues: 376 sheet: 0.70 (0.31), residues: 293 loop : -1.41 (0.25), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 129 TYR 0.012 0.001 TYR S 190 PHE 0.013 0.001 PHE A 189 TRP 0.011 0.001 TRP S 47 HIS 0.005 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 9077) covalent geometry : angle 0.50374 (12299) SS BOND : bond 0.00805 ( 2) SS BOND : angle 1.54446 ( 4) hydrogen bonds : bond 0.04572 ( 414) hydrogen bonds : angle 4.31917 ( 1176) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 180 time to evaluate : 0.310 Fit side-chains REVERT: A 229 ASP cc_start: 0.7681 (m-30) cc_final: 0.7393 (t0) REVERT: A 240 MET cc_start: 0.6604 (mmp) cc_final: 0.6102 (mmp) REVERT: A 248 LYS cc_start: 0.7793 (ttpp) cc_final: 0.7579 (mtpp) REVERT: A 261 ASP cc_start: 0.7385 (t0) cc_final: 0.7085 (t0) REVERT: A 280 LYS cc_start: 0.7588 (mppt) cc_final: 0.7300 (mppt) REVERT: A 304 GLN cc_start: 0.8294 (tm-30) cc_final: 0.7984 (tt0) REVERT: B 187 VAL cc_start: 0.8631 (OUTLIER) cc_final: 0.8286 (t) REVERT: B 212 ASP cc_start: 0.7615 (t70) cc_final: 0.7330 (t70) REVERT: B 217 MET cc_start: 0.7802 (ppp) cc_final: 0.7206 (ppp) REVERT: B 228 ASP cc_start: 0.7834 (m-30) cc_final: 0.7613 (p0) REVERT: B 254 ASP cc_start: 0.7812 (t70) cc_final: 0.7321 (t0) REVERT: D 82 ASP cc_start: 0.7275 (OUTLIER) cc_final: 0.6941 (t70) REVERT: D 236 ARG cc_start: 0.8484 (ttp-110) cc_final: 0.8207 (ttp-110) REVERT: D 263 ILE cc_start: 0.8079 (tp) cc_final: 0.7861 (tp) REVERT: D 282 ASP cc_start: 0.8471 (t0) cc_final: 0.8166 (t70) REVERT: S 21 SER cc_start: 0.8625 (m) cc_final: 0.8320 (p) REVERT: S 119 VAL cc_start: 0.8858 (t) cc_final: 0.8500 (p) REVERT: S 154 SER cc_start: 0.8445 (p) cc_final: 0.8204 (m) REVERT: S 192 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.8188 (ttp) outliers start: 27 outliers final: 16 residues processed: 198 average time/residue: 0.5188 time to fit residues: 109.7159 Evaluate side-chains 199 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 180 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 224 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 46 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 75 GLN C 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.130539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.108758 restraints weight = 13052.569| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.02 r_work: 0.3329 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9079 Z= 0.133 Angle : 0.532 13.255 12303 Z= 0.277 Chirality : 0.042 0.134 1402 Planarity : 0.003 0.034 1548 Dihedral : 6.543 178.354 1235 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.81 % Allowed : 21.41 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.25), residues: 1114 helix: 2.38 (0.27), residues: 376 sheet: 0.66 (0.31), residues: 295 loop : -1.40 (0.25), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 129 TYR 0.012 0.001 TYR S 228 PHE 0.015 0.002 PHE A 189 TRP 0.011 0.001 TRP S 47 HIS 0.003 0.001 HIS S 167 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 9077) covalent geometry : angle 0.53142 (12299) SS BOND : bond 0.00981 ( 2) SS BOND : angle 1.91687 ( 4) hydrogen bonds : bond 0.05063 ( 414) hydrogen bonds : angle 4.37993 ( 1176) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 182 time to evaluate : 0.375 Fit side-chains REVERT: A 229 ASP cc_start: 0.7658 (m-30) cc_final: 0.7373 (t0) REVERT: A 240 MET cc_start: 0.6608 (mmp) cc_final: 0.6123 (mmp) REVERT: A 248 LYS cc_start: 0.7808 (ttpp) cc_final: 0.7598 (mtpp) REVERT: A 261 ASP cc_start: 0.7399 (t0) cc_final: 0.7102 (t0) REVERT: A 280 LYS cc_start: 0.7589 (mppt) cc_final: 0.7333 (mppt) REVERT: A 304 GLN cc_start: 0.8317 (tm-30) cc_final: 0.8018 (tt0) REVERT: B 130 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7541 (mt-10) REVERT: B 187 VAL cc_start: 0.8665 (OUTLIER) cc_final: 0.8322 (t) REVERT: B 212 ASP cc_start: 0.7612 (t70) cc_final: 0.7335 (t70) REVERT: B 217 MET cc_start: 0.7801 (ppp) cc_final: 0.7253 (ppp) REVERT: B 228 ASP cc_start: 0.7850 (m-30) cc_final: 0.7641 (p0) REVERT: B 254 ASP cc_start: 0.7811 (t70) cc_final: 0.7339 (t0) REVERT: D 82 ASP cc_start: 0.7298 (OUTLIER) cc_final: 0.6975 (t70) REVERT: D 136 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8223 (tp) REVERT: D 206 ARG cc_start: 0.8212 (ttp-170) cc_final: 0.7968 (ttp-170) REVERT: D 236 ARG cc_start: 0.8494 (ttp-110) cc_final: 0.8205 (ttp-110) REVERT: D 263 ILE cc_start: 0.8091 (tp) cc_final: 0.7866 (tp) REVERT: D 282 ASP cc_start: 0.8513 (t0) cc_final: 0.8195 (t70) REVERT: S 21 SER cc_start: 0.8636 (m) cc_final: 0.8347 (p) REVERT: S 119 VAL cc_start: 0.8860 (t) cc_final: 0.8502 (p) REVERT: S 192 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8209 (ttp) outliers start: 27 outliers final: 19 residues processed: 194 average time/residue: 0.5567 time to fit residues: 115.0668 Evaluate side-chains 202 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 179 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 224 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 2 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 54 optimal weight: 0.4980 chunk 101 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.130665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.109223 restraints weight = 13085.510| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.01 r_work: 0.3331 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9079 Z= 0.128 Angle : 0.529 13.471 12303 Z= 0.274 Chirality : 0.041 0.137 1402 Planarity : 0.003 0.035 1548 Dihedral : 6.543 177.934 1235 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.49 % Allowed : 21.93 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.25), residues: 1114 helix: 2.41 (0.27), residues: 376 sheet: 0.64 (0.31), residues: 300 loop : -1.38 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 129 TYR 0.012 0.001 TYR S 228 PHE 0.016 0.002 PHE A 189 TRP 0.011 0.001 TRP S 47 HIS 0.007 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 9077) covalent geometry : angle 0.52788 (12299) SS BOND : bond 0.00946 ( 2) SS BOND : angle 1.82889 ( 4) hydrogen bonds : bond 0.04984 ( 414) hydrogen bonds : angle 4.37407 ( 1176) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 182 time to evaluate : 0.242 Fit side-chains REVERT: A 229 ASP cc_start: 0.7643 (m-30) cc_final: 0.7357 (t0) REVERT: A 240 MET cc_start: 0.6642 (mmp) cc_final: 0.6117 (mmp) REVERT: A 248 LYS cc_start: 0.7783 (ttpp) cc_final: 0.7573 (mtpp) REVERT: A 261 ASP cc_start: 0.7412 (t0) cc_final: 0.7116 (t0) REVERT: A 304 GLN cc_start: 0.8312 (tm-30) cc_final: 0.8045 (tt0) REVERT: B 130 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7541 (mt-10) REVERT: B 212 ASP cc_start: 0.7615 (t70) cc_final: 0.7337 (t70) REVERT: B 217 MET cc_start: 0.7808 (ppp) cc_final: 0.7219 (ppp) REVERT: B 228 ASP cc_start: 0.7845 (m-30) cc_final: 0.7642 (p0) REVERT: B 254 ASP cc_start: 0.7817 (t70) cc_final: 0.7342 (t0) REVERT: D 82 ASP cc_start: 0.7253 (OUTLIER) cc_final: 0.6926 (t70) REVERT: D 136 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8227 (tp) REVERT: D 190 VAL cc_start: 0.8449 (m) cc_final: 0.8201 (t) REVERT: D 206 ARG cc_start: 0.8211 (ttp-170) cc_final: 0.7967 (ttp-170) REVERT: D 236 ARG cc_start: 0.8504 (ttp-110) cc_final: 0.8223 (ttp-110) REVERT: D 263 ILE cc_start: 0.8086 (tp) cc_final: 0.7875 (tp) REVERT: D 282 ASP cc_start: 0.8510 (t0) cc_final: 0.8155 (t70) REVERT: S 21 SER cc_start: 0.8627 (m) cc_final: 0.8355 (p) REVERT: S 119 VAL cc_start: 0.8857 (t) cc_final: 0.8520 (p) REVERT: S 192 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.8201 (ttp) outliers start: 24 outliers final: 20 residues processed: 191 average time/residue: 0.5422 time to fit residues: 110.4721 Evaluate side-chains 204 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 181 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 224 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.0980 chunk 61 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 8 optimal weight: 0.3980 chunk 21 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 73 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.131446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.109867 restraints weight = 13065.783| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.00 r_work: 0.3342 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9079 Z= 0.113 Angle : 0.527 13.980 12303 Z= 0.272 Chirality : 0.041 0.137 1402 Planarity : 0.003 0.034 1548 Dihedral : 6.520 178.037 1235 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.29 % Allowed : 22.56 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.25), residues: 1114 helix: 2.45 (0.27), residues: 376 sheet: 0.72 (0.31), residues: 293 loop : -1.39 (0.25), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 129 TYR 0.016 0.001 TYR D 258 PHE 0.014 0.001 PHE A 189 TRP 0.011 0.001 TRP S 47 HIS 0.005 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 9077) covalent geometry : angle 0.52670 (12299) SS BOND : bond 0.00842 ( 2) SS BOND : angle 1.59286 ( 4) hydrogen bonds : bond 0.04676 ( 414) hydrogen bonds : angle 4.36486 ( 1176) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 180 time to evaluate : 0.349 Fit side-chains revert: symmetry clash REVERT: A 229 ASP cc_start: 0.7603 (m-30) cc_final: 0.7282 (t0) REVERT: A 240 MET cc_start: 0.6691 (mmp) cc_final: 0.6128 (mmp) REVERT: A 248 LYS cc_start: 0.7732 (ttpp) cc_final: 0.7520 (mtpp) REVERT: A 261 ASP cc_start: 0.7403 (t0) cc_final: 0.7112 (t0) REVERT: A 304 GLN cc_start: 0.8305 (tm-30) cc_final: 0.8024 (tt0) REVERT: B 129 ARG cc_start: 0.6822 (tpm170) cc_final: 0.6367 (mtp180) REVERT: B 130 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7481 (mt-10) REVERT: B 212 ASP cc_start: 0.7598 (t70) cc_final: 0.7325 (t70) REVERT: B 217 MET cc_start: 0.7830 (ppp) cc_final: 0.7220 (ppp) REVERT: B 254 ASP cc_start: 0.7818 (t70) cc_final: 0.7350 (t0) REVERT: D 82 ASP cc_start: 0.7279 (OUTLIER) cc_final: 0.6959 (t70) REVERT: D 136 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8210 (tp) REVERT: D 190 VAL cc_start: 0.8440 (m) cc_final: 0.8196 (t) REVERT: D 206 ARG cc_start: 0.8202 (ttp-170) cc_final: 0.7962 (ttp-170) REVERT: D 236 ARG cc_start: 0.8501 (ttp-110) cc_final: 0.8231 (ttp-110) REVERT: D 263 ILE cc_start: 0.8085 (tp) cc_final: 0.7863 (tp) REVERT: D 282 ASP cc_start: 0.8508 (t0) cc_final: 0.8142 (t70) REVERT: S 21 SER cc_start: 0.8606 (m) cc_final: 0.8329 (p) REVERT: S 119 VAL cc_start: 0.8869 (t) cc_final: 0.8513 (p) REVERT: S 192 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.8211 (ttp) outliers start: 22 outliers final: 17 residues processed: 190 average time/residue: 0.5573 time to fit residues: 112.7963 Evaluate side-chains 200 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 212 LEU Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 280 LYS Chi-restraints excluded: chain D residue 287 SER Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 192 MET Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 224 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 34 optimal weight: 1.9990 chunk 46 optimal weight: 0.0770 chunk 44 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 60 optimal weight: 0.0170 chunk 88 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.131686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.110103 restraints weight = 12941.665| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.02 r_work: 0.3347 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9079 Z= 0.108 Angle : 0.515 13.960 12303 Z= 0.266 Chirality : 0.041 0.137 1402 Planarity : 0.003 0.034 1548 Dihedral : 6.485 178.052 1235 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.18 % Allowed : 22.77 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.25), residues: 1114 helix: 2.46 (0.27), residues: 378 sheet: 0.73 (0.31), residues: 293 loop : -1.38 (0.25), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 129 TYR 0.013 0.001 TYR D 258 PHE 0.014 0.001 PHE A 189 TRP 0.011 0.001 TRP S 176 HIS 0.006 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 9077) covalent geometry : angle 0.51447 (12299) SS BOND : bond 0.00810 ( 2) SS BOND : angle 1.53586 ( 4) hydrogen bonds : bond 0.04518 ( 414) hydrogen bonds : angle 4.33741 ( 1176) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3795.58 seconds wall clock time: 65 minutes 4.75 seconds (3904.75 seconds total)