Starting phenix.real_space_refine on Mon Jul 28 19:56:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y67_33636/07_2025/7y67_33636_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y67_33636/07_2025/7y67_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7y67_33636/07_2025/7y67_33636.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y67_33636/07_2025/7y67_33636.map" model { file = "/net/cci-nas-00/data/ceres_data/7y67_33636/07_2025/7y67_33636_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y67_33636/07_2025/7y67_33636_neut.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'ZAL:plan-1': 1, 'MEA:plan-2': 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: 5.61, per 1000 atoms: 0.63 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: 2.34 Conformation dependent library (CDL) restraints added in 979.8 milliseconds 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DAR L 6 " Input volumes are d-peptide like pdb=" CB ZAL L 4 " 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: 0.95 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: 3.01 Time building geometry restraints manager: 2.61 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: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.180 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.440 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (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 TRP 0.011 0.001 TRP L 5 HIS 0.004 0.001 HIS A 188 PHE 0.017 0.001 PHE S 177 TYR 0.018 0.001 TYR D 300 ARG 0.007 0.000 ARG D 200 Details of bonding type rmsd hydrogen bonds : bond 0.12174 ( 414) hydrogen bonds : angle 4.81840 ( 1176) SS BOND : bond 0.00789 ( 2) SS BOND : angle 1.28820 ( 4) covalent geometry : bond 0.00283 ( 9077) covalent geometry : angle 0.69141 (12299) *********************** 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 : 0.968 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: 1.1634 time to fit residues: 265.7574 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 : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.9980 chunk 84 optimal weight: 0.0970 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 0.0980 chunk 44 optimal weight: 0.8980 chunk 87 optimal weight: 0.0670 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 64 optimal weight: 0.4980 chunk 100 optimal weight: 2.9990 overall best weight: 0.3116 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.135387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.113970 restraints weight = 13196.584| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.02 r_work: 0.3418 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1093 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= 0.106 Angle : 0.515 6.332 12303 Z= 0.268 Chirality : 0.041 0.136 1402 Planarity : 0.004 0.062 1548 Dihedral : 6.682 177.797 1235 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.66 % Allowed : 12.99 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.25), residues: 1114 helix: 2.05 (0.27), residues: 382 sheet: 0.64 (0.31), residues: 290 loop : -1.24 (0.25), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 211 HIS 0.003 0.001 HIS A 188 PHE 0.016 0.001 PHE B 234 TYR 0.016 0.001 TYR S 190 ARG 0.008 0.000 ARG S 98 Details of bonding type rmsd hydrogen bonds : bond 0.04250 ( 414) hydrogen bonds : angle 4.37328 ( 1176) SS BOND : bond 0.00656 ( 2) SS BOND : angle 1.31651 ( 4) covalent geometry : bond 0.00220 ( 9077) covalent geometry : angle 0.51416 (12299) *********************** 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 193 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 177 time to evaluate : 0.903 Fit side-chains REVERT: A 23 LEU cc_start: 0.7863 (tp) cc_final: 0.7626 (tp) REVERT: A 25 GLU cc_start: 0.7632 (tm-30) cc_final: 0.7093 (tm-30) REVERT: A 26 ASP cc_start: 0.7595 (m-30) cc_final: 0.7186 (m-30) REVERT: A 229 ASP cc_start: 0.7638 (m-30) cc_final: 0.7355 (t0) REVERT: A 248 LYS cc_start: 0.7894 (ttpp) cc_final: 0.7494 (mtpp) REVERT: A 261 ASP cc_start: 0.7292 (t0) cc_final: 0.6969 (t0) REVERT: B 187 VAL cc_start: 0.8656 (OUTLIER) cc_final: 0.8313 (t) REVERT: B 212 ASP cc_start: 0.7568 (t70) cc_final: 0.7245 (t0) REVERT: B 217 MET cc_start: 0.7695 (ppp) cc_final: 0.7179 (ppp) REVERT: B 237 ASN cc_start: 0.7853 (t0) cc_final: 0.7588 (t0) REVERT: D 253 ILE cc_start: 0.8188 (mt) cc_final: 0.7980 (pt) REVERT: D 263 ILE cc_start: 0.8120 (tp) cc_final: 0.7878 (tp) REVERT: D 282 ASP cc_start: 0.8228 (t70) cc_final: 0.7843 (t70) REVERT: S 6 GLU cc_start: 0.7877 (mp0) cc_final: 0.7424 (mp0) REVERT: S 21 SER cc_start: 0.8586 (m) cc_final: 0.8243 (p) REVERT: S 119 VAL cc_start: 0.8769 (t) cc_final: 0.8493 (p) REVERT: S 154 SER cc_start: 0.8449 (p) cc_final: 0.8189 (m) REVERT: S 192 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.8049 (ttp) outliers start: 16 outliers final: 8 residues processed: 187 average time/residue: 1.1234 time to fit residues: 224.4408 Evaluate side-chains 183 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 173 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 LYS 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 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 30 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 54 HIS B 75 GLN B 125 ASN C 44 HIS C 59 ASN D 145 GLN S 35 HIS S 142 GLN S 186 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.130273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.108143 restraints weight = 13144.956| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.05 r_work: 0.3327 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9079 Z= 0.153 Angle : 0.563 6.841 12303 Z= 0.296 Chirality : 0.042 0.135 1402 Planarity : 0.004 0.052 1548 Dihedral : 6.673 178.636 1235 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.91 % Allowed : 14.24 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.25), residues: 1114 helix: 2.02 (0.27), residues: 382 sheet: 0.69 (0.31), residues: 294 loop : -1.34 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 47 HIS 0.006 0.001 HIS B 62 PHE 0.017 0.002 PHE A 189 TYR 0.021 0.002 TYR D 300 ARG 0.007 0.001 ARG S 98 Details of bonding type rmsd hydrogen bonds : bond 0.05573 ( 414) hydrogen bonds : angle 4.47775 ( 1176) SS BOND : bond 0.01174 ( 2) SS BOND : angle 2.21969 ( 4) covalent geometry : bond 0.00353 ( 9077) covalent geometry : angle 0.56152 (12299) *********************** 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 220 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 192 time to evaluate : 0.909 Fit side-chains REVERT: A 25 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7295 (tm-30) REVERT: A 26 ASP cc_start: 0.7723 (m-30) cc_final: 0.7369 (m-30) REVERT: A 33 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7361 (mm-30) REVERT: A 240 MET cc_start: 0.6505 (mmp) cc_final: 0.5937 (mmp) REVERT: A 248 LYS cc_start: 0.7845 (ttpp) cc_final: 0.7569 (mtpp) REVERT: A 261 ASP cc_start: 0.7343 (t0) cc_final: 0.7054 (t0) REVERT: A 304 GLN cc_start: 0.8321 (tm-30) cc_final: 0.7986 (tt0) REVERT: B 52 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.7864 (mtp85) REVERT: B 129 ARG cc_start: 0.6430 (tpm170) cc_final: 0.5982 (tpt90) REVERT: B 187 VAL cc_start: 0.8666 (OUTLIER) cc_final: 0.8300 (t) REVERT: B 212 ASP cc_start: 0.7623 (t70) cc_final: 0.7285 (t70) REVERT: B 217 MET cc_start: 0.7754 (ppp) cc_final: 0.7182 (ppp) REVERT: B 228 ASP cc_start: 0.7866 (m-30) cc_final: 0.7535 (p0) REVERT: B 254 ASP cc_start: 0.7735 (t70) cc_final: 0.7279 (t0) REVERT: B 303 ASP cc_start: 0.7698 (m-30) cc_final: 0.7484 (m-30) REVERT: D 82 ASP cc_start: 0.7266 (OUTLIER) cc_final: 0.6954 (t70) REVERT: D 236 ARG cc_start: 0.8500 (ttp-110) cc_final: 0.8285 (ttp-110) REVERT: D 282 ASP cc_start: 0.8399 (t70) cc_final: 0.8027 (t70) REVERT: S 21 SER cc_start: 0.8579 (m) cc_final: 0.8243 (p) REVERT: S 119 VAL cc_start: 0.8866 (t) cc_final: 0.8521 (p) REVERT: S 154 SER cc_start: 0.8483 (p) cc_final: 0.8255 (m) REVERT: S 192 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.8099 (ttp) outliers start: 28 outliers final: 10 residues processed: 208 average time/residue: 1.0768 time to fit residues: 239.9327 Evaluate side-chains 200 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 186 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain B residue 52 ARG 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 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 158 SER 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 87 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 59 optimal weight: 0.3980 chunk 10 optimal weight: 0.0980 chunk 82 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 237 ASN C 59 ASN D 145 GLN S 186 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.131906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.110099 restraints weight = 13065.395| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.01 r_work: 0.3361 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9079 Z= 0.108 Angle : 0.498 8.397 12303 Z= 0.262 Chirality : 0.041 0.129 1402 Planarity : 0.003 0.047 1548 Dihedral : 6.547 178.851 1235 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.60 % Allowed : 18.19 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.25), residues: 1114 helix: 2.34 (0.27), residues: 375 sheet: 0.67 (0.31), residues: 290 loop : -1.29 (0.25), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 176 HIS 0.004 0.001 HIS B 54 PHE 0.014 0.001 PHE A 189 TYR 0.015 0.001 TYR D 300 ARG 0.004 0.000 ARG B 48 Details of bonding type rmsd hydrogen bonds : bond 0.04570 ( 414) hydrogen bonds : angle 4.31063 ( 1176) SS BOND : bond 0.00806 ( 2) SS BOND : angle 1.51851 ( 4) covalent geometry : bond 0.00234 ( 9077) covalent geometry : angle 0.49724 (12299) *********************** 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 213 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 188 time to evaluate : 0.981 Fit side-chains REVERT: A 25 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7427 (tm-30) REVERT: A 197 LYS cc_start: 0.8123 (tppp) cc_final: 0.7782 (mmmm) REVERT: A 229 ASP cc_start: 0.7681 (m-30) cc_final: 0.7437 (t0) REVERT: A 240 MET cc_start: 0.6486 (mmp) cc_final: 0.5969 (mmp) REVERT: A 248 LYS cc_start: 0.7853 (ttpp) cc_final: 0.7624 (mtpp) REVERT: A 261 ASP cc_start: 0.7309 (t0) cc_final: 0.6997 (t0) REVERT: A 304 GLN cc_start: 0.8308 (tm-30) cc_final: 0.8006 (tt0) REVERT: B 187 VAL cc_start: 0.8653 (OUTLIER) cc_final: 0.8308 (t) REVERT: B 212 ASP cc_start: 0.7624 (t70) cc_final: 0.7329 (t70) REVERT: B 217 MET cc_start: 0.7801 (ppp) cc_final: 0.7302 (ppp) REVERT: B 228 ASP cc_start: 0.7780 (m-30) cc_final: 0.7567 (p0) REVERT: B 254 ASP cc_start: 0.7711 (t70) cc_final: 0.7328 (t0) REVERT: B 303 ASP cc_start: 0.7666 (m-30) cc_final: 0.7464 (m-30) REVERT: D 82 ASP cc_start: 0.7268 (OUTLIER) cc_final: 0.6974 (t70) REVERT: D 134 ARG cc_start: 0.8565 (mtt180) cc_final: 0.8354 (mtt180) REVERT: D 236 ARG cc_start: 0.8528 (ttp-110) cc_final: 0.8311 (ttp-110) REVERT: D 263 ILE cc_start: 0.8153 (tp) cc_final: 0.7924 (tp) REVERT: D 282 ASP cc_start: 0.8388 (t70) cc_final: 0.8029 (t70) REVERT: S 21 SER cc_start: 0.8562 (m) cc_final: 0.8264 (p) REVERT: S 119 VAL cc_start: 0.8856 (t) cc_final: 0.8513 (p) REVERT: S 154 SER cc_start: 0.8503 (p) cc_final: 0.8282 (m) REVERT: S 192 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.8094 (ttp) REVERT: S 199 VAL cc_start: 0.8625 (m) cc_final: 0.8415 (t) outliers start: 25 outliers final: 9 residues processed: 199 average time/residue: 1.0921 time to fit residues: 232.6769 Evaluate side-chains 198 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 186 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 275 GLU 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 265 MET 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 38 optimal weight: 4.9990 chunk 2 optimal weight: 0.4980 chunk 14 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 16 optimal weight: 0.0370 chunk 93 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 74 optimal weight: 0.0980 chunk 42 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.4658 ------------------------------------------------------------------------------- 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 C 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.131844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.110085 restraints weight = 13018.133| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.00 r_work: 0.3361 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9079 Z= 0.104 Angle : 0.498 10.283 12303 Z= 0.260 Chirality : 0.040 0.135 1402 Planarity : 0.003 0.051 1548 Dihedral : 6.499 179.803 1235 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.70 % Allowed : 19.13 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.25), residues: 1114 helix: 2.35 (0.27), residues: 375 sheet: 0.65 (0.31), residues: 290 loop : -1.30 (0.25), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 176 HIS 0.004 0.001 HIS B 54 PHE 0.014 0.001 PHE A 189 TYR 0.014 0.001 TYR D 300 ARG 0.012 0.000 ARG S 98 Details of bonding type rmsd hydrogen bonds : bond 0.04429 ( 414) hydrogen bonds : angle 4.27295 ( 1176) SS BOND : bond 0.00782 ( 2) SS BOND : angle 1.49623 ( 4) covalent geometry : bond 0.00223 ( 9077) covalent geometry : angle 0.49763 (12299) *********************** 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 213 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 187 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7440 (tm-30) REVERT: A 229 ASP cc_start: 0.7672 (m-30) cc_final: 0.7393 (t0) REVERT: A 240 MET cc_start: 0.6538 (mmp) cc_final: 0.6002 (mmp) REVERT: A 248 LYS cc_start: 0.7873 (ttpp) cc_final: 0.7652 (mtpp) REVERT: A 261 ASP cc_start: 0.7296 (t0) cc_final: 0.6991 (t0) REVERT: A 304 GLN cc_start: 0.8284 (tm-30) cc_final: 0.8023 (tt0) REVERT: B 129 ARG cc_start: 0.6616 (tpm170) cc_final: 0.6085 (tpt-90) REVERT: B 187 VAL cc_start: 0.8641 (OUTLIER) cc_final: 0.8306 (t) REVERT: B 212 ASP cc_start: 0.7633 (t70) cc_final: 0.7336 (t70) REVERT: B 217 MET cc_start: 0.7854 (ppp) cc_final: 0.7311 (ppp) REVERT: B 254 ASP cc_start: 0.7720 (t70) cc_final: 0.7313 (t0) REVERT: B 303 ASP cc_start: 0.7650 (m-30) cc_final: 0.7445 (m-30) REVERT: D 82 ASP cc_start: 0.7266 (OUTLIER) cc_final: 0.6970 (t70) REVERT: D 236 ARG cc_start: 0.8536 (ttp-110) cc_final: 0.8290 (ttp-110) REVERT: D 263 ILE cc_start: 0.8145 (tp) cc_final: 0.7905 (tp) REVERT: D 282 ASP cc_start: 0.8398 (t70) cc_final: 0.8066 (t70) REVERT: S 21 SER cc_start: 0.8603 (m) cc_final: 0.8302 (p) REVERT: S 119 VAL cc_start: 0.8872 (t) cc_final: 0.8525 (p) REVERT: S 154 SER cc_start: 0.8472 (p) cc_final: 0.8248 (m) REVERT: S 192 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.8080 (ttp) REVERT: S 199 VAL cc_start: 0.8632 (m) cc_final: 0.8421 (t) outliers start: 26 outliers final: 15 residues processed: 199 average time/residue: 1.0481 time to fit residues: 223.6954 Evaluate side-chains 201 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 183 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 38 ASP 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 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 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 210 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 68 optimal weight: 0.0570 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.1304 ------------------------------------------------------------------------------- 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 ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.129127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.107170 restraints weight = 12969.839| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.01 r_work: 0.3301 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9079 Z= 0.171 Angle : 0.581 11.645 12303 Z= 0.304 Chirality : 0.043 0.134 1402 Planarity : 0.004 0.075 1548 Dihedral : 6.690 179.866 1235 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.60 % Allowed : 20.27 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.25), residues: 1114 helix: 2.18 (0.26), residues: 376 sheet: 0.57 (0.30), residues: 301 loop : -1.39 (0.25), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 47 HIS 0.006 0.001 HIS B 54 PHE 0.017 0.002 PHE A 189 TYR 0.014 0.002 TYR D 300 ARG 0.006 0.000 ARG S 98 Details of bonding type rmsd hydrogen bonds : bond 0.05889 ( 414) hydrogen bonds : angle 4.51598 ( 1176) SS BOND : bond 0.01275 ( 2) SS BOND : angle 2.44353 ( 4) covalent geometry : bond 0.00402 ( 9077) covalent geometry : angle 0.57956 (12299) *********************** 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 209 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 184 time to evaluate : 1.150 Fit side-chains REVERT: A 229 ASP cc_start: 0.7702 (m-30) cc_final: 0.7290 (t0) REVERT: A 232 LEU cc_start: 0.8316 (mm) cc_final: 0.8087 (mt) REVERT: A 240 MET cc_start: 0.6529 (mmp) cc_final: 0.6064 (mmp) REVERT: A 248 LYS cc_start: 0.7828 (ttpp) cc_final: 0.7588 (mtpp) REVERT: A 261 ASP cc_start: 0.7404 (t0) cc_final: 0.7105 (t0) REVERT: A 280 LYS cc_start: 0.7469 (mppt) cc_final: 0.7171 (mppt) REVERT: A 304 GLN cc_start: 0.8312 (tm-30) cc_final: 0.7988 (tt0) REVERT: B 129 ARG cc_start: 0.6718 (tpm170) cc_final: 0.6184 (mtp180) REVERT: B 212 ASP cc_start: 0.7627 (t70) cc_final: 0.7310 (t70) REVERT: B 217 MET cc_start: 0.7778 (ppp) cc_final: 0.7180 (ppp) REVERT: B 254 ASP cc_start: 0.7787 (t70) cc_final: 0.7281 (t0) REVERT: B 303 ASP cc_start: 0.7806 (m-30) cc_final: 0.7581 (m-30) REVERT: D 82 ASP cc_start: 0.7273 (OUTLIER) cc_final: 0.6945 (t70) REVERT: D 136 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8260 (tp) REVERT: D 236 ARG cc_start: 0.8511 (ttp-110) cc_final: 0.8208 (ttp-110) REVERT: D 263 ILE cc_start: 0.8111 (tp) cc_final: 0.7901 (tp) REVERT: S 21 SER cc_start: 0.8566 (m) cc_final: 0.8258 (p) REVERT: S 119 VAL cc_start: 0.8850 (t) cc_final: 0.8490 (p) REVERT: S 154 SER cc_start: 0.8470 (p) cc_final: 0.8248 (m) REVERT: S 192 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.8183 (ttp) outliers start: 25 outliers final: 14 residues processed: 195 average time/residue: 1.1561 time to fit residues: 240.8951 Evaluate side-chains 198 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 181 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 38 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 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 224 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 30 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 105 optimal weight: 0.4980 chunk 106 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 chunk 104 optimal weight: 0.6980 chunk 56 optimal weight: 9.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 237 ASN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 35 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.129946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.108261 restraints weight = 13118.043| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.02 r_work: 0.3330 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9079 Z= 0.123 Angle : 0.531 13.662 12303 Z= 0.277 Chirality : 0.041 0.132 1402 Planarity : 0.004 0.062 1548 Dihedral : 6.566 179.012 1235 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.91 % Allowed : 20.37 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.25), residues: 1114 helix: 2.31 (0.27), residues: 376 sheet: 0.65 (0.31), residues: 293 loop : -1.43 (0.25), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 47 HIS 0.004 0.001 HIS B 54 PHE 0.014 0.001 PHE A 189 TYR 0.012 0.001 TYR D 300 ARG 0.005 0.000 ARG S 98 Details of bonding type rmsd hydrogen bonds : bond 0.04940 ( 414) hydrogen bonds : angle 4.39433 ( 1176) SS BOND : bond 0.00925 ( 2) SS BOND : angle 1.72882 ( 4) covalent geometry : bond 0.00275 ( 9077) covalent geometry : angle 0.52990 (12299) *********************** 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 212 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 1.823 Fit side-chains revert: symmetry clash REVERT: A 229 ASP cc_start: 0.7679 (m-30) cc_final: 0.7258 (t0) REVERT: A 232 LEU cc_start: 0.8272 (mm) cc_final: 0.8061 (mt) REVERT: A 240 MET cc_start: 0.6611 (mmp) cc_final: 0.6112 (mmp) REVERT: A 248 LYS cc_start: 0.7801 (ttpp) cc_final: 0.7586 (mtpp) REVERT: A 261 ASP cc_start: 0.7404 (t0) cc_final: 0.7108 (t0) REVERT: A 280 LYS cc_start: 0.7449 (mppt) cc_final: 0.7168 (mppt) REVERT: A 304 GLN cc_start: 0.8296 (tm-30) cc_final: 0.7977 (tt0) REVERT: B 129 ARG cc_start: 0.6618 (tpm170) cc_final: 0.6216 (mtp180) REVERT: B 187 VAL cc_start: 0.8481 (t) cc_final: 0.8280 (t) REVERT: B 212 ASP cc_start: 0.7610 (t70) cc_final: 0.7314 (t70) REVERT: B 217 MET cc_start: 0.7796 (ppp) cc_final: 0.7253 (ppp) REVERT: B 254 ASP cc_start: 0.7800 (t70) cc_final: 0.7307 (t0) REVERT: B 303 ASP cc_start: 0.7678 (m-30) cc_final: 0.7449 (m-30) REVERT: D 82 ASP cc_start: 0.7269 (OUTLIER) cc_final: 0.6941 (t70) REVERT: D 136 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8243 (tp) REVERT: D 236 ARG cc_start: 0.8491 (ttp-110) cc_final: 0.8188 (ttp-110) REVERT: D 263 ILE cc_start: 0.8093 (tp) cc_final: 0.7882 (tp) REVERT: D 282 ASP cc_start: 0.8455 (t0) cc_final: 0.8206 (t70) REVERT: S 21 SER cc_start: 0.8605 (m) cc_final: 0.8325 (p) REVERT: S 119 VAL cc_start: 0.8867 (t) cc_final: 0.8507 (p) REVERT: S 154 SER cc_start: 0.8436 (p) cc_final: 0.8196 (m) REVERT: S 177 PHE cc_start: 0.7487 (OUTLIER) cc_final: 0.6803 (p90) REVERT: S 192 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.8196 (ttp) outliers start: 28 outliers final: 17 residues processed: 198 average time/residue: 1.5890 time to fit residues: 338.2377 Evaluate side-chains 204 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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 249 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 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 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 177 PHE Chi-restraints excluded: chain S residue 192 MET 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 12 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 45 optimal weight: 0.0370 chunk 19 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 340 ASN C 59 ASN D 145 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.130180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.108480 restraints weight = 13179.906| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.02 r_work: 0.3320 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9079 Z= 0.140 Angle : 0.553 13.074 12303 Z= 0.288 Chirality : 0.042 0.133 1402 Planarity : 0.004 0.068 1548 Dihedral : 6.554 178.477 1235 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.81 % Allowed : 21.21 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.25), residues: 1114 helix: 2.16 (0.27), residues: 383 sheet: 0.67 (0.31), residues: 293 loop : -1.49 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 47 HIS 0.006 0.001 HIS A 188 PHE 0.016 0.002 PHE A 189 TYR 0.013 0.002 TYR D 300 ARG 0.005 0.000 ARG S 98 Details of bonding type rmsd hydrogen bonds : bond 0.05249 ( 414) hydrogen bonds : angle 4.41708 ( 1176) SS BOND : bond 0.01050 ( 2) SS BOND : angle 1.99922 ( 4) covalent geometry : bond 0.00324 ( 9077) covalent geometry : angle 0.55209 (12299) *********************** 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 214 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 187 time to evaluate : 0.953 Fit side-chains revert: symmetry clash REVERT: A 229 ASP cc_start: 0.7699 (m-30) cc_final: 0.7285 (t0) REVERT: A 232 LEU cc_start: 0.8278 (mm) cc_final: 0.8037 (mt) REVERT: A 240 MET cc_start: 0.6594 (mmp) cc_final: 0.6106 (mmp) REVERT: A 261 ASP cc_start: 0.7404 (t0) cc_final: 0.7110 (t0) REVERT: A 280 LYS cc_start: 0.7448 (mppt) cc_final: 0.7192 (mppt) REVERT: A 304 GLN cc_start: 0.8319 (tm-30) cc_final: 0.7994 (tt0) REVERT: B 129 ARG cc_start: 0.6633 (tpm170) cc_final: 0.6224 (mtp180) REVERT: B 187 VAL cc_start: 0.8513 (t) cc_final: 0.8303 (t) REVERT: B 212 ASP cc_start: 0.7615 (t70) cc_final: 0.7323 (t70) REVERT: B 217 MET cc_start: 0.7810 (ppp) cc_final: 0.7242 (ppp) REVERT: B 254 ASP cc_start: 0.7817 (t70) cc_final: 0.7323 (t0) REVERT: B 303 ASP cc_start: 0.7700 (m-30) cc_final: 0.7495 (m-30) REVERT: D 82 ASP cc_start: 0.7287 (OUTLIER) cc_final: 0.6962 (t70) REVERT: D 136 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8242 (tp) REVERT: D 206 ARG cc_start: 0.8221 (ttp-170) cc_final: 0.7978 (ttp-170) REVERT: D 236 ARG cc_start: 0.8481 (ttp-110) cc_final: 0.8168 (ttp-110) REVERT: D 263 ILE cc_start: 0.8091 (tp) cc_final: 0.7867 (tp) REVERT: D 282 ASP cc_start: 0.8490 (t0) cc_final: 0.8194 (t70) REVERT: S 21 SER cc_start: 0.8615 (m) cc_final: 0.8331 (p) REVERT: S 119 VAL cc_start: 0.8860 (t) cc_final: 0.8485 (p) REVERT: S 154 SER cc_start: 0.8463 (p) cc_final: 0.8225 (m) REVERT: S 177 PHE cc_start: 0.7522 (OUTLIER) cc_final: 0.6832 (p90) REVERT: S 192 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.8207 (ttp) outliers start: 27 outliers final: 18 residues processed: 201 average time/residue: 1.1236 time to fit residues: 242.0891 Evaluate side-chains 204 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 182 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 249 LEU 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 177 PHE Chi-restraints excluded: chain S residue 192 MET 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 83 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 19 optimal weight: 0.0020 chunk 100 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 76 optimal weight: 0.0980 chunk 14 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 overall best weight: 0.4788 ------------------------------------------------------------------------------- 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 D 145 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.131871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.110147 restraints weight = 13124.673| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.04 r_work: 0.3346 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9079 Z= 0.106 Angle : 0.513 13.752 12303 Z= 0.265 Chirality : 0.041 0.136 1402 Planarity : 0.003 0.046 1548 Dihedral : 6.447 177.957 1235 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.39 % Allowed : 22.14 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.25), residues: 1114 helix: 2.32 (0.27), residues: 382 sheet: 0.65 (0.31), residues: 293 loop : -1.46 (0.25), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 176 HIS 0.005 0.001 HIS A 188 PHE 0.014 0.001 PHE A 189 TYR 0.021 0.001 TYR S 227 ARG 0.004 0.000 ARG S 98 Details of bonding type rmsd hydrogen bonds : bond 0.04469 ( 414) hydrogen bonds : angle 4.25199 ( 1176) SS BOND : bond 0.00805 ( 2) SS BOND : angle 1.44713 ( 4) covalent geometry : bond 0.00231 ( 9077) covalent geometry : angle 0.51225 (12299) *********************** 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 208 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 185 time to evaluate : 1.046 Fit side-chains revert: symmetry clash REVERT: A 229 ASP cc_start: 0.7647 (m-30) cc_final: 0.7238 (t0) REVERT: A 232 LEU cc_start: 0.8270 (mm) cc_final: 0.8048 (mt) REVERT: A 240 MET cc_start: 0.6608 (mmp) cc_final: 0.6102 (mmp) REVERT: A 261 ASP cc_start: 0.7374 (t0) cc_final: 0.7087 (t0) REVERT: A 280 LYS cc_start: 0.7457 (mppt) cc_final: 0.7214 (mppt) REVERT: A 304 GLN cc_start: 0.8286 (tm-30) cc_final: 0.7997 (tt0) REVERT: B 187 VAL cc_start: 0.8448 (t) cc_final: 0.8225 (t) REVERT: B 212 ASP cc_start: 0.7602 (t70) cc_final: 0.7334 (t70) REVERT: B 217 MET cc_start: 0.7837 (ppp) cc_final: 0.7244 (ppp) REVERT: B 254 ASP cc_start: 0.7823 (t70) cc_final: 0.7328 (t0) REVERT: B 303 ASP cc_start: 0.7656 (m-30) cc_final: 0.7424 (m-30) REVERT: D 82 ASP cc_start: 0.7260 (OUTLIER) cc_final: 0.6938 (t70) REVERT: D 136 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8181 (tp) REVERT: D 206 ARG cc_start: 0.8213 (ttp-170) cc_final: 0.7978 (ttp-170) REVERT: D 236 ARG cc_start: 0.8486 (ttp-110) cc_final: 0.8207 (ttp-110) REVERT: D 263 ILE cc_start: 0.8075 (tp) cc_final: 0.7856 (tp) REVERT: D 282 ASP cc_start: 0.8464 (t0) cc_final: 0.8147 (t70) REVERT: S 21 SER cc_start: 0.8602 (m) cc_final: 0.8324 (p) REVERT: S 119 VAL cc_start: 0.8867 (t) cc_final: 0.8503 (p) REVERT: S 154 SER cc_start: 0.8432 (p) cc_final: 0.8183 (m) REVERT: S 177 PHE cc_start: 0.7294 (OUTLIER) cc_final: 0.6578 (p90) REVERT: S 178 LEU cc_start: 0.8114 (tp) cc_final: 0.7914 (tt) REVERT: S 192 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.8158 (ttp) outliers start: 23 outliers final: 16 residues processed: 194 average time/residue: 1.1696 time to fit residues: 242.0303 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 : 1.005 ------------------------------------------------------------------------------- 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 28 GLU Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain B residue 65 THR 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 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 91 THR Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain S residue 192 MET 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 74 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 chunk 7 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 10 optimal weight: 0.2980 chunk 54 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 47 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 D 145 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.131191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.109446 restraints weight = 13082.108| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.03 r_work: 0.3333 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9079 Z= 0.120 Angle : 0.534 13.878 12303 Z= 0.275 Chirality : 0.041 0.143 1402 Planarity : 0.003 0.034 1548 Dihedral : 6.479 177.960 1235 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.29 % Allowed : 22.25 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.25), residues: 1114 helix: 2.30 (0.27), residues: 382 sheet: 0.70 (0.31), residues: 292 loop : -1.47 (0.25), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 176 HIS 0.006 0.001 HIS A 188 PHE 0.015 0.001 PHE A 189 TYR 0.012 0.001 TYR D 300 ARG 0.004 0.000 ARG B 48 Details of bonding type rmsd hydrogen bonds : bond 0.04795 ( 414) hydrogen bonds : angle 4.28129 ( 1176) SS BOND : bond 0.00927 ( 2) SS BOND : angle 1.74837 ( 4) covalent geometry : bond 0.00270 ( 9077) covalent geometry : angle 0.53303 (12299) ********************** 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 204 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 182 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: A 229 ASP cc_start: 0.7657 (m-30) cc_final: 0.7245 (t0) REVERT: A 232 LEU cc_start: 0.8264 (mm) cc_final: 0.8034 (mt) REVERT: A 240 MET cc_start: 0.6639 (mmp) cc_final: 0.6087 (mmp) REVERT: A 261 ASP cc_start: 0.7370 (t0) cc_final: 0.7086 (t0) REVERT: A 280 LYS cc_start: 0.7468 (mppt) cc_final: 0.7202 (mppt) REVERT: A 304 GLN cc_start: 0.8286 (tm-30) cc_final: 0.8001 (tt0) REVERT: B 129 ARG cc_start: 0.7728 (mtp180) cc_final: 0.7088 (tpm170) REVERT: B 130 GLU cc_start: 0.8056 (mp0) cc_final: 0.7667 (mp0) REVERT: B 187 VAL cc_start: 0.8483 (t) cc_final: 0.8260 (t) REVERT: B 212 ASP cc_start: 0.7613 (t70) cc_final: 0.7325 (t70) REVERT: B 217 MET cc_start: 0.7816 (ppp) cc_final: 0.7212 (ppp) REVERT: B 254 ASP cc_start: 0.7828 (t70) cc_final: 0.7327 (t0) REVERT: B 303 ASP cc_start: 0.7691 (m-30) cc_final: 0.7466 (m-30) REVERT: D 82 ASP cc_start: 0.7276 (OUTLIER) cc_final: 0.6949 (t70) REVERT: D 136 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8214 (tp) REVERT: D 206 ARG cc_start: 0.8211 (ttp-170) cc_final: 0.7968 (ttp-170) REVERT: D 236 ARG cc_start: 0.8492 (ttp-110) cc_final: 0.8206 (ttp-110) REVERT: D 263 ILE cc_start: 0.8065 (tp) cc_final: 0.7849 (tp) REVERT: D 282 ASP cc_start: 0.8494 (t0) cc_final: 0.8161 (t70) REVERT: S 21 SER cc_start: 0.8611 (m) cc_final: 0.8321 (p) REVERT: S 119 VAL cc_start: 0.8864 (t) cc_final: 0.8486 (p) REVERT: S 154 SER cc_start: 0.8433 (p) cc_final: 0.8192 (m) REVERT: S 177 PHE cc_start: 0.7323 (OUTLIER) cc_final: 0.6558 (p90) REVERT: S 192 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.8202 (ttp) outliers start: 22 outliers final: 15 residues processed: 190 average time/residue: 1.3448 time to fit residues: 272.4798 Evaluate side-chains 200 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain B residue 65 THR 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 91 THR Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain S residue 192 MET 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 18 optimal weight: 0.0040 chunk 45 optimal weight: 0.0470 chunk 89 optimal weight: 0.5980 chunk 79 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 93 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 overall best weight: 0.3890 ------------------------------------------------------------------------------- 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 D 145 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.132743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.111181 restraints weight = 13106.648| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.03 r_work: 0.3360 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9079 Z= 0.099 Angle : 0.508 14.007 12303 Z= 0.259 Chirality : 0.041 0.138 1402 Planarity : 0.003 0.034 1548 Dihedral : 6.406 178.134 1235 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.98 % Allowed : 22.66 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.25), residues: 1114 helix: 2.39 (0.27), residues: 383 sheet: 0.71 (0.31), residues: 292 loop : -1.41 (0.25), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 176 HIS 0.006 0.001 HIS A 188 PHE 0.013 0.001 PHE A 189 TYR 0.013 0.001 TYR S 190 ARG 0.004 0.000 ARG B 48 Details of bonding type rmsd hydrogen bonds : bond 0.04183 ( 414) hydrogen bonds : angle 4.17954 ( 1176) SS BOND : bond 0.00730 ( 2) SS BOND : angle 1.35370 ( 4) covalent geometry : bond 0.00208 ( 9077) covalent geometry : angle 0.50760 (12299) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8444.86 seconds wall clock time: 149 minutes 26.88 seconds (8966.88 seconds total)