Starting phenix.real_space_refine on Tue Apr 29 11:31:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jef_36186/04_2025/8jef_36186_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jef_36186/04_2025/8jef_36186.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jef_36186/04_2025/8jef_36186.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jef_36186/04_2025/8jef_36186.map" model { file = "/net/cci-nas-00/data/ceres_data/8jef_36186/04_2025/8jef_36186_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jef_36186/04_2025/8jef_36186_neut.cif" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 5487 2.51 5 N 1477 2.21 5 O 1588 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 8615 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2123 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 52} Link IDs: {'PTRANS': 9, 'TRANS': 274} Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 277 Unresolved non-hydrogen dihedrals: 191 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 3, 'ASP:plan': 2, 'PHE:plan': 5, 'GLU:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 123 Chain: "C" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1701 Classifications: {'peptide': 215} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 212} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 2577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2577 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 431 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1772 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'3HO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.89, per 1000 atoms: 0.68 Number of scatterers: 8615 At special positions: 0 Unit cell: (89.25, 121.55, 131.75, 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 63 16.00 O 1588 8.00 N 1477 7.00 C 5487 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 183 " distance=1.94 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 266 " distance=2.09 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 177 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.18 Conformation dependent library (CDL) restraints added in 993.4 milliseconds 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2104 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 12 sheets defined 33.5% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 30 through 54 removed outlier: 3.993A pdb=" N LEU A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 42 " --> pdb=" O PHE A 38 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU A 43 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY A 44 " --> pdb=" O PHE A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 80 removed outlier: 3.641A pdb=" N ILE A 78 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 96 through 131 removed outlier: 3.653A pdb=" N CYS A 100 " --> pdb=" O GLY A 96 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 138 Processing helix chain 'A' and resid 140 through 159 removed outlier: 4.117A pdb=" N THR A 159 " --> pdb=" O THR A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 163 Processing helix chain 'A' and resid 188 through 215 removed outlier: 3.618A pdb=" N MET A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) Proline residue: A 200 - end of helix Processing helix chain 'A' and resid 231 through 245 removed outlier: 3.756A pdb=" N CYS A 243 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE A 244 " --> pdb=" O PHE A 240 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 245 " --> pdb=" O VAL A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 262 Processing helix chain 'A' and resid 269 through 284 removed outlier: 3.606A pdb=" N LEU A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ALA A 275 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N PHE A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 295 removed outlier: 3.836A pdb=" N LEU A 289 " --> pdb=" O MET A 285 " (cutoff:3.500A) Proline residue: A 291 - end of helix Processing helix chain 'C' and resid 8 through 31 removed outlier: 3.767A pdb=" N ALA C 12 " --> pdb=" O GLU C 8 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU C 14 " --> pdb=" O LYS C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 53 removed outlier: 3.516A pdb=" N MET C 53 " --> pdb=" O ILE C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 211 Processing helix chain 'C' and resid 226 through 230 removed outlier: 3.622A pdb=" N ASP C 229 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TYR C 230 " --> pdb=" O LEU C 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 226 through 230' Processing helix chain 'C' and resid 242 through 255 Processing helix chain 'C' and resid 272 through 281 removed outlier: 4.243A pdb=" N GLU C 276 " --> pdb=" O ASP C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 removed outlier: 3.914A pdb=" N ILE C 285 " --> pdb=" O PRO C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 309 Processing helix chain 'C' and resid 329 through 352 removed outlier: 3.626A pdb=" N GLY C 352 " --> pdb=" O LEU C 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 9 through 23 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.954A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 184 through 191 removed outlier: 4.343A pdb=" N VAL C 201 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLY C 40 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA C 220 " --> pdb=" O LYS C 35 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE C 221 " --> pdb=" O ILE C 265 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.861A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.893A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.152A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.821A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.064A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.645A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.776A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.564A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 128 through 129 Processing sheet with id=AB3, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.536A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU S 162 " --> pdb=" O TYR S 178 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N TYR S 178 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 378 hydrogen bonds defined for protein. 1050 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: 2.44 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1571 1.33 - 1.45: 2314 1.45 - 1.57: 4813 1.57 - 1.69: 8 1.69 - 1.82: 89 Bond restraints: 8795 Sorted by residual: bond pdb=" N CYS A 266 " pdb=" CA CYS A 266 " ideal model delta sigma weight residual 1.457 1.618 -0.161 1.29e-02 6.01e+03 1.55e+02 bond pdb=" N ASN A 265 " pdb=" CA ASN A 265 " ideal model delta sigma weight residual 1.457 1.603 -0.146 1.29e-02 6.01e+03 1.28e+02 bond pdb=" C ASN A 265 " pdb=" N CYS A 266 " ideal model delta sigma weight residual 1.332 1.489 -0.157 1.40e-02 5.10e+03 1.25e+02 bond pdb=" CA ASN A 265 " pdb=" C ASN A 265 " ideal model delta sigma weight residual 1.523 1.662 -0.139 1.34e-02 5.57e+03 1.08e+02 bond pdb=" CB SER A 181 " pdb=" OG SER A 181 " ideal model delta sigma weight residual 1.417 1.618 -0.201 2.00e-02 2.50e+03 1.01e+02 ... (remaining 8790 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.25: 11870 10.25 - 20.50: 36 20.50 - 30.75: 11 30.75 - 41.01: 4 41.01 - 51.26: 1 Bond angle restraints: 11922 Sorted by residual: angle pdb=" O GLN A 264 " pdb=" C GLN A 264 " pdb=" N ASN A 265 " ideal model delta sigma weight residual 122.68 81.78 40.90 1.27e+00 6.20e-01 1.04e+03 angle pdb=" N ASP A 85 " pdb=" CA ASP A 85 " pdb=" C ASP A 85 " ideal model delta sigma weight residual 113.18 146.27 -33.09 1.21e+00 6.83e-01 7.48e+02 angle pdb=" N PRO S 224 " pdb=" CA PRO S 224 " pdb=" C PRO S 224 " ideal model delta sigma weight residual 112.47 61.21 51.26 2.06e+00 2.36e-01 6.19e+02 angle pdb=" N LEU A 167 " pdb=" CA LEU A 167 " pdb=" CB LEU A 167 " ideal model delta sigma weight residual 111.43 76.45 34.98 1.48e+00 4.57e-01 5.59e+02 angle pdb=" N ARG A 22 " pdb=" CA ARG A 22 " pdb=" C ARG A 22 " ideal model delta sigma weight residual 113.18 89.54 23.64 1.21e+00 6.83e-01 3.82e+02 ... (remaining 11917 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.03: 4609 16.03 - 32.07: 450 32.07 - 48.10: 112 48.10 - 64.13: 25 64.13 - 80.16: 7 Dihedral angle restraints: 5203 sinusoidal: 1947 harmonic: 3256 Sorted by residual: dihedral pdb=" C ILE A 169 " pdb=" N ILE A 169 " pdb=" CA ILE A 169 " pdb=" CB ILE A 169 " ideal model delta harmonic sigma weight residual -122.00 -79.06 -42.94 0 2.50e+00 1.60e-01 2.95e+02 dihedral pdb=" N ILE A 169 " pdb=" C ILE A 169 " pdb=" CA ILE A 169 " pdb=" CB ILE A 169 " ideal model delta harmonic sigma weight residual 123.40 80.70 42.70 0 2.50e+00 1.60e-01 2.92e+02 dihedral pdb=" N PRO S 224 " pdb=" C PRO S 224 " pdb=" CA PRO S 224 " pdb=" CB PRO S 224 " ideal model delta harmonic sigma weight residual 115.10 73.40 41.70 0 2.50e+00 1.60e-01 2.78e+02 ... (remaining 5200 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.203: 1333 0.203 - 0.406: 15 0.406 - 0.609: 8 0.609 - 0.812: 1 0.812 - 1.015: 4 Chirality restraints: 1361 Sorted by residual: chirality pdb=" CA CYS A 183 " pdb=" N CYS A 183 " pdb=" C CYS A 183 " pdb=" CB CYS A 183 " both_signs ideal model delta sigma weight residual False 2.51 1.50 1.01 2.00e-01 2.50e+01 2.57e+01 chirality pdb=" CA VAL A 272 " pdb=" N VAL A 272 " pdb=" C VAL A 272 " pdb=" CB VAL A 272 " both_signs ideal model delta sigma weight residual False 2.44 1.53 0.91 2.00e-01 2.50e+01 2.06e+01 chirality pdb=" CA PRO S 224 " pdb=" N PRO S 224 " pdb=" C PRO S 224 " pdb=" CB PRO S 224 " both_signs ideal model delta sigma weight residual False 2.72 1.82 0.89 2.00e-01 2.50e+01 2.00e+01 ... (remaining 1358 not shown) Planarity restraints: 1513 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 264 " -0.144 2.00e-02 2.50e+03 2.20e-01 4.82e+02 pdb=" C GLN A 264 " 0.380 2.00e-02 2.50e+03 pdb=" O GLN A 264 " -0.128 2.00e-02 2.50e+03 pdb=" N ASN A 265 " -0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 167 " -0.047 2.00e-02 2.50e+03 9.52e-02 9.07e+01 pdb=" C LEU A 167 " 0.165 2.00e-02 2.50e+03 pdb=" O LEU A 167 " -0.065 2.00e-02 2.50e+03 pdb=" N LEU A 168 " -0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 165 " -0.042 2.00e-02 2.50e+03 8.88e-02 7.88e+01 pdb=" C LYS A 165 " 0.153 2.00e-02 2.50e+03 pdb=" O LYS A 165 " -0.061 2.00e-02 2.50e+03 pdb=" N LYS A 166 " -0.050 2.00e-02 2.50e+03 ... (remaining 1510 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.13: 7 2.13 - 2.82: 2731 2.82 - 3.51: 11152 3.51 - 4.21: 19116 4.21 - 4.90: 34991 Nonbonded interactions: 67997 Sorted by model distance: nonbonded pdb=" N PRO S 224 " pdb=" O PRO S 224 " model vdw 1.435 2.496 nonbonded pdb=" C TYR S 223 " pdb=" O PRO S 224 " model vdw 1.768 3.270 nonbonded pdb=" O ILE A 169 " pdb=" CD1 ILE A 169 " model vdw 1.955 3.460 nonbonded pdb=" N ILE A 26 " pdb=" O ILE A 26 " model vdw 1.960 2.496 nonbonded pdb=" O ILE A 169 " pdb=" CA ALA A 174 " model vdw 1.960 3.470 ... (remaining 67992 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 23.620 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:12.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 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 : 0.007 0.201 8800 Z= 0.463 Angle : 1.637 51.258 11932 Z= 1.021 Chirality : 0.087 1.015 1361 Planarity : 0.008 0.220 1513 Dihedral : 13.879 80.164 3084 Min Nonbonded Distance : 1.435 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.60 % Favored : 93.95 % Rotamer: Outliers : 1.89 % Allowed : 1.78 % Favored : 96.33 % Cbeta Deviations : 2.19 % Peptide Plane: Cis-proline : 0.00 % 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: -0.30 (0.26), residues: 1108 helix: 0.98 (0.31), residues: 345 sheet: 0.33 (0.30), residues: 292 loop : -1.43 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 142 HIS 0.003 0.000 HIS S 35 PHE 0.090 0.002 PHE A 107 TYR 0.014 0.001 TYR S 223 ARG 0.004 0.000 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.16169 ( 378) hydrogen bonds : angle 6.64299 ( 1050) SS BOND : bond 0.04644 ( 5) SS BOND : angle 5.96830 ( 10) covalent geometry : bond 0.00696 ( 8795) covalent geometry : angle 1.62858 (11922) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: A 23 ASP cc_start: 0.8195 (OUTLIER) cc_final: 0.7897 (p0) REVERT: A 78 ILE cc_start: 0.7176 (pt) cc_final: 0.6956 (pp) REVERT: A 101 ARG cc_start: 0.7023 (mtt180) cc_final: 0.6752 (mtt90) REVERT: A 189 HIS cc_start: 0.4807 (OUTLIER) cc_final: 0.4355 (t-170) REVERT: A 285 MET cc_start: 0.7491 (ptm) cc_final: 0.6447 (tpt) REVERT: A 288 MET cc_start: 0.7662 (mtp) cc_final: 0.6991 (mtm) REVERT: C 242 ARG cc_start: 0.8396 (mtt-85) cc_final: 0.7134 (mmt180) REVERT: C 305 CYS cc_start: 0.8346 (m) cc_final: 0.8126 (p) REVERT: B 42 ARG cc_start: 0.8119 (mmm160) cc_final: 0.7891 (mtp85) REVERT: B 163 ASP cc_start: 0.6850 (t0) cc_final: 0.6581 (t0) REVERT: B 268 ASN cc_start: 0.8700 (m-40) cc_final: 0.8391 (m110) outliers start: 17 outliers final: 4 residues processed: 159 average time/residue: 1.2271 time to fit residues: 207.5484 Evaluate side-chains 126 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 120 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 194 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN S 157 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.140070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.084912 restraints weight = 11966.869| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.81 r_work: 0.2964 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8800 Z= 0.191 Angle : 0.624 9.514 11932 Z= 0.332 Chirality : 0.045 0.171 1361 Planarity : 0.005 0.083 1513 Dihedral : 6.602 56.396 1227 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.32 % Favored : 93.50 % Rotamer: Outliers : 2.33 % Allowed : 12.44 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.09 % 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: 0.04 (0.26), residues: 1108 helix: 1.50 (0.30), residues: 346 sheet: 0.23 (0.30), residues: 300 loop : -1.25 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.005 0.001 HIS S 35 PHE 0.014 0.002 PHE A 232 TYR 0.017 0.001 TYR S 178 ARG 0.004 0.000 ARG A 228 Details of bonding type rmsd hydrogen bonds : bond 0.04916 ( 378) hydrogen bonds : angle 4.68053 ( 1050) SS BOND : bond 0.00784 ( 5) SS BOND : angle 2.51435 ( 10) covalent geometry : bond 0.00439 ( 8795) covalent geometry : angle 0.62002 (11922) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 23 ASP cc_start: 0.8550 (OUTLIER) cc_final: 0.7790 (t0) REVERT: A 76 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7095 (mm) REVERT: A 101 ARG cc_start: 0.7254 (mtt180) cc_final: 0.6888 (mtt90) REVERT: A 182 ILE cc_start: 0.6957 (OUTLIER) cc_final: 0.6554 (tp) REVERT: A 189 HIS cc_start: 0.5078 (OUTLIER) cc_final: 0.4659 (t-170) REVERT: A 228 ARG cc_start: 0.7398 (tmt-80) cc_final: 0.6087 (ptp-170) REVERT: A 285 MET cc_start: 0.7508 (ptm) cc_final: 0.6556 (tpt) REVERT: A 288 MET cc_start: 0.7828 (mtp) cc_final: 0.7312 (mtm) REVERT: C 25 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7892 (tm-30) REVERT: C 242 ARG cc_start: 0.8602 (mtt-85) cc_final: 0.7281 (mmt180) REVERT: C 305 CYS cc_start: 0.8912 (m) cc_final: 0.8501 (p) REVERT: B 42 ARG cc_start: 0.8555 (mmm160) cc_final: 0.8328 (mtp85) REVERT: B 44 GLN cc_start: 0.8489 (mm-40) cc_final: 0.8278 (mm-40) REVERT: B 163 ASP cc_start: 0.7901 (t0) cc_final: 0.7637 (t0) REVERT: B 262 MET cc_start: 0.9136 (OUTLIER) cc_final: 0.8910 (ttp) REVERT: B 268 ASN cc_start: 0.8975 (m-40) cc_final: 0.8644 (m110) REVERT: G 58 GLU cc_start: 0.8050 (pm20) cc_final: 0.7791 (pm20) outliers start: 21 outliers final: 7 residues processed: 145 average time/residue: 1.3796 time to fit residues: 212.2925 Evaluate side-chains 133 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 89 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 106 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN B 88 ASN B 237 ASN S 157 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.138565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.085891 restraints weight = 11960.868| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.76 r_work: 0.2914 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8800 Z= 0.150 Angle : 0.565 7.650 11932 Z= 0.300 Chirality : 0.044 0.191 1361 Planarity : 0.004 0.080 1513 Dihedral : 5.858 56.473 1222 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.05 % Favored : 93.86 % Rotamer: Outliers : 2.00 % Allowed : 15.44 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.09 % 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: 0.14 (0.26), residues: 1108 helix: 1.70 (0.30), residues: 343 sheet: 0.27 (0.30), residues: 300 loop : -1.27 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 47 HIS 0.004 0.001 HIS S 35 PHE 0.012 0.001 PHE C 189 TYR 0.016 0.001 TYR S 178 ARG 0.007 0.000 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.04309 ( 378) hydrogen bonds : angle 4.41895 ( 1050) SS BOND : bond 0.00572 ( 5) SS BOND : angle 1.84425 ( 10) covalent geometry : bond 0.00352 ( 8795) covalent geometry : angle 0.56275 (11922) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 76 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.6964 (mm) REVERT: A 97 ASP cc_start: 0.5973 (t0) cc_final: 0.5660 (t0) REVERT: A 101 ARG cc_start: 0.7112 (mtt180) cc_final: 0.6760 (mtt90) REVERT: A 158 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8310 (mt) REVERT: A 182 ILE cc_start: 0.7054 (OUTLIER) cc_final: 0.6732 (tp) REVERT: A 189 HIS cc_start: 0.5116 (OUTLIER) cc_final: 0.4658 (t-170) REVERT: A 228 ARG cc_start: 0.7420 (tmt-80) cc_final: 0.6014 (ptt180) REVERT: A 285 MET cc_start: 0.7468 (ptm) cc_final: 0.6517 (tpt) REVERT: A 288 MET cc_start: 0.7721 (mtp) cc_final: 0.7352 (mtm) REVERT: C 25 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7749 (tm-30) REVERT: C 242 ARG cc_start: 0.8553 (mtt-85) cc_final: 0.7140 (mmt180) REVERT: C 305 CYS cc_start: 0.8851 (m) cc_final: 0.8445 (p) REVERT: B 42 ARG cc_start: 0.8576 (mmm160) cc_final: 0.8348 (mtp85) REVERT: B 44 GLN cc_start: 0.8528 (mm-40) cc_final: 0.8288 (mm-40) REVERT: B 163 ASP cc_start: 0.7802 (t0) cc_final: 0.7507 (t0) REVERT: B 254 ASP cc_start: 0.8481 (t0) cc_final: 0.8177 (OUTLIER) REVERT: B 268 ASN cc_start: 0.8934 (m-40) cc_final: 0.8593 (m110) REVERT: G 58 GLU cc_start: 0.8049 (pm20) cc_final: 0.7810 (pm20) outliers start: 18 outliers final: 8 residues processed: 140 average time/residue: 1.3162 time to fit residues: 195.8596 Evaluate side-chains 135 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain B residue 275 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 77 optimal weight: 0.7980 chunk 27 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 109 optimal weight: 0.4980 chunk 12 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 346 ASN B 237 ASN S 39 GLN S 157 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.135335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.081985 restraints weight = 11902.772| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.77 r_work: 0.2852 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 8800 Z= 0.263 Angle : 0.632 7.373 11932 Z= 0.337 Chirality : 0.047 0.156 1361 Planarity : 0.005 0.094 1513 Dihedral : 6.008 57.030 1220 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.95 % Favored : 92.96 % Rotamer: Outliers : 2.56 % Allowed : 16.00 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.09 % 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: -0.01 (0.26), residues: 1108 helix: 1.56 (0.30), residues: 343 sheet: 0.16 (0.30), residues: 300 loop : -1.32 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP S 47 HIS 0.004 0.001 HIS S 35 PHE 0.019 0.002 PHE C 196 TYR 0.016 0.002 TYR S 178 ARG 0.008 0.000 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.04982 ( 378) hydrogen bonds : angle 4.63597 ( 1050) SS BOND : bond 0.00756 ( 5) SS BOND : angle 1.68278 ( 10) covalent geometry : bond 0.00638 ( 8795) covalent geometry : angle 0.63012 (11922) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 76 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.6940 (mm) REVERT: A 97 ASP cc_start: 0.6031 (t0) cc_final: 0.5787 (t0) REVERT: A 101 ARG cc_start: 0.7183 (mtt180) cc_final: 0.6805 (mtt90) REVERT: A 158 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8224 (mt) REVERT: A 182 ILE cc_start: 0.7023 (OUTLIER) cc_final: 0.6717 (tp) REVERT: A 189 HIS cc_start: 0.4982 (OUTLIER) cc_final: 0.4713 (t-170) REVERT: A 228 ARG cc_start: 0.7496 (tmt-80) cc_final: 0.5967 (ptp-170) REVERT: A 285 MET cc_start: 0.7641 (ptm) cc_final: 0.6739 (tpt) REVERT: A 288 MET cc_start: 0.7854 (mtp) cc_final: 0.7468 (mtm) REVERT: C 242 ARG cc_start: 0.8583 (mtt-85) cc_final: 0.7223 (mmt180) REVERT: C 305 CYS cc_start: 0.8920 (m) cc_final: 0.8490 (p) REVERT: B 17 GLN cc_start: 0.8360 (tm-30) cc_final: 0.8142 (tm-30) REVERT: B 44 GLN cc_start: 0.8562 (mm-40) cc_final: 0.8343 (mm-40) REVERT: B 163 ASP cc_start: 0.8099 (t0) cc_final: 0.7776 (t0) REVERT: B 254 ASP cc_start: 0.8600 (t0) cc_final: 0.8257 (t0) REVERT: B 268 ASN cc_start: 0.8971 (m-40) cc_final: 0.8632 (m110) REVERT: G 58 GLU cc_start: 0.8137 (pm20) cc_final: 0.7779 (pm20) REVERT: S 76 LYS cc_start: 0.8739 (mtmm) cc_final: 0.8434 (pmtt) REVERT: S 208 GLU cc_start: 0.8512 (pt0) cc_final: 0.8163 (pt0) REVERT: S 222 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8235 (mt-10) REVERT: S 223 TYR cc_start: 0.8753 (OUTLIER) cc_final: 0.7804 (t80) outliers start: 23 outliers final: 9 residues processed: 155 average time/residue: 1.3089 time to fit residues: 215.1630 Evaluate side-chains 141 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 48 optimal weight: 0.7980 chunk 12 optimal weight: 0.3980 chunk 33 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 1 optimal weight: 0.3980 chunk 86 optimal weight: 1.9990 chunk 7 optimal weight: 20.0000 chunk 54 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 346 ASN B 44 GLN B 237 ASN S 157 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.138918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.085439 restraints weight = 11862.845| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.80 r_work: 0.2915 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8800 Z= 0.121 Angle : 0.556 9.464 11932 Z= 0.292 Chirality : 0.043 0.183 1361 Planarity : 0.004 0.085 1513 Dihedral : 5.583 55.120 1220 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.87 % Favored : 94.04 % Rotamer: Outliers : 1.67 % Allowed : 19.11 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: 0.12 (0.26), residues: 1108 helix: 1.86 (0.30), residues: 331 sheet: 0.16 (0.30), residues: 302 loop : -1.27 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 47 HIS 0.002 0.000 HIS S 35 PHE 0.011 0.001 PHE S 29 TYR 0.016 0.001 TYR S 178 ARG 0.012 0.000 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.03801 ( 378) hydrogen bonds : angle 4.32509 ( 1050) SS BOND : bond 0.00464 ( 5) SS BOND : angle 1.10681 ( 10) covalent geometry : bond 0.00268 ( 8795) covalent geometry : angle 0.55545 (11922) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 1.000 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 76 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.6602 (mt) REVERT: A 101 ARG cc_start: 0.7203 (mtt180) cc_final: 0.6935 (mtt90) REVERT: A 158 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8212 (mt) REVERT: A 182 ILE cc_start: 0.7058 (OUTLIER) cc_final: 0.6785 (tp) REVERT: A 189 HIS cc_start: 0.5159 (OUTLIER) cc_final: 0.4881 (t-170) REVERT: A 228 ARG cc_start: 0.7409 (tmt-80) cc_final: 0.5973 (ptp-170) REVERT: A 285 MET cc_start: 0.7571 (ptm) cc_final: 0.6553 (tpt) REVERT: A 288 MET cc_start: 0.7851 (mtp) cc_final: 0.7263 (mtm) REVERT: C 242 ARG cc_start: 0.8545 (mtt-85) cc_final: 0.7189 (mmt180) REVERT: C 305 CYS cc_start: 0.8866 (m) cc_final: 0.8446 (p) REVERT: B 163 ASP cc_start: 0.7858 (t0) cc_final: 0.7561 (t0) REVERT: B 254 ASP cc_start: 0.8516 (t0) cc_final: 0.8168 (OUTLIER) REVERT: B 268 ASN cc_start: 0.8910 (m-40) cc_final: 0.8568 (m110) REVERT: G 58 GLU cc_start: 0.8176 (pm20) cc_final: 0.7825 (pm20) REVERT: S 222 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8056 (mt-10) outliers start: 15 outliers final: 9 residues processed: 141 average time/residue: 1.1967 time to fit residues: 180.0757 Evaluate side-chains 131 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 97 ASP Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 43 optimal weight: 9.9990 chunk 1 optimal weight: 0.1980 chunk 45 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 109 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 346 ASN B 44 GLN B 237 ASN S 157 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.139585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.085335 restraints weight = 11865.722| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.84 r_work: 0.2918 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8800 Z= 0.121 Angle : 0.553 9.634 11932 Z= 0.291 Chirality : 0.043 0.199 1361 Planarity : 0.004 0.085 1513 Dihedral : 5.465 55.989 1220 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.05 % Favored : 93.86 % Rotamer: Outliers : 2.00 % Allowed : 19.33 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: 0.10 (0.26), residues: 1108 helix: 1.66 (0.30), residues: 339 sheet: 0.17 (0.30), residues: 302 loop : -1.20 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.000 HIS S 35 PHE 0.011 0.001 PHE C 189 TYR 0.018 0.001 TYR A 269 ARG 0.011 0.000 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.03721 ( 378) hydrogen bonds : angle 4.26820 ( 1050) SS BOND : bond 0.00460 ( 5) SS BOND : angle 1.03372 ( 10) covalent geometry : bond 0.00277 ( 8795) covalent geometry : angle 0.55227 (11922) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.942 Fit side-chains TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 76 LEU cc_start: 0.7190 (tm) cc_final: 0.6622 (mt) REVERT: A 97 ASP cc_start: 0.6098 (t0) cc_final: 0.5778 (OUTLIER) REVERT: A 101 ARG cc_start: 0.7090 (mtt180) cc_final: 0.6773 (mtt90) REVERT: A 158 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8188 (mt) REVERT: A 189 HIS cc_start: 0.5178 (OUTLIER) cc_final: 0.4890 (t-170) REVERT: A 228 ARG cc_start: 0.7364 (tmt-80) cc_final: 0.5904 (ptp-170) REVERT: A 285 MET cc_start: 0.7559 (ptm) cc_final: 0.6497 (tpt) REVERT: A 288 MET cc_start: 0.7868 (mtp) cc_final: 0.7289 (mtm) REVERT: C 242 ARG cc_start: 0.8528 (mtt-85) cc_final: 0.7181 (mmt180) REVERT: C 305 CYS cc_start: 0.8862 (m) cc_final: 0.8449 (p) REVERT: B 42 ARG cc_start: 0.8419 (mmt-90) cc_final: 0.8065 (mtp85) REVERT: B 163 ASP cc_start: 0.7813 (t0) cc_final: 0.7511 (t0) REVERT: B 254 ASP cc_start: 0.8528 (t0) cc_final: 0.8177 (t0) REVERT: B 268 ASN cc_start: 0.8910 (m-40) cc_final: 0.8563 (m110) REVERT: G 58 GLU cc_start: 0.8191 (pm20) cc_final: 0.7830 (pm20) REVERT: S 76 LYS cc_start: 0.8733 (mtmm) cc_final: 0.8417 (pmtt) REVERT: S 222 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8129 (mt-10) REVERT: S 223 TYR cc_start: 0.8622 (OUTLIER) cc_final: 0.7715 (t80) outliers start: 18 outliers final: 11 residues processed: 145 average time/residue: 1.2709 time to fit residues: 196.4748 Evaluate side-chains 136 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.9980 chunk 103 optimal weight: 0.5980 chunk 62 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 346 ASN B 237 ASN S 157 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.136242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.080441 restraints weight = 12148.186| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.83 r_work: 0.2885 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 8800 Z= 0.312 Angle : 0.677 8.882 11932 Z= 0.359 Chirality : 0.048 0.236 1361 Planarity : 0.005 0.094 1513 Dihedral : 5.935 57.947 1220 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 3.00 % Allowed : 19.56 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: -0.22 (0.26), residues: 1108 helix: 1.34 (0.29), residues: 343 sheet: 0.08 (0.30), residues: 300 loop : -1.43 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP S 47 HIS 0.004 0.001 HIS S 35 PHE 0.020 0.002 PHE C 196 TYR 0.019 0.002 TYR C 296 ARG 0.013 0.001 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.05076 ( 378) hydrogen bonds : angle 4.67798 ( 1050) SS BOND : bond 0.00800 ( 5) SS BOND : angle 1.40508 ( 10) covalent geometry : bond 0.00760 ( 8795) covalent geometry : angle 0.67637 (11922) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 127 time to evaluate : 0.923 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 76 LEU cc_start: 0.7237 (tm) cc_final: 0.6675 (mt) REVERT: A 158 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8276 (mt) REVERT: A 189 HIS cc_start: 0.5223 (OUTLIER) cc_final: 0.4875 (t-170) REVERT: A 228 ARG cc_start: 0.7417 (tmt-80) cc_final: 0.5881 (ptp-170) REVERT: A 285 MET cc_start: 0.7805 (ptm) cc_final: 0.6753 (tpt) REVERT: A 288 MET cc_start: 0.8013 (mtp) cc_final: 0.7507 (mtm) REVERT: C 242 ARG cc_start: 0.8686 (mtt-85) cc_final: 0.7325 (mmt180) REVERT: C 305 CYS cc_start: 0.8974 (m) cc_final: 0.8516 (p) REVERT: C 349 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7637 (mptt) REVERT: B 17 GLN cc_start: 0.8492 (tm-30) cc_final: 0.8255 (tm-30) REVERT: B 42 ARG cc_start: 0.8453 (mmt-90) cc_final: 0.8106 (mtp85) REVERT: B 44 GLN cc_start: 0.8520 (mm-40) cc_final: 0.8290 (mm-40) REVERT: B 146 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8726 (mp) REVERT: B 163 ASP cc_start: 0.8207 (t0) cc_final: 0.7858 (t0) REVERT: B 254 ASP cc_start: 0.8696 (t0) cc_final: 0.8380 (t0) REVERT: B 268 ASN cc_start: 0.8965 (m-40) cc_final: 0.8634 (m110) REVERT: G 58 GLU cc_start: 0.8285 (pm20) cc_final: 0.7899 (pm20) REVERT: S 76 LYS cc_start: 0.8790 (mtmm) cc_final: 0.8508 (pmtt) REVERT: S 222 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8191 (mt-10) REVERT: S 223 TYR cc_start: 0.8741 (OUTLIER) cc_final: 0.7804 (t80) outliers start: 27 outliers final: 12 residues processed: 147 average time/residue: 1.2657 time to fit residues: 197.8678 Evaluate side-chains 136 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 132 THR Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 39 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 94 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 15 optimal weight: 20.0000 chunk 31 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 78 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 346 ASN B 237 ASN S 157 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.139663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.084140 restraints weight = 12093.158| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.84 r_work: 0.2949 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8800 Z= 0.137 Angle : 0.588 9.295 11932 Z= 0.311 Chirality : 0.045 0.228 1361 Planarity : 0.004 0.079 1513 Dihedral : 5.607 56.011 1220 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.33 % Allowed : 20.78 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: -0.00 (0.26), residues: 1108 helix: 1.55 (0.30), residues: 339 sheet: 0.21 (0.30), residues: 294 loop : -1.30 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP S 47 HIS 0.003 0.000 HIS S 35 PHE 0.011 0.001 PHE C 189 TYR 0.024 0.001 TYR A 269 ARG 0.013 0.000 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.03881 ( 378) hydrogen bonds : angle 4.38413 ( 1050) SS BOND : bond 0.00509 ( 5) SS BOND : angle 1.25558 ( 10) covalent geometry : bond 0.00319 ( 8795) covalent geometry : angle 0.58690 (11922) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.937 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 158 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8282 (mt) REVERT: A 189 HIS cc_start: 0.5434 (OUTLIER) cc_final: 0.5175 (t-170) REVERT: A 228 ARG cc_start: 0.7399 (tmt-80) cc_final: 0.5851 (ptp-170) REVERT: A 285 MET cc_start: 0.7733 (ptm) cc_final: 0.6722 (tpt) REVERT: A 288 MET cc_start: 0.7989 (mtp) cc_final: 0.7509 (mtm) REVERT: C 242 ARG cc_start: 0.8611 (mtt-85) cc_final: 0.7246 (mmt180) REVERT: C 305 CYS cc_start: 0.8911 (m) cc_final: 0.8501 (p) REVERT: C 349 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7608 (mptt) REVERT: B 42 ARG cc_start: 0.8423 (mmt-90) cc_final: 0.8091 (mtp85) REVERT: B 146 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8727 (mp) REVERT: B 163 ASP cc_start: 0.8019 (t0) cc_final: 0.7647 (t0) REVERT: B 254 ASP cc_start: 0.8626 (t0) cc_final: 0.8314 (t0) REVERT: B 268 ASN cc_start: 0.8913 (m-40) cc_final: 0.8573 (m110) REVERT: G 58 GLU cc_start: 0.8288 (pm20) cc_final: 0.7901 (pm20) REVERT: S 76 LYS cc_start: 0.8776 (mtmm) cc_final: 0.8492 (pmtt) REVERT: S 222 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8199 (mt-10) REVERT: S 223 TYR cc_start: 0.8628 (OUTLIER) cc_final: 0.7702 (t80) outliers start: 21 outliers final: 12 residues processed: 143 average time/residue: 1.2047 time to fit residues: 183.7572 Evaluate side-chains 137 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 82 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 94 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 48 optimal weight: 0.7980 chunk 4 optimal weight: 10.0000 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 346 ASN B 237 ASN S 157 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.135323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.082332 restraints weight = 12048.975| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.78 r_work: 0.2858 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 8800 Z= 0.236 Angle : 0.651 9.049 11932 Z= 0.343 Chirality : 0.047 0.252 1361 Planarity : 0.005 0.091 1513 Dihedral : 5.778 59.713 1220 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 3.00 % Allowed : 20.33 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: -0.18 (0.26), residues: 1108 helix: 1.37 (0.29), residues: 343 sheet: 0.07 (0.30), residues: 300 loop : -1.38 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS S 35 PHE 0.016 0.002 PHE C 196 TYR 0.022 0.002 TYR C 296 ARG 0.014 0.000 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.04594 ( 378) hydrogen bonds : angle 4.55681 ( 1050) SS BOND : bond 0.00690 ( 5) SS BOND : angle 1.31833 ( 10) covalent geometry : bond 0.00575 ( 8795) covalent geometry : angle 0.65001 (11922) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 158 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8258 (mt) REVERT: A 189 HIS cc_start: 0.5216 (OUTLIER) cc_final: 0.4937 (t-170) REVERT: A 285 MET cc_start: 0.7767 (ptm) cc_final: 0.6742 (tpt) REVERT: A 288 MET cc_start: 0.7989 (mtp) cc_final: 0.7527 (mtm) REVERT: C 242 ARG cc_start: 0.8593 (mtt-85) cc_final: 0.7258 (mmt180) REVERT: C 305 CYS cc_start: 0.8894 (m) cc_final: 0.8465 (p) REVERT: C 349 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7482 (mptt) REVERT: B 17 GLN cc_start: 0.8434 (tm-30) cc_final: 0.8168 (tm-30) REVERT: B 42 ARG cc_start: 0.8446 (mmt-90) cc_final: 0.8092 (mtp85) REVERT: B 44 GLN cc_start: 0.8538 (mm-40) cc_final: 0.8291 (mm-40) REVERT: B 146 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8656 (mp) REVERT: B 163 ASP cc_start: 0.8068 (t0) cc_final: 0.7706 (t0) REVERT: B 254 ASP cc_start: 0.8636 (t0) cc_final: 0.8256 (t0) REVERT: B 262 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8644 (ptm) REVERT: B 268 ASN cc_start: 0.8944 (m-40) cc_final: 0.8598 (m110) REVERT: G 58 GLU cc_start: 0.8256 (pm20) cc_final: 0.7866 (pm20) REVERT: S 222 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8197 (mt-10) REVERT: S 223 TYR cc_start: 0.8754 (OUTLIER) cc_final: 0.7765 (t80) outliers start: 27 outliers final: 13 residues processed: 146 average time/residue: 1.3185 time to fit residues: 204.2510 Evaluate side-chains 141 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain S residue 63 THR Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 54 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 90 optimal weight: 0.5980 chunk 16 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 346 ASN S 157 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.138163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.085258 restraints weight = 11931.596| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.78 r_work: 0.2909 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8800 Z= 0.132 Angle : 0.602 9.387 11932 Z= 0.317 Chirality : 0.045 0.256 1361 Planarity : 0.005 0.076 1513 Dihedral : 5.570 58.534 1220 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.33 % Allowed : 21.44 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: -0.11 (0.26), residues: 1108 helix: 1.41 (0.29), residues: 342 sheet: 0.16 (0.30), residues: 293 loop : -1.34 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP S 47 HIS 0.003 0.000 HIS S 35 PHE 0.011 0.001 PHE C 189 TYR 0.027 0.001 TYR A 269 ARG 0.016 0.000 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.03867 ( 378) hydrogen bonds : angle 4.38362 ( 1050) SS BOND : bond 0.00521 ( 5) SS BOND : angle 1.06818 ( 10) covalent geometry : bond 0.00309 ( 8795) covalent geometry : angle 0.60129 (11922) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 1.543 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 63 " (corrupted residue). Skipping it. REVERT: A 158 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8332 (mt) REVERT: A 189 HIS cc_start: 0.5148 (OUTLIER) cc_final: 0.4888 (t-170) REVERT: A 285 MET cc_start: 0.7722 (ptm) cc_final: 0.6843 (tmt) REVERT: C 242 ARG cc_start: 0.8574 (mtt-85) cc_final: 0.7191 (mmt180) REVERT: C 305 CYS cc_start: 0.8816 (m) cc_final: 0.8387 (p) REVERT: B 42 ARG cc_start: 0.8420 (mmt-90) cc_final: 0.8076 (mtp85) REVERT: B 146 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8611 (mp) REVERT: B 163 ASP cc_start: 0.7878 (t0) cc_final: 0.7491 (t0) REVERT: B 254 ASP cc_start: 0.8552 (t0) cc_final: 0.8160 (t0) REVERT: B 268 ASN cc_start: 0.8890 (m-40) cc_final: 0.8543 (m110) REVERT: G 58 GLU cc_start: 0.8247 (pm20) cc_final: 0.7850 (pm20) REVERT: S 43 LYS cc_start: 0.8958 (mmtm) cc_final: 0.8729 (mmtt) REVERT: S 76 LYS cc_start: 0.8655 (mtmm) cc_final: 0.8433 (pmtt) REVERT: S 222 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8176 (mt-10) REVERT: S 223 TYR cc_start: 0.8622 (OUTLIER) cc_final: 0.7712 (t80) outliers start: 21 outliers final: 15 residues processed: 141 average time/residue: 1.7540 time to fit residues: 262.9558 Evaluate side-chains 138 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 189 HIS Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 198 MET Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain S residue 223 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 81 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 100 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 346 ASN S 157 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.140053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.085609 restraints weight = 12097.399| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.84 r_work: 0.2924 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8800 Z= 0.137 Angle : 0.602 9.294 11932 Z= 0.316 Chirality : 0.044 0.255 1361 Planarity : 0.005 0.084 1513 Dihedral : 5.466 57.882 1220 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.00 % Allowed : 22.11 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: -0.08 (0.26), residues: 1108 helix: 1.40 (0.29), residues: 344 sheet: 0.28 (0.30), residues: 292 loop : -1.37 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS S 35 PHE 0.011 0.001 PHE C 189 TYR 0.028 0.001 TYR A 269 ARG 0.015 0.000 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.03830 ( 378) hydrogen bonds : angle 4.31956 ( 1050) SS BOND : bond 0.00546 ( 5) SS BOND : angle 1.05976 ( 10) covalent geometry : bond 0.00324 ( 8795) covalent geometry : angle 0.60098 (11922) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7854.62 seconds wall clock time: 135 minutes 35.17 seconds (8135.17 seconds total)