Starting phenix.real_space_refine on Wed Jun 3 23:11:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9upu_64402/06_2026/9upu_64402.cif Found real_map, /net/cci-nas-00/data/ceres_data/9upu_64402/06_2026/9upu_64402.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/9upu_64402/06_2026/9upu_64402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9upu_64402/06_2026/9upu_64402.map" model { file = "/net/cci-nas-00/data/ceres_data/9upu_64402/06_2026/9upu_64402.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9upu_64402/06_2026/9upu_64402.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 58 5.16 5 C 5665 2.51 5 N 1480 2.21 5 O 1634 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8837 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 2516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2516 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 5, 'TRANS': 329} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 4, 'GLU:plan': 3, 'ASP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 49 Chain: "C" Number of atoms: 345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 345 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 1803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1803 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "J" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Classifications: {'peptide': 8} Link IDs: {'PTRANS': 1, 'TRANS': 6} Chain: "R" Number of atoms: 2296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2296 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 9, 'TRANS': 275} Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.98, per 1000 atoms: 0.22 Number of scatterers: 8837 At special positions: 0 Unit cell: (87.55, 124.1, 130.9, 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 58 16.00 O 1634 8.00 N 1480 7.00 C 5665 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 186 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 341.6 milliseconds 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2124 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 37.5% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'B' and resid 6 through 26 removed outlier: 3.628A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 13 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 55 through 59 removed outlier: 3.541A pdb=" N ASN C 59 " --> pdb=" O ALA C 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 31 Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.844A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS A 214 " --> pdb=" O TRP A 211 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 279 removed outlier: 4.057A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 327 through 351 removed outlier: 4.492A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.595A pdb=" N SER S 31 " --> pdb=" O ALA S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.041A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.654A pdb=" N ASP S 90 " --> pdb=" O ARG S 87 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 87 through 91' Processing helix chain 'J' and resid 2 through 6 Processing helix chain 'R' and resid 35 through 66 Proline residue: R 42 - end of helix removed outlier: 3.502A pdb=" N GLN R 66 " --> pdb=" O VAL R 62 " (cutoff:3.500A) Processing helix chain 'R' and resid 71 through 89 removed outlier: 3.880A pdb=" N LYS R 75 " --> pdb=" O SER R 71 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR R 76 " --> pdb=" O MET R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 90 through 100 removed outlier: 3.620A pdb=" N TRP R 94 " --> pdb=" O THR R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 140 removed outlier: 4.043A pdb=" N VAL R 124 " --> pdb=" O LEU R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 145 through 154 removed outlier: 3.628A pdb=" N LYS R 149 " --> pdb=" O GLN R 145 " (cutoff:3.500A) Processing helix chain 'R' and resid 160 through 168 removed outlier: 3.825A pdb=" N ALA R 164 " --> pdb=" O VAL R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 168 through 174 Processing helix chain 'R' and resid 193 through 228 removed outlier: 3.753A pdb=" N VAL R 197 " --> pdb=" O ASP R 193 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU R 210 " --> pdb=" O VAL R 206 " (cutoff:3.500A) Proline residue: R 211 - end of helix removed outlier: 3.968A pdb=" N VAL R 214 " --> pdb=" O LEU R 210 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N HIS R 228 " --> pdb=" O SER R 224 " (cutoff:3.500A) Processing helix chain 'R' and resid 231 through 267 Proline residue: R 254 - end of helix Processing helix chain 'R' and resid 273 through 292 removed outlier: 4.125A pdb=" N GLU R 277 " --> pdb=" O GLY R 273 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN R 278 " --> pdb=" O CYS R 274 " (cutoff:3.500A) Processing helix chain 'R' and resid 293 through 303 Proline residue: R 299 - end of helix Processing helix chain 'R' and resid 306 through 317 Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.599A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.679A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.047A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.829A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.828A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.703A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.992A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.604A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.551A pdb=" N SER S 7 " --> pdb=" O SER S 21 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU S 81 " --> pdb=" O LEU S 20 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER S 71 " --> pdb=" O PHE S 80 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.070A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.070A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 141 removed outlier: 3.557A pdb=" N ALA S 211 " --> pdb=" O SER S 208 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.760A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU S 174 " --> pdb=" O TYR S 190 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N TYR S 190 " --> pdb=" O LEU S 174 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 177 through 180 removed outlier: 3.539A pdb=" N ILE R 185 " --> pdb=" O SER R 178 " (cutoff:3.500A) 420 hydrogen bonds defined for protein. 1188 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.51 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1599 1.33 - 1.45: 2363 1.45 - 1.57: 4989 1.57 - 1.69: 0 1.69 - 1.81: 81 Bond restraints: 9032 Sorted by residual: bond pdb=" CA GLU R 288 " pdb=" C GLU R 288 " ideal model delta sigma weight residual 1.524 1.481 0.043 1.29e-02 6.01e+03 1.09e+01 bond pdb=" C GLU R 288 " pdb=" O GLU R 288 " ideal model delta sigma weight residual 1.237 1.205 0.032 1.19e-02 7.06e+03 7.05e+00 bond pdb=" C GLU R 288 " pdb=" N ALA R 289 " ideal model delta sigma weight residual 1.335 1.307 0.028 1.31e-02 5.83e+03 4.45e+00 bond pdb=" CA LYS J 1 " pdb=" C LYS J 1 " ideal model delta sigma weight residual 1.525 1.482 0.043 2.10e-02 2.27e+03 4.10e+00 bond pdb=" CA GLU R 288 " pdb=" CB GLU R 288 " ideal model delta sigma weight residual 1.528 1.502 0.026 1.59e-02 3.96e+03 2.76e+00 ... (remaining 9027 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 12072 1.43 - 2.85: 142 2.85 - 4.28: 24 4.28 - 5.71: 13 5.71 - 7.13: 1 Bond angle restraints: 12252 Sorted by residual: angle pdb=" N LEU R 253 " pdb=" CA LEU R 253 " pdb=" C LEU R 253 " ideal model delta sigma weight residual 109.81 115.18 -5.37 2.21e+00 2.05e-01 5.91e+00 angle pdb=" C THR B 86 " pdb=" N THR B 87 " pdb=" CA THR B 87 " ideal model delta sigma weight residual 121.54 126.11 -4.57 1.91e+00 2.74e-01 5.72e+00 angle pdb=" C GLU R 288 " pdb=" CA GLU R 288 " pdb=" CB GLU R 288 " ideal model delta sigma weight residual 110.85 107.34 3.51 1.70e+00 3.46e-01 4.27e+00 angle pdb=" C GLY A 45 " pdb=" N LYS A 46 " pdb=" CA LYS A 46 " ideal model delta sigma weight residual 121.54 125.30 -3.76 1.91e+00 2.74e-01 3.87e+00 angle pdb=" N ILE B 33 " pdb=" CA ILE B 33 " pdb=" C ILE B 33 " ideal model delta sigma weight residual 109.34 113.12 -3.78 2.08e+00 2.31e-01 3.30e+00 ... (remaining 12247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.11: 4748 14.11 - 28.22: 463 28.22 - 42.33: 134 42.33 - 56.44: 27 56.44 - 70.55: 4 Dihedral angle restraints: 5376 sinusoidal: 2081 harmonic: 3295 Sorted by residual: dihedral pdb=" CA VAL R 160 " pdb=" C VAL R 160 " pdb=" N TRP R 161 " pdb=" CA TRP R 161 " ideal model delta harmonic sigma weight residual -180.00 -159.29 -20.71 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA ARG S 191 " pdb=" C ARG S 191 " pdb=" N MET S 192 " pdb=" CA MET S 192 " ideal model delta harmonic sigma weight residual 180.00 164.24 15.76 0 5.00e+00 4.00e-02 9.94e+00 dihedral pdb=" CG ARG S 67 " pdb=" CD ARG S 67 " pdb=" NE ARG S 67 " pdb=" CZ ARG S 67 " ideal model delta sinusoidal sigma weight residual 90.00 131.86 -41.86 2 1.50e+01 4.44e-03 9.50e+00 ... (remaining 5373 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 883 0.029 - 0.057: 326 0.057 - 0.086: 110 0.086 - 0.114: 69 0.114 - 0.143: 13 Chirality restraints: 1401 Sorted by residual: chirality pdb=" CA TYR S 235 " pdb=" N TYR S 235 " pdb=" C TYR S 235 " pdb=" CB TYR S 235 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.08e-01 chirality pdb=" CA ILE S 189 " pdb=" N ILE S 189 " pdb=" C ILE S 189 " pdb=" CB ILE S 189 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.07e-01 chirality pdb=" CA ILE A 221 " pdb=" N ILE A 221 " pdb=" C ILE A 221 " pdb=" CB ILE A 221 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.05e-01 ... (remaining 1398 not shown) Planarity restraints: 1534 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE R 162 " 0.034 5.00e-02 4.00e+02 5.10e-02 4.16e+00 pdb=" N PRO R 163 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO R 163 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO R 163 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 46 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.14e+00 pdb=" C LYS A 46 " -0.035 2.00e-02 2.50e+03 pdb=" O LYS A 46 " 0.013 2.00e-02 2.50e+03 pdb=" N SER A 47 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.029 5.00e-02 4.00e+02 4.40e-02 3.09e+00 pdb=" N PRO B 236 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.025 5.00e-02 4.00e+02 ... (remaining 1531 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2092 2.79 - 3.32: 7778 3.32 - 3.85: 13521 3.85 - 4.37: 15512 4.37 - 4.90: 29033 Nonbonded interactions: 67936 Sorted by model distance: nonbonded pdb=" OG SER S 154 " pdb=" O SER S 217 " model vdw 2.269 3.040 nonbonded pdb=" O ASP R 97 " pdb=" NH2 ARG R 183 " model vdw 2.272 3.120 nonbonded pdb=" O HIS R 140 " pdb=" OG SER R 144 " model vdw 2.316 3.040 nonbonded pdb=" NH1 ARG S 180 " pdb=" O GLU S 222 " model vdw 2.326 3.120 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.351 3.040 ... (remaining 67931 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: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.440 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 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 : 0.002 0.043 9035 Z= 0.117 Angle : 0.445 7.133 12258 Z= 0.241 Chirality : 0.039 0.143 1401 Planarity : 0.003 0.051 1534 Dihedral : 12.434 70.554 3243 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.26), residues: 1119 helix: 2.96 (0.27), residues: 373 sheet: 0.64 (0.33), residues: 263 loop : -0.72 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 77 TYR 0.010 0.001 TYR R 255 PHE 0.011 0.001 PHE B 234 TRP 0.007 0.001 TRP B 82 HIS 0.003 0.001 HIS R 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.12 ( 9032) covalent geometry : angle 0.44467 / 0.24 (12252) SS BOND : bond 0.00424 / 0.21 ( 3) SS BOND : angle 0.82241 / 0.42 ( 6) hydrogen bonds : bond 0.16391 / 10.79 ( 416) hydrogen bonds : angle 5.90945 / 4.06 ( 1188) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 38 ASP cc_start: 0.8905 (p0) cc_final: 0.8679 (p0) REVERT: B 44 GLN cc_start: 0.8339 (mt0) cc_final: 0.7904 (mp10) REVERT: B 333 ASP cc_start: 0.7058 (t0) cc_final: 0.6602 (t0) REVERT: C 47 GLU cc_start: 0.7728 (mp0) cc_final: 0.7300 (mp0) REVERT: A 209 LYS cc_start: 0.8498 (tmtt) cc_final: 0.8034 (tptp) REVERT: A 261 ASP cc_start: 0.8584 (p0) cc_final: 0.8375 (p0) REVERT: A 312 LYS cc_start: 0.8518 (mptt) cc_final: 0.8315 (mmtt) REVERT: S 234 GLU cc_start: 0.7340 (mm-30) cc_final: 0.7114 (mm-30) REVERT: R 154 LYS cc_start: 0.8012 (mmtt) cc_final: 0.7654 (mtpp) REVERT: R 176 ASN cc_start: 0.7729 (t0) cc_final: 0.7490 (t0) REVERT: R 262 ASP cc_start: 0.7758 (t0) cc_final: 0.7527 (t0) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.6829 time to fit residues: 119.2336 Evaluate side-chains 142 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 176 GLN B 268 ASN B 295 ASN A 188 HIS A 269 ASN A 331 ASN A 346 ASN R 113 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.115637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.092131 restraints weight = 13439.228| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.59 r_work: 0.3260 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9035 Z= 0.149 Angle : 0.539 7.892 12258 Z= 0.282 Chirality : 0.042 0.163 1401 Planarity : 0.004 0.048 1534 Dihedral : 4.998 59.844 1284 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.48 % Allowed : 8.54 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.26), residues: 1119 helix: 2.87 (0.27), residues: 370 sheet: 0.54 (0.31), residues: 282 loop : -0.66 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 70 TYR 0.015 0.001 TYR S 190 PHE 0.013 0.001 PHE R 249 TRP 0.009 0.001 TRP B 211 HIS 0.005 0.001 HIS R 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 9032) covalent geometry : angle 0.53805 / 0.28 (12252) SS BOND : bond 0.00688 / 0.34 ( 3) SS BOND : angle 1.55570 / 0.80 ( 6) hydrogen bonds : bond 0.05459 / 3.77 ( 416) hydrogen bonds : angle 4.48233 / 3.15 ( 1188) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 165 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 ASP cc_start: 0.8993 (p0) cc_final: 0.8769 (p0) REVERT: B 197 ARG cc_start: 0.8348 (mmt-90) cc_final: 0.8045 (mtt-85) REVERT: B 333 ASP cc_start: 0.7185 (t0) cc_final: 0.6752 (t0) REVERT: C 47 GLU cc_start: 0.8020 (mp0) cc_final: 0.7613 (mp0) REVERT: A 29 LYS cc_start: 0.8108 (tmmm) cc_final: 0.7810 (tptp) REVERT: A 209 LYS cc_start: 0.8755 (tmtt) cc_final: 0.8335 (tptp) REVERT: A 261 ASP cc_start: 0.8683 (p0) cc_final: 0.8451 (p0) REVERT: S 218 ARG cc_start: 0.8433 (ttp80) cc_final: 0.8232 (ttp80) REVERT: S 234 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7374 (mm-30) REVERT: R 63 MET cc_start: 0.8099 (tpp) cc_final: 0.7870 (mmp) REVERT: R 145 GLN cc_start: 0.8386 (tt0) cc_final: 0.8083 (mt0) REVERT: R 154 LYS cc_start: 0.8172 (mmtt) cc_final: 0.7776 (mtpp) REVERT: R 176 ASN cc_start: 0.7978 (t0) cc_final: 0.7716 (t0) REVERT: R 262 ASP cc_start: 0.7746 (t0) cc_final: 0.7533 (t0) outliers start: 14 outliers final: 10 residues processed: 166 average time/residue: 0.7059 time to fit residues: 123.3326 Evaluate side-chains 168 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 158 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain S residue 204 SER Chi-restraints excluded: chain R residue 40 PHE Chi-restraints excluded: chain R residue 61 LEU Chi-restraints excluded: chain R residue 149 LYS Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 205 MET Chi-restraints excluded: chain R residue 315 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 109 optimal weight: 3.9990 chunk 36 optimal weight: 0.0170 chunk 101 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 77 optimal weight: 0.0970 chunk 86 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 overall best weight: 0.5816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN S 194 ASN R 113 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.116033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.093933 restraints weight = 12998.245| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.46 r_work: 0.3305 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9035 Z= 0.113 Angle : 0.496 7.051 12258 Z= 0.261 Chirality : 0.041 0.152 1401 Planarity : 0.004 0.046 1534 Dihedral : 4.801 58.728 1284 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.58 % Allowed : 10.65 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.26), residues: 1119 helix: 2.88 (0.27), residues: 369 sheet: 0.58 (0.31), residues: 282 loop : -0.62 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 70 TYR 0.014 0.001 TYR S 190 PHE 0.010 0.001 PHE R 249 TRP 0.009 0.001 TRP B 211 HIS 0.004 0.001 HIS R 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 9032) covalent geometry : angle 0.49543 / 0.26 (12252) SS BOND : bond 0.00521 / 0.26 ( 3) SS BOND : angle 1.14436 / 0.60 ( 6) hydrogen bonds : bond 0.04685 / 3.24 ( 416) hydrogen bonds : angle 4.26231 / 3.01 ( 1188) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 38 ASP cc_start: 0.8989 (p0) cc_final: 0.8784 (p0) REVERT: B 197 ARG cc_start: 0.8306 (mmt-90) cc_final: 0.8034 (mtt-85) REVERT: B 333 ASP cc_start: 0.7048 (t0) cc_final: 0.6577 (t0) REVERT: C 47 GLU cc_start: 0.7993 (mp0) cc_final: 0.7588 (mp0) REVERT: A 29 LYS cc_start: 0.8016 (tmmm) cc_final: 0.7729 (tptp) REVERT: A 209 LYS cc_start: 0.8719 (tmtt) cc_final: 0.8335 (tptp) REVERT: A 256 ASN cc_start: 0.8368 (t0) cc_final: 0.8078 (t0) REVERT: A 261 ASP cc_start: 0.8658 (p0) cc_final: 0.8423 (p0) REVERT: A 350 ASP cc_start: 0.7586 (t0) cc_final: 0.6999 (m-30) REVERT: S 76 LYS cc_start: 0.8362 (mtpt) cc_final: 0.8087 (mtmm) REVERT: S 234 GLU cc_start: 0.7610 (mm-30) cc_final: 0.7342 (mm-30) REVERT: R 63 MET cc_start: 0.8137 (tpp) cc_final: 0.7819 (mmp) REVERT: R 66 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7555 (pp30) REVERT: R 145 GLN cc_start: 0.8314 (tt0) cc_final: 0.8031 (mt0) REVERT: R 154 LYS cc_start: 0.8167 (mmtt) cc_final: 0.7846 (mtpp) REVERT: R 176 ASN cc_start: 0.8008 (t0) cc_final: 0.7715 (t0) REVERT: R 262 ASP cc_start: 0.7738 (t0) cc_final: 0.7494 (t0) outliers start: 15 outliers final: 7 residues processed: 161 average time/residue: 0.7040 time to fit residues: 119.2982 Evaluate side-chains 151 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 143 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain R residue 66 GLN Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 205 MET Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 270 ILE Chi-restraints excluded: chain R residue 315 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 20 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 86 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 53 optimal weight: 0.0060 chunk 93 optimal weight: 0.9980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 54 HIS A 52 GLN R 113 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.116239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.092878 restraints weight = 13452.741| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.58 r_work: 0.3285 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9035 Z= 0.117 Angle : 0.498 7.049 12258 Z= 0.261 Chirality : 0.041 0.151 1401 Planarity : 0.004 0.045 1534 Dihedral : 4.738 58.936 1284 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.58 % Allowed : 11.60 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.26), residues: 1119 helix: 2.88 (0.27), residues: 374 sheet: 0.57 (0.31), residues: 282 loop : -0.58 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 70 TYR 0.013 0.001 TYR S 190 PHE 0.011 0.001 PHE R 249 TRP 0.009 0.001 TRP B 211 HIS 0.004 0.001 HIS R 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 9032) covalent geometry : angle 0.49792 / 0.26 (12252) SS BOND : bond 0.00503 / 0.25 ( 3) SS BOND : angle 1.15777 / 0.59 ( 6) hydrogen bonds : bond 0.04645 / 3.22 ( 416) hydrogen bonds : angle 4.18659 / 2.95 ( 1188) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: B 38 ASP cc_start: 0.8998 (p0) cc_final: 0.8792 (p0) REVERT: B 197 ARG cc_start: 0.8337 (mmt-90) cc_final: 0.8081 (mtt-85) REVERT: B 209 LYS cc_start: 0.8539 (mttp) cc_final: 0.8269 (mttm) REVERT: B 333 ASP cc_start: 0.7057 (t0) cc_final: 0.6538 (t0) REVERT: C 47 GLU cc_start: 0.8018 (mp0) cc_final: 0.7611 (mp0) REVERT: A 29 LYS cc_start: 0.8008 (tmmm) cc_final: 0.7733 (tptp) REVERT: A 209 LYS cc_start: 0.8735 (tmtt) cc_final: 0.8337 (tptp) REVERT: A 256 ASN cc_start: 0.8394 (t0) cc_final: 0.8083 (t0) REVERT: A 281 SER cc_start: 0.7742 (m) cc_final: 0.6887 (p) REVERT: A 350 ASP cc_start: 0.7620 (t0) cc_final: 0.7074 (m-30) REVERT: S 76 LYS cc_start: 0.8383 (mtpt) cc_final: 0.8105 (mtmm) REVERT: S 234 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7340 (mm-30) REVERT: R 63 MET cc_start: 0.8143 (tpp) cc_final: 0.7825 (mmp) REVERT: R 66 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7586 (pp30) REVERT: R 145 GLN cc_start: 0.8366 (tt0) cc_final: 0.8066 (mt0) REVERT: R 154 LYS cc_start: 0.8181 (mmtt) cc_final: 0.7784 (mtpp) REVERT: R 176 ASN cc_start: 0.8049 (t0) cc_final: 0.7729 (t0) REVERT: R 262 ASP cc_start: 0.7750 (t0) cc_final: 0.7509 (t0) outliers start: 15 outliers final: 4 residues processed: 161 average time/residue: 0.7126 time to fit residues: 120.7225 Evaluate side-chains 157 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 152 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 66 GLN Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 270 ILE Chi-restraints excluded: chain R residue 315 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 77 optimal weight: 0.4980 chunk 32 optimal weight: 0.9990 chunk 88 optimal weight: 0.3980 chunk 37 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 54 HIS R 113 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.115159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.092985 restraints weight = 13218.647| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.48 r_work: 0.3283 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9035 Z= 0.125 Angle : 0.517 8.685 12258 Z= 0.268 Chirality : 0.042 0.160 1401 Planarity : 0.004 0.045 1534 Dihedral : 4.748 59.157 1284 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.27 % Allowed : 13.61 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.26), residues: 1119 helix: 2.83 (0.28), residues: 374 sheet: 0.64 (0.31), residues: 277 loop : -0.66 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 42 TYR 0.013 0.001 TYR S 190 PHE 0.012 0.001 PHE R 249 TRP 0.009 0.001 TRP B 211 HIS 0.004 0.001 HIS R 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 9032) covalent geometry : angle 0.51624 / 0.27 (12252) SS BOND : bond 0.00487 / 0.24 ( 3) SS BOND : angle 1.11860 / 0.58 ( 6) hydrogen bonds : bond 0.04827 / 3.36 ( 416) hydrogen bonds : angle 4.17984 / 2.95 ( 1188) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 157 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: B 38 ASP cc_start: 0.9004 (p0) cc_final: 0.8796 (p0) REVERT: B 197 ARG cc_start: 0.8318 (mmt-90) cc_final: 0.8054 (mtt-85) REVERT: B 333 ASP cc_start: 0.7035 (t0) cc_final: 0.6519 (t0) REVERT: C 47 GLU cc_start: 0.8011 (mp0) cc_final: 0.7596 (mp0) REVERT: A 29 LYS cc_start: 0.8016 (tmmm) cc_final: 0.7732 (tptp) REVERT: A 209 LYS cc_start: 0.8791 (tmtt) cc_final: 0.8394 (tptp) REVERT: A 256 ASN cc_start: 0.8410 (t0) cc_final: 0.8093 (t0) REVERT: A 315 ASP cc_start: 0.8520 (p0) cc_final: 0.8180 (p0) REVERT: A 350 ASP cc_start: 0.7692 (t0) cc_final: 0.7166 (m-30) REVERT: S 76 LYS cc_start: 0.8394 (mtpt) cc_final: 0.8118 (mtmm) REVERT: S 230 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8583 (ttt) REVERT: S 234 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7341 (mm-30) REVERT: R 63 MET cc_start: 0.8142 (tpp) cc_final: 0.7763 (mmp) REVERT: R 66 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7537 (pp30) REVERT: R 145 GLN cc_start: 0.8355 (tt0) cc_final: 0.8080 (mt0) REVERT: R 154 LYS cc_start: 0.8182 (mmtt) cc_final: 0.7783 (mtpp) REVERT: R 262 ASP cc_start: 0.7748 (t0) cc_final: 0.7531 (t0) outliers start: 12 outliers final: 5 residues processed: 161 average time/residue: 0.7088 time to fit residues: 120.1265 Evaluate side-chains 151 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 144 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 230 MET Chi-restraints excluded: chain R residue 66 GLN Chi-restraints excluded: chain R residue 133 ASP Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 270 ILE Chi-restraints excluded: chain R residue 315 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 54 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 42 optimal weight: 0.0170 chunk 58 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 38 optimal weight: 0.0070 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN A 52 GLN R 113 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.116295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.094126 restraints weight = 13175.225| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.48 r_work: 0.3303 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9035 Z= 0.106 Angle : 0.513 8.714 12258 Z= 0.266 Chirality : 0.041 0.147 1401 Planarity : 0.004 0.049 1534 Dihedral : 4.654 58.790 1284 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.95 % Allowed : 14.14 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.26), residues: 1119 helix: 2.87 (0.28), residues: 373 sheet: 0.71 (0.32), residues: 276 loop : -0.62 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG R 70 TYR 0.012 0.001 TYR S 190 PHE 0.009 0.001 PHE R 249 TRP 0.009 0.001 TRP B 211 HIS 0.004 0.001 HIS R 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 ( 9032) covalent geometry : angle 0.51240 / 0.27 (12252) SS BOND : bond 0.00430 / 0.22 ( 3) SS BOND : angle 0.89693 / 0.47 ( 6) hydrogen bonds : bond 0.04358 / 3.02 ( 416) hydrogen bonds : angle 4.13537 / 2.91 ( 1188) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 149 time to evaluate : 0.341 Fit side-chains revert: symmetry clash REVERT: B 38 ASP cc_start: 0.9009 (p0) cc_final: 0.8806 (p0) REVERT: B 197 ARG cc_start: 0.8292 (mmt-90) cc_final: 0.7987 (mtt-85) REVERT: B 209 LYS cc_start: 0.8512 (mttp) cc_final: 0.8256 (mttm) REVERT: B 333 ASP cc_start: 0.6995 (t0) cc_final: 0.6528 (t0) REVERT: C 47 GLU cc_start: 0.8002 (mp0) cc_final: 0.7603 (mp0) REVERT: A 29 LYS cc_start: 0.7939 (tmmm) cc_final: 0.7677 (tptp) REVERT: A 51 LYS cc_start: 0.8407 (pptt) cc_final: 0.8154 (pptt) REVERT: A 209 LYS cc_start: 0.8768 (tmtt) cc_final: 0.8367 (tptp) REVERT: A 256 ASN cc_start: 0.8416 (t0) cc_final: 0.8101 (t0) REVERT: A 315 ASP cc_start: 0.8514 (p0) cc_final: 0.8184 (p0) REVERT: A 350 ASP cc_start: 0.7645 (t0) cc_final: 0.7132 (m-30) REVERT: S 76 LYS cc_start: 0.8393 (mtpt) cc_final: 0.8119 (mtmm) REVERT: S 230 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8408 (ttt) REVERT: S 234 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7276 (mm-30) REVERT: R 63 MET cc_start: 0.8127 (tpp) cc_final: 0.7785 (mmp) REVERT: R 66 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7578 (pp30) REVERT: R 145 GLN cc_start: 0.8365 (tt0) cc_final: 0.8082 (mt0) REVERT: R 154 LYS cc_start: 0.8178 (mmtt) cc_final: 0.7865 (mtpp) REVERT: R 262 ASP cc_start: 0.7726 (t0) cc_final: 0.7512 (t0) outliers start: 9 outliers final: 5 residues processed: 152 average time/residue: 0.7417 time to fit residues: 118.2917 Evaluate side-chains 150 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 143 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain S residue 230 MET Chi-restraints excluded: chain R residue 66 GLN Chi-restraints excluded: chain R residue 158 VAL Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 270 ILE Chi-restraints excluded: chain R residue 315 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 64 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 95 optimal weight: 0.0000 chunk 79 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 94 optimal weight: 0.0980 chunk 19 optimal weight: 0.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN R 113 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.116898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.093812 restraints weight = 13426.665| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.53 r_work: 0.3305 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9035 Z= 0.107 Angle : 0.511 9.069 12258 Z= 0.263 Chirality : 0.041 0.148 1401 Planarity : 0.004 0.044 1534 Dihedral : 4.581 59.048 1284 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.16 % Allowed : 14.66 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.26), residues: 1119 helix: 2.89 (0.27), residues: 374 sheet: 0.71 (0.32), residues: 278 loop : -0.63 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 42 TYR 0.012 0.001 TYR S 190 PHE 0.010 0.001 PHE R 249 TRP 0.009 0.001 TRP B 211 HIS 0.004 0.001 HIS R 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 ( 9032) covalent geometry : angle 0.51109 / 0.26 (12252) SS BOND : bond 0.00448 / 0.23 ( 3) SS BOND : angle 0.90312 / 0.47 ( 6) hydrogen bonds : bond 0.04291 / 2.98 ( 416) hydrogen bonds : angle 4.13693 / 2.90 ( 1188) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: B 197 ARG cc_start: 0.8276 (mmt-90) cc_final: 0.8018 (mtt-85) REVERT: B 209 LYS cc_start: 0.8517 (mttp) cc_final: 0.8274 (mttm) REVERT: C 47 GLU cc_start: 0.7985 (mp0) cc_final: 0.7604 (mp0) REVERT: A 51 LYS cc_start: 0.8439 (pptt) cc_final: 0.8185 (pptt) REVERT: A 209 LYS cc_start: 0.8791 (tmtt) cc_final: 0.8388 (tptp) REVERT: A 248 LYS cc_start: 0.8293 (tppt) cc_final: 0.7889 (tppt) REVERT: A 256 ASN cc_start: 0.8439 (t0) cc_final: 0.8103 (t0) REVERT: A 261 ASP cc_start: 0.8682 (p0) cc_final: 0.8472 (p0) REVERT: A 315 ASP cc_start: 0.8512 (p0) cc_final: 0.8180 (p0) REVERT: A 350 ASP cc_start: 0.7591 (t0) cc_final: 0.7050 (m-30) REVERT: S 76 LYS cc_start: 0.8401 (mtpt) cc_final: 0.8121 (mtmm) REVERT: S 218 ARG cc_start: 0.7952 (ttp80) cc_final: 0.7337 (ttp80) REVERT: S 230 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8424 (ttt) REVERT: S 234 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7288 (mm-30) REVERT: R 63 MET cc_start: 0.8132 (tpp) cc_final: 0.7854 (mmm) REVERT: R 66 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7542 (pp30) REVERT: R 145 GLN cc_start: 0.8400 (tt0) cc_final: 0.8100 (mt0) REVERT: R 154 LYS cc_start: 0.8188 (mmtt) cc_final: 0.7881 (mtpp) REVERT: R 176 ASN cc_start: 0.8040 (t0) cc_final: 0.7712 (t0) REVERT: R 262 ASP cc_start: 0.7703 (t0) cc_final: 0.7492 (t0) outliers start: 11 outliers final: 4 residues processed: 153 average time/residue: 0.7401 time to fit residues: 118.9389 Evaluate side-chains 153 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 147 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain S residue 230 MET Chi-restraints excluded: chain R residue 66 GLN Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 270 ILE Chi-restraints excluded: chain R residue 315 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 37 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN R 113 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.114724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.092603 restraints weight = 13164.733| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.47 r_work: 0.3278 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9035 Z= 0.133 Angle : 0.545 9.201 12258 Z= 0.282 Chirality : 0.042 0.168 1401 Planarity : 0.004 0.045 1534 Dihedral : 4.677 59.381 1284 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.95 % Allowed : 16.14 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.26), residues: 1119 helix: 2.79 (0.27), residues: 375 sheet: 0.64 (0.32), residues: 281 loop : -0.61 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 42 TYR 0.012 0.001 TYR B 111 PHE 0.012 0.001 PHE R 249 TRP 0.009 0.001 TRP B 82 HIS 0.005 0.001 HIS R 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 9032) covalent geometry : angle 0.54489 / 0.28 (12252) SS BOND : bond 0.00510 / 0.26 ( 3) SS BOND : angle 1.18325 / 0.60 ( 6) hydrogen bonds : bond 0.04862 / 3.39 ( 416) hydrogen bonds : angle 4.18717 / 2.94 ( 1188) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 150 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: B 197 ARG cc_start: 0.8292 (mmt-90) cc_final: 0.8031 (mtt-85) REVERT: B 209 LYS cc_start: 0.8554 (mttp) cc_final: 0.8311 (mttm) REVERT: C 47 GLU cc_start: 0.7990 (mp0) cc_final: 0.7600 (mp0) REVERT: A 29 LYS cc_start: 0.8023 (tmmm) cc_final: 0.7694 (tmtt) REVERT: A 51 LYS cc_start: 0.8474 (pptt) cc_final: 0.8233 (pptt) REVERT: A 209 LYS cc_start: 0.8805 (tmtt) cc_final: 0.8400 (tptp) REVERT: A 248 LYS cc_start: 0.8312 (tppt) cc_final: 0.7911 (tppt) REVERT: A 256 ASN cc_start: 0.8454 (t0) cc_final: 0.8121 (t0) REVERT: A 315 ASP cc_start: 0.8499 (p0) cc_final: 0.8191 (p0) REVERT: A 350 ASP cc_start: 0.7698 (t0) cc_final: 0.7178 (m-30) REVERT: S 76 LYS cc_start: 0.8410 (mtpt) cc_final: 0.8135 (mtmm) REVERT: S 230 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8463 (ttt) REVERT: S 234 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7354 (mm-30) REVERT: R 63 MET cc_start: 0.8172 (tpp) cc_final: 0.7817 (mmp) REVERT: R 66 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7527 (pp30) REVERT: R 145 GLN cc_start: 0.8400 (tt0) cc_final: 0.8100 (mt0) REVERT: R 154 LYS cc_start: 0.8187 (mmtt) cc_final: 0.7870 (mtpp) REVERT: R 176 ASN cc_start: 0.8116 (t0) cc_final: 0.7797 (t0) REVERT: R 225 LYS cc_start: 0.8019 (ttmm) cc_final: 0.7484 (mtpt) REVERT: R 262 ASP cc_start: 0.7704 (t0) cc_final: 0.7502 (t0) REVERT: R 264 PHE cc_start: 0.7980 (m-10) cc_final: 0.7764 (m-80) outliers start: 9 outliers final: 6 residues processed: 154 average time/residue: 0.7701 time to fit residues: 124.4643 Evaluate side-chains 155 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 147 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain S residue 230 MET Chi-restraints excluded: chain R residue 66 GLN Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 270 ILE Chi-restraints excluded: chain R residue 315 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN R 113 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.114584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.092528 restraints weight = 13158.264| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.46 r_work: 0.3259 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9035 Z= 0.131 Angle : 0.545 9.491 12258 Z= 0.281 Chirality : 0.042 0.172 1401 Planarity : 0.004 0.045 1534 Dihedral : 4.695 59.325 1284 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.95 % Allowed : 16.56 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.26), residues: 1119 helix: 2.82 (0.27), residues: 373 sheet: 0.67 (0.32), residues: 279 loop : -0.64 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 42 TYR 0.013 0.001 TYR B 111 PHE 0.012 0.001 PHE R 249 TRP 0.009 0.001 TRP B 211 HIS 0.004 0.001 HIS R 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 9032) covalent geometry : angle 0.54453 / 0.28 (12252) SS BOND : bond 0.00493 / 0.25 ( 3) SS BOND : angle 1.05864 / 0.54 ( 6) hydrogen bonds : bond 0.04842 / 3.38 ( 416) hydrogen bonds : angle 4.20129 / 2.95 ( 1188) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 151 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: B 197 ARG cc_start: 0.8284 (mmt-90) cc_final: 0.8022 (mtt-85) REVERT: B 209 LYS cc_start: 0.8560 (mttp) cc_final: 0.8316 (mttm) REVERT: C 47 GLU cc_start: 0.7998 (mp0) cc_final: 0.7604 (mp0) REVERT: A 29 LYS cc_start: 0.8048 (tmmm) cc_final: 0.7758 (tptp) REVERT: A 209 LYS cc_start: 0.8835 (tmtt) cc_final: 0.8420 (tptp) REVERT: A 256 ASN cc_start: 0.8473 (t0) cc_final: 0.8137 (t0) REVERT: A 315 ASP cc_start: 0.8496 (p0) cc_final: 0.8192 (p0) REVERT: A 350 ASP cc_start: 0.7717 (t0) cc_final: 0.7151 (m-30) REVERT: S 76 LYS cc_start: 0.8429 (mtpt) cc_final: 0.8165 (mtmm) REVERT: S 234 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7336 (mm-30) REVERT: R 63 MET cc_start: 0.8161 (tpp) cc_final: 0.7811 (mmp) REVERT: R 66 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7513 (pp30) REVERT: R 145 GLN cc_start: 0.8383 (tt0) cc_final: 0.8085 (mt0) REVERT: R 154 LYS cc_start: 0.8195 (mmtt) cc_final: 0.7883 (mtpp) REVERT: R 176 ASN cc_start: 0.8107 (t0) cc_final: 0.7772 (t0) REVERT: R 225 LYS cc_start: 0.8027 (ttmm) cc_final: 0.7509 (mtpt) outliers start: 9 outliers final: 7 residues processed: 155 average time/residue: 0.7276 time to fit residues: 118.2688 Evaluate side-chains 155 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 147 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain R residue 66 GLN Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 270 ILE Chi-restraints excluded: chain R residue 315 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 14 optimal weight: 0.9990 chunk 2 optimal weight: 0.0050 chunk 66 optimal weight: 1.9990 chunk 96 optimal weight: 0.2980 chunk 37 optimal weight: 0.2980 chunk 17 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 58 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN R 113 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.117278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.094370 restraints weight = 13377.675| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.51 r_work: 0.3313 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9035 Z= 0.106 Angle : 0.534 10.215 12258 Z= 0.275 Chirality : 0.041 0.145 1401 Planarity : 0.004 0.044 1534 Dihedral : 4.533 59.239 1284 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.63 % Allowed : 16.67 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.26), residues: 1119 helix: 2.92 (0.27), residues: 371 sheet: 0.69 (0.32), residues: 281 loop : -0.62 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 42 TYR 0.012 0.001 TYR B 111 PHE 0.008 0.001 PHE R 249 TRP 0.009 0.001 TRP B 211 HIS 0.003 0.000 HIS R 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 ( 9032) covalent geometry : angle 0.53420 / 0.27 (12252) SS BOND : bond 0.00420 / 0.21 ( 3) SS BOND : angle 0.84209 / 0.44 ( 6) hydrogen bonds : bond 0.04074 / 2.83 ( 416) hydrogen bonds : angle 4.10876 / 2.89 ( 1188) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 148 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: B 197 ARG cc_start: 0.8283 (mmt-90) cc_final: 0.8023 (mtt-85) REVERT: B 209 LYS cc_start: 0.8512 (mttp) cc_final: 0.8272 (mttm) REVERT: B 258 ASP cc_start: 0.8138 (t0) cc_final: 0.7816 (t0) REVERT: B 262 MET cc_start: 0.8860 (ttp) cc_final: 0.8605 (ttp) REVERT: C 47 GLU cc_start: 0.7944 (mp0) cc_final: 0.7560 (mp0) REVERT: A 29 LYS cc_start: 0.7963 (tmmm) cc_final: 0.7686 (tptp) REVERT: A 51 LYS cc_start: 0.8487 (pptt) cc_final: 0.8239 (pptt) REVERT: A 209 LYS cc_start: 0.8811 (tmtt) cc_final: 0.8478 (tptt) REVERT: A 248 LYS cc_start: 0.8272 (tppt) cc_final: 0.7880 (tppt) REVERT: A 256 ASN cc_start: 0.8428 (t0) cc_final: 0.8094 (t0) REVERT: A 315 ASP cc_start: 0.8457 (p0) cc_final: 0.8133 (p0) REVERT: S 76 LYS cc_start: 0.8408 (mtpt) cc_final: 0.8127 (mtmm) REVERT: S 218 ARG cc_start: 0.7960 (ttp80) cc_final: 0.7297 (ttp80) REVERT: S 234 GLU cc_start: 0.7519 (mm-30) cc_final: 0.7282 (mm-30) REVERT: R 63 MET cc_start: 0.8074 (tpp) cc_final: 0.7707 (mmp) REVERT: R 66 GLN cc_start: 0.7981 (pt0) cc_final: 0.7517 (pp30) REVERT: R 145 GLN cc_start: 0.8386 (tt0) cc_final: 0.8078 (mt0) REVERT: R 154 LYS cc_start: 0.8216 (mmtt) cc_final: 0.7916 (mtpp) REVERT: R 176 ASN cc_start: 0.8100 (t0) cc_final: 0.7776 (t0) REVERT: R 183 ARG cc_start: 0.7937 (mmm160) cc_final: 0.7710 (ttm-80) REVERT: R 225 LYS cc_start: 0.7973 (ttmm) cc_final: 0.7476 (mtpt) outliers start: 6 outliers final: 6 residues processed: 152 average time/residue: 0.7502 time to fit residues: 119.7104 Evaluate side-chains 150 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 144 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 270 ILE Chi-restraints excluded: chain R residue 315 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 106 optimal weight: 0.0070 chunk 95 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 37 optimal weight: 0.3980 chunk 109 optimal weight: 0.5980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN R 113 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.116488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.093531 restraints weight = 13299.080| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.50 r_work: 0.3281 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9035 Z= 0.117 Angle : 0.543 10.541 12258 Z= 0.279 Chirality : 0.041 0.156 1401 Planarity : 0.004 0.045 1534 Dihedral : 4.529 59.321 1284 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.63 % Allowed : 16.88 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.26), residues: 1119 helix: 2.90 (0.27), residues: 371 sheet: 0.68 (0.32), residues: 281 loop : -0.61 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 42 TYR 0.014 0.001 TYR B 111 PHE 0.010 0.001 PHE R 249 TRP 0.008 0.001 TRP B 211 HIS 0.004 0.001 HIS R 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 9032) covalent geometry : angle 0.54295 / 0.28 (12252) SS BOND : bond 0.00477 / 0.24 ( 3) SS BOND : angle 0.99751 / 0.51 ( 6) hydrogen bonds : bond 0.04408 / 3.07 ( 416) hydrogen bonds : angle 4.11708 / 2.89 ( 1188) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3767.88 seconds wall clock time: 64 minutes 46.84 seconds (3886.84 seconds total)