Starting phenix.real_space_refine on Thu Jul 2 22:26:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rpo_24618/07_2026/7rpo_24618.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rpo_24618/07_2026/7rpo_24618.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rpo_24618/07_2026/7rpo_24618.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rpo_24618/07_2026/7rpo_24618.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7rpo_24618/07_2026/7rpo_24618.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rpo_24618/07_2026/7rpo_24618.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rpo_24618/07_2026/7rpo_24618.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rpo_24618/07_2026/7rpo_24618.map" } resolution = 4.16 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= 0.001 sd= 0.026 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: 6 Type Number sf(0) Gaussians Mn 4 7.51 5 P 63 5.49 5 S 25 5.16 5 C 6571 2.51 5 N 1753 2.21 5 O 2186 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10602 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1953 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 8, 'TRANS': 243} Chain: "B" Number of atoms: 1922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1922 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 9, 'TRANS': 233} Chain: "C" Number of atoms: 1941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1941 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 5, 'TRANS': 239} Chain: "X" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 408 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 229 Classifications: {'DNA': 11} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 10} Chain: "Z" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 634 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "E" Number of atoms: 3489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3489 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 13, 'TRANS': 425} Chain: "X" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 24 Unusual residues: {' MN': 2} Classifications: {'RNA': 1, 'undetermined': 2} Modifications used: {'rna2p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 1.78, per 1000 atoms: 0.17 Number of scatterers: 10602 At special positions: 0 Unit cell: (118.5, 109.5, 124.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 4 24.99 S 25 16.00 P 63 15.00 O 2186 8.00 N 1753 7.00 C 6571 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 240.6 milliseconds 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2218 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 9 sheets defined 27.8% alpha, 21.5% beta 30 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 8 through 21 removed outlier: 3.600A pdb=" N PHE A 12 " --> pdb=" O ASN A 8 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 79 removed outlier: 3.929A pdb=" N ILE A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 150 removed outlier: 3.599A pdb=" N VAL A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 165 removed outlier: 3.960A pdb=" N ASP A 164 " --> pdb=" O THR A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 211 removed outlier: 3.538A pdb=" N GLY A 211 " --> pdb=" O ASP A 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 20 Processing helix chain 'B' and resid 73 through 81 removed outlier: 3.572A pdb=" N ASN B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 147 through 151 removed outlier: 3.896A pdb=" N LEU B 150 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLY B 151 " --> pdb=" O SER B 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 147 through 151' Processing helix chain 'B' and resid 199 through 204 Processing helix chain 'B' and resid 205 through 207 No H-bonds generated for 'chain 'B' and resid 205 through 207' Processing helix chain 'C' and resid 9 through 19 removed outlier: 3.935A pdb=" N ASP C 13 " --> pdb=" O ARG C 9 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE C 14 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ILE C 15 " --> pdb=" O LEU C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 77 Processing helix chain 'C' and resid 136 through 147 removed outlier: 3.843A pdb=" N LYS C 140 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER C 141 " --> pdb=" O ASP C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 205 removed outlier: 3.838A pdb=" N VAL C 204 " --> pdb=" O LEU C 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 12 removed outlier: 3.889A pdb=" N LYS E 12 " --> pdb=" O GLU E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 33 removed outlier: 3.778A pdb=" N THR E 23 " --> pdb=" O ARG E 19 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ALA E 24 " --> pdb=" O LEU E 20 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA E 27 " --> pdb=" O THR E 23 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASP E 28 " --> pdb=" O ALA E 24 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU E 29 " --> pdb=" O LEU E 25 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU E 30 " --> pdb=" O LEU E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 47 removed outlier: 3.893A pdb=" N GLN E 46 " --> pdb=" O VAL E 42 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY E 47 " --> pdb=" O TYR E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 75 removed outlier: 3.649A pdb=" N LEU E 66 " --> pdb=" O GLY E 62 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE E 67 " --> pdb=" O GLU E 63 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS E 68 " --> pdb=" O LYS E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 88 removed outlier: 3.727A pdb=" N THR E 87 " --> pdb=" O ASN E 83 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE E 88 " --> pdb=" O LEU E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 97 removed outlier: 4.004A pdb=" N ARG E 97 " --> pdb=" O GLU E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 100 No H-bonds generated for 'chain 'E' and resid 98 through 100' Processing helix chain 'E' and resid 120 through 134 removed outlier: 3.583A pdb=" N LEU E 133 " --> pdb=" O SER E 129 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 153 removed outlier: 3.931A pdb=" N LEU E 142 " --> pdb=" O GLY E 138 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG E 145 " --> pdb=" O ASP E 141 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU E 146 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY E 149 " --> pdb=" O ARG E 145 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LEU E 150 " --> pdb=" O LEU E 146 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU E 151 " --> pdb=" O LEU E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 168 removed outlier: 3.924A pdb=" N ARG E 164 " --> pdb=" O LYS E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 187 Processing helix chain 'E' and resid 190 through 192 No H-bonds generated for 'chain 'E' and resid 190 through 192' Processing helix chain 'E' and resid 193 through 204 removed outlier: 4.138A pdb=" N ILE E 197 " --> pdb=" O ALA E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 218 Processing helix chain 'E' and resid 246 through 252 Processing helix chain 'E' and resid 290 through 293 removed outlier: 3.589A pdb=" N VAL E 293 " --> pdb=" O PRO E 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 290 through 293' Processing helix chain 'E' and resid 294 through 299 Processing helix chain 'E' and resid 323 through 328 Processing helix chain 'E' and resid 339 through 343 Processing helix chain 'E' and resid 366 through 373 Processing helix chain 'E' and resid 392 through 406 removed outlier: 3.582A pdb=" N LYS E 397 " --> pdb=" O VAL E 393 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N SER E 398 " --> pdb=" O GLU E 394 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG E 402 " --> pdb=" O SER E 398 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 removed outlier: 3.520A pdb=" N ILE A 101 " --> pdb=" O GLU A 90 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 100 " --> pdb=" O ILE A 113 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS A 110 " --> pdb=" O GLU C 175 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU C 175 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 71 removed outlier: 3.816A pdb=" N THR A 66 " --> pdb=" O PHE A 30 " (cutoff:3.500A) removed outlier: 10.054A pdb=" N SER A 25 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N LEU A 40 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N ILE A 27 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ARG A 38 " --> pdb=" O ILE A 27 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN A 29 " --> pdb=" O PHE A 36 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE A 36 " --> pdb=" O ASN A 29 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR A 31 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE A 35 " --> pdb=" O ILE A 52 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET A 50 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N HIS A 39 " --> pdb=" O ALA A 48 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA A 48 " --> pdb=" O HIS A 39 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG A 51 " --> pdb=" O HIS A 240 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET A 241 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL A 233 " --> pdb=" O MET A 241 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE A 231 " --> pdb=" O PHE A 243 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN A 135 " --> pdb=" O SER A 191 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER A 191 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A 137 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU A 189 " --> pdb=" O THR A 137 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 181 removed outlier: 3.747A pdb=" N TYR A 177 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA A 170 " --> pdb=" O TYR A 177 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE A 168 " --> pdb=" O ALA A 179 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE A 166 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A 169 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG A 158 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLY A 171 " --> pdb=" O GLU A 156 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLU A 156 " --> pdb=" O GLY A 171 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 61 removed outlier: 5.231A pdb=" N GLY B 59 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N LYS B 5 " --> pdb=" O GLY B 59 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER B 92 " --> pdb=" O THR B 99 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR B 99 " --> pdb=" O SER B 92 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 68 through 72 removed outlier: 3.948A pdb=" N PHE B 71 " --> pdb=" O ALA B 26 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA B 26 " --> pdb=" O PHE B 71 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N GLU B 25 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE B 40 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ASN B 27 " --> pdb=" O SER B 38 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N SER B 38 " --> pdb=" O ASN B 27 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG B 36 " --> pdb=" O ILE B 29 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE B 35 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU B 48 " --> pdb=" O GLY B 39 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP B 49 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR B 236 " --> pdb=" O PHE B 51 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG B 228 " --> pdb=" O GLU B 216 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N SER B 214 " --> pdb=" O LYS B 230 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 194 through 197 removed outlier: 3.839A pdb=" N LEU B 163 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 178 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR B 173 " --> pdb=" O ASN C 110 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS B 175 " --> pdb=" O GLU C 108 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU C 108 " --> pdb=" O LYS B 175 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 66 through 70 removed outlier: 3.714A pdb=" N PHE C 67 " --> pdb=" O LEU C 27 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE C 69 " --> pdb=" O ALA C 25 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA C 25 " --> pdb=" O PHE C 69 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N GLU C 24 " --> pdb=" O LEU C 39 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU C 39 " --> pdb=" O GLU C 24 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N VAL C 26 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N VAL C 37 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA C 38 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE C 47 " --> pdb=" O ALA C 38 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU C 46 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER C 48 " --> pdb=" O THR C 237 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS C 235 " --> pdb=" O ASN C 50 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL C 236 " --> pdb=" O PHE C 228 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE C 228 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR C 238 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU C 226 " --> pdb=" O TYR C 238 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 388 through 389 removed outlier: 3.956A pdb=" N GLY E 410 " --> pdb=" O LYS E 260 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL E 411 " --> pdb=" O LEU E 434 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU E 434 " --> pdb=" O VAL E 411 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE E 432 " --> pdb=" O VAL E 413 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 275 through 278 removed outlier: 3.626A pdb=" N GLY E 309 " --> pdb=" O ALA E 266 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS E 270 " --> pdb=" O PHE E 305 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ILE E 306 " --> pdb=" O LEU E 352 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LEU E 352 " --> pdb=" O ILE E 306 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N GLU E 308 " --> pdb=" O PHE E 350 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL E 312 " --> pdb=" O ASN E 346 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN E 346 " --> pdb=" O VAL E 312 " (cutoff:3.500A) 309 hydrogen bonds defined for protein. 849 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 77 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 1.28 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2890 1.33 - 1.45: 1884 1.45 - 1.57: 5953 1.57 - 1.69: 122 1.69 - 1.80: 50 Bond restraints: 10899 Sorted by residual: bond pdb=" C3' DG Y 9 " pdb=" C2' DG Y 9 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DT X 10 " pdb=" C2' DT X 10 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DG Z 33 " pdb=" C2' DG Z 33 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 bond pdb=" C3' DC Y 7 " pdb=" C2' DC Y 7 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.94e+00 bond pdb=" C3' DC Z 28 " pdb=" C2' DC Z 28 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.86e+00 ... (remaining 10894 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 14485 1.45 - 2.91: 433 2.91 - 4.36: 35 4.36 - 5.81: 8 5.81 - 7.27: 2 Bond angle restraints: 14963 Sorted by residual: angle pdb=" C LEU A 249 " pdb=" CA LEU A 249 " pdb=" CB LEU A 249 " ideal model delta sigma weight residual 117.23 109.96 7.27 1.36e+00 5.41e-01 2.86e+01 angle pdb=" N3 DT X 10 " pdb=" C4 DT X 10 " pdb=" O4 DT X 10 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.01e+01 angle pdb=" N3 DT Z 32 " pdb=" C4 DT Z 32 " pdb=" O4 DT Z 32 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 1.99e+01 angle pdb=" N3 DT Z 18 " pdb=" C4 DT Z 18 " pdb=" O4 DT Z 18 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.89e+01 angle pdb=" N3 DT X 23 " pdb=" C4 DT X 23 " pdb=" O4 DT X 23 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 ... (remaining 14958 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.40: 6078 30.40 - 60.80: 380 60.80 - 91.19: 4 91.19 - 121.59: 0 121.59 - 151.99: 5 Dihedral angle restraints: 6467 sinusoidal: 3035 harmonic: 3432 Sorted by residual: dihedral pdb=" C4' DT Z 30 " pdb=" C3' DT Z 30 " pdb=" O3' DT Z 30 " pdb=" P DC Z 31 " ideal model delta sinusoidal sigma weight residual 220.00 68.01 151.99 1 3.50e+01 8.16e-04 1.48e+01 dihedral pdb=" C4' DA Z 22 " pdb=" C3' DA Z 22 " pdb=" O3' DA Z 22 " pdb=" P DC Z 23 " ideal model delta sinusoidal sigma weight residual 220.00 70.14 149.86 1 3.50e+01 8.16e-04 1.46e+01 dihedral pdb=" C4' DC Z 26 " pdb=" C3' DC Z 26 " pdb=" O3' DC Z 26 " pdb=" P DG Z 27 " ideal model delta sinusoidal sigma weight residual 220.00 71.90 148.10 1 3.50e+01 8.16e-04 1.45e+01 ... (remaining 6464 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1034 0.030 - 0.060: 429 0.060 - 0.089: 128 0.089 - 0.119: 110 0.119 - 0.149: 22 Chirality restraints: 1723 Sorted by residual: chirality pdb=" C3' AMP E 701 " pdb=" C2' AMP E 701 " pdb=" C4' AMP E 701 " pdb=" O3' AMP E 701 " both_signs ideal model delta sigma weight residual False -2.74 -2.60 -0.15 2.00e-01 2.50e+01 5.53e-01 chirality pdb=" CA ILE E 306 " pdb=" N ILE E 306 " pdb=" C ILE E 306 " pdb=" CB ILE E 306 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.18e-01 chirality pdb=" C3' DA Z 22 " pdb=" C4' DA Z 22 " pdb=" O3' DA Z 22 " pdb=" C2' DA Z 22 " both_signs ideal model delta sigma weight residual False -2.73 -2.60 -0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 1720 not shown) Planarity restraints: 1683 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 93 " 0.022 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO C 94 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO C 94 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 94 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 121 " 0.022 5.00e-02 4.00e+02 3.34e-02 1.78e+00 pdb=" N PRO C 122 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO C 122 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 122 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 227 " -0.021 5.00e-02 4.00e+02 3.21e-02 1.65e+00 pdb=" N PRO A 228 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 228 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 228 " -0.018 5.00e-02 4.00e+02 ... (remaining 1680 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 27 2.39 - 3.02: 5691 3.02 - 3.64: 14979 3.64 - 4.27: 21306 4.27 - 4.90: 35049 Nonbonded interactions: 77052 Sorted by model distance: nonbonded pdb=" O1P AMP E 701 " pdb="MN MN E 703 " model vdw 1.759 2.320 nonbonded pdb=" O GLY E 60 " pdb="MN MN X 101 " model vdw 1.776 2.320 nonbonded pdb=" OE2 GLU E 409 " pdb="MN MN E 703 " model vdw 1.815 2.320 nonbonded pdb=" O3' DG X 20 " pdb="MN MN X 101 " model vdw 2.187 2.320 nonbonded pdb=" OG SER C 211 " pdb=" O ASN C 229 " model vdw 2.192 3.040 ... (remaining 77047 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.770 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10900 Z= 0.273 Angle : 0.560 7.267 14963 Z= 0.404 Chirality : 0.043 0.149 1723 Planarity : 0.003 0.034 1683 Dihedral : 16.976 151.990 4249 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 1.64 % Allowed : 9.76 % Favored : 88.60 % 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: -2.01 (0.25), residues: 1171 helix: -0.03 (0.33), residues: 294 sheet: -0.27 (0.32), residues: 303 loop : -2.74 (0.23), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 330 TYR 0.008 0.001 TYR A 177 PHE 0.010 0.001 PHE C 228 TRP 0.004 0.001 TRP E 50 HIS 0.002 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.27 (10899) covalent geometry : angle 0.55961 / 0.40 (14963) hydrogen bonds : bond 0.24462 / 16.12 ( 386) hydrogen bonds : angle 8.23261 / 5.67 ( 1003) Misc. bond : bond 0.05146 / 2.71 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 397 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 VAL cc_start: 0.7540 (t) cc_final: 0.7181 (m) REVERT: A 24 ASP cc_start: 0.5986 (t70) cc_final: 0.5304 (t0) REVERT: A 28 LEU cc_start: 0.7221 (mt) cc_final: 0.6808 (mp) REVERT: A 39 HIS cc_start: 0.7684 (t-90) cc_final: 0.7404 (t-90) REVERT: A 47 MET cc_start: 0.7688 (ttt) cc_final: 0.7285 (ttt) REVERT: A 57 LEU cc_start: 0.8144 (mt) cc_final: 0.7881 (mt) REVERT: A 59 GLU cc_start: 0.8294 (tp30) cc_final: 0.7918 (tp30) REVERT: A 77 LYS cc_start: 0.8708 (pttt) cc_final: 0.8505 (ptpt) REVERT: A 79 LEU cc_start: 0.7529 (mt) cc_final: 0.6939 (mt) REVERT: A 99 LYS cc_start: 0.8536 (ttmt) cc_final: 0.8157 (mtpp) REVERT: A 101 ILE cc_start: 0.7816 (mt) cc_final: 0.7476 (mp) REVERT: A 110 LYS cc_start: 0.7390 (ttmt) cc_final: 0.7137 (ttmm) REVERT: A 136 PHE cc_start: 0.7173 (p90) cc_final: 0.6649 (p90) REVERT: A 156 GLU cc_start: 0.8103 (mp0) cc_final: 0.7807 (mp0) REVERT: A 159 ILE cc_start: 0.8047 (mt) cc_final: 0.7839 (mm) REVERT: A 190 LEU cc_start: 0.7604 (tp) cc_final: 0.7360 (mt) REVERT: A 212 LEU cc_start: 0.7787 (mt) cc_final: 0.7577 (tp) REVERT: A 213 ARG cc_start: 0.7061 (mtt90) cc_final: 0.6718 (mtt90) REVERT: A 221 VAL cc_start: 0.8086 (t) cc_final: 0.7727 (p) REVERT: A 231 ILE cc_start: 0.8109 (mt) cc_final: 0.7564 (tt) REVERT: A 233 VAL cc_start: 0.7705 (OUTLIER) cc_final: 0.7489 (p) REVERT: B 30 VAL cc_start: 0.8305 (t) cc_final: 0.8098 (t) REVERT: B 78 ASP cc_start: 0.6720 (m-30) cc_final: 0.6407 (m-30) REVERT: B 81 LYS cc_start: 0.7912 (ttmm) cc_final: 0.7663 (ttpp) REVERT: B 156 ILE cc_start: 0.8086 (mm) cc_final: 0.7777 (mt) REVERT: B 162 LYS cc_start: 0.8349 (mttp) cc_final: 0.7958 (mmmt) REVERT: B 168 ILE cc_start: 0.8419 (tt) cc_final: 0.8152 (tt) REVERT: B 184 THR cc_start: 0.6611 (OUTLIER) cc_final: 0.6388 (p) REVERT: B 200 GLU cc_start: 0.7219 (tm-30) cc_final: 0.6910 (tm-30) REVERT: C 2 LYS cc_start: 0.7911 (mttt) cc_final: 0.7638 (tppt) REVERT: C 3 VAL cc_start: 0.8648 (t) cc_final: 0.8389 (p) REVERT: C 6 ASP cc_start: 0.7991 (t0) cc_final: 0.7649 (t0) REVERT: C 7 ASP cc_start: 0.7609 (t70) cc_final: 0.7132 (t0) REVERT: C 23 ASP cc_start: 0.8016 (m-30) cc_final: 0.7815 (m-30) REVERT: C 30 LYS cc_start: 0.8021 (mptt) cc_final: 0.7562 (mmmm) REVERT: C 31 GLN cc_start: 0.8039 (mp10) cc_final: 0.7804 (mt0) REVERT: C 75 MET cc_start: 0.6836 (tmm) cc_final: 0.6633 (tpp) REVERT: C 139 PHE cc_start: 0.8027 (t80) cc_final: 0.7575 (t80) REVERT: C 140 LYS cc_start: 0.8082 (ttpt) cc_final: 0.7502 (tttm) REVERT: C 167 GLU cc_start: 0.7801 (pp20) cc_final: 0.7390 (pp20) REVERT: C 191 GLU cc_start: 0.7005 (mp0) cc_final: 0.6749 (mp0) REVERT: C 205 LEU cc_start: 0.8461 (mt) cc_final: 0.7856 (tp) REVERT: C 229 ASN cc_start: 0.7470 (t0) cc_final: 0.7201 (t0) REVERT: E 1 MET cc_start: 0.7067 (mmm) cc_final: 0.6704 (mmm) REVERT: E 2 GLU cc_start: 0.7234 (pm20) cc_final: 0.7029 (pm20) REVERT: E 11 ASP cc_start: 0.6648 (t70) cc_final: 0.6334 (t0) REVERT: E 13 LEU cc_start: 0.7464 (tp) cc_final: 0.7235 (tp) REVERT: E 36 THR cc_start: 0.7292 (p) cc_final: 0.6691 (p) REVERT: E 46 GLN cc_start: 0.7562 (tm-30) cc_final: 0.7351 (tm-30) REVERT: E 48 LYS cc_start: 0.8097 (mmtm) cc_final: 0.7854 (mmmm) REVERT: E 49 LEU cc_start: 0.7264 (mp) cc_final: 0.7025 (mt) REVERT: E 67 ILE cc_start: 0.8020 (mt) cc_final: 0.7668 (pt) REVERT: E 86 LYS cc_start: 0.7898 (tptp) cc_final: 0.7462 (mmmm) REVERT: E 101 LYS cc_start: 0.8699 (pttm) cc_final: 0.8184 (pttm) REVERT: E 111 LEU cc_start: 0.6453 (OUTLIER) cc_final: 0.6244 (pp) REVERT: E 126 SER cc_start: 0.8510 (t) cc_final: 0.7909 (p) REVERT: E 169 ARG cc_start: 0.7185 (ptt180) cc_final: 0.6933 (ptt90) REVERT: E 174 ILE cc_start: 0.7888 (mm) cc_final: 0.7595 (tt) REVERT: E 197 ILE cc_start: 0.7992 (mm) cc_final: 0.7692 (tp) REVERT: E 203 LEU cc_start: 0.7947 (mt) cc_final: 0.7669 (mt) REVERT: E 206 ASP cc_start: 0.7730 (p0) cc_final: 0.7526 (p0) REVERT: E 212 LYS cc_start: 0.7262 (pttm) cc_final: 0.6989 (pttp) REVERT: E 236 MET cc_start: 0.7580 (ptp) cc_final: 0.7362 (ptp) REVERT: E 239 GLU cc_start: 0.7244 (tp30) cc_final: 0.6136 (mp0) REVERT: E 291 ASP cc_start: 0.7755 (p0) cc_final: 0.7513 (p0) REVERT: E 321 MET cc_start: 0.6543 (mmm) cc_final: 0.5649 (mmm) REVERT: E 325 GLN cc_start: 0.7251 (mm-40) cc_final: 0.6995 (tp-100) REVERT: E 326 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7435 (tp30) REVERT: E 328 MET cc_start: 0.7739 (mtm) cc_final: 0.7095 (mtm) REVERT: E 336 ILE cc_start: 0.7362 (mt) cc_final: 0.6787 (mm) REVERT: E 360 TYR cc_start: 0.7426 (m-80) cc_final: 0.6726 (m-80) REVERT: E 373 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7817 (mm-30) REVERT: E 397 LYS cc_start: 0.7841 (mmmt) cc_final: 0.7605 (mmtp) REVERT: E 434 LEU cc_start: 0.8334 (tp) cc_final: 0.7901 (pt) outliers start: 17 outliers final: 4 residues processed: 410 average time/residue: 0.0975 time to fit residues: 53.5756 Evaluate side-chains 350 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 343 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.0670 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 0.4980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 117 optimal weight: 4.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 135 ASN B 116 GLN E 228 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.136893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.115393 restraints weight = 19078.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.118084 restraints weight = 11944.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.119946 restraints weight = 8426.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.121247 restraints weight = 6498.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.122164 restraints weight = 5385.553| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3575 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3575 r_free = 0.3575 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3570 r_free = 0.3570 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3570 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10900 Z= 0.157 Angle : 0.634 6.946 14963 Z= 0.356 Chirality : 0.046 0.227 1723 Planarity : 0.004 0.059 1683 Dihedral : 20.928 155.903 1931 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 0.19 % Allowed : 2.42 % Favored : 97.39 % 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: -2.04 (0.24), residues: 1171 helix: -0.17 (0.32), residues: 295 sheet: 0.19 (0.33), residues: 301 loop : -3.00 (0.22), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 9 TYR 0.018 0.002 TYR E 259 PHE 0.036 0.002 PHE B 60 TRP 0.010 0.002 TRP E 50 HIS 0.003 0.001 HIS C 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.16 (10899) covalent geometry : angle 0.63412 / 0.36 (14963) hydrogen bonds : bond 0.07055 / 4.60 ( 386) hydrogen bonds : angle 6.60640 / 4.48 ( 1003) Misc. bond : bond 0.00805 / 0.42 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 357 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 PHE cc_start: 0.6524 (t80) cc_final: 0.6213 (t80) REVERT: A 24 ASP cc_start: 0.5605 (t70) cc_final: 0.5259 (t0) REVERT: A 57 LEU cc_start: 0.8215 (mt) cc_final: 0.7886 (mt) REVERT: A 59 GLU cc_start: 0.8291 (tp30) cc_final: 0.8085 (tp30) REVERT: A 69 LYS cc_start: 0.7140 (pttp) cc_final: 0.6919 (mmtm) REVERT: A 70 LEU cc_start: 0.7457 (mt) cc_final: 0.7124 (mt) REVERT: A 99 LYS cc_start: 0.8330 (ttmt) cc_final: 0.8018 (mtpp) REVERT: A 110 LYS cc_start: 0.7223 (ttmt) cc_final: 0.6984 (ttmm) REVERT: A 116 LYS cc_start: 0.7975 (mtmm) cc_final: 0.7553 (tppt) REVERT: A 165 LYS cc_start: 0.7237 (mtmm) cc_final: 0.6998 (mtmm) REVERT: A 212 LEU cc_start: 0.7722 (mt) cc_final: 0.7406 (tp) REVERT: A 213 ARG cc_start: 0.6873 (mtt90) cc_final: 0.6539 (mtt90) REVERT: A 220 MET cc_start: 0.7432 (ttt) cc_final: 0.7041 (tmm) REVERT: B 8 ASP cc_start: 0.6342 (t70) cc_final: 0.6103 (t0) REVERT: B 21 ASP cc_start: 0.7429 (t0) cc_final: 0.6740 (t0) REVERT: B 33 GLU cc_start: 0.7580 (pm20) cc_final: 0.7297 (pm20) REVERT: B 52 LEU cc_start: 0.8178 (mt) cc_final: 0.7977 (mt) REVERT: B 62 VAL cc_start: 0.6114 (m) cc_final: 0.5906 (m) REVERT: B 132 LYS cc_start: 0.8367 (ttmt) cc_final: 0.8051 (ttmm) REVERT: B 159 LYS cc_start: 0.7810 (ttpp) cc_final: 0.7555 (ttmm) REVERT: B 195 SER cc_start: 0.6891 (t) cc_final: 0.6429 (p) REVERT: C 3 VAL cc_start: 0.8588 (t) cc_final: 0.8213 (p) REVERT: C 6 ASP cc_start: 0.7575 (t0) cc_final: 0.7375 (t0) REVERT: C 7 ASP cc_start: 0.7671 (t70) cc_final: 0.7089 (t0) REVERT: C 30 LYS cc_start: 0.7816 (mptt) cc_final: 0.7588 (mmmm) REVERT: C 73 TYR cc_start: 0.6472 (t80) cc_final: 0.6261 (t80) REVERT: C 75 MET cc_start: 0.6810 (tmm) cc_final: 0.6548 (tpp) REVERT: C 85 GLU cc_start: 0.7352 (mp0) cc_final: 0.7140 (mp0) REVERT: C 140 LYS cc_start: 0.7990 (ttpt) cc_final: 0.7494 (tttm) REVERT: C 165 LYS cc_start: 0.7848 (pttp) cc_final: 0.7033 (ptpt) REVERT: C 167 GLU cc_start: 0.7642 (pp20) cc_final: 0.7309 (pp20) REVERT: C 190 LYS cc_start: 0.8295 (mttt) cc_final: 0.7986 (mttt) REVERT: C 205 LEU cc_start: 0.8227 (mt) cc_final: 0.7890 (tp) REVERT: C 209 LYS cc_start: 0.8064 (ptmm) cc_final: 0.7588 (ptmm) REVERT: C 215 LYS cc_start: 0.8195 (ttmt) cc_final: 0.7810 (ttmm) REVERT: C 229 ASN cc_start: 0.7569 (t0) cc_final: 0.7301 (t0) REVERT: C 230 MET cc_start: 0.5273 (mtm) cc_final: 0.4888 (mtm) REVERT: E 11 ASP cc_start: 0.6608 (t70) cc_final: 0.6372 (t0) REVERT: E 46 GLN cc_start: 0.7689 (tm-30) cc_final: 0.7381 (tm-30) REVERT: E 101 LYS cc_start: 0.8622 (pttm) cc_final: 0.8199 (pttm) REVERT: E 117 GLU cc_start: 0.5084 (mp0) cc_final: 0.4688 (mp0) REVERT: E 126 SER cc_start: 0.8387 (t) cc_final: 0.7914 (p) REVERT: E 127 THR cc_start: 0.8049 (m) cc_final: 0.7642 (p) REVERT: E 135 THR cc_start: 0.7796 (m) cc_final: 0.7488 (p) REVERT: E 174 ILE cc_start: 0.7946 (mm) cc_final: 0.7596 (tt) REVERT: E 197 ILE cc_start: 0.8026 (mm) cc_final: 0.7789 (tp) REVERT: E 223 LYS cc_start: 0.7675 (mmtp) cc_final: 0.7387 (mmtm) REVERT: E 239 GLU cc_start: 0.7457 (tp30) cc_final: 0.6309 (mp0) REVERT: E 274 LYS cc_start: 0.7022 (mppt) cc_final: 0.6672 (mppt) REVERT: E 290 PRO cc_start: 0.7973 (Cg_endo) cc_final: 0.7598 (Cg_exo) REVERT: E 325 GLN cc_start: 0.7171 (mm-40) cc_final: 0.6784 (tp-100) REVERT: E 326 GLU cc_start: 0.7519 (tp30) cc_final: 0.6848 (tp30) REVERT: E 328 MET cc_start: 0.7506 (mtm) cc_final: 0.7107 (mtm) REVERT: E 329 HIS cc_start: 0.7251 (m90) cc_final: 0.6343 (m-70) REVERT: E 336 ILE cc_start: 0.7261 (mt) cc_final: 0.6985 (mm) REVERT: E 360 TYR cc_start: 0.7387 (m-80) cc_final: 0.6644 (m-80) REVERT: E 363 LYS cc_start: 0.8472 (mmtt) cc_final: 0.8204 (mmtp) REVERT: E 397 LYS cc_start: 0.7858 (mmmt) cc_final: 0.7620 (mmtp) REVERT: E 434 LEU cc_start: 0.8439 (tp) cc_final: 0.7986 (pt) outliers start: 2 outliers final: 0 residues processed: 358 average time/residue: 0.1060 time to fit residues: 50.4142 Evaluate side-chains 326 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 87 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 106 optimal weight: 0.3980 chunk 86 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 288 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.136589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.114972 restraints weight = 19117.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.117652 restraints weight = 11961.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.119495 restraints weight = 8414.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.120762 restraints weight = 6523.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.121682 restraints weight = 5404.924| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3569 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3569 r_free = 0.3569 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3569 r_free = 0.3569 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3569 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10900 Z= 0.146 Angle : 0.623 8.894 14963 Z= 0.343 Chirality : 0.045 0.229 1723 Planarity : 0.004 0.053 1683 Dihedral : 20.983 155.298 1931 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % 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: -2.08 (0.24), residues: 1171 helix: -0.27 (0.31), residues: 295 sheet: 0.21 (0.32), residues: 307 loop : -3.05 (0.22), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 176 TYR 0.018 0.002 TYR C 59 PHE 0.029 0.002 PHE B 60 TRP 0.007 0.001 TRP E 50 HIS 0.003 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.15 (10899) covalent geometry : angle 0.62337 / 0.34 (14963) hydrogen bonds : bond 0.05818 / 3.79 ( 386) hydrogen bonds : angle 6.14339 / 4.17 ( 1003) Misc. bond : bond 0.00275 / 0.14 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.5664 (t70) cc_final: 0.5350 (t0) REVERT: A 57 LEU cc_start: 0.8229 (mt) cc_final: 0.7879 (mt) REVERT: A 59 GLU cc_start: 0.8315 (tp30) cc_final: 0.8094 (tp30) REVERT: A 70 LEU cc_start: 0.7426 (mt) cc_final: 0.7168 (mt) REVERT: A 99 LYS cc_start: 0.8223 (ttmt) cc_final: 0.7945 (mtpp) REVERT: A 110 LYS cc_start: 0.7114 (ttmt) cc_final: 0.6790 (ttmm) REVERT: A 116 LYS cc_start: 0.8006 (mtmm) cc_final: 0.7596 (tppt) REVERT: A 119 LYS cc_start: 0.7108 (mppt) cc_final: 0.6775 (mppt) REVERT: A 190 LEU cc_start: 0.7721 (tp) cc_final: 0.7506 (tt) REVERT: A 212 LEU cc_start: 0.7576 (mt) cc_final: 0.7277 (tp) REVERT: A 213 ARG cc_start: 0.6859 (mtt90) cc_final: 0.6610 (mtt90) REVERT: A 220 MET cc_start: 0.7589 (ttt) cc_final: 0.7255 (tmm) REVERT: A 229 MET cc_start: 0.6543 (ttt) cc_final: 0.6257 (ttt) REVERT: B 21 ASP cc_start: 0.7531 (t0) cc_final: 0.6644 (t0) REVERT: B 33 GLU cc_start: 0.7444 (pm20) cc_final: 0.7232 (pm20) REVERT: B 132 LYS cc_start: 0.8649 (ttmt) cc_final: 0.8178 (ttmm) REVERT: B 145 ASP cc_start: 0.6250 (t0) cc_final: 0.5793 (t0) REVERT: B 159 LYS cc_start: 0.7813 (ttpp) cc_final: 0.7535 (ttmm) REVERT: B 162 LYS cc_start: 0.8325 (mttp) cc_final: 0.7796 (mttp) REVERT: B 195 SER cc_start: 0.6622 (t) cc_final: 0.6392 (t) REVERT: C 2 LYS cc_start: 0.7842 (tppt) cc_final: 0.7385 (tppt) REVERT: C 3 VAL cc_start: 0.8479 (t) cc_final: 0.8005 (p) REVERT: C 6 ASP cc_start: 0.7582 (t0) cc_final: 0.7368 (t0) REVERT: C 7 ASP cc_start: 0.7825 (t70) cc_final: 0.7414 (t0) REVERT: C 23 ASP cc_start: 0.7750 (m-30) cc_final: 0.7547 (m-30) REVERT: C 75 MET cc_start: 0.6979 (tmm) cc_final: 0.6730 (tpp) REVERT: C 85 GLU cc_start: 0.7320 (mp0) cc_final: 0.7086 (mp0) REVERT: C 109 PHE cc_start: 0.8309 (m-80) cc_final: 0.7745 (m-80) REVERT: C 140 LYS cc_start: 0.8052 (ttpt) cc_final: 0.7526 (tttm) REVERT: C 154 VAL cc_start: 0.8130 (t) cc_final: 0.7917 (t) REVERT: C 165 LYS cc_start: 0.7835 (pttp) cc_final: 0.7110 (ptpt) REVERT: C 205 LEU cc_start: 0.8195 (mt) cc_final: 0.7905 (tp) REVERT: C 209 LYS cc_start: 0.8080 (ptmm) cc_final: 0.7546 (ptmm) REVERT: C 215 LYS cc_start: 0.8222 (ttmt) cc_final: 0.7859 (ttmm) REVERT: C 229 ASN cc_start: 0.7590 (t0) cc_final: 0.7309 (t0) REVERT: C 230 MET cc_start: 0.5341 (mtm) cc_final: 0.4855 (mtm) REVERT: E 15 LYS cc_start: 0.8542 (mtmt) cc_final: 0.8073 (mmtm) REVERT: E 36 THR cc_start: 0.7584 (p) cc_final: 0.7141 (p) REVERT: E 46 GLN cc_start: 0.7781 (tm-30) cc_final: 0.7429 (tm-30) REVERT: E 101 LYS cc_start: 0.8670 (pttm) cc_final: 0.8204 (pttm) REVERT: E 117 GLU cc_start: 0.5063 (mp0) cc_final: 0.4649 (mp0) REVERT: E 126 SER cc_start: 0.8335 (t) cc_final: 0.7900 (p) REVERT: E 127 THR cc_start: 0.8162 (m) cc_final: 0.7780 (p) REVERT: E 135 THR cc_start: 0.7838 (m) cc_final: 0.7630 (p) REVERT: E 174 ILE cc_start: 0.8019 (mm) cc_final: 0.7620 (tt) REVERT: E 197 ILE cc_start: 0.7995 (mm) cc_final: 0.7786 (tp) REVERT: E 203 LEU cc_start: 0.7851 (mt) cc_final: 0.7579 (mt) REVERT: E 209 ASN cc_start: 0.6668 (m-40) cc_final: 0.6130 (m-40) REVERT: E 223 LYS cc_start: 0.7629 (mmtp) cc_final: 0.7374 (mmtm) REVERT: E 236 MET cc_start: 0.7735 (ptp) cc_final: 0.7461 (ptp) REVERT: E 239 GLU cc_start: 0.7505 (tp30) cc_final: 0.6232 (mp0) REVERT: E 270 LYS cc_start: 0.7402 (tttt) cc_final: 0.7196 (tttt) REVERT: E 274 LYS cc_start: 0.7121 (mppt) cc_final: 0.6629 (mppt) REVERT: E 290 PRO cc_start: 0.7920 (Cg_endo) cc_final: 0.7618 (Cg_exo) REVERT: E 325 GLN cc_start: 0.7173 (mm-40) cc_final: 0.6925 (tp-100) REVERT: E 328 MET cc_start: 0.7483 (mtm) cc_final: 0.7274 (mtm) REVERT: E 336 ILE cc_start: 0.7265 (mt) cc_final: 0.7047 (mm) REVERT: E 363 LYS cc_start: 0.8403 (mmtt) cc_final: 0.8145 (mmtp) REVERT: E 397 LYS cc_start: 0.7840 (mmmt) cc_final: 0.7578 (mmtp) REVERT: E 434 LEU cc_start: 0.8436 (tp) cc_final: 0.7959 (pt) outliers start: 0 outliers final: 0 residues processed: 351 average time/residue: 0.1098 time to fit residues: 50.8980 Evaluate side-chains 319 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 78 optimal weight: 10.0000 chunk 103 optimal weight: 0.4980 chunk 86 optimal weight: 0.0970 chunk 74 optimal weight: 8.9990 chunk 99 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 106 optimal weight: 0.0970 chunk 60 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.136969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.115208 restraints weight = 19118.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.117951 restraints weight = 11870.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.119862 restraints weight = 8332.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.121184 restraints weight = 6414.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.122130 restraints weight = 5295.528| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3580 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3580 r_free = 0.3580 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3580 r_free = 0.3580 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (15 function evaluations) r_final: 0.3580 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10900 Z= 0.127 Angle : 0.600 9.992 14963 Z= 0.329 Chirality : 0.045 0.228 1723 Planarity : 0.004 0.046 1683 Dihedral : 21.025 154.558 1931 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % 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: -2.00 (0.24), residues: 1171 helix: -0.31 (0.31), residues: 299 sheet: 0.16 (0.32), residues: 314 loop : -2.91 (0.22), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 103 TYR 0.016 0.001 TYR C 59 PHE 0.029 0.002 PHE B 60 TRP 0.006 0.001 TRP E 50 HIS 0.002 0.000 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.13 (10899) covalent geometry : angle 0.59990 / 0.33 (14963) hydrogen bonds : bond 0.04924 / 3.22 ( 386) hydrogen bonds : angle 5.73737 / 3.88 ( 1003) Misc. bond : bond 0.00085 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 345 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.5610 (t70) cc_final: 0.5279 (t0) REVERT: A 55 ASP cc_start: 0.7911 (t70) cc_final: 0.7630 (t0) REVERT: A 57 LEU cc_start: 0.8152 (mt) cc_final: 0.7836 (mt) REVERT: A 59 GLU cc_start: 0.8363 (tp30) cc_final: 0.8056 (tp30) REVERT: A 69 LYS cc_start: 0.7561 (mppt) cc_final: 0.7068 (mmtm) REVERT: A 70 LEU cc_start: 0.7452 (mt) cc_final: 0.7208 (mt) REVERT: A 79 LEU cc_start: 0.7400 (mt) cc_final: 0.7116 (mt) REVERT: A 99 LYS cc_start: 0.7922 (ttmt) cc_final: 0.7692 (mtpp) REVERT: A 110 LYS cc_start: 0.7230 (ttmt) cc_final: 0.6871 (ttmm) REVERT: A 113 ILE cc_start: 0.7940 (mt) cc_final: 0.7691 (mm) REVERT: A 116 LYS cc_start: 0.7910 (mtmm) cc_final: 0.7597 (tppt) REVERT: A 190 LEU cc_start: 0.7701 (tp) cc_final: 0.7496 (tt) REVERT: A 212 LEU cc_start: 0.7485 (mt) cc_final: 0.7108 (tp) REVERT: A 213 ARG cc_start: 0.6878 (mtt90) cc_final: 0.6611 (mtt90) REVERT: A 229 MET cc_start: 0.6553 (ttt) cc_final: 0.6307 (ttt) REVERT: B 21 ASP cc_start: 0.7538 (t0) cc_final: 0.6736 (t0) REVERT: B 107 THR cc_start: 0.8005 (p) cc_final: 0.7730 (t) REVERT: B 132 LYS cc_start: 0.8517 (ttmt) cc_final: 0.8041 (ttmm) REVERT: B 145 ASP cc_start: 0.6167 (t0) cc_final: 0.5699 (t0) REVERT: B 155 ASN cc_start: 0.7394 (t0) cc_final: 0.7178 (t0) REVERT: B 159 LYS cc_start: 0.7810 (ttpp) cc_final: 0.7514 (ttmm) REVERT: B 162 LYS cc_start: 0.8337 (mttp) cc_final: 0.7803 (mttp) REVERT: B 195 SER cc_start: 0.6812 (t) cc_final: 0.6232 (t) REVERT: C 2 LYS cc_start: 0.7775 (tppt) cc_final: 0.7469 (tppt) REVERT: C 3 VAL cc_start: 0.8399 (t) cc_final: 0.7980 (p) REVERT: C 6 ASP cc_start: 0.7555 (t0) cc_final: 0.7327 (t0) REVERT: C 7 ASP cc_start: 0.7735 (t70) cc_final: 0.7328 (t0) REVERT: C 30 LYS cc_start: 0.7603 (mmtm) cc_final: 0.7312 (tppp) REVERT: C 75 MET cc_start: 0.6953 (tmm) cc_final: 0.6678 (tpp) REVERT: C 76 LYS cc_start: 0.8028 (ttpt) cc_final: 0.7802 (ttpt) REVERT: C 77 ILE cc_start: 0.8253 (pt) cc_final: 0.7978 (tt) REVERT: C 112 ARG cc_start: 0.8249 (tpp80) cc_final: 0.7878 (tpp80) REVERT: C 130 ILE cc_start: 0.8649 (mp) cc_final: 0.8387 (mm) REVERT: C 140 LYS cc_start: 0.8052 (ttpt) cc_final: 0.7529 (tttm) REVERT: C 165 LYS cc_start: 0.7885 (pttp) cc_final: 0.7221 (ptpt) REVERT: C 171 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6810 (mm-30) REVERT: C 205 LEU cc_start: 0.8202 (mt) cc_final: 0.7922 (tp) REVERT: C 209 LYS cc_start: 0.8073 (ptmm) cc_final: 0.7523 (ptmm) REVERT: C 215 LYS cc_start: 0.8183 (ttmt) cc_final: 0.7830 (ttmm) REVERT: E 15 LYS cc_start: 0.8489 (mtmt) cc_final: 0.8155 (mmtm) REVERT: E 46 GLN cc_start: 0.7766 (tm-30) cc_final: 0.7491 (tm-30) REVERT: E 49 LEU cc_start: 0.7268 (mt) cc_final: 0.7067 (mt) REVERT: E 86 LYS cc_start: 0.7817 (tptm) cc_final: 0.7544 (mmmm) REVERT: E 101 LYS cc_start: 0.8695 (pttm) cc_final: 0.8195 (pttm) REVERT: E 117 GLU cc_start: 0.5085 (mp0) cc_final: 0.4614 (mp0) REVERT: E 126 SER cc_start: 0.8303 (t) cc_final: 0.7882 (p) REVERT: E 127 THR cc_start: 0.8110 (m) cc_final: 0.7771 (p) REVERT: E 135 THR cc_start: 0.7683 (m) cc_final: 0.7395 (p) REVERT: E 174 ILE cc_start: 0.8053 (mm) cc_final: 0.7729 (tp) REVERT: E 197 ILE cc_start: 0.8046 (mm) cc_final: 0.7742 (tp) REVERT: E 203 LEU cc_start: 0.7838 (mt) cc_final: 0.7636 (mt) REVERT: E 212 LYS cc_start: 0.7325 (pttm) cc_final: 0.7108 (pttp) REVERT: E 236 MET cc_start: 0.7556 (ptp) cc_final: 0.7322 (ptp) REVERT: E 239 GLU cc_start: 0.7553 (tp30) cc_final: 0.6320 (mp0) REVERT: E 277 ILE cc_start: 0.8498 (mp) cc_final: 0.8294 (mt) REVERT: E 281 ARG cc_start: 0.6703 (mtm180) cc_final: 0.6438 (mtm180) REVERT: E 290 PRO cc_start: 0.7973 (Cg_endo) cc_final: 0.7629 (Cg_exo) REVERT: E 328 MET cc_start: 0.7465 (mtm) cc_final: 0.7154 (mmp) REVERT: E 363 LYS cc_start: 0.8376 (mmtt) cc_final: 0.8119 (mmtp) REVERT: E 397 LYS cc_start: 0.7749 (mmmt) cc_final: 0.7440 (mmtp) REVERT: E 434 LEU cc_start: 0.8456 (tp) cc_final: 0.7942 (pt) outliers start: 0 outliers final: 0 residues processed: 345 average time/residue: 0.0959 time to fit residues: 44.0725 Evaluate side-chains 317 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 317 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 56 optimal weight: 0.1980 chunk 38 optimal weight: 0.2980 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 21 optimal weight: 0.4980 chunk 110 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 288 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.136987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.115338 restraints weight = 19090.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.118021 restraints weight = 11859.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.119862 restraints weight = 8387.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.121169 restraints weight = 6500.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.121962 restraints weight = 5393.862| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3579 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3579 r_free = 0.3579 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3578 r_free = 0.3578 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3578 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10900 Z= 0.125 Angle : 0.611 9.479 14963 Z= 0.331 Chirality : 0.045 0.227 1723 Planarity : 0.004 0.046 1683 Dihedral : 21.067 153.844 1931 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % 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: -1.99 (0.24), residues: 1171 helix: -0.46 (0.30), residues: 306 sheet: 0.21 (0.31), residues: 321 loop : -2.91 (0.23), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 103 TYR 0.014 0.001 TYR C 59 PHE 0.025 0.002 PHE B 60 TRP 0.006 0.001 TRP E 50 HIS 0.004 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.13 (10899) covalent geometry : angle 0.61132 / 0.33 (14963) hydrogen bonds : bond 0.04697 / 3.08 ( 386) hydrogen bonds : angle 5.49881 / 3.71 ( 1003) Misc. bond : bond 0.00013 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 341 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.5581 (t70) cc_final: 0.5215 (t0) REVERT: A 55 ASP cc_start: 0.7815 (t70) cc_final: 0.7548 (t0) REVERT: A 57 LEU cc_start: 0.8169 (mt) cc_final: 0.7882 (mt) REVERT: A 59 GLU cc_start: 0.8374 (tp30) cc_final: 0.8067 (tp30) REVERT: A 69 LYS cc_start: 0.7590 (mppt) cc_final: 0.7251 (mmtp) REVERT: A 70 LEU cc_start: 0.7499 (mt) cc_final: 0.7273 (mt) REVERT: A 99 LYS cc_start: 0.7922 (ttmt) cc_final: 0.7622 (mtpp) REVERT: A 110 LYS cc_start: 0.7115 (ttmt) cc_final: 0.6915 (ttmm) REVERT: A 116 LYS cc_start: 0.7948 (mtmm) cc_final: 0.7630 (tppt) REVERT: A 167 LYS cc_start: 0.7207 (tttm) cc_final: 0.6984 (tmmt) REVERT: A 212 LEU cc_start: 0.7500 (mt) cc_final: 0.7194 (tp) REVERT: B 21 ASP cc_start: 0.7582 (t0) cc_final: 0.6731 (t0) REVERT: B 32 LYS cc_start: 0.8119 (tmtt) cc_final: 0.6855 (tptp) REVERT: B 67 GLU cc_start: 0.6597 (mt-10) cc_final: 0.6375 (mt-10) REVERT: B 73 LEU cc_start: 0.6995 (tp) cc_final: 0.6653 (tp) REVERT: B 107 THR cc_start: 0.8011 (p) cc_final: 0.7744 (t) REVERT: B 132 LYS cc_start: 0.8460 (ttmt) cc_final: 0.8078 (ttmm) REVERT: B 145 ASP cc_start: 0.6182 (t0) cc_final: 0.5735 (t0) REVERT: B 153 VAL cc_start: 0.7882 (t) cc_final: 0.7648 (p) REVERT: B 159 LYS cc_start: 0.7761 (ttpp) cc_final: 0.7428 (ttmm) REVERT: B 162 LYS cc_start: 0.7953 (mttp) cc_final: 0.7424 (mttp) REVERT: B 195 SER cc_start: 0.6827 (t) cc_final: 0.6184 (t) REVERT: B 218 TYR cc_start: 0.8037 (m-80) cc_final: 0.7829 (m-80) REVERT: C 2 LYS cc_start: 0.7684 (tppt) cc_final: 0.7372 (tppt) REVERT: C 3 VAL cc_start: 0.8351 (t) cc_final: 0.7896 (p) REVERT: C 6 ASP cc_start: 0.7358 (t0) cc_final: 0.7120 (t0) REVERT: C 7 ASP cc_start: 0.7749 (t70) cc_final: 0.7412 (t0) REVERT: C 28 LYS cc_start: 0.8164 (mttm) cc_final: 0.7478 (mttm) REVERT: C 30 LYS cc_start: 0.7673 (mmtm) cc_final: 0.7147 (tppp) REVERT: C 35 GLU cc_start: 0.6918 (mp0) cc_final: 0.6557 (pm20) REVERT: C 75 MET cc_start: 0.6899 (tmm) cc_final: 0.6650 (tpp) REVERT: C 77 ILE cc_start: 0.8288 (pt) cc_final: 0.8079 (tt) REVERT: C 85 GLU cc_start: 0.7369 (mp0) cc_final: 0.7086 (mp0) REVERT: C 112 ARG cc_start: 0.8226 (tpp80) cc_final: 0.7846 (tpp80) REVERT: C 130 ILE cc_start: 0.8627 (mp) cc_final: 0.8358 (mm) REVERT: C 140 LYS cc_start: 0.7997 (ttpt) cc_final: 0.7465 (tttm) REVERT: C 154 VAL cc_start: 0.8072 (t) cc_final: 0.7626 (p) REVERT: C 165 LYS cc_start: 0.7929 (pttp) cc_final: 0.7210 (ptpt) REVERT: C 171 GLU cc_start: 0.7322 (mm-30) cc_final: 0.6925 (mm-30) REVERT: C 175 GLU cc_start: 0.6805 (pt0) cc_final: 0.6543 (pt0) REVERT: C 205 LEU cc_start: 0.8251 (mt) cc_final: 0.7935 (tp) REVERT: C 209 LYS cc_start: 0.8075 (ptmm) cc_final: 0.7539 (ptmm) REVERT: C 215 LYS cc_start: 0.8189 (ttmt) cc_final: 0.7839 (ttmm) REVERT: E 15 LYS cc_start: 0.8481 (mtmt) cc_final: 0.8063 (mmtm) REVERT: E 32 LYS cc_start: 0.7554 (mmtm) cc_final: 0.7336 (mmmm) REVERT: E 36 THR cc_start: 0.7826 (p) cc_final: 0.7351 (p) REVERT: E 46 GLN cc_start: 0.7806 (tm-30) cc_final: 0.7547 (tm-30) REVERT: E 86 LYS cc_start: 0.7833 (tptm) cc_final: 0.7489 (mmmm) REVERT: E 101 LYS cc_start: 0.8630 (pttm) cc_final: 0.8220 (pttm) REVERT: E 117 GLU cc_start: 0.5065 (mp0) cc_final: 0.4619 (mp0) REVERT: E 126 SER cc_start: 0.8286 (t) cc_final: 0.7861 (p) REVERT: E 127 THR cc_start: 0.8144 (m) cc_final: 0.7770 (p) REVERT: E 135 THR cc_start: 0.7921 (m) cc_final: 0.7700 (p) REVERT: E 174 ILE cc_start: 0.8044 (mm) cc_final: 0.7628 (tt) REVERT: E 197 ILE cc_start: 0.7947 (mm) cc_final: 0.7591 (tp) REVERT: E 236 MET cc_start: 0.7518 (ptp) cc_final: 0.7276 (ptp) REVERT: E 239 GLU cc_start: 0.7565 (tp30) cc_final: 0.6355 (mp0) REVERT: E 271 LYS cc_start: 0.6968 (tmmt) cc_final: 0.6735 (tmtt) REVERT: E 274 LYS cc_start: 0.7056 (mppt) cc_final: 0.6704 (mppt) REVERT: E 277 ILE cc_start: 0.8499 (mp) cc_final: 0.8268 (mt) REVERT: E 283 GLU cc_start: 0.6943 (mp0) cc_final: 0.6710 (mp0) REVERT: E 290 PRO cc_start: 0.8019 (Cg_endo) cc_final: 0.7670 (Cg_exo) REVERT: E 325 GLN cc_start: 0.7310 (tp40) cc_final: 0.6916 (tp-100) REVERT: E 326 GLU cc_start: 0.7746 (tp30) cc_final: 0.6669 (tp30) REVERT: E 329 HIS cc_start: 0.7211 (m90) cc_final: 0.5860 (m90) REVERT: E 363 LYS cc_start: 0.8352 (mmtt) cc_final: 0.8087 (mmtp) REVERT: E 394 GLU cc_start: 0.7372 (tp30) cc_final: 0.7096 (tp30) REVERT: E 397 LYS cc_start: 0.7721 (mmmt) cc_final: 0.7382 (mmtp) REVERT: E 434 LEU cc_start: 0.8453 (tp) cc_final: 0.7924 (pt) outliers start: 0 outliers final: 0 residues processed: 341 average time/residue: 0.1090 time to fit residues: 48.9353 Evaluate side-chains 323 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 323 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 57 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 115 optimal weight: 0.0870 chunk 100 optimal weight: 0.6980 overall best weight: 1.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 155 ASN B 204 ASN E 102 GLN E 288 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.134400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.112849 restraints weight = 19289.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.115471 restraints weight = 12107.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.117270 restraints weight = 8605.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.118539 restraints weight = 6691.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.119437 restraints weight = 5552.051| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3540 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3540 r_free = 0.3540 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3540 r_free = 0.3540 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.3540 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10900 Z= 0.185 Angle : 0.640 8.655 14963 Z= 0.351 Chirality : 0.046 0.236 1723 Planarity : 0.004 0.049 1683 Dihedral : 21.168 155.172 1931 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 0.10 % Allowed : 2.22 % Favored : 97.68 % 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: -2.05 (0.24), residues: 1171 helix: -0.41 (0.31), residues: 300 sheet: 0.09 (0.31), residues: 320 loop : -2.91 (0.23), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 103 TYR 0.017 0.002 TYR C 59 PHE 0.027 0.002 PHE E 10 TRP 0.014 0.002 TRP E 50 HIS 0.004 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.19 (10899) covalent geometry : angle 0.63965 / 0.35 (14963) hydrogen bonds : bond 0.05284 / 3.44 ( 386) hydrogen bonds : angle 5.46463 / 3.69 ( 1003) Misc. bond : bond 0.00064 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 345 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.5521 (t70) cc_final: 0.5150 (t0) REVERT: A 55 ASP cc_start: 0.7916 (t70) cc_final: 0.7633 (t0) REVERT: A 57 LEU cc_start: 0.8172 (mt) cc_final: 0.7892 (mt) REVERT: A 59 GLU cc_start: 0.8415 (tp30) cc_final: 0.8132 (tp30) REVERT: A 69 LYS cc_start: 0.7628 (mppt) cc_final: 0.7298 (mmtp) REVERT: A 99 LYS cc_start: 0.7928 (ttmt) cc_final: 0.7659 (mtpp) REVERT: A 110 LYS cc_start: 0.7029 (ttmt) cc_final: 0.6530 (ttmm) REVERT: A 116 LYS cc_start: 0.7910 (mtmm) cc_final: 0.7564 (tptt) REVERT: B 21 ASP cc_start: 0.7545 (t0) cc_final: 0.6725 (t0) REVERT: B 33 GLU cc_start: 0.7434 (mp0) cc_final: 0.7117 (mp0) REVERT: B 103 ASP cc_start: 0.6944 (m-30) cc_final: 0.6675 (m-30) REVERT: B 107 THR cc_start: 0.8040 (p) cc_final: 0.7769 (t) REVERT: B 132 LYS cc_start: 0.8277 (ttmt) cc_final: 0.7969 (ttmm) REVERT: B 145 ASP cc_start: 0.6286 (t0) cc_final: 0.5796 (t0) REVERT: B 159 LYS cc_start: 0.7774 (ttpp) cc_final: 0.7534 (ttmm) REVERT: B 162 LYS cc_start: 0.8048 (mttp) cc_final: 0.7538 (mttp) REVERT: B 204 ASN cc_start: 0.8344 (OUTLIER) cc_final: 0.7971 (t0) REVERT: C 3 VAL cc_start: 0.8539 (t) cc_final: 0.8181 (p) REVERT: C 7 ASP cc_start: 0.7386 (t70) cc_final: 0.6887 (t0) REVERT: C 28 LYS cc_start: 0.8259 (mttm) cc_final: 0.7610 (mttm) REVERT: C 30 LYS cc_start: 0.7751 (mmtm) cc_final: 0.7171 (tppp) REVERT: C 35 GLU cc_start: 0.6932 (mp0) cc_final: 0.6550 (pm20) REVERT: C 72 GLN cc_start: 0.7592 (tt0) cc_final: 0.7163 (mt0) REVERT: C 75 MET cc_start: 0.7062 (tmm) cc_final: 0.6811 (tpp) REVERT: C 85 GLU cc_start: 0.7526 (mp0) cc_final: 0.7096 (mp0) REVERT: C 88 GLU cc_start: 0.6900 (tm-30) cc_final: 0.6616 (tm-30) REVERT: C 109 PHE cc_start: 0.8420 (m-80) cc_final: 0.7914 (m-80) REVERT: C 112 ARG cc_start: 0.8204 (tpp80) cc_final: 0.7860 (tpp80) REVERT: C 130 ILE cc_start: 0.8662 (mp) cc_final: 0.8412 (mm) REVERT: C 140 LYS cc_start: 0.8121 (ttpt) cc_final: 0.7605 (tttm) REVERT: C 154 VAL cc_start: 0.8191 (t) cc_final: 0.7780 (p) REVERT: C 165 LYS cc_start: 0.8019 (pttp) cc_final: 0.7339 (ptpt) REVERT: C 171 GLU cc_start: 0.7290 (mm-30) cc_final: 0.6962 (mm-30) REVERT: C 205 LEU cc_start: 0.8263 (mt) cc_final: 0.7992 (tp) REVERT: C 209 LYS cc_start: 0.8098 (ptmm) cc_final: 0.7625 (ptmm) REVERT: C 215 LYS cc_start: 0.8207 (ttmt) cc_final: 0.7810 (ttmm) REVERT: C 229 ASN cc_start: 0.7558 (t0) cc_final: 0.7290 (t0) REVERT: E 14 GLU cc_start: 0.7289 (tp30) cc_final: 0.7054 (tp30) REVERT: E 15 LYS cc_start: 0.8512 (mtmt) cc_final: 0.8124 (mmtm) REVERT: E 32 LYS cc_start: 0.7608 (mmtm) cc_final: 0.7378 (mmmm) REVERT: E 36 THR cc_start: 0.7792 (p) cc_final: 0.7339 (p) REVERT: E 46 GLN cc_start: 0.7895 (tm-30) cc_final: 0.7554 (tm-30) REVERT: E 49 LEU cc_start: 0.7317 (mt) cc_final: 0.6960 (mt) REVERT: E 86 LYS cc_start: 0.7869 (tptm) cc_final: 0.7641 (mmmm) REVERT: E 117 GLU cc_start: 0.5100 (mp0) cc_final: 0.4670 (mp0) REVERT: E 126 SER cc_start: 0.8323 (t) cc_final: 0.7886 (p) REVERT: E 127 THR cc_start: 0.8176 (m) cc_final: 0.7793 (p) REVERT: E 135 THR cc_start: 0.7938 (m) cc_final: 0.7724 (p) REVERT: E 174 ILE cc_start: 0.8013 (mm) cc_final: 0.7660 (tt) REVERT: E 194 SER cc_start: 0.7908 (p) cc_final: 0.7612 (p) REVERT: E 197 ILE cc_start: 0.7993 (mm) cc_final: 0.7607 (tp) REVERT: E 203 LEU cc_start: 0.7917 (mt) cc_final: 0.7674 (mt) REVERT: E 239 GLU cc_start: 0.7546 (tp30) cc_final: 0.6345 (mp0) REVERT: E 274 LYS cc_start: 0.6964 (mppt) cc_final: 0.6637 (mppt) REVERT: E 277 ILE cc_start: 0.8484 (mp) cc_final: 0.8276 (mt) REVERT: E 283 GLU cc_start: 0.6910 (mp0) cc_final: 0.6551 (mp0) REVERT: E 290 PRO cc_start: 0.8021 (Cg_endo) cc_final: 0.7634 (Cg_exo) REVERT: E 325 GLN cc_start: 0.7243 (tp40) cc_final: 0.6828 (tp-100) REVERT: E 326 GLU cc_start: 0.7699 (tp30) cc_final: 0.6647 (tp30) REVERT: E 329 HIS cc_start: 0.7220 (m90) cc_final: 0.5838 (m90) REVERT: E 363 LYS cc_start: 0.8232 (mmtt) cc_final: 0.7978 (mmtp) REVERT: E 394 GLU cc_start: 0.7396 (tp30) cc_final: 0.7151 (tp30) REVERT: E 397 LYS cc_start: 0.7760 (mmmt) cc_final: 0.7396 (mmtp) REVERT: E 434 LEU cc_start: 0.8479 (tp) cc_final: 0.7980 (pt) outliers start: 1 outliers final: 0 residues processed: 346 average time/residue: 0.1036 time to fit residues: 47.7293 Evaluate side-chains 327 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 326 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.133268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.111669 restraints weight = 19061.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.114331 restraints weight = 12089.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.116150 restraints weight = 8599.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.117404 restraints weight = 6694.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.118325 restraints weight = 5576.285| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3525 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3525 r_free = 0.3525 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3525 r_free = 0.3525 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3525 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 10900 Z= 0.215 Angle : 0.697 10.630 14963 Z= 0.379 Chirality : 0.048 0.251 1723 Planarity : 0.005 0.048 1683 Dihedral : 21.262 157.113 1931 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.08 % Favored : 89.92 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % 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: -2.19 (0.24), residues: 1171 helix: -0.59 (0.30), residues: 299 sheet: 0.03 (0.31), residues: 324 loop : -2.99 (0.23), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 176 TYR 0.020 0.002 TYR C 59 PHE 0.029 0.003 PHE E 10 TRP 0.023 0.003 TRP E 50 HIS 0.007 0.001 HIS C 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.21 (10899) covalent geometry : angle 0.69741 / 0.38 (14963) hydrogen bonds : bond 0.05656 / 3.66 ( 386) hydrogen bonds : angle 5.51661 / 3.73 ( 1003) Misc. bond : bond 0.00092 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 340 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 THR cc_start: 0.7544 (p) cc_final: 0.7335 (p) REVERT: A 55 ASP cc_start: 0.7931 (t70) cc_final: 0.7682 (t0) REVERT: A 57 LEU cc_start: 0.8170 (mt) cc_final: 0.7884 (mt) REVERT: A 59 GLU cc_start: 0.8411 (tp30) cc_final: 0.8096 (tp30) REVERT: A 69 LYS cc_start: 0.7662 (mppt) cc_final: 0.7334 (pttm) REVERT: A 99 LYS cc_start: 0.7932 (ttmt) cc_final: 0.7614 (mtpp) REVERT: A 116 LYS cc_start: 0.7960 (mtmm) cc_final: 0.7633 (tppt) REVERT: A 156 GLU cc_start: 0.7983 (mp0) cc_final: 0.7749 (mm-30) REVERT: B 21 ASP cc_start: 0.7551 (t0) cc_final: 0.6558 (t0) REVERT: B 32 LYS cc_start: 0.7520 (tmtt) cc_final: 0.7313 (tptp) REVERT: B 103 ASP cc_start: 0.6955 (m-30) cc_final: 0.6659 (m-30) REVERT: B 132 LYS cc_start: 0.8462 (ttmt) cc_final: 0.7932 (ttmm) REVERT: B 145 ASP cc_start: 0.6400 (t0) cc_final: 0.5929 (t0) REVERT: B 162 LYS cc_start: 0.8027 (mttp) cc_final: 0.7541 (mttp) REVERT: B 199 MET cc_start: 0.7493 (tpp) cc_final: 0.7266 (tpp) REVERT: C 3 VAL cc_start: 0.8603 (t) cc_final: 0.8184 (p) REVERT: C 7 ASP cc_start: 0.7421 (t70) cc_final: 0.7006 (t0) REVERT: C 28 LYS cc_start: 0.8296 (mttm) cc_final: 0.7696 (mttm) REVERT: C 30 LYS cc_start: 0.7774 (mmtm) cc_final: 0.7268 (tppp) REVERT: C 35 GLU cc_start: 0.6963 (mp0) cc_final: 0.6552 (pm20) REVERT: C 72 GLN cc_start: 0.7662 (tt0) cc_final: 0.7295 (mt0) REVERT: C 75 MET cc_start: 0.7097 (tmm) cc_final: 0.6806 (tpp) REVERT: C 154 VAL cc_start: 0.8209 (t) cc_final: 0.7805 (p) REVERT: C 165 LYS cc_start: 0.8066 (pttp) cc_final: 0.7382 (ptpt) REVERT: C 171 GLU cc_start: 0.7316 (mm-30) cc_final: 0.6968 (mm-30) REVERT: C 205 LEU cc_start: 0.8324 (mt) cc_final: 0.8009 (tp) REVERT: C 209 LYS cc_start: 0.8104 (ptmm) cc_final: 0.7678 (ptmm) REVERT: C 215 LYS cc_start: 0.8221 (ttmt) cc_final: 0.7849 (ttmm) REVERT: E 1 MET cc_start: 0.7072 (mtm) cc_final: 0.6859 (mtm) REVERT: E 6 ILE cc_start: 0.6830 (tp) cc_final: 0.6360 (tp) REVERT: E 15 LYS cc_start: 0.8544 (mtmt) cc_final: 0.8165 (mmtm) REVERT: E 32 LYS cc_start: 0.7650 (mmtm) cc_final: 0.7390 (mmmm) REVERT: E 46 GLN cc_start: 0.7914 (tm-30) cc_final: 0.7545 (tm-30) REVERT: E 49 LEU cc_start: 0.7329 (mt) cc_final: 0.6966 (mt) REVERT: E 86 LYS cc_start: 0.7910 (tptm) cc_final: 0.7698 (mmmm) REVERT: E 101 LYS cc_start: 0.8637 (pttm) cc_final: 0.8254 (pttm) REVERT: E 117 GLU cc_start: 0.5142 (mp0) cc_final: 0.4696 (mp0) REVERT: E 126 SER cc_start: 0.8366 (t) cc_final: 0.7854 (p) REVERT: E 135 THR cc_start: 0.7966 (m) cc_final: 0.7705 (p) REVERT: E 174 ILE cc_start: 0.8016 (mm) cc_final: 0.7694 (tp) REVERT: E 194 SER cc_start: 0.7952 (p) cc_final: 0.7637 (p) REVERT: E 197 ILE cc_start: 0.7982 (mm) cc_final: 0.7641 (tp) REVERT: E 224 THR cc_start: 0.7141 (p) cc_final: 0.6918 (p) REVERT: E 226 LYS cc_start: 0.6730 (tptm) cc_final: 0.6513 (tptt) REVERT: E 236 MET cc_start: 0.7499 (ptp) cc_final: 0.7213 (ptp) REVERT: E 239 GLU cc_start: 0.7595 (tp30) cc_final: 0.6433 (mp0) REVERT: E 270 LYS cc_start: 0.7431 (ttmt) cc_final: 0.7205 (ttmt) REVERT: E 283 GLU cc_start: 0.6893 (mp0) cc_final: 0.6497 (mp0) REVERT: E 290 PRO cc_start: 0.8007 (Cg_endo) cc_final: 0.7634 (Cg_exo) REVERT: E 325 GLN cc_start: 0.7348 (tp40) cc_final: 0.6930 (tp-100) REVERT: E 326 GLU cc_start: 0.7754 (tp30) cc_final: 0.6641 (tp30) REVERT: E 329 HIS cc_start: 0.7165 (m90) cc_final: 0.5815 (m90) REVERT: E 363 LYS cc_start: 0.8265 (mmtt) cc_final: 0.8024 (mmtp) REVERT: E 394 GLU cc_start: 0.7391 (tp30) cc_final: 0.7154 (tp30) REVERT: E 397 LYS cc_start: 0.7765 (mmmt) cc_final: 0.7402 (mmtp) outliers start: 0 outliers final: 0 residues processed: 340 average time/residue: 0.1053 time to fit residues: 47.2042 Evaluate side-chains 311 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 311 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 7 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 111 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.134407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.112742 restraints weight = 19086.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.115335 restraints weight = 12231.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.116972 restraints weight = 8795.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.118340 restraints weight = 6932.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.119135 restraints weight = 5780.892| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3538 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3538 r_free = 0.3538 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3538 r_free = 0.3538 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3538 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10900 Z= 0.169 Angle : 0.684 10.913 14963 Z= 0.370 Chirality : 0.047 0.241 1723 Planarity : 0.004 0.047 1683 Dihedral : 21.282 157.793 1931 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % 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: -2.23 (0.24), residues: 1171 helix: -0.67 (0.30), residues: 307 sheet: 0.08 (0.32), residues: 315 loop : -3.02 (0.23), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 103 TYR 0.024 0.002 TYR E 381 PHE 0.028 0.002 PHE E 10 TRP 0.029 0.003 TRP E 50 HIS 0.004 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 (10899) covalent geometry : angle 0.68366 / 0.37 (14963) hydrogen bonds : bond 0.05176 / 3.35 ( 386) hydrogen bonds : angle 5.44296 / 3.68 ( 1003) Misc. bond : bond 0.00107 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 338 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASP cc_start: 0.7904 (t70) cc_final: 0.7621 (t0) REVERT: A 57 LEU cc_start: 0.8124 (mt) cc_final: 0.7822 (mt) REVERT: A 59 GLU cc_start: 0.8374 (tp30) cc_final: 0.8109 (tp30) REVERT: A 69 LYS cc_start: 0.7673 (mppt) cc_final: 0.7339 (pttm) REVERT: A 99 LYS cc_start: 0.7962 (ttmt) cc_final: 0.7645 (mtpp) REVERT: A 116 LYS cc_start: 0.7930 (mtmm) cc_final: 0.7622 (tppt) REVERT: A 156 GLU cc_start: 0.7949 (mp0) cc_final: 0.7736 (mm-30) REVERT: B 21 ASP cc_start: 0.7472 (t0) cc_final: 0.6506 (t0) REVERT: B 33 GLU cc_start: 0.7300 (mp0) cc_final: 0.6969 (mp0) REVERT: B 103 ASP cc_start: 0.7032 (m-30) cc_final: 0.6709 (m-30) REVERT: B 107 THR cc_start: 0.8126 (p) cc_final: 0.7744 (t) REVERT: B 132 LYS cc_start: 0.8264 (ttmt) cc_final: 0.7929 (ttmm) REVERT: B 145 ASP cc_start: 0.6279 (t0) cc_final: 0.5841 (t0) REVERT: B 162 LYS cc_start: 0.7904 (mttp) cc_final: 0.7622 (mttp) REVERT: C 3 VAL cc_start: 0.8526 (t) cc_final: 0.8169 (p) REVERT: C 7 ASP cc_start: 0.7492 (t70) cc_final: 0.7062 (t0) REVERT: C 28 LYS cc_start: 0.8266 (mttm) cc_final: 0.7128 (mttm) REVERT: C 30 LYS cc_start: 0.7769 (mmtm) cc_final: 0.7484 (tppp) REVERT: C 35 GLU cc_start: 0.7002 (mp0) cc_final: 0.6410 (mp0) REVERT: C 72 GLN cc_start: 0.7714 (tt0) cc_final: 0.7318 (mt0) REVERT: C 75 MET cc_start: 0.7092 (tmm) cc_final: 0.6837 (tpp) REVERT: C 85 GLU cc_start: 0.7467 (mp0) cc_final: 0.6921 (mp0) REVERT: C 156 GLU cc_start: 0.7250 (tp30) cc_final: 0.6869 (tp30) REVERT: C 165 LYS cc_start: 0.8033 (pttp) cc_final: 0.7344 (ptpt) REVERT: C 171 GLU cc_start: 0.7392 (mm-30) cc_final: 0.7002 (mm-30) REVERT: C 190 LYS cc_start: 0.8195 (mttt) cc_final: 0.7986 (mmtt) REVERT: C 205 LEU cc_start: 0.8334 (mt) cc_final: 0.7996 (tp) REVERT: C 209 LYS cc_start: 0.8124 (ptmm) cc_final: 0.7638 (ptmm) REVERT: C 215 LYS cc_start: 0.8212 (ttmt) cc_final: 0.7827 (ttmm) REVERT: E 6 ILE cc_start: 0.6810 (tp) cc_final: 0.6315 (tp) REVERT: E 15 LYS cc_start: 0.8512 (mtmt) cc_final: 0.8167 (mmtp) REVERT: E 36 THR cc_start: 0.7536 (p) cc_final: 0.7074 (p) REVERT: E 46 GLN cc_start: 0.7919 (tm-30) cc_final: 0.7554 (tm-30) REVERT: E 49 LEU cc_start: 0.7398 (mt) cc_final: 0.7114 (mt) REVERT: E 101 LYS cc_start: 0.8548 (pttm) cc_final: 0.8230 (pttm) REVERT: E 117 GLU cc_start: 0.5116 (mp0) cc_final: 0.4707 (mp0) REVERT: E 126 SER cc_start: 0.8368 (t) cc_final: 0.7832 (p) REVERT: E 127 THR cc_start: 0.7995 (m) cc_final: 0.7683 (m) REVERT: E 135 THR cc_start: 0.7930 (m) cc_final: 0.7668 (p) REVERT: E 174 ILE cc_start: 0.7999 (mm) cc_final: 0.7666 (tp) REVERT: E 194 SER cc_start: 0.7881 (p) cc_final: 0.6801 (p) REVERT: E 197 ILE cc_start: 0.7945 (mm) cc_final: 0.7549 (tp) REVERT: E 203 LEU cc_start: 0.7835 (mt) cc_final: 0.7631 (mt) REVERT: E 206 ASP cc_start: 0.7760 (p0) cc_final: 0.7527 (p0) REVERT: E 209 ASN cc_start: 0.6884 (m-40) cc_final: 0.6545 (m-40) REVERT: E 220 GLU cc_start: 0.8126 (mp0) cc_final: 0.7879 (mp0) REVERT: E 224 THR cc_start: 0.7073 (p) cc_final: 0.6846 (p) REVERT: E 274 LYS cc_start: 0.7066 (mppt) cc_final: 0.6591 (mppt) REVERT: E 283 GLU cc_start: 0.6929 (mp0) cc_final: 0.6595 (mp0) REVERT: E 290 PRO cc_start: 0.7966 (Cg_endo) cc_final: 0.7563 (Cg_exo) REVERT: E 325 GLN cc_start: 0.7256 (tp40) cc_final: 0.6844 (tp-100) REVERT: E 326 GLU cc_start: 0.7663 (tp30) cc_final: 0.6403 (tp30) REVERT: E 329 HIS cc_start: 0.7206 (m90) cc_final: 0.6029 (m90) REVERT: E 363 LYS cc_start: 0.8252 (mmtt) cc_final: 0.8009 (mmtp) REVERT: E 397 LYS cc_start: 0.7750 (mmmt) cc_final: 0.7370 (mmtp) outliers start: 0 outliers final: 0 residues processed: 338 average time/residue: 0.1285 time to fit residues: 57.3666 Evaluate side-chains 315 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 3 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 73 optimal weight: 10.0000 chunk 45 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 157 HIS ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.133725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.111990 restraints weight = 19005.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.114671 restraints weight = 12049.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.116496 restraints weight = 8526.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.117664 restraints weight = 6632.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.118643 restraints weight = 5535.553| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3522 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3522 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 10900 Z= 0.192 Angle : 0.714 11.805 14963 Z= 0.386 Chirality : 0.048 0.249 1723 Planarity : 0.005 0.048 1683 Dihedral : 21.335 158.224 1931 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.33 % Favored : 89.67 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: -2.29 (0.24), residues: 1171 helix: -0.77 (0.29), residues: 307 sheet: 0.03 (0.31), residues: 319 loop : -3.03 (0.23), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 103 TYR 0.023 0.002 TYR B 197 PHE 0.030 0.002 PHE E 10 TRP 0.029 0.003 TRP E 50 HIS 0.008 0.001 HIS B 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.19 (10899) covalent geometry : angle 0.71424 / 0.39 (14963) hydrogen bonds : bond 0.05508 / 3.63 ( 386) hydrogen bonds : angle 5.41474 / 3.66 ( 1003) Misc. bond : bond 0.00117 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASP cc_start: 0.7845 (t70) cc_final: 0.7558 (t0) REVERT: A 57 LEU cc_start: 0.8083 (mt) cc_final: 0.7764 (mt) REVERT: A 59 GLU cc_start: 0.8391 (tp30) cc_final: 0.8121 (tp30) REVERT: A 69 LYS cc_start: 0.7699 (mppt) cc_final: 0.7313 (pttm) REVERT: A 91 LEU cc_start: 0.8205 (tp) cc_final: 0.7857 (tp) REVERT: A 93 GLU cc_start: 0.8757 (pp20) cc_final: 0.8207 (pp20) REVERT: A 99 LYS cc_start: 0.7951 (ttmt) cc_final: 0.7569 (mtpp) REVERT: A 116 LYS cc_start: 0.7927 (mtmm) cc_final: 0.7631 (tppt) REVERT: B 21 ASP cc_start: 0.7496 (t0) cc_final: 0.6538 (t0) REVERT: B 32 LYS cc_start: 0.7493 (tttt) cc_final: 0.7195 (tmmt) REVERT: B 103 ASP cc_start: 0.7072 (m-30) cc_final: 0.6717 (m-30) REVERT: B 107 THR cc_start: 0.8156 (p) cc_final: 0.7761 (t) REVERT: B 132 LYS cc_start: 0.8432 (ttmt) cc_final: 0.7895 (ttmm) REVERT: B 145 ASP cc_start: 0.6408 (t0) cc_final: 0.5892 (t0) REVERT: B 159 LYS cc_start: 0.7828 (ttmm) cc_final: 0.7550 (ttmm) REVERT: B 162 LYS cc_start: 0.7937 (mttp) cc_final: 0.7621 (mttp) REVERT: C 3 VAL cc_start: 0.8568 (t) cc_final: 0.8232 (p) REVERT: C 7 ASP cc_start: 0.7510 (t70) cc_final: 0.7169 (t0) REVERT: C 28 LYS cc_start: 0.8240 (mttm) cc_final: 0.7157 (mttm) REVERT: C 30 LYS cc_start: 0.7760 (mmtm) cc_final: 0.7485 (tppp) REVERT: C 35 GLU cc_start: 0.7002 (mp0) cc_final: 0.6422 (mp0) REVERT: C 72 GLN cc_start: 0.7711 (tt0) cc_final: 0.7249 (mt0) REVERT: C 75 MET cc_start: 0.7085 (tmm) cc_final: 0.6794 (tpp) REVERT: C 85 GLU cc_start: 0.7479 (mp0) cc_final: 0.6946 (mp0) REVERT: C 156 GLU cc_start: 0.7421 (tp30) cc_final: 0.6040 (tp30) REVERT: C 165 LYS cc_start: 0.7931 (pttp) cc_final: 0.7586 (ptpt) REVERT: C 171 GLU cc_start: 0.7343 (mm-30) cc_final: 0.6978 (mm-30) REVERT: C 193 LYS cc_start: 0.7430 (mptt) cc_final: 0.6548 (mptt) REVERT: C 205 LEU cc_start: 0.8412 (mt) cc_final: 0.7986 (tp) REVERT: C 209 LYS cc_start: 0.8113 (ptmm) cc_final: 0.7697 (ptmm) REVERT: C 215 LYS cc_start: 0.8210 (ttmt) cc_final: 0.7828 (ttmm) REVERT: E 1 MET cc_start: 0.7055 (mtm) cc_final: 0.6826 (mtm) REVERT: E 6 ILE cc_start: 0.6877 (tp) cc_final: 0.6415 (tp) REVERT: E 15 LYS cc_start: 0.8516 (mtmt) cc_final: 0.8057 (mmtm) REVERT: E 36 THR cc_start: 0.7537 (p) cc_final: 0.7087 (p) REVERT: E 46 GLN cc_start: 0.7944 (tm-30) cc_final: 0.7553 (tm-30) REVERT: E 49 LEU cc_start: 0.7339 (mt) cc_final: 0.7040 (mt) REVERT: E 101 LYS cc_start: 0.8606 (pttm) cc_final: 0.8228 (pttm) REVERT: E 126 SER cc_start: 0.8370 (t) cc_final: 0.7853 (p) REVERT: E 127 THR cc_start: 0.7999 (m) cc_final: 0.7700 (m) REVERT: E 135 THR cc_start: 0.7899 (m) cc_final: 0.7641 (p) REVERT: E 174 ILE cc_start: 0.8017 (mm) cc_final: 0.7663 (tp) REVERT: E 209 ASN cc_start: 0.6688 (m-40) cc_final: 0.6342 (m-40) REVERT: E 236 MET cc_start: 0.7459 (ptp) cc_final: 0.7258 (ptp) REVERT: E 274 LYS cc_start: 0.7088 (mppt) cc_final: 0.6604 (mppt) REVERT: E 283 GLU cc_start: 0.6919 (mp0) cc_final: 0.6544 (mp0) REVERT: E 290 PRO cc_start: 0.8035 (Cg_endo) cc_final: 0.7590 (Cg_exo) REVERT: E 325 GLN cc_start: 0.7339 (tp40) cc_final: 0.6972 (tp-100) REVERT: E 326 GLU cc_start: 0.7668 (tp30) cc_final: 0.6505 (tp30) REVERT: E 329 HIS cc_start: 0.7157 (m90) cc_final: 0.5792 (m90) REVERT: E 363 LYS cc_start: 0.8309 (mmtt) cc_final: 0.8052 (mmtp) REVERT: E 397 LYS cc_start: 0.7721 (mmmt) cc_final: 0.7378 (mmtp) outliers start: 0 outliers final: 0 residues processed: 343 average time/residue: 0.1181 time to fit residues: 53.5106 Evaluate side-chains 309 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 309 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 34 optimal weight: 0.1980 chunk 101 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 109 optimal weight: 0.0870 chunk 36 optimal weight: 2.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 ASN E 288 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.134943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.113552 restraints weight = 18742.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.116106 restraints weight = 11941.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.117884 restraints weight = 8540.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.119148 restraints weight = 6661.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.120029 restraints weight = 5543.605| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3543 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3543 r_free = 0.3543 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3543 r_free = 0.3543 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3543 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10900 Z= 0.152 Angle : 0.690 11.513 14963 Z= 0.372 Chirality : 0.047 0.238 1723 Planarity : 0.004 0.048 1683 Dihedral : 21.339 158.125 1931 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 0.10 % Allowed : 0.29 % Favored : 99.61 % 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: -2.23 (0.24), residues: 1171 helix: -0.63 (0.30), residues: 305 sheet: 0.02 (0.31), residues: 317 loop : -3.00 (0.23), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 103 TYR 0.021 0.002 TYR B 197 PHE 0.038 0.002 PHE C 65 TRP 0.027 0.002 TRP E 50 HIS 0.004 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (10899) covalent geometry : angle 0.68970 / 0.37 (14963) hydrogen bonds : bond 0.05077 / 3.35 ( 386) hydrogen bonds : angle 5.33828 / 3.62 ( 1003) Misc. bond : bond 0.00067 / 0.04 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 342 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 ASP cc_start: 0.7881 (t70) cc_final: 0.7576 (t0) REVERT: A 57 LEU cc_start: 0.8107 (mt) cc_final: 0.7795 (mt) REVERT: A 59 GLU cc_start: 0.8395 (tp30) cc_final: 0.8117 (tp30) REVERT: A 69 LYS cc_start: 0.7709 (mppt) cc_final: 0.7272 (pttm) REVERT: A 93 GLU cc_start: 0.8771 (pp20) cc_final: 0.8213 (pp20) REVERT: A 99 LYS cc_start: 0.7937 (ttmt) cc_final: 0.7584 (mtpp) REVERT: A 116 LYS cc_start: 0.7948 (mtmm) cc_final: 0.7641 (tppt) REVERT: A 144 ASN cc_start: 0.7474 (OUTLIER) cc_final: 0.7246 (t0) REVERT: A 206 LYS cc_start: 0.8095 (ttmm) cc_final: 0.7874 (ttmm) REVERT: B 21 ASP cc_start: 0.7520 (t0) cc_final: 0.6530 (t0) REVERT: B 33 GLU cc_start: 0.7375 (mp0) cc_final: 0.7146 (mm-30) REVERT: B 107 THR cc_start: 0.8150 (p) cc_final: 0.7761 (t) REVERT: B 132 LYS cc_start: 0.8216 (ttmt) cc_final: 0.7891 (ttmm) REVERT: B 145 ASP cc_start: 0.6404 (t0) cc_final: 0.5920 (t70) REVERT: B 159 LYS cc_start: 0.7830 (ttmm) cc_final: 0.7526 (ttmm) REVERT: B 162 LYS cc_start: 0.7829 (mttp) cc_final: 0.7481 (mttp) REVERT: C 3 VAL cc_start: 0.8578 (t) cc_final: 0.8145 (p) REVERT: C 7 ASP cc_start: 0.7492 (t70) cc_final: 0.7172 (t0) REVERT: C 28 LYS cc_start: 0.8199 (mttm) cc_final: 0.7100 (mttm) REVERT: C 30 LYS cc_start: 0.7779 (mmtm) cc_final: 0.7438 (tppp) REVERT: C 35 GLU cc_start: 0.7053 (mp0) cc_final: 0.6418 (mp0) REVERT: C 72 GLN cc_start: 0.7687 (tt0) cc_final: 0.7298 (mt0) REVERT: C 75 MET cc_start: 0.7107 (tmm) cc_final: 0.6832 (tpp) REVERT: C 88 GLU cc_start: 0.6984 (pp20) cc_final: 0.6149 (pp20) REVERT: C 156 GLU cc_start: 0.7483 (tp30) cc_final: 0.6530 (tp30) REVERT: C 165 LYS cc_start: 0.7924 (pttp) cc_final: 0.7514 (ptpt) REVERT: C 171 GLU cc_start: 0.7367 (mm-30) cc_final: 0.6970 (mm-30) REVERT: C 193 LYS cc_start: 0.7391 (mptt) cc_final: 0.7028 (mptt) REVERT: C 205 LEU cc_start: 0.8255 (mt) cc_final: 0.7919 (tp) REVERT: C 209 LYS cc_start: 0.8113 (ptmm) cc_final: 0.7660 (ptmm) REVERT: C 215 LYS cc_start: 0.8086 (ttmt) cc_final: 0.7662 (ttmm) REVERT: E 6 ILE cc_start: 0.6723 (tp) cc_final: 0.6265 (tp) REVERT: E 15 LYS cc_start: 0.8496 (mtmt) cc_final: 0.8133 (mmtp) REVERT: E 36 THR cc_start: 0.7683 (p) cc_final: 0.7270 (p) REVERT: E 46 GLN cc_start: 0.7896 (tm-30) cc_final: 0.7567 (tm-30) REVERT: E 49 LEU cc_start: 0.7362 (mt) cc_final: 0.7118 (mt) REVERT: E 86 LYS cc_start: 0.7854 (tptm) cc_final: 0.7578 (mmmm) REVERT: E 101 LYS cc_start: 0.8555 (pttm) cc_final: 0.8268 (pttm) REVERT: E 126 SER cc_start: 0.8367 (t) cc_final: 0.7835 (p) REVERT: E 127 THR cc_start: 0.8026 (m) cc_final: 0.7691 (m) REVERT: E 135 THR cc_start: 0.7822 (m) cc_final: 0.7565 (p) REVERT: E 141 ASP cc_start: 0.7272 (m-30) cc_final: 0.7059 (m-30) REVERT: E 174 ILE cc_start: 0.8065 (mm) cc_final: 0.7677 (tp) REVERT: E 203 LEU cc_start: 0.7872 (mt) cc_final: 0.7563 (mt) REVERT: E 209 ASN cc_start: 0.6969 (m-40) cc_final: 0.6676 (m-40) REVERT: E 224 THR cc_start: 0.7192 (p) cc_final: 0.6924 (p) REVERT: E 225 LEU cc_start: 0.6940 (tp) cc_final: 0.6667 (tp) REVERT: E 283 GLU cc_start: 0.6847 (mp0) cc_final: 0.6489 (mp0) REVERT: E 290 PRO cc_start: 0.7931 (Cg_endo) cc_final: 0.7548 (Cg_exo) REVERT: E 325 GLN cc_start: 0.7339 (tp40) cc_final: 0.6959 (tp-100) REVERT: E 326 GLU cc_start: 0.7661 (tp30) cc_final: 0.6487 (tp30) REVERT: E 329 HIS cc_start: 0.7147 (m90) cc_final: 0.5798 (m90) REVERT: E 363 LYS cc_start: 0.8313 (mmtt) cc_final: 0.8057 (mmtp) REVERT: E 397 LYS cc_start: 0.7699 (mmmt) cc_final: 0.7348 (mmtp) outliers start: 1 outliers final: 0 residues processed: 342 average time/residue: 0.1329 time to fit residues: 59.9534 Evaluate side-chains 318 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 317 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 77 optimal weight: 9.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 ASN ** E 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.137373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.114241 restraints weight = 19061.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.117098 restraints weight = 11811.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.119132 restraints weight = 8363.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.120538 restraints weight = 6459.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.121409 restraints weight = 5341.492| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3559 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3559 r_free = 0.3559 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3559 r_free = 0.3559 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3559 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 10900 Z= 0.195 Angle : 0.730 12.123 14963 Z= 0.393 Chirality : 0.048 0.253 1723 Planarity : 0.005 0.048 1683 Dihedral : 21.406 158.711 1931 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.93 % Favored : 89.07 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: -2.30 (0.24), residues: 1171 helix: -0.75 (0.29), residues: 306 sheet: 0.15 (0.31), residues: 312 loop : -3.10 (0.22), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 103 TYR 0.022 0.002 TYR B 197 PHE 0.037 0.003 PHE C 65 TRP 0.035 0.003 TRP E 50 HIS 0.004 0.001 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.19 (10899) covalent geometry : angle 0.72960 / 0.39 (14963) hydrogen bonds : bond 0.05512 / 3.62 ( 386) hydrogen bonds : angle 5.39632 / 3.66 ( 1003) Misc. bond : bond 0.00079 / 0.04 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1794.80 seconds wall clock time: 31 minutes 42.28 seconds (1902.28 seconds total)