Starting phenix.real_space_refine on Sun Apr 5 18:14:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xjm_66940/04_2026/9xjm_66940.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xjm_66940/04_2026/9xjm_66940.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xjm_66940/04_2026/9xjm_66940.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xjm_66940/04_2026/9xjm_66940.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xjm_66940/04_2026/9xjm_66940.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xjm_66940/04_2026/9xjm_66940.map" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 7724 2.51 5 N 2112 2.21 5 O 2224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12112 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3028 Classifications: {'peptide': 377} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 362} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3028 Classifications: {'peptide': 377} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 362} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 3028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3028 Classifications: {'peptide': 377} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 362} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 3028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3028 Classifications: {'peptide': 377} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 362} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 2.70, per 1000 atoms: 0.22 Number of scatterers: 12112 At special positions: 0 Unit cell: (150.45, 130.05, 86.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 2224 8.00 N 2112 7.00 C 7724 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 311 " distance=2.04 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 311 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 311 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 311 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 535.8 milliseconds 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2808 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 16 sheets defined 39.4% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 18 through 33 removed outlier: 3.572A pdb=" N THR A 22 " --> pdb=" O ASP A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 69 removed outlier: 3.774A pdb=" N ARG A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 90 removed outlier: 3.549A pdb=" N CYS A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 130 removed outlier: 3.958A pdb=" N ASP A 127 " --> pdb=" O LEU A 123 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N HIS A 128 " --> pdb=" O SER A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 155 Processing helix chain 'A' and resid 170 through 184 removed outlier: 3.687A pdb=" N TYR A 174 " --> pdb=" O ASN A 170 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG A 175 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU A 179 " --> pdb=" O ARG A 175 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU A 180 " --> pdb=" O GLN A 176 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASP A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 208 removed outlier: 3.823A pdb=" N ASN A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A 203 " --> pdb=" O GLN A 199 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A 208 " --> pdb=" O GLN A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 236 removed outlier: 3.719A pdb=" N HIS A 234 " --> pdb=" O GLU A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 261 removed outlier: 3.877A pdb=" N LEU A 255 " --> pdb=" O MET A 251 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS A 260 " --> pdb=" O MET A 256 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS A 261 " --> pdb=" O ASP A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 298 removed outlier: 3.868A pdb=" N TYR A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 321 No H-bonds generated for 'chain 'A' and resid 319 through 321' Processing helix chain 'A' and resid 322 through 330 removed outlier: 3.504A pdb=" N GLU A 326 " --> pdb=" O GLY A 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 33 removed outlier: 3.576A pdb=" N THR B 22 " --> pdb=" O ASP B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 69 removed outlier: 3.778A pdb=" N ARG B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 90 removed outlier: 3.541A pdb=" N CYS B 90 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 130 removed outlier: 3.960A pdb=" N ASP B 127 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N HIS B 128 " --> pdb=" O SER B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 158 removed outlier: 3.633A pdb=" N GLN B 156 " --> pdb=" O GLU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 184 removed outlier: 3.878A pdb=" N TYR B 174 " --> pdb=" O ASN B 170 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ARG B 175 " --> pdb=" O ASP B 171 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN B 176 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU B 179 " --> pdb=" O ARG B 175 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU B 180 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASP B 182 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 208 removed outlier: 4.173A pdb=" N ASN B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 236 removed outlier: 3.710A pdb=" N HIS B 234 " --> pdb=" O GLU B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 261 removed outlier: 3.881A pdb=" N LEU B 255 " --> pdb=" O MET B 251 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS B 260 " --> pdb=" O MET B 256 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 298 removed outlier: 3.867A pdb=" N TYR B 282 " --> pdb=" O SER B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 330 removed outlier: 3.698A pdb=" N GLU B 326 " --> pdb=" O GLY B 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 33 removed outlier: 3.572A pdb=" N THR C 22 " --> pdb=" O ASP C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 69 removed outlier: 3.773A pdb=" N ARG C 69 " --> pdb=" O SER C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 90 removed outlier: 3.549A pdb=" N CYS C 90 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 130 removed outlier: 3.958A pdb=" N ASP C 127 " --> pdb=" O LEU C 123 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N HIS C 128 " --> pdb=" O SER C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 155 Processing helix chain 'C' and resid 170 through 184 removed outlier: 3.688A pdb=" N TYR C 174 " --> pdb=" O ASN C 170 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG C 175 " --> pdb=" O ASP C 171 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU C 179 " --> pdb=" O ARG C 175 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU C 180 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASP C 182 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG C 184 " --> pdb=" O GLU C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 208 removed outlier: 3.823A pdb=" N ASN C 200 " --> pdb=" O GLU C 196 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU C 203 " --> pdb=" O GLN C 199 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL C 206 " --> pdb=" O LEU C 202 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL C 208 " --> pdb=" O GLN C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 236 removed outlier: 3.719A pdb=" N HIS C 234 " --> pdb=" O GLU C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 261 removed outlier: 3.878A pdb=" N LEU C 255 " --> pdb=" O MET C 251 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS C 260 " --> pdb=" O MET C 256 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS C 261 " --> pdb=" O ASP C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 298 removed outlier: 3.868A pdb=" N TYR C 282 " --> pdb=" O SER C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 321 No H-bonds generated for 'chain 'C' and resid 319 through 321' Processing helix chain 'C' and resid 322 through 330 removed outlier: 3.504A pdb=" N GLU C 326 " --> pdb=" O GLY C 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 33 removed outlier: 3.575A pdb=" N THR D 22 " --> pdb=" O ASP D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 69 removed outlier: 3.778A pdb=" N ARG D 69 " --> pdb=" O SER D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 90 removed outlier: 3.541A pdb=" N CYS D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 130 removed outlier: 3.959A pdb=" N ASP D 127 " --> pdb=" O LEU D 123 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N HIS D 128 " --> pdb=" O SER D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 158 removed outlier: 3.633A pdb=" N GLN D 156 " --> pdb=" O GLU D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 184 removed outlier: 3.878A pdb=" N TYR D 174 " --> pdb=" O ASN D 170 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ARG D 175 " --> pdb=" O ASP D 171 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN D 176 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU D 179 " --> pdb=" O ARG D 175 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU D 180 " --> pdb=" O GLN D 176 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASP D 182 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG D 184 " --> pdb=" O GLU D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 208 removed outlier: 4.172A pdb=" N ASN D 200 " --> pdb=" O GLU D 196 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL D 206 " --> pdb=" O LEU D 202 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL D 208 " --> pdb=" O GLN D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 236 removed outlier: 3.710A pdb=" N HIS D 234 " --> pdb=" O GLU D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 261 removed outlier: 3.881A pdb=" N LEU D 255 " --> pdb=" O MET D 251 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS D 260 " --> pdb=" O MET D 256 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS D 261 " --> pdb=" O ASP D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 298 removed outlier: 3.867A pdb=" N TYR D 282 " --> pdb=" O SER D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 330 removed outlier: 3.699A pdb=" N GLU D 326 " --> pdb=" O GLY D 322 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 48 removed outlier: 7.615A pdb=" N GLN A 8 " --> pdb=" O ALA A 73 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N PHE A 75 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLY A 10 " --> pdb=" O PHE A 75 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU A 97 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 164 through 165 removed outlier: 6.394A pdb=" N LEU A 137 " --> pdb=" O ASP A 192 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 216 through 217 removed outlier: 4.826A pdb=" N VAL A 239 " --> pdb=" O LEU A 359 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N MET A 354 " --> pdb=" O TYR A 369 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N TYR A 369 " --> pdb=" O MET A 354 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL A 356 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 333 through 336 Processing sheet with id=AA5, first strand: chain 'B' and resid 45 through 48 removed outlier: 7.617A pdb=" N GLN B 8 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 8.799A pdb=" N PHE B 75 " --> pdb=" O GLN B 8 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLY B 10 " --> pdb=" O PHE B 75 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU B 97 " --> pdb=" O LEU B 112 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 164 through 165 removed outlier: 6.459A pdb=" N LEU B 137 " --> pdb=" O ASP B 192 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 216 through 217 removed outlier: 4.839A pdb=" N VAL B 239 " --> pdb=" O LEU B 359 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N MET B 354 " --> pdb=" O TYR B 369 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N TYR B 369 " --> pdb=" O MET B 354 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL B 356 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 333 through 336 Processing sheet with id=AA9, first strand: chain 'C' and resid 45 through 48 removed outlier: 7.615A pdb=" N GLN C 8 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N PHE C 75 " --> pdb=" O GLN C 8 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLY C 10 " --> pdb=" O PHE C 75 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU C 97 " --> pdb=" O LEU C 112 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 164 through 165 removed outlier: 6.394A pdb=" N LEU C 137 " --> pdb=" O ASP C 192 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 216 through 217 removed outlier: 4.826A pdb=" N VAL C 239 " --> pdb=" O LEU C 359 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N MET C 354 " --> pdb=" O TYR C 369 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N TYR C 369 " --> pdb=" O MET C 354 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL C 356 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 333 through 336 Processing sheet with id=AB4, first strand: chain 'D' and resid 45 through 48 removed outlier: 7.619A pdb=" N GLN D 8 " --> pdb=" O ALA D 73 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N PHE D 75 " --> pdb=" O GLN D 8 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLY D 10 " --> pdb=" O PHE D 75 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU D 97 " --> pdb=" O LEU D 112 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 164 through 165 removed outlier: 6.458A pdb=" N LEU D 137 " --> pdb=" O ASP D 192 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 216 through 217 removed outlier: 4.840A pdb=" N VAL D 239 " --> pdb=" O LEU D 359 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N MET D 354 " --> pdb=" O TYR D 369 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N TYR D 369 " --> pdb=" O MET D 354 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL D 356 " --> pdb=" O VAL D 367 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 333 through 336 420 hydrogen bonds defined for protein. 1248 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.94 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3992 1.34 - 1.46: 2835 1.46 - 1.58: 5489 1.58 - 1.70: 0 1.70 - 1.82: 80 Bond restraints: 12396 Sorted by residual: bond pdb=" N GLU B 203 " pdb=" CA GLU B 203 " ideal model delta sigma weight residual 1.457 1.485 -0.027 1.29e-02 6.01e+03 4.43e+00 bond pdb=" N GLN B 204 " pdb=" CA GLN B 204 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.23e-02 6.61e+03 4.24e+00 bond pdb=" N GLU D 203 " pdb=" CA GLU D 203 " ideal model delta sigma weight residual 1.459 1.482 -0.023 1.24e-02 6.50e+03 3.48e+00 bond pdb=" N LEU B 202 " pdb=" CA LEU B 202 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.21e-02 6.83e+03 3.42e+00 bond pdb=" C ALA A 40 " pdb=" N PRO A 41 " ideal model delta sigma weight residual 1.334 1.372 -0.038 2.34e-02 1.83e+03 2.64e+00 ... (remaining 12391 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 16362 1.81 - 3.62: 350 3.62 - 5.43: 56 5.43 - 7.24: 14 7.24 - 9.04: 6 Bond angle restraints: 16788 Sorted by residual: angle pdb=" N LEU B 202 " pdb=" CA LEU B 202 " pdb=" C LEU B 202 " ideal model delta sigma weight residual 111.28 107.03 4.25 1.09e+00 8.42e-01 1.52e+01 angle pdb=" N GLU D 203 " pdb=" CA GLU D 203 " pdb=" C GLU D 203 " ideal model delta sigma weight residual 111.40 107.24 4.16 1.22e+00 6.72e-01 1.16e+01 angle pdb=" CG1 ILE B 300 " pdb=" CB ILE B 300 " pdb=" CG2 ILE B 300 " ideal model delta sigma weight residual 110.70 101.66 9.04 3.00e+00 1.11e-01 9.09e+00 angle pdb=" CG1 ILE D 300 " pdb=" CB ILE D 300 " pdb=" CG2 ILE D 300 " ideal model delta sigma weight residual 110.70 101.66 9.04 3.00e+00 1.11e-01 9.08e+00 angle pdb=" CG1 ILE C 300 " pdb=" CB ILE C 300 " pdb=" CG2 ILE C 300 " ideal model delta sigma weight residual 110.70 101.94 8.76 3.00e+00 1.11e-01 8.53e+00 ... (remaining 16783 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 6249 17.44 - 34.87: 821 34.87 - 52.31: 235 52.31 - 69.74: 45 69.74 - 87.18: 6 Dihedral angle restraints: 7356 sinusoidal: 2984 harmonic: 4372 Sorted by residual: dihedral pdb=" CA ASN C 170 " pdb=" C ASN C 170 " pdb=" N ASP C 171 " pdb=" CA ASP C 171 " ideal model delta harmonic sigma weight residual 180.00 162.50 17.50 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA ASN A 170 " pdb=" C ASN A 170 " pdb=" N ASP A 171 " pdb=" CA ASP A 171 " ideal model delta harmonic sigma weight residual 180.00 162.50 17.50 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA PHE D 134 " pdb=" C PHE D 134 " pdb=" N VAL D 135 " pdb=" CA VAL D 135 " ideal model delta harmonic sigma weight residual -180.00 -162.82 -17.18 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 7353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1243 0.044 - 0.088: 484 0.088 - 0.132: 83 0.132 - 0.175: 14 0.175 - 0.219: 4 Chirality restraints: 1828 Sorted by residual: chirality pdb=" CB ILE D 300 " pdb=" CA ILE D 300 " pdb=" CG1 ILE D 300 " pdb=" CG2 ILE D 300 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB ILE B 300 " pdb=" CA ILE B 300 " pdb=" CG1 ILE B 300 " pdb=" CG2 ILE B 300 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CB ILE C 300 " pdb=" CA ILE C 300 " pdb=" CG1 ILE C 300 " pdb=" CG2 ILE C 300 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 1825 not shown) Planarity restraints: 2180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 363 " 0.027 5.00e-02 4.00e+02 4.05e-02 2.63e+00 pdb=" N PRO C 364 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO C 364 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 364 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 363 " -0.027 5.00e-02 4.00e+02 4.05e-02 2.62e+00 pdb=" N PRO A 364 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 364 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 364 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 218 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.61e+00 pdb=" C ILE C 218 " -0.028 2.00e-02 2.50e+03 pdb=" O ILE C 218 " 0.010 2.00e-02 2.50e+03 pdb=" N ILE C 219 " 0.009 2.00e-02 2.50e+03 ... (remaining 2177 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 183 2.68 - 3.23: 10517 3.23 - 3.79: 16373 3.79 - 4.34: 22265 4.34 - 4.90: 39569 Nonbonded interactions: 88907 Sorted by model distance: nonbonded pdb=" NE2 HIS B 211 " pdb=" O SER D 207 " model vdw 2.124 3.120 nonbonded pdb=" O SER B 207 " pdb=" NE2 HIS D 211 " model vdw 2.126 3.120 nonbonded pdb=" OD2 ASP C 139 " pdb=" NH1 ARG C 197 " model vdw 2.206 3.120 nonbonded pdb=" OD2 ASP A 139 " pdb=" NH1 ARG A 197 " model vdw 2.206 3.120 nonbonded pdb=" OD2 ASP D 139 " pdb=" NH1 ARG D 197 " model vdw 2.216 3.120 ... (remaining 88902 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 11.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.650 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 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 : 0.005 0.038 12400 Z= 0.211 Angle : 0.699 9.045 16796 Z= 0.377 Chirality : 0.046 0.219 1828 Planarity : 0.004 0.041 2180 Dihedral : 17.172 87.179 4536 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 0.00 % Allowed : 26.37 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.91 (0.21), residues: 1500 helix: -1.33 (0.20), residues: 628 sheet: -2.02 (0.33), residues: 232 loop : -2.42 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 293 TYR 0.014 0.002 TYR D 282 PHE 0.018 0.002 PHE A 134 TRP 0.007 0.001 TRP D 259 HIS 0.004 0.001 HIS B 211 Details of bonding type rmsd covalent geometry : bond 0.00496 (12396) covalent geometry : angle 0.69866 (16788) SS BOND : bond 0.00295 ( 4) SS BOND : angle 1.26702 ( 8) hydrogen bonds : bond 0.20679 ( 420) hydrogen bonds : angle 5.94824 ( 1248) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 0.470 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: A 63 PHE cc_start: 0.6469 (t80) cc_final: 0.6049 (t80) REVERT: B 29 PHE cc_start: 0.7191 (t80) cc_final: 0.6954 (t80) REVERT: C 332 VAL cc_start: 0.7411 (p) cc_final: 0.6409 (p) outliers start: 0 outliers final: 0 residues processed: 363 average time/residue: 0.1376 time to fit residues: 67.0356 Evaluate side-chains 140 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.0970 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 GLN A 148 GLN A 160 HIS A 298 GLN A 335 GLN A 340 ASN B 66 GLN ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 16 ASN C 61 ASN C 160 HIS C 199 GLN ** C 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 GLN C 340 ASN ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 HIS D 345 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.104167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.086953 restraints weight = 37948.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.089656 restraints weight = 21795.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.091481 restraints weight = 14951.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.092764 restraints weight = 11498.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.093678 restraints weight = 9485.360| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12400 Z= 0.160 Angle : 0.705 11.888 16796 Z= 0.361 Chirality : 0.045 0.198 1828 Planarity : 0.004 0.050 2180 Dihedral : 4.524 20.098 1660 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 2.96 % Allowed : 26.29 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 (0.21), residues: 1500 helix: -0.44 (0.21), residues: 600 sheet: -0.77 (0.37), residues: 212 loop : -2.35 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 231 TYR 0.028 0.002 TYR B 369 PHE 0.013 0.001 PHE D 42 TRP 0.015 0.002 TRP A 370 HIS 0.008 0.002 HIS D 94 Details of bonding type rmsd covalent geometry : bond 0.00361 (12396) covalent geometry : angle 0.70489 (16788) SS BOND : bond 0.00227 ( 4) SS BOND : angle 1.50431 ( 8) hydrogen bonds : bond 0.04761 ( 420) hydrogen bonds : angle 4.13901 ( 1248) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 149 time to evaluate : 0.387 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 63 PHE cc_start: 0.7289 (t80) cc_final: 0.6791 (t80) REVERT: A 141 ASP cc_start: 0.7154 (t0) cc_final: 0.6949 (t70) REVERT: A 208 VAL cc_start: 0.8693 (t) cc_final: 0.8399 (p) REVERT: A 221 ASN cc_start: 0.7486 (OUTLIER) cc_final: 0.6870 (t0) REVERT: A 325 MET cc_start: 0.7566 (tmm) cc_final: 0.7345 (tmm) REVERT: B 49 ASP cc_start: 0.7454 (t0) cc_final: 0.6898 (p0) REVERT: B 196 GLU cc_start: 0.8305 (pm20) cc_final: 0.7860 (pp20) REVERT: D 278 SER cc_start: 0.9338 (m) cc_final: 0.8799 (t) REVERT: D 374 ASP cc_start: 0.7640 (p0) cc_final: 0.7420 (p0) outliers start: 39 outliers final: 19 residues processed: 184 average time/residue: 0.1127 time to fit residues: 29.5917 Evaluate side-chains 128 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain D residue 5 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 182 ASP Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 345 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 61 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 114 optimal weight: 0.5980 chunk 42 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 0.4980 chunk 91 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS A 113 GLN ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 GLN C 160 HIS C 176 GLN C 298 GLN D 16 ASN D 47 HIS ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 HIS ** D 345 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.098583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.081066 restraints weight = 39803.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.083583 restraints weight = 23778.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.085297 restraints weight = 16818.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.086466 restraints weight = 13274.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.087290 restraints weight = 11206.798| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.4554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 12400 Z= 0.212 Angle : 0.693 10.211 16796 Z= 0.354 Chirality : 0.044 0.184 1828 Planarity : 0.005 0.052 2180 Dihedral : 4.577 21.140 1660 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 4.86 % Allowed : 24.32 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.60 (0.22), residues: 1500 helix: 0.13 (0.21), residues: 632 sheet: -1.48 (0.33), residues: 268 loop : -2.11 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 231 TYR 0.019 0.002 TYR A 144 PHE 0.017 0.002 PHE C 136 TRP 0.025 0.002 TRP A 319 HIS 0.038 0.002 HIS D 345 Details of bonding type rmsd covalent geometry : bond 0.00475 (12396) covalent geometry : angle 0.69230 (16788) SS BOND : bond 0.00362 ( 4) SS BOND : angle 1.04693 ( 8) hydrogen bonds : bond 0.04463 ( 420) hydrogen bonds : angle 4.10423 ( 1248) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 124 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ASP cc_start: 0.7246 (t0) cc_final: 0.6946 (t0) REVERT: A 325 MET cc_start: 0.7755 (tmm) cc_final: 0.7489 (tmm) REVERT: B 49 ASP cc_start: 0.7544 (t0) cc_final: 0.7235 (p0) REVERT: B 265 ARG cc_start: 0.7339 (mmp80) cc_final: 0.6912 (mmp80) REVERT: C 151 MET cc_start: 0.8576 (mmp) cc_final: 0.8355 (mmp) REVERT: D 15 ARG cc_start: 0.7109 (OUTLIER) cc_final: 0.6738 (ptp-170) REVERT: D 221 ASN cc_start: 0.8551 (t0) cc_final: 0.8342 (t0) outliers start: 64 outliers final: 35 residues processed: 184 average time/residue: 0.1139 time to fit residues: 29.9603 Evaluate side-chains 135 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 99 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain D residue 5 SER Chi-restraints excluded: chain D residue 15 ARG Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 182 ASP Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 345 HIS Chi-restraints excluded: chain D residue 378 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 69 optimal weight: 0.3980 chunk 5 optimal weight: 0.9980 chunk 68 optimal weight: 6.9990 chunk 7 optimal weight: 0.3980 chunk 143 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 141 optimal weight: 6.9990 chunk 70 optimal weight: 0.0040 chunk 80 optimal weight: 0.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 GLN D 298 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.100323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.082963 restraints weight = 38251.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.085605 restraints weight = 22206.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.087404 restraints weight = 15366.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.088661 restraints weight = 11875.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.089476 restraints weight = 9855.269| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.4838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12400 Z= 0.114 Angle : 0.636 11.950 16796 Z= 0.314 Chirality : 0.042 0.157 1828 Planarity : 0.004 0.114 2180 Dihedral : 4.219 20.060 1660 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.96 % Allowed : 25.76 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.32 (0.22), residues: 1500 helix: 0.39 (0.22), residues: 624 sheet: -1.49 (0.32), residues: 276 loop : -1.87 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 69 TYR 0.025 0.001 TYR B 369 PHE 0.018 0.001 PHE A 224 TRP 0.021 0.001 TRP A 319 HIS 0.005 0.001 HIS D 345 Details of bonding type rmsd covalent geometry : bond 0.00262 (12396) covalent geometry : angle 0.63644 (16788) SS BOND : bond 0.00241 ( 4) SS BOND : angle 0.64186 ( 8) hydrogen bonds : bond 0.03308 ( 420) hydrogen bonds : angle 3.75079 ( 1248) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 115 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ASP cc_start: 0.7004 (t0) cc_final: 0.6733 (t0) REVERT: A 221 ASN cc_start: 0.7697 (OUTLIER) cc_final: 0.7118 (t0) REVERT: A 370 TRP cc_start: 0.8495 (t-100) cc_final: 0.8103 (t60) REVERT: B 49 ASP cc_start: 0.7592 (t0) cc_final: 0.7225 (p0) REVERT: B 265 ARG cc_start: 0.7403 (mmp80) cc_final: 0.6950 (mmp80) REVERT: B 325 MET cc_start: 0.8132 (tpp) cc_final: 0.7789 (tpt) REVERT: D 221 ASN cc_start: 0.8499 (t0) cc_final: 0.8183 (t0) outliers start: 39 outliers final: 21 residues processed: 150 average time/residue: 0.1126 time to fit residues: 24.2360 Evaluate side-chains 120 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain D residue 5 SER Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 378 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 86 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 42 optimal weight: 0.1980 chunk 111 optimal weight: 7.9990 chunk 131 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 113 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 = 0.3778 r_free = 0.3778 target = 0.100010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.082528 restraints weight = 39571.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.085133 restraints weight = 23243.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.086940 restraints weight = 16201.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.088187 restraints weight = 12600.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.089049 restraints weight = 10524.744| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.5137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12400 Z= 0.115 Angle : 0.614 11.472 16796 Z= 0.304 Chirality : 0.042 0.170 1828 Planarity : 0.003 0.065 2180 Dihedral : 4.068 18.867 1660 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 3.19 % Allowed : 25.30 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.20 (0.22), residues: 1500 helix: 0.51 (0.21), residues: 620 sheet: -1.41 (0.33), residues: 276 loop : -1.83 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 69 TYR 0.027 0.001 TYR B 369 PHE 0.018 0.001 PHE A 63 TRP 0.010 0.001 TRP A 259 HIS 0.004 0.001 HIS D 47 Details of bonding type rmsd covalent geometry : bond 0.00272 (12396) covalent geometry : angle 0.61363 (16788) SS BOND : bond 0.00147 ( 4) SS BOND : angle 0.50151 ( 8) hydrogen bonds : bond 0.03169 ( 420) hydrogen bonds : angle 3.67608 ( 1248) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 108 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ASP cc_start: 0.7108 (t0) cc_final: 0.6866 (t0) REVERT: A 221 ASN cc_start: 0.7658 (OUTLIER) cc_final: 0.6959 (t0) REVERT: A 224 PHE cc_start: 0.7621 (t80) cc_final: 0.7323 (t80) REVERT: A 370 TRP cc_start: 0.8495 (t-100) cc_final: 0.8162 (t60) REVERT: B 49 ASP cc_start: 0.7630 (t0) cc_final: 0.7286 (p0) REVERT: B 265 ARG cc_start: 0.7450 (mmp80) cc_final: 0.6971 (mmp80) REVERT: D 221 ASN cc_start: 0.8498 (t0) cc_final: 0.8154 (t0) REVERT: D 267 TYR cc_start: 0.6521 (m-10) cc_final: 0.6263 (m-80) outliers start: 42 outliers final: 25 residues processed: 147 average time/residue: 0.1090 time to fit residues: 23.3524 Evaluate side-chains 127 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain D residue 5 SER Chi-restraints excluded: chain D residue 15 ARG Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 378 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 63 optimal weight: 9.9990 chunk 31 optimal weight: 8.9990 chunk 113 optimal weight: 0.9990 chunk 73 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 146 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 HIS B 84 HIS ** D 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 HIS D 345 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.094888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.077611 restraints weight = 39639.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.080065 restraints weight = 23600.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.081750 restraints weight = 16658.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.082911 restraints weight = 13061.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.083740 restraints weight = 11011.141| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.5845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 12400 Z= 0.217 Angle : 0.700 11.949 16796 Z= 0.355 Chirality : 0.045 0.225 1828 Planarity : 0.005 0.057 2180 Dihedral : 4.500 19.204 1660 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 4.26 % Allowed : 24.47 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.19 (0.22), residues: 1500 helix: 0.53 (0.21), residues: 640 sheet: -1.66 (0.32), residues: 276 loop : -1.78 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 296 TYR 0.028 0.002 TYR B 369 PHE 0.028 0.002 PHE C 136 TRP 0.015 0.002 TRP A 259 HIS 0.005 0.001 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00494 (12396) covalent geometry : angle 0.69974 (16788) SS BOND : bond 0.00169 ( 4) SS BOND : angle 0.49066 ( 8) hydrogen bonds : bond 0.04319 ( 420) hydrogen bonds : angle 4.10537 ( 1248) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 107 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.7314 (ttm-80) REVERT: A 141 ASP cc_start: 0.6712 (t0) cc_final: 0.6470 (t70) REVERT: A 216 HIS cc_start: 0.7674 (t-170) cc_final: 0.7364 (t-90) REVERT: A 224 PHE cc_start: 0.7810 (t80) cc_final: 0.7603 (t80) REVERT: A 370 TRP cc_start: 0.8596 (t-100) cc_final: 0.8234 (t60) REVERT: B 265 ARG cc_start: 0.7545 (mmp80) cc_final: 0.7076 (mmp80) REVERT: C 12 LEU cc_start: 0.8592 (tp) cc_final: 0.8382 (tp) REVERT: C 151 MET cc_start: 0.8671 (mmp) cc_final: 0.8459 (mmp) REVERT: C 187 LYS cc_start: 0.6903 (mmtt) cc_final: 0.6264 (mmtm) REVERT: C 217 TYR cc_start: 0.7127 (m-10) cc_final: 0.6886 (m-10) REVERT: D 221 ASN cc_start: 0.8679 (t0) cc_final: 0.8399 (t0) outliers start: 56 outliers final: 42 residues processed: 160 average time/residue: 0.1138 time to fit residues: 26.0821 Evaluate side-chains 131 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 88 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 119 ARG Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 334 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 355 ASP Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 182 ASP Chi-restraints excluded: chain C residue 216 HIS Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain D residue 5 SER Chi-restraints excluded: chain D residue 15 ARG Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 182 ASP Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 287 VAL Chi-restraints excluded: chain D residue 345 HIS Chi-restraints excluded: chain D residue 378 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 65 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 100 optimal weight: 0.3980 chunk 78 optimal weight: 5.9990 chunk 26 optimal weight: 0.0020 chunk 133 optimal weight: 5.9990 chunk 105 optimal weight: 0.0770 chunk 140 optimal weight: 0.8980 chunk 143 optimal weight: 0.7980 chunk 13 optimal weight: 7.9990 overall best weight: 0.4346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 113 GLN D 345 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.093678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.075687 restraints weight = 38638.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.078226 restraints weight = 22427.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.079977 restraints weight = 15598.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.081192 restraints weight = 12153.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.082053 restraints weight = 10173.611| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.5956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12400 Z= 0.113 Angle : 0.630 11.322 16796 Z= 0.314 Chirality : 0.043 0.190 1828 Planarity : 0.004 0.043 2180 Dihedral : 4.155 19.520 1660 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 2.81 % Allowed : 27.13 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.02 (0.22), residues: 1500 helix: 0.64 (0.21), residues: 628 sheet: -1.53 (0.32), residues: 276 loop : -1.61 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 183 TYR 0.022 0.001 TYR B 369 PHE 0.026 0.001 PHE D 29 TRP 0.026 0.001 TRP A 319 HIS 0.013 0.001 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00260 (12396) covalent geometry : angle 0.63024 (16788) SS BOND : bond 0.00171 ( 4) SS BOND : angle 0.46688 ( 8) hydrogen bonds : bond 0.03180 ( 420) hydrogen bonds : angle 3.76959 ( 1248) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 112 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ASP cc_start: 0.6749 (t0) cc_final: 0.6472 (t70) REVERT: A 221 ASN cc_start: 0.7710 (OUTLIER) cc_final: 0.7129 (t0) REVERT: A 224 PHE cc_start: 0.7908 (t80) cc_final: 0.7680 (t80) REVERT: A 370 TRP cc_start: 0.8518 (t-100) cc_final: 0.8255 (t60) REVERT: B 196 GLU cc_start: 0.8535 (pm20) cc_final: 0.8053 (pp20) REVERT: B 265 ARG cc_start: 0.7586 (mmp80) cc_final: 0.7106 (mmp80) REVERT: C 81 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7035 (mtm-85) REVERT: C 151 MET cc_start: 0.8559 (mmp) cc_final: 0.8343 (mmp) REVERT: C 187 LYS cc_start: 0.6749 (mmtt) cc_final: 0.6216 (mmtm) REVERT: C 217 TYR cc_start: 0.7220 (m-10) cc_final: 0.6998 (m-10) REVERT: D 99 THR cc_start: 0.8991 (OUTLIER) cc_final: 0.8707 (p) REVERT: D 221 ASN cc_start: 0.8677 (t0) cc_final: 0.8322 (t0) outliers start: 37 outliers final: 28 residues processed: 146 average time/residue: 0.1053 time to fit residues: 22.5831 Evaluate side-chains 129 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 98 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 319 TRP Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 81 ARG Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain D residue 5 SER Chi-restraints excluded: chain D residue 15 ARG Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 345 HIS Chi-restraints excluded: chain D residue 378 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 59 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 26 optimal weight: 0.0170 chunk 98 optimal weight: 0.7980 chunk 125 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 107 optimal weight: 0.0030 chunk 105 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 overall best weight: 1.3430 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 HIS A 216 HIS D 345 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.092592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.074789 restraints weight = 38922.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.077286 restraints weight = 22598.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.079004 restraints weight = 15697.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.080204 restraints weight = 12220.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.081056 restraints weight = 10222.309| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.6145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12400 Z= 0.130 Angle : 0.623 10.967 16796 Z= 0.312 Chirality : 0.042 0.173 1828 Planarity : 0.003 0.038 2180 Dihedral : 4.091 20.635 1660 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 3.19 % Allowed : 27.05 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.22), residues: 1500 helix: 0.74 (0.22), residues: 632 sheet: -1.55 (0.32), residues: 276 loop : -1.54 (0.26), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 119 TYR 0.022 0.001 TYR B 369 PHE 0.030 0.001 PHE D 29 TRP 0.025 0.001 TRP A 319 HIS 0.012 0.001 HIS D 345 Details of bonding type rmsd covalent geometry : bond 0.00305 (12396) covalent geometry : angle 0.62337 (16788) SS BOND : bond 0.00120 ( 4) SS BOND : angle 0.39517 ( 8) hydrogen bonds : bond 0.03208 ( 420) hydrogen bonds : angle 3.75578 ( 1248) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 96 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 ASN cc_start: 0.7621 (OUTLIER) cc_final: 0.7033 (t0) REVERT: A 224 PHE cc_start: 0.7971 (t80) cc_final: 0.7755 (t80) REVERT: A 231 ARG cc_start: 0.8014 (mpp-170) cc_final: 0.6745 (mmm160) REVERT: A 370 TRP cc_start: 0.8562 (t-100) cc_final: 0.8275 (t60) REVERT: B 196 GLU cc_start: 0.8579 (pm20) cc_final: 0.8136 (pp20) REVERT: B 265 ARG cc_start: 0.7611 (mmp80) cc_final: 0.7128 (mmp80) REVERT: C 81 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.6941 (mtm-85) REVERT: C 151 MET cc_start: 0.8562 (mmp) cc_final: 0.8305 (mmp) REVERT: C 187 LYS cc_start: 0.6831 (mmtt) cc_final: 0.6023 (mmtm) REVERT: D 99 THR cc_start: 0.9053 (OUTLIER) cc_final: 0.8737 (p) REVERT: D 221 ASN cc_start: 0.8721 (t0) cc_final: 0.8331 (t0) outliers start: 42 outliers final: 33 residues processed: 135 average time/residue: 0.1093 time to fit residues: 21.3752 Evaluate side-chains 127 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 91 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 82 SER Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 211 HIS Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 319 TRP Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 81 ARG Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain D residue 5 SER Chi-restraints excluded: chain D residue 15 ARG Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 345 HIS Chi-restraints excluded: chain D residue 378 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 69 optimal weight: 0.8980 chunk 47 optimal weight: 0.3980 chunk 124 optimal weight: 0.9990 chunk 105 optimal weight: 8.9990 chunk 82 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 49 optimal weight: 0.0970 chunk 57 optimal weight: 4.9990 chunk 20 optimal weight: 0.0870 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.093883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.075973 restraints weight = 38745.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.078502 restraints weight = 22583.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.080235 restraints weight = 15716.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.081451 restraints weight = 12274.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.082243 restraints weight = 10272.665| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.6198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12400 Z= 0.108 Angle : 0.624 11.170 16796 Z= 0.310 Chirality : 0.042 0.275 1828 Planarity : 0.003 0.035 2180 Dihedral : 3.988 21.061 1660 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.36 % Allowed : 27.81 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.23), residues: 1500 helix: 0.81 (0.22), residues: 628 sheet: -1.49 (0.32), residues: 276 loop : -1.45 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 69 TYR 0.021 0.001 TYR B 369 PHE 0.033 0.001 PHE D 29 TRP 0.023 0.001 TRP A 319 HIS 0.014 0.001 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00250 (12396) covalent geometry : angle 0.62382 (16788) SS BOND : bond 0.00155 ( 4) SS BOND : angle 0.41684 ( 8) hydrogen bonds : bond 0.02919 ( 420) hydrogen bonds : angle 3.65268 ( 1248) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 ASN cc_start: 0.7578 (OUTLIER) cc_final: 0.7016 (t0) REVERT: A 231 ARG cc_start: 0.7863 (mpp-170) cc_final: 0.6643 (mmm160) REVERT: A 370 TRP cc_start: 0.8548 (t-100) cc_final: 0.8307 (t60) REVERT: B 196 GLU cc_start: 0.8526 (pm20) cc_final: 0.8112 (pp20) REVERT: B 265 ARG cc_start: 0.7621 (mmp80) cc_final: 0.7142 (mmp80) REVERT: C 81 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.6961 (mtm-85) REVERT: C 151 MET cc_start: 0.8557 (mmp) cc_final: 0.8279 (mmp) REVERT: C 187 LYS cc_start: 0.6755 (mmtt) cc_final: 0.5983 (mmtm) REVERT: D 99 THR cc_start: 0.8950 (OUTLIER) cc_final: 0.8666 (p) REVERT: D 221 ASN cc_start: 0.8681 (t0) cc_final: 0.8292 (t0) outliers start: 31 outliers final: 26 residues processed: 125 average time/residue: 0.1110 time to fit residues: 20.2901 Evaluate side-chains 122 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 93 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 319 TRP Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 81 ARG Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain D residue 5 SER Chi-restraints excluded: chain D residue 15 ARG Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 378 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 116 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 chunk 108 optimal weight: 8.9990 chunk 110 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 98 optimal weight: 0.5980 chunk 125 optimal weight: 0.9980 chunk 16 optimal weight: 10.0000 chunk 94 optimal weight: 0.9980 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.090181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.072611 restraints weight = 38971.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.075020 restraints weight = 22870.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.076694 restraints weight = 16016.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.077827 restraints weight = 12503.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.078658 restraints weight = 10509.036| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.6558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12400 Z= 0.169 Angle : 0.655 10.802 16796 Z= 0.331 Chirality : 0.044 0.247 1828 Planarity : 0.004 0.050 2180 Dihedral : 4.234 19.261 1660 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 2.43 % Allowed : 28.19 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.23), residues: 1500 helix: 0.94 (0.21), residues: 652 sheet: -1.68 (0.31), residues: 276 loop : -1.48 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 119 TYR 0.022 0.002 TYR B 369 PHE 0.030 0.002 PHE D 29 TRP 0.024 0.002 TRP A 319 HIS 0.006 0.001 HIS A 211 Details of bonding type rmsd covalent geometry : bond 0.00390 (12396) covalent geometry : angle 0.65483 (16788) SS BOND : bond 0.00170 ( 4) SS BOND : angle 0.39349 ( 8) hydrogen bonds : bond 0.03797 ( 420) hydrogen bonds : angle 3.88121 ( 1248) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 93 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 TRP cc_start: 0.8629 (t-100) cc_final: 0.8363 (t60) REVERT: B 196 GLU cc_start: 0.8620 (pm20) cc_final: 0.8286 (pp20) REVERT: B 265 ARG cc_start: 0.7650 (mmp80) cc_final: 0.7169 (mmp80) REVERT: C 12 LEU cc_start: 0.8642 (tp) cc_final: 0.8382 (tp) REVERT: C 81 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.6966 (mtm-85) REVERT: C 151 MET cc_start: 0.8603 (mmp) cc_final: 0.8359 (mmp) REVERT: C 187 LYS cc_start: 0.6854 (mmtt) cc_final: 0.6349 (mmtm) REVERT: D 99 THR cc_start: 0.9155 (OUTLIER) cc_final: 0.8828 (p) REVERT: D 221 ASN cc_start: 0.8799 (t0) cc_final: 0.7917 (p0) outliers start: 32 outliers final: 27 residues processed: 124 average time/residue: 0.1061 time to fit residues: 19.2515 Evaluate side-chains 116 residues out of total 1320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 87 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASN Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 345 HIS Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 81 ARG Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 265 ARG Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain D residue 5 SER Chi-restraints excluded: chain D residue 15 ARG Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 99 THR Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 272 THR Chi-restraints excluded: chain D residue 345 HIS Chi-restraints excluded: chain D residue 378 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 17 optimal weight: 0.9980 chunk 139 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 89 optimal weight: 0.0030 chunk 48 optimal weight: 0.7980 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 HIS A 221 ASN D 345 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.091838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.074554 restraints weight = 38504.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.076907 restraints weight = 23134.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.078540 restraints weight = 16418.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.079684 restraints weight = 12912.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.080486 restraints weight = 10872.780| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.6590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12400 Z= 0.112 Angle : 0.632 10.106 16796 Z= 0.314 Chirality : 0.043 0.236 1828 Planarity : 0.003 0.030 2180 Dihedral : 4.060 19.696 1660 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 2.58 % Allowed : 28.42 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.23), residues: 1500 helix: 1.12 (0.22), residues: 640 sheet: -1.60 (0.32), residues: 276 loop : -1.45 (0.27), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 349 TYR 0.021 0.001 TYR B 369 PHE 0.032 0.001 PHE D 29 TRP 0.033 0.002 TRP A 319 HIS 0.007 0.001 HIS D 345 Details of bonding type rmsd covalent geometry : bond 0.00262 (12396) covalent geometry : angle 0.63163 (16788) SS BOND : bond 0.00142 ( 4) SS BOND : angle 0.41360 ( 8) hydrogen bonds : bond 0.03060 ( 420) hydrogen bonds : angle 3.70203 ( 1248) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1932.20 seconds wall clock time: 34 minutes 8.28 seconds (2048.28 seconds total)