Starting phenix.real_space_refine on Wed Aug 5 09:38:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/23bt_68840/08_2026/23bt_68840.cif Found real_map, /net/cci-nas-00/data/ceres_data/23bt_68840/08_2026/23bt_68840.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/23bt_68840/08_2026/23bt_68840.map" default_real_map = "/net/cci-nas-00/data/ceres_data/23bt_68840/08_2026/23bt_68840.map" model { file = "/net/cci-nas-00/data/ceres_data/23bt_68840/08_2026/23bt_68840.cif" } default_model = "/net/cci-nas-00/data/ceres_data/23bt_68840/08_2026/23bt_68840.cif" } resolution = 2.42 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= 0.052 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 40 5.16 5 C 5960 2.51 5 N 1628 2.21 5 O 1696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9324 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2319 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 12, 'TRANS': 272} Chain: "B" Number of atoms: 2319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2319 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 12, 'TRANS': 272} Chain: "C" Number of atoms: 2319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2319 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 12, 'TRANS': 272} Chain: "D" Number of atoms: 2319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2319 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 12, 'TRANS': 272} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'URC': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'URC': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'URC': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'URC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.70, per 1000 atoms: 0.18 Number of scatterers: 9324 At special positions: 0 Unit cell: (89.54, 86.58, 86.58, 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 40 16.00 O 1696 8.00 N 1628 7.00 C 5960 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.79 Conformation dependent library (CDL) restraints added in 302.0 milliseconds 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 1 sheets defined 26.3% alpha, 32.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 54 through 59 Processing helix chain 'A' and resid 67 through 83 Processing helix chain 'A' and resid 86 through 102 removed outlier: 3.714A pdb=" N PHE A 102 " --> pdb=" O PHE A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 223 Processing helix chain 'A' and resid 233 through 249 Processing helix chain 'B' and resid 54 through 59 Processing helix chain 'B' and resid 67 through 83 Processing helix chain 'B' and resid 86 through 102 removed outlier: 3.718A pdb=" N PHE B 102 " --> pdb=" O PHE B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 223 Processing helix chain 'B' and resid 233 through 249 Processing helix chain 'C' and resid 54 through 59 Processing helix chain 'C' and resid 67 through 83 Processing helix chain 'C' and resid 86 through 102 removed outlier: 3.716A pdb=" N PHE C 102 " --> pdb=" O PHE C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 223 Processing helix chain 'C' and resid 233 through 249 Processing helix chain 'D' and resid 54 through 59 Processing helix chain 'D' and resid 67 through 83 Processing helix chain 'D' and resid 86 through 102 removed outlier: 3.718A pdb=" N PHE D 102 " --> pdb=" O PHE D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 223 Processing helix chain 'D' and resid 233 through 249 Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 34 removed outlier: 7.390A pdb=" N THR A 19 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N LEU A 51 " --> pdb=" O THR A 19 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N THR A 45 " --> pdb=" O MET A 25 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYS A 27 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL A 43 " --> pdb=" O LYS A 27 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU A 29 " --> pdb=" O LYS A 41 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS A 41 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE A 31 " --> pdb=" O SER A 39 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N SER A 39 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ARG A 33 " --> pdb=" O TYR A 37 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TYR A 37 " --> pdb=" O ARG A 33 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N GLU A 42 " --> pdb=" O GLU A 114 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N GLU A 114 " --> pdb=" O GLU A 42 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ALA A 44 " --> pdb=" O VAL A 112 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N VAL A 112 " --> pdb=" O ALA A 44 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N SER A 46 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL A 110 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLN A 48 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ALA A 108 " --> pdb=" O GLN A 48 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N THR A 50 " --> pdb=" O THR A 106 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 105 through 114 current: chain 'A' and resid 125 through 133 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 125 through 133 current: chain 'A' and resid 152 through 164 removed outlier: 6.666A pdb=" N HIS A 154 " --> pdb=" O TYR A 199 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N TYR A 199 " --> pdb=" O HIS A 154 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N GLY A 156 " --> pdb=" O TRP A 197 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N TRP A 197 " --> pdb=" O GLY A 156 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N LYS A 158 " --> pdb=" O CYS A 195 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N CYS A 195 " --> pdb=" O LYS A 158 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU A 160 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ALA A 190 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLN A 192 " --> pdb=" O PRO A 260 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP A 254 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY A 289 " --> pdb=" O ASN A 261 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N HIS A 263 " --> pdb=" O PRO A 287 " (cutoff:3.500A) removed outlier: 11.324A pdb=" N PHE A 265 " --> pdb=" O ASP A 285 " (cutoff:3.500A) removed outlier: 10.683A pdb=" N ASP A 285 " --> pdb=" O PHE A 265 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 280 through 296 current: chain 'B' and resid 37 through 51 removed outlier: 7.445A pdb=" N GLU B 42 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N GLU B 114 " --> pdb=" O GLU B 42 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA B 44 " --> pdb=" O VAL B 112 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL B 112 " --> pdb=" O ALA B 44 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N SER B 46 " --> pdb=" O VAL B 110 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL B 110 " --> pdb=" O SER B 46 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLN B 48 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ALA B 108 " --> pdb=" O GLN B 48 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N THR B 50 " --> pdb=" O THR B 106 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 105 through 114 current: chain 'B' and resid 125 through 133 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 125 through 133 current: chain 'B' and resid 152 through 164 removed outlier: 6.666A pdb=" N HIS B 154 " --> pdb=" O TYR B 199 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TYR B 199 " --> pdb=" O HIS B 154 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N GLY B 156 " --> pdb=" O TRP B 197 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N TRP B 197 " --> pdb=" O GLY B 156 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N LYS B 158 " --> pdb=" O CYS B 195 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N CYS B 195 " --> pdb=" O LYS B 158 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU B 160 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ALA B 190 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLN B 192 " --> pdb=" O PRO B 260 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASP B 254 " --> pdb=" O ARG B 198 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY B 289 " --> pdb=" O ASN B 261 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N HIS B 263 " --> pdb=" O PRO B 287 " (cutoff:3.500A) removed outlier: 11.349A pdb=" N PHE B 265 " --> pdb=" O ASP B 285 " (cutoff:3.500A) removed outlier: 10.729A pdb=" N ASP B 285 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LYS C 27 " --> pdb=" O PRO B 283 " (cutoff:3.500A) removed outlier: 9.916A pdb=" N ASP B 285 " --> pdb=" O MET C 25 " (cutoff:3.500A) removed outlier: 15.723A pdb=" N MET C 25 " --> pdb=" O ASP B 285 " (cutoff:3.500A) removed outlier: 23.076A pdb=" N LYS C 23 " --> pdb=" O PRO B 287 " (cutoff:3.500A) removed outlier: 32.706A pdb=" N GLY B 289 " --> pdb=" O TYR C 21 " (cutoff:3.500A) removed outlier: 35.948A pdb=" N TYR C 21 " --> pdb=" O GLY B 289 " (cutoff:3.500A) removed outlier: 44.945A pdb=" N ILE B 291 " --> pdb=" O THR C 19 " (cutoff:3.500A) removed outlier: 48.229A pdb=" N THR C 19 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 56.295A pdb=" N GLY B 293 " --> pdb=" O VAL C 17 " (cutoff:3.500A) removed outlier: 58.879A pdb=" N VAL C 17 " --> pdb=" O GLY B 293 " (cutoff:3.500A) removed outlier: 65.278A pdb=" N VAL B 295 " --> pdb=" O GLU C 15 " (cutoff:3.500A) removed outlier: 69.522A pdb=" N GLU C 15 " --> pdb=" O VAL B 295 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N THR C 19 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N LEU C 51 " --> pdb=" O THR C 19 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N THR C 45 " --> pdb=" O MET C 25 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYS C 27 " --> pdb=" O VAL C 43 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL C 43 " --> pdb=" O LYS C 27 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU C 29 " --> pdb=" O LYS C 41 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS C 41 " --> pdb=" O LEU C 29 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE C 31 " --> pdb=" O SER C 39 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N SER C 39 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ARG C 33 " --> pdb=" O TYR C 37 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N TYR C 37 " --> pdb=" O ARG C 33 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N GLU C 42 " --> pdb=" O GLU C 114 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N GLU C 114 " --> pdb=" O GLU C 42 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA C 44 " --> pdb=" O VAL C 112 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N VAL C 112 " --> pdb=" O ALA C 44 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N SER C 46 " --> pdb=" O VAL C 110 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL C 110 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLN C 48 " --> pdb=" O ALA C 108 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ALA C 108 " --> pdb=" O GLN C 48 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N THR C 50 " --> pdb=" O THR C 106 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 105 through 114 current: chain 'C' and resid 125 through 133 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 125 through 133 current: chain 'C' and resid 152 through 164 removed outlier: 6.666A pdb=" N HIS C 154 " --> pdb=" O TYR C 199 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TYR C 199 " --> pdb=" O HIS C 154 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N GLY C 156 " --> pdb=" O TRP C 197 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N TRP C 197 " --> pdb=" O GLY C 156 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N LYS C 158 " --> pdb=" O CYS C 195 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N CYS C 195 " --> pdb=" O LYS C 158 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU C 160 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ALA C 190 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLN C 192 " --> pdb=" O PRO C 260 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASP C 254 " --> pdb=" O ARG C 198 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY C 289 " --> pdb=" O ASN C 261 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N HIS C 263 " --> pdb=" O PRO C 287 " (cutoff:3.500A) removed outlier: 11.324A pdb=" N PHE C 265 " --> pdb=" O ASP C 285 " (cutoff:3.500A) removed outlier: 10.682A pdb=" N ASP C 285 " --> pdb=" O PHE C 265 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 280 through 296 current: chain 'D' and resid 37 through 51 removed outlier: 7.441A pdb=" N GLU D 42 " --> pdb=" O GLU D 114 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N GLU D 114 " --> pdb=" O GLU D 42 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA D 44 " --> pdb=" O VAL D 112 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL D 112 " --> pdb=" O ALA D 44 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N SER D 46 " --> pdb=" O VAL D 110 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL D 110 " --> pdb=" O SER D 46 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLN D 48 " --> pdb=" O ALA D 108 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ALA D 108 " --> pdb=" O GLN D 48 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N THR D 50 " --> pdb=" O THR D 106 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 105 through 114 current: chain 'D' and resid 125 through 133 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 125 through 133 current: chain 'D' and resid 152 through 164 removed outlier: 6.666A pdb=" N HIS D 154 " --> pdb=" O TYR D 199 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TYR D 199 " --> pdb=" O HIS D 154 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N GLY D 156 " --> pdb=" O TRP D 197 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N TRP D 197 " --> pdb=" O GLY D 156 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N LYS D 158 " --> pdb=" O CYS D 195 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N CYS D 195 " --> pdb=" O LYS D 158 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU D 160 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ALA D 190 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLN D 192 " --> pdb=" O PRO D 260 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP D 254 " --> pdb=" O ARG D 198 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY D 289 " --> pdb=" O ASN D 261 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N HIS D 263 " --> pdb=" O PRO D 287 " (cutoff:3.500A) removed outlier: 11.349A pdb=" N PHE D 265 " --> pdb=" O ASP D 285 " (cutoff:3.500A) removed outlier: 10.730A pdb=" N ASP D 285 " --> pdb=" O PHE D 265 " (cutoff:3.500A) 304 hydrogen bonds defined for protein. 900 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: 1.26 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1520 1.30 - 1.43: 2509 1.43 - 1.56: 5455 1.56 - 1.68: 0 1.68 - 1.81: 64 Bond restraints: 9548 Sorted by residual: bond pdb=" C6 URC C 301 " pdb=" N1 URC C 301 " ideal model delta sigma weight residual 1.398 1.317 0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" C6 URC D 301 " pdb=" N1 URC D 301 " ideal model delta sigma weight residual 1.398 1.318 0.080 2.00e-02 2.50e+03 1.62e+01 bond pdb=" C6 URC B 301 " pdb=" N1 URC B 301 " ideal model delta sigma weight residual 1.398 1.318 0.080 2.00e-02 2.50e+03 1.61e+01 bond pdb=" C6 URC A 301 " pdb=" N1 URC A 301 " ideal model delta sigma weight residual 1.398 1.318 0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C8 URC C 301 " pdb=" N9 URC C 301 " ideal model delta sigma weight residual 1.396 1.330 0.066 2.00e-02 2.50e+03 1.10e+01 ... (remaining 9543 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 12673 1.90 - 3.80: 194 3.80 - 5.70: 28 5.70 - 7.60: 5 7.60 - 9.50: 8 Bond angle restraints: 12908 Sorted by residual: angle pdb=" C2 URC B 301 " pdb=" N1 URC B 301 " pdb=" C6 URC B 301 " ideal model delta sigma weight residual 129.31 119.81 9.50 3.00e+00 1.11e-01 1.00e+01 angle pdb=" C2 URC D 301 " pdb=" N1 URC D 301 " pdb=" C6 URC D 301 " ideal model delta sigma weight residual 129.31 119.84 9.47 3.00e+00 1.11e-01 9.97e+00 angle pdb=" C2 URC A 301 " pdb=" N1 URC A 301 " pdb=" C6 URC A 301 " ideal model delta sigma weight residual 129.31 119.86 9.45 3.00e+00 1.11e-01 9.93e+00 angle pdb=" C2 URC C 301 " pdb=" N1 URC C 301 " pdb=" C6 URC C 301 " ideal model delta sigma weight residual 129.31 119.89 9.42 3.00e+00 1.11e-01 9.87e+00 angle pdb=" C5 URC B 301 " pdb=" C6 URC B 301 " pdb=" N1 URC B 301 " ideal model delta sigma weight residual 111.19 120.08 -8.89 3.00e+00 1.11e-01 8.77e+00 ... (remaining 12903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.04: 5040 15.04 - 30.09: 512 30.09 - 45.13: 116 45.13 - 60.17: 28 60.17 - 75.22: 8 Dihedral angle restraints: 5704 sinusoidal: 2380 harmonic: 3324 Sorted by residual: dihedral pdb=" CA VAL C 193 " pdb=" C VAL C 193 " pdb=" N TYR C 194 " pdb=" CA TYR C 194 " ideal model delta harmonic sigma weight residual 180.00 164.01 15.99 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA VAL D 193 " pdb=" C VAL D 193 " pdb=" N TYR D 194 " pdb=" CA TYR D 194 " ideal model delta harmonic sigma weight residual 180.00 164.05 15.95 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" CA VAL A 193 " pdb=" C VAL A 193 " pdb=" N TYR A 194 " pdb=" CA TYR A 194 " ideal model delta harmonic sigma weight residual 180.00 164.07 15.93 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 5701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 666 0.028 - 0.057: 459 0.057 - 0.085: 161 0.085 - 0.113: 91 0.113 - 0.141: 39 Chirality restraints: 1416 Sorted by residual: chirality pdb=" CA ILE A 66 " pdb=" N ILE A 66 " pdb=" C ILE A 66 " pdb=" CB ILE A 66 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.00e-01 chirality pdb=" CA ILE D 66 " pdb=" N ILE D 66 " pdb=" C ILE D 66 " pdb=" CB ILE D 66 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.95e-01 chirality pdb=" CA ASN C 286 " pdb=" N ASN C 286 " pdb=" C ASN C 286 " pdb=" CB ASN C 286 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.91e-01 ... (remaining 1413 not shown) Planarity restraints: 1636 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 231 " -0.040 5.00e-02 4.00e+02 6.10e-02 5.95e+00 pdb=" N PRO D 232 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO D 232 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 232 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 231 " 0.040 5.00e-02 4.00e+02 6.08e-02 5.91e+00 pdb=" N PRO B 232 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 232 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 232 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 231 " 0.040 5.00e-02 4.00e+02 6.08e-02 5.91e+00 pdb=" N PRO A 232 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 232 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 232 " 0.034 5.00e-02 4.00e+02 ... (remaining 1633 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 3443 2.91 - 3.40: 8063 3.40 - 3.90: 15988 3.90 - 4.40: 18187 4.40 - 4.90: 30797 Nonbonded interactions: 76478 Sorted by model distance: nonbonded pdb=" OH TYR C 21 " pdb=" O ILE C 66 " model vdw 2.408 3.040 nonbonded pdb=" OH TYR D 21 " pdb=" O ILE D 66 " model vdw 2.411 3.040 nonbonded pdb=" OH TYR A 21 " pdb=" O ILE A 66 " model vdw 2.412 3.040 nonbonded pdb=" OH TYR B 21 " pdb=" O ILE B 66 " model vdw 2.412 3.040 nonbonded pdb=" OD1 ASN D 266 " pdb=" ND2 ASN D 276 " model vdw 2.446 3.120 ... (remaining 76473 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: 0.03 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.660 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 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 0.081 9548 Z= 0.223 Angle : 0.673 9.501 12908 Z= 0.356 Chirality : 0.047 0.141 1416 Planarity : 0.005 0.061 1636 Dihedral : 13.334 75.218 3560 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.25), residues: 1132 helix: 1.19 (0.32), residues: 280 sheet: 0.35 (0.26), residues: 400 loop : -1.50 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 107 TYR 0.007 0.001 TYR A 57 PHE 0.012 0.002 PHE B 120 TRP 0.009 0.001 TRP C 117 HIS 0.014 0.002 HIS B 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.22 ( 9548) covalent geometry : angle 0.67322 / 0.36 (12908) hydrogen bonds : bond 0.13412 / 9.42 ( 304) hydrogen bonds : angle 6.28234 / 4.58 ( 900) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.274 Fit side-chains REVERT: A 96 GLU cc_start: 0.7711 (tp30) cc_final: 0.7305 (tp30) REVERT: B 96 GLU cc_start: 0.7699 (tp30) cc_final: 0.7285 (tp30) REVERT: C 96 GLU cc_start: 0.7697 (tp30) cc_final: 0.7297 (tp30) REVERT: D 96 GLU cc_start: 0.7707 (tp30) cc_final: 0.7292 (tp30) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.8718 time to fit residues: 127.5757 Evaluate side-chains 116 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.0570 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 overall best weight: 3.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 73 ASN A 219 GLN ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 ASN B 219 GLN ** C 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN C 219 GLN ** D 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 ASN D 219 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.126070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.108715 restraints weight = 9605.715| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.66 r_work: 0.3259 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.0798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 9548 Z= 0.157 Angle : 0.552 5.580 12908 Z= 0.297 Chirality : 0.047 0.147 1416 Planarity : 0.005 0.042 1636 Dihedral : 4.847 16.182 1236 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.16 % Allowed : 5.02 % Favored : 93.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.25), residues: 1132 helix: 1.43 (0.31), residues: 284 sheet: 0.13 (0.25), residues: 404 loop : -1.43 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 107 TYR 0.005 0.001 TYR A 57 PHE 0.012 0.002 PHE D 120 TRP 0.006 0.001 TRP A 117 HIS 0.012 0.002 HIS C 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 9548) covalent geometry : angle 0.55169 / 0.30 (12908) hydrogen bonds : bond 0.05994 / 4.08 ( 304) hydrogen bonds : angle 5.20006 / 3.77 ( 900) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.472 Fit side-chains REVERT: A 96 GLU cc_start: 0.7879 (tp30) cc_final: 0.7382 (tp30) REVERT: B 96 GLU cc_start: 0.7880 (tp30) cc_final: 0.7371 (tp30) REVERT: C 96 GLU cc_start: 0.7876 (tp30) cc_final: 0.7376 (tp30) REVERT: D 96 GLU cc_start: 0.7887 (tp30) cc_final: 0.7380 (tp30) outliers start: 12 outliers final: 4 residues processed: 136 average time/residue: 0.8224 time to fit residues: 117.3982 Evaluate side-chains 112 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain D residue 166 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 46 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 11 optimal weight: 20.0000 chunk 67 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 HIS A 86 ASN A 219 GLN B 30 HIS B 86 ASN B 219 GLN C 30 HIS C 86 ASN C 219 GLN D 30 HIS D 86 ASN D 219 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.122665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.105135 restraints weight = 9768.276| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.69 r_work: 0.3208 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 9548 Z= 0.257 Angle : 0.652 6.240 12908 Z= 0.350 Chirality : 0.051 0.224 1416 Planarity : 0.005 0.049 1636 Dihedral : 5.176 19.074 1236 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.77 % Allowed : 8.88 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.24), residues: 1132 helix: 1.08 (0.30), residues: 284 sheet: -0.12 (0.24), residues: 404 loop : -1.54 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 107 TYR 0.007 0.002 TYR C 21 PHE 0.018 0.002 PHE D 120 TRP 0.007 0.002 TRP B 117 HIS 0.014 0.002 HIS B 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00630 / 0.26 ( 9548) covalent geometry : angle 0.65214 / 0.35 (12908) hydrogen bonds : bond 0.07689 / 5.26 ( 304) hydrogen bonds : angle 5.34747 / 3.86 ( 900) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 0.386 Fit side-chains REVERT: A 96 GLU cc_start: 0.7945 (tp30) cc_final: 0.7444 (tp30) REVERT: B 96 GLU cc_start: 0.7908 (tp30) cc_final: 0.7407 (tp30) REVERT: C 96 GLU cc_start: 0.7905 (tp30) cc_final: 0.7402 (tp30) REVERT: D 96 GLU cc_start: 0.7901 (tp30) cc_final: 0.7392 (tp30) outliers start: 8 outliers final: 8 residues processed: 116 average time/residue: 0.7839 time to fit residues: 95.6985 Evaluate side-chains 112 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 200 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 9 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 21 optimal weight: 0.0370 chunk 44 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 2 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 overall best weight: 1.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 HIS A 286 ASN B 154 HIS C 154 HIS C 286 ASN D 154 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.128130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.110627 restraints weight = 9738.244| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.68 r_work: 0.3280 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9548 Z= 0.097 Angle : 0.467 5.328 12908 Z= 0.253 Chirality : 0.044 0.135 1416 Planarity : 0.004 0.043 1636 Dihedral : 4.578 15.441 1236 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.58 % Allowed : 9.65 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.25), residues: 1132 helix: 1.83 (0.33), residues: 284 sheet: -0.00 (0.25), residues: 404 loop : -1.36 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 201 TYR 0.006 0.001 TYR A 57 PHE 0.006 0.001 PHE B 120 TRP 0.004 0.001 TRP C 117 HIS 0.003 0.001 HIS A 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 ( 9548) covalent geometry : angle 0.46684 / 0.25 (12908) hydrogen bonds : bond 0.04258 / 2.89 ( 304) hydrogen bonds : angle 4.91319 / 3.57 ( 900) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 112 time to evaluate : 0.388 Fit side-chains REVERT: A 96 GLU cc_start: 0.7877 (tp30) cc_final: 0.7370 (tp30) REVERT: A 121 GLU cc_start: 0.8146 (tt0) cc_final: 0.7794 (mt-10) REVERT: A 126 LYS cc_start: 0.7751 (OUTLIER) cc_final: 0.7379 (mttm) REVERT: B 96 GLU cc_start: 0.7886 (tp30) cc_final: 0.7373 (tp30) REVERT: B 121 GLU cc_start: 0.8152 (tt0) cc_final: 0.7797 (mt-10) REVERT: B 126 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7370 (mttm) REVERT: C 96 GLU cc_start: 0.7884 (tp30) cc_final: 0.7377 (tp30) REVERT: C 121 GLU cc_start: 0.8153 (tt0) cc_final: 0.7801 (mt-10) REVERT: C 126 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7375 (mttm) REVERT: D 96 GLU cc_start: 0.7884 (tp30) cc_final: 0.7373 (tp30) REVERT: D 121 GLU cc_start: 0.8142 (tt0) cc_final: 0.7807 (mt-10) outliers start: 6 outliers final: 1 residues processed: 118 average time/residue: 0.8282 time to fit residues: 102.7419 Evaluate side-chains 116 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 112 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain C residue 126 LYS Chi-restraints excluded: chain D residue 126 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 52 optimal weight: 9.9990 chunk 91 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 82 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 chunk 6 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 GLN B 219 GLN C 219 GLN D 219 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.122478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.105013 restraints weight = 9812.195| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.69 r_work: 0.3205 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.035 9548 Z= 0.269 Angle : 0.650 6.386 12908 Z= 0.349 Chirality : 0.051 0.223 1416 Planarity : 0.005 0.049 1636 Dihedral : 5.113 19.431 1236 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.03 % Allowed : 10.62 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.24), residues: 1132 helix: 1.17 (0.30), residues: 284 sheet: -0.17 (0.24), residues: 404 loop : -1.49 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 107 TYR 0.008 0.002 TYR C 21 PHE 0.018 0.003 PHE B 120 TRP 0.007 0.002 TRP B 117 HIS 0.012 0.002 HIS C 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00662 / 0.27 ( 9548) covalent geometry : angle 0.65009 / 0.35 (12908) hydrogen bonds : bond 0.07580 / 5.19 ( 304) hydrogen bonds : angle 5.29404 / 3.83 ( 900) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.377 Fit side-chains REVERT: A 96 GLU cc_start: 0.7955 (tp30) cc_final: 0.7449 (tp30) REVERT: A 121 GLU cc_start: 0.8150 (tt0) cc_final: 0.7766 (mt-10) REVERT: A 272 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.7223 (mpp) REVERT: B 96 GLU cc_start: 0.7935 (tp30) cc_final: 0.7428 (tp30) REVERT: B 121 GLU cc_start: 0.8163 (tt0) cc_final: 0.7780 (mt-10) REVERT: B 272 MET cc_start: 0.7690 (OUTLIER) cc_final: 0.7225 (mpp) REVERT: C 96 GLU cc_start: 0.7957 (tp30) cc_final: 0.7452 (tp30) REVERT: C 121 GLU cc_start: 0.8154 (tt0) cc_final: 0.7771 (mt-10) REVERT: C 272 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.7214 (mpp) REVERT: D 96 GLU cc_start: 0.7932 (tp30) cc_final: 0.7420 (tp30) REVERT: D 121 GLU cc_start: 0.8154 (tt0) cc_final: 0.7772 (mt-10) REVERT: D 272 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.7212 (mpp) outliers start: 21 outliers final: 9 residues processed: 117 average time/residue: 0.8387 time to fit residues: 102.9352 Evaluate side-chains 121 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 272 MET Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain C residue 272 MET Chi-restraints excluded: chain D residue 126 LYS Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 200 GLN Chi-restraints excluded: chain D residue 272 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 49 optimal weight: 4.9990 chunk 58 optimal weight: 8.9990 chunk 79 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 chunk 109 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 HIS A 219 GLN B 109 HIS B 219 GLN C 109 HIS C 219 GLN D 109 HIS D 219 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.125486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.107929 restraints weight = 9642.948| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.68 r_work: 0.3243 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9548 Z= 0.139 Angle : 0.525 5.404 12908 Z= 0.283 Chirality : 0.046 0.140 1416 Planarity : 0.004 0.047 1636 Dihedral : 4.798 16.331 1236 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.16 % Allowed : 12.93 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.25), residues: 1132 helix: 1.55 (0.32), residues: 284 sheet: -0.16 (0.24), residues: 404 loop : -1.38 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 107 TYR 0.005 0.001 TYR A 57 PHE 0.010 0.001 PHE D 120 TRP 0.005 0.001 TRP A 117 HIS 0.005 0.001 HIS C 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 ( 9548) covalent geometry : angle 0.52471 / 0.28 (12908) hydrogen bonds : bond 0.05505 / 3.75 ( 304) hydrogen bonds : angle 5.04767 / 3.66 ( 900) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.369 Fit side-chains REVERT: A 96 GLU cc_start: 0.7905 (tp30) cc_final: 0.7390 (tp30) REVERT: A 121 GLU cc_start: 0.8139 (tt0) cc_final: 0.7769 (mt-10) REVERT: B 96 GLU cc_start: 0.7913 (tp30) cc_final: 0.7397 (tp30) REVERT: B 121 GLU cc_start: 0.8152 (tt0) cc_final: 0.7780 (mt-10) REVERT: C 96 GLU cc_start: 0.7909 (tp30) cc_final: 0.7391 (tp30) REVERT: C 121 GLU cc_start: 0.8139 (tt0) cc_final: 0.7768 (mt-10) REVERT: D 96 GLU cc_start: 0.7911 (tp30) cc_final: 0.7393 (tp30) REVERT: D 121 GLU cc_start: 0.8132 (tt0) cc_final: 0.7759 (mt-10) outliers start: 12 outliers final: 12 residues processed: 120 average time/residue: 0.7530 time to fit residues: 94.9960 Evaluate side-chains 134 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 200 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 53 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 13 optimal weight: 0.3980 chunk 61 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 92 optimal weight: 9.9990 overall best weight: 5.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 86 ASN A 219 GLN B 86 ASN B 219 GLN C 86 ASN C 219 GLN D 86 ASN D 219 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.122795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.105436 restraints weight = 9767.182| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.68 r_work: 0.3211 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 9548 Z= 0.231 Angle : 0.617 6.006 12908 Z= 0.331 Chirality : 0.050 0.205 1416 Planarity : 0.005 0.049 1636 Dihedral : 5.043 18.903 1236 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.35 % Allowed : 13.32 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.24), residues: 1132 helix: 1.22 (0.31), residues: 284 sheet: -0.19 (0.24), residues: 404 loop : -1.48 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 107 TYR 0.007 0.002 TYR A 21 PHE 0.017 0.002 PHE A 120 TRP 0.006 0.002 TRP B 117 HIS 0.009 0.001 HIS A 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.23 ( 9548) covalent geometry : angle 0.61675 / 0.33 (12908) hydrogen bonds : bond 0.07060 / 4.83 ( 304) hydrogen bonds : angle 5.23539 / 3.78 ( 900) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 108 time to evaluate : 0.379 Fit side-chains REVERT: A 96 GLU cc_start: 0.7912 (tp30) cc_final: 0.7407 (tp30) REVERT: A 121 GLU cc_start: 0.8147 (tt0) cc_final: 0.7763 (mt-10) REVERT: B 96 GLU cc_start: 0.7934 (tp30) cc_final: 0.7430 (tp30) REVERT: B 121 GLU cc_start: 0.8167 (tt0) cc_final: 0.7786 (mt-10) REVERT: C 96 GLU cc_start: 0.7912 (tp30) cc_final: 0.7407 (tp30) REVERT: C 121 GLU cc_start: 0.8153 (tt0) cc_final: 0.7770 (mt-10) REVERT: D 96 GLU cc_start: 0.7933 (tp30) cc_final: 0.7425 (tp30) REVERT: D 121 GLU cc_start: 0.8152 (tt0) cc_final: 0.7768 (mt-10) outliers start: 14 outliers final: 14 residues processed: 118 average time/residue: 0.7931 time to fit residues: 98.4776 Evaluate side-chains 128 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain C residue 126 LYS Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 200 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 105 optimal weight: 0.9990 chunk 62 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 64 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 GLN B 219 GLN C 219 GLN D 219 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.126075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.108716 restraints weight = 9611.768| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.67 r_work: 0.3254 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9548 Z= 0.120 Angle : 0.504 5.868 12908 Z= 0.271 Chirality : 0.045 0.138 1416 Planarity : 0.004 0.046 1636 Dihedral : 4.699 15.665 1236 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.16 % Allowed : 14.38 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.25), residues: 1132 helix: 1.69 (0.32), residues: 284 sheet: -0.13 (0.24), residues: 404 loop : -1.36 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 107 TYR 0.006 0.001 TYR A 57 PHE 0.009 0.001 PHE D 120 TRP 0.005 0.001 TRP A 117 HIS 0.004 0.001 HIS D 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 ( 9548) covalent geometry : angle 0.50373 / 0.27 (12908) hydrogen bonds : bond 0.04972 / 3.38 ( 304) hydrogen bonds : angle 4.98658 / 3.61 ( 900) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.375 Fit side-chains REVERT: A 96 GLU cc_start: 0.7877 (tp30) cc_final: 0.7375 (tp30) REVERT: A 121 GLU cc_start: 0.8132 (tt0) cc_final: 0.7754 (mt-10) REVERT: B 96 GLU cc_start: 0.7887 (tp30) cc_final: 0.7381 (tp30) REVERT: B 121 GLU cc_start: 0.8148 (tt0) cc_final: 0.7776 (mt-10) REVERT: C 96 GLU cc_start: 0.7884 (tp30) cc_final: 0.7379 (tp30) REVERT: C 121 GLU cc_start: 0.8137 (tt0) cc_final: 0.7760 (mt-10) REVERT: D 96 GLU cc_start: 0.7878 (tp30) cc_final: 0.7374 (tp30) REVERT: D 121 GLU cc_start: 0.8132 (tt0) cc_final: 0.7755 (mt-10) outliers start: 12 outliers final: 12 residues processed: 124 average time/residue: 0.7511 time to fit residues: 98.2290 Evaluate side-chains 138 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 200 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 chunk 9 optimal weight: 0.6980 chunk 71 optimal weight: 9.9990 chunk 96 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 76 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 GLN B 219 GLN C 219 GLN D 219 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.123465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.106067 restraints weight = 9654.035| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.67 r_work: 0.3219 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 9548 Z= 0.206 Angle : 0.601 5.907 12908 Z= 0.321 Chirality : 0.048 0.189 1416 Planarity : 0.005 0.049 1636 Dihedral : 4.950 18.183 1236 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.25 % Allowed : 14.29 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.24), residues: 1132 helix: 1.33 (0.31), residues: 284 sheet: -0.18 (0.24), residues: 404 loop : -1.46 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 107 TYR 0.006 0.002 TYR B 57 PHE 0.015 0.002 PHE B 120 TRP 0.005 0.001 TRP B 117 HIS 0.007 0.001 HIS B 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.21 ( 9548) covalent geometry : angle 0.60051 / 0.32 (12908) hydrogen bonds : bond 0.06651 / 4.55 ( 304) hydrogen bonds : angle 5.18425 / 3.75 ( 900) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.373 Fit side-chains REVERT: A 96 GLU cc_start: 0.7916 (tp30) cc_final: 0.7412 (tp30) REVERT: A 121 GLU cc_start: 0.8143 (tt0) cc_final: 0.7767 (mt-10) REVERT: B 96 GLU cc_start: 0.7905 (tp30) cc_final: 0.7420 (tp30) REVERT: B 121 GLU cc_start: 0.8162 (tt0) cc_final: 0.7786 (mt-10) REVERT: C 96 GLU cc_start: 0.7903 (tp30) cc_final: 0.7400 (tp30) REVERT: C 121 GLU cc_start: 0.8145 (tt0) cc_final: 0.7766 (mt-10) REVERT: D 96 GLU cc_start: 0.7901 (tp30) cc_final: 0.7412 (tp30) REVERT: D 121 GLU cc_start: 0.8137 (tt0) cc_final: 0.7759 (mt-10) outliers start: 13 outliers final: 13 residues processed: 123 average time/residue: 0.7782 time to fit residues: 100.8575 Evaluate side-chains 125 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain B residue 126 LYS Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 200 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 44 optimal weight: 0.0770 chunk 29 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 overall best weight: 3.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 GLN B 86 ASN B 219 GLN C 86 ASN C 219 GLN D 86 ASN D 219 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.125178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.107779 restraints weight = 9658.363| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.67 r_work: 0.3242 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9548 Z= 0.143 Angle : 0.536 5.837 12908 Z= 0.288 Chirality : 0.046 0.140 1416 Planarity : 0.004 0.047 1636 Dihedral : 4.776 16.506 1236 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.16 % Allowed : 15.15 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.25), residues: 1132 helix: 1.60 (0.32), residues: 284 sheet: -0.15 (0.24), residues: 404 loop : -1.42 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 107 TYR 0.006 0.001 TYR C 57 PHE 0.010 0.002 PHE B 120 TRP 0.005 0.001 TRP A 117 HIS 0.005 0.001 HIS C 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.14 ( 9548) covalent geometry : angle 0.53573 / 0.29 (12908) hydrogen bonds : bond 0.05498 / 3.75 ( 304) hydrogen bonds : angle 5.04616 / 3.65 ( 900) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.401 Fit side-chains REVERT: A 96 GLU cc_start: 0.7871 (tp30) cc_final: 0.7361 (tp30) REVERT: A 121 GLU cc_start: 0.8134 (tt0) cc_final: 0.7762 (mt-10) REVERT: B 96 GLU cc_start: 0.7883 (tp30) cc_final: 0.7390 (tp30) REVERT: B 121 GLU cc_start: 0.8152 (tt0) cc_final: 0.7782 (mt-10) REVERT: C 96 GLU cc_start: 0.7894 (tp30) cc_final: 0.7383 (tp30) REVERT: C 121 GLU cc_start: 0.8145 (tt0) cc_final: 0.7774 (mt-10) REVERT: D 96 GLU cc_start: 0.7880 (tp30) cc_final: 0.7388 (tp30) REVERT: D 121 GLU cc_start: 0.8132 (tt0) cc_final: 0.7757 (mt-10) outliers start: 12 outliers final: 12 residues processed: 120 average time/residue: 0.7583 time to fit residues: 95.9142 Evaluate side-chains 126 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 200 GLN Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 200 GLN Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 200 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 86 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 73 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 90 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 219 GLN B 219 GLN C 219 GLN D 219 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.121870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.104549 restraints weight = 9693.443| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.67 r_work: 0.3199 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 9548 Z= 0.295 Angle : 0.687 6.806 12908 Z= 0.368 Chirality : 0.053 0.253 1416 Planarity : 0.005 0.050 1636 Dihedral : 5.194 19.574 1236 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.35 % Allowed : 14.77 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.24), residues: 1132 helix: 0.97 (0.30), residues: 284 sheet: -0.24 (0.24), residues: 404 loop : -1.55 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 107 TYR 0.008 0.002 TYR C 21 PHE 0.020 0.003 PHE D 120 TRP 0.006 0.002 TRP A 210 HIS 0.011 0.002 HIS A 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00725 / 0.30 ( 9548) covalent geometry : angle 0.68724 / 0.37 (12908) hydrogen bonds : bond 0.07947 / 5.44 ( 304) hydrogen bonds : angle 5.36021 / 3.87 ( 900) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3061.38 seconds wall clock time: 52 minutes 58.30 seconds (3178.30 seconds total)