Starting phenix.real_space_refine on Tue Aug 26 11:46:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6c9k_7437/08_2025/6c9k_7437.cif Found real_map, /net/cci-nas-00/data/ceres_data/6c9k_7437/08_2025/6c9k_7437.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6c9k_7437/08_2025/6c9k_7437.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6c9k_7437/08_2025/6c9k_7437.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6c9k_7437/08_2025/6c9k_7437.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6c9k_7437/08_2025/6c9k_7437.map" } resolution = 3.49 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= 0.001 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 108 5.16 5 C 23733 2.51 5 N 6510 2.21 5 O 7281 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 104 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37632 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2255 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 6, 'TRANS': 286} Chain breaks: 1 Chain: "B" Number of atoms: 2249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2249 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 6, 'TRANS': 285} Chain breaks: 1 Chain: "C" Number of atoms: 2241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2241 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 6, 'TRANS': 284} Chain breaks: 1 Chain: "D" Number of atoms: 2264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2264 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 6, 'TRANS': 287} Chain: "E" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "F" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "G" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "H" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 880 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Chain: "I" Number of atoms: 2255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2255 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 6, 'TRANS': 286} Chain breaks: 1 Chain: "J" Number of atoms: 2249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2249 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 6, 'TRANS': 285} Chain breaks: 1 Chain: "K" Number of atoms: 2241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2241 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 6, 'TRANS': 284} Chain breaks: 1 Chain: "L" Number of atoms: 2264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2264 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 6, 'TRANS': 287} Chain: "M" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "N" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "O" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "P" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 880 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Chain: "Q" Number of atoms: 2255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2255 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 6, 'TRANS': 286} Chain: "R" Number of atoms: 2249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2249 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 6, 'TRANS': 285} Chain breaks: 1 Chain: "S" Number of atoms: 2241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2241 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 6, 'TRANS': 284} Chain breaks: 1 Chain: "T" Number of atoms: 2264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2264 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 6, 'TRANS': 287} Chain: "U" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "V" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "W" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 885 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "X" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 880 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Time building chain proxies: 8.05, per 1000 atoms: 0.21 Number of scatterers: 37632 At special positions: 0 Unit cell: (191.915, 195.19, 161.13, 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 108 16.00 O 7281 8.00 N 6510 7.00 C 23733 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: 3.19 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 1.2 microseconds 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9006 Finding SS restraints... Secondary structure from input PDB file: 206 helices and 24 sheets defined 62.5% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 24 through 45 Processing helix chain 'A' and resid 49 through 72 Processing helix chain 'A' and resid 80 through 96 removed outlier: 3.531A pdb=" N ILE A 84 " --> pdb=" O SER A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 137 removed outlier: 3.552A pdb=" N LEU A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 175 Processing helix chain 'A' and resid 176 through 186 Processing helix chain 'A' and resid 199 through 208 Processing helix chain 'A' and resid 209 through 219 Processing helix chain 'A' and resid 232 through 240 Processing helix chain 'A' and resid 242 through 252 Processing helix chain 'A' and resid 265 through 273 Processing helix chain 'A' and resid 275 through 285 Processing helix chain 'A' and resid 298 through 306 Processing helix chain 'A' and resid 308 through 315 Processing helix chain 'B' and resid 24 through 45 Processing helix chain 'B' and resid 49 through 72 Processing helix chain 'B' and resid 81 through 96 removed outlier: 3.725A pdb=" N GLU B 96 " --> pdb=" O LEU B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 137 removed outlier: 3.543A pdb=" N LEU B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 175 Processing helix chain 'B' and resid 176 through 186 removed outlier: 3.601A pdb=" N ARG B 181 " --> pdb=" O ASP B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 208 Processing helix chain 'B' and resid 209 through 219 Processing helix chain 'B' and resid 232 through 240 Processing helix chain 'B' and resid 242 through 252 Processing helix chain 'B' and resid 265 through 273 Processing helix chain 'B' and resid 275 through 285 Processing helix chain 'B' and resid 298 through 306 Processing helix chain 'B' and resid 308 through 315 Processing helix chain 'C' and resid 24 through 45 Processing helix chain 'C' and resid 49 through 72 Processing helix chain 'C' and resid 80 through 96 removed outlier: 3.688A pdb=" N ILE C 84 " --> pdb=" O SER C 80 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU C 96 " --> pdb=" O LEU C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 137 removed outlier: 3.504A pdb=" N LEU C 115 " --> pdb=" O GLU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 175 Processing helix chain 'C' and resid 176 through 186 Processing helix chain 'C' and resid 199 through 208 Processing helix chain 'C' and resid 209 through 219 Processing helix chain 'C' and resid 232 through 240 Processing helix chain 'C' and resid 242 through 252 Processing helix chain 'C' and resid 265 through 273 Processing helix chain 'C' and resid 275 through 285 Processing helix chain 'C' and resid 298 through 306 Processing helix chain 'C' and resid 308 through 315 Processing helix chain 'D' and resid 24 through 45 Processing helix chain 'D' and resid 49 through 72 Processing helix chain 'D' and resid 80 through 96 removed outlier: 4.059A pdb=" N ILE D 84 " --> pdb=" O SER D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 137 Processing helix chain 'D' and resid 139 through 175 Processing helix chain 'D' and resid 176 through 186 Processing helix chain 'D' and resid 199 through 208 Processing helix chain 'D' and resid 209 through 219 Processing helix chain 'D' and resid 232 through 240 Processing helix chain 'D' and resid 242 through 252 Processing helix chain 'D' and resid 265 through 273 Processing helix chain 'D' and resid 275 through 285 Processing helix chain 'D' and resid 298 through 306 Processing helix chain 'D' and resid 308 through 315 Processing helix chain 'E' and resid 17 through 31 Processing helix chain 'E' and resid 36 through 39 Processing helix chain 'E' and resid 73 through 91 Processing helix chain 'F' and resid 17 through 31 Processing helix chain 'F' and resid 36 through 39 Processing helix chain 'F' and resid 73 through 91 Processing helix chain 'G' and resid 17 through 31 Processing helix chain 'G' and resid 36 through 39 Processing helix chain 'G' and resid 73 through 91 Processing helix chain 'H' and resid 17 through 31 Processing helix chain 'H' and resid 36 through 39 Processing helix chain 'H' and resid 73 through 91 Processing helix chain 'I' and resid 24 through 45 Processing helix chain 'I' and resid 49 through 72 Processing helix chain 'I' and resid 80 through 96 removed outlier: 3.530A pdb=" N ILE I 84 " --> pdb=" O SER I 80 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU I 96 " --> pdb=" O LEU I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 137 removed outlier: 3.569A pdb=" N LEU I 115 " --> pdb=" O GLU I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 139 through 175 Processing helix chain 'I' and resid 176 through 186 Processing helix chain 'I' and resid 199 through 208 Processing helix chain 'I' and resid 209 through 219 Processing helix chain 'I' and resid 232 through 240 Processing helix chain 'I' and resid 242 through 252 Processing helix chain 'I' and resid 265 through 273 Processing helix chain 'I' and resid 275 through 285 Processing helix chain 'I' and resid 298 through 306 Processing helix chain 'I' and resid 308 through 315 Processing helix chain 'J' and resid 24 through 45 Processing helix chain 'J' and resid 46 through 48 No H-bonds generated for 'chain 'J' and resid 46 through 48' Processing helix chain 'J' and resid 49 through 72 Processing helix chain 'J' and resid 80 through 96 removed outlier: 4.174A pdb=" N ILE J 84 " --> pdb=" O SER J 80 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU J 96 " --> pdb=" O LEU J 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 137 Processing helix chain 'J' and resid 139 through 175 Processing helix chain 'J' and resid 176 through 186 Processing helix chain 'J' and resid 199 through 208 Processing helix chain 'J' and resid 209 through 219 Processing helix chain 'J' and resid 232 through 240 Processing helix chain 'J' and resid 242 through 252 Processing helix chain 'J' and resid 265 through 273 Processing helix chain 'J' and resid 275 through 285 Processing helix chain 'J' and resid 298 through 306 Processing helix chain 'J' and resid 308 through 315 Processing helix chain 'K' and resid 24 through 45 Processing helix chain 'K' and resid 49 through 72 Processing helix chain 'K' and resid 80 through 96 removed outlier: 3.560A pdb=" N ILE K 84 " --> pdb=" O SER K 80 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU K 96 " --> pdb=" O LEU K 92 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 137 Processing helix chain 'K' and resid 139 through 175 Processing helix chain 'K' and resid 176 through 186 Processing helix chain 'K' and resid 199 through 208 Processing helix chain 'K' and resid 209 through 219 Processing helix chain 'K' and resid 232 through 240 Processing helix chain 'K' and resid 242 through 252 Processing helix chain 'K' and resid 265 through 273 Processing helix chain 'K' and resid 275 through 285 Processing helix chain 'K' and resid 298 through 306 Processing helix chain 'K' and resid 308 through 315 Processing helix chain 'L' and resid 24 through 45 Processing helix chain 'L' and resid 49 through 72 Processing helix chain 'L' and resid 80 through 96 removed outlier: 4.030A pdb=" N ILE L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 109 through 137 removed outlier: 3.548A pdb=" N LEU L 115 " --> pdb=" O GLU L 111 " (cutoff:3.500A) Processing helix chain 'L' and resid 139 through 175 Processing helix chain 'L' and resid 176 through 186 Processing helix chain 'L' and resid 199 through 208 Processing helix chain 'L' and resid 209 through 219 Processing helix chain 'L' and resid 232 through 240 Processing helix chain 'L' and resid 242 through 252 Processing helix chain 'L' and resid 265 through 273 Processing helix chain 'L' and resid 275 through 285 Processing helix chain 'L' and resid 298 through 306 Processing helix chain 'L' and resid 308 through 315 Processing helix chain 'M' and resid 17 through 31 Processing helix chain 'M' and resid 36 through 39 Processing helix chain 'M' and resid 73 through 91 Processing helix chain 'N' and resid 17 through 31 Processing helix chain 'N' and resid 36 through 39 Processing helix chain 'N' and resid 73 through 91 Processing helix chain 'O' and resid 17 through 31 Processing helix chain 'O' and resid 36 through 39 Processing helix chain 'O' and resid 73 through 91 Processing helix chain 'P' and resid 17 through 31 Processing helix chain 'P' and resid 36 through 39 Processing helix chain 'P' and resid 73 through 91 Processing helix chain 'Q' and resid 24 through 45 Processing helix chain 'Q' and resid 49 through 72 Processing helix chain 'Q' and resid 80 through 96 removed outlier: 3.553A pdb=" N ILE Q 84 " --> pdb=" O SER Q 80 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU Q 96 " --> pdb=" O LEU Q 92 " (cutoff:3.500A) Processing helix chain 'Q' and resid 109 through 137 removed outlier: 3.549A pdb=" N LEU Q 115 " --> pdb=" O GLU Q 111 " (cutoff:3.500A) Processing helix chain 'Q' and resid 139 through 175 Processing helix chain 'Q' and resid 176 through 186 Processing helix chain 'Q' and resid 199 through 208 Processing helix chain 'Q' and resid 209 through 219 Processing helix chain 'Q' and resid 232 through 240 Processing helix chain 'Q' and resid 242 through 252 Processing helix chain 'Q' and resid 265 through 273 Processing helix chain 'Q' and resid 275 through 285 Processing helix chain 'Q' and resid 298 through 306 Processing helix chain 'Q' and resid 308 through 315 Processing helix chain 'R' and resid 24 through 45 Processing helix chain 'R' and resid 46 through 48 No H-bonds generated for 'chain 'R' and resid 46 through 48' Processing helix chain 'R' and resid 49 through 72 Processing helix chain 'R' and resid 80 through 97 removed outlier: 4.117A pdb=" N ILE R 84 " --> pdb=" O SER R 80 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU R 96 " --> pdb=" O LEU R 92 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N MET R 97 " --> pdb=" O ARG R 93 " (cutoff:3.500A) Processing helix chain 'R' and resid 109 through 137 removed outlier: 3.507A pdb=" N LYS R 114 " --> pdb=" O LEU R 110 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU R 115 " --> pdb=" O GLU R 111 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 175 Processing helix chain 'R' and resid 176 through 186 Processing helix chain 'R' and resid 199 through 208 Processing helix chain 'R' and resid 209 through 219 Processing helix chain 'R' and resid 232 through 240 Processing helix chain 'R' and resid 242 through 252 Processing helix chain 'R' and resid 265 through 273 Processing helix chain 'R' and resid 275 through 285 Processing helix chain 'R' and resid 298 through 306 Processing helix chain 'R' and resid 308 through 315 Processing helix chain 'S' and resid 24 through 45 Processing helix chain 'S' and resid 49 through 72 Processing helix chain 'S' and resid 80 through 96 removed outlier: 3.681A pdb=" N ILE S 84 " --> pdb=" O SER S 80 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU S 96 " --> pdb=" O LEU S 92 " (cutoff:3.500A) Processing helix chain 'S' and resid 109 through 137 removed outlier: 3.532A pdb=" N LEU S 115 " --> pdb=" O GLU S 111 " (cutoff:3.500A) Processing helix chain 'S' and resid 139 through 175 Processing helix chain 'S' and resid 176 through 186 Processing helix chain 'S' and resid 199 through 208 Processing helix chain 'S' and resid 209 through 219 Processing helix chain 'S' and resid 232 through 240 Processing helix chain 'S' and resid 242 through 252 Processing helix chain 'S' and resid 265 through 273 Processing helix chain 'S' and resid 275 through 285 Processing helix chain 'S' and resid 298 through 306 Processing helix chain 'S' and resid 308 through 315 Processing helix chain 'T' and resid 24 through 45 Processing helix chain 'T' and resid 49 through 72 Processing helix chain 'T' and resid 80 through 96 removed outlier: 4.132A pdb=" N ILE T 84 " --> pdb=" O SER T 80 " (cutoff:3.500A) Processing helix chain 'T' and resid 109 through 137 Processing helix chain 'T' and resid 139 through 175 Processing helix chain 'T' and resid 176 through 186 Processing helix chain 'T' and resid 199 through 208 Processing helix chain 'T' and resid 209 through 219 Processing helix chain 'T' and resid 232 through 240 Processing helix chain 'T' and resid 242 through 252 Processing helix chain 'T' and resid 265 through 273 Processing helix chain 'T' and resid 275 through 285 Processing helix chain 'T' and resid 298 through 306 Processing helix chain 'T' and resid 308 through 315 Processing helix chain 'U' and resid 17 through 31 Processing helix chain 'U' and resid 36 through 39 Processing helix chain 'U' and resid 73 through 91 Processing helix chain 'V' and resid 17 through 31 Processing helix chain 'V' and resid 36 through 39 Processing helix chain 'V' and resid 73 through 91 Processing helix chain 'W' and resid 17 through 31 Processing helix chain 'W' and resid 36 through 39 Processing helix chain 'W' and resid 73 through 91 Processing helix chain 'X' and resid 17 through 31 Processing helix chain 'X' and resid 36 through 39 Processing helix chain 'X' and resid 73 through 91 Processing sheet with id=AA1, first strand: chain 'M' and resid 50 through 52 removed outlier: 6.548A pdb=" N LEU E 4 " --> pdb=" O ARG E 43 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N VAL E 45 " --> pdb=" O LEU E 4 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE E 6 " --> pdb=" O VAL E 45 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N LEU E 47 " --> pdb=" O ILE E 6 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ALA E 8 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N TYR E 61 " --> pdb=" O THR E 9 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU E 62 " --> pdb=" O SER E 103 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N GLU E 105 " --> pdb=" O LEU E 62 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ALA E 64 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N ARG E 107 " --> pdb=" O ALA E 64 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU E 66 " --> pdb=" O ARG E 107 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N MET E 109 " --> pdb=" O LEU E 66 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE E 68 " --> pdb=" O MET E 109 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 13 through 14 removed outlier: 6.637A pdb=" N ARG E 13 " --> pdb=" O ALA E 93 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 50 through 52 removed outlier: 6.591A pdb=" N LEU U 4 " --> pdb=" O ARG U 43 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N VAL U 45 " --> pdb=" O LEU U 4 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE U 6 " --> pdb=" O VAL U 45 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU U 47 " --> pdb=" O ILE U 6 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ALA U 8 " --> pdb=" O LEU U 47 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N TYR U 61 " --> pdb=" O THR U 9 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 115 through 119 removed outlier: 6.640A pdb=" N LEU M 62 " --> pdb=" O SER M 103 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N GLU M 105 " --> pdb=" O LEU M 62 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA M 64 " --> pdb=" O GLU M 105 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N ARG M 107 " --> pdb=" O ALA M 64 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU M 66 " --> pdb=" O ARG M 107 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N MET M 109 " --> pdb=" O LEU M 66 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE M 68 " --> pdb=" O MET M 109 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N TYR M 61 " --> pdb=" O THR M 9 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU M 4 " --> pdb=" O ARG M 43 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N VAL M 45 " --> pdb=" O LEU M 4 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE M 6 " --> pdb=" O VAL M 45 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N LEU M 47 " --> pdb=" O ILE M 6 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ALA M 8 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 50 through 52 removed outlier: 6.501A pdb=" N LEU F 4 " --> pdb=" O ARG F 43 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N VAL F 45 " --> pdb=" O LEU F 4 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE F 6 " --> pdb=" O VAL F 45 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N LEU F 47 " --> pdb=" O ILE F 6 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA F 8 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N TYR F 61 " --> pdb=" O THR F 9 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU F 62 " --> pdb=" O SER F 103 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N GLU F 105 " --> pdb=" O LEU F 62 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA F 64 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ARG F 107 " --> pdb=" O ALA F 64 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU F 66 " --> pdb=" O ARG F 107 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N MET F 109 " --> pdb=" O LEU F 66 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE F 68 " --> pdb=" O MET F 109 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 13 through 14 Processing sheet with id=AA7, first strand: chain 'F' and resid 50 through 52 removed outlier: 6.593A pdb=" N LEU P 4 " --> pdb=" O ARG P 43 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N VAL P 45 " --> pdb=" O LEU P 4 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE P 6 " --> pdb=" O VAL P 45 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LEU P 47 " --> pdb=" O ILE P 6 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ALA P 8 " --> pdb=" O LEU P 47 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N TYR P 61 " --> pdb=" O THR P 9 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 115 through 119 removed outlier: 6.015A pdb=" N TYR G 61 " --> pdb=" O THR G 9 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU G 4 " --> pdb=" O ARG G 43 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N VAL G 45 " --> pdb=" O LEU G 4 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE G 6 " --> pdb=" O VAL G 45 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N LEU G 47 " --> pdb=" O ILE G 6 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA G 8 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 13 through 14 removed outlier: 6.627A pdb=" N ARG G 13 " --> pdb=" O ALA G 93 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'V' and resid 50 through 52 removed outlier: 6.538A pdb=" N LEU H 4 " --> pdb=" O ARG H 43 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N VAL H 45 " --> pdb=" O LEU H 4 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE H 6 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU H 47 " --> pdb=" O ILE H 6 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ALA H 8 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N TYR H 61 " --> pdb=" O THR H 9 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU H 62 " --> pdb=" O SER H 103 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N GLU H 105 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA H 64 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N ARG H 107 " --> pdb=" O ALA H 64 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU H 66 " --> pdb=" O ARG H 107 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N MET H 109 " --> pdb=" O LEU H 66 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE H 68 " --> pdb=" O MET H 109 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 13 through 14 removed outlier: 6.451A pdb=" N ARG H 13 " --> pdb=" O ALA H 93 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 50 through 52 removed outlier: 6.520A pdb=" N LEU W 4 " --> pdb=" O ARG W 43 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N VAL W 45 " --> pdb=" O LEU W 4 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE W 6 " --> pdb=" O VAL W 45 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N LEU W 47 " --> pdb=" O ILE W 6 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ALA W 8 " --> pdb=" O LEU W 47 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N TYR W 61 " --> pdb=" O THR W 9 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU W 62 " --> pdb=" O SER W 103 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N GLU W 105 " --> pdb=" O LEU W 62 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA W 64 " --> pdb=" O GLU W 105 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ARG W 107 " --> pdb=" O ALA W 64 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU W 66 " --> pdb=" O ARG W 107 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N MET W 109 " --> pdb=" O LEU W 66 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE W 68 " --> pdb=" O MET W 109 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 115 through 119 removed outlier: 5.987A pdb=" N TYR V 61 " --> pdb=" O THR V 9 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LEU V 4 " --> pdb=" O ARG V 43 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N VAL V 45 " --> pdb=" O LEU V 4 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE V 6 " --> pdb=" O VAL V 45 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N LEU V 47 " --> pdb=" O ILE V 6 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ALA V 8 " --> pdb=" O LEU V 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 12 through 14 Processing sheet with id=AB6, first strand: chain 'O' and resid 50 through 52 removed outlier: 6.490A pdb=" N LEU N 4 " --> pdb=" O ARG N 43 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N VAL N 45 " --> pdb=" O LEU N 4 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE N 6 " --> pdb=" O VAL N 45 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LEU N 47 " --> pdb=" O ILE N 6 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ALA N 8 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N TYR N 61 " --> pdb=" O THR N 9 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 13 through 14 Processing sheet with id=AB8, first strand: chain 'N' and resid 50 through 52 removed outlier: 6.596A pdb=" N LEU X 4 " --> pdb=" O ARG X 43 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N VAL X 45 " --> pdb=" O LEU X 4 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE X 6 " --> pdb=" O VAL X 45 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LEU X 47 " --> pdb=" O ILE X 6 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ALA X 8 " --> pdb=" O LEU X 47 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N TYR X 61 " --> pdb=" O THR X 9 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU X 62 " --> pdb=" O SER X 103 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N GLU X 105 " --> pdb=" O LEU X 62 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA X 64 " --> pdb=" O GLU X 105 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ARG X 107 " --> pdb=" O ALA X 64 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LEU X 66 " --> pdb=" O ARG X 107 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N MET X 109 " --> pdb=" O LEU X 66 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE X 68 " --> pdb=" O MET X 109 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 115 through 119 removed outlier: 6.571A pdb=" N LEU O 62 " --> pdb=" O SER O 103 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N GLU O 105 " --> pdb=" O LEU O 62 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA O 64 " --> pdb=" O GLU O 105 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ARG O 107 " --> pdb=" O ALA O 64 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU O 66 " --> pdb=" O ARG O 107 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N MET O 109 " --> pdb=" O LEU O 66 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE O 68 " --> pdb=" O MET O 109 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N TYR O 61 " --> pdb=" O THR O 9 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU O 4 " --> pdb=" O ARG O 43 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N VAL O 45 " --> pdb=" O LEU O 4 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ILE O 6 " --> pdb=" O VAL O 45 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU O 47 " --> pdb=" O ILE O 6 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ALA O 8 " --> pdb=" O LEU O 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'O' and resid 13 through 14 removed outlier: 6.522A pdb=" N ARG O 13 " --> pdb=" O ALA O 93 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'P' and resid 13 through 14 removed outlier: 6.446A pdb=" N ARG P 13 " --> pdb=" O ALA P 93 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'U' and resid 13 through 14 Processing sheet with id=AC4, first strand: chain 'V' and resid 13 through 14 Processing sheet with id=AC5, first strand: chain 'W' and resid 13 through 14 removed outlier: 6.556A pdb=" N ARG W 13 " --> pdb=" O ALA W 93 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'X' and resid 13 through 14 removed outlier: 6.429A pdb=" N ARG X 13 " --> pdb=" O ALA X 93 " (cutoff:3.500A) 2475 hydrogen bonds defined for protein. 7269 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: 6.49 Time building geometry restraints manager: 4.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.54: 36161 1.54 - 1.90: 1963 1.90 - 2.26: 0 2.26 - 2.63: 0 2.63 - 2.99: 1 Bond restraints: 38125 Sorted by residual: bond pdb=" C LEU Q 100 " pdb=" N SER Q 102 " ideal model delta sigma weight residual 1.330 2.991 -1.660 1.30e-02 5.92e+03 1.63e+04 bond pdb=" C GLU B 163 " pdb=" N LEU B 164 " ideal model delta sigma weight residual 1.335 1.559 -0.224 1.38e-02 5.25e+03 2.63e+02 bond pdb=" C GLU R 163 " pdb=" N LEU R 164 " ideal model delta sigma weight residual 1.335 1.559 -0.224 1.38e-02 5.25e+03 2.63e+02 bond pdb=" C GLU J 163 " pdb=" N LEU J 164 " ideal model delta sigma weight residual 1.335 1.558 -0.223 1.38e-02 5.25e+03 2.62e+02 bond pdb=" C GLU D 163 " pdb=" N LEU D 164 " ideal model delta sigma weight residual 1.335 1.544 -0.209 1.34e-02 5.57e+03 2.44e+02 ... (remaining 38120 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.97: 51157 3.97 - 7.93: 368 7.93 - 11.90: 17 11.90 - 15.86: 3 15.86 - 19.83: 1 Bond angle restraints: 51546 Sorted by residual: angle pdb=" CA LEU Q 100 " pdb=" C LEU Q 100 " pdb=" N SER Q 102 " ideal model delta sigma weight residual 115.51 95.68 19.83 1.27e+00 6.20e-01 2.44e+02 angle pdb=" C GLU S 163 " pdb=" N LEU S 164 " pdb=" CA LEU S 164 " ideal model delta sigma weight residual 120.31 108.19 12.12 1.52e+00 4.33e-01 6.36e+01 angle pdb=" C GLU C 163 " pdb=" N LEU C 164 " pdb=" CA LEU C 164 " ideal model delta sigma weight residual 120.31 108.25 12.06 1.52e+00 4.33e-01 6.29e+01 angle pdb=" C GLU K 163 " pdb=" N LEU K 164 " pdb=" CA LEU K 164 " ideal model delta sigma weight residual 120.31 108.27 12.04 1.52e+00 4.33e-01 6.28e+01 angle pdb=" C GLU Q 163 " pdb=" N LEU Q 164 " pdb=" CA LEU Q 164 " ideal model delta sigma weight residual 120.31 109.40 10.91 1.52e+00 4.33e-01 5.15e+01 ... (remaining 51541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 22117 17.70 - 35.39: 580 35.39 - 53.09: 149 53.09 - 70.78: 125 70.78 - 88.48: 31 Dihedral angle restraints: 23002 sinusoidal: 9000 harmonic: 14002 Sorted by residual: dihedral pdb=" CA LEU Q 100 " pdb=" C LEU Q 100 " pdb=" N SER Q 102 " pdb=" CA SER Q 102 " ideal model delta harmonic sigma weight residual 180.00 110.32 69.68 0 5.00e+00 4.00e-02 1.94e+02 dihedral pdb=" CA ASP U 70 " pdb=" CB ASP U 70 " pdb=" CG ASP U 70 " pdb=" OD1 ASP U 70 " ideal model delta sinusoidal sigma weight residual -30.00 -87.07 57.07 1 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" CA ASP W 70 " pdb=" CB ASP W 70 " pdb=" CG ASP W 70 " pdb=" OD1 ASP W 70 " ideal model delta sinusoidal sigma weight residual -30.00 -86.94 56.94 1 2.00e+01 2.50e-03 1.09e+01 ... (remaining 22999 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 4307 0.067 - 0.134: 1429 0.134 - 0.201: 269 0.201 - 0.268: 32 0.268 - 0.335: 23 Chirality restraints: 6060 Sorted by residual: chirality pdb=" CA HIS T 202 " pdb=" N HIS T 202 " pdb=" C HIS T 202 " pdb=" CB HIS T 202 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CA HIS B 202 " pdb=" N HIS B 202 " pdb=" C HIS B 202 " pdb=" CB HIS B 202 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CA HIS K 202 " pdb=" N HIS K 202 " pdb=" C HIS K 202 " pdb=" CB HIS K 202 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.77e+00 ... (remaining 6057 not shown) Planarity restraints: 6688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU Q 100 " 0.078 2.00e-02 2.50e+03 1.52e-01 2.31e+02 pdb=" C LEU Q 100 " -0.257 2.00e-02 2.50e+03 pdb=" O LEU Q 100 " 0.137 2.00e-02 2.50e+03 pdb=" N SER Q 102 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS K 235 " -0.041 2.00e-02 2.50e+03 3.12e-02 1.46e+01 pdb=" CG HIS K 235 " 0.046 2.00e-02 2.50e+03 pdb=" ND1 HIS K 235 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 HIS K 235 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 HIS K 235 " -0.012 2.00e-02 2.50e+03 pdb=" NE2 HIS K 235 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 235 " -0.041 2.00e-02 2.50e+03 3.11e-02 1.45e+01 pdb=" CG HIS C 235 " 0.046 2.00e-02 2.50e+03 pdb=" ND1 HIS C 235 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 HIS C 235 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 HIS C 235 " -0.012 2.00e-02 2.50e+03 pdb=" NE2 HIS C 235 " -0.033 2.00e-02 2.50e+03 ... (remaining 6685 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 13727 2.89 - 3.39: 39608 3.39 - 3.90: 66114 3.90 - 4.40: 76938 4.40 - 4.90: 122795 Nonbonded interactions: 319182 Sorted by model distance: nonbonded pdb=" O ARG H 72 " pdb=" NH1 ARG H 77 " model vdw 2.388 3.120 nonbonded pdb=" O ARG P 72 " pdb=" NH1 ARG P 77 " model vdw 2.405 3.120 nonbonded pdb=" O ARG F 72 " pdb=" NH1 ARG F 77 " model vdw 2.409 3.120 nonbonded pdb=" O ARG N 72 " pdb=" NH1 ARG N 77 " model vdw 2.412 3.120 nonbonded pdb=" O ARG X 72 " pdb=" NH1 ARG X 77 " model vdw 2.427 3.120 ... (remaining 319177 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' and (resid 23 through 99 or resid 103 through 316)) selection = (chain 'B' and (resid 23 through 99 or resid 103 through 316)) selection = chain 'C' selection = (chain 'D' and (resid 23 through 99 or resid 103 through 316)) selection = (chain 'I' and (resid 23 through 99 or resid 103 through 316)) selection = (chain 'J' and (resid 23 through 99 or resid 103 through 316)) selection = chain 'K' selection = (chain 'L' and (resid 23 through 99 or resid 103 through 316)) selection = (chain 'Q' and (resid 23 through 99 or resid 103 through 316)) selection = (chain 'R' and (resid 23 through 99 or resid 103 through 316)) selection = chain 'S' selection = (chain 'T' and (resid 23 through 99 or resid 103 through 316)) } ncs_group { reference = (chain 'E' and (resid 2 through 55 or resid 57 through 119)) selection = (chain 'F' and (resid 2 through 55 or resid 57 through 119)) selection = (chain 'G' and (resid 2 through 55 or resid 57 through 119)) selection = chain 'H' selection = (chain 'M' and (resid 2 through 55 or resid 57 through 119)) selection = (chain 'N' and (resid 2 through 55 or resid 57 through 119)) selection = (chain 'O' and (resid 2 through 55 or resid 57 through 119)) selection = chain 'P' selection = (chain 'U' and (resid 2 through 55 or resid 57 through 119)) selection = (chain 'V' and (resid 2 through 55 or resid 57 through 119)) selection = (chain 'W' and (resid 2 through 55 or resid 57 through 119)) selection = chain 'X' } 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: 4.840 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: 0.040 Extract box with map and model: 1.210 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 29.980 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.070 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2992 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 : 0.016 1.660 38125 Z= 1.066 Angle : 1.083 19.826 51546 Z= 0.785 Chirality : 0.066 0.335 6060 Planarity : 0.005 0.152 6688 Dihedral : 11.333 88.476 13996 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 0.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % 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 aren not related in a simple way. whole: 1.74 (0.11), residues: 4851 helix: 0.95 (0.08), residues: 3057 sheet: 2.60 (0.23), residues: 396 loop : 1.54 (0.16), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG W 77 TYR 0.028 0.002 TYR A 262 PHE 0.003 0.000 PHE A 154 TRP 0.008 0.001 TRP J 86 HIS 0.011 0.001 HIS D 268 Details of bonding type rmsd covalent geometry : bond 0.01550 (38125) covalent geometry : angle 1.08343 (51546) hydrogen bonds : bond 0.18163 ( 2475) hydrogen bonds : angle 5.90429 ( 7269) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9702 Ramachandran restraints generated. 4851 Oldfield, 0 Emsley, 4851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 895 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 895 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 121 ILE cc_start: 0.4728 (mm) cc_final: 0.4457 (mm) REVERT: L 120 THR cc_start: 0.5082 (p) cc_final: 0.3848 (p) REVERT: Q 120 THR cc_start: 0.5185 (p) cc_final: 0.4977 (p) REVERT: T 120 THR cc_start: 0.4756 (p) cc_final: 0.4471 (p) outliers start: 0 outliers final: 0 residues processed: 895 average time/residue: 0.2219 time to fit residues: 310.7041 Evaluate side-chains 425 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 425 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 7.9990 chunk 455 optimal weight: 8.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 10.0000 chunk 470 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 ASN ** C 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN H 3 HIS ** I 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 202 HIS ** K 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 HIS ** Q 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 3 HIS X 3 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.120460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.104681 restraints weight = 124393.525| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 6.13 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6388 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 38125 Z= 0.216 Angle : 0.602 9.156 51546 Z= 0.327 Chirality : 0.040 0.188 6060 Planarity : 0.004 0.039 6688 Dihedral : 3.894 46.498 5248 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.67 % Allowed : 9.89 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: 3.21 (0.11), residues: 4853 helix: 2.29 (0.08), residues: 3084 sheet: 2.87 (0.23), residues: 396 loop : 1.70 (0.17), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 107 TYR 0.020 0.002 TYR B 47 PHE 0.023 0.002 PHE D 136 TRP 0.021 0.001 TRP L 86 HIS 0.010 0.001 HIS S 219 Details of bonding type rmsd covalent geometry : bond 0.00427 (38125) covalent geometry : angle 0.60181 (51546) hydrogen bonds : bond 0.04936 ( 2475) hydrogen bonds : angle 4.69326 ( 7269) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9706 Ramachandran restraints generated. 4853 Oldfield, 0 Emsley, 4853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9706 Ramachandran restraints generated. 4853 Oldfield, 0 Emsley, 4853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 395 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.9408 (mm-30) cc_final: 0.9208 (mm-30) REVERT: A 93 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8482 (ttt-90) REVERT: A 97 MET cc_start: 0.9361 (mmm) cc_final: 0.9140 (mmm) REVERT: A 98 VAL cc_start: 0.8955 (OUTLIER) cc_final: 0.8621 (t) REVERT: A 99 ASN cc_start: 0.8648 (p0) cc_final: 0.7902 (p0) REVERT: A 193 HIS cc_start: 0.9140 (p90) cc_final: 0.8879 (p90) REVERT: B 36 GLU cc_start: 0.9437 (mm-30) cc_final: 0.9067 (mm-30) REVERT: B 184 MET cc_start: 0.7682 (OUTLIER) cc_final: 0.7367 (ptp) REVERT: C 67 MET cc_start: 0.9492 (mtp) cc_final: 0.8880 (mmm) REVERT: C 97 MET cc_start: 0.9396 (mpp) cc_final: 0.9102 (mpp) REVERT: C 130 LEU cc_start: 0.9670 (tp) cc_final: 0.9414 (mm) REVERT: D 43 GLU cc_start: 0.9274 (tm-30) cc_final: 0.9062 (tm-30) REVERT: D 67 MET cc_start: 0.9554 (mtp) cc_final: 0.9115 (mmt) REVERT: H 35 PHE cc_start: 0.8501 (m-10) cc_final: 0.8113 (m-10) REVERT: I 134 ARG cc_start: 0.9151 (ptp-170) cc_final: 0.8940 (ptp-170) REVERT: J 52 MET cc_start: 0.8917 (mmm) cc_final: 0.8682 (mmm) REVERT: J 97 MET cc_start: 0.9021 (ptp) cc_final: 0.8741 (ptp) REVERT: J 163 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8854 (mt-10) REVERT: J 184 MET cc_start: 0.7503 (ppp) cc_final: 0.7218 (ptm) REVERT: K 43 GLU cc_start: 0.9302 (tm-30) cc_final: 0.9017 (tm-30) REVERT: K 97 MET cc_start: 0.9428 (mpp) cc_final: 0.9122 (mpp) REVERT: K 130 LEU cc_start: 0.9699 (tp) cc_final: 0.9404 (mm) REVERT: L 52 MET cc_start: 0.9204 (mmm) cc_final: 0.8910 (mmm) REVERT: L 67 MET cc_start: 0.9489 (mtp) cc_final: 0.8823 (mmm) REVERT: L 99 ASN cc_start: 0.8337 (p0) cc_final: 0.7952 (p0) REVERT: L 130 LEU cc_start: 0.9638 (tp) cc_final: 0.9317 (mm) REVERT: M 72 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8282 (mmp80) REVERT: P 72 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.8113 (mmp80) REVERT: Q 99 ASN cc_start: 0.8946 (p0) cc_final: 0.8197 (p0) REVERT: Q 130 LEU cc_start: 0.9659 (tp) cc_final: 0.9311 (mm) REVERT: R 52 MET cc_start: 0.9151 (mmm) cc_final: 0.8941 (mmm) REVERT: R 67 MET cc_start: 0.9491 (mtp) cc_final: 0.8783 (mmm) REVERT: R 82 GLU cc_start: 0.9583 (mt-10) cc_final: 0.9262 (mp0) REVERT: R 97 MET cc_start: 0.9284 (mmm) cc_final: 0.9075 (mpp) REVERT: R 136 PHE cc_start: 0.8100 (m-80) cc_final: 0.7888 (m-80) REVERT: S 130 LEU cc_start: 0.9678 (tp) cc_final: 0.9442 (mm) REVERT: T 67 MET cc_start: 0.9359 (mtp) cc_final: 0.9050 (mtp) REVERT: T 79 ILE cc_start: 0.7236 (pt) cc_final: 0.6875 (mm) REVERT: T 99 ASN cc_start: 0.8396 (p0) cc_final: 0.6809 (p0) REVERT: T 130 LEU cc_start: 0.9674 (tp) cc_final: 0.9402 (mt) outliers start: 65 outliers final: 37 residues processed: 442 average time/residue: 0.1901 time to fit residues: 138.1012 Evaluate side-chains 336 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 294 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 202 HIS Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 99 ASN Chi-restraints excluded: chain J residue 31 ASN Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 72 ARG Chi-restraints excluded: chain N residue 24 GLN Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain O residue 68 ILE Chi-restraints excluded: chain O residue 73 ASP Chi-restraints excluded: chain P residue 72 ARG Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain R residue 151 ASP Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 117 VAL Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain W residue 24 GLN Chi-restraints excluded: chain W residue 79 LEU Chi-restraints excluded: chain X residue 68 ILE Chi-restraints excluded: chain X residue 79 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 316 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 294 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 255 optimal weight: 7.9990 chunk 215 optimal weight: 0.0980 chunk 396 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 86 optimal weight: 50.0000 chunk 426 optimal weight: 20.0000 chunk 280 optimal weight: 6.9990 overall best weight: 3.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 HIS ** D 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 202 HIS ** S 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 219 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.113250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.092105 restraints weight = 137472.324| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 6.65 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6527 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 38125 Z= 0.145 Angle : 0.519 9.139 51546 Z= 0.276 Chirality : 0.038 0.162 6060 Planarity : 0.004 0.075 6688 Dihedral : 3.577 32.957 5248 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.62 % Allowed : 11.17 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 aren not related in a simple way. whole: 3.52 (0.11), residues: 4853 helix: 2.64 (0.09), residues: 3069 sheet: 3.14 (0.23), residues: 396 loop : 1.49 (0.17), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 13 TYR 0.014 0.002 TYR R 145 PHE 0.014 0.001 PHE T 103 TRP 0.019 0.001 TRP L 86 HIS 0.011 0.001 HIS Q 219 Details of bonding type rmsd covalent geometry : bond 0.00296 (38125) covalent geometry : angle 0.51927 (51546) hydrogen bonds : bond 0.04261 ( 2475) hydrogen bonds : angle 4.31093 ( 7269) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9706 Ramachandran restraints generated. 4853 Oldfield, 0 Emsley, 4853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9706 Ramachandran restraints generated. 4853 Oldfield, 0 Emsley, 4853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 346 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8520 (tp30) REVERT: A 95 MET cc_start: 0.9567 (tpp) cc_final: 0.9076 (tmm) REVERT: A 99 ASN cc_start: 0.8555 (p0) cc_final: 0.8025 (p0) REVERT: A 193 HIS cc_start: 0.9128 (p90) cc_final: 0.8750 (p90) REVERT: B 95 MET cc_start: 0.9596 (ttm) cc_final: 0.9164 (tmm) REVERT: B 97 MET cc_start: 0.9369 (mpp) cc_final: 0.9063 (mpp) REVERT: B 184 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.7074 (ptp) REVERT: C 67 MET cc_start: 0.9523 (mtp) cc_final: 0.8682 (tpp) REVERT: C 95 MET cc_start: 0.9473 (ttm) cc_final: 0.8973 (tmm) REVERT: C 97 MET cc_start: 0.9440 (mpp) cc_final: 0.9049 (mpp) REVERT: D 43 GLU cc_start: 0.9281 (tm-30) cc_final: 0.9024 (tm-30) REVERT: D 52 MET cc_start: 0.9398 (ptp) cc_final: 0.9030 (ptt) REVERT: D 67 MET cc_start: 0.9580 (mtp) cc_final: 0.9136 (mmt) REVERT: D 82 GLU cc_start: 0.9627 (mt-10) cc_final: 0.9313 (mp0) REVERT: D 95 MET cc_start: 0.9555 (tpp) cc_final: 0.9046 (tmm) REVERT: D 103 PHE cc_start: 0.7926 (t80) cc_final: 0.7500 (t80) REVERT: D 134 ARG cc_start: 0.8877 (ptp90) cc_final: 0.8646 (ptt-90) REVERT: H 35 PHE cc_start: 0.8450 (m-10) cc_final: 0.8211 (m-10) REVERT: I 99 ASN cc_start: 0.8797 (p0) cc_final: 0.8163 (p0) REVERT: J 95 MET cc_start: 0.9568 (ttm) cc_final: 0.9059 (tmm) REVERT: J 97 MET cc_start: 0.9114 (ptp) cc_final: 0.8911 (ptp) REVERT: J 130 LEU cc_start: 0.9712 (tp) cc_final: 0.9476 (mt) REVERT: J 184 MET cc_start: 0.7591 (ppp) cc_final: 0.7305 (ptm) REVERT: K 43 GLU cc_start: 0.9347 (tm-30) cc_final: 0.9043 (tm-30) REVERT: K 69 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8529 (tp30) REVERT: K 95 MET cc_start: 0.9409 (OUTLIER) cc_final: 0.8886 (tmm) REVERT: K 97 MET cc_start: 0.9525 (mpp) cc_final: 0.9250 (mpp) REVERT: L 67 MET cc_start: 0.9441 (mtp) cc_final: 0.8712 (tpp) REVERT: L 99 ASN cc_start: 0.8541 (p0) cc_final: 0.8098 (p0) REVERT: O 70 ASP cc_start: 0.9473 (p0) cc_final: 0.9261 (p0) REVERT: P 68 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8907 (mm) REVERT: P 72 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.8034 (mmp80) REVERT: Q 95 MET cc_start: 0.9497 (tpp) cc_final: 0.8831 (tmm) REVERT: Q 97 MET cc_start: 0.9548 (mmm) cc_final: 0.9319 (mmm) REVERT: Q 99 ASN cc_start: 0.8819 (p0) cc_final: 0.8324 (p0) REVERT: Q 126 LEU cc_start: 0.9598 (tt) cc_final: 0.9284 (tp) REVERT: Q 146 LEU cc_start: 0.9345 (tt) cc_final: 0.8974 (tp) REVERT: R 67 MET cc_start: 0.9353 (mtp) cc_final: 0.8733 (mmm) REVERT: R 82 GLU cc_start: 0.9562 (mt-10) cc_final: 0.9259 (mp0) REVERT: R 134 ARG cc_start: 0.9026 (ptp-110) cc_final: 0.8658 (ptp-170) REVERT: R 184 MET cc_start: 0.8101 (ppp) cc_final: 0.7636 (ptm) REVERT: S 95 MET cc_start: 0.9452 (ttm) cc_final: 0.8973 (tmm) REVERT: S 97 MET cc_start: 0.9465 (mpp) cc_final: 0.9222 (mpp) REVERT: S 184 MET cc_start: 0.7962 (ppp) cc_final: 0.7704 (ppp) REVERT: T 79 ILE cc_start: 0.7391 (pt) cc_final: 0.6835 (mm) REVERT: T 82 GLU cc_start: 0.9648 (mt-10) cc_final: 0.9378 (mp0) REVERT: T 95 MET cc_start: 0.9558 (tpp) cc_final: 0.9077 (tmm) REVERT: T 99 ASN cc_start: 0.8478 (p0) cc_final: 0.7128 (p0) REVERT: T 101 LYS cc_start: 0.9055 (mmmt) cc_final: 0.8656 (mmmt) REVERT: T 145 TYR cc_start: 0.9183 (t80) cc_final: 0.8960 (t80) REVERT: T 158 ARG cc_start: 0.8823 (mmp80) cc_final: 0.8537 (mmp80) REVERT: T 163 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8548 (tp30) REVERT: U 68 ILE cc_start: 0.9361 (OUTLIER) cc_final: 0.9131 (mm) outliers start: 63 outliers final: 35 residues processed: 385 average time/residue: 0.2024 time to fit residues: 128.9968 Evaluate side-chains 334 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 292 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 202 HIS Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain F residue 109 MET Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain K residue 69 GLU Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 109 MET Chi-restraints excluded: chain N residue 24 GLN Chi-restraints excluded: chain O residue 24 GLN Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 72 ARG Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 31 ASN Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain S residue 117 VAL Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain T residue 105 LEU Chi-restraints excluded: chain T residue 117 VAL Chi-restraints excluded: chain U residue 24 GLN Chi-restraints excluded: chain U residue 68 ILE Chi-restraints excluded: chain V residue 39 ASP Chi-restraints excluded: chain W residue 24 GLN Chi-restraints excluded: chain W residue 68 ILE Chi-restraints excluded: chain X residue 68 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 294 optimal weight: 9.9990 chunk 346 optimal weight: 50.0000 chunk 463 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 237 optimal weight: 20.0000 chunk 140 optimal weight: 10.0000 chunk 348 optimal weight: 30.0000 chunk 443 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 25 optimal weight: 50.0000 chunk 322 optimal weight: 0.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 202 HIS ** L 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.113354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.092101 restraints weight = 138930.354| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 6.38 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 38125 Z= 0.140 Angle : 0.497 7.294 51546 Z= 0.266 Chirality : 0.038 0.171 6060 Planarity : 0.003 0.044 6688 Dihedral : 3.505 28.671 5248 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.98 % Allowed : 10.89 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.54 (0.11), residues: 4853 helix: 2.67 (0.09), residues: 3081 sheet: 3.17 (0.23), residues: 396 loop : 1.44 (0.17), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 134 TYR 0.014 0.001 TYR O 61 PHE 0.014 0.001 PHE R 136 TRP 0.021 0.001 TRP L 86 HIS 0.008 0.001 HIS S 219 Details of bonding type rmsd covalent geometry : bond 0.00286 (38125) covalent geometry : angle 0.49654 (51546) hydrogen bonds : bond 0.03993 ( 2475) hydrogen bonds : angle 4.13576 ( 7269) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9706 Ramachandran restraints generated. 4853 Oldfield, 0 Emsley, 4853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9706 Ramachandran restraints generated. 4853 Oldfield, 0 Emsley, 4853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 317 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.8858 (OUTLIER) cc_final: 0.8489 (tp30) REVERT: A 95 MET cc_start: 0.9567 (tpp) cc_final: 0.9047 (tmm) REVERT: A 99 ASN cc_start: 0.8598 (p0) cc_final: 0.8084 (p0) REVERT: A 193 HIS cc_start: 0.9161 (p90) cc_final: 0.8789 (p90) REVERT: B 95 MET cc_start: 0.9618 (ttm) cc_final: 0.9264 (tmm) REVERT: B 97 MET cc_start: 0.9326 (mpp) cc_final: 0.8703 (mpp) REVERT: C 67 MET cc_start: 0.9499 (mtp) cc_final: 0.8881 (mmm) REVERT: C 95 MET cc_start: 0.9496 (ttm) cc_final: 0.8973 (tmm) REVERT: C 97 MET cc_start: 0.9431 (mpp) cc_final: 0.8997 (mpp) REVERT: D 43 GLU cc_start: 0.9343 (tm-30) cc_final: 0.9070 (tm-30) REVERT: D 67 MET cc_start: 0.9565 (mtp) cc_final: 0.9144 (mmm) REVERT: D 82 GLU cc_start: 0.9626 (mt-10) cc_final: 0.9311 (mp0) REVERT: D 95 MET cc_start: 0.9531 (tpp) cc_final: 0.9001 (tmm) REVERT: H 35 PHE cc_start: 0.8506 (m-10) cc_final: 0.8273 (m-10) REVERT: I 97 MET cc_start: 0.9457 (mmm) cc_final: 0.9255 (mmm) REVERT: I 99 ASN cc_start: 0.8705 (p0) cc_final: 0.8109 (p0) REVERT: J 82 GLU cc_start: 0.9632 (mt-10) cc_final: 0.9304 (mp0) REVERT: J 95 MET cc_start: 0.9508 (OUTLIER) cc_final: 0.8969 (tmm) REVERT: J 97 MET cc_start: 0.9186 (ptp) cc_final: 0.8916 (ptp) REVERT: J 184 MET cc_start: 0.7760 (ppp) cc_final: 0.7431 (ptm) REVERT: K 43 GLU cc_start: 0.9340 (tm-30) cc_final: 0.9014 (tm-30) REVERT: K 69 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8560 (tp30) REVERT: K 95 MET cc_start: 0.9406 (ttm) cc_final: 0.8885 (tmm) REVERT: K 97 MET cc_start: 0.9472 (mpp) cc_final: 0.9160 (mpp) REVERT: L 67 MET cc_start: 0.9540 (mtp) cc_final: 0.8841 (tpp) REVERT: L 99 ASN cc_start: 0.8497 (p0) cc_final: 0.7991 (p0) REVERT: L 129 VAL cc_start: 0.9671 (OUTLIER) cc_final: 0.9415 (p) REVERT: L 134 ARG cc_start: 0.9235 (ttm110) cc_final: 0.8789 (ptp-110) REVERT: M 72 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.8410 (mmp80) REVERT: N 68 ILE cc_start: 0.9324 (tt) cc_final: 0.8969 (mm) REVERT: P 68 ILE cc_start: 0.9191 (OUTLIER) cc_final: 0.8957 (mm) REVERT: P 72 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.8091 (mmp80) REVERT: Q 95 MET cc_start: 0.9500 (tpp) cc_final: 0.8805 (tmm) REVERT: Q 99 ASN cc_start: 0.8872 (p0) cc_final: 0.8489 (p0) REVERT: R 67 MET cc_start: 0.9418 (mtp) cc_final: 0.8726 (mmm) REVERT: R 82 GLU cc_start: 0.9552 (mt-10) cc_final: 0.9241 (mp0) REVERT: R 97 MET cc_start: 0.9295 (mpp) cc_final: 0.8983 (mpp) REVERT: R 184 MET cc_start: 0.8186 (ppp) cc_final: 0.7753 (ptm) REVERT: S 67 MET cc_start: 0.9365 (ptt) cc_final: 0.8902 (ptp) REVERT: S 97 MET cc_start: 0.9454 (mpp) cc_final: 0.9200 (mpp) REVERT: T 67 MET cc_start: 0.9457 (mtp) cc_final: 0.9156 (mtp) REVERT: T 79 ILE cc_start: 0.7431 (pt) cc_final: 0.6851 (mm) REVERT: T 82 GLU cc_start: 0.9646 (mt-10) cc_final: 0.9381 (mp0) REVERT: T 95 MET cc_start: 0.9516 (tpp) cc_final: 0.9062 (tmm) REVERT: T 99 ASN cc_start: 0.8345 (p0) cc_final: 0.6791 (p0) REVERT: T 101 LYS cc_start: 0.8773 (mmmt) cc_final: 0.8546 (mmmt) REVERT: T 145 TYR cc_start: 0.9177 (t80) cc_final: 0.8935 (t80) REVERT: T 163 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8481 (tp30) REVERT: U 68 ILE cc_start: 0.9332 (OUTLIER) cc_final: 0.9117 (mm) outliers start: 77 outliers final: 47 residues processed: 370 average time/residue: 0.1903 time to fit residues: 116.7929 Evaluate side-chains 341 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 286 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 86 TRP Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 202 HIS Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 109 MET Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain K residue 69 GLU Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain L residue 101 LYS Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 72 ARG Chi-restraints excluded: chain N residue 24 GLN Chi-restraints excluded: chain O residue 24 GLN Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 72 ARG Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain R residue 86 TRP Chi-restraints excluded: chain R residue 151 ASP Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain S residue 117 VAL Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain T residue 105 LEU Chi-restraints excluded: chain T residue 117 VAL Chi-restraints excluded: chain U residue 24 GLN Chi-restraints excluded: chain U residue 68 ILE Chi-restraints excluded: chain V residue 39 ASP Chi-restraints excluded: chain W residue 24 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 197 optimal weight: 5.9990 chunk 133 optimal weight: 20.0000 chunk 319 optimal weight: 6.9990 chunk 159 optimal weight: 7.9990 chunk 403 optimal weight: 8.9990 chunk 323 optimal weight: 10.0000 chunk 279 optimal weight: 10.0000 chunk 114 optimal weight: 40.0000 chunk 230 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 282 optimal weight: 30.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 202 HIS U 3 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.113973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.093750 restraints weight = 136963.204| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 6.38 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 moved from start: 0.4844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 38125 Z= 0.163 Angle : 0.511 10.861 51546 Z= 0.273 Chirality : 0.037 0.150 6060 Planarity : 0.004 0.046 6688 Dihedral : 3.490 24.345 5248 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.13 % Allowed : 11.07 % Favored : 86.80 % 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 aren not related in a simple way. whole: 3.43 (0.11), residues: 4853 helix: 2.61 (0.09), residues: 3084 sheet: 3.02 (0.22), residues: 396 loop : 1.35 (0.17), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 134 TYR 0.014 0.002 TYR O 61 PHE 0.022 0.001 PHE D 103 TRP 0.020 0.001 TRP L 86 HIS 0.006 0.001 HIS D 219 Details of bonding type rmsd covalent geometry : bond 0.00326 (38125) covalent geometry : angle 0.51063 (51546) hydrogen bonds : bond 0.03969 ( 2475) hydrogen bonds : angle 4.11104 ( 7269) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9706 Ramachandran restraints generated. 4853 Oldfield, 0 Emsley, 4853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9706 Ramachandran restraints generated. 4853 Oldfield, 0 Emsley, 4853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 290 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.9253 (ptt) cc_final: 0.8841 (ptp) REVERT: A 69 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8465 (tp30) REVERT: A 99 ASN cc_start: 0.8601 (p0) cc_final: 0.8118 (p0) REVERT: A 193 HIS cc_start: 0.9223 (p90) cc_final: 0.8844 (p90) REVERT: B 67 MET cc_start: 0.9435 (ptp) cc_final: 0.8842 (ptp) REVERT: B 97 MET cc_start: 0.9320 (mpp) cc_final: 0.8648 (mpp) REVERT: C 36 GLU cc_start: 0.9732 (tt0) cc_final: 0.9481 (tt0) REVERT: C 67 MET cc_start: 0.9445 (mtp) cc_final: 0.8567 (tpp) REVERT: C 97 MET cc_start: 0.9389 (mpp) cc_final: 0.8904 (mpp) REVERT: C 134 ARG cc_start: 0.9058 (ptp-170) cc_final: 0.8797 (ptp-170) REVERT: D 43 GLU cc_start: 0.9359 (tm-30) cc_final: 0.9066 (tm-30) REVERT: D 67 MET cc_start: 0.9577 (mtp) cc_final: 0.9164 (mmm) REVERT: D 82 GLU cc_start: 0.9624 (mt-10) cc_final: 0.9316 (mp0) REVERT: D 95 MET cc_start: 0.9524 (tpp) cc_final: 0.8983 (tmm) REVERT: D 103 PHE cc_start: 0.7848 (t80) cc_final: 0.7521 (t80) REVERT: D 177 ASP cc_start: 0.9427 (p0) cc_final: 0.9167 (m-30) REVERT: G 109 MET cc_start: 0.8704 (ptm) cc_final: 0.8414 (ptm) REVERT: H 35 PHE cc_start: 0.8555 (m-10) cc_final: 0.8303 (m-10) REVERT: H 72 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8112 (mmp80) REVERT: I 67 MET cc_start: 0.9126 (ptt) cc_final: 0.8198 (ttp) REVERT: I 69 GLU cc_start: 0.9188 (OUTLIER) cc_final: 0.8729 (tp30) REVERT: I 97 MET cc_start: 0.9512 (mmm) cc_final: 0.9286 (mmm) REVERT: I 99 ASN cc_start: 0.8717 (p0) cc_final: 0.8225 (p0) REVERT: I 126 LEU cc_start: 0.9696 (tp) cc_final: 0.9372 (tp) REVERT: I 146 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9089 (tt) REVERT: J 82 GLU cc_start: 0.9644 (mt-10) cc_final: 0.9298 (mp0) REVERT: J 95 MET cc_start: 0.9486 (OUTLIER) cc_final: 0.8879 (tmm) REVERT: J 146 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.9248 (tt) REVERT: J 184 MET cc_start: 0.7966 (OUTLIER) cc_final: 0.7746 (ptm) REVERT: K 43 GLU cc_start: 0.9304 (tm-30) cc_final: 0.8973 (tm-30) REVERT: K 69 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8522 (tp30) REVERT: K 97 MET cc_start: 0.9405 (mpp) cc_final: 0.9052 (mpp) REVERT: L 67 MET cc_start: 0.9507 (mtp) cc_final: 0.9289 (mtp) REVERT: L 99 ASN cc_start: 0.8498 (p0) cc_final: 0.7974 (p0) REVERT: L 103 PHE cc_start: 0.8220 (t80) cc_final: 0.7944 (t80) REVERT: L 129 VAL cc_start: 0.9487 (OUTLIER) cc_final: 0.9266 (p) REVERT: M 72 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.8396 (mmp80) REVERT: N 68 ILE cc_start: 0.9353 (tt) cc_final: 0.9020 (mm) REVERT: P 72 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.8129 (mmp80) REVERT: Q 69 GLU cc_start: 0.9157 (OUTLIER) cc_final: 0.8788 (tm-30) REVERT: Q 99 ASN cc_start: 0.8834 (p0) cc_final: 0.8512 (p0) REVERT: R 67 MET cc_start: 0.9378 (mtp) cc_final: 0.8655 (tpp) REVERT: R 82 GLU cc_start: 0.9573 (mt-10) cc_final: 0.9280 (mp0) REVERT: R 95 MET cc_start: 0.9553 (ttm) cc_final: 0.9144 (tmm) REVERT: R 97 MET cc_start: 0.9306 (mpp) cc_final: 0.9009 (mpp) REVERT: R 184 MET cc_start: 0.8307 (ppp) cc_final: 0.7866 (ptm) REVERT: S 97 MET cc_start: 0.9442 (mpp) cc_final: 0.9209 (mpp) REVERT: T 82 GLU cc_start: 0.9650 (mt-10) cc_final: 0.9396 (mp0) REVERT: T 95 MET cc_start: 0.9485 (tpp) cc_final: 0.9025 (tmm) REVERT: T 99 ASN cc_start: 0.8368 (p0) cc_final: 0.7410 (p0) REVERT: T 145 TYR cc_start: 0.9219 (t80) cc_final: 0.9013 (t80) outliers start: 83 outliers final: 55 residues processed: 346 average time/residue: 0.1960 time to fit residues: 112.5450 Evaluate side-chains 335 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 268 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain B residue 31 ASN Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 202 HIS Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 69 GLU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 146 LEU Chi-restraints excluded: chain J residue 95 MET Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 146 LEU Chi-restraints excluded: chain J residue 184 MET Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain K residue 69 GLU Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 86 TRP Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain L residue 101 LYS Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 120 THR Chi-restraints excluded: chain L residue 121 ILE Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 72 ARG Chi-restraints excluded: chain N residue 24 GLN Chi-restraints excluded: chain O residue 24 GLN Chi-restraints excluded: chain P residue 72 ARG Chi-restraints excluded: chain Q residue 69 GLU Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain R residue 31 ASN Chi-restraints excluded: chain R residue 86 TRP Chi-restraints excluded: chain R residue 151 ASP Chi-restraints excluded: chain S residue 31 ASN Chi-restraints excluded: chain S residue 86 TRP Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain S residue 117 VAL Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain T residue 105 LEU Chi-restraints excluded: chain T residue 117 VAL Chi-restraints excluded: chain U residue 24 GLN Chi-restraints excluded: chain V residue 39 ASP Chi-restraints excluded: chain V residue 109 MET Chi-restraints excluded: chain W residue 24 GLN Chi-restraints excluded: chain X residue 68 ILE Chi-restraints excluded: chain X residue 109 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 112 optimal weight: 50.0000 chunk 138 optimal weight: 9.9990 chunk 162 optimal weight: 2.9990 chunk 449 optimal weight: 6.9990 chunk 450 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 437 optimal weight: 1.9990 chunk 417 optimal weight: 5.9990 chunk 181 optimal weight: 50.0000 chunk 414 optimal weight: 8.9990 chunk 378 optimal weight: 0.0980 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 202 HIS R 202 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.107865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.084188 restraints weight = 148322.461| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 6.53 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 38125 Z= 0.108 Angle : 0.476 11.705 51546 Z= 0.250 Chirality : 0.037 0.153 6060 Planarity : 0.003 0.047 6688 Dihedral : 3.372 21.709 5248 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.77 % Allowed : 11.81 % Favored : 86.41 % 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 aren not related in a simple way. whole: 3.76 (0.12), residues: 4853 helix: 2.89 (0.09), residues: 3081 sheet: 3.06 (0.22), residues: 396 loop : 1.45 (0.17), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 134 TYR 0.017 0.001 TYR D 145 PHE 0.016 0.001 PHE T 103 TRP 0.018 0.001 TRP L 86 HIS 0.006 0.001 HIS S 219 Details of bonding type rmsd covalent geometry : bond 0.00223 (38125) covalent geometry : angle 0.47575 (51546) hydrogen bonds : bond 0.03671 ( 2475) hydrogen bonds : angle 3.83560 ( 7269) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9706 Ramachandran restraints generated. 4853 Oldfield, 0 Emsley, 4853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9706 Ramachandran restraints generated. 4853 Oldfield, 0 Emsley, 4853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 314 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.9483 (mm-30) cc_final: 0.9278 (mm-30) REVERT: A 67 MET cc_start: 0.9253 (ptt) cc_final: 0.9049 (ptp) REVERT: A 69 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8449 (tp30) REVERT: A 99 ASN cc_start: 0.8740 (p0) cc_final: 0.8261 (p0) REVERT: A 151 ASP cc_start: 0.9528 (OUTLIER) cc_final: 0.9054 (t0) REVERT: A 193 HIS cc_start: 0.9251 (p90) cc_final: 0.8907 (p90) REVERT: B 36 GLU cc_start: 0.9541 (mm-30) cc_final: 0.9168 (mm-30) REVERT: B 97 MET cc_start: 0.9325 (mpp) cc_final: 0.8715 (mpp) REVERT: C 36 GLU cc_start: 0.9710 (tt0) cc_final: 0.9409 (tt0) REVERT: C 67 MET cc_start: 0.9407 (mtp) cc_final: 0.8567 (tpp) REVERT: C 97 MET cc_start: 0.9380 (mpp) cc_final: 0.8908 (mpp) REVERT: D 43 GLU cc_start: 0.9308 (tm-30) cc_final: 0.9030 (tm-30) REVERT: D 67 MET cc_start: 0.9579 (mtp) cc_final: 0.9192 (mmm) REVERT: D 82 GLU cc_start: 0.9611 (mt-10) cc_final: 0.9339 (mp0) REVERT: D 95 MET cc_start: 0.9566 (tpp) cc_final: 0.9029 (tmm) REVERT: D 177 ASP cc_start: 0.9459 (p0) cc_final: 0.9124 (t0) REVERT: G 72 ARG cc_start: 0.8527 (mpt180) cc_final: 0.8250 (mpt180) REVERT: H 35 PHE cc_start: 0.8417 (m-10) cc_final: 0.8205 (m-10) REVERT: I 67 MET cc_start: 0.9239 (ptt) cc_final: 0.8309 (ttp) REVERT: I 69 GLU cc_start: 0.9280 (OUTLIER) cc_final: 0.8826 (tp30) REVERT: I 97 MET cc_start: 0.9504 (mmm) cc_final: 0.9286 (mmm) REVERT: I 99 ASN cc_start: 0.8843 (p0) cc_final: 0.8385 (p0) REVERT: I 126 LEU cc_start: 0.9695 (tp) cc_final: 0.9383 (tp) REVERT: I 146 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9155 (tt) REVERT: I 153 LEU cc_start: 0.9840 (mp) cc_final: 0.9573 (tp) REVERT: J 82 GLU cc_start: 0.9646 (mt-10) cc_final: 0.9321 (mp0) REVERT: J 95 MET cc_start: 0.9553 (ttm) cc_final: 0.8954 (tmm) REVERT: J 184 MET cc_start: 0.7924 (OUTLIER) cc_final: 0.7696 (ptm) REVERT: K 43 GLU cc_start: 0.9326 (tm-30) cc_final: 0.8998 (tm-30) REVERT: K 69 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8525 (tp30) REVERT: K 97 MET cc_start: 0.9432 (mpp) cc_final: 0.9098 (mpp) REVERT: L 99 ASN cc_start: 0.8696 (p0) cc_final: 0.8199 (p0) REVERT: L 177 ASP cc_start: 0.9485 (p0) cc_final: 0.9112 (m-30) REVERT: N 68 ILE cc_start: 0.9276 (tt) cc_final: 0.8951 (mm) REVERT: Q 69 GLU cc_start: 0.9172 (OUTLIER) cc_final: 0.8771 (tp30) REVERT: Q 99 ASN cc_start: 0.8986 (p0) cc_final: 0.8712 (p0) REVERT: R 67 MET cc_start: 0.9429 (mtp) cc_final: 0.8695 (tpp) REVERT: R 82 GLU cc_start: 0.9584 (mt-10) cc_final: 0.9243 (mp0) REVERT: R 95 MET cc_start: 0.9556 (ttm) cc_final: 0.9146 (tmm) REVERT: R 97 MET cc_start: 0.9352 (mpp) cc_final: 0.9054 (mpp) REVERT: R 184 MET cc_start: 0.8201 (ppp) cc_final: 0.7807 (ptm) REVERT: S 67 MET cc_start: 0.9322 (ptt) cc_final: 0.8927 (ptp) REVERT: S 97 MET cc_start: 0.9468 (mpp) cc_final: 0.9257 (mpp) REVERT: S 177 ASP cc_start: 0.9430 (p0) cc_final: 0.8980 (t0) REVERT: T 67 MET cc_start: 0.9517 (mtp) cc_final: 0.8504 (tpp) REVERT: T 82 GLU cc_start: 0.9661 (mt-10) cc_final: 0.9438 (mp0) REVERT: T 95 MET cc_start: 0.9506 (tpp) cc_final: 0.9023 (tmm) REVERT: T 99 ASN cc_start: 0.8641 (p0) cc_final: 0.8177 (p0) REVERT: T 130 LEU cc_start: 0.9780 (tt) cc_final: 0.9471 (mt) REVERT: T 134 ARG cc_start: 0.9337 (ptp-110) cc_final: 0.9129 (ptp-170) REVERT: U 70 ASP cc_start: 0.9601 (p0) cc_final: 0.9371 (p0) outliers start: 69 outliers final: 46 residues processed: 359 average time/residue: 0.1981 time to fit residues: 119.2323 Evaluate side-chains 331 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 278 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 86 TRP Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 202 HIS Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain I residue 52 MET Chi-restraints excluded: chain I residue 69 GLU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 146 LEU Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 138 ILE Chi-restraints excluded: chain J residue 184 MET Chi-restraints excluded: chain K residue 31 ASN Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain K residue 69 GLU Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 86 TRP Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain L residue 101 LYS Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 121 ILE Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain N residue 24 GLN Chi-restraints excluded: chain O residue 24 GLN Chi-restraints excluded: chain Q residue 69 GLU Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain R residue 31 ASN Chi-restraints excluded: chain R residue 86 TRP Chi-restraints excluded: chain S residue 86 TRP Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain T residue 105 LEU Chi-restraints excluded: chain T residue 117 VAL Chi-restraints excluded: chain U residue 24 GLN Chi-restraints excluded: chain V residue 109 MET Chi-restraints excluded: chain W residue 24 GLN Chi-restraints excluded: chain X residue 68 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 152 optimal weight: 7.9990 chunk 369 optimal weight: 9.9990 chunk 290 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 chunk 108 optimal weight: 8.9990 chunk 134 optimal weight: 9.9990 chunk 47 optimal weight: 50.0000 chunk 294 optimal weight: 9.9990 chunk 104 optimal weight: 0.1980 chunk 462 optimal weight: 20.0000 chunk 423 optimal weight: 20.0000 overall best weight: 7.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 24 GLN G 3 HIS J 202 HIS J 240 ASN M 24 GLN O 3 HIS P 3 HIS W 3 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.109426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.083603 restraints weight = 149131.363| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 6.20 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 moved from start: 0.5429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 38125 Z= 0.223 Angle : 0.575 13.201 51546 Z= 0.309 Chirality : 0.038 0.151 6060 Planarity : 0.004 0.046 6688 Dihedral : 3.561 22.161 5248 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.52 % Allowed : 12.04 % Favored : 85.44 % 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 aren not related in a simple way. whole: 3.17 (0.11), residues: 4853 helix: 2.43 (0.09), residues: 3084 sheet: 2.71 (0.22), residues: 396 loop : 1.27 (0.17), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 134 TYR 0.021 0.002 TYR B 64 PHE 0.029 0.002 PHE L 103 TRP 0.019 0.001 TRP L 86 HIS 0.007 0.001 HIS C 46 Details of bonding type rmsd covalent geometry : bond 0.00435 (38125) covalent geometry : angle 0.57456 (51546) hydrogen bonds : bond 0.04138 ( 2475) hydrogen bonds : angle 4.31183 ( 7269) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9706 Ramachandran restraints generated. 4853 Oldfield, 0 Emsley, 4853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9706 Ramachandran restraints generated. 4853 Oldfield, 0 Emsley, 4853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 280 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.9621 (mtp) cc_final: 0.9186 (mpp) REVERT: A 67 MET cc_start: 0.9327 (ptt) cc_final: 0.9127 (ptp) REVERT: A 69 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8398 (tp30) REVERT: A 99 ASN cc_start: 0.8787 (p0) cc_final: 0.8322 (p0) REVERT: A 151 ASP cc_start: 0.9583 (OUTLIER) cc_final: 0.9132 (t70) REVERT: A 193 HIS cc_start: 0.9278 (p90) cc_final: 0.8907 (p90) REVERT: B 36 GLU cc_start: 0.9499 (mm-30) cc_final: 0.9258 (mm-30) REVERT: B 151 ASP cc_start: 0.9625 (OUTLIER) cc_final: 0.9252 (t70) REVERT: C 36 GLU cc_start: 0.9750 (tt0) cc_final: 0.9434 (tt0) REVERT: C 67 MET cc_start: 0.9442 (mtp) cc_final: 0.8626 (tpp) REVERT: C 97 MET cc_start: 0.9330 (mpp) cc_final: 0.8837 (mpp) REVERT: C 158 ARG cc_start: 0.8512 (mmp80) cc_final: 0.8311 (mmp80) REVERT: D 43 GLU cc_start: 0.9359 (tm-30) cc_final: 0.8987 (tm-30) REVERT: D 67 MET cc_start: 0.9525 (mtp) cc_final: 0.9205 (mmm) REVERT: D 82 GLU cc_start: 0.9618 (mt-10) cc_final: 0.9305 (mp0) REVERT: D 103 PHE cc_start: 0.8167 (t80) cc_final: 0.7911 (t80) REVERT: D 177 ASP cc_start: 0.9414 (p0) cc_final: 0.9141 (m-30) REVERT: H 35 PHE cc_start: 0.8426 (m-10) cc_final: 0.7922 (m-10) REVERT: H 72 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7933 (mmp80) REVERT: I 69 GLU cc_start: 0.9209 (OUTLIER) cc_final: 0.8723 (tp30) REVERT: I 99 ASN cc_start: 0.8875 (p0) cc_final: 0.8453 (p0) REVERT: I 146 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9321 (tt) REVERT: J 82 GLU cc_start: 0.9677 (mt-10) cc_final: 0.9339 (mp0) REVERT: J 95 MET cc_start: 0.9597 (ttm) cc_final: 0.9008 (tmm) REVERT: J 105 LEU cc_start: 0.9549 (OUTLIER) cc_final: 0.9047 (tt) REVERT: J 184 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7802 (ptm) REVERT: K 43 GLU cc_start: 0.9349 (tm-30) cc_final: 0.8954 (tm-30) REVERT: K 69 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8128 (tp30) REVERT: K 97 MET cc_start: 0.9302 (mpp) cc_final: 0.8941 (mpp) REVERT: L 67 MET cc_start: 0.9496 (mtp) cc_final: 0.8806 (tpp) REVERT: L 99 ASN cc_start: 0.8858 (p0) cc_final: 0.8424 (p0) REVERT: M 72 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8489 (mmp80) REVERT: N 68 ILE cc_start: 0.9302 (tt) cc_final: 0.8968 (mm) REVERT: Q 69 GLU cc_start: 0.9108 (OUTLIER) cc_final: 0.8774 (tm-30) REVERT: Q 99 ASN cc_start: 0.8962 (p0) cc_final: 0.8704 (p0) REVERT: R 67 MET cc_start: 0.9377 (mtp) cc_final: 0.8760 (tpp) REVERT: R 82 GLU cc_start: 0.9618 (mt-10) cc_final: 0.9333 (mp0) REVERT: R 95 MET cc_start: 0.9582 (ttm) cc_final: 0.9199 (tmm) REVERT: R 97 MET cc_start: 0.9305 (mpp) cc_final: 0.9092 (mpp) REVERT: R 184 MET cc_start: 0.8265 (ppp) cc_final: 0.7896 (ptm) REVERT: S 67 MET cc_start: 0.9364 (ptt) cc_final: 0.9066 (ppp) REVERT: S 97 MET cc_start: 0.9381 (mpp) cc_final: 0.9146 (mpp) REVERT: S 177 ASP cc_start: 0.9396 (p0) cc_final: 0.9010 (m-30) REVERT: T 67 MET cc_start: 0.9498 (mtp) cc_final: 0.8582 (tpp) REVERT: T 82 GLU cc_start: 0.9658 (mt-10) cc_final: 0.9436 (mp0) REVERT: T 95 MET cc_start: 0.9542 (tpp) cc_final: 0.9042 (tmm) REVERT: T 99 ASN cc_start: 0.8954 (p0) cc_final: 0.8510 (p0) outliers start: 98 outliers final: 66 residues processed: 348 average time/residue: 0.2038 time to fit residues: 117.6651 Evaluate side-chains 341 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 264 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 31 ASN Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 202 HIS Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 52 MET Chi-restraints excluded: chain I residue 69 GLU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 86 TRP Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 146 LEU Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain J residue 138 ILE Chi-restraints excluded: chain J residue 184 MET Chi-restraints excluded: chain K residue 31 ASN Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain K residue 69 GLU Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 86 TRP Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 101 LYS Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 120 THR Chi-restraints excluded: chain L residue 121 ILE Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 72 ARG Chi-restraints excluded: chain N residue 24 GLN Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain O residue 24 GLN Chi-restraints excluded: chain Q residue 69 GLU Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain R residue 31 ASN Chi-restraints excluded: chain R residue 86 TRP Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 133 THR Chi-restraints excluded: chain R residue 151 ASP Chi-restraints excluded: chain S residue 31 ASN Chi-restraints excluded: chain S residue 86 TRP Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain S residue 117 VAL Chi-restraints excluded: chain T residue 52 MET Chi-restraints excluded: chain T residue 105 LEU Chi-restraints excluded: chain T residue 117 VAL Chi-restraints excluded: chain U residue 24 GLN Chi-restraints excluded: chain V residue 109 MET Chi-restraints excluded: chain W residue 24 GLN Chi-restraints excluded: chain W residue 68 ILE Chi-restraints excluded: chain X residue 68 ILE Chi-restraints excluded: chain X residue 85 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 343 optimal weight: 50.0000 chunk 267 optimal weight: 0.0770 chunk 259 optimal weight: 0.9990 chunk 395 optimal weight: 9.9990 chunk 109 optimal weight: 50.0000 chunk 378 optimal weight: 0.0570 chunk 106 optimal weight: 30.0000 chunk 117 optimal weight: 30.0000 chunk 122 optimal weight: 20.0000 chunk 354 optimal weight: 8.9990 chunk 202 optimal weight: 2.9990 overall best weight: 2.6262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 219 HIS J 202 HIS R 202 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.109013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.086208 restraints weight = 143057.798| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 6.54 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6558 moved from start: 0.5525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 38125 Z= 0.114 Angle : 0.499 12.984 51546 Z= 0.258 Chirality : 0.038 0.190 6060 Planarity : 0.003 0.047 6688 Dihedral : 3.402 22.885 5248 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.90 % Allowed : 13.25 % Favored : 84.85 % 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 aren not related in a simple way. whole: 3.63 (0.12), residues: 4853 helix: 2.83 (0.09), residues: 3081 sheet: 2.76 (0.22), residues: 396 loop : 1.40 (0.17), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 134 TYR 0.021 0.001 TYR B 64 PHE 0.023 0.001 PHE L 103 TRP 0.017 0.001 TRP L 86 HIS 0.004 0.001 HIS J 219 Details of bonding type rmsd covalent geometry : bond 0.00238 (38125) covalent geometry : angle 0.49903 (51546) hydrogen bonds : bond 0.03679 ( 2475) hydrogen bonds : angle 3.87939 ( 7269) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9706 Ramachandran restraints generated. 4853 Oldfield, 0 Emsley, 4853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9706 Ramachandran restraints generated. 4853 Oldfield, 0 Emsley, 4853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 278 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8400 (tp30) REVERT: A 97 MET cc_start: 0.9395 (mmm) cc_final: 0.9112 (tpp) REVERT: A 99 ASN cc_start: 0.8787 (p0) cc_final: 0.8338 (p0) REVERT: A 193 HIS cc_start: 0.9346 (p90) cc_final: 0.8985 (p90) REVERT: B 36 GLU cc_start: 0.9500 (mm-30) cc_final: 0.9153 (mm-30) REVERT: B 52 MET cc_start: 0.9548 (mtp) cc_final: 0.9087 (mpp) REVERT: C 36 GLU cc_start: 0.9737 (tt0) cc_final: 0.9369 (tt0) REVERT: C 67 MET cc_start: 0.9407 (mtp) cc_final: 0.8621 (tpp) REVERT: C 97 MET cc_start: 0.9346 (mpp) cc_final: 0.8880 (mpp) REVERT: D 43 GLU cc_start: 0.9301 (tm-30) cc_final: 0.9000 (tm-30) REVERT: D 67 MET cc_start: 0.9548 (mtp) cc_final: 0.9201 (mmm) REVERT: D 82 GLU cc_start: 0.9592 (mt-10) cc_final: 0.9331 (mp0) REVERT: D 134 ARG cc_start: 0.8674 (ptp-170) cc_final: 0.8379 (ptp90) REVERT: D 177 ASP cc_start: 0.9442 (p0) cc_final: 0.9180 (m-30) REVERT: G 109 MET cc_start: 0.8714 (ptm) cc_final: 0.8421 (ptm) REVERT: I 69 GLU cc_start: 0.9229 (OUTLIER) cc_final: 0.8781 (tp30) REVERT: J 67 MET cc_start: 0.9357 (ptt) cc_final: 0.9018 (ptp) REVERT: J 82 GLU cc_start: 0.9665 (mt-10) cc_final: 0.9331 (mp0) REVERT: J 93 ARG cc_start: 0.9425 (OUTLIER) cc_final: 0.9162 (ttt-90) REVERT: J 184 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7746 (ptm) REVERT: K 43 GLU cc_start: 0.9311 (tm-30) cc_final: 0.8955 (tm-30) REVERT: K 67 MET cc_start: 0.9271 (ptt) cc_final: 0.8953 (ptp) REVERT: K 69 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8416 (tp30) REVERT: K 97 MET cc_start: 0.9383 (mpp) cc_final: 0.9038 (mpp) REVERT: L 67 MET cc_start: 0.9407 (mtp) cc_final: 0.8816 (tpp) REVERT: L 99 ASN cc_start: 0.8906 (p0) cc_final: 0.8442 (p0) REVERT: L 177 ASP cc_start: 0.9490 (p0) cc_final: 0.9121 (m-30) REVERT: N 68 ILE cc_start: 0.9231 (tt) cc_final: 0.8917 (mm) REVERT: Q 67 MET cc_start: 0.9268 (ptt) cc_final: 0.8229 (ttp) REVERT: Q 69 GLU cc_start: 0.9138 (OUTLIER) cc_final: 0.8804 (tm-30) REVERT: Q 99 ASN cc_start: 0.9034 (p0) cc_final: 0.8797 (p0) REVERT: Q 177 ASP cc_start: 0.9556 (p0) cc_final: 0.9195 (t0) REVERT: R 36 GLU cc_start: 0.9446 (mm-30) cc_final: 0.9233 (mm-30) REVERT: R 67 MET cc_start: 0.9312 (mtp) cc_final: 0.8696 (tpp) REVERT: R 82 GLU cc_start: 0.9610 (mt-10) cc_final: 0.9317 (mp0) REVERT: R 95 MET cc_start: 0.9547 (ttm) cc_final: 0.9163 (tmm) REVERT: R 97 MET cc_start: 0.9342 (mpp) cc_final: 0.8899 (mpp) REVERT: R 118 CYS cc_start: 0.9824 (m) cc_final: 0.9612 (m) REVERT: R 184 MET cc_start: 0.8271 (ppp) cc_final: 0.7861 (ptm) REVERT: S 67 MET cc_start: 0.9305 (ptt) cc_final: 0.9024 (ppp) REVERT: S 97 MET cc_start: 0.9425 (mpp) cc_final: 0.9208 (mpp) REVERT: S 177 ASP cc_start: 0.9418 (p0) cc_final: 0.9013 (m-30) REVERT: T 36 GLU cc_start: 0.9307 (tm-30) cc_final: 0.9008 (tm-30) REVERT: T 67 MET cc_start: 0.9500 (mtp) cc_final: 0.8626 (tpp) REVERT: T 82 GLU cc_start: 0.9647 (mt-10) cc_final: 0.9374 (mp0) REVERT: T 99 ASN cc_start: 0.8950 (p0) cc_final: 0.8468 (p0) REVERT: T 130 LEU cc_start: 0.9796 (tt) cc_final: 0.9469 (mt) REVERT: T 134 ARG cc_start: 0.9378 (ttm110) cc_final: 0.9042 (ptp-170) outliers start: 74 outliers final: 55 residues processed: 329 average time/residue: 0.2096 time to fit residues: 114.8153 Evaluate side-chains 326 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 265 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 86 TRP Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 93 ARG Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 202 HIS Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain I residue 52 MET Chi-restraints excluded: chain I residue 69 GLU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain J residue 52 MET Chi-restraints excluded: chain J residue 93 ARG Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 138 ILE Chi-restraints excluded: chain J residue 184 MET Chi-restraints excluded: chain K residue 31 ASN Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain K residue 69 GLU Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 86 TRP Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 97 MET Chi-restraints excluded: chain L residue 101 LYS Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain N residue 24 GLN Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain O residue 24 GLN Chi-restraints excluded: chain Q residue 69 GLU Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain R residue 31 ASN Chi-restraints excluded: chain R residue 86 TRP Chi-restraints excluded: chain S residue 86 TRP Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain S residue 117 VAL Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain T residue 105 LEU Chi-restraints excluded: chain T residue 117 VAL Chi-restraints excluded: chain U residue 24 GLN Chi-restraints excluded: chain V residue 109 MET Chi-restraints excluded: chain W residue 24 GLN Chi-restraints excluded: chain X residue 68 ILE Chi-restraints excluded: chain X residue 85 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 257 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 303 optimal weight: 7.9990 chunk 320 optimal weight: 7.9990 chunk 236 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 chunk 430 optimal weight: 30.0000 chunk 237 optimal weight: 9.9990 chunk 170 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN J 202 HIS K 202 HIS L 219 HIS R 202 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.108854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.082421 restraints weight = 154166.360| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 6.21 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 moved from start: 0.5709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 38125 Z= 0.178 Angle : 0.543 12.390 51546 Z= 0.286 Chirality : 0.038 0.173 6060 Planarity : 0.004 0.047 6688 Dihedral : 3.444 19.569 5248 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.03 % Allowed : 13.28 % Favored : 84.69 % 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 aren not related in a simple way. whole: 3.38 (0.12), residues: 4853 helix: 2.64 (0.09), residues: 3081 sheet: 2.61 (0.22), residues: 396 loop : 1.31 (0.18), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG T 134 TYR 0.042 0.002 TYR B 64 PHE 0.032 0.002 PHE D 103 TRP 0.016 0.001 TRP L 86 HIS 0.005 0.001 HIS C 46 Details of bonding type rmsd covalent geometry : bond 0.00355 (38125) covalent geometry : angle 0.54263 (51546) hydrogen bonds : bond 0.03854 ( 2475) hydrogen bonds : angle 4.13938 ( 7269) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9706 Ramachandran restraints generated. 4853 Oldfield, 0 Emsley, 4853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9706 Ramachandran restraints generated. 4853 Oldfield, 0 Emsley, 4853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 269 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.9639 (mtm) cc_final: 0.9419 (mtm) REVERT: A 69 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8429 (tp30) REVERT: A 99 ASN cc_start: 0.8817 (p0) cc_final: 0.8360 (p0) REVERT: B 36 GLU cc_start: 0.9461 (mm-30) cc_final: 0.9166 (mm-30) REVERT: B 52 MET cc_start: 0.9484 (OUTLIER) cc_final: 0.9173 (mtm) REVERT: C 36 GLU cc_start: 0.9753 (tt0) cc_final: 0.9383 (tt0) REVERT: C 67 MET cc_start: 0.9456 (mtp) cc_final: 0.8670 (tpp) REVERT: C 97 MET cc_start: 0.9357 (mpp) cc_final: 0.8871 (mpp) REVERT: D 43 GLU cc_start: 0.9376 (tm-30) cc_final: 0.9036 (tm-30) REVERT: D 67 MET cc_start: 0.9561 (mtp) cc_final: 0.9248 (mmm) REVERT: D 82 GLU cc_start: 0.9596 (mt-10) cc_final: 0.9298 (mp0) REVERT: D 177 ASP cc_start: 0.9421 (p0) cc_final: 0.9172 (m-30) REVERT: G 109 MET cc_start: 0.8638 (ptm) cc_final: 0.8395 (ptm) REVERT: I 69 GLU cc_start: 0.9252 (OUTLIER) cc_final: 0.8751 (tp30) REVERT: J 67 MET cc_start: 0.9399 (ptt) cc_final: 0.9126 (ptm) REVERT: J 82 GLU cc_start: 0.9683 (mt-10) cc_final: 0.9339 (mp0) REVERT: J 93 ARG cc_start: 0.9439 (OUTLIER) cc_final: 0.9151 (ttt-90) REVERT: J 105 LEU cc_start: 0.9532 (OUTLIER) cc_final: 0.9045 (tt) REVERT: J 184 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7818 (ptm) REVERT: K 43 GLU cc_start: 0.9362 (tm-30) cc_final: 0.8997 (tm-30) REVERT: K 67 MET cc_start: 0.9319 (ptt) cc_final: 0.8998 (ptp) REVERT: K 69 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8428 (tp30) REVERT: K 97 MET cc_start: 0.9319 (mpp) cc_final: 0.8977 (mpp) REVERT: L 67 MET cc_start: 0.9427 (mtp) cc_final: 0.8737 (tpp) REVERT: L 99 ASN cc_start: 0.8899 (p0) cc_final: 0.8461 (p0) REVERT: L 134 ARG cc_start: 0.9328 (ttm110) cc_final: 0.9078 (ttm110) REVERT: L 177 ASP cc_start: 0.9493 (p0) cc_final: 0.9116 (m-30) REVERT: M 69 LEU cc_start: 0.9255 (mt) cc_final: 0.9044 (mm) REVERT: N 68 ILE cc_start: 0.9245 (tt) cc_final: 0.8950 (mm) REVERT: O 109 MET cc_start: 0.8209 (mmm) cc_final: 0.7958 (mmm) REVERT: Q 67 MET cc_start: 0.9282 (ptt) cc_final: 0.8274 (ttp) REVERT: Q 69 GLU cc_start: 0.9168 (OUTLIER) cc_final: 0.8820 (tm-30) REVERT: Q 99 ASN cc_start: 0.8994 (p0) cc_final: 0.8769 (p0) REVERT: Q 177 ASP cc_start: 0.9538 (p0) cc_final: 0.9189 (t0) REVERT: R 52 MET cc_start: 0.9559 (ptp) cc_final: 0.8888 (pmm) REVERT: R 67 MET cc_start: 0.9329 (mtp) cc_final: 0.8698 (tpp) REVERT: R 82 GLU cc_start: 0.9626 (mt-10) cc_final: 0.9322 (mp0) REVERT: R 95 MET cc_start: 0.9571 (ttm) cc_final: 0.9183 (tmm) REVERT: R 97 MET cc_start: 0.9310 (mpp) cc_final: 0.9097 (mpp) REVERT: R 184 MET cc_start: 0.8341 (ppp) cc_final: 0.7944 (ptm) REVERT: S 67 MET cc_start: 0.9305 (ptt) cc_final: 0.8948 (ptp) REVERT: S 97 MET cc_start: 0.9362 (mpp) cc_final: 0.9144 (mpp) REVERT: S 177 ASP cc_start: 0.9390 (p0) cc_final: 0.9010 (m-30) REVERT: T 36 GLU cc_start: 0.9360 (tm-30) cc_final: 0.9088 (tm-30) REVERT: T 67 MET cc_start: 0.9537 (mtp) cc_final: 0.8623 (tpp) REVERT: T 82 GLU cc_start: 0.9648 (mt-10) cc_final: 0.9432 (mp0) REVERT: T 99 ASN cc_start: 0.8944 (p0) cc_final: 0.8474 (p0) REVERT: T 134 ARG cc_start: 0.9376 (ttm110) cc_final: 0.8858 (ptp-170) REVERT: X 116 LYS cc_start: 0.9410 (ttpt) cc_final: 0.9148 (tptp) outliers start: 79 outliers final: 56 residues processed: 326 average time/residue: 0.2010 time to fit residues: 108.3568 Evaluate side-chains 328 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 264 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 86 TRP Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 93 ARG Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 202 HIS Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain I residue 52 MET Chi-restraints excluded: chain I residue 69 GLU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain J residue 31 ASN Chi-restraints excluded: chain J residue 93 ARG Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 138 ILE Chi-restraints excluded: chain J residue 184 MET Chi-restraints excluded: chain K residue 31 ASN Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain K residue 69 GLU Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 86 TRP Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 101 LYS Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain N residue 24 GLN Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain O residue 24 GLN Chi-restraints excluded: chain Q residue 69 GLU Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 86 TRP Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain R residue 31 ASN Chi-restraints excluded: chain R residue 86 TRP Chi-restraints excluded: chain S residue 31 ASN Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain S residue 117 VAL Chi-restraints excluded: chain T residue 31 ASN Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain T residue 117 VAL Chi-restraints excluded: chain U residue 24 GLN Chi-restraints excluded: chain V residue 109 MET Chi-restraints excluded: chain W residue 24 GLN Chi-restraints excluded: chain X residue 68 ILE Chi-restraints excluded: chain X residue 85 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 130 optimal weight: 4.9990 chunk 438 optimal weight: 6.9990 chunk 165 optimal weight: 20.0000 chunk 394 optimal weight: 20.0000 chunk 50 optimal weight: 40.0000 chunk 453 optimal weight: 8.9990 chunk 213 optimal weight: 50.0000 chunk 309 optimal weight: 7.9990 chunk 476 optimal weight: 6.9990 chunk 23 optimal weight: 40.0000 chunk 21 optimal weight: 30.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 202 HIS F 3 HIS K 202 HIS R 202 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.122151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.090143 restraints weight = 148625.772| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 6.54 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.5938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 38125 Z= 0.228 Angle : 0.596 12.146 51546 Z= 0.317 Chirality : 0.038 0.153 6060 Planarity : 0.004 0.071 6688 Dihedral : 3.617 29.252 5248 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.98 % Allowed : 13.43 % Favored : 84.59 % 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 aren not related in a simple way. whole: 2.96 (0.12), residues: 4853 helix: 2.32 (0.09), residues: 3081 sheet: 2.27 (0.22), residues: 396 loop : 1.18 (0.17), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 134 TYR 0.031 0.002 TYR B 64 PHE 0.032 0.002 PHE L 103 TRP 0.017 0.001 TRP Q 86 HIS 0.007 0.001 HIS C 46 Details of bonding type rmsd covalent geometry : bond 0.00448 (38125) covalent geometry : angle 0.59602 (51546) hydrogen bonds : bond 0.04114 ( 2475) hydrogen bonds : angle 4.40454 ( 7269) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9706 Ramachandran restraints generated. 4853 Oldfield, 0 Emsley, 4853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9706 Ramachandran restraints generated. 4853 Oldfield, 0 Emsley, 4853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 267 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8397 (tp30) REVERT: A 99 ASN cc_start: 0.8983 (p0) cc_final: 0.8579 (p0) REVERT: B 36 GLU cc_start: 0.9397 (mm-30) cc_final: 0.9115 (mm-30) REVERT: C 36 GLU cc_start: 0.9724 (tt0) cc_final: 0.9335 (tt0) REVERT: C 67 MET cc_start: 0.9514 (mtp) cc_final: 0.8711 (tpp) REVERT: C 95 MET cc_start: 0.9584 (ttm) cc_final: 0.9078 (tmm) REVERT: C 97 MET cc_start: 0.9307 (mpp) cc_final: 0.8869 (mpp) REVERT: C 184 MET cc_start: 0.6679 (ttp) cc_final: 0.6373 (ptm) REVERT: D 43 GLU cc_start: 0.9302 (tm-30) cc_final: 0.8858 (tm-30) REVERT: D 67 MET cc_start: 0.9545 (mtp) cc_final: 0.9214 (mmm) REVERT: D 82 GLU cc_start: 0.9631 (mt-10) cc_final: 0.9320 (mp0) REVERT: D 177 ASP cc_start: 0.9404 (p0) cc_final: 0.9107 (m-30) REVERT: H 72 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7948 (mmp80) REVERT: I 69 GLU cc_start: 0.9156 (OUTLIER) cc_final: 0.8701 (tp30) REVERT: I 134 ARG cc_start: 0.8605 (ptp90) cc_final: 0.8330 (ptp90) REVERT: J 67 MET cc_start: 0.9451 (ptt) cc_final: 0.9171 (ptp) REVERT: J 82 GLU cc_start: 0.9708 (mt-10) cc_final: 0.9355 (mp0) REVERT: J 105 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9015 (tt) REVERT: J 184 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.7773 (ptm) REVERT: K 43 GLU cc_start: 0.9336 (tm-30) cc_final: 0.8944 (tm-30) REVERT: K 67 MET cc_start: 0.9369 (ptt) cc_final: 0.9043 (ptp) REVERT: K 69 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8099 (tp30) REVERT: K 97 MET cc_start: 0.9288 (mpp) cc_final: 0.8941 (mpp) REVERT: L 67 MET cc_start: 0.9475 (mtp) cc_final: 0.8754 (tpp) REVERT: L 99 ASN cc_start: 0.8983 (p0) cc_final: 0.8633 (p0) REVERT: L 134 ARG cc_start: 0.9321 (ttm110) cc_final: 0.9063 (ttm110) REVERT: L 177 ASP cc_start: 0.9497 (p0) cc_final: 0.9106 (m-30) REVERT: N 68 ILE cc_start: 0.9142 (tt) cc_final: 0.8895 (mm) REVERT: Q 67 MET cc_start: 0.9419 (ptt) cc_final: 0.9114 (ppp) REVERT: Q 69 GLU cc_start: 0.9092 (OUTLIER) cc_final: 0.8845 (tm-30) REVERT: Q 99 ASN cc_start: 0.9018 (p0) cc_final: 0.8789 (p0) REVERT: Q 177 ASP cc_start: 0.9534 (p0) cc_final: 0.9172 (t0) REVERT: R 52 MET cc_start: 0.9573 (ptp) cc_final: 0.8912 (pmm) REVERT: R 67 MET cc_start: 0.9367 (mtp) cc_final: 0.8739 (tpp) REVERT: R 82 GLU cc_start: 0.9642 (mt-10) cc_final: 0.9327 (mp0) REVERT: R 95 MET cc_start: 0.9591 (ttm) cc_final: 0.9226 (tmm) REVERT: R 184 MET cc_start: 0.8377 (ppp) cc_final: 0.8001 (ptm) REVERT: S 67 MET cc_start: 0.9365 (ptt) cc_final: 0.9001 (ptp) REVERT: S 97 MET cc_start: 0.9279 (mpp) cc_final: 0.9048 (mpp) REVERT: S 177 ASP cc_start: 0.9387 (p0) cc_final: 0.8985 (m-30) REVERT: T 67 MET cc_start: 0.9569 (mtp) cc_final: 0.8654 (tpp) REVERT: T 82 GLU cc_start: 0.9687 (mt-10) cc_final: 0.9477 (mp0) REVERT: T 99 ASN cc_start: 0.9101 (p0) cc_final: 0.8752 (p0) REVERT: T 134 ARG cc_start: 0.9385 (ttm110) cc_final: 0.8859 (ptp-110) REVERT: X 116 LYS cc_start: 0.9285 (ttpt) cc_final: 0.9044 (tptp) outliers start: 77 outliers final: 62 residues processed: 317 average time/residue: 0.1957 time to fit residues: 102.0747 Evaluate side-chains 325 residues out of total 3894 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 256 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 69 GLU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 202 HIS Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 31 ASN Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 93 ARG Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 202 HIS Chi-restraints excluded: chain C residue 86 TRP Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 117 VAL Chi-restraints excluded: chain D residue 121 ILE Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain H residue 72 ARG Chi-restraints excluded: chain I residue 31 ASN Chi-restraints excluded: chain I residue 52 MET Chi-restraints excluded: chain I residue 69 GLU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain J residue 31 ASN Chi-restraints excluded: chain J residue 97 MET Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 138 ILE Chi-restraints excluded: chain J residue 184 MET Chi-restraints excluded: chain K residue 31 ASN Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain K residue 69 GLU Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 101 LYS Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 120 THR Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain N residue 24 GLN Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain O residue 24 GLN Chi-restraints excluded: chain Q residue 69 GLU Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 86 TRP Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain R residue 31 ASN Chi-restraints excluded: chain R residue 86 TRP Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 133 THR Chi-restraints excluded: chain S residue 31 ASN Chi-restraints excluded: chain S residue 98 VAL Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain S residue 117 VAL Chi-restraints excluded: chain S residue 158 ARG Chi-restraints excluded: chain T residue 31 ASN Chi-restraints excluded: chain T residue 98 VAL Chi-restraints excluded: chain T residue 117 VAL Chi-restraints excluded: chain U residue 24 GLN Chi-restraints excluded: chain V residue 109 MET Chi-restraints excluded: chain W residue 24 GLN Chi-restraints excluded: chain X residue 68 ILE Chi-restraints excluded: chain X residue 85 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 288 optimal weight: 1.9990 chunk 455 optimal weight: 9.9990 chunk 294 optimal weight: 7.9990 chunk 458 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 243 optimal weight: 40.0000 chunk 393 optimal weight: 20.0000 chunk 214 optimal weight: 3.9990 chunk 409 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 79 optimal weight: 50.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 202 HIS R 202 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.109310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.083120 restraints weight = 152550.061| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 6.21 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.5992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 38125 Z= 0.142 Angle : 0.532 13.129 51546 Z= 0.275 Chirality : 0.038 0.180 6060 Planarity : 0.003 0.046 6688 Dihedral : 3.462 19.453 5248 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.64 % Allowed : 14.05 % Favored : 84.31 % 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 aren not related in a simple way. whole: 3.30 (0.12), residues: 4853 helix: 2.61 (0.09), residues: 3090 sheet: 2.34 (0.22), residues: 396 loop : 1.25 (0.18), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 134 TYR 0.038 0.002 TYR B 64 PHE 0.034 0.001 PHE L 103 TRP 0.017 0.001 TRP L 86 HIS 0.004 0.001 HIS Q 209 Details of bonding type rmsd covalent geometry : bond 0.00291 (38125) covalent geometry : angle 0.53227 (51546) hydrogen bonds : bond 0.03772 ( 2475) hydrogen bonds : angle 4.07101 ( 7269) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8792.37 seconds wall clock time: 151 minutes 28.47 seconds (9088.47 seconds total)