Starting phenix.real_space_refine on Sat Feb 7 00:35:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xlj_38450/02_2026/8xlj_38450_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xlj_38450/02_2026/8xlj_38450.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xlj_38450/02_2026/8xlj_38450.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xlj_38450/02_2026/8xlj_38450.map" model { file = "/net/cci-nas-00/data/ceres_data/8xlj_38450/02_2026/8xlj_38450_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xlj_38450/02_2026/8xlj_38450_neut.cif" } resolution = 3.9 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= 0.023 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 260 5.16 5 C 18557 2.51 5 N 5273 2.21 5 O 5466 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 153 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29556 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2958 Classifications: {'peptide': 372} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 348} Chain: "B" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2958 Classifications: {'peptide': 372} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 348} Chain: "C" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2958 Classifications: {'peptide': 372} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 348} Chain: "D" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2958 Classifications: {'peptide': 372} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 348} Chain: "E" Number of atoms: 2942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2942 Classifications: {'peptide': 372} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 348} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "F" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2958 Classifications: {'peptide': 372} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 348} Chain: "G" Number of atoms: 2954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2954 Classifications: {'peptide': 372} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 348} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2958 Classifications: {'peptide': 372} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 348} Chain: "I" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2958 Classifications: {'peptide': 372} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 348} Chain: "J" Number of atoms: 2954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2954 Classifications: {'peptide': 372} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 348} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 6.54, per 1000 atoms: 0.22 Number of scatterers: 29556 At special positions: 0 Unit cell: (149.94, 153.153, 140.301, 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 260 16.00 O 5466 8.00 N 5273 7.00 C 18557 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: 2.54 Conformation dependent library (CDL) restraints added in 1.1 seconds 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6760 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 20 sheets defined 36.7% alpha, 32.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 5 through 9 Processing helix chain 'A' and resid 10 through 19 removed outlier: 3.750A pdb=" N LYS A 14 " --> pdb=" O ASN A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 57 Processing helix chain 'A' and resid 65 through 67 No H-bonds generated for 'chain 'A' and resid 65 through 67' Processing helix chain 'A' and resid 113 through 124 Processing helix chain 'A' and resid 125 through 128 Processing helix chain 'A' and resid 172 through 187 removed outlier: 3.667A pdb=" N VAL A 176 " --> pdb=" O GLY A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 233 Processing helix chain 'A' and resid 258 through 263 Processing helix chain 'A' and resid 266 through 288 removed outlier: 6.373A pdb=" N GLN A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N TYR A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 300 removed outlier: 4.264A pdb=" N ARG A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 333 Processing helix chain 'A' and resid 347 through 360 Processing helix chain 'B' and resid 5 through 9 Processing helix chain 'B' and resid 10 through 19 removed outlier: 3.740A pdb=" N LYS B 14 " --> pdb=" O ASN B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 57 Processing helix chain 'B' and resid 65 through 67 No H-bonds generated for 'chain 'B' and resid 65 through 67' Processing helix chain 'B' and resid 113 through 124 Processing helix chain 'B' and resid 125 through 128 Processing helix chain 'B' and resid 172 through 187 removed outlier: 3.570A pdb=" N VAL B 176 " --> pdb=" O GLY B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 233 removed outlier: 4.342A pdb=" N GLY B 215 " --> pdb=" O GLY B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 263 Processing helix chain 'B' and resid 266 through 280 Processing helix chain 'B' and resid 280 through 288 Processing helix chain 'B' and resid 293 through 300 removed outlier: 3.983A pdb=" N ARG B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG B 299 " --> pdb=" O ASP B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 333 Processing helix chain 'B' and resid 347 through 360 Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 10 through 19 removed outlier: 3.732A pdb=" N LYS C 14 " --> pdb=" O ASN C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 57 Processing helix chain 'C' and resid 65 through 67 No H-bonds generated for 'chain 'C' and resid 65 through 67' Processing helix chain 'C' and resid 113 through 124 Processing helix chain 'C' and resid 125 through 128 Processing helix chain 'C' and resid 172 through 187 removed outlier: 3.568A pdb=" N VAL C 176 " --> pdb=" O GLY C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 233 removed outlier: 4.293A pdb=" N GLY C 215 " --> pdb=" O GLY C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 263 Processing helix chain 'C' and resid 266 through 280 Processing helix chain 'C' and resid 280 through 288 Processing helix chain 'C' and resid 293 through 300 removed outlier: 3.997A pdb=" N ARG C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG C 299 " --> pdb=" O ASP C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 333 Processing helix chain 'C' and resid 347 through 360 Processing helix chain 'D' and resid 4 through 9 Processing helix chain 'D' and resid 10 through 19 removed outlier: 3.727A pdb=" N LYS D 14 " --> pdb=" O ASN D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 57 Processing helix chain 'D' and resid 65 through 67 No H-bonds generated for 'chain 'D' and resid 65 through 67' Processing helix chain 'D' and resid 113 through 124 Processing helix chain 'D' and resid 125 through 128 Processing helix chain 'D' and resid 172 through 187 removed outlier: 3.593A pdb=" N VAL D 176 " --> pdb=" O GLY D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 233 removed outlier: 4.219A pdb=" N GLY D 215 " --> pdb=" O GLY D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 263 Processing helix chain 'D' and resid 265 through 280 removed outlier: 4.069A pdb=" N CYS D 269 " --> pdb=" O ASN D 265 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS D 279 " --> pdb=" O ASP D 275 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ARG D 280 " --> pdb=" O LYS D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 288 Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 326 through 333 Processing helix chain 'D' and resid 347 through 362 Processing helix chain 'E' and resid 5 through 9 Processing helix chain 'E' and resid 10 through 19 removed outlier: 3.678A pdb=" N LYS E 14 " --> pdb=" O ASN E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 57 Processing helix chain 'E' and resid 65 through 68 removed outlier: 4.017A pdb=" N PHE E 68 " --> pdb=" O SER E 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 65 through 68' Processing helix chain 'E' and resid 113 through 124 Processing helix chain 'E' and resid 125 through 128 Processing helix chain 'E' and resid 172 through 187 removed outlier: 3.578A pdb=" N VAL E 176 " --> pdb=" O GLY E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 233 Processing helix chain 'E' and resid 258 through 263 Processing helix chain 'E' and resid 266 through 280 Processing helix chain 'E' and resid 280 through 288 Processing helix chain 'E' and resid 293 through 300 removed outlier: 3.703A pdb=" N ARG E 298 " --> pdb=" O LEU E 294 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ARG E 299 " --> pdb=" O ASP E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 333 Processing helix chain 'E' and resid 347 through 360 Processing helix chain 'F' and resid 5 through 9 Processing helix chain 'F' and resid 10 through 19 removed outlier: 3.773A pdb=" N LYS F 14 " --> pdb=" O ASN F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 57 Processing helix chain 'F' and resid 65 through 67 No H-bonds generated for 'chain 'F' and resid 65 through 67' Processing helix chain 'F' and resid 113 through 124 Processing helix chain 'F' and resid 125 through 128 Processing helix chain 'F' and resid 172 through 187 removed outlier: 3.559A pdb=" N VAL F 176 " --> pdb=" O GLY F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 233 Processing helix chain 'F' and resid 258 through 263 Processing helix chain 'F' and resid 266 through 280 Processing helix chain 'F' and resid 280 through 288 Processing helix chain 'F' and resid 293 through 298 removed outlier: 3.944A pdb=" N ARG F 298 " --> pdb=" O LEU F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 333 Processing helix chain 'F' and resid 347 through 360 Processing helix chain 'G' and resid 5 through 9 Processing helix chain 'G' and resid 10 through 19 removed outlier: 3.713A pdb=" N LYS G 14 " --> pdb=" O ASN G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 57 Processing helix chain 'G' and resid 113 through 124 Processing helix chain 'G' and resid 125 through 128 Processing helix chain 'G' and resid 172 through 187 removed outlier: 3.543A pdb=" N VAL G 176 " --> pdb=" O GLY G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 233 removed outlier: 4.127A pdb=" N GLY G 215 " --> pdb=" O GLY G 211 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 263 Processing helix chain 'G' and resid 266 through 280 Processing helix chain 'G' and resid 280 through 288 Processing helix chain 'G' and resid 295 through 300 removed outlier: 4.035A pdb=" N ARG G 299 " --> pdb=" O ASP G 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 333 Processing helix chain 'G' and resid 347 through 360 Processing helix chain 'H' and resid 5 through 9 Processing helix chain 'H' and resid 10 through 19 removed outlier: 3.793A pdb=" N LYS H 14 " --> pdb=" O ASN H 10 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 57 Processing helix chain 'H' and resid 65 through 67 No H-bonds generated for 'chain 'H' and resid 65 through 67' Processing helix chain 'H' and resid 113 through 124 Processing helix chain 'H' and resid 125 through 128 Processing helix chain 'H' and resid 172 through 187 Processing helix chain 'H' and resid 211 through 233 removed outlier: 4.218A pdb=" N GLY H 215 " --> pdb=" O GLY H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 258 through 263 Processing helix chain 'H' and resid 266 through 280 Processing helix chain 'H' and resid 281 through 287 Processing helix chain 'H' and resid 292 through 297 removed outlier: 4.597A pdb=" N ASN H 296 " --> pdb=" O GLY H 292 " (cutoff:3.500A) Processing helix chain 'H' and resid 326 through 331 Processing helix chain 'H' and resid 347 through 360 Processing helix chain 'I' and resid 5 through 9 Processing helix chain 'I' and resid 10 through 19 removed outlier: 3.718A pdb=" N LYS I 14 " --> pdb=" O ASN I 10 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 57 Processing helix chain 'I' and resid 65 through 67 No H-bonds generated for 'chain 'I' and resid 65 through 67' Processing helix chain 'I' and resid 113 through 124 Processing helix chain 'I' and resid 125 through 128 Processing helix chain 'I' and resid 172 through 187 removed outlier: 3.578A pdb=" N VAL I 176 " --> pdb=" O GLY I 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 212 through 233 Processing helix chain 'I' and resid 258 through 263 Processing helix chain 'I' and resid 266 through 280 Processing helix chain 'I' and resid 280 through 288 Processing helix chain 'I' and resid 293 through 300 removed outlier: 3.970A pdb=" N ARG I 298 " --> pdb=" O LEU I 294 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG I 299 " --> pdb=" O ASP I 295 " (cutoff:3.500A) Processing helix chain 'I' and resid 326 through 333 Processing helix chain 'I' and resid 347 through 360 Processing helix chain 'J' and resid 5 through 9 Processing helix chain 'J' and resid 10 through 19 removed outlier: 3.707A pdb=" N LYS J 14 " --> pdb=" O ASN J 10 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 57 Processing helix chain 'J' and resid 65 through 67 No H-bonds generated for 'chain 'J' and resid 65 through 67' Processing helix chain 'J' and resid 113 through 124 Processing helix chain 'J' and resid 125 through 128 Processing helix chain 'J' and resid 172 through 187 removed outlier: 3.632A pdb=" N VAL J 176 " --> pdb=" O GLY J 172 " (cutoff:3.500A) Processing helix chain 'J' and resid 212 through 233 Processing helix chain 'J' and resid 258 through 263 Processing helix chain 'J' and resid 266 through 280 Processing helix chain 'J' and resid 280 through 288 Processing helix chain 'J' and resid 293 through 300 removed outlier: 4.055A pdb=" N ARG J 298 " --> pdb=" O LEU J 294 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG J 299 " --> pdb=" O ASP J 295 " (cutoff:3.500A) Processing helix chain 'J' and resid 326 through 333 Processing helix chain 'J' and resid 347 through 360 Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 63 removed outlier: 6.702A pdb=" N PHE A 98 " --> pdb=" O VAL A 82 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N MET A 84 " --> pdb=" O LEU A 96 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU A 96 " --> pdb=" O MET A 84 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLN A 27 " --> pdb=" O LYS A 95 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N VAL A 97 " --> pdb=" O GLN A 27 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N MET A 29 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N CYS A 99 " --> pdb=" O MET A 29 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE A 31 " --> pdb=" O CYS A 99 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N VAL A 101 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N VAL A 33 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N CYS A 42 " --> pdb=" O ALA B 195 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ALA B 195 " --> pdb=" O CYS A 42 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N THR B 191 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLN B 205 " --> pdb=" O THR B 191 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR B 193 " --> pdb=" O GLU B 203 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLU B 203 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ALA B 195 " --> pdb=" O GLN B 201 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N GLN B 201 " --> pdb=" O ALA B 195 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N PHE B 131 " --> pdb=" O PRO B 208 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 63 removed outlier: 6.702A pdb=" N PHE A 98 " --> pdb=" O VAL A 82 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N MET A 84 " --> pdb=" O LEU A 96 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU A 96 " --> pdb=" O MET A 84 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLN A 27 " --> pdb=" O LYS A 95 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N VAL A 97 " --> pdb=" O GLN A 27 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N MET A 29 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N CYS A 99 " --> pdb=" O MET A 29 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE A 31 " --> pdb=" O CYS A 99 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N VAL A 101 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N VAL A 33 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N CYS A 42 " --> pdb=" O ALA B 195 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ALA B 195 " --> pdb=" O CYS A 42 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N THR B 191 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLN B 205 " --> pdb=" O THR B 191 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR B 193 " --> pdb=" O GLU B 203 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLU B 203 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ALA B 195 " --> pdb=" O GLN B 201 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N GLN B 201 " --> pdb=" O ALA B 195 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N PHE B 131 " --> pdb=" O PRO B 208 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS B 253 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLY B 315 " --> pdb=" O ILE B 325 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 235 through 237 removed outlier: 6.974A pdb=" N GLY A 315 " --> pdb=" O ILE A 325 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 235 through 237 removed outlier: 6.188A pdb=" N PHE A 131 " --> pdb=" O PRO A 208 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N GLN A 201 " --> pdb=" O ALA A 195 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ALA A 195 " --> pdb=" O GLN A 201 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLU A 203 " --> pdb=" O THR A 193 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N THR A 193 " --> pdb=" O GLU A 203 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLN A 205 " --> pdb=" O THR A 191 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N THR A 191 " --> pdb=" O THR E 46 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ALA A 195 " --> pdb=" O CYS E 42 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N CYS E 42 " --> pdb=" O ALA A 195 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN E 27 " --> pdb=" O LYS E 95 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N VAL E 97 " --> pdb=" O GLN E 27 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N MET E 29 " --> pdb=" O VAL E 97 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N CYS E 99 " --> pdb=" O MET E 29 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE E 31 " --> pdb=" O CYS E 99 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N VAL E 101 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N VAL E 33 " --> pdb=" O VAL E 101 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU E 96 " --> pdb=" O MET E 84 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N MET E 84 " --> pdb=" O LEU E 96 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N PHE E 98 " --> pdb=" O VAL E 82 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 60 through 63 removed outlier: 6.734A pdb=" N PHE B 98 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N MET B 84 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU B 96 " --> pdb=" O MET B 84 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLN B 27 " --> pdb=" O LYS B 95 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N VAL B 97 " --> pdb=" O GLN B 27 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N MET B 29 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N CYS B 99 " --> pdb=" O MET B 29 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE B 31 " --> pdb=" O CYS B 99 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N VAL B 101 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N VAL B 33 " --> pdb=" O VAL B 101 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N CYS B 42 " --> pdb=" O ALA C 195 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ALA C 195 " --> pdb=" O CYS B 42 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N THR C 191 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLN C 205 " --> pdb=" O THR C 191 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N THR C 193 " --> pdb=" O GLU C 203 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU C 203 " --> pdb=" O THR C 193 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ALA C 195 " --> pdb=" O GLN C 201 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N GLN C 201 " --> pdb=" O ALA C 195 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N PHE C 131 " --> pdb=" O PRO C 208 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 60 through 63 removed outlier: 6.734A pdb=" N PHE B 98 " --> pdb=" O VAL B 82 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N MET B 84 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU B 96 " --> pdb=" O MET B 84 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLN B 27 " --> pdb=" O LYS B 95 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N VAL B 97 " --> pdb=" O GLN B 27 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N MET B 29 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N CYS B 99 " --> pdb=" O MET B 29 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE B 31 " --> pdb=" O CYS B 99 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N VAL B 101 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N VAL B 33 " --> pdb=" O VAL B 101 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N CYS B 42 " --> pdb=" O ALA C 195 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ALA C 195 " --> pdb=" O CYS B 42 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N THR C 191 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLN C 205 " --> pdb=" O THR C 191 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N THR C 193 " --> pdb=" O GLU C 203 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU C 203 " --> pdb=" O THR C 193 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ALA C 195 " --> pdb=" O GLN C 201 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N GLN C 201 " --> pdb=" O ALA C 195 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N PHE C 131 " --> pdb=" O PRO C 208 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N HIS C 253 " --> pdb=" O GLU C 134 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLY C 315 " --> pdb=" O ILE C 325 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 60 through 63 removed outlier: 6.750A pdb=" N PHE C 98 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N MET C 84 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU C 96 " --> pdb=" O MET C 84 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N GLN C 27 " --> pdb=" O LYS C 95 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N VAL C 97 " --> pdb=" O GLN C 27 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N MET C 29 " --> pdb=" O VAL C 97 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N CYS C 99 " --> pdb=" O MET C 29 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE C 31 " --> pdb=" O CYS C 99 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N VAL C 101 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 8.755A pdb=" N VAL C 33 " --> pdb=" O VAL C 101 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N CYS C 42 " --> pdb=" O ALA D 195 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N ALA D 195 " --> pdb=" O CYS C 42 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N THR D 191 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLN D 205 " --> pdb=" O THR D 191 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N THR D 193 " --> pdb=" O GLU D 203 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLU D 203 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ALA D 195 " --> pdb=" O GLN D 201 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N GLN D 201 " --> pdb=" O ALA D 195 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N PHE D 131 " --> pdb=" O PRO D 208 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 60 through 63 removed outlier: 6.750A pdb=" N PHE C 98 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N MET C 84 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU C 96 " --> pdb=" O MET C 84 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N GLN C 27 " --> pdb=" O LYS C 95 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N VAL C 97 " --> pdb=" O GLN C 27 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N MET C 29 " --> pdb=" O VAL C 97 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N CYS C 99 " --> pdb=" O MET C 29 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE C 31 " --> pdb=" O CYS C 99 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N VAL C 101 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 8.755A pdb=" N VAL C 33 " --> pdb=" O VAL C 101 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N CYS C 42 " --> pdb=" O ALA D 195 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N ALA D 195 " --> pdb=" O CYS C 42 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N THR D 191 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLN D 205 " --> pdb=" O THR D 191 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N THR D 193 " --> pdb=" O GLU D 203 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLU D 203 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ALA D 195 " --> pdb=" O GLN D 201 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N GLN D 201 " --> pdb=" O ALA D 195 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N PHE D 131 " --> pdb=" O PRO D 208 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS D 253 " --> pdb=" O GLU D 134 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N GLY D 315 " --> pdb=" O ILE D 325 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 60 through 63 removed outlier: 6.782A pdb=" N PHE D 98 " --> pdb=" O VAL D 82 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N MET D 84 " --> pdb=" O LEU D 96 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU D 96 " --> pdb=" O MET D 84 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLN D 27 " --> pdb=" O LYS D 95 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL D 97 " --> pdb=" O GLN D 27 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N MET D 29 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N CYS D 99 " --> pdb=" O MET D 29 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE D 31 " --> pdb=" O CYS D 99 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N VAL D 101 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N VAL D 33 " --> pdb=" O VAL D 101 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N CYS D 42 " --> pdb=" O ALA E 195 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ALA E 195 " --> pdb=" O CYS D 42 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N THR E 191 " --> pdb=" O THR D 46 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLN E 205 " --> pdb=" O THR E 191 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N THR E 193 " --> pdb=" O GLU E 203 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLU E 203 " --> pdb=" O THR E 193 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ALA E 195 " --> pdb=" O GLN E 201 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N GLN E 201 " --> pdb=" O ALA E 195 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N GLN E 201 " --> pdb=" O LEU E 139 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU E 139 " --> pdb=" O GLN E 201 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N GLU E 203 " --> pdb=" O TYR E 137 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N TYR E 137 " --> pdb=" O GLU E 203 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N GLN E 205 " --> pdb=" O GLN E 135 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLN E 135 " --> pdb=" O GLN E 205 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N GLY E 207 " --> pdb=" O MET E 133 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N MET E 133 " --> pdb=" O GLY E 207 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 60 through 63 removed outlier: 6.782A pdb=" N PHE D 98 " --> pdb=" O VAL D 82 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N MET D 84 " --> pdb=" O LEU D 96 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU D 96 " --> pdb=" O MET D 84 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLN D 27 " --> pdb=" O LYS D 95 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL D 97 " --> pdb=" O GLN D 27 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N MET D 29 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N CYS D 99 " --> pdb=" O MET D 29 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE D 31 " --> pdb=" O CYS D 99 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N VAL D 101 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N VAL D 33 " --> pdb=" O VAL D 101 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N CYS D 42 " --> pdb=" O ALA E 195 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ALA E 195 " --> pdb=" O CYS D 42 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N THR E 191 " --> pdb=" O THR D 46 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLN E 205 " --> pdb=" O THR E 191 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N THR E 193 " --> pdb=" O GLU E 203 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLU E 203 " --> pdb=" O THR E 193 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ALA E 195 " --> pdb=" O GLN E 201 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N GLN E 201 " --> pdb=" O ALA E 195 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N GLN E 201 " --> pdb=" O LEU E 139 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU E 139 " --> pdb=" O GLN E 201 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N GLU E 203 " --> pdb=" O TYR E 137 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N TYR E 137 " --> pdb=" O GLU E 203 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N GLN E 205 " --> pdb=" O GLN E 135 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLN E 135 " --> pdb=" O GLN E 205 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N GLY E 207 " --> pdb=" O MET E 133 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N MET E 133 " --> pdb=" O GLY E 207 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLY E 315 " --> pdb=" O ILE E 325 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 60 through 63 removed outlier: 6.730A pdb=" N PHE F 98 " --> pdb=" O VAL F 82 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N MET F 84 " --> pdb=" O LEU F 96 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU F 96 " --> pdb=" O MET F 84 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLN F 27 " --> pdb=" O LYS F 95 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL F 97 " --> pdb=" O GLN F 27 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N MET F 29 " --> pdb=" O VAL F 97 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N CYS F 99 " --> pdb=" O MET F 29 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE F 31 " --> pdb=" O CYS F 99 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N VAL F 101 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 8.868A pdb=" N VAL F 33 " --> pdb=" O VAL F 101 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N CYS F 42 " --> pdb=" O ALA G 195 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ALA G 195 " --> pdb=" O CYS F 42 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N THR G 191 " --> pdb=" O THR F 46 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLN G 205 " --> pdb=" O THR G 191 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N THR G 193 " --> pdb=" O GLU G 203 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLU G 203 " --> pdb=" O THR G 193 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ALA G 195 " --> pdb=" O GLN G 201 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N GLN G 201 " --> pdb=" O ALA G 195 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLN G 201 " --> pdb=" O LEU G 139 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU G 139 " --> pdb=" O GLN G 201 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N GLU G 203 " --> pdb=" O TYR G 137 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N TYR G 137 " --> pdb=" O GLU G 203 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N GLN G 205 " --> pdb=" O GLN G 135 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLN G 135 " --> pdb=" O GLN G 205 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N GLY G 207 " --> pdb=" O MET G 133 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N MET G 133 " --> pdb=" O GLY G 207 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 60 through 63 removed outlier: 6.730A pdb=" N PHE F 98 " --> pdb=" O VAL F 82 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N MET F 84 " --> pdb=" O LEU F 96 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N LEU F 96 " --> pdb=" O MET F 84 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLN F 27 " --> pdb=" O LYS F 95 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL F 97 " --> pdb=" O GLN F 27 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N MET F 29 " --> pdb=" O VAL F 97 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N CYS F 99 " --> pdb=" O MET F 29 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE F 31 " --> pdb=" O CYS F 99 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N VAL F 101 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 8.868A pdb=" N VAL F 33 " --> pdb=" O VAL F 101 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N CYS F 42 " --> pdb=" O ALA G 195 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ALA G 195 " --> pdb=" O CYS F 42 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N THR G 191 " --> pdb=" O THR F 46 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLN G 205 " --> pdb=" O THR G 191 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N THR G 193 " --> pdb=" O GLU G 203 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLU G 203 " --> pdb=" O THR G 193 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ALA G 195 " --> pdb=" O GLN G 201 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N GLN G 201 " --> pdb=" O ALA G 195 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLN G 201 " --> pdb=" O LEU G 139 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU G 139 " --> pdb=" O GLN G 201 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N GLU G 203 " --> pdb=" O TYR G 137 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N TYR G 137 " --> pdb=" O GLU G 203 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N GLN G 205 " --> pdb=" O GLN G 135 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLN G 135 " --> pdb=" O GLN G 205 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N GLY G 207 " --> pdb=" O MET G 133 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N MET G 133 " --> pdb=" O GLY G 207 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N HIS G 253 " --> pdb=" O GLU G 134 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 235 through 237 removed outlier: 3.593A pdb=" N HIS F 253 " --> pdb=" O GLU F 134 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLY F 315 " --> pdb=" O ILE F 325 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 235 through 237 removed outlier: 6.180A pdb=" N PHE F 131 " --> pdb=" O PRO F 208 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N GLN F 201 " --> pdb=" O ALA F 195 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ALA F 195 " --> pdb=" O GLN F 201 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLU F 203 " --> pdb=" O THR F 193 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N THR F 193 " --> pdb=" O GLU F 203 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLN F 205 " --> pdb=" O THR F 191 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N THR F 191 " --> pdb=" O THR J 46 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N ALA F 195 " --> pdb=" O CYS J 42 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N CYS J 42 " --> pdb=" O ALA F 195 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N VAL J 33 " --> pdb=" O CYS J 99 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL J 101 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU J 96 " --> pdb=" O MET J 84 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N MET J 84 " --> pdb=" O LEU J 96 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N PHE J 98 " --> pdb=" O VAL J 82 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 60 through 63 removed outlier: 6.756A pdb=" N PHE G 98 " --> pdb=" O VAL G 82 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N MET G 84 " --> pdb=" O LEU G 96 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU G 96 " --> pdb=" O MET G 84 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLN G 27 " --> pdb=" O LYS G 95 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL G 97 " --> pdb=" O GLN G 27 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N MET G 29 " --> pdb=" O VAL G 97 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N CYS G 99 " --> pdb=" O MET G 29 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE G 31 " --> pdb=" O CYS G 99 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N VAL G 101 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 8.832A pdb=" N VAL G 33 " --> pdb=" O VAL G 101 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N CYS G 42 " --> pdb=" O ALA H 195 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ALA H 195 " --> pdb=" O CYS G 42 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N THR H 191 " --> pdb=" O THR G 46 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLN H 205 " --> pdb=" O THR H 191 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N THR H 193 " --> pdb=" O GLU H 203 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLU H 203 " --> pdb=" O THR H 193 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ALA H 195 " --> pdb=" O GLN H 201 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N GLN H 201 " --> pdb=" O ALA H 195 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N GLN H 201 " --> pdb=" O LEU H 139 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU H 139 " --> pdb=" O GLN H 201 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N GLU H 203 " --> pdb=" O TYR H 137 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N TYR H 137 " --> pdb=" O GLU H 203 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N GLN H 205 " --> pdb=" O GLN H 135 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLN H 135 " --> pdb=" O GLN H 205 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLY H 207 " --> pdb=" O MET H 133 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N MET H 133 " --> pdb=" O GLY H 207 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 60 through 63 removed outlier: 6.756A pdb=" N PHE G 98 " --> pdb=" O VAL G 82 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N MET G 84 " --> pdb=" O LEU G 96 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU G 96 " --> pdb=" O MET G 84 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLN G 27 " --> pdb=" O LYS G 95 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL G 97 " --> pdb=" O GLN G 27 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N MET G 29 " --> pdb=" O VAL G 97 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N CYS G 99 " --> pdb=" O MET G 29 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE G 31 " --> pdb=" O CYS G 99 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N VAL G 101 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 8.832A pdb=" N VAL G 33 " --> pdb=" O VAL G 101 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N CYS G 42 " --> pdb=" O ALA H 195 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ALA H 195 " --> pdb=" O CYS G 42 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N THR H 191 " --> pdb=" O THR G 46 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLN H 205 " --> pdb=" O THR H 191 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N THR H 193 " --> pdb=" O GLU H 203 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLU H 203 " --> pdb=" O THR H 193 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ALA H 195 " --> pdb=" O GLN H 201 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N GLN H 201 " --> pdb=" O ALA H 195 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N GLN H 201 " --> pdb=" O LEU H 139 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU H 139 " --> pdb=" O GLN H 201 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N GLU H 203 " --> pdb=" O TYR H 137 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N TYR H 137 " --> pdb=" O GLU H 203 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N GLN H 205 " --> pdb=" O GLN H 135 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLN H 135 " --> pdb=" O GLN H 205 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLY H 207 " --> pdb=" O MET H 133 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N MET H 133 " --> pdb=" O GLY H 207 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE H 337 " --> pdb=" O PHE H 256 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 60 through 63 removed outlier: 5.553A pdb=" N LEU H 79 " --> pdb=" O PHE H 102 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N PHE H 102 " --> pdb=" O LEU H 79 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N GLU H 100 " --> pdb=" O PRO H 81 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLN H 27 " --> pdb=" O LYS H 95 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N VAL H 97 " --> pdb=" O GLN H 27 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N MET H 29 " --> pdb=" O VAL H 97 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N CYS H 99 " --> pdb=" O MET H 29 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE H 31 " --> pdb=" O CYS H 99 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL H 101 " --> pdb=" O ILE H 31 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N VAL H 33 " --> pdb=" O VAL H 101 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N CYS H 42 " --> pdb=" O ALA I 195 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ALA I 195 " --> pdb=" O CYS H 42 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N THR I 191 " --> pdb=" O THR H 46 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLN I 205 " --> pdb=" O THR I 191 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N THR I 193 " --> pdb=" O GLU I 203 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLU I 203 " --> pdb=" O THR I 193 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ALA I 195 " --> pdb=" O GLN I 201 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N GLN I 201 " --> pdb=" O ALA I 195 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N PHE I 131 " --> pdb=" O PRO I 208 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 60 through 63 removed outlier: 5.553A pdb=" N LEU H 79 " --> pdb=" O PHE H 102 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N PHE H 102 " --> pdb=" O LEU H 79 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N GLU H 100 " --> pdb=" O PRO H 81 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLN H 27 " --> pdb=" O LYS H 95 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N VAL H 97 " --> pdb=" O GLN H 27 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N MET H 29 " --> pdb=" O VAL H 97 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N CYS H 99 " --> pdb=" O MET H 29 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE H 31 " --> pdb=" O CYS H 99 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL H 101 " --> pdb=" O ILE H 31 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N VAL H 33 " --> pdb=" O VAL H 101 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N CYS H 42 " --> pdb=" O ALA I 195 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ALA I 195 " --> pdb=" O CYS H 42 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N THR I 191 " --> pdb=" O THR H 46 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLN I 205 " --> pdb=" O THR I 191 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N THR I 193 " --> pdb=" O GLU I 203 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLU I 203 " --> pdb=" O THR I 193 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ALA I 195 " --> pdb=" O GLN I 201 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N GLN I 201 " --> pdb=" O ALA I 195 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N PHE I 131 " --> pdb=" O PRO I 208 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS I 253 " --> pdb=" O GLU I 134 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLY I 315 " --> pdb=" O ILE I 325 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 60 through 63 removed outlier: 6.722A pdb=" N PHE I 98 " --> pdb=" O VAL I 82 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N MET I 84 " --> pdb=" O LEU I 96 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU I 96 " --> pdb=" O MET I 84 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLN I 27 " --> pdb=" O LYS I 95 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N VAL I 97 " --> pdb=" O GLN I 27 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N MET I 29 " --> pdb=" O VAL I 97 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N CYS I 99 " --> pdb=" O MET I 29 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE I 31 " --> pdb=" O CYS I 99 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N VAL I 101 " --> pdb=" O ILE I 31 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N VAL I 33 " --> pdb=" O VAL I 101 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N CYS I 42 " --> pdb=" O ALA J 195 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ALA J 195 " --> pdb=" O CYS I 42 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR J 191 " --> pdb=" O THR I 46 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLN J 205 " --> pdb=" O THR J 191 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N THR J 193 " --> pdb=" O GLU J 203 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLU J 203 " --> pdb=" O THR J 193 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ALA J 195 " --> pdb=" O GLN J 201 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N GLN J 201 " --> pdb=" O ALA J 195 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N PHE J 131 " --> pdb=" O PRO J 208 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 60 through 63 removed outlier: 6.722A pdb=" N PHE I 98 " --> pdb=" O VAL I 82 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N MET I 84 " --> pdb=" O LEU I 96 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU I 96 " --> pdb=" O MET I 84 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLN I 27 " --> pdb=" O LYS I 95 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N VAL I 97 " --> pdb=" O GLN I 27 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N MET I 29 " --> pdb=" O VAL I 97 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N CYS I 99 " --> pdb=" O MET I 29 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE I 31 " --> pdb=" O CYS I 99 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N VAL I 101 " --> pdb=" O ILE I 31 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N VAL I 33 " --> pdb=" O VAL I 101 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N CYS I 42 " --> pdb=" O ALA J 195 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ALA J 195 " --> pdb=" O CYS I 42 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR J 191 " --> pdb=" O THR I 46 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLN J 205 " --> pdb=" O THR J 191 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N THR J 193 " --> pdb=" O GLU J 203 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLU J 203 " --> pdb=" O THR J 193 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ALA J 195 " --> pdb=" O GLN J 201 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N GLN J 201 " --> pdb=" O ALA J 195 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N PHE J 131 " --> pdb=" O PRO J 208 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS J 253 " --> pdb=" O GLU J 134 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLY J 315 " --> pdb=" O ILE J 325 " (cutoff:3.500A) 1433 hydrogen bonds defined for protein. 3939 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: 5.84 Time building geometry restraints manager: 3.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5971 1.33 - 1.45: 7776 1.45 - 1.57: 16229 1.57 - 1.69: 0 1.69 - 1.82: 390 Bond restraints: 30366 Sorted by residual: bond pdb=" N ILE H 243 " pdb=" CA ILE H 243 " ideal model delta sigma weight residual 1.457 1.492 -0.035 9.00e-03 1.23e+04 1.51e+01 bond pdb=" N ARG A 280 " pdb=" CA ARG A 280 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.08e-02 8.57e+03 1.21e+01 bond pdb=" N ILE H 285 " pdb=" CA ILE H 285 " ideal model delta sigma weight residual 1.462 1.497 -0.035 1.06e-02 8.90e+03 1.07e+01 bond pdb=" CA SER H 322 " pdb=" CB SER H 322 " ideal model delta sigma weight residual 1.531 1.487 0.044 1.57e-02 4.06e+03 7.98e+00 bond pdb=" N GLN H 331 " pdb=" CA GLN H 331 " ideal model delta sigma weight residual 1.458 1.488 -0.031 1.12e-02 7.97e+03 7.51e+00 ... (remaining 30361 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 39834 2.30 - 4.61: 1065 4.61 - 6.91: 123 6.91 - 9.21: 23 9.21 - 11.51: 7 Bond angle restraints: 41052 Sorted by residual: angle pdb=" N ARG H 298 " pdb=" CA ARG H 298 " pdb=" C ARG H 298 " ideal model delta sigma weight residual 113.72 107.03 6.69 1.30e+00 5.92e-01 2.65e+01 angle pdb=" N ARG H 340 " pdb=" CA ARG H 340 " pdb=" C ARG H 340 " ideal model delta sigma weight residual 113.21 108.00 5.21 1.15e+00 7.56e-01 2.05e+01 angle pdb=" N PHE H 238 " pdb=" CA PHE H 238 " pdb=" C PHE H 238 " ideal model delta sigma weight residual 113.30 107.34 5.96 1.34e+00 5.57e-01 1.98e+01 angle pdb=" N ARG H 286 " pdb=" CA ARG H 286 " pdb=" C ARG H 286 " ideal model delta sigma weight residual 113.72 108.05 5.67 1.30e+00 5.92e-01 1.90e+01 angle pdb=" N GLU E 272 " pdb=" CA GLU E 272 " pdb=" CB GLU E 272 " ideal model delta sigma weight residual 110.01 116.25 -6.24 1.45e+00 4.76e-01 1.85e+01 ... (remaining 41047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 16134 17.98 - 35.96: 1481 35.96 - 53.94: 343 53.94 - 71.92: 88 71.92 - 89.90: 34 Dihedral angle restraints: 18080 sinusoidal: 7460 harmonic: 10620 Sorted by residual: dihedral pdb=" CD ARG H 298 " pdb=" NE ARG H 298 " pdb=" CZ ARG H 298 " pdb=" NH1 ARG H 298 " ideal model delta sinusoidal sigma weight residual 0.00 -87.49 87.49 1 1.00e+01 1.00e-02 9.18e+01 dihedral pdb=" CD ARG H 286 " pdb=" NE ARG H 286 " pdb=" CZ ARG H 286 " pdb=" NH1 ARG H 286 " ideal model delta sinusoidal sigma weight residual 0.00 -85.80 85.80 1 1.00e+01 1.00e-02 8.90e+01 dihedral pdb=" CD ARG D 268 " pdb=" NE ARG D 268 " pdb=" CZ ARG D 268 " pdb=" NH1 ARG D 268 " ideal model delta sinusoidal sigma weight residual 0.00 -72.03 72.03 1 1.00e+01 1.00e-02 6.64e+01 ... (remaining 18077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 3200 0.056 - 0.112: 772 0.112 - 0.168: 122 0.168 - 0.224: 14 0.224 - 0.280: 2 Chirality restraints: 4110 Sorted by residual: chirality pdb=" CG LEU C 225 " pdb=" CB LEU C 225 " pdb=" CD1 LEU C 225 " pdb=" CD2 LEU C 225 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CA GLU E 272 " pdb=" N GLU E 272 " pdb=" C GLU E 272 " pdb=" CB GLU E 272 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA TYR G 288 " pdb=" N TYR G 288 " pdb=" C TYR G 288 " pdb=" CB TYR G 288 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 4107 not shown) Planarity restraints: 5476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 298 " -1.101 9.50e-02 1.11e+02 4.93e-01 1.47e+02 pdb=" NE ARG H 298 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG H 298 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG H 298 " -0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG H 298 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 286 " 1.090 9.50e-02 1.11e+02 4.89e-01 1.44e+02 pdb=" NE ARG H 286 " -0.067 2.00e-02 2.50e+03 pdb=" CZ ARG H 286 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG H 286 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG H 286 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 340 " -1.050 9.50e-02 1.11e+02 4.70e-01 1.34e+02 pdb=" NE ARG H 340 " 0.062 2.00e-02 2.50e+03 pdb=" CZ ARG H 340 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG H 340 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG H 340 " -0.022 2.00e-02 2.50e+03 ... (remaining 5473 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 310 2.61 - 3.19: 26301 3.19 - 3.76: 46431 3.76 - 4.33: 65497 4.33 - 4.90: 107649 Nonbonded interactions: 246188 Sorted by model distance: nonbonded pdb=" OG SER F 116 " pdb=" OE2 GLU F 353 " model vdw 2.043 3.040 nonbonded pdb=" OG1 THR I 46 " pdb=" OH TYR J 180 " model vdw 2.063 3.040 nonbonded pdb=" OG SER D 73 " pdb=" OD1 ASN D 74 " model vdw 2.067 3.040 nonbonded pdb=" OH TYR A 180 " pdb=" OG1 THR E 46 " model vdw 2.111 3.040 nonbonded pdb=" O ASN J 19 " pdb=" ND2 ASN J 19 " model vdw 2.121 3.120 ... (remaining 246183 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 202 or (resid 203 and (name N or name CA or name \ C or name O or name CB )) or resid 204 through 267 or (resid 268 and (name N or \ name CA or name C or name O or name CB )) or resid 269 through 271 or (resid 27 \ 2 through 273 and (name N or name CA or name C or name O or name CB )) or resid \ 274 through 318 or (resid 319 and (name N or name CA or name C or name O or name \ CB )) or resid 320 through 371 or (resid 372 and (name N or name CA or name C o \ r name O or name CB )))) selection = (chain 'B' and (resid 1 through 202 or (resid 203 and (name N or name CA or name \ C or name O or name CB )) or resid 204 through 267 or (resid 268 and (name N or \ name CA or name C or name O or name CB )) or resid 269 through 271 or (resid 27 \ 2 through 273 and (name N or name CA or name C or name O or name CB )) or resid \ 274 through 318 or (resid 319 and (name N or name CA or name C or name O or name \ CB )) or resid 320 through 371 or (resid 372 and (name N or name CA or name C o \ r name O or name CB )))) selection = (chain 'C' and (resid 1 through 202 or (resid 203 and (name N or name CA or name \ C or name O or name CB )) or resid 204 through 267 or (resid 268 and (name N or \ name CA or name C or name O or name CB )) or resid 269 through 271 or (resid 27 \ 2 through 273 and (name N or name CA or name C or name O or name CB )) or resid \ 274 through 318 or (resid 319 and (name N or name CA or name C or name O or name \ CB )) or resid 320 through 371 or (resid 372 and (name N or name CA or name C o \ r name O or name CB )))) selection = (chain 'D' and (resid 1 through 202 or (resid 203 and (name N or name CA or name \ C or name O or name CB )) or resid 204 through 267 or (resid 268 and (name N or \ name CA or name C or name O or name CB )) or resid 269 through 271 or (resid 27 \ 2 through 273 and (name N or name CA or name C or name O or name CB )) or resid \ 274 through 318 or (resid 319 and (name N or name CA or name C or name O or name \ CB )) or resid 320 through 371 or (resid 372 and (name N or name CA or name C o \ r name O or name CB )))) selection = (chain 'E' and (resid 1 through 202 or (resid 203 and (name N or name CA or name \ C or name O or name CB )) or resid 204 through 371 or (resid 372 and (name N or \ name CA or name C or name O or name CB )))) selection = (chain 'F' and (resid 1 through 202 or (resid 203 and (name N or name CA or name \ C or name O or name CB )) or resid 204 through 267 or (resid 268 and (name N or \ name CA or name C or name O or name CB )) or resid 269 through 271 or (resid 27 \ 2 through 273 and (name N or name CA or name C or name O or name CB )) or resid \ 274 through 318 or (resid 319 and (name N or name CA or name C or name O or name \ CB )) or resid 320 through 371 or (resid 372 and (name N or name CA or name C o \ r name O or name CB )))) selection = (chain 'G' and (resid 1 through 202 or (resid 203 and (name N or name CA or name \ C or name O or name CB )) or resid 204 through 267 or (resid 268 and (name N or \ name CA or name C or name O or name CB )) or resid 269 through 271 or (resid 27 \ 2 through 273 and (name N or name CA or name C or name O or name CB )) or resid \ 274 through 318 or (resid 319 and (name N or name CA or name C or name O or name \ CB )) or resid 320 through 372)) selection = (chain 'H' and (resid 1 through 202 or (resid 203 and (name N or name CA or name \ C or name O or name CB )) or resid 204 through 267 or (resid 268 and (name N or \ name CA or name C or name O or name CB )) or resid 269 through 271 or (resid 27 \ 2 through 273 and (name N or name CA or name C or name O or name CB )) or resid \ 274 through 318 or (resid 319 and (name N or name CA or name C or name O or name \ CB )) or resid 320 through 371 or (resid 372 and (name N or name CA or name C o \ r name O or name CB )))) selection = (chain 'I' and (resid 1 through 202 or (resid 203 and (name N or name CA or name \ C or name O or name CB )) or resid 204 through 267 or (resid 268 and (name N or \ name CA or name C or name O or name CB )) or resid 269 through 271 or (resid 27 \ 2 through 273 and (name N or name CA or name C or name O or name CB )) or resid \ 274 through 318 or (resid 319 and (name N or name CA or name C or name O or name \ CB )) or resid 320 through 371 or (resid 372 and (name N or name CA or name C o \ r name O or name CB )))) selection = (chain 'J' and (resid 1 through 267 or (resid 268 and (name N or name CA or name \ C or name O or name CB )) or resid 269 through 271 or (resid 272 through 273 an \ d (name N or name CA or name C or name O or name CB )) or resid 274 through 318 \ or (resid 319 and (name N or name CA or name C or name O or name CB )) or resid \ 320 through 371 or (resid 372 and (name N or name CA or name C or name O or name \ CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.680 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: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 25.940 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 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 : 0.004 0.069 30366 Z= 0.227 Angle : 0.867 11.515 41052 Z= 0.491 Chirality : 0.049 0.280 4110 Planarity : 0.019 0.493 5476 Dihedral : 15.340 89.896 11320 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.59 % Allowed : 4.68 % Favored : 94.73 % Rotamer: Outliers : 1.44 % Allowed : 16.11 % Favored : 82.46 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.13), residues: 3700 helix: 0.65 (0.14), residues: 1080 sheet: -0.43 (0.16), residues: 790 loop : -0.21 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.061 0.001 ARG E 280 TYR 0.039 0.002 TYR J 288 PHE 0.032 0.002 PHE C 312 TRP 0.051 0.002 TRP E 149 HIS 0.013 0.001 HIS D 80 Details of bonding type rmsd covalent geometry : bond 0.00431 (30366) covalent geometry : angle 0.86706 (41052) hydrogen bonds : bond 0.15385 ( 1222) hydrogen bonds : angle 7.23972 ( 3939) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 479 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 MET cc_start: 0.8575 (mtt) cc_final: 0.8247 (mtt) REVERT: B 133 MET cc_start: 0.7513 (mmm) cc_final: 0.7278 (mmm) REVERT: C 336 TYR cc_start: 0.8612 (OUTLIER) cc_final: 0.8006 (p90) REVERT: D 1 MET cc_start: 0.3312 (tmm) cc_final: 0.2769 (tpp) REVERT: D 104 TYR cc_start: 0.7332 (p90) cc_final: 0.7054 (p90) REVERT: D 214 MET cc_start: 0.7968 (tpp) cc_final: 0.7673 (tpp) REVERT: D 255 ASN cc_start: 0.8154 (m-40) cc_final: 0.7901 (m-40) REVERT: E 336 TYR cc_start: 0.7744 (p90) cc_final: 0.7465 (p90) REVERT: F 283 TYR cc_start: 0.7928 (t80) cc_final: 0.7646 (t80) REVERT: G 162 TYR cc_start: 0.8495 (t80) cc_final: 0.8059 (t80) REVERT: G 198 MET cc_start: 0.7770 (ttp) cc_final: 0.7463 (ttp) REVERT: H 337 PHE cc_start: 0.8241 (p90) cc_final: 0.7678 (p90) REVERT: J 18 MET cc_start: 0.8955 (mmt) cc_final: 0.8693 (tpp) REVERT: J 140 MET cc_start: 0.8014 (mtp) cc_final: 0.7798 (mtm) REVERT: J 149 TRP cc_start: 0.9245 (m-10) cc_final: 0.8951 (m-10) REVERT: J 214 MET cc_start: 0.9023 (tpp) cc_final: 0.8612 (tpp) REVERT: J 333 LYS cc_start: 0.8602 (mttp) cc_final: 0.8222 (mmtp) outliers start: 45 outliers final: 9 residues processed: 509 average time/residue: 0.1696 time to fit residues: 140.5218 Evaluate side-chains 384 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 374 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain C residue 336 TYR Chi-restraints excluded: chain D residue 366 ASP Chi-restraints excluded: chain D residue 369 PHE Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 274 ILE Chi-restraints excluded: chain E residue 307 SER Chi-restraints excluded: chain E residue 310 ASN Chi-restraints excluded: chain G residue 294 LEU Chi-restraints excluded: chain J residue 19 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.1980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 158 GLN C 27 GLN C 69 GLN C 80 HIS C 112 ASN ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 ASN E 158 GLN F 22 GLN F 112 ASN G 22 GLN G 194 ASN G 362 ASN H 19 ASN H 265 ASN ** I 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 201 GLN J 112 ASN J 152 ASN J 158 GLN ** J 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.149840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.118643 restraints weight = 43939.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.122218 restraints weight = 24869.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.124579 restraints weight = 17673.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.126035 restraints weight = 14356.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.126791 restraints weight = 12661.704| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30366 Z= 0.148 Angle : 0.652 9.681 41052 Z= 0.342 Chirality : 0.044 0.188 4110 Planarity : 0.005 0.098 5476 Dihedral : 4.662 55.488 4127 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.97 % Favored : 98.00 % Rotamer: Outliers : 1.47 % Allowed : 15.98 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.14), residues: 3700 helix: 1.48 (0.16), residues: 1080 sheet: -0.13 (0.17), residues: 800 loop : 0.25 (0.15), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 357 TYR 0.038 0.001 TYR A 288 PHE 0.027 0.002 PHE G 62 TRP 0.020 0.001 TRP D 130 HIS 0.009 0.001 HIS D 80 Details of bonding type rmsd covalent geometry : bond 0.00347 (30366) covalent geometry : angle 0.65217 (41052) hydrogen bonds : bond 0.04982 ( 1222) hydrogen bonds : angle 5.39976 ( 3939) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 430 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 SER cc_start: 0.8395 (p) cc_final: 0.8175 (p) REVERT: B 1 MET cc_start: 0.5059 (tmm) cc_final: 0.1793 (tpt) REVERT: C 87 ASP cc_start: 0.8561 (t0) cc_final: 0.8315 (t0) REVERT: C 214 MET cc_start: 0.8790 (tpp) cc_final: 0.8575 (tpp) REVERT: C 288 TYR cc_start: 0.8476 (m-10) cc_final: 0.8137 (m-10) REVERT: D 1 MET cc_start: 0.3182 (tmm) cc_final: 0.2830 (tmm) REVERT: D 255 ASN cc_start: 0.8360 (m-40) cc_final: 0.7833 (m-40) REVERT: D 341 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.8349 (ttp-110) REVERT: E 92 ASP cc_start: 0.8331 (m-30) cc_final: 0.8118 (m-30) REVERT: E 133 MET cc_start: 0.8308 (mtt) cc_final: 0.7363 (mtp) REVERT: E 311 ASP cc_start: 0.6373 (t0) cc_final: 0.6030 (m-30) REVERT: E 312 PHE cc_start: 0.7762 (t80) cc_final: 0.7441 (t80) REVERT: E 336 TYR cc_start: 0.7794 (p90) cc_final: 0.7536 (p90) REVERT: F 15 GLN cc_start: 0.8366 (tp-100) cc_final: 0.7552 (mm-40) REVERT: F 77 MET cc_start: 0.7569 (mmm) cc_final: 0.6781 (mmt) REVERT: F 162 TYR cc_start: 0.9044 (t80) cc_final: 0.8839 (t80) REVERT: F 261 MET cc_start: 0.8358 (mmt) cc_final: 0.7917 (mmt) REVERT: G 30 TYR cc_start: 0.8264 (m-80) cc_final: 0.7945 (m-80) REVERT: G 63 ASP cc_start: 0.8116 (t0) cc_final: 0.7620 (t0) REVERT: G 133 MET cc_start: 0.7710 (mtp) cc_final: 0.7450 (mtp) REVERT: G 162 TYR cc_start: 0.8572 (t80) cc_final: 0.8351 (t80) REVERT: G 362 ASN cc_start: 0.6556 (t0) cc_final: 0.6316 (t0) REVERT: H 214 MET cc_start: 0.8434 (tpp) cc_final: 0.8217 (tmm) REVERT: H 337 PHE cc_start: 0.8068 (p90) cc_final: 0.7508 (p90) REVERT: I 52 LYS cc_start: 0.7229 (pttm) cc_final: 0.6974 (pttm) REVERT: I 291 LYS cc_start: 0.8424 (mmtm) cc_final: 0.7345 (mttp) REVERT: I 296 ASN cc_start: 0.8131 (t0) cc_final: 0.7827 (t0) REVERT: J 133 MET cc_start: 0.7836 (mtp) cc_final: 0.7304 (mtp) REVERT: J 140 MET cc_start: 0.8141 (mtp) cc_final: 0.7927 (mtm) REVERT: J 149 TRP cc_start: 0.9266 (m-10) cc_final: 0.9031 (m-10) REVERT: J 214 MET cc_start: 0.9149 (tpp) cc_final: 0.8721 (tpp) REVERT: J 261 MET cc_start: 0.8255 (mmt) cc_final: 0.8054 (mmt) outliers start: 46 outliers final: 28 residues processed: 462 average time/residue: 0.1753 time to fit residues: 131.5367 Evaluate side-chains 395 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 366 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 341 ARG Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 145 HIS Chi-restraints excluded: chain E residue 255 ASN Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain F residue 99 CYS Chi-restraints excluded: chain F residue 112 ASN Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 145 HIS Chi-restraints excluded: chain F residue 152 ASN Chi-restraints excluded: chain G residue 294 LEU Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain H residue 145 HIS Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain H residue 243 ILE Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain H residue 309 ILE Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain J residue 307 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 139 optimal weight: 0.9980 chunk 297 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 270 optimal weight: 0.8980 chunk 137 optimal weight: 9.9990 chunk 307 optimal weight: 3.9990 chunk 42 optimal weight: 0.0000 chunk 95 optimal weight: 0.8980 chunk 169 optimal weight: 0.5980 chunk 251 optimal weight: 4.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 27 GLN C 194 ASN D 15 GLN D 22 GLN E 15 GLN E 158 GLN G 194 ASN H 27 GLN ** I 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 194 ASN J 112 ASN J 296 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.148050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.117027 restraints weight = 44028.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.120509 restraints weight = 24873.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.122814 restraints weight = 17772.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.124252 restraints weight = 14484.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.125101 restraints weight = 12797.468| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 30366 Z= 0.131 Angle : 0.589 8.488 41052 Z= 0.307 Chirality : 0.043 0.166 4110 Planarity : 0.004 0.050 5476 Dihedral : 4.193 54.556 4110 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.46 % Favored : 97.51 % Rotamer: Outliers : 1.72 % Allowed : 16.01 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.14), residues: 3700 helix: 1.69 (0.16), residues: 1080 sheet: -0.10 (0.17), residues: 840 loop : 0.26 (0.16), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 340 TYR 0.027 0.001 TYR E 162 PHE 0.026 0.001 PHE G 62 TRP 0.019 0.001 TRP D 130 HIS 0.010 0.001 HIS D 80 Details of bonding type rmsd covalent geometry : bond 0.00309 (30366) covalent geometry : angle 0.58914 (41052) hydrogen bonds : bond 0.04187 ( 1222) hydrogen bonds : angle 4.97236 ( 3939) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 419 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8732 (mt) REVERT: B 1 MET cc_start: 0.5191 (tmm) cc_final: 0.4860 (tmm) REVERT: B 77 MET cc_start: 0.8109 (mtp) cc_final: 0.7849 (mtt) REVERT: C 52 LYS cc_start: 0.7745 (mptt) cc_final: 0.7436 (mppt) REVERT: C 87 ASP cc_start: 0.8626 (t0) cc_final: 0.8405 (t0) REVERT: C 143 ASP cc_start: 0.8421 (p0) cc_final: 0.8182 (p0) REVERT: C 288 TYR cc_start: 0.8517 (m-10) cc_final: 0.8116 (m-10) REVERT: D 1 MET cc_start: 0.3416 (tmm) cc_final: 0.2992 (mmm) REVERT: D 340 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.8223 (ttm170) REVERT: E 92 ASP cc_start: 0.8364 (m-30) cc_final: 0.8155 (m-30) REVERT: E 140 MET cc_start: 0.7837 (mtp) cc_final: 0.7540 (mtp) REVERT: E 361 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7443 (mp) REVERT: F 15 GLN cc_start: 0.8407 (tp-100) cc_final: 0.7527 (mm-40) REVERT: F 77 MET cc_start: 0.7629 (mmm) cc_final: 0.6833 (mmt) REVERT: F 123 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.8060 (mtt) REVERT: F 212 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8559 (mp) REVERT: F 261 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.7934 (mmt) REVERT: G 30 TYR cc_start: 0.8362 (m-80) cc_final: 0.8076 (m-80) REVERT: G 63 ASP cc_start: 0.8158 (t0) cc_final: 0.7658 (t0) REVERT: G 77 MET cc_start: 0.8265 (mmm) cc_final: 0.7961 (mmm) REVERT: G 121 MET cc_start: 0.7238 (tmm) cc_final: 0.6948 (tmm) REVERT: G 185 TYR cc_start: 0.9499 (t80) cc_final: 0.8986 (t80) REVERT: G 188 ILE cc_start: 0.9189 (mm) cc_final: 0.8986 (mm) REVERT: G 362 ASN cc_start: 0.6787 (t0) cc_final: 0.6482 (t0) REVERT: H 24 GLU cc_start: 0.6204 (tp30) cc_final: 0.5772 (tp30) REVERT: H 117 CYS cc_start: 0.8411 (OUTLIER) cc_final: 0.7177 (t) REVERT: H 130 TRP cc_start: 0.8579 (m-10) cc_final: 0.8127 (m-10) REVERT: H 337 PHE cc_start: 0.8238 (p90) cc_final: 0.7753 (p90) REVERT: I 52 LYS cc_start: 0.7067 (pttm) cc_final: 0.6792 (pttm) REVERT: I 87 ASP cc_start: 0.8535 (t0) cc_final: 0.8296 (t0) REVERT: I 291 LYS cc_start: 0.8399 (mmtm) cc_final: 0.7229 (mttp) REVERT: I 296 ASN cc_start: 0.8189 (t0) cc_final: 0.7851 (t0) REVERT: J 133 MET cc_start: 0.7845 (mtp) cc_final: 0.7573 (mtp) REVERT: J 149 TRP cc_start: 0.9259 (m-10) cc_final: 0.9045 (m-10) REVERT: J 201 GLN cc_start: 0.8566 (tt0) cc_final: 0.8356 (tt0) REVERT: J 214 MET cc_start: 0.9096 (tpp) cc_final: 0.8836 (tpp) outliers start: 54 outliers final: 34 residues processed: 457 average time/residue: 0.1741 time to fit residues: 129.4864 Evaluate side-chains 419 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 378 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 49 CYS Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 99 CYS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 340 ARG Chi-restraints excluded: chain D residue 369 PHE Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 145 HIS Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 255 ASN Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 99 CYS Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 145 HIS Chi-restraints excluded: chain F residue 152 ASN Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 261 MET Chi-restraints excluded: chain G residue 294 LEU Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 117 CYS Chi-restraints excluded: chain H residue 145 HIS Chi-restraints excluded: chain H residue 191 THR Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain H residue 243 ILE Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain J residue 307 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 233 optimal weight: 0.9990 chunk 325 optimal weight: 6.9990 chunk 202 optimal weight: 3.9990 chunk 224 optimal weight: 0.7980 chunk 260 optimal weight: 0.6980 chunk 206 optimal weight: 0.5980 chunk 155 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 293 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 311 optimal weight: 0.0970 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 ASN E 158 GLN ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN H 15 GLN I 15 GLN J 112 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.146477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.115380 restraints weight = 43889.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.118847 restraints weight = 25050.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.121122 restraints weight = 17986.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.122555 restraints weight = 14708.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.123329 restraints weight = 13010.250| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30366 Z= 0.131 Angle : 0.572 8.880 41052 Z= 0.296 Chirality : 0.042 0.163 4110 Planarity : 0.004 0.053 5476 Dihedral : 4.055 55.930 4110 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.14 % Favored : 97.84 % Rotamer: Outliers : 2.42 % Allowed : 16.01 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.14), residues: 3700 helix: 1.83 (0.16), residues: 1080 sheet: -0.10 (0.18), residues: 820 loop : 0.23 (0.16), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 91 TYR 0.025 0.001 TYR F 162 PHE 0.025 0.001 PHE G 62 TRP 0.018 0.001 TRP D 130 HIS 0.009 0.001 HIS F 80 Details of bonding type rmsd covalent geometry : bond 0.00307 (30366) covalent geometry : angle 0.57184 (41052) hydrogen bonds : bond 0.03921 ( 1222) hydrogen bonds : angle 4.74553 ( 3939) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 411 time to evaluate : 0.792 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: B 1 MET cc_start: 0.5195 (tmm) cc_final: 0.4532 (tmm) REVERT: B 77 MET cc_start: 0.8096 (mtp) cc_final: 0.7807 (mtt) REVERT: B 203 GLU cc_start: 0.7927 (tt0) cc_final: 0.7519 (pt0) REVERT: C 52 LYS cc_start: 0.7801 (mptt) cc_final: 0.7554 (mppt) REVERT: C 77 MET cc_start: 0.7902 (mmm) cc_final: 0.7615 (mmp) REVERT: C 143 ASP cc_start: 0.8555 (p0) cc_final: 0.8238 (p0) REVERT: C 214 MET cc_start: 0.8628 (tpp) cc_final: 0.7925 (tpp) REVERT: D 1 MET cc_start: 0.3616 (tmm) cc_final: 0.2241 (mmm) REVERT: D 203 GLU cc_start: 0.7547 (tt0) cc_final: 0.7143 (tt0) REVERT: D 255 ASN cc_start: 0.8660 (m-40) cc_final: 0.8329 (m110) REVERT: D 265 ASN cc_start: 0.8306 (t0) cc_final: 0.7987 (t0) REVERT: D 267 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8380 (mt) REVERT: D 333 LYS cc_start: 0.8064 (mmmt) cc_final: 0.7840 (mmmt) REVERT: D 341 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8185 (ttp-110) REVERT: E 17 TYR cc_start: 0.8968 (m-10) cc_final: 0.8766 (m-10) REVERT: E 92 ASP cc_start: 0.8364 (m-30) cc_final: 0.8123 (m-30) REVERT: E 140 MET cc_start: 0.7859 (mtp) cc_final: 0.7659 (mtm) REVERT: E 162 TYR cc_start: 0.9014 (t80) cc_final: 0.8794 (t80) REVERT: E 205 GLN cc_start: 0.8404 (mp10) cc_final: 0.8174 (mt0) REVERT: E 361 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7564 (mp) REVERT: F 15 GLN cc_start: 0.8383 (tp-100) cc_final: 0.7499 (mm-40) REVERT: F 123 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.8025 (mtt) REVERT: F 261 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.8030 (mmt) REVERT: F 288 TYR cc_start: 0.8160 (m-10) cc_final: 0.7113 (m-80) REVERT: G 30 TYR cc_start: 0.8421 (m-80) cc_final: 0.8199 (m-80) REVERT: G 63 ASP cc_start: 0.8131 (t0) cc_final: 0.7727 (t0) REVERT: G 77 MET cc_start: 0.8393 (mmm) cc_final: 0.8176 (mmm) REVERT: G 121 MET cc_start: 0.7171 (tmm) cc_final: 0.6709 (tmm) REVERT: G 122 ASP cc_start: 0.7395 (m-30) cc_final: 0.6928 (m-30) REVERT: G 133 MET cc_start: 0.7730 (mtp) cc_final: 0.7519 (mtp) REVERT: G 168 ASP cc_start: 0.8188 (p0) cc_final: 0.7976 (t0) REVERT: G 185 TYR cc_start: 0.9494 (t80) cc_final: 0.9257 (t80) REVERT: G 362 ASN cc_start: 0.6938 (t0) cc_final: 0.6598 (t0) REVERT: H 24 GLU cc_start: 0.6192 (tp30) cc_final: 0.5741 (tp30) REVERT: H 117 CYS cc_start: 0.8440 (OUTLIER) cc_final: 0.7173 (t) REVERT: H 214 MET cc_start: 0.8567 (tpp) cc_final: 0.8300 (tmm) REVERT: H 337 PHE cc_start: 0.8379 (p90) cc_final: 0.8130 (p90) REVERT: I 52 LYS cc_start: 0.7153 (pttm) cc_final: 0.6677 (pttm) REVERT: I 104 TYR cc_start: 0.7540 (p90) cc_final: 0.7280 (p90) REVERT: I 291 LYS cc_start: 0.8290 (mmtm) cc_final: 0.7221 (mttp) REVERT: I 296 ASN cc_start: 0.8232 (t0) cc_final: 0.7905 (t0) REVERT: J 133 MET cc_start: 0.7884 (mtp) cc_final: 0.7478 (mtp) REVERT: J 145 HIS cc_start: 0.8373 (OUTLIER) cc_final: 0.7942 (t70) REVERT: J 149 TRP cc_start: 0.9304 (m-10) cc_final: 0.9067 (m-10) REVERT: J 214 MET cc_start: 0.9076 (tpp) cc_final: 0.8837 (tpp) outliers start: 76 outliers final: 44 residues processed: 466 average time/residue: 0.1717 time to fit residues: 130.7039 Evaluate side-chains 440 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 389 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 49 CYS Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 99 CYS Chi-restraints excluded: chain C residue 112 ASN Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 341 ARG Chi-restraints excluded: chain D residue 369 PHE Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 145 HIS Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 255 ASN Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 99 CYS Chi-restraints excluded: chain F residue 112 ASN Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 145 HIS Chi-restraints excluded: chain F residue 152 ASN Chi-restraints excluded: chain F residue 261 MET Chi-restraints excluded: chain F residue 307 SER Chi-restraints excluded: chain G residue 145 HIS Chi-restraints excluded: chain G residue 294 LEU Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 117 CYS Chi-restraints excluded: chain H residue 145 HIS Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain H residue 243 ILE Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 261 MET Chi-restraints excluded: chain J residue 145 HIS Chi-restraints excluded: chain J residue 307 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 7 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 199 optimal weight: 0.8980 chunk 329 optimal weight: 7.9990 chunk 254 optimal weight: 0.9980 chunk 299 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 189 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 178 optimal weight: 6.9990 chunk 211 optimal weight: 9.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN B 246 ASN C 217 HIS D 253 HIS E 27 GLN E 194 ASN F 80 HIS F 152 ASN F 217 HIS F 253 HIS ** G 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 15 GLN H 281 HIS ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 112 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.132298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.101223 restraints weight = 45602.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.104330 restraints weight = 26774.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.106400 restraints weight = 19503.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.107709 restraints weight = 16087.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.108371 restraints weight = 14319.140| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 30366 Z= 0.351 Angle : 0.803 12.571 41052 Z= 0.416 Chirality : 0.051 0.206 4110 Planarity : 0.006 0.067 5476 Dihedral : 4.934 57.844 4110 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.38 % Favored : 96.59 % Rotamer: Outliers : 3.48 % Allowed : 15.57 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.14), residues: 3700 helix: 1.08 (0.15), residues: 1090 sheet: -0.70 (0.17), residues: 860 loop : 0.05 (0.16), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 41 TYR 0.033 0.003 TYR G 349 PHE 0.027 0.003 PHE G 62 TRP 0.028 0.002 TRP D 130 HIS 0.018 0.002 HIS G 217 Details of bonding type rmsd covalent geometry : bond 0.00835 (30366) covalent geometry : angle 0.80322 (41052) hydrogen bonds : bond 0.05584 ( 1222) hydrogen bonds : angle 5.44014 ( 3939) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 391 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 GLU cc_start: 0.7617 (tt0) cc_final: 0.6913 (pt0) REVERT: A 235 ILE cc_start: 0.9417 (mt) cc_final: 0.9047 (tt) REVERT: B 88 PRO cc_start: 0.9406 (Cg_endo) cc_final: 0.9016 (Cg_exo) REVERT: B 203 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7551 (pt0) REVERT: B 214 MET cc_start: 0.8706 (tpp) cc_final: 0.8446 (tpp) REVERT: C 27 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8120 (mm-40) REVERT: C 52 LYS cc_start: 0.7768 (mptt) cc_final: 0.7481 (mppt) REVERT: C 77 MET cc_start: 0.8186 (mmm) cc_final: 0.7854 (mmm) REVERT: C 214 MET cc_start: 0.8852 (tpp) cc_final: 0.8450 (tpp) REVERT: C 353 GLU cc_start: 0.7429 (tt0) cc_final: 0.7065 (mt-10) REVERT: D 77 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.8144 (mmp) REVERT: D 203 GLU cc_start: 0.7705 (tt0) cc_final: 0.7216 (tt0) REVERT: D 265 ASN cc_start: 0.8300 (t0) cc_final: 0.8089 (t0) REVERT: D 341 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.8745 (ttp-110) REVERT: E 92 ASP cc_start: 0.8135 (m-30) cc_final: 0.7930 (m-30) REVERT: E 123 MET cc_start: 0.7087 (mtp) cc_final: 0.6873 (mtp) REVERT: E 149 TRP cc_start: 0.9484 (m-10) cc_final: 0.9212 (m-10) REVERT: E 181 ARG cc_start: 0.9031 (tpp80) cc_final: 0.8749 (tpp80) REVERT: E 261 MET cc_start: 0.8109 (mtt) cc_final: 0.7689 (mtt) REVERT: E 361 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8317 (mp) REVERT: F 133 MET cc_start: 0.8696 (mtp) cc_final: 0.8427 (mtp) REVERT: F 214 MET cc_start: 0.8711 (tpp) cc_final: 0.8317 (tmm) REVERT: F 235 ILE cc_start: 0.9270 (mt) cc_final: 0.8866 (tt) REVERT: F 261 MET cc_start: 0.8843 (OUTLIER) cc_final: 0.7901 (mmt) REVERT: G 63 ASP cc_start: 0.8387 (t0) cc_final: 0.7913 (t0) REVERT: G 77 MET cc_start: 0.8693 (mmm) cc_final: 0.8272 (mmm) REVERT: G 84 MET cc_start: 0.8053 (tpp) cc_final: 0.7655 (ttt) REVERT: G 168 ASP cc_start: 0.8497 (p0) cc_final: 0.8024 (t0) REVERT: G 184 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.9060 (mt) REVERT: G 188 ILE cc_start: 0.9317 (mm) cc_final: 0.9010 (mt) REVERT: G 294 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.7999 (tt) REVERT: G 296 ASN cc_start: 0.8362 (t0) cc_final: 0.7658 (t0) REVERT: G 362 ASN cc_start: 0.7730 (t0) cc_final: 0.7512 (t0) REVERT: H 24 GLU cc_start: 0.6543 (tp30) cc_final: 0.6104 (tp30) REVERT: H 78 TYR cc_start: 0.8851 (m-80) cc_final: 0.8651 (m-80) REVERT: H 106 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8554 (mmm-85) REVERT: I 7 SER cc_start: 0.9179 (OUTLIER) cc_final: 0.8847 (t) REVERT: I 52 LYS cc_start: 0.7461 (pttm) cc_final: 0.7248 (pttp) REVERT: I 180 TYR cc_start: 0.9189 (t80) cc_final: 0.8815 (t80) REVERT: I 239 ASP cc_start: 0.8526 (t0) cc_final: 0.8287 (t0) REVERT: I 291 LYS cc_start: 0.8337 (mmtm) cc_final: 0.7348 (mttp) REVERT: J 87 ASP cc_start: 0.8748 (t0) cc_final: 0.8323 (t0) REVERT: J 106 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7805 (mpt180) REVERT: J 133 MET cc_start: 0.8141 (mtp) cc_final: 0.7743 (mtp) REVERT: J 140 MET cc_start: 0.8439 (mtm) cc_final: 0.8216 (mtm) REVERT: J 145 HIS cc_start: 0.8373 (OUTLIER) cc_final: 0.7893 (t70) REVERT: J 214 MET cc_start: 0.9181 (tpp) cc_final: 0.8934 (tpp) outliers start: 109 outliers final: 70 residues processed: 472 average time/residue: 0.1858 time to fit residues: 140.1591 Evaluate side-chains 427 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 345 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 145 HIS Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 49 CYS Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 341 ARG Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain E residue 145 HIS Chi-restraints excluded: chain E residue 255 ASN Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 288 TYR Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 145 HIS Chi-restraints excluded: chain F residue 152 ASN Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 261 MET Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 307 SER Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 123 MET Chi-restraints excluded: chain G residue 145 HIS Chi-restraints excluded: chain G residue 184 LEU Chi-restraints excluded: chain G residue 274 ILE Chi-restraints excluded: chain G residue 294 LEU Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 106 ARG Chi-restraints excluded: chain H residue 117 CYS Chi-restraints excluded: chain H residue 145 HIS Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain H residue 191 THR Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain H residue 243 ILE Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain H residue 313 SER Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 106 ARG Chi-restraints excluded: chain I residue 123 MET Chi-restraints excluded: chain I residue 145 HIS Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain I residue 261 MET Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 106 ARG Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 145 HIS Chi-restraints excluded: chain J residue 307 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 203 optimal weight: 0.7980 chunk 178 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 chunk 148 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 320 optimal weight: 0.0370 chunk 219 optimal weight: 0.9990 chunk 230 optimal weight: 0.8980 chunk 158 optimal weight: 0.0470 chunk 76 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 GLN C 112 ASN E 15 GLN F 15 GLN F 296 ASN H 15 GLN ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 112 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.138821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.108119 restraints weight = 44366.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.111481 restraints weight = 25178.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.113756 restraints weight = 17989.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.115160 restraints weight = 14646.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.116026 restraints weight = 12939.778| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30366 Z= 0.129 Angle : 0.592 9.382 41052 Z= 0.309 Chirality : 0.042 0.169 4110 Planarity : 0.005 0.056 5476 Dihedral : 4.369 58.621 4110 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.27 % Favored : 97.70 % Rotamer: Outliers : 2.36 % Allowed : 17.22 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.14), residues: 3700 helix: 1.58 (0.15), residues: 1080 sheet: -0.56 (0.17), residues: 860 loop : 0.16 (0.16), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 319 TYR 0.027 0.001 TYR G 349 PHE 0.037 0.002 PHE E 312 TRP 0.018 0.001 TRP D 130 HIS 0.008 0.001 HIS G 284 Details of bonding type rmsd covalent geometry : bond 0.00288 (30366) covalent geometry : angle 0.59228 (41052) hydrogen bonds : bond 0.04149 ( 1222) hydrogen bonds : angle 4.79986 ( 3939) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 417 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 GLU cc_start: 0.7557 (tt0) cc_final: 0.6791 (pt0) REVERT: A 235 ILE cc_start: 0.9297 (mt) cc_final: 0.8919 (tt) REVERT: A 369 PHE cc_start: 0.7262 (OUTLIER) cc_final: 0.7012 (t80) REVERT: B 77 MET cc_start: 0.8156 (mtp) cc_final: 0.7908 (mtt) REVERT: B 88 PRO cc_start: 0.9277 (Cg_endo) cc_final: 0.8893 (Cg_exo) REVERT: B 203 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7460 (pt0) REVERT: C 27 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.8164 (mm110) REVERT: C 77 MET cc_start: 0.8169 (mmm) cc_final: 0.7814 (mmm) REVERT: C 143 ASP cc_start: 0.8700 (p0) cc_final: 0.8407 (p0) REVERT: C 214 MET cc_start: 0.8602 (tpp) cc_final: 0.8209 (tpp) REVERT: C 353 GLU cc_start: 0.7409 (tt0) cc_final: 0.7044 (mt-10) REVERT: D 77 MET cc_start: 0.8341 (mmp) cc_final: 0.8122 (mmp) REVERT: D 79 LEU cc_start: 0.9443 (mt) cc_final: 0.9197 (mt) REVERT: D 188 ILE cc_start: 0.9295 (mm) cc_final: 0.9091 (mm) REVERT: D 203 GLU cc_start: 0.7654 (tt0) cc_final: 0.7204 (tt0) REVERT: D 255 ASN cc_start: 0.8665 (m-40) cc_final: 0.8400 (m110) REVERT: D 341 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8509 (ttp-110) REVERT: D 353 GLU cc_start: 0.8716 (pp20) cc_final: 0.8188 (tt0) REVERT: E 92 ASP cc_start: 0.8214 (OUTLIER) cc_final: 0.8009 (m-30) REVERT: E 121 MET cc_start: 0.8022 (mmp) cc_final: 0.7260 (mmp) REVERT: E 149 TRP cc_start: 0.9594 (m-10) cc_final: 0.9180 (m-10) REVERT: E 181 ARG cc_start: 0.8805 (tpp80) cc_final: 0.8392 (tpp80) REVERT: E 361 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8117 (mp) REVERT: F 77 MET cc_start: 0.7684 (mmt) cc_final: 0.6746 (mmt) REVERT: F 121 MET cc_start: 0.8047 (mmt) cc_final: 0.7739 (mmp) REVERT: F 140 MET cc_start: 0.8594 (mtp) cc_final: 0.8104 (mtp) REVERT: F 214 MET cc_start: 0.8529 (tpp) cc_final: 0.8194 (tpp) REVERT: F 235 ILE cc_start: 0.9232 (mt) cc_final: 0.8820 (tt) REVERT: F 261 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.7928 (mmt) REVERT: G 30 TYR cc_start: 0.8501 (m-80) cc_final: 0.8043 (m-80) REVERT: G 63 ASP cc_start: 0.8350 (t0) cc_final: 0.7960 (t0) REVERT: G 110 GLU cc_start: 0.7847 (pm20) cc_final: 0.7181 (pt0) REVERT: G 121 MET cc_start: 0.7355 (tmm) cc_final: 0.7145 (tmm) REVERT: G 168 ASP cc_start: 0.8514 (p0) cc_final: 0.8028 (t0) REVERT: G 188 ILE cc_start: 0.9253 (mm) cc_final: 0.8910 (mt) REVERT: G 283 TYR cc_start: 0.7325 (t80) cc_final: 0.6988 (t80) REVERT: G 294 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8209 (tt) REVERT: G 296 ASN cc_start: 0.8293 (t0) cc_final: 0.7341 (t0) REVERT: G 300 LEU cc_start: 0.8178 (mt) cc_final: 0.7948 (mt) REVERT: G 362 ASN cc_start: 0.7485 (t0) cc_final: 0.7217 (t0) REVERT: H 1 MET cc_start: 0.2670 (mmm) cc_final: 0.1456 (tmm) REVERT: H 24 GLU cc_start: 0.6327 (tp30) cc_final: 0.6119 (tp30) REVERT: H 71 GLU cc_start: 0.6732 (mp0) cc_final: 0.6201 (pt0) REVERT: H 106 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8592 (mmm-85) REVERT: H 117 CYS cc_start: 0.8407 (OUTLIER) cc_final: 0.7369 (t) REVERT: I 7 SER cc_start: 0.9241 (p) cc_final: 0.8873 (t) REVERT: I 52 LYS cc_start: 0.7216 (pttm) cc_final: 0.6953 (pttp) REVERT: I 181 ARG cc_start: 0.8830 (tpp80) cc_final: 0.8582 (mmt90) REVERT: I 291 LYS cc_start: 0.8338 (mmtm) cc_final: 0.7232 (mttm) REVERT: I 324 ARG cc_start: 0.8179 (ttp80) cc_final: 0.7849 (ttp80) REVERT: J 1 MET cc_start: 0.1118 (tmm) cc_final: 0.0852 (mmt) REVERT: J 145 HIS cc_start: 0.8281 (OUTLIER) cc_final: 0.7703 (t70) outliers start: 74 outliers final: 39 residues processed: 469 average time/residue: 0.1815 time to fit residues: 136.1740 Evaluate side-chains 414 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 364 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 145 HIS Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 369 PHE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 341 ARG Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 145 HIS Chi-restraints excluded: chain E residue 255 ASN Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 145 HIS Chi-restraints excluded: chain F residue 152 ASN Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 259 LYS Chi-restraints excluded: chain F residue 261 MET Chi-restraints excluded: chain F residue 307 SER Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 145 HIS Chi-restraints excluded: chain G residue 274 ILE Chi-restraints excluded: chain G residue 294 LEU Chi-restraints excluded: chain H residue 106 ARG Chi-restraints excluded: chain H residue 117 CYS Chi-restraints excluded: chain H residue 145 HIS Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain H residue 243 ILE Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 145 HIS Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain J residue 145 HIS Chi-restraints excluded: chain J residue 307 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 310 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 190 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 283 optimal weight: 0.0770 chunk 123 optimal weight: 0.6980 chunk 272 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 104 optimal weight: 0.0170 chunk 84 optimal weight: 2.9990 chunk 303 optimal weight: 4.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 GLN C 112 ASN E 194 ASN E 282 GLN E 318 ASN F 15 GLN G 27 GLN ** G 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 15 GLN ** I 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 265 ASN J 112 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.139828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.109080 restraints weight = 44531.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.112493 restraints weight = 25248.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.114779 restraints weight = 18044.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.116210 restraints weight = 14706.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.116849 restraints weight = 12994.680| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 30366 Z= 0.120 Angle : 0.576 9.371 41052 Z= 0.298 Chirality : 0.042 0.207 4110 Planarity : 0.004 0.069 5476 Dihedral : 4.197 57.970 4110 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.68 % Favored : 97.30 % Rotamer: Outliers : 2.58 % Allowed : 17.58 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.14), residues: 3700 helix: 1.70 (0.15), residues: 1080 sheet: -0.45 (0.18), residues: 840 loop : 0.16 (0.16), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG I 319 TYR 0.025 0.001 TYR C 104 PHE 0.033 0.002 PHE G 62 TRP 0.016 0.001 TRP D 130 HIS 0.007 0.001 HIS G 284 Details of bonding type rmsd covalent geometry : bond 0.00281 (30366) covalent geometry : angle 0.57587 (41052) hydrogen bonds : bond 0.03819 ( 1222) hydrogen bonds : angle 4.64219 ( 3939) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 398 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 GLU cc_start: 0.7576 (tt0) cc_final: 0.6799 (pt0) REVERT: A 235 ILE cc_start: 0.9252 (mt) cc_final: 0.8871 (tt) REVERT: A 369 PHE cc_start: 0.7313 (OUTLIER) cc_final: 0.7033 (t80) REVERT: B 1 MET cc_start: 0.5424 (tmm) cc_final: 0.2271 (mmp) REVERT: B 77 MET cc_start: 0.8200 (mtp) cc_final: 0.7926 (mtt) REVERT: B 203 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7392 (pt0) REVERT: C 77 MET cc_start: 0.8152 (mmm) cc_final: 0.7812 (mmm) REVERT: C 121 MET cc_start: 0.8839 (mmp) cc_final: 0.8590 (mmp) REVERT: C 143 ASP cc_start: 0.8666 (p0) cc_final: 0.8338 (p0) REVERT: C 214 MET cc_start: 0.8483 (tpp) cc_final: 0.8088 (tpp) REVERT: C 323 ILE cc_start: 0.9112 (mm) cc_final: 0.8713 (mt) REVERT: C 353 GLU cc_start: 0.7420 (tt0) cc_final: 0.7026 (mt-10) REVERT: D 77 MET cc_start: 0.8371 (mmp) cc_final: 0.8121 (mmp) REVERT: D 79 LEU cc_start: 0.9427 (mt) cc_final: 0.9182 (mt) REVERT: D 80 HIS cc_start: 0.7776 (t-170) cc_final: 0.7503 (t-90) REVERT: D 203 GLU cc_start: 0.7678 (tt0) cc_final: 0.7272 (tt0) REVERT: D 255 ASN cc_start: 0.8604 (m-40) cc_final: 0.8284 (m110) REVERT: D 298 ARG cc_start: 0.8362 (mtp85) cc_final: 0.7985 (ttp80) REVERT: D 299 ARG cc_start: 0.7140 (OUTLIER) cc_final: 0.6867 (tmm-80) REVERT: D 338 GLU cc_start: 0.7727 (tt0) cc_final: 0.7338 (tt0) REVERT: D 341 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8692 (ttp-110) REVERT: D 353 GLU cc_start: 0.8723 (pp20) cc_final: 0.8182 (tt0) REVERT: E 121 MET cc_start: 0.7944 (mmp) cc_final: 0.7217 (mmp) REVERT: E 140 MET cc_start: 0.7904 (mtp) cc_final: 0.7648 (mtm) REVERT: E 181 ARG cc_start: 0.8824 (tpp80) cc_final: 0.8468 (tpp80) REVERT: E 214 MET cc_start: 0.8338 (tmm) cc_final: 0.8087 (tmm) REVERT: E 361 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8065 (mp) REVERT: F 77 MET cc_start: 0.7638 (mmt) cc_final: 0.6723 (mmt) REVERT: F 96 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8836 (tp) REVERT: F 140 MET cc_start: 0.8552 (mtp) cc_final: 0.7972 (mtp) REVERT: F 214 MET cc_start: 0.8457 (tpp) cc_final: 0.8134 (tpp) REVERT: F 235 ILE cc_start: 0.9225 (mt) cc_final: 0.8797 (tt) REVERT: F 261 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8220 (mmt) REVERT: G 30 TYR cc_start: 0.8489 (m-80) cc_final: 0.8104 (m-80) REVERT: G 63 ASP cc_start: 0.8219 (t0) cc_final: 0.7947 (t0) REVERT: G 168 ASP cc_start: 0.8532 (p0) cc_final: 0.8000 (t0) REVERT: G 188 ILE cc_start: 0.9255 (mm) cc_final: 0.8909 (mt) REVERT: G 283 TYR cc_start: 0.7372 (t80) cc_final: 0.7034 (t80) REVERT: G 294 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8204 (tt) REVERT: G 296 ASN cc_start: 0.8235 (t0) cc_final: 0.7275 (t0) REVERT: G 300 LEU cc_start: 0.8250 (mt) cc_final: 0.7989 (mt) REVERT: G 362 ASN cc_start: 0.7592 (t0) cc_final: 0.7183 (t0) REVERT: G 363 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7181 (tt0) REVERT: H 1 MET cc_start: 0.2536 (mmm) cc_final: 0.1398 (tmm) REVERT: H 24 GLU cc_start: 0.6366 (tp30) cc_final: 0.6153 (tp30) REVERT: H 106 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8569 (mmm-85) REVERT: H 117 CYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7381 (t) REVERT: I 7 SER cc_start: 0.9241 (p) cc_final: 0.8861 (t) REVERT: I 121 MET cc_start: 0.8285 (tpp) cc_final: 0.8030 (tpp) REVERT: I 291 LYS cc_start: 0.8235 (mmtm) cc_final: 0.7096 (mttm) REVERT: I 296 ASN cc_start: 0.8397 (t0) cc_final: 0.7935 (t0) REVERT: I 324 ARG cc_start: 0.8168 (ttp80) cc_final: 0.7872 (ttp80) REVERT: J 53 CYS cc_start: 0.7858 (p) cc_final: 0.7437 (m) REVERT: J 140 MET cc_start: 0.8307 (mtm) cc_final: 0.7951 (mtm) REVERT: J 145 HIS cc_start: 0.8336 (OUTLIER) cc_final: 0.7725 (t70) REVERT: J 311 ASP cc_start: 0.8088 (m-30) cc_final: 0.7775 (m-30) outliers start: 81 outliers final: 42 residues processed: 456 average time/residue: 0.1746 time to fit residues: 128.4815 Evaluate side-chains 424 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 371 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 145 HIS Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 369 PHE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 49 CYS Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 299 ARG Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 341 ARG Chi-restraints excluded: chain E residue 145 HIS Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain F residue 15 GLN Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 99 CYS Chi-restraints excluded: chain F residue 145 HIS Chi-restraints excluded: chain F residue 152 ASN Chi-restraints excluded: chain F residue 259 LYS Chi-restraints excluded: chain F residue 261 MET Chi-restraints excluded: chain F residue 307 SER Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 145 HIS Chi-restraints excluded: chain G residue 274 ILE Chi-restraints excluded: chain G residue 294 LEU Chi-restraints excluded: chain H residue 106 ARG Chi-restraints excluded: chain H residue 117 CYS Chi-restraints excluded: chain H residue 145 HIS Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain H residue 191 THR Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain H residue 243 ILE Chi-restraints excluded: chain H residue 261 MET Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 248 ASN Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain J residue 145 HIS Chi-restraints excluded: chain J residue 307 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 266 optimal weight: 2.9990 chunk 179 optimal weight: 9.9990 chunk 245 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 276 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 354 optimal weight: 2.9990 chunk 199 optimal weight: 0.0470 chunk 356 optimal weight: 2.9990 chunk 159 optimal weight: 6.9990 chunk 237 optimal weight: 0.2980 overall best weight: 1.4682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 74 ASN C 112 ASN ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 201 GLN J 112 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.135027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.104546 restraints weight = 45266.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.108805 restraints weight = 25732.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.110941 restraints weight = 17013.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.111158 restraints weight = 13599.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.111335 restraints weight = 13839.634| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 30366 Z= 0.219 Angle : 0.645 11.531 41052 Z= 0.333 Chirality : 0.045 0.169 4110 Planarity : 0.005 0.058 5476 Dihedral : 4.380 59.431 4110 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.89 % Favored : 97.08 % Rotamer: Outliers : 2.55 % Allowed : 17.74 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.14), residues: 3700 helix: 1.53 (0.15), residues: 1080 sheet: -0.64 (0.17), residues: 860 loop : 0.18 (0.16), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 268 TYR 0.027 0.002 TYR B 288 PHE 0.036 0.002 PHE G 62 TRP 0.021 0.002 TRP D 130 HIS 0.009 0.001 HIS G 217 Details of bonding type rmsd covalent geometry : bond 0.00525 (30366) covalent geometry : angle 0.64507 (41052) hydrogen bonds : bond 0.04380 ( 1222) hydrogen bonds : angle 4.84195 ( 3939) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 380 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 GLU cc_start: 0.7488 (tt0) cc_final: 0.6731 (pt0) REVERT: A 235 ILE cc_start: 0.9346 (mt) cc_final: 0.9017 (tt) REVERT: A 369 PHE cc_start: 0.7424 (OUTLIER) cc_final: 0.7114 (t80) REVERT: B 88 PRO cc_start: 0.9338 (Cg_endo) cc_final: 0.8970 (Cg_exo) REVERT: B 203 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7385 (pt0) REVERT: B 268 ARG cc_start: 0.8477 (ttp-110) cc_final: 0.7915 (tmt170) REVERT: B 320 SER cc_start: 0.8674 (OUTLIER) cc_final: 0.8214 (t) REVERT: C 77 MET cc_start: 0.8225 (mmm) cc_final: 0.7854 (mmm) REVERT: C 214 MET cc_start: 0.8749 (tpp) cc_final: 0.8414 (tpp) REVERT: C 353 GLU cc_start: 0.7455 (tt0) cc_final: 0.7218 (tt0) REVERT: D 77 MET cc_start: 0.8426 (mmp) cc_final: 0.8109 (mmp) REVERT: D 203 GLU cc_start: 0.7751 (tt0) cc_final: 0.7291 (tt0) REVERT: D 255 ASN cc_start: 0.8695 (m-40) cc_final: 0.8442 (m110) REVERT: D 298 ARG cc_start: 0.8404 (mtp85) cc_final: 0.8042 (ttp80) REVERT: D 353 GLU cc_start: 0.8747 (pp20) cc_final: 0.8301 (tt0) REVERT: E 121 MET cc_start: 0.8313 (mmp) cc_final: 0.7502 (mmp) REVERT: E 181 ARG cc_start: 0.8949 (tpp80) cc_final: 0.8682 (tpp80) REVERT: E 214 MET cc_start: 0.8529 (tmm) cc_final: 0.8237 (tmm) REVERT: E 361 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8156 (mp) REVERT: F 77 MET cc_start: 0.7794 (mmt) cc_final: 0.6846 (mmt) REVERT: F 87 ASP cc_start: 0.8479 (t0) cc_final: 0.8238 (t0) REVERT: F 235 ILE cc_start: 0.9265 (mt) cc_final: 0.8885 (tt) REVERT: F 261 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8149 (mmt) REVERT: G 30 TYR cc_start: 0.8558 (m-80) cc_final: 0.8163 (m-80) REVERT: G 63 ASP cc_start: 0.8193 (t0) cc_final: 0.7801 (t0) REVERT: G 84 MET cc_start: 0.8021 (tpp) cc_final: 0.7524 (ttt) REVERT: G 99 CYS cc_start: 0.8746 (m) cc_final: 0.8471 (m) REVERT: G 168 ASP cc_start: 0.8543 (p0) cc_final: 0.7949 (t0) REVERT: G 188 ILE cc_start: 0.9277 (mm) cc_final: 0.8966 (mt) REVERT: G 272 GLU cc_start: 0.6876 (mt-10) cc_final: 0.6437 (pt0) REVERT: G 283 TYR cc_start: 0.7776 (t80) cc_final: 0.7534 (t80) REVERT: G 296 ASN cc_start: 0.8443 (t0) cc_final: 0.7699 (t0) REVERT: G 357 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7764 (ttm170) REVERT: G 362 ASN cc_start: 0.8121 (t0) cc_final: 0.7693 (t0) REVERT: G 363 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7246 (tt0) REVERT: H 1 MET cc_start: 0.2514 (mmm) cc_final: 0.1715 (tmm) REVERT: H 117 CYS cc_start: 0.8592 (OUTLIER) cc_final: 0.7607 (t) REVERT: I 7 SER cc_start: 0.9242 (p) cc_final: 0.8834 (t) REVERT: I 239 ASP cc_start: 0.8500 (t0) cc_final: 0.8173 (t0) REVERT: I 291 LYS cc_start: 0.8242 (mmtm) cc_final: 0.7075 (mttm) REVERT: J 53 CYS cc_start: 0.7938 (p) cc_final: 0.7425 (m) REVERT: J 140 MET cc_start: 0.8399 (mtm) cc_final: 0.8020 (mtm) REVERT: J 145 HIS cc_start: 0.8288 (OUTLIER) cc_final: 0.7825 (t70) REVERT: J 261 MET cc_start: 0.8560 (mmt) cc_final: 0.8010 (mmt) outliers start: 80 outliers final: 59 residues processed: 434 average time/residue: 0.1793 time to fit residues: 124.5278 Evaluate side-chains 412 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 345 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 145 HIS Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 369 PHE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 49 CYS Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain E residue 145 HIS Chi-restraints excluded: chain E residue 288 TYR Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 145 HIS Chi-restraints excluded: chain F residue 152 ASN Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 259 LYS Chi-restraints excluded: chain F residue 261 MET Chi-restraints excluded: chain F residue 307 SER Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 274 ILE Chi-restraints excluded: chain G residue 357 ARG Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 117 CYS Chi-restraints excluded: chain H residue 145 HIS Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain H residue 191 THR Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain H residue 243 ILE Chi-restraints excluded: chain H residue 261 MET Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 56 GLU Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 145 HIS Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain I residue 248 ASN Chi-restraints excluded: chain I residue 261 MET Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 145 HIS Chi-restraints excluded: chain J residue 307 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 215 optimal weight: 10.0000 chunk 295 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 261 optimal weight: 0.0020 chunk 179 optimal weight: 1.9990 chunk 165 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 203 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 279 optimal weight: 1.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 74 ASN C 112 ASN E 15 GLN F 112 ASN ** G 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 112 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.138511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.107867 restraints weight = 44530.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.111246 restraints weight = 25325.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.113495 restraints weight = 18130.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.114768 restraints weight = 14807.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.115750 restraints weight = 13133.173| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 30366 Z= 0.129 Angle : 0.593 9.747 41052 Z= 0.307 Chirality : 0.043 0.179 4110 Planarity : 0.004 0.054 5476 Dihedral : 4.133 17.630 4108 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.76 % Favored : 97.22 % Rotamer: Outliers : 2.52 % Allowed : 18.02 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.14), residues: 3700 helix: 1.68 (0.16), residues: 1080 sheet: -0.50 (0.18), residues: 840 loop : 0.16 (0.16), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 268 TYR 0.032 0.001 TYR B 288 PHE 0.036 0.001 PHE G 62 TRP 0.018 0.001 TRP E 149 HIS 0.009 0.001 HIS G 284 Details of bonding type rmsd covalent geometry : bond 0.00304 (30366) covalent geometry : angle 0.59305 (41052) hydrogen bonds : bond 0.03841 ( 1222) hydrogen bonds : angle 4.59375 ( 3939) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 390 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 GLU cc_start: 0.7539 (tt0) cc_final: 0.6682 (pt0) REVERT: A 235 ILE cc_start: 0.9272 (mt) cc_final: 0.8915 (tt) REVERT: A 369 PHE cc_start: 0.7314 (OUTLIER) cc_final: 0.7020 (t80) REVERT: B 1 MET cc_start: 0.5115 (tmm) cc_final: 0.2260 (mmp) REVERT: B 140 MET cc_start: 0.7958 (mtt) cc_final: 0.7553 (mtt) REVERT: B 203 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7358 (pt0) REVERT: B 268 ARG cc_start: 0.8499 (ttp-110) cc_final: 0.7885 (tmt170) REVERT: B 320 SER cc_start: 0.8634 (OUTLIER) cc_final: 0.8262 (t) REVERT: C 77 MET cc_start: 0.8165 (mmm) cc_final: 0.7794 (mmm) REVERT: C 214 MET cc_start: 0.8575 (tpp) cc_final: 0.8263 (tpp) REVERT: C 353 GLU cc_start: 0.7512 (tt0) cc_final: 0.7168 (tt0) REVERT: D 77 MET cc_start: 0.8376 (mmp) cc_final: 0.8084 (mmp) REVERT: D 79 LEU cc_start: 0.9410 (mt) cc_final: 0.9207 (mt) REVERT: D 80 HIS cc_start: 0.7817 (t-170) cc_final: 0.7533 (t-90) REVERT: D 203 GLU cc_start: 0.7724 (tt0) cc_final: 0.7304 (tt0) REVERT: D 298 ARG cc_start: 0.8366 (mtp85) cc_final: 0.8101 (ttp80) REVERT: D 353 GLU cc_start: 0.8716 (pp20) cc_final: 0.8267 (tt0) REVERT: E 121 MET cc_start: 0.8227 (mmp) cc_final: 0.7357 (mmp) REVERT: E 181 ARG cc_start: 0.8867 (tpp80) cc_final: 0.8477 (tpp80) REVERT: E 214 MET cc_start: 0.8526 (tmm) cc_final: 0.8241 (tmm) REVERT: E 331 GLN cc_start: 0.8476 (mm-40) cc_final: 0.8140 (mt0) REVERT: F 77 MET cc_start: 0.7665 (mmt) cc_final: 0.6748 (mmt) REVERT: F 87 ASP cc_start: 0.8369 (t0) cc_final: 0.8124 (t0) REVERT: F 140 MET cc_start: 0.8605 (mtp) cc_final: 0.8074 (mtp) REVERT: F 235 ILE cc_start: 0.9225 (mt) cc_final: 0.8818 (tt) REVERT: F 261 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8341 (mmt) REVERT: G 30 TYR cc_start: 0.8511 (m-80) cc_final: 0.8126 (m-80) REVERT: G 63 ASP cc_start: 0.8229 (t0) cc_final: 0.7946 (t0) REVERT: G 84 MET cc_start: 0.8099 (tpp) cc_final: 0.7494 (ttt) REVERT: G 99 CYS cc_start: 0.8656 (m) cc_final: 0.8400 (m) REVERT: G 110 GLU cc_start: 0.7857 (pm20) cc_final: 0.7256 (pt0) REVERT: G 133 MET cc_start: 0.8067 (mmm) cc_final: 0.7679 (mmm) REVERT: G 168 ASP cc_start: 0.8568 (p0) cc_final: 0.7952 (t0) REVERT: G 188 ILE cc_start: 0.9241 (mm) cc_final: 0.8887 (mt) REVERT: G 296 ASN cc_start: 0.8408 (t0) cc_final: 0.7645 (t0) REVERT: G 362 ASN cc_start: 0.8059 (t0) cc_final: 0.7640 (t0) REVERT: G 363 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7461 (tt0) REVERT: H 1 MET cc_start: 0.2586 (mmm) cc_final: 0.1738 (tmm) REVERT: H 117 CYS cc_start: 0.8490 (OUTLIER) cc_final: 0.7480 (t) REVERT: H 214 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8162 (tmm) REVERT: I 7 SER cc_start: 0.9178 (p) cc_final: 0.8801 (t) REVERT: I 52 LYS cc_start: 0.7387 (pttp) cc_final: 0.6629 (mtmm) REVERT: I 121 MET cc_start: 0.8169 (tpp) cc_final: 0.7794 (mmp) REVERT: I 268 ARG cc_start: 0.8112 (ttm110) cc_final: 0.7867 (mtm-85) REVERT: I 291 LYS cc_start: 0.8196 (mmtm) cc_final: 0.7051 (mttm) REVERT: I 324 ARG cc_start: 0.8202 (ttp80) cc_final: 0.7831 (ttp80) REVERT: J 53 CYS cc_start: 0.7824 (p) cc_final: 0.7391 (m) REVERT: J 140 MET cc_start: 0.8275 (mtm) cc_final: 0.7912 (mtm) REVERT: J 145 HIS cc_start: 0.8345 (OUTLIER) cc_final: 0.7806 (t70) REVERT: J 261 MET cc_start: 0.8551 (mmt) cc_final: 0.7982 (mmt) REVERT: J 311 ASP cc_start: 0.7884 (m-30) cc_final: 0.7681 (m-30) outliers start: 79 outliers final: 55 residues processed: 442 average time/residue: 0.1688 time to fit residues: 121.8483 Evaluate side-chains 423 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 361 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 145 HIS Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 369 PHE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain E residue 145 HIS Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 145 HIS Chi-restraints excluded: chain F residue 152 ASN Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 259 LYS Chi-restraints excluded: chain F residue 261 MET Chi-restraints excluded: chain F residue 307 SER Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 123 MET Chi-restraints excluded: chain G residue 198 MET Chi-restraints excluded: chain G residue 274 ILE Chi-restraints excluded: chain G residue 355 ILE Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 117 CYS Chi-restraints excluded: chain H residue 145 HIS Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain H residue 191 THR Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain H residue 214 MET Chi-restraints excluded: chain H residue 243 ILE Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 56 GLU Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 145 HIS Chi-restraints excluded: chain I residue 248 ASN Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 145 HIS Chi-restraints excluded: chain J residue 267 LEU Chi-restraints excluded: chain J residue 307 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 202 optimal weight: 0.5980 chunk 110 optimal weight: 0.0060 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 221 optimal weight: 0.0970 chunk 346 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 270 optimal weight: 0.4980 chunk 10 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 chunk 362 optimal weight: 1.9990 overall best weight: 0.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 ASN D 255 ASN F 112 ASN ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 158 GLN J 112 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.139731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.109287 restraints weight = 44277.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.112739 restraints weight = 25117.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.115016 restraints weight = 17864.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.116349 restraints weight = 14527.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.117282 restraints weight = 12881.005| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 30366 Z= 0.118 Angle : 0.587 10.202 41052 Z= 0.305 Chirality : 0.042 0.173 4110 Planarity : 0.004 0.050 5476 Dihedral : 4.032 16.937 4108 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.84 % Favored : 97.14 % Rotamer: Outliers : 2.26 % Allowed : 18.72 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.14), residues: 3700 helix: 1.76 (0.16), residues: 1080 sheet: -0.39 (0.18), residues: 840 loop : 0.19 (0.16), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 268 TYR 0.032 0.001 TYR B 288 PHE 0.035 0.001 PHE G 62 TRP 0.024 0.001 TRP J 149 HIS 0.008 0.001 HIS G 284 Details of bonding type rmsd covalent geometry : bond 0.00276 (30366) covalent geometry : angle 0.58737 (41052) hydrogen bonds : bond 0.03694 ( 1222) hydrogen bonds : angle 4.50324 ( 3939) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 388 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 GLU cc_start: 0.7546 (tt0) cc_final: 0.6696 (pt0) REVERT: A 235 ILE cc_start: 0.9235 (mt) cc_final: 0.8861 (tt) REVERT: A 338 GLU cc_start: 0.8262 (tt0) cc_final: 0.8046 (tt0) REVERT: A 369 PHE cc_start: 0.7273 (OUTLIER) cc_final: 0.6972 (t80) REVERT: B 1 MET cc_start: 0.5098 (tmm) cc_final: 0.2304 (mmp) REVERT: B 77 MET cc_start: 0.8240 (mtp) cc_final: 0.7953 (mtt) REVERT: B 203 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7403 (pt0) REVERT: B 268 ARG cc_start: 0.8465 (ttp-110) cc_final: 0.7789 (tmt170) REVERT: B 320 SER cc_start: 0.8686 (OUTLIER) cc_final: 0.8302 (t) REVERT: C 77 MET cc_start: 0.8151 (mmm) cc_final: 0.7776 (mmm) REVERT: C 214 MET cc_start: 0.8566 (tpp) cc_final: 0.8193 (tpp) REVERT: C 239 ASP cc_start: 0.8438 (t0) cc_final: 0.8220 (t0) REVERT: C 288 TYR cc_start: 0.8446 (m-10) cc_final: 0.8192 (m-10) REVERT: C 353 GLU cc_start: 0.7469 (tt0) cc_final: 0.7162 (tt0) REVERT: D 77 MET cc_start: 0.8329 (mmp) cc_final: 0.8027 (mmp) REVERT: D 79 LEU cc_start: 0.9389 (mt) cc_final: 0.9170 (mt) REVERT: D 80 HIS cc_start: 0.7774 (t-170) cc_final: 0.7449 (t-90) REVERT: D 203 GLU cc_start: 0.7728 (tt0) cc_final: 0.7284 (tt0) REVERT: D 298 ARG cc_start: 0.8349 (mtp85) cc_final: 0.8107 (ttp80) REVERT: D 353 GLU cc_start: 0.8692 (pp20) cc_final: 0.8261 (tt0) REVERT: E 17 TYR cc_start: 0.8938 (m-10) cc_final: 0.8691 (m-10) REVERT: E 121 MET cc_start: 0.8168 (mmp) cc_final: 0.7250 (mmp) REVERT: E 181 ARG cc_start: 0.8875 (tpp80) cc_final: 0.8363 (tpp80) REVERT: E 214 MET cc_start: 0.8507 (tmm) cc_final: 0.8251 (tmm) REVERT: E 331 GLN cc_start: 0.8472 (mm-40) cc_final: 0.8120 (mt0) REVERT: F 77 MET cc_start: 0.7656 (mmt) cc_final: 0.6709 (mmt) REVERT: F 87 ASP cc_start: 0.8318 (t0) cc_final: 0.8079 (t70) REVERT: F 140 MET cc_start: 0.8592 (mtp) cc_final: 0.8055 (mtp) REVERT: F 214 MET cc_start: 0.8535 (tmm) cc_final: 0.8225 (tpp) REVERT: F 235 ILE cc_start: 0.9272 (mt) cc_final: 0.8843 (tt) REVERT: F 261 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.8504 (mmt) REVERT: G 30 TYR cc_start: 0.8483 (m-80) cc_final: 0.8201 (m-80) REVERT: G 63 ASP cc_start: 0.8194 (t0) cc_final: 0.7951 (t0) REVERT: G 110 GLU cc_start: 0.7887 (pm20) cc_final: 0.7205 (pt0) REVERT: G 168 ASP cc_start: 0.8580 (p0) cc_final: 0.7966 (t0) REVERT: G 188 ILE cc_start: 0.9238 (mm) cc_final: 0.8866 (mt) REVERT: G 296 ASN cc_start: 0.8375 (t0) cc_final: 0.7580 (t0) REVERT: G 362 ASN cc_start: 0.8072 (t0) cc_final: 0.7651 (t0) REVERT: G 363 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7512 (tt0) REVERT: H 1 MET cc_start: 0.2372 (mmm) cc_final: 0.1795 (tmm) REVERT: H 117 CYS cc_start: 0.8471 (OUTLIER) cc_final: 0.7467 (t) REVERT: H 214 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8199 (tmm) REVERT: I 7 SER cc_start: 0.9219 (p) cc_final: 0.8814 (t) REVERT: I 52 LYS cc_start: 0.7295 (pttp) cc_final: 0.6619 (mtmm) REVERT: I 121 MET cc_start: 0.8001 (tpp) cc_final: 0.7633 (mmp) REVERT: I 214 MET cc_start: 0.8247 (tpp) cc_final: 0.7931 (tpp) REVERT: I 268 ARG cc_start: 0.8134 (ttm110) cc_final: 0.7890 (mtm-85) REVERT: I 291 LYS cc_start: 0.8123 (mmtm) cc_final: 0.6972 (mttm) REVERT: I 324 ARG cc_start: 0.8213 (ttp80) cc_final: 0.7863 (ttp80) REVERT: J 53 CYS cc_start: 0.7853 (p) cc_final: 0.7377 (m) REVERT: J 87 ASP cc_start: 0.8548 (t0) cc_final: 0.7976 (t0) REVERT: J 140 MET cc_start: 0.8221 (mtm) cc_final: 0.8005 (mtm) REVERT: J 145 HIS cc_start: 0.8348 (OUTLIER) cc_final: 0.7712 (t70) REVERT: J 261 MET cc_start: 0.8568 (mmt) cc_final: 0.7984 (mmt) REVERT: J 311 ASP cc_start: 0.7876 (m-30) cc_final: 0.7457 (t0) outliers start: 71 outliers final: 56 residues processed: 435 average time/residue: 0.1644 time to fit residues: 116.9845 Evaluate side-chains 432 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 369 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 145 HIS Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 369 PHE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 121 MET Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 145 HIS Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain E residue 145 HIS Chi-restraints excluded: chain F residue 92 ASP Chi-restraints excluded: chain F residue 142 THR Chi-restraints excluded: chain F residue 145 HIS Chi-restraints excluded: chain F residue 152 ASN Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 259 LYS Chi-restraints excluded: chain F residue 261 MET Chi-restraints excluded: chain F residue 307 SER Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 123 MET Chi-restraints excluded: chain G residue 198 MET Chi-restraints excluded: chain G residue 274 ILE Chi-restraints excluded: chain G residue 355 ILE Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 117 CYS Chi-restraints excluded: chain H residue 145 HIS Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 190 ILE Chi-restraints excluded: chain H residue 191 THR Chi-restraints excluded: chain H residue 197 VAL Chi-restraints excluded: chain H residue 214 MET Chi-restraints excluded: chain H residue 243 ILE Chi-restraints excluded: chain H residue 261 MET Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 56 GLU Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 145 HIS Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 145 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 370 random chunks: chunk 198 optimal weight: 0.7980 chunk 78 optimal weight: 0.6980 chunk 302 optimal weight: 3.9990 chunk 336 optimal weight: 3.9990 chunk 326 optimal weight: 0.6980 chunk 308 optimal weight: 0.0670 chunk 304 optimal weight: 0.9980 chunk 102 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 237 optimal weight: 0.5980 chunk 357 optimal weight: 1.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 74 ASN C 112 ASN F 112 ASN F 217 HIS ** G 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 112 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.139600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.109169 restraints weight = 44406.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.112518 restraints weight = 25199.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.114765 restraints weight = 18048.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.116080 restraints weight = 14721.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.117006 restraints weight = 13066.720| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 30366 Z= 0.126 Angle : 0.587 10.239 41052 Z= 0.302 Chirality : 0.042 0.163 4110 Planarity : 0.004 0.047 5476 Dihedral : 3.962 19.640 4108 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.86 % Favored : 97.11 % Rotamer: Outliers : 2.26 % Allowed : 18.69 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.14), residues: 3700 helix: 1.82 (0.16), residues: 1080 sheet: -0.35 (0.18), residues: 840 loop : 0.21 (0.16), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 286 TYR 0.031 0.001 TYR B 288 PHE 0.035 0.001 PHE G 62 TRP 0.017 0.001 TRP E 149 HIS 0.008 0.001 HIS G 284 Details of bonding type rmsd covalent geometry : bond 0.00299 (30366) covalent geometry : angle 0.58730 (41052) hydrogen bonds : bond 0.03634 ( 1222) hydrogen bonds : angle 4.46596 ( 3939) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4227.01 seconds wall clock time: 74 minutes 16.67 seconds (4456.67 seconds total)