Starting phenix.real_space_refine on Tue May 27 09:29:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xlj_38450/05_2025/8xlj_38450_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xlj_38450/05_2025/8xlj_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_38450/05_2025/8xlj_38450.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xlj_38450/05_2025/8xlj_38450.map" model { file = "/net/cci-nas-00/data/ceres_data/8xlj_38450/05_2025/8xlj_38450_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xlj_38450/05_2025/8xlj_38450_neut.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLU:plan': 1, 'ARG:plan': 2} 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: 16.64, per 1000 atoms: 0.56 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: 6.27 Conformation dependent library (CDL) restraints added in 3.6 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: 3.76 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: 11.44 Time building geometry restraints manager: 7.47 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: 4.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.980 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 62.020 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.120 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:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.830 ------------------------------------------------------------------------------- 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 : 12.27 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.051 0.002 TRP E 149 HIS 0.013 0.001 HIS D 80 PHE 0.032 0.002 PHE C 312 TYR 0.039 0.002 TYR J 288 ARG 0.061 0.001 ARG E 280 Details of bonding type rmsd hydrogen bonds : bond 0.15385 ( 1222) hydrogen bonds : angle 7.23972 ( 3939) covalent geometry : bond 0.00431 (30366) covalent geometry : angle 0.86706 (41052) *********************** 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 : 3.327 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: 0.8155 (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: 0.7462 (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: 0.3994 time to fit residues: 327.6652 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 : 3.252 ------------------------------------------------------------------------------- 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 312 optimal weight: 0.9980 chunk 280 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 189 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 290 optimal weight: 2.9990 chunk 112 optimal weight: 0.5980 chunk 176 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 chunk 336 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 ASN E 15 GLN E 158 GLN F 22 GLN F 112 ASN G 22 GLN G 253 HIS 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 = 0.3703 r_free = 0.3703 target = 0.144575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.113313 restraints weight = 44296.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.116566 restraints weight = 25426.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.118943 restraints weight = 18336.175| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 30366 Z= 0.211 Angle : 0.690 10.128 41052 Z= 0.360 Chirality : 0.046 0.186 4110 Planarity : 0.006 0.106 5476 Dihedral : 4.777 56.302 4127 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.03 % Favored : 97.95 % Rotamer: Outliers : 2.07 % Allowed : 15.53 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.14), residues: 3700 helix: 1.33 (0.16), residues: 1080 sheet: -0.23 (0.17), residues: 840 loop : 0.22 (0.16), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 130 HIS 0.011 0.001 HIS I 217 PHE 0.027 0.002 PHE G 62 TYR 0.042 0.002 TYR A 288 ARG 0.013 0.001 ARG D 357 Details of bonding type rmsd hydrogen bonds : bond 0.04988 ( 1222) hydrogen bonds : angle 5.40807 ( 3939) covalent geometry : bond 0.00506 (30366) covalent geometry : angle 0.68967 (41052) *********************** 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 478 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 413 time to evaluate : 3.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 133 MET cc_start: 0.7892 (mmm) cc_final: 0.7639 (mmm) REVERT: B 288 TYR cc_start: 0.8193 (m-10) cc_final: 0.7912 (m-10) REVERT: C 52 LYS cc_start: 0.7779 (mptt) cc_final: 0.7438 (mppt) REVERT: C 87 ASP cc_start: 0.8647 (t0) cc_final: 0.8442 (t0) REVERT: C 99 CYS cc_start: 0.8649 (m) cc_final: 0.8338 (m) REVERT: C 203 GLU cc_start: 0.7907 (tt0) cc_final: 0.7682 (tt0) REVERT: C 288 TYR cc_start: 0.8625 (m-10) cc_final: 0.8194 (m-10) REVERT: C 296 ASN cc_start: 0.8077 (t0) cc_final: 0.7863 (t0) REVERT: D 1 MET cc_start: 0.3610 (tmm) cc_final: 0.2309 (mmm) REVERT: D 84 MET cc_start: 0.7863 (tmm) cc_final: 0.7533 (tmm) REVERT: D 265 ASN cc_start: 0.8136 (t0) cc_final: 0.7814 (t0) REVERT: D 341 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.8410 (ttp-110) REVERT: E 92 ASP cc_start: 0.8385 (m-30) cc_final: 0.8183 (m-30) REVERT: E 311 ASP cc_start: 0.6371 (t0) cc_final: 0.5985 (m-30) REVERT: E 312 PHE cc_start: 0.7861 (t80) cc_final: 0.7500 (t80) REVERT: E 360 LEU cc_start: 0.8592 (mt) cc_final: 0.8122 (tt) REVERT: F 15 GLN cc_start: 0.8456 (tp-100) cc_final: 0.7602 (mm-40) REVERT: F 140 MET cc_start: 0.8508 (mtp) cc_final: 0.7949 (mtp) REVERT: F 261 MET cc_start: 0.8507 (mmt) cc_final: 0.8033 (mmt) REVERT: G 30 TYR cc_start: 0.8407 (m-80) cc_final: 0.8068 (m-80) REVERT: G 63 ASP cc_start: 0.8208 (t0) cc_final: 0.7700 (t0) REVERT: G 84 MET cc_start: 0.8028 (ttt) cc_final: 0.7559 (ttt) REVERT: G 133 MET cc_start: 0.7798 (mtp) cc_final: 0.7591 (mtp) REVERT: G 362 ASN cc_start: 0.6818 (t0) cc_final: 0.6586 (t0) REVERT: H 117 CYS cc_start: 0.8505 (OUTLIER) cc_final: 0.7321 (t) REVERT: H 214 MET cc_start: 0.8561 (tpp) cc_final: 0.8278 (tmm) REVERT: I 213 ARG cc_start: 0.7877 (mtm180) cc_final: 0.7669 (mtp85) REVERT: I 291 LYS cc_start: 0.8459 (mmtm) cc_final: 0.7279 (mttp) REVERT: I 296 ASN cc_start: 0.8273 (t0) cc_final: 0.7991 (t0) REVERT: J 140 MET cc_start: 0.8244 (mtp) cc_final: 0.8000 (mtm) REVERT: J 214 MET cc_start: 0.9191 (tpp) cc_final: 0.8880 (tpp) outliers start: 65 outliers final: 39 residues processed: 458 average time/residue: 0.3847 time to fit residues: 284.8109 Evaluate side-chains 403 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 362 time to evaluate : 3.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 53 CYS 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 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 151 SER 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 D residue 343 SER 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 255 ASN Chi-restraints excluded: chain E residue 294 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 270 ILE Chi-restraints excluded: chain G residue 123 MET Chi-restraints excluded: chain G residue 294 LEU Chi-restraints excluded: chain G residue 316 VAL Chi-restraints excluded: chain H residue 117 CYS 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 I residue 7 SER Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 190 ILE 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 16 optimal weight: 2.9990 chunk 233 optimal weight: 0.9990 chunk 159 optimal weight: 5.9990 chunk 322 optimal weight: 9.9990 chunk 127 optimal weight: 2.9990 chunk 325 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 238 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 323 optimal weight: 0.9990 chunk 123 optimal weight: 0.0670 overall best weight: 0.9724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN C 69 GLN ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 15 GLN D 22 GLN E 15 GLN E 158 GLN ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN ** I 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 27 GLN J 112 ASN ** J 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.142772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.111838 restraints weight = 44227.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.115207 restraints weight = 25300.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.117449 restraints weight = 18221.911| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 30366 Z= 0.162 Angle : 0.606 7.002 41052 Z= 0.316 Chirality : 0.044 0.170 4110 Planarity : 0.004 0.056 5476 Dihedral : 4.299 58.483 4110 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.73 % Favored : 97.24 % Rotamer: Outliers : 2.46 % Allowed : 15.69 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.14), residues: 3700 helix: 1.60 (0.15), residues: 1080 sheet: -0.21 (0.17), residues: 840 loop : 0.23 (0.16), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 130 HIS 0.007 0.001 HIS G 217 PHE 0.026 0.002 PHE G 62 TYR 0.026 0.001 TYR J 288 ARG 0.006 0.000 ARG C 91 Details of bonding type rmsd hydrogen bonds : bond 0.04392 ( 1222) hydrogen bonds : angle 4.98121 ( 3939) covalent geometry : bond 0.00384 (30366) covalent geometry : angle 0.60606 (41052) *********************** 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 475 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 398 time to evaluate : 3.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3375 (tpt) cc_final: 0.2964 (tpt) REVERT: A 261 MET cc_start: 0.8623 (mtt) cc_final: 0.8101 (mtt) REVERT: B 77 MET cc_start: 0.8073 (mtp) cc_final: 0.7840 (mtt) REVERT: B 88 PRO cc_start: 0.9160 (Cg_endo) cc_final: 0.8681 (Cg_exo) REVERT: B 203 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7485 (pt0) REVERT: C 18 MET cc_start: 0.9013 (mmt) cc_final: 0.8792 (mmt) REVERT: C 52 LYS cc_start: 0.7865 (mptt) cc_final: 0.7499 (mppt) REVERT: C 92 ASP cc_start: 0.8291 (OUTLIER) cc_final: 0.7976 (m-30) REVERT: C 143 ASP cc_start: 0.8505 (p0) cc_final: 0.8265 (p0) REVERT: C 214 MET cc_start: 0.8894 (tpp) cc_final: 0.8645 (tpp) REVERT: C 323 ILE cc_start: 0.9034 (mm) cc_final: 0.8682 (mt) REVERT: D 1 MET cc_start: 0.3748 (tmm) cc_final: 0.3273 (mmm) REVERT: D 87 ASP cc_start: 0.8938 (t0) cc_final: 0.8736 (t0) REVERT: D 203 GLU cc_start: 0.7637 (tt0) cc_final: 0.7217 (tt0) REVERT: D 255 ASN cc_start: 0.8642 (m-40) cc_final: 0.8292 (m-40) REVERT: D 265 ASN cc_start: 0.8179 (t0) cc_final: 0.7828 (t0) REVERT: D 353 GLU cc_start: 0.8629 (pp20) cc_final: 0.8416 (tm-30) REVERT: E 140 MET cc_start: 0.7963 (mtp) cc_final: 0.7667 (mtm) REVERT: E 205 GLN cc_start: 0.8611 (mp10) cc_final: 0.8330 (mt0) REVERT: E 361 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7768 (mp) REVERT: F 15 GLN cc_start: 0.8422 (tp-100) cc_final: 0.7987 (tp40) REVERT: F 77 MET cc_start: 0.7873 (mmm) cc_final: 0.7022 (mmt) REVERT: F 121 MET cc_start: 0.7832 (mmt) cc_final: 0.7502 (mmp) REVERT: F 261 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.7811 (mmt) REVERT: F 288 TYR cc_start: 0.8330 (m-10) cc_final: 0.7945 (m-80) REVERT: G 30 TYR cc_start: 0.8467 (m-80) cc_final: 0.8104 (m-80) REVERT: G 63 ASP cc_start: 0.8185 (t0) cc_final: 0.7725 (t0) REVERT: G 77 MET cc_start: 0.8385 (mmm) cc_final: 0.8039 (mmm) REVERT: G 133 MET cc_start: 0.7784 (mtp) cc_final: 0.7505 (mtp) REVERT: G 362 ASN cc_start: 0.7246 (t0) cc_final: 0.6945 (t0) REVERT: H 24 GLU cc_start: 0.6299 (tp30) cc_final: 0.6061 (tp30) REVERT: H 87 ASP cc_start: 0.8721 (t0) cc_final: 0.8450 (t0) REVERT: H 117 CYS cc_start: 0.8478 (OUTLIER) cc_final: 0.7242 (t) REVERT: I 104 TYR cc_start: 0.7554 (p90) cc_final: 0.7307 (p90) REVERT: I 121 MET cc_start: 0.8580 (tpp) cc_final: 0.7924 (mmt) REVERT: I 213 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7621 (mtp85) REVERT: I 291 LYS cc_start: 0.8335 (mmtm) cc_final: 0.7277 (mttp) REVERT: I 296 ASN cc_start: 0.8251 (t0) cc_final: 0.7933 (t0) REVERT: J 214 MET cc_start: 0.9141 (tpp) cc_final: 0.8587 (tpp) outliers start: 77 outliers final: 42 residues processed: 453 average time/residue: 0.3995 time to fit residues: 292.4555 Evaluate side-chains 409 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 361 time to evaluate : 3.113 ------------------------------------------------------------------------------- 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 44 THR 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 145 HIS Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 44 THR 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 301 THR Chi-restraints excluded: chain D residue 343 SER 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 255 ASN Chi-restraints excluded: chain E residue 361 LEU Chi-restraints excluded: chain F residue 112 ASN 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 328 ILE Chi-restraints excluded: chain G residue 145 HIS 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 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 I residue 44 THR Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 198 MET Chi-restraints excluded: chain I residue 213 ARG Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain J residue 44 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 125 optimal weight: 1.9990 chunk 277 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 300 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 173 optimal weight: 0.6980 chunk 365 optimal weight: 0.0370 chunk 145 optimal weight: 0.8980 chunk 24 optimal weight: 0.2980 chunk 353 optimal weight: 0.6980 chunk 338 optimal weight: 0.0980 overall best weight: 0.3658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN C 112 ASN E 27 GLN E 158 GLN ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 80 HIS ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 296 ASN H 15 GLN H 27 GLN ** I 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 112 ASN J 296 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.145088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.114031 restraints weight = 44325.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.117587 restraints weight = 25504.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.119903 restraints weight = 18135.491| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30366 Z= 0.113 Angle : 0.569 9.938 41052 Z= 0.294 Chirality : 0.042 0.165 4110 Planarity : 0.004 0.056 5476 Dihedral : 4.124 57.444 4110 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.05 % Favored : 97.92 % Rotamer: Outliers : 2.36 % Allowed : 16.24 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.14), residues: 3700 helix: 1.77 (0.16), residues: 1080 sheet: -0.16 (0.17), residues: 840 loop : 0.23 (0.16), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 130 HIS 0.006 0.001 HIS D 80 PHE 0.026 0.001 PHE G 62 TYR 0.026 0.001 TYR C 104 ARG 0.006 0.000 ARG H 340 Details of bonding type rmsd hydrogen bonds : bond 0.03880 ( 1222) hydrogen bonds : angle 4.70949 ( 3939) covalent geometry : bond 0.00263 (30366) covalent geometry : angle 0.56905 (41052) *********************** 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 486 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 412 time to evaluate : 3.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3049 (tpt) cc_final: 0.2697 (tpt) REVERT: B 77 MET cc_start: 0.8061 (mtp) cc_final: 0.7828 (mtt) REVERT: B 133 MET cc_start: 0.7881 (mmm) cc_final: 0.7614 (mmm) REVERT: B 203 GLU cc_start: 0.7893 (tt0) cc_final: 0.7526 (pt0) REVERT: C 52 LYS cc_start: 0.7940 (mptt) cc_final: 0.7561 (mppt) REVERT: C 77 MET cc_start: 0.7922 (mmm) cc_final: 0.7468 (mmm) REVERT: C 92 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.7917 (m-30) REVERT: C 143 ASP cc_start: 0.8531 (p0) cc_final: 0.8255 (p0) REVERT: D 1 MET cc_start: 0.3712 (tmm) cc_final: 0.2440 (mmm) REVERT: D 185 TYR cc_start: 0.9106 (t80) cc_final: 0.8898 (t80) REVERT: D 203 GLU cc_start: 0.7543 (tt0) cc_final: 0.7093 (tt0) REVERT: D 255 ASN cc_start: 0.8668 (m-40) cc_final: 0.8400 (m110) REVERT: D 265 ASN cc_start: 0.8183 (t0) cc_final: 0.7764 (t0) REVERT: D 267 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8532 (mt) REVERT: D 341 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.8388 (ttp-110) REVERT: D 353 GLU cc_start: 0.8665 (pp20) cc_final: 0.7965 (tt0) REVERT: E 36 THR cc_start: 0.9192 (p) cc_final: 0.8907 (t) REVERT: E 121 MET cc_start: 0.7543 (OUTLIER) cc_final: 0.6942 (mmp) REVERT: E 133 MET cc_start: 0.8427 (mmm) cc_final: 0.8221 (mmm) REVERT: E 140 MET cc_start: 0.7863 (mtp) cc_final: 0.7643 (mtm) REVERT: E 205 GLN cc_start: 0.8622 (mp10) cc_final: 0.8353 (mt0) REVERT: E 312 PHE cc_start: 0.7741 (t80) cc_final: 0.7425 (t80) REVERT: E 361 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7723 (mp) REVERT: F 15 GLN cc_start: 0.8370 (tp-100) cc_final: 0.7901 (tp40) REVERT: F 77 MET cc_start: 0.7760 (mmm) cc_final: 0.6945 (mmt) REVERT: F 121 MET cc_start: 0.7695 (mmt) cc_final: 0.7494 (mmp) REVERT: F 214 MET cc_start: 0.8290 (tpp) cc_final: 0.7919 (tpp) REVERT: F 261 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.7778 (mmt) REVERT: G 30 TYR cc_start: 0.8434 (m-80) cc_final: 0.8113 (m-80) REVERT: G 63 ASP cc_start: 0.8167 (t0) cc_final: 0.7767 (t0) REVERT: G 77 MET cc_start: 0.8449 (mmm) cc_final: 0.8244 (mmm) REVERT: G 133 MET cc_start: 0.7767 (mtp) cc_final: 0.7524 (mtp) REVERT: G 294 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.8001 (tt) REVERT: G 362 ASN cc_start: 0.7165 (t0) cc_final: 0.6838 (t0) REVERT: H 24 GLU cc_start: 0.6239 (tp30) cc_final: 0.5761 (tp30) REVERT: H 117 CYS cc_start: 0.8370 (OUTLIER) cc_final: 0.7165 (t) REVERT: H 130 TRP cc_start: 0.8719 (m-10) cc_final: 0.8441 (m-10) REVERT: H 337 PHE cc_start: 0.8549 (p90) cc_final: 0.8183 (p90) REVERT: I 57 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9191 (mm) REVERT: I 104 TYR cc_start: 0.7548 (p90) cc_final: 0.7294 (p90) REVERT: I 180 TYR cc_start: 0.8848 (t80) cc_final: 0.8412 (t80) REVERT: I 213 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7558 (mtp85) REVERT: I 291 LYS cc_start: 0.8272 (mmtm) cc_final: 0.7208 (mttp) REVERT: J 133 MET cc_start: 0.8056 (mmm) cc_final: 0.7204 (mtp) REVERT: J 140 MET cc_start: 0.8129 (mtm) cc_final: 0.7787 (mtm) REVERT: J 145 HIS cc_start: 0.8310 (OUTLIER) cc_final: 0.7787 (t70) REVERT: J 282 GLN cc_start: 0.8476 (tp40) cc_final: 0.8262 (tp40) outliers start: 74 outliers final: 39 residues processed: 469 average time/residue: 0.4187 time to fit residues: 317.7377 Evaluate side-chains 425 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 375 time to evaluate : 3.039 ------------------------------------------------------------------------------- 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 191 THR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 99 CYS Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 145 HIS 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 255 ASN Chi-restraints excluded: chain E residue 288 TYR Chi-restraints excluded: chain E residue 361 LEU 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 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 44 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 243 ILE Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 145 HIS Chi-restraints excluded: chain I residue 213 ARG 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 351 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 266 optimal weight: 1.9990 chunk 322 optimal weight: 10.0000 chunk 321 optimal weight: 2.9990 chunk 365 optimal weight: 1.9990 chunk 332 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 238 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 189 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN C 27 GLN ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 ASN ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN F 253 HIS ** H 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 253 HIS H 281 HIS ** I 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 194 ASN J 27 GLN J 112 ASN J 255 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.137960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.107186 restraints weight = 44464.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.110476 restraints weight = 25797.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.112545 restraints weight = 18558.673| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 30366 Z= 0.207 Angle : 0.634 8.438 41052 Z= 0.327 Chirality : 0.045 0.163 4110 Planarity : 0.005 0.053 5476 Dihedral : 4.277 59.713 4110 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.84 % Favored : 97.14 % Rotamer: Outliers : 2.90 % Allowed : 16.24 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.14), residues: 3700 helix: 1.64 (0.16), residues: 1080 sheet: -0.30 (0.18), residues: 840 loop : 0.23 (0.16), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 130 HIS 0.009 0.001 HIS G 217 PHE 0.026 0.002 PHE G 62 TYR 0.028 0.002 TYR G 349 ARG 0.015 0.001 ARG H 90 Details of bonding type rmsd hydrogen bonds : bond 0.04396 ( 1222) hydrogen bonds : angle 4.85545 ( 3939) covalent geometry : bond 0.00496 (30366) covalent geometry : angle 0.63426 (41052) *********************** 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 485 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 394 time to evaluate : 3.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 GLU cc_start: 0.7647 (tt0) cc_final: 0.7057 (pt0) REVERT: A 235 ILE cc_start: 0.9333 (mt) cc_final: 0.8895 (tt) REVERT: A 369 PHE cc_start: 0.7418 (OUTLIER) cc_final: 0.7144 (t80) REVERT: B 77 MET cc_start: 0.8210 (mtp) cc_final: 0.7943 (mtt) REVERT: B 88 PRO cc_start: 0.9237 (Cg_endo) cc_final: 0.8823 (Cg_exo) REVERT: B 140 MET cc_start: 0.7773 (mtt) cc_final: 0.7396 (mtt) REVERT: B 203 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7442 (pt0) REVERT: C 52 LYS cc_start: 0.8046 (mptt) cc_final: 0.7623 (mppt) REVERT: C 92 ASP cc_start: 0.8245 (OUTLIER) cc_final: 0.7850 (m-30) REVERT: C 143 ASP cc_start: 0.8716 (p0) cc_final: 0.8436 (p0) REVERT: C 203 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7756 (pt0) REVERT: C 214 MET cc_start: 0.8964 (tpp) cc_final: 0.8202 (tpp) REVERT: D 1 MET cc_start: 0.3993 (tmm) cc_final: 0.2965 (mmm) REVERT: D 112 ASN cc_start: 0.8158 (t0) cc_final: 0.7906 (t0) REVERT: D 203 GLU cc_start: 0.7691 (tt0) cc_final: 0.7122 (tt0) REVERT: D 255 ASN cc_start: 0.8739 (m-40) cc_final: 0.8534 (m110) REVERT: D 265 ASN cc_start: 0.8273 (t0) cc_final: 0.7814 (t0) REVERT: D 341 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.8557 (ttp-110) REVERT: D 353 GLU cc_start: 0.8729 (pp20) cc_final: 0.8086 (tt0) REVERT: E 36 THR cc_start: 0.9225 (p) cc_final: 0.8855 (t) REVERT: E 133 MET cc_start: 0.8475 (mmm) cc_final: 0.8228 (mmm) REVERT: E 181 ARG cc_start: 0.8903 (tpp80) cc_final: 0.8638 (tpp80) REVERT: E 198 MET cc_start: 0.7974 (ptm) cc_final: 0.7626 (ptm) REVERT: E 201 GLN cc_start: 0.8781 (mt0) cc_final: 0.8120 (mt0) REVERT: E 282 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8013 (mm-40) REVERT: E 361 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8153 (mp) REVERT: F 15 GLN cc_start: 0.8572 (tp-100) cc_final: 0.8059 (tp40) REVERT: F 87 ASP cc_start: 0.8565 (t0) cc_final: 0.8138 (t0) REVERT: F 261 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.7932 (mmt) REVERT: G 30 TYR cc_start: 0.8523 (m-80) cc_final: 0.8182 (m-80) REVERT: G 63 ASP cc_start: 0.8302 (t0) cc_final: 0.7876 (t0) REVERT: G 77 MET cc_start: 0.8542 (mmm) cc_final: 0.8125 (mmm) REVERT: G 84 MET cc_start: 0.7922 (ttt) cc_final: 0.7593 (ttt) REVERT: G 133 MET cc_start: 0.7767 (mtp) cc_final: 0.7544 (mtp) REVERT: G 294 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7909 (tt) REVERT: G 296 ASN cc_start: 0.8201 (t0) cc_final: 0.7671 (t0) REVERT: G 362 ASN cc_start: 0.7388 (t0) cc_final: 0.7057 (t0) REVERT: H 24 GLU cc_start: 0.6391 (tp30) cc_final: 0.5912 (tp30) REVERT: H 71 GLU cc_start: 0.6765 (mp0) cc_final: 0.6059 (pt0) REVERT: H 106 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.8547 (mmm-85) REVERT: H 117 CYS cc_start: 0.8543 (OUTLIER) cc_final: 0.7467 (t) REVERT: H 214 MET cc_start: 0.8660 (tpp) cc_final: 0.8324 (tmm) REVERT: H 252 CYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8627 (t) REVERT: I 7 SER cc_start: 0.9237 (p) cc_final: 0.8824 (t) REVERT: I 57 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9287 (mm) REVERT: I 180 TYR cc_start: 0.9021 (t80) cc_final: 0.8804 (t80) REVERT: I 213 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.7590 (mtp85) REVERT: I 239 ASP cc_start: 0.8458 (t0) cc_final: 0.8142 (t0) REVERT: I 291 LYS cc_start: 0.8267 (mmtm) cc_final: 0.7157 (mttp) REVERT: J 106 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7739 (mpt180) REVERT: J 140 MET cc_start: 0.8380 (mtm) cc_final: 0.8061 (mtm) REVERT: J 145 HIS cc_start: 0.8346 (OUTLIER) cc_final: 0.7782 (t70) outliers start: 91 outliers final: 60 residues processed: 463 average time/residue: 0.4054 time to fit residues: 301.1096 Evaluate side-chains 428 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 352 time to evaluate : 3.222 ------------------------------------------------------------------------------- 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 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 C residue 4 SER Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 203 GLU Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 111 THR 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 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 282 GLN 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 112 ASN 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 44 THR Chi-restraints excluded: chain G residue 123 MET Chi-restraints excluded: chain G residue 145 HIS Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 274 ILE Chi-restraints excluded: chain G residue 294 LEU 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 123 MET 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 252 CYS Chi-restraints excluded: chain H residue 285 ILE Chi-restraints excluded: chain H residue 316 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 145 HIS Chi-restraints excluded: chain I residue 213 ARG 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 79 LEU Chi-restraints excluded: chain J residue 106 ARG 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 19 optimal weight: 0.6980 chunk 156 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 201 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 192 optimal weight: 5.9990 chunk 139 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 74 ASN C 112 ASN E 15 GLN ** E 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 ASN ** H 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 158 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 = 0.3637 r_free = 0.3637 target = 0.139058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.108238 restraints weight = 44710.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.111668 restraints weight = 25412.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.113936 restraints weight = 18040.191| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 30366 Z= 0.150 Angle : 0.588 8.525 41052 Z= 0.303 Chirality : 0.043 0.187 4110 Planarity : 0.004 0.056 5476 Dihedral : 4.201 59.491 4110 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.62 % Favored : 97.35 % Rotamer: Outliers : 2.78 % Allowed : 16.84 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.14), residues: 3700 helix: 1.71 (0.16), residues: 1080 sheet: -0.44 (0.17), residues: 860 loop : 0.25 (0.16), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 130 HIS 0.009 0.001 HIS D 80 PHE 0.030 0.002 PHE G 62 TYR 0.027 0.001 TYR G 349 ARG 0.005 0.000 ARG I 319 Details of bonding type rmsd hydrogen bonds : bond 0.04012 ( 1222) hydrogen bonds : angle 4.69194 ( 3939) covalent geometry : bond 0.00359 (30366) covalent geometry : angle 0.58833 (41052) *********************** 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 477 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 390 time to evaluate : 3.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 GLU cc_start: 0.7567 (tt0) cc_final: 0.6980 (pt0) REVERT: A 235 ILE cc_start: 0.9304 (mt) cc_final: 0.8878 (tt) REVERT: A 369 PHE cc_start: 0.7382 (OUTLIER) cc_final: 0.7106 (t80) REVERT: B 77 MET cc_start: 0.8174 (mtp) cc_final: 0.7868 (mtt) REVERT: B 88 PRO cc_start: 0.9227 (Cg_endo) cc_final: 0.8831 (Cg_exo) REVERT: B 140 MET cc_start: 0.7803 (mtt) cc_final: 0.7438 (mtt) REVERT: B 203 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7392 (pt0) REVERT: C 18 MET cc_start: 0.8984 (mmt) cc_final: 0.8747 (mmt) REVERT: C 52 LYS cc_start: 0.8076 (mptt) cc_final: 0.7675 (mppt) REVERT: C 92 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.7918 (m-30) REVERT: C 143 ASP cc_start: 0.8690 (p0) cc_final: 0.8392 (p0) REVERT: D 1 MET cc_start: 0.4000 (tmm) cc_final: 0.2976 (mmm) REVERT: D 80 HIS cc_start: 0.7707 (t-170) cc_final: 0.7460 (t-90) REVERT: D 203 GLU cc_start: 0.7704 (tt0) cc_final: 0.7185 (tt0) REVERT: D 255 ASN cc_start: 0.8659 (m-40) cc_final: 0.8379 (m110) REVERT: D 265 ASN cc_start: 0.8241 (t0) cc_final: 0.7789 (t0) REVERT: D 341 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8580 (ttp-110) REVERT: D 353 GLU cc_start: 0.8759 (pp20) cc_final: 0.8173 (tt0) REVERT: E 36 THR cc_start: 0.9212 (p) cc_final: 0.8873 (t) REVERT: E 121 MET cc_start: 0.7977 (mmp) cc_final: 0.7260 (mmp) REVERT: E 133 MET cc_start: 0.8471 (mmm) cc_final: 0.8151 (mmm) REVERT: E 181 ARG cc_start: 0.8874 (tpp80) cc_final: 0.8610 (tpp80) REVERT: E 282 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7998 (mm-40) REVERT: E 356 VAL cc_start: 0.8876 (p) cc_final: 0.8600 (p) REVERT: E 361 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8107 (mp) REVERT: F 15 GLN cc_start: 0.8498 (tp-100) cc_final: 0.7957 (tp40) REVERT: F 77 MET cc_start: 0.8115 (mmm) cc_final: 0.7176 (mmt) REVERT: F 87 ASP cc_start: 0.8582 (t0) cc_final: 0.7854 (t0) REVERT: F 121 MET cc_start: 0.8013 (mmt) cc_final: 0.7674 (mmp) REVERT: F 140 MET cc_start: 0.8562 (mtp) cc_final: 0.8192 (mtp) REVERT: F 261 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.7993 (mmt) REVERT: F 288 TYR cc_start: 0.8019 (m-80) cc_final: 0.7747 (m-80) REVERT: G 30 TYR cc_start: 0.8501 (m-80) cc_final: 0.8144 (m-80) REVERT: G 63 ASP cc_start: 0.8273 (t0) cc_final: 0.7849 (t0) REVERT: G 84 MET cc_start: 0.7876 (ttt) cc_final: 0.7521 (ttt) REVERT: G 168 ASP cc_start: 0.8296 (p0) cc_final: 0.7930 (t0) REVERT: G 294 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8128 (tt) REVERT: G 296 ASN cc_start: 0.8188 (t0) cc_final: 0.7590 (t0) REVERT: G 362 ASN cc_start: 0.7451 (t0) cc_final: 0.7123 (t0) REVERT: H 24 GLU cc_start: 0.6488 (tp30) cc_final: 0.6226 (tp30) REVERT: H 71 GLU cc_start: 0.7129 (mp0) cc_final: 0.6286 (pt0) REVERT: H 106 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8555 (mmm-85) REVERT: H 117 CYS cc_start: 0.8473 (OUTLIER) cc_final: 0.7420 (t) REVERT: H 214 MET cc_start: 0.8669 (tpp) cc_final: 0.8265 (tmm) REVERT: I 7 SER cc_start: 0.9238 (p) cc_final: 0.8844 (t) REVERT: I 49 CYS cc_start: 0.8275 (m) cc_final: 0.7766 (p) REVERT: I 57 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9248 (mm) REVERT: I 121 MET cc_start: 0.8350 (tpp) cc_final: 0.8022 (tpp) REVERT: I 291 LYS cc_start: 0.8286 (mmtm) cc_final: 0.7111 (mttm) REVERT: J 106 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7724 (mpt180) REVERT: J 140 MET cc_start: 0.8346 (mtm) cc_final: 0.8126 (mtm) REVERT: J 145 HIS cc_start: 0.8322 (OUTLIER) cc_final: 0.7760 (t70) outliers start: 87 outliers final: 52 residues processed: 456 average time/residue: 0.3913 time to fit residues: 287.8362 Evaluate side-chains 425 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 360 time to evaluate : 3.403 ------------------------------------------------------------------------------- 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 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 203 GLU Chi-restraints excluded: chain B residue 288 TYR Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain D residue 34 ASP Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 123 MET 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 D residue 341 ARG Chi-restraints excluded: chain E residue 145 HIS Chi-restraints excluded: chain E residue 255 ASN Chi-restraints excluded: chain E residue 282 GLN 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 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 193 THR Chi-restraints excluded: chain G residue 274 ILE Chi-restraints excluded: chain G residue 294 LEU 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 I residue 44 THR Chi-restraints excluded: chain I residue 57 LEU Chi-restraints excluded: chain I residue 145 HIS 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 106 ARG 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 68 optimal weight: 3.9990 chunk 278 optimal weight: 0.9990 chunk 361 optimal weight: 0.9980 chunk 199 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 185 optimal weight: 4.9990 chunk 214 optimal weight: 4.9990 chunk 285 optimal weight: 5.9990 chunk 209 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN ** A 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 ASN E 15 GLN ** E 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 318 ASN ** H 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 265 ASN J 112 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.138391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.107822 restraints weight = 44555.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.111248 restraints weight = 25330.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.113526 restraints weight = 17986.831| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 30366 Z= 0.153 Angle : 0.587 9.492 41052 Z= 0.303 Chirality : 0.043 0.183 4110 Planarity : 0.004 0.053 5476 Dihedral : 4.173 58.281 4110 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.68 % Favored : 97.30 % Rotamer: Outliers : 3.13 % Allowed : 16.78 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.14), residues: 3700 helix: 1.74 (0.16), residues: 1080 sheet: -0.43 (0.17), residues: 860 loop : 0.25 (0.16), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 130 HIS 0.007 0.001 HIS I 217 PHE 0.033 0.002 PHE G 62 TYR 0.025 0.001 TYR F 288 ARG 0.011 0.000 ARG D 327 Details of bonding type rmsd hydrogen bonds : bond 0.03940 ( 1222) hydrogen bonds : angle 4.64612 ( 3939) covalent geometry : bond 0.00367 (30366) covalent geometry : angle 0.58672 (41052) *********************** 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 481 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 383 time to evaluate : 3.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 GLU cc_start: 0.7576 (tt0) cc_final: 0.6950 (pt0) REVERT: A 235 ILE cc_start: 0.9302 (mt) cc_final: 0.8897 (tt) REVERT: A 369 PHE cc_start: 0.7362 (OUTLIER) cc_final: 0.7092 (t80) REVERT: B 77 MET cc_start: 0.8244 (mtp) cc_final: 0.7973 (mtt) REVERT: B 88 PRO cc_start: 0.9237 (Cg_endo) cc_final: 0.8882 (Cg_exo) REVERT: B 140 MET cc_start: 0.7889 (mtt) cc_final: 0.7567 (mtt) REVERT: B 203 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7383 (pt0) REVERT: B 320 SER cc_start: 0.8652 (OUTLIER) cc_final: 0.8238 (t) REVERT: C 18 MET cc_start: 0.8963 (mmt) cc_final: 0.8754 (mmt) REVERT: C 52 LYS cc_start: 0.8137 (mptt) cc_final: 0.7740 (mppt) REVERT: C 92 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.7916 (m-30) REVERT: C 143 ASP cc_start: 0.8688 (p0) cc_final: 0.8374 (p0) REVERT: C 214 MET cc_start: 0.8921 (tpp) cc_final: 0.8192 (tpp) REVERT: D 1 MET cc_start: 0.4074 (OUTLIER) cc_final: 0.2978 (mmm) REVERT: D 80 HIS cc_start: 0.7761 (t-170) cc_final: 0.7493 (t-90) REVERT: D 203 GLU cc_start: 0.7711 (tt0) cc_final: 0.7197 (tt0) REVERT: D 255 ASN cc_start: 0.8651 (m-40) cc_final: 0.8422 (m110) REVERT: D 265 ASN cc_start: 0.8249 (t0) cc_final: 0.7763 (t0) REVERT: D 353 GLU cc_start: 0.8743 (pp20) cc_final: 0.8189 (tt0) REVERT: E 36 THR cc_start: 0.9212 (p) cc_final: 0.8897 (t) REVERT: E 121 MET cc_start: 0.8005 (mmp) cc_final: 0.7190 (mmp) REVERT: E 133 MET cc_start: 0.8376 (mmm) cc_final: 0.8169 (mmm) REVERT: E 181 ARG cc_start: 0.8893 (tpp80) cc_final: 0.8614 (tpp80) REVERT: E 201 GLN cc_start: 0.8748 (mt0) cc_final: 0.8472 (mt0) REVERT: E 356 VAL cc_start: 0.8836 (p) cc_final: 0.8586 (p) REVERT: E 361 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8063 (mp) REVERT: F 15 GLN cc_start: 0.8513 (tp-100) cc_final: 0.7970 (tp40) REVERT: F 87 ASP cc_start: 0.8532 (t0) cc_final: 0.8118 (t0) REVERT: F 121 MET cc_start: 0.7989 (mmt) cc_final: 0.7676 (mmp) REVERT: F 140 MET cc_start: 0.8557 (mtp) cc_final: 0.8206 (mtp) REVERT: F 214 MET cc_start: 0.8456 (tpp) cc_final: 0.8236 (tmm) REVERT: F 261 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.7993 (mmt) REVERT: G 30 TYR cc_start: 0.8500 (m-80) cc_final: 0.8166 (m-80) REVERT: G 63 ASP cc_start: 0.8253 (t0) cc_final: 0.7867 (t0) REVERT: G 84 MET cc_start: 0.7904 (ttt) cc_final: 0.7550 (ttt) REVERT: G 135 GLN cc_start: 0.8549 (tp40) cc_final: 0.8303 (tp40) REVERT: G 168 ASP cc_start: 0.8392 (p0) cc_final: 0.7873 (t0) REVERT: G 283 TYR cc_start: 0.7353 (t80) cc_final: 0.7053 (t80) REVERT: G 294 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8166 (tt) REVERT: G 296 ASN cc_start: 0.8207 (t0) cc_final: 0.7272 (t0) REVERT: G 300 LEU cc_start: 0.8147 (mt) cc_final: 0.7933 (mt) REVERT: G 357 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7221 (ttm-80) REVERT: G 362 ASN cc_start: 0.7513 (t0) cc_final: 0.7190 (t0) REVERT: H 24 GLU cc_start: 0.6471 (tp30) cc_final: 0.6209 (tp30) REVERT: H 106 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8550 (mmm-85) REVERT: H 117 CYS cc_start: 0.8495 (OUTLIER) cc_final: 0.7418 (t) REVERT: H 214 MET cc_start: 0.8700 (tpp) cc_final: 0.8253 (tmm) REVERT: I 7 SER cc_start: 0.9236 (p) cc_final: 0.8845 (t) REVERT: I 49 CYS cc_start: 0.8296 (m) cc_final: 0.7789 (p) REVERT: I 57 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9222 (mm) REVERT: I 214 MET cc_start: 0.8449 (tpp) cc_final: 0.8033 (tpp) REVERT: I 291 LYS cc_start: 0.8256 (mmtm) cc_final: 0.7090 (mttm) REVERT: J 53 CYS cc_start: 0.7943 (p) cc_final: 0.7349 (m) REVERT: J 106 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7767 (mpt180) REVERT: J 140 MET cc_start: 0.8361 (mtm) cc_final: 0.8101 (mtm) REVERT: J 145 HIS cc_start: 0.8329 (OUTLIER) cc_final: 0.7786 (t70) outliers start: 98 outliers final: 65 residues processed: 456 average time/residue: 0.3923 time to fit residues: 288.9974 Evaluate side-chains 443 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 364 time to evaluate : 3.173 ------------------------------------------------------------------------------- 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 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 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 288 TYR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain C residue 4 SER 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 C residue 92 ASP Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 111 THR 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 D residue 343 SER Chi-restraints excluded: chain E residue 145 HIS Chi-restraints excluded: chain E residue 282 GLN 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 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 F residue 355 ILE Chi-restraints excluded: chain G residue 145 HIS Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 274 ILE Chi-restraints excluded: chain G residue 294 LEU 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 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 352 THR Chi-restraints excluded: chain I residue 34 ASP Chi-restraints excluded: chain I residue 56 GLU Chi-restraints excluded: chain I residue 57 LEU 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 261 MET Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 106 ARG 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 287 optimal weight: 2.9990 chunk 246 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 187 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 138 optimal weight: 7.9990 chunk 186 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 173 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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** B 246 ASN ** C 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 282 GLN ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.136810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.106645 restraints weight = 44628.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.109914 restraints weight = 25866.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.112080 restraints weight = 18540.889| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 30366 Z= 0.171 Angle : 0.597 10.119 41052 Z= 0.308 Chirality : 0.043 0.225 4110 Planarity : 0.005 0.054 5476 Dihedral : 4.217 57.165 4110 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.95 % Favored : 97.03 % Rotamer: Outliers : 2.87 % Allowed : 17.16 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.14), residues: 3700 helix: 1.74 (0.16), residues: 1080 sheet: -0.47 (0.18), residues: 860 loop : 0.24 (0.16), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 130 HIS 0.007 0.001 HIS I 217 PHE 0.035 0.002 PHE G 62 TYR 0.023 0.001 TYR G 349 ARG 0.004 0.000 ARG J 319 Details of bonding type rmsd hydrogen bonds : bond 0.04008 ( 1222) hydrogen bonds : angle 4.65600 ( 3939) covalent geometry : bond 0.00411 (30366) covalent geometry : angle 0.59707 (41052) *********************** 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 467 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 377 time to evaluate : 3.312 Fit side-chains revert: symmetry clash REVERT: A 203 GLU cc_start: 0.7555 (tt0) cc_final: 0.6786 (pt0) REVERT: A 235 ILE cc_start: 0.9307 (mt) cc_final: 0.8918 (tt) REVERT: A 369 PHE cc_start: 0.7395 (OUTLIER) cc_final: 0.7095 (t80) REVERT: B 77 MET cc_start: 0.8288 (mtp) cc_final: 0.8003 (mtt) REVERT: B 88 PRO cc_start: 0.9284 (Cg_endo) cc_final: 0.8947 (Cg_exo) REVERT: B 140 MET cc_start: 0.8012 (mtt) cc_final: 0.7754 (mtt) REVERT: B 203 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7411 (pt0) REVERT: B 320 SER cc_start: 0.8648 (OUTLIER) cc_final: 0.8201 (t) REVERT: C 18 MET cc_start: 0.8976 (mmt) cc_final: 0.8773 (mmt) REVERT: C 52 LYS cc_start: 0.8127 (mptt) cc_final: 0.7738 (mppt) REVERT: C 214 MET cc_start: 0.8999 (tpp) cc_final: 0.8416 (tpp) REVERT: C 353 GLU cc_start: 0.7386 (tt0) cc_final: 0.7022 (mt-10) REVERT: D 1 MET cc_start: 0.4051 (OUTLIER) cc_final: 0.2858 (tpp) REVERT: D 80 HIS cc_start: 0.7788 (t-170) cc_final: 0.7502 (t-90) REVERT: D 203 GLU cc_start: 0.7763 (tt0) cc_final: 0.7228 (tt0) REVERT: D 255 ASN cc_start: 0.8630 (m-40) cc_final: 0.8377 (m110) REVERT: D 265 ASN cc_start: 0.8316 (t0) cc_final: 0.7867 (t0) REVERT: D 296 ASN cc_start: 0.6966 (t0) cc_final: 0.6681 (t0) REVERT: D 353 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8271 (tt0) REVERT: E 36 THR cc_start: 0.9207 (p) cc_final: 0.8916 (t) REVERT: E 133 MET cc_start: 0.8345 (mmm) cc_final: 0.8141 (mmm) REVERT: E 181 ARG cc_start: 0.8913 (tpp80) cc_final: 0.8597 (tpp80) REVERT: E 331 GLN cc_start: 0.8402 (mm-40) cc_final: 0.7968 (mt0) REVERT: F 15 GLN cc_start: 0.8535 (tp-100) cc_final: 0.8009 (tp40) REVERT: F 47 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8636 (mt) REVERT: F 87 ASP cc_start: 0.8596 (t0) cc_final: 0.8212 (t0) REVERT: F 121 MET cc_start: 0.8082 (mmt) cc_final: 0.7789 (mmp) REVERT: F 140 MET cc_start: 0.8591 (mtp) cc_final: 0.8239 (mtp) REVERT: F 214 MET cc_start: 0.8521 (tpp) cc_final: 0.8283 (tmm) REVERT: F 261 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.7973 (mmt) REVERT: G 30 TYR cc_start: 0.8529 (m-80) cc_final: 0.8144 (m-80) REVERT: G 63 ASP cc_start: 0.8242 (t0) cc_final: 0.7889 (t0) REVERT: G 84 MET cc_start: 0.7933 (ttt) cc_final: 0.7623 (ttt) REVERT: G 99 CYS cc_start: 0.8655 (m) cc_final: 0.8384 (m) REVERT: G 135 GLN cc_start: 0.8547 (tp40) cc_final: 0.8315 (tp40) REVERT: G 168 ASP cc_start: 0.8488 (p0) cc_final: 0.7901 (t0) REVERT: G 283 TYR cc_start: 0.7623 (t80) cc_final: 0.7308 (t80) REVERT: G 296 ASN cc_start: 0.8343 (t0) cc_final: 0.7628 (t0) REVERT: G 362 ASN cc_start: 0.7794 (t0) cc_final: 0.7386 (t0) REVERT: H 24 GLU cc_start: 0.6511 (tp30) cc_final: 0.6279 (tp30) REVERT: H 106 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8538 (mmm-85) REVERT: H 117 CYS cc_start: 0.8528 (OUTLIER) cc_final: 0.7528 (t) REVERT: I 7 SER cc_start: 0.9244 (p) cc_final: 0.8867 (t) REVERT: I 49 CYS cc_start: 0.8112 (m) cc_final: 0.7693 (p) REVERT: I 121 MET cc_start: 0.8309 (tpp) cc_final: 0.8073 (tpp) REVERT: I 214 MET cc_start: 0.8530 (tpp) cc_final: 0.8138 (tpp) REVERT: I 239 ASP cc_start: 0.8515 (t0) cc_final: 0.8147 (t0) REVERT: I 291 LYS cc_start: 0.8182 (mmtm) cc_final: 0.7026 (mttm) REVERT: I 296 ASN cc_start: 0.8423 (t0) cc_final: 0.8016 (t0) REVERT: J 53 CYS cc_start: 0.7898 (p) cc_final: 0.7371 (m) REVERT: J 140 MET cc_start: 0.8402 (mtm) cc_final: 0.8112 (mtm) REVERT: J 145 HIS cc_start: 0.8364 (OUTLIER) cc_final: 0.7762 (t70) REVERT: J 261 MET cc_start: 0.8497 (mmt) cc_final: 0.7952 (mmt) REVERT: J 311 ASP cc_start: 0.7987 (m-30) cc_final: 0.7721 (m-30) outliers start: 90 outliers final: 67 residues processed: 444 average time/residue: 0.4177 time to fit residues: 301.3168 Evaluate side-chains 434 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 357 time to evaluate : 3.069 ------------------------------------------------------------------------------- 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 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 49 CYS Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain B residue 288 TYR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 26 ILE 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 C residue 92 ASP Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 111 THR 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 257 SER Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 353 GLU Chi-restraints excluded: chain E residue 145 HIS Chi-restraints excluded: chain E residue 288 TYR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 47 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 F residue 355 ILE Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 193 THR Chi-restraints excluded: chain G residue 274 ILE 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 352 THR Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 145 HIS Chi-restraints excluded: chain I residue 198 MET 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 I residue 360 LEU Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 79 LEU 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 350 optimal weight: 2.9990 chunk 245 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 301 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 286 optimal weight: 1.9990 chunk 328 optimal weight: 0.9980 chunk 221 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 254 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 HIS F 112 ASN ** H 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 201 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.131718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.101412 restraints weight = 45239.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.104528 restraints weight = 26287.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.106599 restraints weight = 19045.213| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 30366 Z= 0.283 Angle : 0.712 12.704 41052 Z= 0.367 Chirality : 0.047 0.158 4110 Planarity : 0.005 0.082 5476 Dihedral : 4.561 20.264 4108 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.46 % Favored : 96.51 % Rotamer: Outliers : 3.13 % Allowed : 16.97 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.14), residues: 3700 helix: 1.43 (0.15), residues: 1080 sheet: -0.70 (0.17), residues: 860 loop : 0.08 (0.16), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 130 HIS 0.012 0.001 HIS G 217 PHE 0.038 0.002 PHE G 62 TYR 0.024 0.002 TYR B 180 ARG 0.005 0.001 ARG I 106 Details of bonding type rmsd hydrogen bonds : bond 0.04819 ( 1222) hydrogen bonds : angle 5.03105 ( 3939) covalent geometry : bond 0.00674 (30366) covalent geometry : angle 0.71184 (41052) *********************** 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 480 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 382 time to evaluate : 3.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.8545 (ttm) cc_final: 0.8326 (ttp) REVERT: A 203 GLU cc_start: 0.7583 (tt0) cc_final: 0.6745 (pt0) REVERT: A 235 ILE cc_start: 0.9391 (mt) cc_final: 0.9057 (tt) REVERT: A 369 PHE cc_start: 0.7526 (OUTLIER) cc_final: 0.7217 (t80) REVERT: B 88 PRO cc_start: 0.9372 (Cg_endo) cc_final: 0.9048 (Cg_exo) REVERT: B 140 MET cc_start: 0.8031 (mtt) cc_final: 0.7714 (mtt) REVERT: B 203 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7459 (pt0) REVERT: B 320 SER cc_start: 0.8668 (OUTLIER) cc_final: 0.8171 (t) REVERT: B 369 PHE cc_start: 0.7717 (t80) cc_final: 0.7468 (t80) REVERT: C 92 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.7995 (m-30) REVERT: C 99 CYS cc_start: 0.8930 (m) cc_final: 0.8517 (m) REVERT: C 121 MET cc_start: 0.8921 (mmp) cc_final: 0.8721 (mmp) REVERT: D 203 GLU cc_start: 0.7771 (tt0) cc_final: 0.7211 (tt0) REVERT: D 255 ASN cc_start: 0.8661 (m-40) cc_final: 0.8440 (m110) REVERT: D 265 ASN cc_start: 0.8425 (t0) cc_final: 0.7891 (t0) REVERT: D 296 ASN cc_start: 0.7078 (t0) cc_final: 0.6666 (t0) REVERT: D 353 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8360 (tt0) REVERT: E 121 MET cc_start: 0.8633 (mmp) cc_final: 0.8007 (mmp) REVERT: E 181 ARG cc_start: 0.8998 (tpp80) cc_final: 0.8678 (tpp80) REVERT: E 331 GLN cc_start: 0.8487 (mm-40) cc_final: 0.8120 (mt0) REVERT: F 15 GLN cc_start: 0.8756 (tp-100) cc_final: 0.8508 (tp40) REVERT: F 47 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8653 (mt) REVERT: F 140 MET cc_start: 0.8648 (mtp) cc_final: 0.8232 (mtp) REVERT: F 261 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8046 (mmt) REVERT: G 30 TYR cc_start: 0.8611 (m-80) cc_final: 0.8157 (m-80) REVERT: G 63 ASP cc_start: 0.8290 (t0) cc_final: 0.7919 (t0) REVERT: G 99 CYS cc_start: 0.8734 (m) cc_final: 0.8464 (m) REVERT: G 168 ASP cc_start: 0.8537 (p0) cc_final: 0.7911 (t0) REVERT: G 283 TYR cc_start: 0.8247 (t80) cc_final: 0.7935 (t80) REVERT: G 357 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7882 (ttm170) REVERT: G 362 ASN cc_start: 0.8245 (t0) cc_final: 0.7906 (t0) REVERT: H 24 GLU cc_start: 0.6509 (tp30) cc_final: 0.6262 (tp30) REVERT: H 106 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.8569 (mmm-85) REVERT: H 117 CYS cc_start: 0.8637 (OUTLIER) cc_final: 0.7754 (t) REVERT: H 214 MET cc_start: 0.8409 (tpp) cc_final: 0.8138 (tmm) REVERT: I 7 SER cc_start: 0.9150 (OUTLIER) cc_final: 0.8835 (t) REVERT: I 49 CYS cc_start: 0.8173 (m) cc_final: 0.7742 (p) REVERT: I 52 LYS cc_start: 0.7187 (pttm) cc_final: 0.6395 (mtmm) REVERT: I 214 MET cc_start: 0.8598 (tpp) cc_final: 0.8216 (tpp) REVERT: I 239 ASP cc_start: 0.8551 (t0) cc_final: 0.8242 (t0) REVERT: I 268 ARG cc_start: 0.8280 (ttm110) cc_final: 0.7863 (mtm-85) REVERT: I 291 LYS cc_start: 0.8221 (mmtm) cc_final: 0.7111 (mttm) REVERT: J 53 CYS cc_start: 0.7739 (p) cc_final: 0.7430 (m) REVERT: J 145 HIS cc_start: 0.8397 (OUTLIER) cc_final: 0.7852 (t70) REVERT: J 261 MET cc_start: 0.8626 (mmt) cc_final: 0.8038 (mmt) outliers start: 98 outliers final: 74 residues processed: 454 average time/residue: 0.4007 time to fit residues: 292.1799 Evaluate side-chains 445 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 359 time to evaluate : 3.318 ------------------------------------------------------------------------------- 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 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 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 234 VAL Chi-restraints excluded: chain B residue 288 TYR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 26 ILE 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 C residue 92 ASP 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 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 257 SER Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 341 ARG Chi-restraints excluded: chain D residue 343 SER Chi-restraints excluded: chain D residue 353 GLU Chi-restraints excluded: chain E residue 145 HIS Chi-restraints excluded: chain E residue 288 TYR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 92 ASP 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 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 F residue 355 ILE Chi-restraints excluded: chain G residue 33 VAL Chi-restraints excluded: chain G residue 145 HIS Chi-restraints excluded: chain G residue 193 THR 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 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 316 VAL Chi-restraints excluded: chain H residue 352 THR Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 145 HIS Chi-restraints excluded: chain I residue 190 ILE Chi-restraints excluded: chain I residue 198 MET 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 26 ILE Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain J residue 145 HIS 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 124 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 337 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 248 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 243 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 181 optimal weight: 0.0270 chunk 298 optimal weight: 0.8980 chunk 247 optimal weight: 0.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 GLN A 265 ASN C 112 ASN C 201 GLN F 112 ASN ** H 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.136189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.105949 restraints weight = 44937.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.109243 restraints weight = 25527.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.111451 restraints weight = 18265.551| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 30366 Z= 0.141 Angle : 0.617 10.338 41052 Z= 0.317 Chirality : 0.044 0.193 4110 Planarity : 0.005 0.054 5476 Dihedral : 4.284 19.987 4108 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.95 % Favored : 97.03 % Rotamer: Outliers : 2.49 % Allowed : 18.31 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.14), residues: 3700 helix: 1.70 (0.16), residues: 1080 sheet: -0.58 (0.17), residues: 860 loop : 0.15 (0.16), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP J 149 HIS 0.008 0.001 HIS I 217 PHE 0.036 0.002 PHE G 62 TYR 0.022 0.001 TYR C 104 ARG 0.007 0.000 ARG E 227 Details of bonding type rmsd hydrogen bonds : bond 0.03992 ( 1222) hydrogen bonds : angle 4.68400 ( 3939) covalent geometry : bond 0.00338 (30366) covalent geometry : angle 0.61652 (41052) ********************** 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 466 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 388 time to evaluate : 3.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 GLU cc_start: 0.7523 (tt0) cc_final: 0.6756 (pt0) REVERT: A 235 ILE cc_start: 0.9295 (mt) cc_final: 0.8958 (tt) REVERT: A 369 PHE cc_start: 0.7462 (OUTLIER) cc_final: 0.7165 (t80) REVERT: B 88 PRO cc_start: 0.9297 (Cg_endo) cc_final: 0.8971 (Cg_exo) REVERT: B 140 MET cc_start: 0.7971 (mtt) cc_final: 0.7733 (mtt) REVERT: B 203 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7426 (pt0) REVERT: B 320 SER cc_start: 0.8735 (OUTLIER) cc_final: 0.8284 (t) REVERT: C 92 ASP cc_start: 0.8237 (OUTLIER) cc_final: 0.7973 (m-30) REVERT: D 1 MET cc_start: 0.4175 (OUTLIER) cc_final: 0.3166 (tpp) REVERT: D 18 MET cc_start: 0.9006 (tpp) cc_final: 0.8777 (mmm) REVERT: D 255 ASN cc_start: 0.8589 (m-40) cc_final: 0.8381 (m110) REVERT: D 265 ASN cc_start: 0.8380 (t0) cc_final: 0.7835 (t0) REVERT: D 296 ASN cc_start: 0.6931 (t0) cc_final: 0.6616 (t0) REVERT: D 353 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8344 (tt0) REVERT: E 121 MET cc_start: 0.8482 (mmp) cc_final: 0.7810 (mmp) REVERT: E 181 ARG cc_start: 0.8879 (tpp80) cc_final: 0.8532 (tpp80) REVERT: E 263 GLU cc_start: 0.6472 (mt-10) cc_final: 0.6271 (mt-10) REVERT: E 331 GLN cc_start: 0.8438 (mm-40) cc_final: 0.8171 (mt0) REVERT: F 15 GLN cc_start: 0.8540 (tp-100) cc_final: 0.7990 (tp40) REVERT: F 140 MET cc_start: 0.8546 (mtp) cc_final: 0.8096 (mtp) REVERT: F 214 MET cc_start: 0.8667 (tmm) cc_final: 0.8294 (tpp) REVERT: F 235 ILE cc_start: 0.9227 (mt) cc_final: 0.8863 (tt) REVERT: F 261 MET cc_start: 0.8938 (OUTLIER) cc_final: 0.8132 (mmt) REVERT: G 30 TYR cc_start: 0.8536 (m-80) cc_final: 0.8107 (m-80) REVERT: G 63 ASP cc_start: 0.8235 (t0) cc_final: 0.7960 (t0) REVERT: G 110 GLU cc_start: 0.7988 (pm20) cc_final: 0.7474 (pt0) REVERT: G 168 ASP cc_start: 0.8536 (p0) cc_final: 0.7936 (t0) REVERT: G 283 TYR cc_start: 0.8222 (t80) cc_final: 0.7979 (t80) REVERT: G 296 ASN cc_start: 0.8454 (t0) cc_final: 0.7767 (t0) REVERT: G 357 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7987 (ttm-80) REVERT: G 362 ASN cc_start: 0.8207 (t0) cc_final: 0.7772 (t0) REVERT: H 24 GLU cc_start: 0.6424 (tp30) cc_final: 0.6199 (tp30) REVERT: H 117 CYS cc_start: 0.8585 (OUTLIER) cc_final: 0.7638 (t) REVERT: H 214 MET cc_start: 0.8494 (tpp) cc_final: 0.8248 (tmm) REVERT: I 7 SER cc_start: 0.9172 (p) cc_final: 0.8842 (t) REVERT: I 49 CYS cc_start: 0.8108 (m) cc_final: 0.7751 (p) REVERT: I 52 LYS cc_start: 0.6950 (pttm) cc_final: 0.6358 (mtmm) REVERT: I 121 MET cc_start: 0.8232 (tpp) cc_final: 0.7949 (tpp) REVERT: I 239 ASP cc_start: 0.8510 (t0) cc_final: 0.8159 (t0) REVERT: I 268 ARG cc_start: 0.8257 (ttm110) cc_final: 0.7836 (mtm-85) REVERT: I 291 LYS cc_start: 0.8159 (mmtm) cc_final: 0.7039 (mttm) REVERT: J 53 CYS cc_start: 0.7753 (p) cc_final: 0.7408 (m) REVERT: J 145 HIS cc_start: 0.8284 (OUTLIER) cc_final: 0.7690 (t70) REVERT: J 261 MET cc_start: 0.8584 (mmt) cc_final: 0.8014 (mmt) REVERT: J 311 ASP cc_start: 0.7883 (m-30) cc_final: 0.7423 (t0) outliers start: 78 outliers final: 53 residues processed: 443 average time/residue: 0.3995 time to fit residues: 286.3238 Evaluate side-chains 428 residues out of total 3140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 365 time to evaluate : 3.227 ------------------------------------------------------------------------------- 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 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 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 4 SER Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 92 ASP Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 111 THR 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 D residue 353 GLU Chi-restraints excluded: chain E residue 145 HIS Chi-restraints excluded: chain F residue 44 THR 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 145 HIS Chi-restraints excluded: chain G residue 193 THR 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 197 VAL Chi-restraints excluded: chain H residue 243 ILE Chi-restraints excluded: chain H residue 352 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain I residue 261 MET Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain J residue 145 HIS 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 48 optimal weight: 6.9990 chunk 252 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 124 optimal weight: 0.5980 chunk 136 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 351 optimal weight: 0.8980 chunk 230 optimal weight: 0.4980 chunk 183 optimal weight: 2.9990 chunk 344 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 ASN D 265 ASN F 112 ASN ** H 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.136691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.106499 restraints weight = 44696.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.109800 restraints weight = 25425.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.112030 restraints weight = 18193.082| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30366 Z= 0.144 Angle : 0.614 12.278 41052 Z= 0.314 Chirality : 0.043 0.165 4110 Planarity : 0.005 0.046 5476 Dihedral : 4.166 19.490 4108 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.86 % Favored : 97.11 % Rotamer: Outliers : 2.04 % Allowed : 18.76 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.14), residues: 3700 helix: 1.77 (0.16), residues: 1080 sheet: -0.49 (0.18), residues: 840 loop : 0.13 (0.16), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 149 HIS 0.008 0.001 HIS I 217 PHE 0.036 0.002 PHE G 62 TYR 0.034 0.001 TYR F 283 ARG 0.006 0.000 ARG F 340 Details of bonding type rmsd hydrogen bonds : bond 0.03874 ( 1222) hydrogen bonds : angle 4.61184 ( 3939) covalent geometry : bond 0.00346 (30366) covalent geometry : angle 0.61365 (41052) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8687.52 seconds wall clock time: 154 minutes 0.34 seconds (9240.34 seconds total)