Starting phenix.real_space_refine on Mon Aug 25 18:51:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8s7g_19771/08_2025/8s7g_19771_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s7g_19771/08_2025/8s7g_19771.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8s7g_19771/08_2025/8s7g_19771_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s7g_19771/08_2025/8s7g_19771_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8s7g_19771/08_2025/8s7g_19771.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s7g_19771/08_2025/8s7g_19771.map" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.021 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: 6 Type Number sf(0) Gaussians P 69 5.49 5 Mg 11 5.21 5 S 116 5.16 5 C 18641 2.51 5 N 5242 2.21 5 O 5957 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 83 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30036 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 963 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 6, 'TRANS': 117} Chain: "B" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 963 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 6, 'TRANS': 117} Chain: "D" Number of atoms: 2458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2458 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 10, 'TRANS': 317} Chain: "E" Number of atoms: 2458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2458 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 10, 'TRANS': 317} Chain: "F" Number of atoms: 2458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2458 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 10, 'TRANS': 317} Chain: "G" Number of atoms: 2458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2458 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 10, 'TRANS': 317} Chain: "H" Number of atoms: 2458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2458 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 10, 'TRANS': 317} Chain: "I" Number of atoms: 2458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2458 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 10, 'TRANS': 317} Chain: "J" Number of atoms: 2458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2458 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 10, 'TRANS': 317} Chain: "K" Number of atoms: 2458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2458 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 10, 'TRANS': 317} Chain: "L" Number of atoms: 2458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2458 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 10, 'TRANS': 317} Chain: "T" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 720 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "C" Number of atoms: 2458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2458 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 10, 'TRANS': 317} Chain: "M" Number of atoms: 2458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2458 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 10, 'TRANS': 317} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.99, per 1000 atoms: 0.23 Number of scatterers: 30036 At special positions: 0 Unit cell: (233.52, 177.24, 137.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 116 16.00 P 69 15.00 Mg 11 11.99 O 5957 8.00 N 5242 7.00 C 18641 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.76 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 1.4 microseconds 7660 Ramachandran restraints generated. 3830 Oldfield, 0 Emsley, 3830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6832 Finding SS restraints... Secondary structure from input PDB file: 139 helices and 51 sheets defined 43.9% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 107 through 111 removed outlier: 4.336A pdb=" N PHE A 111 " --> pdb=" O PRO A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 130 Processing helix chain 'D' and resid 2 through 21 Processing helix chain 'D' and resid 43 through 50 Processing helix chain 'D' and resid 70 through 86 Processing helix chain 'D' and resid 99 through 107 Processing helix chain 'D' and resid 120 through 134 Processing helix chain 'D' and resid 144 through 148 Processing helix chain 'D' and resid 150 through 156 Processing helix chain 'D' and resid 164 through 185 removed outlier: 3.534A pdb=" N LYS D 176 " --> pdb=" O GLN D 172 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N GLY D 179 " --> pdb=" O ARG D 175 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ASN D 180 " --> pdb=" O LYS D 176 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN D 183 " --> pdb=" O GLY D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 218 removed outlier: 3.872A pdb=" N TYR D 217 " --> pdb=" O ALA D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 281 removed outlier: 3.521A pdb=" N ILE D 274 " --> pdb=" O THR D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 311 removed outlier: 3.779A pdb=" N ASN D 311 " --> pdb=" O TYR D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 327 Processing helix chain 'E' and resid 2 through 21 Processing helix chain 'E' and resid 43 through 50 Processing helix chain 'E' and resid 70 through 86 removed outlier: 3.596A pdb=" N GLN E 85 " --> pdb=" O GLU E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 107 Processing helix chain 'E' and resid 109 through 113 Processing helix chain 'E' and resid 120 through 135 removed outlier: 3.675A pdb=" N LEU E 125 " --> pdb=" O GLY E 121 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR E 128 " --> pdb=" O ALA E 124 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN E 135 " --> pdb=" O LEU E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 148 Processing helix chain 'E' and resid 150 through 155 removed outlier: 3.555A pdb=" N GLU E 155 " --> pdb=" O LYS E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 178 Processing helix chain 'E' and resid 179 through 184 Processing helix chain 'E' and resid 213 through 218 removed outlier: 3.608A pdb=" N TYR E 217 " --> pdb=" O ALA E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 280 Processing helix chain 'E' and resid 300 through 310 removed outlier: 4.000A pdb=" N LYS E 306 " --> pdb=" O ALA E 302 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TYR E 307 " --> pdb=" O ASN E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 326 removed outlier: 3.606A pdb=" N GLY E 315 " --> pdb=" O ASN E 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 21 Processing helix chain 'F' and resid 43 through 51 Processing helix chain 'F' and resid 70 through 85 removed outlier: 3.813A pdb=" N GLN F 85 " --> pdb=" O GLU F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 107 Processing helix chain 'F' and resid 120 through 134 removed outlier: 3.807A pdb=" N VAL F 132 " --> pdb=" O THR F 128 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER F 134 " --> pdb=" O MET F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 148 Processing helix chain 'F' and resid 150 through 155 Processing helix chain 'F' and resid 164 through 185 removed outlier: 4.437A pdb=" N GLY F 179 " --> pdb=" O ARG F 175 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ASN F 180 " --> pdb=" O LYS F 176 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS F 182 " --> pdb=" O THR F 178 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASN F 183 " --> pdb=" O GLY F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 218 removed outlier: 4.159A pdb=" N TYR F 217 " --> pdb=" O ALA F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 281 removed outlier: 3.634A pdb=" N ASP F 275 " --> pdb=" O GLY F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 311 removed outlier: 3.885A pdb=" N ASN F 311 " --> pdb=" O TYR F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 328 removed outlier: 3.669A pdb=" N GLY F 315 " --> pdb=" O ASN F 311 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA F 328 " --> pdb=" O ASP F 324 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 20 Processing helix chain 'G' and resid 43 through 51 removed outlier: 3.529A pdb=" N GLY G 51 " --> pdb=" O ASP G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 86 removed outlier: 3.508A pdb=" N LEU G 74 " --> pdb=" O GLY G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 107 Processing helix chain 'G' and resid 120 through 134 Processing helix chain 'G' and resid 144 through 148 removed outlier: 3.549A pdb=" N LEU G 148 " --> pdb=" O VAL G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 150 through 156 Processing helix chain 'G' and resid 164 through 185 removed outlier: 3.551A pdb=" N ARG G 168 " --> pdb=" O GLY G 164 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N GLY G 179 " --> pdb=" O ARG G 175 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ASN G 180 " --> pdb=" O LYS G 176 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS G 182 " --> pdb=" O THR G 178 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASN G 183 " --> pdb=" O GLY G 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 218 removed outlier: 4.237A pdb=" N TYR G 217 " --> pdb=" O ALA G 213 " (cutoff:3.500A) Processing helix chain 'G' and resid 268 through 281 removed outlier: 3.505A pdb=" N ILE G 274 " --> pdb=" O THR G 270 " (cutoff:3.500A) Processing helix chain 'G' and resid 300 through 310 Processing helix chain 'G' and resid 311 through 327 Processing helix chain 'H' and resid 2 through 18 Processing helix chain 'H' and resid 30 through 34 removed outlier: 3.606A pdb=" N GLN H 34 " --> pdb=" O HIS H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 51 Processing helix chain 'H' and resid 70 through 86 Processing helix chain 'H' and resid 99 through 107 Processing helix chain 'H' and resid 109 through 113 Processing helix chain 'H' and resid 120 through 134 Processing helix chain 'H' and resid 150 through 156 Processing helix chain 'H' and resid 164 through 185 removed outlier: 4.427A pdb=" N GLY H 179 " --> pdb=" O ARG H 175 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASN H 180 " --> pdb=" O LYS H 176 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS H 182 " --> pdb=" O THR H 178 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASN H 183 " --> pdb=" O GLY H 179 " (cutoff:3.500A) Processing helix chain 'H' and resid 213 through 218 removed outlier: 4.012A pdb=" N TYR H 217 " --> pdb=" O ALA H 213 " (cutoff:3.500A) Processing helix chain 'H' and resid 268 through 281 Processing helix chain 'H' and resid 300 through 311 removed outlier: 3.917A pdb=" N ASN H 311 " --> pdb=" O TYR H 307 " (cutoff:3.500A) Processing helix chain 'H' and resid 311 through 327 removed outlier: 3.712A pdb=" N GLY H 315 " --> pdb=" O ASN H 311 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 21 Processing helix chain 'I' and resid 43 through 51 removed outlier: 3.605A pdb=" N GLY I 51 " --> pdb=" O ASP I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 85 removed outlier: 3.591A pdb=" N GLN I 85 " --> pdb=" O GLU I 81 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 107 Processing helix chain 'I' and resid 109 through 113 removed outlier: 3.891A pdb=" N LEU I 113 " --> pdb=" O VAL I 110 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 133 removed outlier: 3.580A pdb=" N VAL I 132 " --> pdb=" O THR I 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 150 through 156 removed outlier: 3.784A pdb=" N GLY I 156 " --> pdb=" O ALA I 152 " (cutoff:3.500A) Processing helix chain 'I' and resid 164 through 185 removed outlier: 4.668A pdb=" N GLY I 179 " --> pdb=" O ARG I 175 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ASN I 180 " --> pdb=" O LYS I 176 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS I 182 " --> pdb=" O THR I 178 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASN I 183 " --> pdb=" O GLY I 179 " (cutoff:3.500A) Processing helix chain 'I' and resid 213 through 218 removed outlier: 3.962A pdb=" N TYR I 217 " --> pdb=" O ALA I 213 " (cutoff:3.500A) Processing helix chain 'I' and resid 268 through 281 removed outlier: 3.639A pdb=" N GLU I 272 " --> pdb=" O TYR I 268 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE I 274 " --> pdb=" O THR I 270 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN I 279 " --> pdb=" O ASP I 275 " (cutoff:3.500A) Processing helix chain 'I' and resid 300 through 311 removed outlier: 3.947A pdb=" N ASN I 311 " --> pdb=" O TYR I 307 " (cutoff:3.500A) Processing helix chain 'I' and resid 311 through 327 removed outlier: 3.518A pdb=" N GLY I 315 " --> pdb=" O ASN I 311 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 21 Processing helix chain 'J' and resid 43 through 50 removed outlier: 3.587A pdb=" N ALA J 49 " --> pdb=" O GLY J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 86 Processing helix chain 'J' and resid 99 through 107 Processing helix chain 'J' and resid 120 through 135 removed outlier: 4.016A pdb=" N ASN J 135 " --> pdb=" O LEU J 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 144 through 148 removed outlier: 3.559A pdb=" N LEU J 148 " --> pdb=" O VAL J 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 156 Processing helix chain 'J' and resid 164 through 185 removed outlier: 4.539A pdb=" N GLY J 179 " --> pdb=" O ARG J 175 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ASN J 180 " --> pdb=" O LYS J 176 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS J 182 " --> pdb=" O THR J 178 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASN J 183 " --> pdb=" O GLY J 179 " (cutoff:3.500A) Processing helix chain 'J' and resid 213 through 218 removed outlier: 4.108A pdb=" N TYR J 217 " --> pdb=" O ALA J 213 " (cutoff:3.500A) Processing helix chain 'J' and resid 268 through 281 removed outlier: 3.739A pdb=" N GLU J 272 " --> pdb=" O TYR J 268 " (cutoff:3.500A) Processing helix chain 'J' and resid 300 through 311 removed outlier: 4.043A pdb=" N ASN J 311 " --> pdb=" O TYR J 307 " (cutoff:3.500A) Processing helix chain 'J' and resid 311 through 327 removed outlier: 3.569A pdb=" N GLY J 315 " --> pdb=" O ASN J 311 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 21 Processing helix chain 'K' and resid 43 through 51 Processing helix chain 'K' and resid 70 through 86 Processing helix chain 'K' and resid 99 through 107 removed outlier: 3.547A pdb=" N LYS K 105 " --> pdb=" O ASP K 101 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU K 106 " --> pdb=" O TYR K 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 113 removed outlier: 3.550A pdb=" N LEU K 113 " --> pdb=" O VAL K 110 " (cutoff:3.500A) Processing helix chain 'K' and resid 120 through 134 removed outlier: 3.676A pdb=" N SER K 134 " --> pdb=" O MET K 130 " (cutoff:3.500A) Processing helix chain 'K' and resid 144 through 148 Processing helix chain 'K' and resid 150 through 156 Processing helix chain 'K' and resid 164 through 185 removed outlier: 3.620A pdb=" N LYS K 176 " --> pdb=" O GLN K 172 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N GLY K 179 " --> pdb=" O ARG K 175 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ASN K 180 " --> pdb=" O LYS K 176 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS K 182 " --> pdb=" O THR K 178 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN K 183 " --> pdb=" O GLY K 179 " (cutoff:3.500A) Processing helix chain 'K' and resid 213 through 218 removed outlier: 3.866A pdb=" N TYR K 217 " --> pdb=" O ALA K 213 " (cutoff:3.500A) Processing helix chain 'K' and resid 268 through 281 Processing helix chain 'K' and resid 300 through 311 removed outlier: 4.327A pdb=" N ASN K 311 " --> pdb=" O TYR K 307 " (cutoff:3.500A) Processing helix chain 'K' and resid 311 through 327 removed outlier: 3.866A pdb=" N GLY K 315 " --> pdb=" O ASN K 311 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 20 Processing helix chain 'L' and resid 43 through 50 Processing helix chain 'L' and resid 70 through 85 removed outlier: 3.832A pdb=" N LEU L 74 " --> pdb=" O GLY L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 99 through 107 Processing helix chain 'L' and resid 109 through 113 removed outlier: 3.706A pdb=" N LEU L 113 " --> pdb=" O VAL L 110 " (cutoff:3.500A) Processing helix chain 'L' and resid 120 through 134 Processing helix chain 'L' and resid 144 through 148 Processing helix chain 'L' and resid 150 through 156 Processing helix chain 'L' and resid 164 through 185 removed outlier: 4.485A pdb=" N GLY L 179 " --> pdb=" O ARG L 175 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ASN L 180 " --> pdb=" O LYS L 176 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS L 182 " --> pdb=" O THR L 178 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN L 183 " --> pdb=" O GLY L 179 " (cutoff:3.500A) Processing helix chain 'L' and resid 212 through 218 removed outlier: 3.905A pdb=" N PHE L 216 " --> pdb=" O ASN L 212 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR L 217 " --> pdb=" O ALA L 213 " (cutoff:3.500A) Processing helix chain 'L' and resid 268 through 281 Processing helix chain 'L' and resid 300 through 310 Processing helix chain 'L' and resid 311 through 327 removed outlier: 3.585A pdb=" N GLY L 315 " --> pdb=" O ASN L 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 21 Processing helix chain 'C' and resid 43 through 50 Processing helix chain 'C' and resid 70 through 85 Processing helix chain 'C' and resid 99 through 107 Processing helix chain 'C' and resid 120 through 135 removed outlier: 3.519A pdb=" N ASN C 135 " --> pdb=" O LEU C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 148 Processing helix chain 'C' and resid 150 through 156 Processing helix chain 'C' and resid 164 through 185 removed outlier: 4.444A pdb=" N GLY C 179 " --> pdb=" O ARG C 175 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ASN C 180 " --> pdb=" O LYS C 176 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS C 182 " --> pdb=" O THR C 178 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ASN C 183 " --> pdb=" O GLY C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 218 removed outlier: 3.806A pdb=" N TYR C 217 " --> pdb=" O ALA C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 281 Processing helix chain 'C' and resid 300 through 311 removed outlier: 3.846A pdb=" N ASN C 311 " --> pdb=" O TYR C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 327 removed outlier: 3.680A pdb=" N GLY C 315 " --> pdb=" O ASN C 311 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 21 Processing helix chain 'M' and resid 43 through 51 Processing helix chain 'M' and resid 70 through 85 Processing helix chain 'M' and resid 99 through 107 Processing helix chain 'M' and resid 120 through 135 removed outlier: 3.589A pdb=" N ASN M 135 " --> pdb=" O LEU M 131 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 148 Processing helix chain 'M' and resid 150 through 156 Processing helix chain 'M' and resid 165 through 185 removed outlier: 4.551A pdb=" N GLY M 179 " --> pdb=" O ARG M 175 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ASN M 180 " --> pdb=" O LYS M 176 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS M 182 " --> pdb=" O THR M 178 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN M 183 " --> pdb=" O GLY M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 213 through 217 removed outlier: 3.719A pdb=" N TYR M 217 " --> pdb=" O ALA M 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 213 through 217' Processing helix chain 'M' and resid 268 through 281 Processing helix chain 'M' and resid 300 through 311 removed outlier: 3.979A pdb=" N ASN M 311 " --> pdb=" O TYR M 307 " (cutoff:3.500A) Processing helix chain 'M' and resid 311 through 327 Processing sheet with id=AA1, first strand: chain 'A' and resid 94 through 95 removed outlier: 3.536A pdb=" N ILE A 94 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N VAL A 150 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N LEU A 197 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL A 152 " --> pdb=" O GLU A 195 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA A 138 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR A 117 " --> pdb=" O VAL A 139 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 95 removed outlier: 3.536A pdb=" N ILE A 94 " --> pdb=" O VAL A 159 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.771A pdb=" N GLY B 200 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N HIS B 140 " --> pdb=" O SER B 198 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N SER B 198 " --> pdb=" O HIS B 140 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL B 152 " --> pdb=" O GLU B 195 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N LEU B 197 " --> pdb=" O VAL B 150 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N VAL B 150 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN B 149 " --> pdb=" O PHE B 164 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR B 160 " --> pdb=" O ALA B 153 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 38 through 39 Processing sheet with id=AA5, first strand: chain 'D' and resid 190 through 191 removed outlier: 6.407A pdb=" N VAL D 61 " --> pdb=" O PHE D 190 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 115 through 116 removed outlier: 3.690A pdb=" N ASP D 93 " --> pdb=" O SER D 116 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 224 through 228 removed outlier: 6.301A pdb=" N GLU D 240 " --> pdb=" O THR D 227 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 231 through 232 removed outlier: 3.909A pdb=" N GLU D 235 " --> pdb=" O GLU D 232 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 284 through 285 Processing sheet with id=AB1, first strand: chain 'E' and resid 25 through 26 removed outlier: 3.751A pdb=" N VAL F 115 " --> pdb=" O MET E 26 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N PHE F 91 " --> pdb=" O SER F 116 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE F 141 " --> pdb=" O ALA F 90 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL F 61 " --> pdb=" O PHE F 190 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ASN F 192 " --> pdb=" O VAL F 61 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE F 63 " --> pdb=" O ASN F 192 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLU F 62 " --> pdb=" O LEU F 222 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ILE F 224 " --> pdb=" O GLU F 62 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N TYR F 64 " --> pdb=" O ILE F 224 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N ARG F 226 " --> pdb=" O TYR F 64 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL F 220 " --> pdb=" O ASN F 248 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASN F 248 " --> pdb=" O VAL F 220 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LEU F 222 " --> pdb=" O VAL F 246 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N VAL F 246 " --> pdb=" O LEU F 222 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ILE F 224 " --> pdb=" O LYS F 244 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LYS F 244 " --> pdb=" O ILE F 224 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ARG F 226 " --> pdb=" O ARG F 242 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG F 242 " --> pdb=" O ARG F 226 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLU F 232 " --> pdb=" O VAL F 236 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL F 236 " --> pdb=" O GLU F 232 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 38 through 39 Processing sheet with id=AB3, first strand: chain 'E' and resid 114 through 116 removed outlier: 6.288A pdb=" N CYS E 89 " --> pdb=" O LEU E 114 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N SER E 116 " --> pdb=" O CYS E 89 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N PHE E 91 " --> pdb=" O SER E 116 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE E 141 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LYS E 247 " --> pdb=" O ARG E 221 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 114 through 116 removed outlier: 6.288A pdb=" N CYS E 89 " --> pdb=" O LEU E 114 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N SER E 116 " --> pdb=" O CYS E 89 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N PHE E 91 " --> pdb=" O SER E 116 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE E 141 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP E 223 " --> pdb=" O LYS E 244 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N GLU E 240 " --> pdb=" O THR E 227 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE E 259 " --> pdb=" O THR E 241 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 195 through 196 Processing sheet with id=AB6, first strand: chain 'E' and resid 261 through 262 removed outlier: 3.557A pdb=" N GLY E 266 " --> pdb=" O LEU E 262 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 38 through 39 Processing sheet with id=AB8, first strand: chain 'F' and resid 194 through 196 Processing sheet with id=AB9, first strand: chain 'F' and resid 284 through 285 removed outlier: 7.597A pdb=" N TYR F 290 " --> pdb=" O ILE F 297 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE F 297 " --> pdb=" O TYR F 290 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 38 through 39 Processing sheet with id=AC2, first strand: chain 'G' and resid 114 through 116 removed outlier: 3.554A pdb=" N LEU G 114 " --> pdb=" O CYS G 89 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL G 61 " --> pdb=" O PHE G 190 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLU G 62 " --> pdb=" O LEU G 222 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ILE G 224 " --> pdb=" O GLU G 62 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N TYR G 64 " --> pdb=" O ILE G 224 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N ARG G 226 " --> pdb=" O TYR G 64 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 230 through 231 removed outlier: 3.732A pdb=" N GLY G 238 " --> pdb=" O VAL G 230 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 220 through 226 current: chain 'G' and resid 266 through 267 Processing sheet with id=AC4, first strand: chain 'G' and resid 284 through 285 Processing sheet with id=AC5, first strand: chain 'H' and resid 38 through 39 Processing sheet with id=AC6, first strand: chain 'H' and resid 114 through 116 removed outlier: 6.652A pdb=" N ILE H 140 " --> pdb=" O ILE H 189 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ILE H 191 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL H 142 " --> pdb=" O ILE H 191 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLU H 62 " --> pdb=" O LEU H 222 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ILE H 224 " --> pdb=" O GLU H 62 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N TYR H 64 " --> pdb=" O ILE H 224 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N ARG H 226 " --> pdb=" O TYR H 64 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ARG H 221 " --> pdb=" O VAL H 246 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY H 238 " --> pdb=" O VAL H 230 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 114 through 116 removed outlier: 6.652A pdb=" N ILE H 140 " --> pdb=" O ILE H 189 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ILE H 191 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL H 142 " --> pdb=" O ILE H 191 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLU H 62 " --> pdb=" O LEU H 222 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ILE H 224 " --> pdb=" O GLU H 62 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N TYR H 64 " --> pdb=" O ILE H 224 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N ARG H 226 " --> pdb=" O TYR H 64 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ARG H 221 " --> pdb=" O VAL H 246 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 283 through 285 Processing sheet with id=AC9, first strand: chain 'I' and resid 24 through 25 removed outlier: 3.759A pdb=" N VAL J 115 " --> pdb=" O VAL I 25 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU J 114 " --> pdb=" O CYS J 89 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE J 189 " --> pdb=" O ILE J 140 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL J 220 " --> pdb=" O ASN J 248 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASN J 248 " --> pdb=" O VAL J 220 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N LEU J 222 " --> pdb=" O VAL J 246 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N VAL J 246 " --> pdb=" O LEU J 222 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ILE J 224 " --> pdb=" O LYS J 244 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LYS J 244 " --> pdb=" O ILE J 224 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ARG J 226 " --> pdb=" O ARG J 242 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ARG J 242 " --> pdb=" O ARG J 226 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N GLU J 232 " --> pdb=" O VAL J 236 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N VAL J 236 " --> pdb=" O GLU J 232 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 38 through 39 Processing sheet with id=AD2, first strand: chain 'I' and resid 114 through 116 removed outlier: 3.959A pdb=" N LEU I 114 " --> pdb=" O CYS I 89 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR I 64 " --> pdb=" O LEU I 222 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 226 through 232 removed outlier: 6.027A pdb=" N ARG I 226 " --> pdb=" O ARG I 242 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ARG I 242 " --> pdb=" O ARG I 226 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLU I 232 " --> pdb=" O VAL I 236 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL I 236 " --> pdb=" O GLU I 232 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE I 259 " --> pdb=" O THR I 241 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 284 through 285 removed outlier: 7.566A pdb=" N TYR I 290 " --> pdb=" O ILE I 297 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 38 through 39 Processing sheet with id=AD6, first strand: chain 'J' and resid 194 through 196 Processing sheet with id=AD7, first strand: chain 'J' and resid 290 through 292 removed outlier: 8.056A pdb=" N TYR J 290 " --> pdb=" O ILE J 297 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE J 297 " --> pdb=" O TYR J 290 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 38 through 39 Processing sheet with id=AD9, first strand: chain 'K' and resid 114 through 116 removed outlier: 3.751A pdb=" N LEU K 114 " --> pdb=" O CYS K 89 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL K 61 " --> pdb=" O PHE K 190 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 224 through 232 removed outlier: 6.919A pdb=" N ILE K 224 " --> pdb=" O VAL K 243 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL K 243 " --> pdb=" O ILE K 224 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ARG K 226 " --> pdb=" O THR K 241 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N THR K 241 " --> pdb=" O ARG K 226 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLY K 228 " --> pdb=" O SER K 239 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N SER K 239 " --> pdb=" O GLY K 228 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL K 230 " --> pdb=" O VAL K 237 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU K 235 " --> pdb=" O GLU K 232 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 290 through 292 removed outlier: 7.433A pdb=" N TYR K 290 " --> pdb=" O ILE K 297 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 38 through 39 Processing sheet with id=AE4, first strand: chain 'L' and resid 114 through 116 removed outlier: 3.674A pdb=" N SER L 116 " --> pdb=" O PHE L 91 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLU L 62 " --> pdb=" O LEU L 222 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 225 through 228 removed outlier: 5.499A pdb=" N ARG L 226 " --> pdb=" O ARG L 242 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ARG L 242 " --> pdb=" O ARG L 226 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 284 through 285 removed outlier: 7.206A pdb=" N TYR L 290 " --> pdb=" O ILE L 297 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE L 297 " --> pdb=" O TYR L 290 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 38 through 39 Processing sheet with id=AE8, first strand: chain 'C' and resid 114 through 116 removed outlier: 3.723A pdb=" N LEU C 114 " --> pdb=" O CYS C 89 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ARG C 221 " --> pdb=" O VAL C 246 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLU C 240 " --> pdb=" O THR C 227 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLN C 260 " --> pdb=" O TYR C 268 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 231 through 232 removed outlier: 3.913A pdb=" N GLU C 235 " --> pdb=" O GLU C 232 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 284 through 285 removed outlier: 7.626A pdb=" N TYR C 290 " --> pdb=" O ILE C 297 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE C 297 " --> pdb=" O TYR C 290 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 38 through 39 Processing sheet with id=AF3, first strand: chain 'M' and resid 114 through 116 removed outlier: 7.277A pdb=" N ILE M 60 " --> pdb=" O SER M 219 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ARG M 221 " --> pdb=" O ILE M 60 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLU M 62 " --> pdb=" O ARG M 221 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ASP M 223 " --> pdb=" O GLU M 62 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N TYR M 64 " --> pdb=" O ASP M 223 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ARG M 225 " --> pdb=" O TYR M 64 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ARG M 221 " --> pdb=" O VAL M 246 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N GLU M 240 " --> pdb=" O THR M 227 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 194 through 196 Processing sheet with id=AF5, first strand: chain 'M' and resid 231 through 232 removed outlier: 3.641A pdb=" N GLU M 235 " --> pdb=" O GLU M 232 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 290 through 292 removed outlier: 7.232A pdb=" N TYR M 290 " --> pdb=" O ILE M 297 " (cutoff:3.500A) 1439 hydrogen bonds defined for protein. 4035 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.99 Time building geometry restraints manager: 3.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 10178 1.36 - 1.50: 7445 1.50 - 1.65: 12643 1.65 - 1.80: 124 1.80 - 1.95: 73 Bond restraints: 30463 Sorted by residual: bond pdb=" N VAL G 61 " pdb=" CA VAL G 61 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.14e-02 7.69e+03 1.04e+01 bond pdb=" N VAL J 132 " pdb=" CA VAL J 132 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.33e-02 5.65e+03 1.04e+01 bond pdb=" N ASN J 311 " pdb=" CA ASN J 311 " ideal model delta sigma weight residual 1.462 1.493 -0.031 1.00e-02 1.00e+04 9.54e+00 bond pdb=" N ILE G 198 " pdb=" CA ILE G 198 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.15e-02 7.56e+03 9.34e+00 bond pdb=" N GLU H 284 " pdb=" CA GLU H 284 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.29e-02 6.01e+03 9.23e+00 ... (remaining 30458 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 40338 2.05 - 4.10: 904 4.10 - 6.16: 62 6.16 - 8.21: 4 8.21 - 10.26: 3 Bond angle restraints: 41311 Sorted by residual: angle pdb=" CA GLY F 300 " pdb=" C GLY F 300 " pdb=" O GLY F 300 " ideal model delta sigma weight residual 121.88 118.23 3.65 7.80e-01 1.64e+00 2.18e+01 angle pdb=" CA PRO B 113 " pdb=" N PRO B 113 " pdb=" CD PRO B 113 " ideal model delta sigma weight residual 112.00 106.11 5.89 1.40e+00 5.10e-01 1.77e+01 angle pdb=" C LYS H 285 " pdb=" N SER H 286 " pdb=" CA SER H 286 " ideal model delta sigma weight residual 122.16 115.95 6.21 1.50e+00 4.44e-01 1.71e+01 angle pdb=" CA GLY H 45 " pdb=" C GLY H 45 " pdb=" O GLY H 45 " ideal model delta sigma weight residual 121.00 116.85 4.15 1.08e+00 8.57e-01 1.48e+01 angle pdb=" CB ARG B 105 " pdb=" CG ARG B 105 " pdb=" CD ARG B 105 " ideal model delta sigma weight residual 111.30 120.06 -8.76 2.30e+00 1.89e-01 1.45e+01 ... (remaining 41306 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 16349 18.00 - 36.00: 1486 36.00 - 53.99: 480 53.99 - 71.99: 111 71.99 - 89.99: 31 Dihedral angle restraints: 18457 sinusoidal: 7692 harmonic: 10765 Sorted by residual: dihedral pdb=" CA ASN J 303 " pdb=" CB ASN J 303 " pdb=" CG ASN J 303 " pdb=" OD1 ASN J 303 " ideal model delta sinusoidal sigma weight residual -90.00 -161.92 71.92 2 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CB GLU A 101 " pdb=" CG GLU A 101 " pdb=" CD GLU A 101 " pdb=" OE1 GLU A 101 " ideal model delta sinusoidal sigma weight residual 0.00 89.99 -89.99 1 3.00e+01 1.11e-03 1.07e+01 dihedral pdb=" CB GLU J 206 " pdb=" CG GLU J 206 " pdb=" CD GLU J 206 " pdb=" OE1 GLU J 206 " ideal model delta sinusoidal sigma weight residual 0.00 89.91 -89.91 1 3.00e+01 1.11e-03 1.07e+01 ... (remaining 18454 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 4122 0.065 - 0.129: 604 0.129 - 0.194: 40 0.194 - 0.259: 2 0.259 - 0.324: 3 Chirality restraints: 4771 Sorted by residual: chirality pdb=" CB VAL J 132 " pdb=" CA VAL J 132 " pdb=" CG1 VAL J 132 " pdb=" CG2 VAL J 132 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CA VAL G 61 " pdb=" N VAL G 61 " pdb=" C VAL G 61 " pdb=" CB VAL G 61 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA VAL C 283 " pdb=" N VAL C 283 " pdb=" C VAL C 283 " pdb=" CB VAL C 283 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 4768 not shown) Planarity restraints: 5235 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 112 " 0.079 5.00e-02 4.00e+02 1.17e-01 2.18e+01 pdb=" N PRO B 113 " -0.202 5.00e-02 4.00e+02 pdb=" CA PRO B 113 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO B 113 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET J 130 " -0.020 2.00e-02 2.50e+03 3.93e-02 1.54e+01 pdb=" C MET J 130 " 0.068 2.00e-02 2.50e+03 pdb=" O MET J 130 " -0.026 2.00e-02 2.50e+03 pdb=" N LEU J 131 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 107 " 0.058 5.00e-02 4.00e+02 8.63e-02 1.19e+01 pdb=" N PRO B 108 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO B 108 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 108 " 0.047 5.00e-02 4.00e+02 ... (remaining 5232 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.33: 105 2.33 - 2.97: 17637 2.97 - 3.62: 44675 3.62 - 4.26: 67299 4.26 - 4.90: 112855 Nonbonded interactions: 242571 Sorted by model distance: nonbonded pdb="MG MG F 401 " pdb=" O3B AGS F 402 " model vdw 1.689 2.170 nonbonded pdb=" OG1 THR C 72 " pdb="MG MG C 401 " model vdw 1.744 2.170 nonbonded pdb="MG MG D 401 " pdb=" O2B AGS D 402 " model vdw 1.744 2.170 nonbonded pdb="MG MG L 401 " pdb=" O2B AGS L 402 " model vdw 1.781 2.170 nonbonded pdb=" OG1 THR I 72 " pdb="MG MG I 401 " model vdw 1.789 2.170 ... (remaining 242566 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' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 26.900 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 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 : 0.007 0.856 30464 Z= 0.566 Angle : 0.667 10.262 41311 Z= 0.413 Chirality : 0.046 0.324 4771 Planarity : 0.005 0.117 5235 Dihedral : 15.829 89.990 11625 Min Nonbonded Distance : 1.689 Molprobity Statistics. All-atom Clashscore : 45.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.25 % Favored : 94.62 % Rotamer: Outliers : 1.95 % Allowed : 20.37 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.14), residues: 3830 helix: 1.64 (0.14), residues: 1565 sheet: -1.09 (0.21), residues: 605 loop : -1.80 (0.14), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 18 TYR 0.013 0.001 TYR D 64 PHE 0.028 0.001 PHE E 202 TRP 0.017 0.002 TRP G 289 HIS 0.003 0.001 HIS K 96 Details of bonding type rmsd covalent geometry : bond 0.00508 (30463) covalent geometry : angle 0.66722 (41311) hydrogen bonds : bond 0.18865 ( 1408) hydrogen bonds : angle 7.53299 ( 4035) Misc. bond : bond 0.85556 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7660 Ramachandran restraints generated. 3830 Oldfield, 0 Emsley, 3830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7660 Ramachandran restraints generated. 3830 Oldfield, 0 Emsley, 3830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 3029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 571 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 ASP cc_start: 0.9004 (t70) cc_final: 0.8632 (t0) REVERT: B 126 MET cc_start: 0.8861 (mmt) cc_final: 0.8460 (mmm) REVERT: B 127 LYS cc_start: 0.9467 (ptmm) cc_final: 0.9182 (pptt) REVERT: B 146 ARG cc_start: 0.8878 (ptm160) cc_final: 0.8674 (ttp80) REVERT: D 126 GLU cc_start: 0.9079 (tp30) cc_final: 0.8584 (tm-30) REVERT: D 130 MET cc_start: 0.8615 (mmm) cc_final: 0.8142 (mmm) REVERT: D 170 MET cc_start: 0.9065 (mmm) cc_final: 0.8777 (mmm) REVERT: D 263 TYR cc_start: 0.7895 (m-10) cc_final: 0.7528 (m-10) REVERT: E 68 SER cc_start: 0.9020 (OUTLIER) cc_final: 0.8614 (p) REVERT: E 151 LYS cc_start: 0.9083 (tptt) cc_final: 0.8646 (tppt) REVERT: E 204 ASN cc_start: 0.8489 (t0) cc_final: 0.8239 (t0) REVERT: E 290 TYR cc_start: 0.8627 (m-10) cc_final: 0.8398 (m-10) REVERT: E 306 LYS cc_start: 0.9599 (mppt) cc_final: 0.9193 (pttm) REVERT: E 324 ASP cc_start: 0.9284 (t0) cc_final: 0.8912 (m-30) REVERT: F 130 MET cc_start: 0.8833 (ptp) cc_final: 0.8594 (mtm) REVERT: F 151 LYS cc_start: 0.9257 (tptp) cc_final: 0.9025 (tppt) REVERT: F 319 GLU cc_start: 0.9043 (OUTLIER) cc_final: 0.8800 (pp20) REVERT: G 68 SER cc_start: 0.9531 (OUTLIER) cc_final: 0.9228 (t) REVERT: G 290 TYR cc_start: 0.7410 (m-10) cc_final: 0.6859 (m-80) REVERT: H 151 LYS cc_start: 0.8802 (tptt) cc_final: 0.8214 (tppt) REVERT: H 290 TYR cc_start: 0.7971 (m-80) cc_final: 0.5742 (m-80) REVERT: H 301 LYS cc_start: 0.9001 (mmtp) cc_final: 0.8738 (mmmt) REVERT: I 27 ARG cc_start: 0.7980 (mtt-85) cc_final: 0.7486 (mtt-85) REVERT: I 162 HIS cc_start: 0.7518 (m90) cc_final: 0.7190 (m-70) REVERT: I 290 TYR cc_start: 0.8173 (m-80) cc_final: 0.7745 (m-80) REVERT: I 307 TYR cc_start: 0.8785 (t80) cc_final: 0.8528 (t80) REVERT: J 319 GLU cc_start: 0.9155 (pt0) cc_final: 0.8791 (pp20) REVERT: K 26 MET cc_start: 0.2515 (ppp) cc_final: 0.1900 (ppp) REVERT: K 130 MET cc_start: 0.8995 (mtt) cc_final: 0.8352 (mtp) REVERT: K 151 LYS cc_start: 0.9233 (tmmt) cc_final: 0.8633 (tppt) REVERT: K 204 ASN cc_start: 0.8891 (t0) cc_final: 0.8636 (t0) REVERT: K 206 GLU cc_start: 0.8843 (mm-30) cc_final: 0.8456 (mt-10) REVERT: L 28 MET cc_start: 0.6894 (mmm) cc_final: 0.6501 (mmm) REVERT: L 57 LYS cc_start: 0.9338 (mtpt) cc_final: 0.8904 (ttmm) REVERT: L 68 SER cc_start: 0.9633 (OUTLIER) cc_final: 0.8910 (t) REVERT: L 102 TYR cc_start: 0.8991 (t80) cc_final: 0.8328 (t80) REVERT: L 130 MET cc_start: 0.8541 (mtp) cc_final: 0.8061 (ttm) REVERT: L 244 LYS cc_start: 0.9034 (tttp) cc_final: 0.8719 (tptt) REVERT: L 268 TYR cc_start: 0.8678 (t80) cc_final: 0.8341 (t80) REVERT: L 323 ARG cc_start: 0.9228 (ttm-80) cc_final: 0.9016 (ttm110) REVERT: C 31 HIS cc_start: 0.7249 (m90) cc_final: 0.6988 (m170) REVERT: C 85 GLN cc_start: 0.9294 (tp40) cc_final: 0.9018 (tm-30) REVERT: C 130 MET cc_start: 0.9144 (mmp) cc_final: 0.8633 (ttt) REVERT: C 215 LYS cc_start: 0.9225 (ptpt) cc_final: 0.8873 (ptpp) REVERT: C 221 ARG cc_start: 0.8774 (ttp80) cc_final: 0.8173 (mtp-110) REVERT: C 254 PHE cc_start: 0.9027 (m-80) cc_final: 0.8817 (m-80) REVERT: C 290 TYR cc_start: 0.8686 (m-10) cc_final: 0.8411 (m-10) REVERT: C 292 TYR cc_start: 0.7663 (t80) cc_final: 0.7162 (t80) REVERT: C 313 GLU cc_start: 0.9214 (mp0) cc_final: 0.8987 (pm20) REVERT: M 151 LYS cc_start: 0.9223 (tptt) cc_final: 0.8989 (tppt) REVERT: M 204 ASN cc_start: 0.8858 (p0) cc_final: 0.8587 (p0) outliers start: 59 outliers final: 8 residues processed: 618 average time/residue: 0.2529 time to fit residues: 223.8669 Evaluate side-chains 407 residues out of total 3029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 395 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 ARG Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 303 ASN Chi-restraints excluded: chain I residue 196 MET Chi-restraints excluded: chain J residue 299 GLN Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 237 VAL Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 286 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 10.0000 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 GLN A 190 GLN ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 GLN ** F 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 ASN F 325 GLN ** G 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 311 ASN ** I 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 85 GLN K 162 HIS L 299 GLN C 15 GLN C 19 GLN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 HIS ** M 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.056726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.041429 restraints weight = 145418.498| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 4.25 r_work: 0.2807 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 30464 Z= 0.227 Angle : 0.751 12.311 41311 Z= 0.389 Chirality : 0.048 0.180 4771 Planarity : 0.005 0.083 5235 Dihedral : 13.236 84.094 4734 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.11 % Favored : 96.84 % Rotamer: Outliers : 4.03 % Allowed : 19.15 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.13), residues: 3830 helix: 1.28 (0.13), residues: 1596 sheet: -0.72 (0.21), residues: 595 loop : -1.66 (0.14), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 323 TYR 0.029 0.002 TYR G 307 PHE 0.029 0.002 PHE I 20 TRP 0.022 0.003 TRP D 289 HIS 0.008 0.001 HIS K 162 Details of bonding type rmsd covalent geometry : bond 0.00533 (30463) covalent geometry : angle 0.75140 (41311) hydrogen bonds : bond 0.04861 ( 1408) hydrogen bonds : angle 5.77642 ( 4035) Misc. bond : bond 0.00229 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7660 Ramachandran restraints generated. 3830 Oldfield, 0 Emsley, 3830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7660 Ramachandran restraints generated. 3830 Oldfield, 0 Emsley, 3830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 3029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 438 time to evaluate : 1.066 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.8783 (mmm) cc_final: 0.8433 (mmm) REVERT: A 165 LYS cc_start: 0.9370 (tppt) cc_final: 0.8998 (tppt) REVERT: B 95 LEU cc_start: 0.9386 (pt) cc_final: 0.8962 (mm) REVERT: B 117 TYR cc_start: 0.8702 (p90) cc_final: 0.8500 (p90) REVERT: B 126 MET cc_start: 0.8953 (mmt) cc_final: 0.8428 (mmm) REVERT: B 127 LYS cc_start: 0.9422 (ptmm) cc_final: 0.9208 (ptmm) REVERT: B 146 ARG cc_start: 0.9329 (ptm160) cc_final: 0.9128 (ttp80) REVERT: D 126 GLU cc_start: 0.9258 (tp30) cc_final: 0.8712 (tm-30) REVERT: D 162 HIS cc_start: 0.8638 (m-70) cc_final: 0.8418 (m-70) REVERT: D 170 MET cc_start: 0.9232 (mmm) cc_final: 0.8975 (mmm) REVERT: D 197 LYS cc_start: 0.9446 (ptmm) cc_final: 0.9211 (ptpp) REVERT: D 263 TYR cc_start: 0.8204 (m-10) cc_final: 0.7705 (m-10) REVERT: D 268 TYR cc_start: 0.8603 (t80) cc_final: 0.8327 (t80) REVERT: E 7 ARG cc_start: 0.9529 (ttm-80) cc_final: 0.9249 (ttm110) REVERT: E 68 SER cc_start: 0.9373 (OUTLIER) cc_final: 0.9017 (p) REVERT: E 130 MET cc_start: 0.9270 (mtp) cc_final: 0.8899 (mtp) REVERT: E 151 LYS cc_start: 0.9236 (tptt) cc_final: 0.8749 (tppt) REVERT: E 158 MET cc_start: 0.8635 (tpp) cc_final: 0.8078 (tpp) REVERT: E 204 ASN cc_start: 0.8820 (t0) cc_final: 0.8390 (t0) REVERT: E 276 LEU cc_start: 0.9512 (mm) cc_final: 0.9304 (tp) REVERT: E 324 ASP cc_start: 0.9470 (OUTLIER) cc_final: 0.9086 (m-30) REVERT: F 112 ASP cc_start: 0.9162 (t0) cc_final: 0.8792 (p0) REVERT: F 144 SER cc_start: 0.9319 (OUTLIER) cc_final: 0.8949 (p) REVERT: F 151 LYS cc_start: 0.9459 (tptp) cc_final: 0.9127 (tppt) REVERT: F 280 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9112 (tt) REVERT: G 6 LYS cc_start: 0.9637 (mtmt) cc_final: 0.9271 (mtmt) REVERT: G 7 ARG cc_start: 0.9414 (mtm-85) cc_final: 0.9086 (ptp90) REVERT: G 25 VAL cc_start: 0.7094 (OUTLIER) cc_final: 0.6873 (t) REVERT: G 105 LYS cc_start: 0.9500 (ttpt) cc_final: 0.9275 (ttpp) REVERT: G 158 MET cc_start: 0.8200 (mtm) cc_final: 0.7810 (mtm) REVERT: G 265 LYS cc_start: 0.9497 (mmmt) cc_final: 0.9091 (tmtt) REVERT: H 151 LYS cc_start: 0.9133 (tptt) cc_final: 0.8876 (tppt) REVERT: H 158 MET cc_start: 0.7824 (tpp) cc_final: 0.7560 (tpp) REVERT: H 320 LYS cc_start: 0.9533 (mmmt) cc_final: 0.9153 (ptpp) REVERT: I 7 ARG cc_start: 0.8940 (ptp-170) cc_final: 0.8342 (ptt90) REVERT: I 18 ARG cc_start: 0.9430 (ptp-170) cc_final: 0.9225 (ptp90) REVERT: I 26 MET cc_start: 0.8040 (tmm) cc_final: 0.7552 (tmm) REVERT: I 143 ASP cc_start: 0.8028 (t0) cc_final: 0.7798 (t0) REVERT: I 162 HIS cc_start: 0.7861 (m90) cc_final: 0.7580 (m-70) REVERT: I 197 LYS cc_start: 0.9215 (ptpp) cc_final: 0.8785 (ptpp) REVERT: I 265 LYS cc_start: 0.9400 (mmmt) cc_final: 0.9118 (mtmm) REVERT: I 290 TYR cc_start: 0.8285 (m-80) cc_final: 0.7318 (m-80) REVERT: I 307 TYR cc_start: 0.8894 (t80) cc_final: 0.8661 (t80) REVERT: I 320 LYS cc_start: 0.9524 (tppt) cc_final: 0.9276 (tppt) REVERT: J 215 LYS cc_start: 0.9345 (ptpt) cc_final: 0.9100 (ptpp) REVERT: J 256 GLN cc_start: 0.9472 (pp30) cc_final: 0.8839 (pp30) REVERT: J 306 LYS cc_start: 0.9453 (pttp) cc_final: 0.9213 (pttm) REVERT: J 319 GLU cc_start: 0.9354 (pt0) cc_final: 0.8975 (pp20) REVERT: K 151 LYS cc_start: 0.9016 (tmmt) cc_final: 0.8687 (tppt) REVERT: K 162 HIS cc_start: 0.8211 (m-70) cc_final: 0.8006 (m-70) REVERT: K 204 ASN cc_start: 0.8881 (t0) cc_final: 0.8652 (t0) REVERT: K 206 GLU cc_start: 0.9086 (OUTLIER) cc_final: 0.8645 (mt-10) REVERT: K 268 TYR cc_start: 0.9165 (t80) cc_final: 0.8472 (t80) REVERT: K 323 ARG cc_start: 0.8993 (ttp-110) cc_final: 0.8791 (mtm110) REVERT: L 67 GLU cc_start: 0.8570 (pp20) cc_final: 0.8139 (tm-30) REVERT: L 68 SER cc_start: 0.9527 (OUTLIER) cc_final: 0.8863 (p) REVERT: L 196 MET cc_start: 0.9101 (ptp) cc_final: 0.8882 (pmm) REVERT: L 268 TYR cc_start: 0.9231 (t80) cc_final: 0.8426 (t80) REVERT: L 289 TRP cc_start: 0.8763 (t60) cc_final: 0.8526 (t-100) REVERT: L 323 ARG cc_start: 0.9460 (ttm-80) cc_final: 0.9149 (ttm110) REVERT: C 85 GLN cc_start: 0.9511 (tp40) cc_final: 0.9271 (tm-30) REVERT: C 215 LYS cc_start: 0.9420 (ptpt) cc_final: 0.9014 (ptpp) REVERT: C 221 ARG cc_start: 0.9099 (ttp80) cc_final: 0.8572 (mtp-110) REVERT: C 254 PHE cc_start: 0.9234 (m-80) cc_final: 0.8941 (m-80) REVERT: C 268 TYR cc_start: 0.8874 (t80) cc_final: 0.8485 (t80) REVERT: C 292 TYR cc_start: 0.7997 (t80) cc_final: 0.7437 (t80) REVERT: M 64 TYR cc_start: 0.8660 (p90) cc_final: 0.8416 (p90) REVERT: M 151 LYS cc_start: 0.9274 (tptt) cc_final: 0.9036 (tppt) REVERT: M 158 MET cc_start: 0.9138 (tpp) cc_final: 0.8686 (tpp) REVERT: M 162 HIS cc_start: 0.8350 (m-70) cc_final: 0.7869 (m-70) REVERT: M 242 ARG cc_start: 0.8277 (ttp80) cc_final: 0.7836 (ttp80) REVERT: M 268 TYR cc_start: 0.8925 (t80) cc_final: 0.8660 (t80) REVERT: M 324 ASP cc_start: 0.9183 (p0) cc_final: 0.8488 (p0) outliers start: 122 outliers final: 59 residues processed: 546 average time/residue: 0.2385 time to fit residues: 191.0799 Evaluate side-chains 453 residues out of total 3029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 387 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 207 THR Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 297 ILE Chi-restraints excluded: chain E residue 324 ASP Chi-restraints excluded: chain F residue 77 SER Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 144 SER Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 220 VAL Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 186 CYS Chi-restraints excluded: chain G residue 215 LYS Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain G residue 289 TRP Chi-restraints excluded: chain G residue 303 ASN Chi-restraints excluded: chain G residue 318 LEU Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 311 ASN Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain J residue 326 LEU Chi-restraints excluded: chain K residue 28 MET Chi-restraints excluded: chain K residue 149 VAL Chi-restraints excluded: chain K residue 206 GLU Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 111 ASP Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain L residue 157 GLU Chi-restraints excluded: chain L residue 162 HIS Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain L residue 239 SER Chi-restraints excluded: chain L residue 245 VAL Chi-restraints excluded: chain L residue 272 GLU Chi-restraints excluded: chain L residue 276 LEU Chi-restraints excluded: chain L residue 327 LEU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain M residue 27 ARG Chi-restraints excluded: chain M residue 31 HIS Chi-restraints excluded: chain M residue 260 GLN Chi-restraints excluded: chain M residue 263 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 334 optimal weight: 8.9990 chunk 177 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 333 optimal weight: 7.9990 chunk 179 optimal weight: 5.9990 chunk 197 optimal weight: 3.9990 chunk 136 optimal weight: 9.9990 chunk 256 optimal weight: 10.0000 chunk 169 optimal weight: 1.9990 chunk 349 optimal weight: 20.0000 chunk 192 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 GLN ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 ASN E 256 GLN ** G 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 117 GLN ** I 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 GLN ** L 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 GLN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN ** C 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.055743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.040631 restraints weight = 145353.548| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 4.18 r_work: 0.2777 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 30464 Z= 0.254 Angle : 0.703 10.822 41311 Z= 0.364 Chirality : 0.047 0.219 4771 Planarity : 0.005 0.082 5235 Dihedral : 13.106 84.963 4718 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.99 % Favored : 95.98 % Rotamer: Outliers : 4.59 % Allowed : 19.45 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.13), residues: 3830 helix: 1.34 (0.13), residues: 1535 sheet: -0.73 (0.20), residues: 656 loop : -1.54 (0.15), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 120 TYR 0.031 0.002 TYR L 102 PHE 0.018 0.002 PHE E 202 TRP 0.028 0.002 TRP E 289 HIS 0.016 0.001 HIS M 31 Details of bonding type rmsd covalent geometry : bond 0.00581 (30463) covalent geometry : angle 0.70281 (41311) hydrogen bonds : bond 0.04165 ( 1408) hydrogen bonds : angle 5.41775 ( 4035) Misc. bond : bond 0.00086 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7660 Ramachandran restraints generated. 3830 Oldfield, 0 Emsley, 3830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7660 Ramachandran restraints generated. 3830 Oldfield, 0 Emsley, 3830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 3029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 410 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.8767 (mmm) cc_final: 0.8379 (mmm) REVERT: A 127 LYS cc_start: 0.9468 (ptmt) cc_final: 0.9254 (ptpt) REVERT: A 165 LYS cc_start: 0.9338 (tppt) cc_final: 0.9077 (tppt) REVERT: B 114 ARG cc_start: 0.9207 (tpt90) cc_final: 0.8562 (tpt90) REVERT: B 126 MET cc_start: 0.9027 (mmt) cc_final: 0.8589 (mmm) REVERT: B 172 TRP cc_start: 0.9293 (m-10) cc_final: 0.8868 (m-10) REVERT: D 26 MET cc_start: 0.4819 (ppp) cc_final: 0.3135 (ppp) REVERT: D 28 MET cc_start: 0.2972 (mmt) cc_final: 0.2508 (mmp) REVERT: D 126 GLU cc_start: 0.9147 (tp30) cc_final: 0.8843 (tm-30) REVERT: D 162 HIS cc_start: 0.8687 (m-70) cc_final: 0.8286 (m90) REVERT: D 197 LYS cc_start: 0.9399 (ptmm) cc_final: 0.9196 (ptpp) REVERT: D 299 GLN cc_start: 0.8434 (mp-120) cc_final: 0.8013 (tp40) REVERT: E 68 SER cc_start: 0.9430 (OUTLIER) cc_final: 0.9164 (p) REVERT: E 151 LYS cc_start: 0.9226 (tptt) cc_final: 0.8764 (tppt) REVERT: E 204 ASN cc_start: 0.8683 (t0) cc_final: 0.8322 (t0) REVERT: E 276 LEU cc_start: 0.9528 (mm) cc_final: 0.9306 (tp) REVERT: E 324 ASP cc_start: 0.9478 (OUTLIER) cc_final: 0.9091 (m-30) REVERT: F 151 LYS cc_start: 0.9430 (tptp) cc_final: 0.9121 (tppt) REVERT: F 206 GLU cc_start: 0.8237 (mp0) cc_final: 0.7932 (mp0) REVERT: F 280 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9150 (tt) REVERT: G 7 ARG cc_start: 0.9427 (mtm-85) cc_final: 0.9028 (ptp-110) REVERT: G 105 LYS cc_start: 0.9475 (ttpt) cc_final: 0.9265 (ttpt) REVERT: G 158 MET cc_start: 0.8358 (mtm) cc_final: 0.7918 (mtm) REVERT: G 290 TYR cc_start: 0.8210 (m-80) cc_final: 0.6829 (m-80) REVERT: G 306 LYS cc_start: 0.9586 (pttm) cc_final: 0.9364 (ptpp) REVERT: H 105 LYS cc_start: 0.9462 (OUTLIER) cc_final: 0.8949 (mtmm) REVERT: H 151 LYS cc_start: 0.9315 (tptt) cc_final: 0.9024 (tppt) REVERT: H 320 LYS cc_start: 0.9575 (mmmt) cc_final: 0.9248 (ptpt) REVERT: I 27 ARG cc_start: 0.8170 (ptt-90) cc_final: 0.7963 (ptt-90) REVERT: I 162 HIS cc_start: 0.7904 (m90) cc_final: 0.7585 (m-70) REVERT: I 307 TYR cc_start: 0.8892 (t80) cc_final: 0.8666 (t80) REVERT: I 320 LYS cc_start: 0.9549 (tppt) cc_final: 0.9219 (tppt) REVERT: J 196 MET cc_start: 0.8754 (mpp) cc_final: 0.8532 (mpp) REVERT: J 215 LYS cc_start: 0.9390 (ptpt) cc_final: 0.9152 (ptpp) REVERT: J 256 GLN cc_start: 0.9491 (pp30) cc_final: 0.8865 (pp30) REVERT: J 319 GLU cc_start: 0.9325 (pt0) cc_final: 0.8936 (pp20) REVERT: K 18 ARG cc_start: 0.9387 (ptt-90) cc_final: 0.9149 (ptt90) REVERT: K 22 LYS cc_start: 0.9177 (mmmt) cc_final: 0.8956 (pptt) REVERT: K 151 LYS cc_start: 0.9119 (tmmt) cc_final: 0.8805 (tppt) REVERT: K 204 ASN cc_start: 0.8867 (t0) cc_final: 0.8648 (t0) REVERT: K 206 GLU cc_start: 0.9099 (OUTLIER) cc_final: 0.8664 (mt-10) REVERT: K 268 TYR cc_start: 0.9061 (t80) cc_final: 0.8825 (t80) REVERT: L 196 MET cc_start: 0.9177 (ptp) cc_final: 0.8953 (pmm) REVERT: L 244 LYS cc_start: 0.9049 (tttp) cc_final: 0.8757 (tptt) REVERT: L 268 TYR cc_start: 0.9110 (t80) cc_final: 0.8313 (t80) REVERT: L 289 TRP cc_start: 0.8914 (t60) cc_final: 0.8450 (t-100) REVERT: L 290 TYR cc_start: 0.9044 (m-80) cc_final: 0.8654 (m-10) REVERT: L 307 TYR cc_start: 0.8113 (t80) cc_final: 0.7532 (t80) REVERT: L 323 ARG cc_start: 0.9440 (ttm-80) cc_final: 0.9160 (ttm110) REVERT: C 85 GLN cc_start: 0.9528 (tp40) cc_final: 0.9298 (tm-30) REVERT: C 91 PHE cc_start: 0.8721 (t80) cc_final: 0.8471 (t80) REVERT: C 151 LYS cc_start: 0.8904 (tppt) cc_final: 0.8487 (tppt) REVERT: C 155 GLU cc_start: 0.9253 (mt-10) cc_final: 0.9044 (pp20) REVERT: C 215 LYS cc_start: 0.9466 (ptpt) cc_final: 0.9075 (ptpp) REVERT: C 221 ARG cc_start: 0.9119 (ttp80) cc_final: 0.8563 (mtp-110) REVERT: C 254 PHE cc_start: 0.9274 (m-80) cc_final: 0.8951 (m-80) REVERT: C 292 TYR cc_start: 0.8033 (t80) cc_final: 0.7560 (t80) REVERT: C 320 LYS cc_start: 0.9722 (mmmt) cc_final: 0.9483 (tppt) REVERT: M 26 MET cc_start: 0.7057 (ppp) cc_final: 0.6022 (tmm) REVERT: M 64 TYR cc_start: 0.8804 (p90) cc_final: 0.8556 (p90) REVERT: M 151 LYS cc_start: 0.9300 (tptt) cc_final: 0.9075 (tppt) REVERT: M 162 HIS cc_start: 0.8322 (m-70) cc_final: 0.7817 (m-70) REVERT: M 320 LYS cc_start: 0.9743 (tppt) cc_final: 0.9478 (mmmt) REVERT: M 324 ASP cc_start: 0.9148 (OUTLIER) cc_final: 0.8693 (p0) outliers start: 139 outliers final: 77 residues processed: 523 average time/residue: 0.2222 time to fit residues: 171.6302 Evaluate side-chains 457 residues out of total 3029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 374 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 112 ASN Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 297 ILE Chi-restraints excluded: chain E residue 324 ASP Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 220 VAL Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain G residue 28 MET Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 186 CYS Chi-restraints excluded: chain G residue 215 LYS Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain G residue 289 TRP Chi-restraints excluded: chain G residue 303 ASN Chi-restraints excluded: chain G residue 318 LEU Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 105 LYS Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 230 VAL Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 158 MET Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 230 VAL Chi-restraints excluded: chain I residue 261 ILE Chi-restraints excluded: chain J residue 119 ASP Chi-restraints excluded: chain J residue 220 VAL Chi-restraints excluded: chain J residue 230 VAL Chi-restraints excluded: chain K residue 28 MET Chi-restraints excluded: chain K residue 149 VAL Chi-restraints excluded: chain K residue 206 GLU Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 303 ASN Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 111 ASP Chi-restraints excluded: chain L residue 130 MET Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain L residue 149 VAL Chi-restraints excluded: chain L residue 157 GLU Chi-restraints excluded: chain L residue 162 HIS Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain L residue 236 VAL Chi-restraints excluded: chain L residue 245 VAL Chi-restraints excluded: chain L residue 272 GLU Chi-restraints excluded: chain L residue 276 LEU Chi-restraints excluded: chain L residue 327 LEU Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 289 TRP Chi-restraints excluded: chain M residue 27 ARG Chi-restraints excluded: chain M residue 130 MET Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 197 LYS Chi-restraints excluded: chain M residue 208 THR Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain M residue 324 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 84 optimal weight: 9.9990 chunk 291 optimal weight: 10.0000 chunk 204 optimal weight: 7.9990 chunk 135 optimal weight: 6.9990 chunk 312 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 348 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 265 optimal weight: 0.9980 chunk 189 optimal weight: 0.8980 chunk 133 optimal weight: 0.8980 overall best weight: 2.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 279 GLN ** H 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 85 GLN ** K 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 166 GLN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 303 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.056887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.041442 restraints weight = 143380.621| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 4.22 r_work: 0.2823 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 30464 Z= 0.157 Angle : 0.663 11.873 41311 Z= 0.341 Chirality : 0.045 0.293 4771 Planarity : 0.004 0.096 5235 Dihedral : 12.933 86.061 4714 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.34 % Favored : 96.63 % Rotamer: Outliers : 3.93 % Allowed : 20.86 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.13), residues: 3830 helix: 1.28 (0.13), residues: 1545 sheet: -0.56 (0.20), residues: 665 loop : -1.46 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 146 TYR 0.034 0.002 TYR L 102 PHE 0.020 0.001 PHE J 91 TRP 0.032 0.003 TRP E 289 HIS 0.010 0.001 HIS M 31 Details of bonding type rmsd covalent geometry : bond 0.00367 (30463) covalent geometry : angle 0.66316 (41311) hydrogen bonds : bond 0.03609 ( 1408) hydrogen bonds : angle 5.23602 ( 4035) Misc. bond : bond 0.00057 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7660 Ramachandran restraints generated. 3830 Oldfield, 0 Emsley, 3830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7660 Ramachandran restraints generated. 3830 Oldfield, 0 Emsley, 3830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 397 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.8797 (mmm) cc_final: 0.8572 (mmm) REVERT: A 165 LYS cc_start: 0.9336 (tppt) cc_final: 0.9067 (tppt) REVERT: B 126 MET cc_start: 0.9152 (mmt) cc_final: 0.8605 (mmm) REVERT: D 126 GLU cc_start: 0.9115 (tp30) cc_final: 0.8828 (tm-30) REVERT: D 162 HIS cc_start: 0.8679 (m-70) cc_final: 0.8314 (m90) REVERT: D 196 MET cc_start: 0.8604 (ppp) cc_final: 0.8235 (ppp) REVERT: D 299 GLN cc_start: 0.8447 (mp-120) cc_final: 0.8047 (tp40) REVERT: E 151 LYS cc_start: 0.9189 (tptt) cc_final: 0.8658 (tppt) REVERT: E 204 ASN cc_start: 0.8653 (t0) cc_final: 0.8322 (t0) REVERT: E 242 ARG cc_start: 0.8896 (mtm110) cc_final: 0.8657 (mtp-110) REVERT: E 276 LEU cc_start: 0.9542 (mm) cc_final: 0.9314 (tp) REVERT: E 290 TYR cc_start: 0.9079 (m-10) cc_final: 0.8807 (m-10) REVERT: E 324 ASP cc_start: 0.9454 (OUTLIER) cc_final: 0.9088 (m-30) REVERT: F 28 MET cc_start: 0.3919 (mmt) cc_final: 0.2896 (mmp) REVERT: F 112 ASP cc_start: 0.9171 (t0) cc_final: 0.8878 (p0) REVERT: F 151 LYS cc_start: 0.9382 (tptp) cc_final: 0.9066 (tppt) REVERT: F 157 GLU cc_start: 0.8364 (tm-30) cc_final: 0.8117 (tm-30) REVERT: F 158 MET cc_start: 0.7955 (tpp) cc_final: 0.7612 (tpp) REVERT: F 206 GLU cc_start: 0.8257 (mp0) cc_final: 0.8030 (mp0) REVERT: F 241 THR cc_start: 0.9158 (OUTLIER) cc_final: 0.8923 (p) REVERT: G 2 ASP cc_start: 0.9346 (t0) cc_final: 0.9100 (t0) REVERT: G 6 LYS cc_start: 0.9563 (mtmt) cc_final: 0.9340 (mtmt) REVERT: G 7 ARG cc_start: 0.9412 (mtm-85) cc_final: 0.9032 (ptp-110) REVERT: G 84 LYS cc_start: 0.9100 (tmmt) cc_final: 0.8831 (ptpp) REVERT: G 105 LYS cc_start: 0.9454 (ttpt) cc_final: 0.9238 (ttpt) REVERT: G 158 MET cc_start: 0.8339 (mtm) cc_final: 0.7920 (mtm) REVERT: G 265 LYS cc_start: 0.9536 (mmmt) cc_final: 0.9234 (mtmm) REVERT: G 290 TYR cc_start: 0.7733 (m-80) cc_final: 0.7124 (m-80) REVERT: H 320 LYS cc_start: 0.9602 (mmmt) cc_final: 0.9361 (mttt) REVERT: I 18 ARG cc_start: 0.9370 (ptp-170) cc_final: 0.9117 (ptt-90) REVERT: I 143 ASP cc_start: 0.7996 (t0) cc_final: 0.7727 (t0) REVERT: I 151 LYS cc_start: 0.9443 (tppt) cc_final: 0.9213 (tppt) REVERT: I 162 HIS cc_start: 0.7853 (m90) cc_final: 0.7567 (m-70) REVERT: I 252 PRO cc_start: 0.9208 (Cg_exo) cc_final: 0.8996 (Cg_endo) REVERT: I 265 LYS cc_start: 0.9398 (mmmt) cc_final: 0.9195 (mtmm) REVERT: I 278 VAL cc_start: 0.9585 (p) cc_final: 0.9360 (m) REVERT: I 307 TYR cc_start: 0.8895 (t80) cc_final: 0.8603 (t80) REVERT: I 320 LYS cc_start: 0.9570 (tppt) cc_final: 0.9264 (tppt) REVERT: J 151 LYS cc_start: 0.9387 (tppt) cc_final: 0.9169 (tppt) REVERT: J 196 MET cc_start: 0.8715 (mpp) cc_final: 0.8462 (mpp) REVERT: J 206 GLU cc_start: 0.8748 (mp0) cc_final: 0.8518 (pm20) REVERT: J 215 LYS cc_start: 0.9349 (ptpt) cc_final: 0.9113 (ptpp) REVERT: J 242 ARG cc_start: 0.8737 (ptm-80) cc_final: 0.8484 (ptm-80) REVERT: J 256 GLN cc_start: 0.9461 (pp30) cc_final: 0.8872 (pp30) REVERT: J 319 GLU cc_start: 0.9277 (pt0) cc_final: 0.8882 (pp20) REVERT: K 18 ARG cc_start: 0.9406 (ptt-90) cc_final: 0.9191 (ptt90) REVERT: K 84 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.9000 (ptpp) REVERT: K 151 LYS cc_start: 0.9119 (tmmt) cc_final: 0.8819 (tppt) REVERT: K 204 ASN cc_start: 0.8814 (t0) cc_final: 0.8512 (t0) REVERT: K 268 TYR cc_start: 0.9120 (t80) cc_final: 0.8886 (t80) REVERT: L 196 MET cc_start: 0.9183 (ptp) cc_final: 0.8932 (pmm) REVERT: L 268 TYR cc_start: 0.9004 (t80) cc_final: 0.8155 (t80) REVERT: L 290 TYR cc_start: 0.8967 (m-80) cc_final: 0.8256 (m-10) REVERT: L 307 TYR cc_start: 0.8107 (t80) cc_final: 0.7493 (t80) REVERT: L 323 ARG cc_start: 0.9466 (ttm-80) cc_final: 0.9169 (ttm110) REVERT: C 89 CYS cc_start: 0.5741 (t) cc_final: 0.5530 (t) REVERT: C 151 LYS cc_start: 0.8970 (tppt) cc_final: 0.8544 (tppt) REVERT: C 155 GLU cc_start: 0.9275 (mt-10) cc_final: 0.9058 (pp20) REVERT: C 215 LYS cc_start: 0.9450 (ptpt) cc_final: 0.9062 (ptpp) REVERT: C 254 PHE cc_start: 0.9240 (m-80) cc_final: 0.8919 (m-80) REVERT: C 292 TYR cc_start: 0.8087 (t80) cc_final: 0.7686 (t80) REVERT: C 320 LYS cc_start: 0.9726 (mmmt) cc_final: 0.9492 (tppt) REVERT: M 26 MET cc_start: 0.6540 (ppp) cc_final: 0.5960 (ppp) REVERT: M 64 TYR cc_start: 0.8845 (p90) cc_final: 0.8577 (p90) REVERT: M 151 LYS cc_start: 0.9286 (tptt) cc_final: 0.9061 (tppt) REVERT: M 162 HIS cc_start: 0.8257 (m-70) cc_final: 0.7728 (m-70) REVERT: M 324 ASP cc_start: 0.8942 (OUTLIER) cc_final: 0.8548 (p0) outliers start: 119 outliers final: 72 residues processed: 493 average time/residue: 0.2231 time to fit residues: 161.7043 Evaluate side-chains 444 residues out of total 3029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 368 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 112 ASN Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 324 ASP Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 220 VAL Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 197 LYS Chi-restraints excluded: chain G residue 289 TRP Chi-restraints excluded: chain G residue 303 ASN Chi-restraints excluded: chain G residue 318 LEU Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 105 LYS Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 230 VAL Chi-restraints excluded: chain H residue 239 SER Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 158 MET Chi-restraints excluded: chain I residue 230 VAL Chi-restraints excluded: chain I residue 261 ILE Chi-restraints excluded: chain J residue 119 ASP Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 220 VAL Chi-restraints excluded: chain J residue 230 VAL Chi-restraints excluded: chain K residue 28 MET Chi-restraints excluded: chain K residue 84 LYS Chi-restraints excluded: chain K residue 149 VAL Chi-restraints excluded: chain K residue 206 GLU Chi-restraints excluded: chain K residue 303 ASN Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 111 ASP Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain L residue 149 VAL Chi-restraints excluded: chain L residue 162 HIS Chi-restraints excluded: chain L residue 200 VAL Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain L residue 245 VAL Chi-restraints excluded: chain L residue 272 GLU Chi-restraints excluded: chain L residue 276 LEU Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain M residue 324 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 359 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 197 optimal weight: 3.9990 chunk 266 optimal weight: 2.9990 chunk 108 optimal weight: 0.0060 chunk 361 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 300 optimal weight: 8.9990 chunk 256 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 230 optimal weight: 3.9990 overall best weight: 3.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 162 HIS ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 192 ASN ** H 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 260 GLN ** 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 = 0.3502 r_free = 0.3502 target = 0.056124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.040714 restraints weight = 144455.684| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 4.21 r_work: 0.2800 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 30464 Z= 0.201 Angle : 0.671 10.738 41311 Z= 0.346 Chirality : 0.045 0.304 4771 Planarity : 0.004 0.056 5235 Dihedral : 12.938 86.103 4712 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.73 % Favored : 96.24 % Rotamer: Outliers : 4.16 % Allowed : 21.29 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.14), residues: 3830 helix: 1.27 (0.13), residues: 1545 sheet: -0.56 (0.20), residues: 665 loop : -1.43 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 323 TYR 0.034 0.002 TYR L 102 PHE 0.020 0.001 PHE E 202 TRP 0.035 0.003 TRP J 289 HIS 0.006 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00463 (30463) covalent geometry : angle 0.67107 (41311) hydrogen bonds : bond 0.03551 ( 1408) hydrogen bonds : angle 5.12015 ( 4035) Misc. bond : bond 0.00068 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7660 Ramachandran restraints generated. 3830 Oldfield, 0 Emsley, 3830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7660 Ramachandran restraints generated. 3830 Oldfield, 0 Emsley, 3830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 3029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 381 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 MET cc_start: 0.8792 (mmm) cc_final: 0.8359 (mmm) REVERT: A 165 LYS cc_start: 0.9355 (tppt) cc_final: 0.9003 (tppt) REVERT: B 126 MET cc_start: 0.8984 (mmt) cc_final: 0.8525 (mmm) REVERT: B 166 ARG cc_start: 0.8973 (tpp-160) cc_final: 0.8650 (tpp-160) REVERT: D 26 MET cc_start: 0.5361 (ppp) cc_final: 0.3660 (ppp) REVERT: D 126 GLU cc_start: 0.9124 (tp30) cc_final: 0.8827 (tm-30) REVERT: D 196 MET cc_start: 0.8573 (ppp) cc_final: 0.8185 (ppp) REVERT: D 206 GLU cc_start: 0.9005 (pm20) cc_final: 0.8426 (pm20) REVERT: D 232 GLU cc_start: 0.9210 (mp0) cc_final: 0.8931 (mp0) REVERT: D 263 TYR cc_start: 0.8224 (m-10) cc_final: 0.7637 (m-80) REVERT: E 151 LYS cc_start: 0.9207 (tptt) cc_final: 0.8692 (tppt) REVERT: E 196 MET cc_start: 0.9061 (ttp) cc_final: 0.8785 (ttp) REVERT: E 204 ASN cc_start: 0.8644 (t0) cc_final: 0.8309 (t0) REVERT: E 242 ARG cc_start: 0.8974 (mtm110) cc_final: 0.8741 (mtp-110) REVERT: E 276 LEU cc_start: 0.9544 (mm) cc_final: 0.9319 (tp) REVERT: E 290 TYR cc_start: 0.9185 (m-10) cc_final: 0.8883 (m-10) REVERT: E 324 ASP cc_start: 0.9443 (OUTLIER) cc_final: 0.9112 (m-30) REVERT: F 151 LYS cc_start: 0.9383 (tptp) cc_final: 0.9075 (tppt) REVERT: F 158 MET cc_start: 0.8069 (tpp) cc_final: 0.7710 (tpp) REVERT: F 306 LYS cc_start: 0.9545 (pptt) cc_final: 0.9308 (ptpt) REVERT: G 6 LYS cc_start: 0.9552 (mtmt) cc_final: 0.9232 (mtmt) REVERT: G 105 LYS cc_start: 0.9445 (ttpt) cc_final: 0.9229 (ttpt) REVERT: G 158 MET cc_start: 0.8392 (mtm) cc_final: 0.8048 (mtp) REVERT: G 197 LYS cc_start: 0.9413 (OUTLIER) cc_final: 0.8986 (ptmt) REVERT: G 265 LYS cc_start: 0.9552 (mmmt) cc_final: 0.9231 (mtmm) REVERT: G 290 TYR cc_start: 0.7709 (m-80) cc_final: 0.7264 (m-80) REVERT: H 151 LYS cc_start: 0.9314 (tppt) cc_final: 0.8926 (tppt) REVERT: H 320 LYS cc_start: 0.9620 (mmmt) cc_final: 0.9376 (mttt) REVERT: I 18 ARG cc_start: 0.9362 (ptp-170) cc_final: 0.9095 (ptt-90) REVERT: I 151 LYS cc_start: 0.9459 (tppt) cc_final: 0.9154 (tppt) REVERT: I 162 HIS cc_start: 0.7923 (m90) cc_final: 0.7589 (m-70) REVERT: I 265 LYS cc_start: 0.9431 (mmmt) cc_final: 0.9172 (mtmm) REVERT: I 290 TYR cc_start: 0.8530 (m-10) cc_final: 0.7352 (m-80) REVERT: I 307 TYR cc_start: 0.8905 (t80) cc_final: 0.8617 (t80) REVERT: I 320 LYS cc_start: 0.9597 (tppt) cc_final: 0.9281 (tppt) REVERT: J 196 MET cc_start: 0.8764 (mpp) cc_final: 0.8516 (mpp) REVERT: J 206 GLU cc_start: 0.8784 (mp0) cc_final: 0.8531 (pm20) REVERT: J 215 LYS cc_start: 0.9382 (ptpt) cc_final: 0.9161 (ptpp) REVERT: J 256 GLN cc_start: 0.9468 (pp30) cc_final: 0.8798 (pp30) REVERT: J 319 GLU cc_start: 0.9285 (pt0) cc_final: 0.8901 (pp20) REVERT: K 151 LYS cc_start: 0.9160 (tmmt) cc_final: 0.8918 (tppt) REVERT: K 204 ASN cc_start: 0.8835 (t0) cc_final: 0.8541 (t0) REVERT: K 268 TYR cc_start: 0.9150 (t80) cc_final: 0.8897 (t80) REVERT: L 196 MET cc_start: 0.9199 (ptp) cc_final: 0.8709 (pmm) REVERT: L 231 LYS cc_start: 0.9264 (mtmt) cc_final: 0.8944 (ttmm) REVERT: L 268 TYR cc_start: 0.9072 (t80) cc_final: 0.8175 (t80) REVERT: L 290 TYR cc_start: 0.8800 (m-80) cc_final: 0.8234 (m-10) REVERT: L 307 TYR cc_start: 0.8105 (t80) cc_final: 0.7536 (t80) REVERT: L 323 ARG cc_start: 0.9476 (ttm-80) cc_final: 0.9170 (ttm110) REVERT: C 20 PHE cc_start: 0.9243 (m-10) cc_final: 0.8380 (m-10) REVERT: C 89 CYS cc_start: 0.5753 (t) cc_final: 0.4885 (t) REVERT: C 91 PHE cc_start: 0.8636 (t80) cc_final: 0.8363 (t80) REVERT: C 151 LYS cc_start: 0.9018 (tppt) cc_final: 0.8808 (tppt) REVERT: C 162 HIS cc_start: 0.8253 (m90) cc_final: 0.7674 (m90) REVERT: C 196 MET cc_start: 0.9271 (ptt) cc_final: 0.8940 (tmm) REVERT: C 215 LYS cc_start: 0.9464 (ptpt) cc_final: 0.9086 (ptpp) REVERT: C 254 PHE cc_start: 0.9250 (m-80) cc_final: 0.8931 (m-80) REVERT: C 292 TYR cc_start: 0.8140 (t80) cc_final: 0.7752 (t80) REVERT: C 320 LYS cc_start: 0.9722 (mmmt) cc_final: 0.9476 (tppt) REVERT: M 26 MET cc_start: 0.6465 (ppp) cc_final: 0.6221 (ppp) REVERT: M 105 LYS cc_start: 0.9306 (mttt) cc_final: 0.9078 (ptpp) REVERT: M 151 LYS cc_start: 0.9295 (tptt) cc_final: 0.9071 (tppt) REVERT: M 162 HIS cc_start: 0.8304 (m-70) cc_final: 0.7762 (m-70) REVERT: M 323 ARG cc_start: 0.9118 (ppt170) cc_final: 0.8766 (ppt170) outliers start: 126 outliers final: 91 residues processed: 478 average time/residue: 0.2107 time to fit residues: 149.6509 Evaluate side-chains 455 residues out of total 3029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 362 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 112 ASN Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 289 TRP Chi-restraints excluded: chain E residue 297 ILE Chi-restraints excluded: chain E residue 306 LYS Chi-restraints excluded: chain E residue 324 ASP Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 220 VAL Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 192 ASN Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 197 LYS Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain G residue 289 TRP Chi-restraints excluded: chain G residue 303 ASN Chi-restraints excluded: chain H residue 105 LYS Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 230 VAL Chi-restraints excluded: chain H residue 239 SER Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 158 MET Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 230 VAL Chi-restraints excluded: chain I residue 261 ILE Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 220 VAL Chi-restraints excluded: chain J residue 230 VAL Chi-restraints excluded: chain K residue 28 MET Chi-restraints excluded: chain K residue 149 VAL Chi-restraints excluded: chain K residue 206 GLU Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 289 TRP Chi-restraints excluded: chain K residue 303 ASN Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 111 ASP Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain L residue 149 VAL Chi-restraints excluded: chain L residue 157 GLU Chi-restraints excluded: chain L residue 162 HIS Chi-restraints excluded: chain L residue 200 VAL Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain L residue 230 VAL Chi-restraints excluded: chain L residue 236 VAL Chi-restraints excluded: chain L residue 245 VAL Chi-restraints excluded: chain L residue 272 GLU Chi-restraints excluded: chain L residue 276 LEU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain M residue 130 MET Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 197 LYS Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain M residue 260 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 231 optimal weight: 6.9990 chunk 364 optimal weight: 9.9990 chunk 201 optimal weight: 0.9990 chunk 309 optimal weight: 1.9990 chunk 339 optimal weight: 9.9990 chunk 194 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 285 optimal weight: 7.9990 chunk 141 optimal weight: 3.9990 chunk 376 optimal weight: 8.9990 chunk 131 optimal weight: 0.3980 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 192 ASN ** H 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.056165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.040972 restraints weight = 143162.529| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 4.12 r_work: 0.2809 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 30464 Z= 0.178 Angle : 0.659 10.987 41311 Z= 0.340 Chirality : 0.045 0.258 4771 Planarity : 0.004 0.047 5235 Dihedral : 12.894 86.327 4712 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.68 % Favored : 96.29 % Rotamer: Outliers : 4.29 % Allowed : 21.66 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.14), residues: 3830 helix: 1.24 (0.13), residues: 1545 sheet: -0.49 (0.20), residues: 665 loop : -1.36 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 146 TYR 0.038 0.002 TYR C 268 PHE 0.017 0.001 PHE E 202 TRP 0.036 0.003 TRP J 289 HIS 0.006 0.001 HIS K 162 Details of bonding type rmsd covalent geometry : bond 0.00412 (30463) covalent geometry : angle 0.65898 (41311) hydrogen bonds : bond 0.03405 ( 1408) hydrogen bonds : angle 5.01976 ( 4035) Misc. bond : bond 0.00065 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7660 Ramachandran restraints generated. 3830 Oldfield, 0 Emsley, 3830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7660 Ramachandran restraints generated. 3830 Oldfield, 0 Emsley, 3830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 3029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 377 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 LYS cc_start: 0.9374 (tppt) cc_final: 0.8997 (tppt) REVERT: B 114 ARG cc_start: 0.9033 (mmm160) cc_final: 0.8776 (mmm160) REVERT: B 126 MET cc_start: 0.9065 (mmt) cc_final: 0.8623 (mmm) REVERT: B 140 HIS cc_start: 0.9147 (t70) cc_final: 0.8684 (t70) REVERT: B 163 ARG cc_start: 0.9068 (tpp80) cc_final: 0.8861 (tpp80) REVERT: B 166 ARG cc_start: 0.8969 (tpp-160) cc_final: 0.8707 (tpp-160) REVERT: D 26 MET cc_start: 0.5296 (ppp) cc_final: 0.3660 (ppp) REVERT: D 126 GLU cc_start: 0.9154 (tp30) cc_final: 0.8791 (tm-30) REVERT: D 196 MET cc_start: 0.8595 (ppp) cc_final: 0.8224 (ppp) REVERT: D 263 TYR cc_start: 0.8206 (m-10) cc_final: 0.7618 (m-80) REVERT: E 151 LYS cc_start: 0.9194 (tptt) cc_final: 0.8660 (tppt) REVERT: E 204 ASN cc_start: 0.8649 (t0) cc_final: 0.8311 (t0) REVERT: E 242 ARG cc_start: 0.8980 (mtm110) cc_final: 0.8745 (mtp-110) REVERT: E 276 LEU cc_start: 0.9552 (mm) cc_final: 0.9323 (tp) REVERT: E 290 TYR cc_start: 0.9239 (m-10) cc_final: 0.8948 (m-10) REVERT: E 324 ASP cc_start: 0.9456 (OUTLIER) cc_final: 0.9116 (m-30) REVERT: F 28 MET cc_start: 0.3844 (mmt) cc_final: 0.2851 (mmp) REVERT: F 112 ASP cc_start: 0.9175 (t0) cc_final: 0.8912 (p0) REVERT: F 151 LYS cc_start: 0.9371 (tptp) cc_final: 0.9059 (tppt) REVERT: F 241 THR cc_start: 0.9146 (OUTLIER) cc_final: 0.8911 (p) REVERT: G 6 LYS cc_start: 0.9563 (mtmt) cc_final: 0.9336 (mtmt) REVERT: G 105 LYS cc_start: 0.9450 (ttpt) cc_final: 0.9217 (ttpt) REVERT: G 158 MET cc_start: 0.8378 (mtm) cc_final: 0.8027 (mtp) REVERT: G 197 LYS cc_start: 0.9380 (OUTLIER) cc_final: 0.8909 (ptmt) REVERT: G 265 LYS cc_start: 0.9546 (mmmt) cc_final: 0.9315 (mmmm) REVERT: H 320 LYS cc_start: 0.9637 (mmmt) cc_final: 0.9412 (mttt) REVERT: I 143 ASP cc_start: 0.8023 (t0) cc_final: 0.7664 (t0) REVERT: I 151 LYS cc_start: 0.9475 (tppt) cc_final: 0.9140 (tppt) REVERT: I 162 HIS cc_start: 0.7941 (m90) cc_final: 0.7588 (m-70) REVERT: I 252 PRO cc_start: 0.9212 (Cg_exo) cc_final: 0.8987 (Cg_endo) REVERT: I 265 LYS cc_start: 0.9420 (mmmt) cc_final: 0.9141 (mtmm) REVERT: I 307 TYR cc_start: 0.8968 (t80) cc_final: 0.8616 (t80) REVERT: I 320 LYS cc_start: 0.9596 (tppt) cc_final: 0.9270 (tppt) REVERT: J 196 MET cc_start: 0.8789 (mpp) cc_final: 0.8510 (mpp) REVERT: J 215 LYS cc_start: 0.9381 (ptpt) cc_final: 0.9144 (ptpp) REVERT: J 256 GLN cc_start: 0.9448 (pp30) cc_final: 0.8898 (pp30) REVERT: J 319 GLU cc_start: 0.9273 (pt0) cc_final: 0.8878 (pp20) REVERT: K 84 LYS cc_start: 0.9087 (ptpp) cc_final: 0.8833 (ptpp) REVERT: K 151 LYS cc_start: 0.9161 (tmmt) cc_final: 0.8856 (tppt) REVERT: K 155 GLU cc_start: 0.8997 (mm-30) cc_final: 0.8665 (mm-30) REVERT: K 204 ASN cc_start: 0.8828 (t0) cc_final: 0.8559 (t0) REVERT: K 268 TYR cc_start: 0.9173 (t80) cc_final: 0.8922 (t80) REVERT: L 196 MET cc_start: 0.9226 (ptp) cc_final: 0.8685 (pmm) REVERT: L 244 LYS cc_start: 0.8966 (tttp) cc_final: 0.8748 (tptt) REVERT: L 268 TYR cc_start: 0.9004 (t80) cc_final: 0.8118 (t80) REVERT: L 290 TYR cc_start: 0.8744 (m-80) cc_final: 0.8386 (m-10) REVERT: L 307 TYR cc_start: 0.8104 (t80) cc_final: 0.7526 (t80) REVERT: L 323 ARG cc_start: 0.9466 (ttm-80) cc_final: 0.9151 (ttm110) REVERT: C 151 LYS cc_start: 0.9026 (tppt) cc_final: 0.8803 (tppt) REVERT: C 162 HIS cc_start: 0.8274 (m90) cc_final: 0.7442 (m90) REVERT: C 196 MET cc_start: 0.9259 (ptt) cc_final: 0.8934 (tmm) REVERT: C 215 LYS cc_start: 0.9446 (ptpt) cc_final: 0.9062 (ptpp) REVERT: C 225 ARG cc_start: 0.7803 (mtm180) cc_final: 0.7574 (mtm180) REVERT: C 254 PHE cc_start: 0.9231 (m-80) cc_final: 0.8903 (m-80) REVERT: C 292 TYR cc_start: 0.8182 (t80) cc_final: 0.7827 (t80) REVERT: C 320 LYS cc_start: 0.9727 (mmmt) cc_final: 0.9500 (tppt) REVERT: M 111 ASP cc_start: 0.9110 (t0) cc_final: 0.8857 (p0) REVERT: M 151 LYS cc_start: 0.9297 (tptt) cc_final: 0.9071 (tppt) REVERT: M 162 HIS cc_start: 0.8310 (m-70) cc_final: 0.7756 (m-70) REVERT: M 324 ASP cc_start: 0.8715 (p0) cc_final: 0.8406 (p0) outliers start: 130 outliers final: 97 residues processed: 480 average time/residue: 0.2019 time to fit residues: 145.2692 Evaluate side-chains 461 residues out of total 3029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 361 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 112 ASN Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain D residue 28 MET Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 265 LYS Chi-restraints excluded: chain E residue 324 ASP Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 220 VAL Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 192 ASN Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 197 LYS Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 289 TRP Chi-restraints excluded: chain G residue 303 ASN Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 105 LYS Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 230 VAL Chi-restraints excluded: chain H residue 239 SER Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 158 MET Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 261 ILE Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 220 VAL Chi-restraints excluded: chain K residue 28 MET Chi-restraints excluded: chain K residue 92 VAL Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain K residue 149 VAL Chi-restraints excluded: chain K residue 206 GLU Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 289 TRP Chi-restraints excluded: chain K residue 303 ASN Chi-restraints excluded: chain L residue 9 LEU Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 111 ASP Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain L residue 149 VAL Chi-restraints excluded: chain L residue 162 HIS Chi-restraints excluded: chain L residue 200 VAL Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain L residue 230 VAL Chi-restraints excluded: chain L residue 236 VAL Chi-restraints excluded: chain L residue 245 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain M residue 130 MET Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 197 LYS Chi-restraints excluded: chain M residue 208 THR Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain M residue 260 GLN Chi-restraints excluded: chain M residue 289 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 68 optimal weight: 6.9990 chunk 280 optimal weight: 0.0870 chunk 102 optimal weight: 0.8980 chunk 39 optimal weight: 0.0040 chunk 306 optimal weight: 3.9990 chunk 199 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 64 optimal weight: 10.0000 chunk 337 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 276 optimal weight: 9.9990 overall best weight: 0.9972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 303 ASN ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 260 GLN G 192 ASN ** H 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 31 HIS ** J 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 162 HIS K 325 GLN C 19 GLN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.057275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.041884 restraints weight = 142592.975| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 4.23 r_work: 0.2846 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30464 Z= 0.129 Angle : 0.661 12.394 41311 Z= 0.339 Chirality : 0.044 0.237 4771 Planarity : 0.004 0.044 5235 Dihedral : 12.746 86.232 4712 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.58 % Favored : 96.40 % Rotamer: Outliers : 3.80 % Allowed : 22.71 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.14), residues: 3830 helix: 1.22 (0.13), residues: 1545 sheet: -0.32 (0.20), residues: 654 loop : -1.28 (0.15), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 133 TYR 0.026 0.002 TYR L 102 PHE 0.018 0.001 PHE E 202 TRP 0.044 0.004 TRP D 289 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00298 (30463) covalent geometry : angle 0.66141 (41311) hydrogen bonds : bond 0.03207 ( 1408) hydrogen bonds : angle 4.92468 ( 4035) Misc. bond : bond 0.00051 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7660 Ramachandran restraints generated. 3830 Oldfield, 0 Emsley, 3830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7660 Ramachandran restraints generated. 3830 Oldfield, 0 Emsley, 3830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 3029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 374 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 LYS cc_start: 0.9333 (tppt) cc_final: 0.8964 (tppt) REVERT: B 114 ARG cc_start: 0.8999 (mmm160) cc_final: 0.8738 (mmm160) REVERT: B 126 MET cc_start: 0.8984 (mmt) cc_final: 0.8222 (mmm) REVERT: B 140 HIS cc_start: 0.9078 (t70) cc_final: 0.8635 (t70) REVERT: D 26 MET cc_start: 0.5618 (ppp) cc_final: 0.3968 (ppp) REVERT: D 28 MET cc_start: 0.2435 (OUTLIER) cc_final: 0.2061 (mmt) REVERT: D 84 LYS cc_start: 0.9337 (tmmt) cc_final: 0.8870 (pttm) REVERT: D 126 GLU cc_start: 0.9106 (tp30) cc_final: 0.8811 (tm-30) REVERT: D 158 MET cc_start: 0.8670 (tpp) cc_final: 0.8452 (tpp) REVERT: D 196 MET cc_start: 0.8541 (ppp) cc_final: 0.8203 (ppp) REVERT: D 252 PRO cc_start: 0.9003 (Cg_exo) cc_final: 0.8745 (Cg_endo) REVERT: D 263 TYR cc_start: 0.8120 (m-10) cc_final: 0.7628 (m-80) REVERT: E 151 LYS cc_start: 0.9159 (tptt) cc_final: 0.8559 (tppt) REVERT: E 196 MET cc_start: 0.8940 (ttp) cc_final: 0.8665 (ttp) REVERT: E 204 ASN cc_start: 0.8642 (t0) cc_final: 0.8261 (t0) REVERT: E 242 ARG cc_start: 0.8986 (mtm110) cc_final: 0.8783 (mtp-110) REVERT: E 276 LEU cc_start: 0.9555 (mm) cc_final: 0.9323 (tp) REVERT: E 290 TYR cc_start: 0.9204 (m-10) cc_final: 0.8912 (m-10) REVERT: E 324 ASP cc_start: 0.9433 (OUTLIER) cc_final: 0.9087 (m-30) REVERT: F 28 MET cc_start: 0.3887 (mmt) cc_final: 0.2916 (mmp) REVERT: F 151 LYS cc_start: 0.9342 (tptp) cc_final: 0.9013 (tppt) REVERT: F 196 MET cc_start: 0.8539 (tpp) cc_final: 0.7694 (tpp) REVERT: F 241 THR cc_start: 0.9167 (OUTLIER) cc_final: 0.8946 (p) REVERT: G 151 LYS cc_start: 0.9179 (mptt) cc_final: 0.8862 (mmtt) REVERT: G 158 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.8062 (mtp) REVERT: G 197 LYS cc_start: 0.9300 (OUTLIER) cc_final: 0.8967 (ptmt) REVERT: G 263 TYR cc_start: 0.9281 (m-10) cc_final: 0.8887 (m-80) REVERT: G 265 LYS cc_start: 0.9524 (mmmt) cc_final: 0.9294 (mmmm) REVERT: H 28 MET cc_start: 0.3624 (mmt) cc_final: 0.3406 (mmt) REVERT: H 158 MET cc_start: 0.8105 (tpp) cc_final: 0.7700 (tpp) REVERT: H 320 LYS cc_start: 0.9637 (mmmt) cc_final: 0.9406 (mttt) REVERT: I 18 ARG cc_start: 0.9314 (ptp-170) cc_final: 0.9034 (ptp90) REVERT: I 151 LYS cc_start: 0.9480 (tppt) cc_final: 0.9210 (tppt) REVERT: I 162 HIS cc_start: 0.7888 (m90) cc_final: 0.7536 (m-70) REVERT: I 170 MET cc_start: 0.8877 (tpp) cc_final: 0.8668 (tpp) REVERT: I 252 PRO cc_start: 0.9184 (Cg_exo) cc_final: 0.8962 (Cg_endo) REVERT: I 307 TYR cc_start: 0.8944 (t80) cc_final: 0.8573 (t80) REVERT: I 320 LYS cc_start: 0.9597 (tppt) cc_final: 0.9264 (tppt) REVERT: J 196 MET cc_start: 0.8785 (mpp) cc_final: 0.8493 (mpp) REVERT: J 242 ARG cc_start: 0.8733 (ptm-80) cc_final: 0.8356 (ptm-80) REVERT: J 256 GLN cc_start: 0.9420 (pp30) cc_final: 0.8815 (pp30) REVERT: J 268 TYR cc_start: 0.8653 (t80) cc_final: 0.8184 (t80) REVERT: J 319 GLU cc_start: 0.9233 (pt0) cc_final: 0.8814 (pp20) REVERT: K 151 LYS cc_start: 0.9120 (tmmt) cc_final: 0.8818 (tppt) REVERT: K 155 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8656 (mm-30) REVERT: K 204 ASN cc_start: 0.8774 (t0) cc_final: 0.8510 (t0) REVERT: K 268 TYR cc_start: 0.9159 (t80) cc_final: 0.8897 (t80) REVERT: L 26 MET cc_start: 0.4679 (ppp) cc_final: 0.4400 (ppp) REVERT: L 196 MET cc_start: 0.9194 (ptp) cc_final: 0.8713 (pmm) REVERT: L 268 TYR cc_start: 0.8908 (t80) cc_final: 0.8576 (t80) REVERT: L 290 TYR cc_start: 0.8730 (m-80) cc_final: 0.8172 (m-10) REVERT: L 307 TYR cc_start: 0.8192 (t80) cc_final: 0.7547 (t80) REVERT: L 323 ARG cc_start: 0.9450 (ttm-80) cc_final: 0.8952 (ttm110) REVERT: L 327 LEU cc_start: 0.8961 (tt) cc_final: 0.8759 (mm) REVERT: C 20 PHE cc_start: 0.9264 (m-10) cc_final: 0.8356 (m-10) REVERT: C 133 ARG cc_start: 0.8368 (mtm110) cc_final: 0.8127 (mtm180) REVERT: C 151 LYS cc_start: 0.9050 (tppt) cc_final: 0.8809 (tppt) REVERT: C 196 MET cc_start: 0.9257 (ptt) cc_final: 0.8980 (tmm) REVERT: C 215 LYS cc_start: 0.9430 (ptpt) cc_final: 0.9040 (ptpp) REVERT: C 225 ARG cc_start: 0.7785 (mtm180) cc_final: 0.7541 (mtm180) REVERT: C 254 PHE cc_start: 0.9244 (m-80) cc_final: 0.8922 (m-80) REVERT: C 292 TYR cc_start: 0.8016 (t80) cc_final: 0.7702 (t80) REVERT: C 320 LYS cc_start: 0.9722 (mmmt) cc_final: 0.9481 (tppt) REVERT: M 111 ASP cc_start: 0.9080 (t0) cc_final: 0.8816 (p0) REVERT: M 151 LYS cc_start: 0.9280 (tptt) cc_final: 0.9051 (tppt) REVERT: M 162 HIS cc_start: 0.8248 (m-70) cc_final: 0.7720 (m-70) outliers start: 115 outliers final: 95 residues processed: 466 average time/residue: 0.2117 time to fit residues: 147.1562 Evaluate side-chains 458 residues out of total 3029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 358 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 112 ASN Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain D residue 28 MET Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 324 ASP Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 220 VAL Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 192 ASN Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 197 LYS Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 289 TRP Chi-restraints excluded: chain G residue 290 TYR Chi-restraints excluded: chain G residue 303 ASN Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 105 LYS Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 230 VAL Chi-restraints excluded: chain H residue 239 SER Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 158 MET Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 261 ILE Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 165 LEU Chi-restraints excluded: chain J residue 220 VAL Chi-restraints excluded: chain K residue 28 MET Chi-restraints excluded: chain K residue 92 VAL Chi-restraints excluded: chain K residue 149 VAL Chi-restraints excluded: chain K residue 206 GLU Chi-restraints excluded: chain K residue 289 TRP Chi-restraints excluded: chain K residue 303 ASN Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 92 VAL Chi-restraints excluded: chain L residue 111 ASP Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain L residue 149 VAL Chi-restraints excluded: chain L residue 162 HIS Chi-restraints excluded: chain L residue 200 VAL Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain L residue 230 VAL Chi-restraints excluded: chain L residue 236 VAL Chi-restraints excluded: chain L residue 245 VAL Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain M residue 130 MET Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 197 LYS Chi-restraints excluded: chain M residue 208 THR Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain M residue 260 GLN Chi-restraints excluded: chain M residue 289 TRP Chi-restraints excluded: chain M residue 311 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 318 optimal weight: 10.0000 chunk 196 optimal weight: 7.9990 chunk 76 optimal weight: 9.9990 chunk 200 optimal weight: 10.0000 chunk 190 optimal weight: 0.9980 chunk 374 optimal weight: 7.9990 chunk 291 optimal weight: 7.9990 chunk 226 optimal weight: 5.9990 chunk 350 optimal weight: 0.0870 chunk 306 optimal weight: 9.9990 chunk 193 optimal weight: 8.9990 overall best weight: 4.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 325 GLN C 15 GLN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 260 GLN ** 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 = 0.3486 r_free = 0.3486 target = 0.055463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.040440 restraints weight = 144628.543| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 4.01 r_work: 0.2797 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 30464 Z= 0.254 Angle : 0.716 13.074 41311 Z= 0.366 Chirality : 0.046 0.230 4771 Planarity : 0.004 0.045 5235 Dihedral : 12.897 85.663 4712 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.92 % Favored : 96.06 % Rotamer: Outliers : 4.13 % Allowed : 23.11 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.14), residues: 3830 helix: 1.19 (0.13), residues: 1545 sheet: -0.38 (0.20), residues: 677 loop : -1.35 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 166 TYR 0.034 0.002 TYR C 268 PHE 0.022 0.002 PHE E 202 TRP 0.048 0.004 TRP L 289 HIS 0.006 0.001 HIS I 31 Details of bonding type rmsd covalent geometry : bond 0.00576 (30463) covalent geometry : angle 0.71610 (41311) hydrogen bonds : bond 0.03504 ( 1408) hydrogen bonds : angle 4.99684 ( 4035) Misc. bond : bond 0.00109 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7660 Ramachandran restraints generated. 3830 Oldfield, 0 Emsley, 3830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7660 Ramachandran restraints generated. 3830 Oldfield, 0 Emsley, 3830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 3029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 360 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 LYS cc_start: 0.9374 (tppt) cc_final: 0.8995 (tppt) REVERT: B 114 ARG cc_start: 0.9032 (mmm160) cc_final: 0.8790 (mmm160) REVERT: B 126 MET cc_start: 0.8828 (mmt) cc_final: 0.8402 (mmm) REVERT: B 127 LYS cc_start: 0.9502 (pptt) cc_final: 0.9233 (pptt) REVERT: B 140 HIS cc_start: 0.9150 (t70) cc_final: 0.8652 (t70) REVERT: D 26 MET cc_start: 0.5537 (ppp) cc_final: 0.4010 (ppp) REVERT: D 28 MET cc_start: 0.2651 (OUTLIER) cc_final: 0.2370 (mmt) REVERT: D 84 LYS cc_start: 0.9322 (tmmt) cc_final: 0.8791 (pttm) REVERT: D 126 GLU cc_start: 0.9107 (tp30) cc_final: 0.8680 (tm-30) REVERT: D 196 MET cc_start: 0.8567 (ppp) cc_final: 0.8273 (ppp) REVERT: D 263 TYR cc_start: 0.8237 (m-10) cc_final: 0.7672 (m-80) REVERT: D 268 TYR cc_start: 0.8466 (t80) cc_final: 0.8088 (t80) REVERT: E 33 ARG cc_start: 0.8654 (ptp90) cc_final: 0.8452 (ptp90) REVERT: E 151 LYS cc_start: 0.9207 (tptt) cc_final: 0.8670 (tppt) REVERT: E 204 ASN cc_start: 0.8779 (t0) cc_final: 0.8549 (t0) REVERT: E 276 LEU cc_start: 0.9559 (mm) cc_final: 0.9323 (tp) REVERT: E 290 TYR cc_start: 0.9278 (m-10) cc_final: 0.8973 (m-10) REVERT: E 324 ASP cc_start: 0.9444 (OUTLIER) cc_final: 0.9106 (m-30) REVERT: F 25 VAL cc_start: 0.8317 (OUTLIER) cc_final: 0.7983 (t) REVERT: F 28 MET cc_start: 0.3930 (mmt) cc_final: 0.2962 (mmp) REVERT: F 112 ASP cc_start: 0.9179 (t0) cc_final: 0.8951 (p0) REVERT: F 151 LYS cc_start: 0.9389 (tptp) cc_final: 0.9088 (tppt) REVERT: G 6 LYS cc_start: 0.9599 (mtmt) cc_final: 0.9371 (mtmt) REVERT: G 158 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.8050 (mtp) REVERT: G 197 LYS cc_start: 0.9318 (OUTLIER) cc_final: 0.9032 (ptmt) REVERT: G 265 LYS cc_start: 0.9544 (mmmt) cc_final: 0.9344 (mmmm) REVERT: H 162 HIS cc_start: 0.8272 (m170) cc_final: 0.8045 (m170) REVERT: H 320 LYS cc_start: 0.9644 (mmmt) cc_final: 0.9405 (mttt) REVERT: I 18 ARG cc_start: 0.9303 (ptp-170) cc_final: 0.9052 (ptp90) REVERT: I 143 ASP cc_start: 0.7985 (t0) cc_final: 0.7670 (t0) REVERT: I 151 LYS cc_start: 0.9480 (tppt) cc_final: 0.9164 (tppp) REVERT: I 162 HIS cc_start: 0.7791 (m90) cc_final: 0.7446 (m-70) REVERT: I 252 PRO cc_start: 0.9228 (Cg_exo) cc_final: 0.8997 (Cg_endo) REVERT: I 307 TYR cc_start: 0.8961 (t80) cc_final: 0.8578 (t80) REVERT: I 320 LYS cc_start: 0.9605 (tppt) cc_final: 0.9266 (tppt) REVERT: J 151 LYS cc_start: 0.9325 (tppt) cc_final: 0.9119 (tppt) REVERT: J 196 MET cc_start: 0.8774 (mpp) cc_final: 0.8543 (mpp) REVERT: J 242 ARG cc_start: 0.8733 (ptm-80) cc_final: 0.8339 (ptm-80) REVERT: J 256 GLN cc_start: 0.9447 (pp30) cc_final: 0.8717 (pp30) REVERT: J 319 GLU cc_start: 0.9246 (pt0) cc_final: 0.8932 (pp20) REVERT: J 320 LYS cc_start: 0.9703 (tppt) cc_final: 0.9259 (tppt) REVERT: K 151 LYS cc_start: 0.9192 (tmmt) cc_final: 0.8985 (tppt) REVERT: K 204 ASN cc_start: 0.8851 (t0) cc_final: 0.8589 (t0) REVERT: K 268 TYR cc_start: 0.9171 (t80) cc_final: 0.8948 (t80) REVERT: L 196 MET cc_start: 0.9193 (ptp) cc_final: 0.8738 (pmm) REVERT: L 268 TYR cc_start: 0.8944 (t80) cc_final: 0.8143 (t80) REVERT: L 290 TYR cc_start: 0.8766 (m-80) cc_final: 0.8201 (m-10) REVERT: L 307 TYR cc_start: 0.8127 (t80) cc_final: 0.7528 (t80) REVERT: L 323 ARG cc_start: 0.9453 (ttm-80) cc_final: 0.9124 (ttm110) REVERT: C 20 PHE cc_start: 0.9282 (m-10) cc_final: 0.8617 (m-80) REVERT: C 89 CYS cc_start: 0.5827 (t) cc_final: 0.5605 (t) REVERT: C 91 PHE cc_start: 0.8573 (t80) cc_final: 0.8283 (t80) REVERT: C 151 LYS cc_start: 0.9103 (tppt) cc_final: 0.8871 (tppt) REVERT: C 196 MET cc_start: 0.9199 (ptt) cc_final: 0.8921 (tmm) REVERT: C 215 LYS cc_start: 0.9466 (ptpt) cc_final: 0.9098 (ptpp) REVERT: C 226 ARG cc_start: 0.9153 (tmt170) cc_final: 0.8875 (tmt170) REVERT: C 254 PHE cc_start: 0.9219 (m-80) cc_final: 0.8899 (m-80) REVERT: C 292 TYR cc_start: 0.8135 (t80) cc_final: 0.7754 (t80) REVERT: C 320 LYS cc_start: 0.9724 (mmmt) cc_final: 0.9493 (tppt) REVERT: M 28 MET cc_start: 0.6591 (mmp) cc_final: 0.6333 (mmp) REVERT: M 111 ASP cc_start: 0.9128 (t0) cc_final: 0.8907 (p0) REVERT: M 151 LYS cc_start: 0.9308 (tptt) cc_final: 0.9095 (tppt) REVERT: M 162 HIS cc_start: 0.8348 (m-70) cc_final: 0.7757 (m-70) outliers start: 125 outliers final: 99 residues processed: 453 average time/residue: 0.2036 time to fit residues: 139.0841 Evaluate side-chains 445 residues out of total 3029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 341 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 112 ASN Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain D residue 28 MET Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 263 TYR Chi-restraints excluded: chain E residue 324 ASP Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 220 VAL Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 197 LYS Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 289 TRP Chi-restraints excluded: chain G residue 290 TYR Chi-restraints excluded: chain G residue 303 ASN Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 105 LYS Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain H residue 230 VAL Chi-restraints excluded: chain H residue 239 SER Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 158 MET Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 261 ILE Chi-restraints excluded: chain J residue 144 SER Chi-restraints excluded: chain J residue 220 VAL Chi-restraints excluded: chain J residue 289 TRP Chi-restraints excluded: chain K residue 28 MET Chi-restraints excluded: chain K residue 92 VAL Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain K residue 149 VAL Chi-restraints excluded: chain K residue 206 GLU Chi-restraints excluded: chain K residue 289 TRP Chi-restraints excluded: chain K residue 303 ASN Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 92 VAL Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 111 ASP Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain L residue 149 VAL Chi-restraints excluded: chain L residue 162 HIS Chi-restraints excluded: chain L residue 200 VAL Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain L residue 230 VAL Chi-restraints excluded: chain L residue 236 VAL Chi-restraints excluded: chain L residue 245 VAL Chi-restraints excluded: chain L residue 276 LEU Chi-restraints excluded: chain L residue 327 LEU Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain M residue 130 MET Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 197 LYS Chi-restraints excluded: chain M residue 208 THR Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain M residue 260 GLN Chi-restraints excluded: chain M residue 289 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 16 optimal weight: 0.4980 chunk 108 optimal weight: 5.9990 chunk 227 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 184 optimal weight: 0.0970 chunk 323 optimal weight: 8.9990 chunk 237 optimal weight: 0.9980 chunk 376 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 chunk 203 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 192 ASN G 303 ASN ** H 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 293 GLN ** I 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 31 HIS ** J 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 GLN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 260 GLN ** 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 = 0.3537 r_free = 0.3537 target = 0.057293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.042122 restraints weight = 142554.775| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 4.19 r_work: 0.2853 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30464 Z= 0.131 Angle : 0.709 12.934 41311 Z= 0.362 Chirality : 0.045 0.215 4771 Planarity : 0.004 0.070 5235 Dihedral : 12.698 86.162 4712 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.47 % Favored : 96.50 % Rotamer: Outliers : 3.47 % Allowed : 23.90 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.14), residues: 3830 helix: 1.17 (0.13), residues: 1539 sheet: -0.32 (0.20), residues: 663 loop : -1.23 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 225 TYR 0.032 0.002 TYR C 268 PHE 0.022 0.001 PHE E 202 TRP 0.072 0.005 TRP L 289 HIS 0.004 0.001 HIS K 162 Details of bonding type rmsd covalent geometry : bond 0.00304 (30463) covalent geometry : angle 0.70913 (41311) hydrogen bonds : bond 0.03211 ( 1408) hydrogen bonds : angle 4.90584 ( 4035) Misc. bond : bond 0.00064 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7660 Ramachandran restraints generated. 3830 Oldfield, 0 Emsley, 3830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7660 Ramachandran restraints generated. 3830 Oldfield, 0 Emsley, 3830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 359 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ARG cc_start: 0.8362 (ttm110) cc_final: 0.8114 (ttm110) REVERT: A 165 LYS cc_start: 0.9371 (tppt) cc_final: 0.9009 (tppt) REVERT: B 126 MET cc_start: 0.8831 (mmt) cc_final: 0.8411 (mmm) REVERT: B 127 LYS cc_start: 0.9495 (pptt) cc_final: 0.9206 (pptt) REVERT: B 140 HIS cc_start: 0.9086 (t70) cc_final: 0.8602 (t70) REVERT: D 26 MET cc_start: 0.5352 (ppp) cc_final: 0.3951 (ppp) REVERT: D 84 LYS cc_start: 0.9337 (tmmt) cc_final: 0.8882 (pttm) REVERT: D 196 MET cc_start: 0.8587 (ppp) cc_final: 0.8312 (ppp) REVERT: D 252 PRO cc_start: 0.9028 (Cg_exo) cc_final: 0.8772 (Cg_endo) REVERT: D 263 TYR cc_start: 0.8114 (m-10) cc_final: 0.7562 (m-80) REVERT: D 268 TYR cc_start: 0.8438 (t80) cc_final: 0.8023 (t80) REVERT: E 151 LYS cc_start: 0.9146 (tptt) cc_final: 0.8595 (tppt) REVERT: E 196 MET cc_start: 0.8940 (ttp) cc_final: 0.8331 (ppp) REVERT: E 204 ASN cc_start: 0.8689 (t0) cc_final: 0.8343 (t0) REVERT: E 276 LEU cc_start: 0.9560 (mm) cc_final: 0.9323 (tp) REVERT: E 290 TYR cc_start: 0.9276 (m-10) cc_final: 0.9044 (m-10) REVERT: E 324 ASP cc_start: 0.9437 (OUTLIER) cc_final: 0.9108 (m-30) REVERT: F 151 LYS cc_start: 0.9337 (tptp) cc_final: 0.9010 (tppt) REVERT: G 6 LYS cc_start: 0.9599 (mtmt) cc_final: 0.9369 (mtmt) REVERT: G 151 LYS cc_start: 0.9188 (mptt) cc_final: 0.8883 (mmtt) REVERT: G 158 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.8149 (mtp) REVERT: G 197 LYS cc_start: 0.9237 (OUTLIER) cc_final: 0.8993 (ptmt) REVERT: G 263 TYR cc_start: 0.9226 (m-10) cc_final: 0.8950 (m-80) REVERT: G 265 LYS cc_start: 0.9523 (mmmt) cc_final: 0.9313 (mmmm) REVERT: H 158 MET cc_start: 0.8083 (tpp) cc_final: 0.7683 (tpp) REVERT: H 162 HIS cc_start: 0.8287 (m170) cc_final: 0.8060 (m170) REVERT: H 320 LYS cc_start: 0.9650 (mmmt) cc_final: 0.9419 (mttt) REVERT: I 18 ARG cc_start: 0.9310 (ptp-170) cc_final: 0.9042 (ptp90) REVERT: I 151 LYS cc_start: 0.9486 (tppt) cc_final: 0.9224 (tppt) REVERT: I 162 HIS cc_start: 0.7780 (m90) cc_final: 0.7432 (m-70) REVERT: I 252 PRO cc_start: 0.9207 (Cg_exo) cc_final: 0.8987 (Cg_endo) REVERT: I 307 TYR cc_start: 0.8970 (t80) cc_final: 0.8644 (t80) REVERT: I 320 LYS cc_start: 0.9594 (tppt) cc_final: 0.9248 (tppt) REVERT: J 242 ARG cc_start: 0.8730 (ptm-80) cc_final: 0.8292 (ptm-80) REVERT: J 256 GLN cc_start: 0.9433 (pp30) cc_final: 0.8717 (pp30) REVERT: J 319 GLU cc_start: 0.9232 (pt0) cc_final: 0.8798 (pp20) REVERT: K 84 LYS cc_start: 0.9099 (ptpp) cc_final: 0.8865 (pttm) REVERT: K 151 LYS cc_start: 0.9142 (tmmt) cc_final: 0.8841 (tppt) REVERT: K 155 GLU cc_start: 0.8995 (mm-30) cc_final: 0.8659 (mm-30) REVERT: K 268 TYR cc_start: 0.9170 (t80) cc_final: 0.8920 (t80) REVERT: L 196 MET cc_start: 0.9175 (ptp) cc_final: 0.8708 (pmm) REVERT: L 242 ARG cc_start: 0.8246 (ttp80) cc_final: 0.7723 (ttp80) REVERT: L 268 TYR cc_start: 0.8780 (t80) cc_final: 0.7932 (t80) REVERT: L 290 TYR cc_start: 0.8674 (m-80) cc_final: 0.8189 (m-10) REVERT: L 307 TYR cc_start: 0.8196 (t80) cc_final: 0.7580 (t80) REVERT: L 323 ARG cc_start: 0.9436 (ttm-80) cc_final: 0.8906 (ttm110) REVERT: C 89 CYS cc_start: 0.5763 (t) cc_final: 0.5528 (t) REVERT: C 91 PHE cc_start: 0.8564 (t80) cc_final: 0.8248 (t80) REVERT: C 151 LYS cc_start: 0.9085 (tppt) cc_final: 0.8837 (tppt) REVERT: C 196 MET cc_start: 0.9203 (ptt) cc_final: 0.8969 (tmm) REVERT: C 215 LYS cc_start: 0.9415 (ptpt) cc_final: 0.9031 (ptpp) REVERT: C 254 PHE cc_start: 0.9209 (m-80) cc_final: 0.8883 (m-80) REVERT: C 292 TYR cc_start: 0.8111 (t80) cc_final: 0.7764 (t80) REVERT: C 320 LYS cc_start: 0.9734 (mmmt) cc_final: 0.9514 (tppt) REVERT: M 111 ASP cc_start: 0.9147 (t0) cc_final: 0.8915 (p0) REVERT: M 151 LYS cc_start: 0.9232 (tptt) cc_final: 0.9002 (tppt) outliers start: 105 outliers final: 91 residues processed: 440 average time/residue: 0.2456 time to fit residues: 161.3457 Evaluate side-chains 447 residues out of total 3029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 353 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 112 ASN Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 202 PHE Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 263 TYR Chi-restraints excluded: chain E residue 324 ASP Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 220 VAL Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 192 ASN Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 197 LYS Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 289 TRP Chi-restraints excluded: chain G residue 290 TYR Chi-restraints excluded: chain G residue 303 ASN Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 105 LYS Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 230 VAL Chi-restraints excluded: chain H residue 239 SER Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 158 MET Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 232 GLU Chi-restraints excluded: chain I residue 261 ILE Chi-restraints excluded: chain K residue 28 MET Chi-restraints excluded: chain K residue 149 VAL Chi-restraints excluded: chain K residue 206 GLU Chi-restraints excluded: chain K residue 289 TRP Chi-restraints excluded: chain K residue 303 ASN Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 92 VAL Chi-restraints excluded: chain L residue 111 ASP Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain L residue 149 VAL Chi-restraints excluded: chain L residue 162 HIS Chi-restraints excluded: chain L residue 200 VAL Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain L residue 230 VAL Chi-restraints excluded: chain L residue 236 VAL Chi-restraints excluded: chain L residue 245 VAL Chi-restraints excluded: chain L residue 276 LEU Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain M residue 130 MET Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 197 LYS Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain M residue 289 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 230 optimal weight: 4.9990 chunk 196 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 210 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 322 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 chunk 18 optimal weight: 9.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 299 GLN ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 279 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.056789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.041658 restraints weight = 142273.520| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 4.15 r_work: 0.2837 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 30464 Z= 0.164 Angle : 0.744 16.022 41311 Z= 0.377 Chirality : 0.045 0.205 4771 Planarity : 0.004 0.048 5235 Dihedral : 12.704 86.058 4712 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.47 % Favored : 96.50 % Rotamer: Outliers : 3.30 % Allowed : 24.07 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.14), residues: 3830 helix: 1.17 (0.13), residues: 1539 sheet: -0.27 (0.20), residues: 655 loop : -1.24 (0.15), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG I 7 TYR 0.055 0.002 TYR M 268 PHE 0.021 0.001 PHE E 202 TRP 0.074 0.004 TRP L 289 HIS 0.005 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00383 (30463) covalent geometry : angle 0.74369 (41311) hydrogen bonds : bond 0.03239 ( 1408) hydrogen bonds : angle 4.88870 ( 4035) Misc. bond : bond 0.00062 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7660 Ramachandran restraints generated. 3830 Oldfield, 0 Emsley, 3830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7660 Ramachandran restraints generated. 3830 Oldfield, 0 Emsley, 3830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 350 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 ARG cc_start: 0.8480 (ttm110) cc_final: 0.8061 (mpt-90) REVERT: A 165 LYS cc_start: 0.9367 (tppt) cc_final: 0.8983 (tppt) REVERT: B 126 MET cc_start: 0.8840 (mmt) cc_final: 0.8418 (mmm) REVERT: B 127 LYS cc_start: 0.9501 (pptt) cc_final: 0.9224 (pptt) REVERT: B 140 HIS cc_start: 0.9095 (t70) cc_final: 0.8606 (t70) REVERT: D 26 MET cc_start: 0.5205 (ppp) cc_final: 0.4012 (ppp) REVERT: D 28 MET cc_start: 0.2854 (mmt) cc_final: 0.2536 (mmp) REVERT: D 84 LYS cc_start: 0.9341 (tmmt) cc_final: 0.8886 (pttm) REVERT: D 196 MET cc_start: 0.8562 (ppp) cc_final: 0.8251 (ppp) REVERT: D 252 PRO cc_start: 0.9043 (Cg_exo) cc_final: 0.8790 (Cg_endo) REVERT: D 263 TYR cc_start: 0.8144 (m-10) cc_final: 0.7721 (m-10) REVERT: D 268 TYR cc_start: 0.8449 (t80) cc_final: 0.8025 (t80) REVERT: E 151 LYS cc_start: 0.9181 (tptt) cc_final: 0.8680 (tppt) REVERT: E 196 MET cc_start: 0.8951 (ttp) cc_final: 0.8264 (ppp) REVERT: E 276 LEU cc_start: 0.9568 (mm) cc_final: 0.9333 (tp) REVERT: E 290 TYR cc_start: 0.9306 (m-10) cc_final: 0.9073 (m-10) REVERT: E 324 ASP cc_start: 0.9443 (OUTLIER) cc_final: 0.9111 (m-30) REVERT: F 28 MET cc_start: 0.3913 (mmt) cc_final: 0.2973 (mmp) REVERT: F 112 ASP cc_start: 0.9186 (t0) cc_final: 0.8918 (p0) REVERT: F 151 LYS cc_start: 0.9350 (tptp) cc_final: 0.9025 (tppt) REVERT: G 6 LYS cc_start: 0.9587 (mtmt) cc_final: 0.9376 (mtmt) REVERT: G 28 MET cc_start: 0.3490 (mmt) cc_final: 0.3107 (mmp) REVERT: G 158 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.8159 (mtp) REVERT: G 192 ASN cc_start: 0.9260 (OUTLIER) cc_final: 0.8937 (t0) REVERT: G 197 LYS cc_start: 0.9243 (OUTLIER) cc_final: 0.8943 (ptmt) REVERT: G 263 TYR cc_start: 0.9230 (m-10) cc_final: 0.8950 (m-80) REVERT: G 265 LYS cc_start: 0.9546 (mmmt) cc_final: 0.9335 (mmmm) REVERT: H 158 MET cc_start: 0.8076 (tpp) cc_final: 0.7687 (tpp) REVERT: H 162 HIS cc_start: 0.8308 (m170) cc_final: 0.8082 (m170) REVERT: H 201 MET cc_start: 0.9140 (ptp) cc_final: 0.8837 (pmm) REVERT: H 320 LYS cc_start: 0.9659 (mmmt) cc_final: 0.9425 (mttt) REVERT: I 18 ARG cc_start: 0.9321 (ptp-170) cc_final: 0.9054 (ptp90) REVERT: I 143 ASP cc_start: 0.7920 (t0) cc_final: 0.7586 (t0) REVERT: I 151 LYS cc_start: 0.9489 (tppt) cc_final: 0.9211 (tppt) REVERT: I 162 HIS cc_start: 0.7820 (m90) cc_final: 0.7436 (m-70) REVERT: I 252 PRO cc_start: 0.9209 (Cg_exo) cc_final: 0.8984 (Cg_endo) REVERT: I 307 TYR cc_start: 0.8994 (t80) cc_final: 0.8614 (t80) REVERT: I 320 LYS cc_start: 0.9604 (tppt) cc_final: 0.9257 (tppt) REVERT: J 242 ARG cc_start: 0.8762 (ptm-80) cc_final: 0.8320 (ptm-80) REVERT: J 256 GLN cc_start: 0.9438 (pp30) cc_final: 0.8681 (pp30) REVERT: J 279 GLN cc_start: 0.9384 (pp30) cc_final: 0.9172 (pp30) REVERT: J 319 GLU cc_start: 0.9229 (pt0) cc_final: 0.8800 (pp20) REVERT: K 18 ARG cc_start: 0.9262 (ptp90) cc_final: 0.8965 (ptp90) REVERT: K 151 LYS cc_start: 0.9145 (tmmt) cc_final: 0.8850 (tppt) REVERT: K 155 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8698 (mm-30) REVERT: K 268 TYR cc_start: 0.9170 (t80) cc_final: 0.8923 (t80) REVERT: L 196 MET cc_start: 0.9206 (ptp) cc_final: 0.8732 (pmm) REVERT: L 242 ARG cc_start: 0.8259 (ttp80) cc_final: 0.7729 (ttp80) REVERT: L 268 TYR cc_start: 0.8822 (t80) cc_final: 0.7993 (t80) REVERT: L 290 TYR cc_start: 0.8723 (m-80) cc_final: 0.8227 (m-10) REVERT: L 307 TYR cc_start: 0.8215 (t80) cc_final: 0.7596 (t80) REVERT: L 323 ARG cc_start: 0.9418 (ttm-80) cc_final: 0.9091 (ttm110) REVERT: C 28 MET cc_start: 0.7433 (mmp) cc_final: 0.6775 (mmp) REVERT: C 89 CYS cc_start: 0.5762 (t) cc_final: 0.5541 (t) REVERT: C 91 PHE cc_start: 0.8574 (t80) cc_final: 0.8259 (t80) REVERT: C 151 LYS cc_start: 0.9095 (tppt) cc_final: 0.8853 (tppt) REVERT: C 196 MET cc_start: 0.9159 (ptt) cc_final: 0.8934 (tmm) REVERT: C 215 LYS cc_start: 0.9432 (ptpt) cc_final: 0.8975 (ptpp) REVERT: C 221 ARG cc_start: 0.9033 (ttp80) cc_final: 0.8713 (mtp-110) REVERT: C 254 PHE cc_start: 0.9229 (m-80) cc_final: 0.8912 (m-80) REVERT: C 292 TYR cc_start: 0.8073 (t80) cc_final: 0.7685 (t80) REVERT: C 320 LYS cc_start: 0.9730 (mmmt) cc_final: 0.9497 (tppt) REVERT: M 111 ASP cc_start: 0.9145 (t0) cc_final: 0.8918 (p0) REVERT: M 151 LYS cc_start: 0.9257 (tptt) cc_final: 0.9023 (tppt) outliers start: 100 outliers final: 90 residues processed: 427 average time/residue: 0.2408 time to fit residues: 153.2326 Evaluate side-chains 433 residues out of total 3029 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 339 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 105 ARG Chi-restraints excluded: chain A residue 112 ASN Chi-restraints excluded: chain A residue 135 ASP Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 165 LYS Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 149 VAL Chi-restraints excluded: chain E residue 202 PHE Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain E residue 263 TYR Chi-restraints excluded: chain E residue 324 ASP Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 220 VAL Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 320 LYS Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 120 THR Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 158 MET Chi-restraints excluded: chain G residue 192 ASN Chi-restraints excluded: chain G residue 194 ILE Chi-restraints excluded: chain G residue 197 LYS Chi-restraints excluded: chain G residue 220 VAL Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 289 TRP Chi-restraints excluded: chain G residue 290 TYR Chi-restraints excluded: chain G residue 303 ASN Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 105 LYS Chi-restraints excluded: chain H residue 110 VAL Chi-restraints excluded: chain H residue 149 VAL Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 230 VAL Chi-restraints excluded: chain H residue 239 SER Chi-restraints excluded: chain I residue 106 LEU Chi-restraints excluded: chain I residue 149 VAL Chi-restraints excluded: chain I residue 158 MET Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 232 GLU Chi-restraints excluded: chain I residue 261 ILE Chi-restraints excluded: chain J residue 220 VAL Chi-restraints excluded: chain K residue 28 MET Chi-restraints excluded: chain K residue 149 VAL Chi-restraints excluded: chain K residue 206 GLU Chi-restraints excluded: chain K residue 289 TRP Chi-restraints excluded: chain K residue 303 ASN Chi-restraints excluded: chain L residue 52 ILE Chi-restraints excluded: chain L residue 92 VAL Chi-restraints excluded: chain L residue 111 ASP Chi-restraints excluded: chain L residue 145 VAL Chi-restraints excluded: chain L residue 149 VAL Chi-restraints excluded: chain L residue 162 HIS Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain L residue 230 VAL Chi-restraints excluded: chain L residue 245 VAL Chi-restraints excluded: chain L residue 276 LEU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 224 ILE Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain M residue 130 MET Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 197 LYS Chi-restraints excluded: chain M residue 220 VAL Chi-restraints excluded: chain M residue 289 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 362 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 116 optimal weight: 0.0870 chunk 25 optimal weight: 5.9990 chunk 203 optimal weight: 0.8980 chunk 302 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 chunk 154 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 overall best weight: 2.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 192 ASN ** H 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 325 GLN J 15 GLN ** J 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 260 GLN ** 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 = 0.3511 r_free = 0.3511 target = 0.056303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.041112 restraints weight = 144047.668| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 4.17 r_work: 0.2820 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 30464 Z= 0.173 Angle : 0.734 14.365 41311 Z= 0.374 Chirality : 0.045 0.216 4771 Planarity : 0.004 0.055 5235 Dihedral : 12.716 85.611 4712 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.50 % Favored : 96.48 % Rotamer: Outliers : 3.53 % Allowed : 23.74 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.14), residues: 3830 helix: 1.15 (0.13), residues: 1538 sheet: -0.30 (0.20), residues: 653 loop : -1.24 (0.15), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG I 7 TYR 0.047 0.002 TYR M 268 PHE 0.021 0.001 PHE E 202 TRP 0.059 0.004 TRP L 289 HIS 0.010 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00402 (30463) covalent geometry : angle 0.73355 (41311) hydrogen bonds : bond 0.03332 ( 1408) hydrogen bonds : angle 4.90620 ( 4035) Misc. bond : bond 0.00063 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7797.98 seconds wall clock time: 134 minutes 18.41 seconds (8058.41 seconds total)