Starting phenix.real_space_refine on Wed Aug 27 02:17:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8trg_41579/08_2025/8trg_41579_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8trg_41579/08_2025/8trg_41579.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8trg_41579/08_2025/8trg_41579_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8trg_41579/08_2025/8trg_41579_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8trg_41579/08_2025/8trg_41579.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8trg_41579/08_2025/8trg_41579.map" } resolution = 2.93 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= 0.002 sd= 0.030 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: 7 Type Number sf(0) Gaussians P 50 5.49 5 Mg 8 5.21 5 S 111 5.16 5 C 14198 2.51 5 N 3989 2.21 5 O 4510 1.98 5 H 22935 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 85 residue(s): 0.01s 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: 45801 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 4971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 4971 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 8, 'TRANS': 316} Chain: "B" Number of atoms: 4971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 4971 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 8, 'TRANS': 316} Chain: "C" Number of atoms: 4971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 4971 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 8, 'TRANS': 316} Chain: "D" Number of atoms: 4971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 4971 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 8, 'TRANS': 316} Chain: "E" Number of atoms: 4971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 4971 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 8, 'TRANS': 316} Chain: "F" Number of atoms: 4971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 4971 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 8, 'TRANS': 316} Chain: "G" Number of atoms: 4971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 4971 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 8, 'TRANS': 316} Chain: "H" Number of atoms: 4971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 4971 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 8, 'TRANS': 316} Chain: "I" Number of atoms: 2916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 2916 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 9, 'TRANS': 177} Chain breaks: 1 Chain: "J" Number of atoms: 1980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1980 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 6, 'TRANS': 120} Chain: "L" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 881 Classifications: {'DNA': 27} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 26} Chain: "A" 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: "B" 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: "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} Time building chain proxies: 7.52, per 1000 atoms: 0.16 Number of scatterers: 45801 At special positions: 0 Unit cell: (144.9, 131.1, 208.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 111 16.00 P 50 15.00 Mg 8 11.99 O 4510 8.00 N 3989 7.00 C 14198 6.00 H 22935 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.99 Conformation dependent library (CDL) restraints added in 923.0 milliseconds Enol-peptide restraints added in 1.7 microseconds 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5226 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 37 sheets defined 43.5% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 3 through 22 Processing helix chain 'A' and resid 44 through 51 Processing helix chain 'A' and resid 71 through 86 Processing helix chain 'A' and resid 100 through 108 Processing helix chain 'A' and resid 121 through 135 removed outlier: 3.570A pdb=" N SER A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 149 removed outlier: 3.836A pdb=" N LEU A 149 " --> pdb=" O VAL A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 165 through 186 removed outlier: 4.722A pdb=" N GLY A 180 " --> pdb=" O ARG A 176 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASN A 181 " --> pdb=" O LYS A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 219 removed outlier: 3.886A pdb=" N PHE A 217 " --> pdb=" O ASN A 213 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 281 Processing helix chain 'A' and resid 301 through 312 Processing helix chain 'A' and resid 312 through 327 removed outlier: 4.078A pdb=" N GLU A 318 " --> pdb=" O GLU A 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 22 removed outlier: 3.680A pdb=" N ALA B 9 " --> pdb=" O ASN B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 36 removed outlier: 6.026A pdb=" N ARG B 33 " --> pdb=" O GLY B 30 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N SER B 34 " --> pdb=" O GLU B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 52 Processing helix chain 'B' and resid 71 through 86 removed outlier: 4.032A pdb=" N GLU B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 108 Processing helix chain 'B' and resid 110 through 113 removed outlier: 3.664A pdb=" N ASN B 113 " --> pdb=" O ASP B 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 110 through 113' Processing helix chain 'B' and resid 121 through 135 Processing helix chain 'B' and resid 151 through 157 Processing helix chain 'B' and resid 165 through 186 removed outlier: 3.747A pdb=" N ARG B 176 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS B 177 " --> pdb=" O GLN B 173 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLY B 180 " --> pdb=" O ARG B 176 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN B 181 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS B 183 " --> pdb=" O ALA B 179 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN B 184 " --> pdb=" O GLY B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 219 removed outlier: 3.538A pdb=" N PHE B 217 " --> pdb=" O ASN B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 281 removed outlier: 3.546A pdb=" N ASP B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 312 Processing helix chain 'B' and resid 312 through 327 removed outlier: 3.951A pdb=" N ALA B 316 " --> pdb=" O ASN B 312 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS B 322 " --> pdb=" O GLU B 318 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU B 325 " --> pdb=" O LYS B 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 22 Processing helix chain 'C' and resid 32 through 36 removed outlier: 3.669A pdb=" N MET C 35 " --> pdb=" O ASP C 32 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP C 36 " --> pdb=" O ARG C 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 32 through 36' Processing helix chain 'C' and resid 44 through 52 removed outlier: 3.633A pdb=" N GLY C 52 " --> pdb=" O ASP C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 86 removed outlier: 3.792A pdb=" N ARG C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU C 86 " --> pdb=" O ALA C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 107 Processing helix chain 'C' and resid 110 through 113 Processing helix chain 'C' and resid 121 through 136 removed outlier: 3.941A pdb=" N GLY C 136 " --> pdb=" O LEU C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 149 removed outlier: 3.576A pdb=" N LEU C 149 " --> pdb=" O VAL C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 157 Processing helix chain 'C' and resid 165 through 186 removed outlier: 3.640A pdb=" N ARG C 176 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLY C 180 " --> pdb=" O ARG C 176 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASN C 181 " --> pdb=" O LYS C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 219 Processing helix chain 'C' and resid 269 through 281 removed outlier: 3.661A pdb=" N GLU C 273 " --> pdb=" O ASN C 269 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL C 275 " --> pdb=" O TYR C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 312 Processing helix chain 'C' and resid 312 through 327 removed outlier: 3.605A pdb=" N LYS C 322 " --> pdb=" O GLU C 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 22 removed outlier: 3.640A pdb=" N LYS D 8 " --> pdb=" O GLU D 4 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 36 Processing helix chain 'D' and resid 44 through 52 removed outlier: 3.603A pdb=" N GLY D 52 " --> pdb=" O ASP D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 86 removed outlier: 3.564A pdb=" N ALA D 83 " --> pdb=" O VAL D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 108 removed outlier: 3.563A pdb=" N GLY D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 136 removed outlier: 3.861A pdb=" N GLY D 136 " --> pdb=" O LEU D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 156 Processing helix chain 'D' and resid 165 through 186 removed outlier: 3.784A pdb=" N ARG D 169 " --> pdb=" O GLY D 165 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N GLY D 180 " --> pdb=" O ARG D 176 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ASN D 181 " --> pdb=" O LYS D 177 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS D 183 " --> pdb=" O ALA D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 219 removed outlier: 3.618A pdb=" N PHE D 217 " --> pdb=" O ASN D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 281 removed outlier: 3.547A pdb=" N GLU D 273 " --> pdb=" O ASN D 269 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL D 275 " --> pdb=" O TYR D 271 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP D 276 " --> pdb=" O GLY D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 312 Processing helix chain 'D' and resid 312 through 327 removed outlier: 3.505A pdb=" N LYS D 322 " --> pdb=" O GLU D 318 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLU D 325 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU D 326 " --> pdb=" O LYS D 322 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU D 327 " --> pdb=" O VAL D 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 22 removed outlier: 3.605A pdb=" N ALA E 9 " --> pdb=" O ASN E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 36 removed outlier: 6.386A pdb=" N ARG E 33 " --> pdb=" O GLY E 30 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N SER E 34 " --> pdb=" O GLU E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 51 Processing helix chain 'E' and resid 71 through 85 Processing helix chain 'E' and resid 100 through 107 Processing helix chain 'E' and resid 121 through 136 removed outlier: 3.578A pdb=" N GLY E 136 " --> pdb=" O LEU E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 157 removed outlier: 3.581A pdb=" N ILE E 155 " --> pdb=" O PRO E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 186 removed outlier: 3.549A pdb=" N ARG E 169 " --> pdb=" O GLY E 165 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N GLY E 180 " --> pdb=" O ARG E 176 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASN E 181 " --> pdb=" O LYS E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 219 Processing helix chain 'E' and resid 269 through 281 removed outlier: 4.035A pdb=" N GLU E 273 " --> pdb=" O ASN E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 312 Processing helix chain 'E' and resid 312 through 327 removed outlier: 3.549A pdb=" N ALA E 316 " --> pdb=" O ASN E 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 22 Processing helix chain 'F' and resid 44 through 52 removed outlier: 3.923A pdb=" N GLY F 52 " --> pdb=" O ASP F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 85 removed outlier: 3.618A pdb=" N ARG F 85 " --> pdb=" O ALA F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 108 removed outlier: 3.663A pdb=" N GLY F 108 " --> pdb=" O ALA F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 113 Processing helix chain 'F' and resid 121 through 136 removed outlier: 3.564A pdb=" N CYS F 129 " --> pdb=" O ALA F 125 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY F 136 " --> pdb=" O LEU F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 157 removed outlier: 3.643A pdb=" N GLY F 157 " --> pdb=" O ALA F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 186 removed outlier: 3.589A pdb=" N ARG F 169 " --> pdb=" O GLY F 165 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N GLY F 180 " --> pdb=" O ARG F 176 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ASN F 181 " --> pdb=" O LYS F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 219 removed outlier: 3.704A pdb=" N PHE F 217 " --> pdb=" O ASN F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 281 removed outlier: 3.581A pdb=" N GLU F 273 " --> pdb=" O ASN F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 312 removed outlier: 3.603A pdb=" N ASP F 311 " --> pdb=" O ALA F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 327 removed outlier: 3.624A pdb=" N GLU F 318 " --> pdb=" O GLU F 314 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LYS F 321 " --> pdb=" O LYS F 317 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 22 Processing helix chain 'G' and resid 30 through 36 removed outlier: 5.812A pdb=" N ARG G 33 " --> pdb=" O GLY G 30 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N SER G 34 " --> pdb=" O GLU G 31 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N MET G 35 " --> pdb=" O ASP G 32 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP G 36 " --> pdb=" O ARG G 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 30 through 36' Processing helix chain 'G' and resid 44 through 51 Processing helix chain 'G' and resid 71 through 85 Processing helix chain 'G' and resid 100 through 108 Processing helix chain 'G' and resid 121 through 136 removed outlier: 3.776A pdb=" N GLY G 136 " --> pdb=" O LEU G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 157 Processing helix chain 'G' and resid 165 through 186 removed outlier: 5.169A pdb=" N GLY G 180 " --> pdb=" O ARG G 176 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ASN G 181 " --> pdb=" O LYS G 177 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS G 183 " --> pdb=" O ALA G 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 219 removed outlier: 3.917A pdb=" N PHE G 217 " --> pdb=" O ASN G 213 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR G 218 " --> pdb=" O ALA G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 281 removed outlier: 3.545A pdb=" N GLU G 273 " --> pdb=" O ASN G 269 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL G 279 " --> pdb=" O VAL G 275 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 312 Processing helix chain 'G' and resid 312 through 327 Processing helix chain 'H' and resid 4 through 22 removed outlier: 4.080A pdb=" N ALA H 11 " --> pdb=" O GLN H 7 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ALA H 12 " --> pdb=" O LYS H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 36 removed outlier: 3.699A pdb=" N MET H 35 " --> pdb=" O ASP H 32 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASP H 36 " --> pdb=" O ARG H 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 32 through 36' Processing helix chain 'H' and resid 44 through 51 Processing helix chain 'H' and resid 71 through 85 removed outlier: 3.752A pdb=" N THR H 76 " --> pdb=" O LYS H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 107 Processing helix chain 'H' and resid 121 through 135 removed outlier: 4.296A pdb=" N GLU H 127 " --> pdb=" O GLU H 123 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER H 135 " --> pdb=" O ALA H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 149 removed outlier: 3.529A pdb=" N ALA H 148 " --> pdb=" O SER H 145 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU H 149 " --> pdb=" O VAL H 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 145 through 149' Processing helix chain 'H' and resid 151 through 157 Processing helix chain 'H' and resid 165 through 179 Processing helix chain 'H' and resid 180 through 186 Processing helix chain 'H' and resid 213 through 219 removed outlier: 3.743A pdb=" N PHE H 217 " --> pdb=" O ASN H 213 " (cutoff:3.500A) Processing helix chain 'H' and resid 269 through 281 removed outlier: 3.751A pdb=" N GLU H 273 " --> pdb=" O ASN H 269 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP H 276 " --> pdb=" O GLY H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 301 through 312 Processing helix chain 'H' and resid 312 through 327 Processing helix chain 'I' and resid 9 through 23 removed outlier: 3.735A pdb=" N SER I 20 " --> pdb=" O ARG I 16 " (cutoff:3.500A) Processing helix chain 'I' and resid 27 through 36 Processing helix chain 'I' and resid 39 through 53 removed outlier: 4.337A pdb=" N ALA I 43 " --> pdb=" O SER I 39 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N HIS I 46 " --> pdb=" O ALA I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 105 Processing helix chain 'J' and resid 90 through 92 No H-bonds generated for 'chain 'J' and resid 90 through 92' Processing helix chain 'J' and resid 101 through 105 removed outlier: 3.752A pdb=" N LEU J 104 " --> pdb=" O ASP J 101 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N PHE J 105 " --> pdb=" O PRO J 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 101 through 105' Processing helix chain 'J' and resid 118 through 121 removed outlier: 4.069A pdb=" N LYS J 121 " --> pdb=" O MET J 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 118 through 121' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 28 removed outlier: 7.114A pdb=" N CYS B 90 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N SER B 117 " --> pdb=" O CYS B 90 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N PHE B 92 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL B 62 " --> pdb=" O PHE B 191 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE B 61 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N LEU B 223 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N GLU B 63 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ILE B 225 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR B 65 " --> pdb=" O ILE B 225 " (cutoff:3.500A) removed outlier: 9.162A pdb=" N ARG B 227 " --> pdb=" O TYR B 65 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL B 221 " --> pdb=" O LYS B 248 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LYS B 248 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LEU B 223 " --> pdb=" O VAL B 246 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL B 246 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE B 225 " --> pdb=" O VAL B 244 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL B 244 " --> pdb=" O ILE B 225 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ARG B 227 " --> pdb=" O THR B 242 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR B 242 " --> pdb=" O ARG B 227 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N GLY B 229 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N SER B 240 " --> pdb=" O GLY B 229 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL B 231 " --> pdb=" O VAL B 238 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 40 Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 65 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 61 through 65 current: chain 'A' and resid 188 through 193 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 188 through 193 current: chain 'A' and resid 236 through 248 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 257 through 258 current: chain 'A' and resid 267 through 268 Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 93 removed outlier: 6.908A pdb=" N CYS A 90 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 8.777A pdb=" N SER A 117 " --> pdb=" O CYS A 90 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N PHE A 92 " --> pdb=" O SER A 117 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 196 through 197 Processing sheet with id=AA6, first strand: chain 'A' and resid 285 through 287 removed outlier: 6.561A pdb=" N TYR A 291 " --> pdb=" O ILE A 298 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 27 through 28 removed outlier: 6.523A pdb=" N VAL C 62 " --> pdb=" O PHE C 191 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ASN C 193 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE C 64 " --> pdb=" O ASN C 193 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL C 221 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ARG C 222 " --> pdb=" O VAL C 247 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N GLU C 241 " --> pdb=" O ILE C 228 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ALA C 230 " --> pdb=" O GLY C 239 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N GLY C 239 " --> pdb=" O ALA C 230 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LYS C 232 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N VAL C 237 " --> pdb=" O LYS C 232 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 39 through 40 Processing sheet with id=AA9, first strand: chain 'B' and resid 195 through 197 Processing sheet with id=AB1, first strand: chain 'B' and resid 285 through 287 removed outlier: 3.659A pdb=" N GLY B 299 " --> pdb=" O TYR B 291 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N TYR B 293 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N LYS B 297 " --> pdb=" O TYR B 293 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 27 through 28 removed outlier: 7.286A pdb=" N CYS D 90 " --> pdb=" O LEU D 115 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N SER D 117 " --> pdb=" O CYS D 90 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N PHE D 92 " --> pdb=" O SER D 117 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL D 221 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N VAL D 221 " --> pdb=" O LYS D 248 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LYS D 248 " --> pdb=" O VAL D 221 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LEU D 223 " --> pdb=" O VAL D 246 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL D 246 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ILE D 225 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL D 244 " --> pdb=" O ILE D 225 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ARG D 227 " --> pdb=" O THR D 242 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N THR D 242 " --> pdb=" O ARG D 227 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLY D 229 " --> pdb=" O SER D 240 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N SER D 240 " --> pdb=" O GLY D 229 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL D 231 " --> pdb=" O VAL D 238 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 39 through 40 Processing sheet with id=AB4, first strand: chain 'C' and resid 196 through 197 Processing sheet with id=AB5, first strand: chain 'C' and resid 285 through 287 removed outlier: 6.969A pdb=" N TYR C 291 " --> pdb=" O ILE C 298 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 27 through 28 removed outlier: 3.568A pdb=" N MET D 27 " --> pdb=" O CYS E 116 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU E 115 " --> pdb=" O CYS E 90 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL E 221 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N VAL E 221 " --> pdb=" O LYS E 248 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LYS E 248 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU E 223 " --> pdb=" O VAL E 246 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL E 246 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE E 225 " --> pdb=" O VAL E 244 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL E 244 " --> pdb=" O ILE E 225 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ARG E 227 " --> pdb=" O THR E 242 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N THR E 242 " --> pdb=" O ARG E 227 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLY E 229 " --> pdb=" O SER E 240 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N SER E 240 " --> pdb=" O GLY E 229 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL E 231 " --> pdb=" O VAL E 238 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE E 260 " --> pdb=" O THR E 242 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 39 through 40 Processing sheet with id=AB8, first strand: chain 'D' and resid 196 through 197 Processing sheet with id=AB9, first strand: chain 'D' and resid 285 through 287 removed outlier: 6.497A pdb=" N TYR D 291 " --> pdb=" O ILE D 298 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 27 through 28 Processing sheet with id=AC2, first strand: chain 'E' and resid 39 through 40 Processing sheet with id=AC3, first strand: chain 'E' and resid 195 through 197 Processing sheet with id=AC4, first strand: chain 'E' and resid 285 through 287 removed outlier: 3.564A pdb=" N GLY E 299 " --> pdb=" O TYR E 291 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N TYR E 293 " --> pdb=" O LYS E 297 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N LYS E 297 " --> pdb=" O TYR E 293 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 27 through 28 removed outlier: 6.890A pdb=" N CYS G 90 " --> pdb=" O LEU G 115 " (cutoff:3.500A) removed outlier: 8.801A pdb=" N SER G 117 " --> pdb=" O CYS G 90 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N PHE G 92 " --> pdb=" O SER G 117 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL G 62 " --> pdb=" O PHE G 191 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ILE G 61 " --> pdb=" O VAL G 221 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N LEU G 223 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLU G 63 " --> pdb=" O LEU G 223 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N ILE G 225 " --> pdb=" O GLU G 63 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TYR G 65 " --> pdb=" O ILE G 225 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N ARG G 227 " --> pdb=" O TYR G 65 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ARG G 222 " --> pdb=" O VAL G 247 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLU G 241 " --> pdb=" O ILE G 228 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ALA G 230 " --> pdb=" O GLY G 239 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLY G 239 " --> pdb=" O ALA G 230 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LYS G 232 " --> pdb=" O VAL G 237 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL G 237 " --> pdb=" O LYS G 232 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 39 through 40 Processing sheet with id=AC7, first strand: chain 'F' and resid 140 through 143 removed outlier: 6.505A pdb=" N ILE F 141 " --> pdb=" O ILE F 190 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ILE F 192 " --> pdb=" O ILE F 141 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL F 143 " --> pdb=" O ILE F 192 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL F 62 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE F 61 " --> pdb=" O VAL F 221 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N LEU F 223 " --> pdb=" O ILE F 61 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLU F 63 " --> pdb=" O LEU F 223 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N ILE F 225 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TYR F 65 " --> pdb=" O ILE F 225 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N ARG F 227 " --> pdb=" O TYR F 65 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL F 221 " --> pdb=" O LYS F 248 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LYS F 248 " --> pdb=" O VAL F 221 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LEU F 223 " --> pdb=" O VAL F 246 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N VAL F 246 " --> pdb=" O LEU F 223 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE F 225 " --> pdb=" O VAL F 244 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL F 244 " --> pdb=" O ILE F 225 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ARG F 227 " --> pdb=" O THR F 242 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N THR F 242 " --> pdb=" O ARG F 227 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLY F 229 " --> pdb=" O SER F 240 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N SER F 240 " --> pdb=" O GLY F 229 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL F 231 " --> pdb=" O VAL F 238 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE F 260 " --> pdb=" O THR F 242 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 195 through 197 Processing sheet with id=AC9, first strand: chain 'F' and resid 285 through 287 removed outlier: 6.505A pdb=" N TYR F 291 " --> pdb=" O ILE F 298 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 27 through 28 removed outlier: 6.583A pdb=" N PHE H 92 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 39 through 40 Processing sheet with id=AD3, first strand: chain 'G' and resid 195 through 197 Processing sheet with id=AD4, first strand: chain 'G' and resid 285 through 287 removed outlier: 6.824A pdb=" N TYR G 291 " --> pdb=" O ILE G 298 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 39 through 40 Processing sheet with id=AD6, first strand: chain 'H' and resid 140 through 143 removed outlier: 6.526A pdb=" N VAL H 62 " --> pdb=" O PHE H 191 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL H 221 " --> pdb=" O ILE H 61 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL H 221 " --> pdb=" O ASN H 249 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ASN H 249 " --> pdb=" O VAL H 221 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N LEU H 223 " --> pdb=" O VAL H 247 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL H 247 " --> pdb=" O LEU H 223 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ILE H 225 " --> pdb=" O LYS H 245 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N LYS H 245 " --> pdb=" O ILE H 225 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ARG H 227 " --> pdb=" O ARG H 243 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ARG H 243 " --> pdb=" O ARG H 227 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLY H 229 " --> pdb=" O GLU H 241 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLU H 233 " --> pdb=" O VAL H 237 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N VAL H 237 " --> pdb=" O GLU H 233 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE H 260 " --> pdb=" O THR H 242 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 195 through 197 Processing sheet with id=AD8, first strand: chain 'H' and resid 291 through 293 removed outlier: 6.521A pdb=" N TYR H 293 " --> pdb=" O LYS H 297 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N LYS H 297 " --> pdb=" O TYR H 293 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 57 through 59 removed outlier: 6.236A pdb=" N GLU I 57 " --> pdb=" O ARG I 64 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 76 through 83 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 76 through 83 current: chain 'I' and resid 130 through 134 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 130 through 134 current: chain 'I' and resid 152 through 161 removed outlier: 3.629A pdb=" N ARG I 157 " --> pdb=" O LEU I 168 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 177 through 180 current: chain 'J' and resid 94 through 98 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 94 through 98 current: chain 'J' and resid 127 through 135 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 127 through 135 current: chain 'J' and resid 152 through 160 1000 hydrogen bonds defined for protein. 2817 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: 8.80 Time building geometry restraints manager: 5.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.06: 7612 1.06 - 1.27: 19252 1.27 - 1.47: 8564 1.47 - 1.67: 10510 1.67 - 1.88: 200 Bond restraints: 46138 Sorted by residual: bond pdb=" C3' AGS A 401 " pdb=" C4' AGS A 401 " ideal model delta sigma weight residual 1.526 1.324 0.202 1.10e-02 8.26e+03 3.37e+02 bond pdb=" C3' AGS F 401 " pdb=" C4' AGS F 401 " ideal model delta sigma weight residual 1.526 1.330 0.196 1.10e-02 8.26e+03 3.17e+02 bond pdb=" C3' AGS C 401 " pdb=" C4' AGS C 401 " ideal model delta sigma weight residual 1.526 1.331 0.195 1.10e-02 8.26e+03 3.16e+02 bond pdb=" C3' AGS E 401 " pdb=" C4' AGS E 401 " ideal model delta sigma weight residual 1.526 1.331 0.195 1.10e-02 8.26e+03 3.13e+02 bond pdb=" C3' AGS G 401 " pdb=" C4' AGS G 401 " ideal model delta sigma weight residual 1.526 1.335 0.191 1.10e-02 8.26e+03 3.02e+02 ... (remaining 46133 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.62: 83172 3.62 - 7.23: 593 7.23 - 10.85: 36 10.85 - 14.46: 1 14.46 - 18.08: 1 Bond angle restraints: 83803 Sorted by residual: angle pdb=" C5 AGS E 401 " pdb=" C4 AGS E 401 " pdb=" N3 AGS E 401 " ideal model delta sigma weight residual 126.80 118.35 8.45 7.41e-01 1.82e+00 1.30e+02 angle pdb=" C5 AGS D 401 " pdb=" C4 AGS D 401 " pdb=" N3 AGS D 401 " ideal model delta sigma weight residual 126.80 118.36 8.44 7.41e-01 1.82e+00 1.30e+02 angle pdb=" C5 AGS G 401 " pdb=" N7 AGS G 401 " pdb=" C8 AGS G 401 " ideal model delta sigma weight residual 103.67 108.36 -4.69 4.26e-01 5.51e+00 1.21e+02 angle pdb=" C5 AGS B 401 " pdb=" C4 AGS B 401 " pdb=" N3 AGS B 401 " ideal model delta sigma weight residual 126.80 118.88 7.92 7.41e-01 1.82e+00 1.14e+02 angle pdb=" C5 AGS C 401 " pdb=" C4 AGS C 401 " pdb=" N3 AGS C 401 " ideal model delta sigma weight residual 126.80 118.92 7.88 7.41e-01 1.82e+00 1.13e+02 ... (remaining 83798 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.72: 20169 34.72 - 69.44: 924 69.44 - 104.16: 42 104.16 - 138.88: 3 138.88 - 173.60: 6 Dihedral angle restraints: 21144 sinusoidal: 12180 harmonic: 8964 Sorted by residual: dihedral pdb=" CA LYS I 106 " pdb=" C LYS I 106 " pdb=" N PRO I 107 " pdb=" CA PRO I 107 " ideal model delta harmonic sigma weight residual 180.00 154.57 25.43 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" O1A AGS E 401 " pdb=" O3A AGS E 401 " pdb=" PA AGS E 401 " pdb=" PB AGS E 401 " ideal model delta sinusoidal sigma weight residual 292.27 118.67 173.60 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1B AGS H 401 " pdb=" O3B AGS H 401 " pdb=" PB AGS H 401 " pdb=" PG AGS H 401 " ideal model delta sinusoidal sigma weight residual 68.91 -99.84 168.75 1 3.00e+01 1.11e-03 2.11e+01 ... (remaining 21141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 3437 0.110 - 0.221: 135 0.221 - 0.331: 18 0.331 - 0.441: 0 0.441 - 0.552: 1 Chirality restraints: 3591 Sorted by residual: chirality pdb=" PB AGS G 401 " pdb=" O2B AGS G 401 " pdb=" O3A AGS G 401 " pdb=" O3B AGS G 401 " both_signs ideal model delta sigma weight residual True 3.18 -2.63 0.55 2.00e-01 2.50e+01 7.60e+00 chirality pdb=" C3' AGS C 401 " pdb=" C2' AGS C 401 " pdb=" C4' AGS C 401 " pdb=" O3' AGS C 401 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" C3' AGS F 401 " pdb=" C2' AGS F 401 " pdb=" C4' AGS F 401 " pdb=" O3' AGS F 401 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.42e+00 ... (remaining 3588 not shown) Planarity restraints: 6782 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 134 " 0.276 9.50e-02 1.11e+02 9.38e-02 1.62e+01 pdb=" NE ARG G 134 " 0.000 2.00e-02 2.50e+03 pdb=" CZ ARG G 134 " 0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG G 134 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG G 134 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG G 134 " -0.035 2.00e-02 2.50e+03 pdb="HH12 ARG G 134 " 0.014 2.00e-02 2.50e+03 pdb="HH21 ARG G 134 " -0.030 2.00e-02 2.50e+03 pdb="HH22 ARG G 134 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS I 106 " -0.059 5.00e-02 4.00e+02 8.92e-02 1.27e+01 pdb=" N PRO I 107 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO I 107 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO I 107 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 105 " -0.240 9.50e-02 1.11e+02 8.10e-02 1.03e+01 pdb=" NE ARG C 105 " 0.002 2.00e-02 2.50e+03 pdb=" CZ ARG C 105 " -0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG C 105 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 105 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG C 105 " 0.025 2.00e-02 2.50e+03 pdb="HH12 ARG C 105 " -0.011 2.00e-02 2.50e+03 pdb="HH21 ARG C 105 " 0.021 2.00e-02 2.50e+03 pdb="HH22 ARG C 105 " -0.011 2.00e-02 2.50e+03 ... (remaining 6779 not shown) Histogram of nonbonded interaction distances: 1.29 - 1.95: 538 1.95 - 2.61: 52947 2.61 - 3.28: 132240 3.28 - 3.94: 167336 3.94 - 4.60: 262960 Nonbonded interactions: 616021 Sorted by model distance: nonbonded pdb=" OE2 GLU E 18 " pdb=" HZ3 LYS E 23 " model vdw 1.291 2.450 nonbonded pdb=" HB2 LYS A 19 " pdb=" HZ3 LYS A 19 " model vdw 1.320 2.270 nonbonded pdb=" HB2 LYS F 245 " pdb=" HZ3 LYS F 245 " model vdw 1.354 2.270 nonbonded pdb=" HB3 LYS F 317 " pdb=" HZ2 LYS F 317 " model vdw 1.363 2.270 nonbonded pdb=" HB3 LYS H 106 " pdb=" HZ2 LYS H 106 " model vdw 1.380 2.270 ... (remaining 616016 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' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 1.050 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: 0.220 Extract box with map and model: 0.590 Check model and map are aligned: 0.140 Set scattering table: 0.130 Process input model: 36.050 Find NCS groups from input model: 0.690 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:5.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 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 : 0.009 0.202 23203 Z= 0.641 Angle : 0.846 10.986 31402 Z= 0.581 Chirality : 0.051 0.552 3591 Planarity : 0.006 0.109 3940 Dihedral : 17.979 173.599 8884 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.78 % Allowed : 20.20 % Favored : 79.02 % 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: -0.52 (0.15), residues: 2892 helix: 0.77 (0.16), residues: 1094 sheet: 0.02 (0.23), residues: 487 loop : -1.45 (0.16), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG G 134 TYR 0.012 0.002 TYR G 218 PHE 0.014 0.002 PHE E 217 TRP 0.020 0.001 TRP A 308 HIS 0.007 0.002 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00943 (23203) covalent geometry : angle 0.84629 (31402) hydrogen bonds : bond 0.20002 ( 1000) hydrogen bonds : angle 6.96490 ( 2817) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 606 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7581 (mm-30) REVERT: D 68 GLU cc_start: 0.7893 (pm20) cc_final: 0.7508 (pm20) REVERT: H 63 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7486 (tt0) REVERT: H 113 ASN cc_start: 0.7997 (p0) cc_final: 0.7747 (p0) REVERT: H 123 GLU cc_start: 0.5165 (mm-30) cc_final: 0.4756 (mm-30) REVERT: H 233 GLU cc_start: 0.7915 (pp20) cc_final: 0.7712 (pp20) REVERT: I 108 ASN cc_start: 0.7860 (m-40) cc_final: 0.7599 (m-40) REVERT: I 110 ASP cc_start: 0.8066 (m-30) cc_final: 0.7777 (m-30) REVERT: I 171 ASN cc_start: 0.8275 (t0) cc_final: 0.7914 (t0) outliers start: 18 outliers final: 13 residues processed: 618 average time/residue: 1.3530 time to fit residues: 948.7994 Evaluate side-chains 582 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 568 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 173 GLN Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 242 THR Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain J residue 168 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.6980 chunk 111 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 GLN B 20 GLN D 312 ASN E 84 GLN F 163 HIS F 257 GLN F 300 GLN H 181 ASN I 184 GLN ** I 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.133163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.108244 restraints weight = 96855.593| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.84 r_work: 0.3231 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23203 Z= 0.147 Angle : 0.627 6.812 31402 Z= 0.337 Chirality : 0.044 0.156 3591 Planarity : 0.005 0.084 3940 Dihedral : 14.656 174.610 3542 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.87 % Allowed : 19.20 % Favored : 78.93 % 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: -0.19 (0.15), residues: 2892 helix: 1.10 (0.15), residues: 1125 sheet: 0.29 (0.22), residues: 492 loop : -1.44 (0.16), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 134 TYR 0.013 0.001 TYR D 65 PHE 0.013 0.001 PHE C 260 TRP 0.016 0.002 TRP G 308 HIS 0.004 0.001 HIS G 97 Details of bonding type rmsd covalent geometry : bond 0.00328 (23203) covalent geometry : angle 0.62729 (31402) hydrogen bonds : bond 0.05422 ( 1000) hydrogen bonds : angle 5.45075 ( 2817) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 567 time to evaluate : 1.148 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: A 68 GLU cc_start: 0.6047 (mt-10) cc_final: 0.4092 (pm20) REVERT: A 110 ASP cc_start: 0.7605 (t0) cc_final: 0.7374 (p0) REVERT: A 127 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7579 (mm-30) REVERT: A 202 MET cc_start: 0.7488 (mmm) cc_final: 0.7273 (tmm) REVERT: A 283 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.7983 (tt) REVERT: C 281 GLU cc_start: 0.6497 (tm-30) cc_final: 0.6281 (tm-30) REVERT: D 16 GLN cc_start: 0.7970 (tp40) cc_final: 0.7554 (tm-30) REVERT: D 48 ASP cc_start: 0.8037 (m-30) cc_final: 0.7822 (m-30) REVERT: D 68 GLU cc_start: 0.7843 (pm20) cc_final: 0.7437 (pm20) REVERT: E 32 ASP cc_start: 0.7766 (t0) cc_final: 0.7502 (t0) REVERT: E 63 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7789 (tt0) REVERT: E 156 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7857 (mm-30) REVERT: F 202 MET cc_start: 0.6983 (mmt) cc_final: 0.6488 (mmt) REVERT: G 16 GLN cc_start: 0.8257 (tp-100) cc_final: 0.7894 (tp-100) REVERT: G 199 ILE cc_start: 0.8560 (tp) cc_final: 0.8300 (tt) REVERT: G 282 LYS cc_start: 0.8143 (mmtm) cc_final: 0.7883 (mmtm) REVERT: H 63 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7464 (tt0) REVERT: H 123 GLU cc_start: 0.4902 (mm-30) cc_final: 0.4637 (mm-30) REVERT: H 213 ASN cc_start: 0.8501 (m110) cc_final: 0.8220 (m110) REVERT: H 233 GLU cc_start: 0.8040 (pp20) cc_final: 0.7733 (pp20) REVERT: I 110 ASP cc_start: 0.7969 (m-30) cc_final: 0.7576 (m-30) REVERT: I 151 ASP cc_start: 0.7216 (t0) cc_final: 0.6773 (t0) REVERT: I 159 LYS cc_start: 0.8383 (tttt) cc_final: 0.7970 (tttt) REVERT: I 171 ASN cc_start: 0.8167 (t0) cc_final: 0.7933 (t0) REVERT: I 180 ASP cc_start: 0.7543 (t0) cc_final: 0.6787 (p0) REVERT: J 110 ASP cc_start: 0.7631 (m-30) cc_final: 0.7372 (m-30) outliers start: 43 outliers final: 25 residues processed: 583 average time/residue: 1.2916 time to fit residues: 856.5934 Evaluate side-chains 583 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 555 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain D residue 120 ASP Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain F residue 170 MET Chi-restraints excluded: chain G residue 27 MET Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 242 THR Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain I residue 187 THR Chi-restraints excluded: chain J residue 121 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 213 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 192 optimal weight: 6.9990 chunk 170 optimal weight: 1.9990 chunk 236 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 251 optimal weight: 5.9990 chunk 161 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 97 HIS C 173 GLN G 184 GLN G 213 ASN ** I 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.132492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.107554 restraints weight = 96234.505| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.83 r_work: 0.3244 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 23203 Z= 0.235 Angle : 0.628 6.360 31402 Z= 0.339 Chirality : 0.045 0.165 3591 Planarity : 0.005 0.085 3940 Dihedral : 14.395 177.681 3528 Min Nonbonded Distance : 1.655 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.35 % Allowed : 19.42 % Favored : 78.24 % 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: -0.31 (0.15), residues: 2892 helix: 1.11 (0.15), residues: 1125 sheet: 0.08 (0.23), residues: 499 loop : -1.56 (0.16), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 134 TYR 0.018 0.002 TYR A 271 PHE 0.014 0.002 PHE G 270 TRP 0.015 0.002 TRP F 308 HIS 0.007 0.001 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00538 (23203) covalent geometry : angle 0.62811 (31402) hydrogen bonds : bond 0.05861 ( 1000) hydrogen bonds : angle 5.25224 ( 2817) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 568 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: A 127 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7617 (mm-30) REVERT: A 202 MET cc_start: 0.7495 (mmm) cc_final: 0.7277 (tmm) REVERT: A 283 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8099 (tt) REVERT: B 155 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.8277 (tp) REVERT: B 159 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8352 (tt) REVERT: D 16 GLN cc_start: 0.8044 (tp40) cc_final: 0.7563 (tm-30) REVERT: D 68 GLU cc_start: 0.7814 (pm20) cc_final: 0.7392 (pm20) REVERT: D 105 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.7971 (ttt180) REVERT: F 154 GLU cc_start: 0.8524 (tt0) cc_final: 0.8262 (tt0) REVERT: F 202 MET cc_start: 0.6981 (mmt) cc_final: 0.6513 (mmt) REVERT: F 280 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.8056 (ttmm) REVERT: G 16 GLN cc_start: 0.8245 (tp-100) cc_final: 0.7530 (tm-30) REVERT: H 63 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7425 (tt0) REVERT: H 123 GLU cc_start: 0.5098 (mm-30) cc_final: 0.4835 (mm-30) REVERT: H 213 ASN cc_start: 0.8555 (m110) cc_final: 0.8278 (m110) REVERT: H 233 GLU cc_start: 0.8141 (pp20) cc_final: 0.7795 (pp20) REVERT: I 110 ASP cc_start: 0.7920 (m-30) cc_final: 0.7577 (m-30) REVERT: I 141 ASN cc_start: 0.8459 (m-40) cc_final: 0.8226 (m-40) REVERT: I 151 ASP cc_start: 0.7237 (t0) cc_final: 0.6843 (t0) REVERT: I 159 LYS cc_start: 0.8483 (tttt) cc_final: 0.8049 (tttt) REVERT: I 171 ASN cc_start: 0.8109 (t0) cc_final: 0.7847 (t0) REVERT: I 180 ASP cc_start: 0.7509 (t0) cc_final: 0.7030 (p0) REVERT: J 110 ASP cc_start: 0.7794 (m-30) cc_final: 0.7557 (m-30) outliers start: 54 outliers final: 28 residues processed: 587 average time/residue: 1.2966 time to fit residues: 863.5973 Evaluate side-chains 588 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 553 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain D residue 27 MET Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 105 ARG Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 152 LYS Chi-restraints excluded: chain F residue 170 MET Chi-restraints excluded: chain F residue 280 LYS Chi-restraints excluded: chain G residue 27 MET Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain I residue 187 THR Chi-restraints excluded: chain J residue 121 LYS Chi-restraints excluded: chain J residue 168 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 88 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 271 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 231 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 206 optimal weight: 0.7980 chunk 189 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 173 GLN ** F 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 213 ASN I 198 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.133090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.108068 restraints weight = 96294.701| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.84 r_work: 0.3236 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23203 Z= 0.184 Angle : 0.595 6.308 31402 Z= 0.319 Chirality : 0.044 0.166 3591 Planarity : 0.005 0.087 3940 Dihedral : 14.114 167.222 3527 Min Nonbonded Distance : 1.714 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.48 % Allowed : 19.72 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.15), residues: 2892 helix: 1.29 (0.15), residues: 1123 sheet: 0.07 (0.23), residues: 499 loop : -1.57 (0.16), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 134 TYR 0.013 0.001 TYR A 271 PHE 0.011 0.001 PHE C 260 TRP 0.015 0.002 TRP F 308 HIS 0.005 0.001 HIS B 97 Details of bonding type rmsd covalent geometry : bond 0.00420 (23203) covalent geometry : angle 0.59521 (31402) hydrogen bonds : bond 0.05072 ( 1000) hydrogen bonds : angle 5.00364 ( 2817) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 558 time to evaluate : 0.905 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: A 68 GLU cc_start: 0.6203 (mt-10) cc_final: 0.3759 (tt0) REVERT: A 127 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7592 (mm-30) REVERT: A 202 MET cc_start: 0.7467 (mmm) cc_final: 0.7249 (tmm) REVERT: A 283 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8090 (tt) REVERT: B 155 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.8284 (tp) REVERT: B 159 ILE cc_start: 0.8950 (OUTLIER) cc_final: 0.8339 (tt) REVERT: D 16 GLN cc_start: 0.8139 (tp40) cc_final: 0.7625 (tm-30) REVERT: D 68 GLU cc_start: 0.7824 (pm20) cc_final: 0.7383 (pm20) REVERT: E 86 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7600 (mm-30) REVERT: F 202 MET cc_start: 0.6993 (mmt) cc_final: 0.6512 (mmt) REVERT: F 280 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.8036 (ttmm) REVERT: G 16 GLN cc_start: 0.8227 (tp-100) cc_final: 0.7917 (tp-100) REVERT: G 118 GLN cc_start: 0.8313 (mt0) cc_final: 0.8012 (mt0) REVERT: H 63 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7402 (tt0) REVERT: H 123 GLU cc_start: 0.5036 (mm-30) cc_final: 0.4779 (mm-30) REVERT: H 213 ASN cc_start: 0.8541 (m110) cc_final: 0.8256 (m110) REVERT: H 233 GLU cc_start: 0.8173 (pp20) cc_final: 0.7776 (pp20) REVERT: H 241 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7504 (mt-10) REVERT: I 110 ASP cc_start: 0.7919 (m-30) cc_final: 0.7547 (m-30) REVERT: I 141 ASN cc_start: 0.8416 (m-40) cc_final: 0.8204 (m-40) REVERT: I 151 ASP cc_start: 0.7206 (t0) cc_final: 0.6805 (t0) REVERT: I 159 LYS cc_start: 0.8445 (tttt) cc_final: 0.8019 (tttt) REVERT: I 171 ASN cc_start: 0.8078 (t0) cc_final: 0.7830 (t0) REVERT: J 110 ASP cc_start: 0.7820 (m-30) cc_final: 0.7554 (m-30) outliers start: 57 outliers final: 33 residues processed: 582 average time/residue: 1.3173 time to fit residues: 870.9466 Evaluate side-chains 586 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 547 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 310 LYS Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 116 CYS Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 152 LYS Chi-restraints excluded: chain F residue 170 MET Chi-restraints excluded: chain F residue 280 LYS Chi-restraints excluded: chain G residue 27 MET Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 279 VAL Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 242 THR Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain I residue 187 THR Chi-restraints excluded: chain J residue 121 LYS Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain J residue 168 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 214 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 184 optimal weight: 0.0980 chunk 16 optimal weight: 2.9990 chunk 275 optimal weight: 20.0000 chunk 18 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 255 optimal weight: 5.9990 chunk 176 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 HIS C 173 GLN ** F 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 184 GLN ** G 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 213 ASN I 198 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.130361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.105632 restraints weight = 96658.201| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.82 r_work: 0.3229 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 23203 Z= 0.242 Angle : 0.622 6.454 31402 Z= 0.334 Chirality : 0.045 0.168 3591 Planarity : 0.005 0.086 3940 Dihedral : 14.123 168.019 3527 Min Nonbonded Distance : 1.687 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.69 % Allowed : 19.68 % Favored : 77.63 % 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: -0.32 (0.15), residues: 2892 helix: 1.22 (0.15), residues: 1123 sheet: -0.05 (0.23), residues: 502 loop : -1.63 (0.16), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 134 TYR 0.012 0.002 TYR C 65 PHE 0.016 0.002 PHE G 270 TRP 0.017 0.002 TRP B 290 HIS 0.005 0.001 HIS E 97 Details of bonding type rmsd covalent geometry : bond 0.00559 (23203) covalent geometry : angle 0.62181 (31402) hydrogen bonds : bond 0.05379 ( 1000) hydrogen bonds : angle 5.01112 ( 2817) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 551 time to evaluate : 0.869 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: A 68 GLU cc_start: 0.6344 (mt-10) cc_final: 0.4042 (pm20) REVERT: A 127 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7612 (mm-30) REVERT: A 202 MET cc_start: 0.7481 (mmm) cc_final: 0.7260 (tmm) REVERT: A 283 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8126 (tt) REVERT: B 155 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.8415 (tp) REVERT: B 159 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8371 (tt) REVERT: B 205 ASN cc_start: 0.8135 (p0) cc_final: 0.7912 (p0) REVERT: D 16 GLN cc_start: 0.8118 (tp40) cc_final: 0.7657 (tm-30) REVERT: D 68 GLU cc_start: 0.7840 (pm20) cc_final: 0.7402 (pm20) REVERT: D 243 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8190 (ttm170) REVERT: E 14 LEU cc_start: 0.8457 (mt) cc_final: 0.8242 (mt) REVERT: E 86 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7645 (mm-30) REVERT: F 202 MET cc_start: 0.7001 (mmt) cc_final: 0.6525 (mmt) REVERT: F 280 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.8033 (ttmm) REVERT: G 16 GLN cc_start: 0.8193 (tp-100) cc_final: 0.7470 (tm-30) REVERT: G 118 GLN cc_start: 0.8271 (mt0) cc_final: 0.7984 (mt0) REVERT: H 63 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7415 (tt0) REVERT: H 106 LYS cc_start: 0.8378 (mtpp) cc_final: 0.8137 (ttmm) REVERT: H 123 GLU cc_start: 0.5153 (mm-30) cc_final: 0.4894 (mm-30) REVERT: H 213 ASN cc_start: 0.8564 (m110) cc_final: 0.8270 (m110) REVERT: H 233 GLU cc_start: 0.8225 (pp20) cc_final: 0.7812 (pp20) REVERT: I 110 ASP cc_start: 0.7929 (m-30) cc_final: 0.7560 (m-30) REVERT: I 141 ASN cc_start: 0.8417 (m-40) cc_final: 0.8204 (m-40) REVERT: I 151 ASP cc_start: 0.7192 (t0) cc_final: 0.6784 (t0) REVERT: I 159 LYS cc_start: 0.8456 (tttt) cc_final: 0.8031 (tttt) REVERT: I 171 ASN cc_start: 0.8043 (t0) cc_final: 0.7783 (t0) outliers start: 62 outliers final: 37 residues processed: 577 average time/residue: 1.1078 time to fit residues: 732.0446 Evaluate side-chains 593 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 549 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain D residue 27 MET Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 116 CYS Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 243 ARG Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 152 LYS Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 170 MET Chi-restraints excluded: chain F residue 280 LYS Chi-restraints excluded: chain G residue 27 MET Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 279 VAL Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 242 THR Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 187 THR Chi-restraints excluded: chain J residue 121 LYS Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain J residue 197 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 116 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 283 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 199 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 169 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 173 GLN ** F 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 213 ASN I 198 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.132542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.107639 restraints weight = 96306.804| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.83 r_work: 0.3248 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 23203 Z= 0.226 Angle : 0.616 6.575 31402 Z= 0.331 Chirality : 0.045 0.164 3591 Planarity : 0.005 0.094 3940 Dihedral : 14.110 164.720 3527 Min Nonbonded Distance : 1.697 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.87 % Allowed : 20.46 % Favored : 76.67 % 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: -0.33 (0.15), residues: 2892 helix: 1.24 (0.15), residues: 1123 sheet: -0.15 (0.23), residues: 502 loop : -1.63 (0.16), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG H 134 TYR 0.019 0.002 TYR A 293 PHE 0.012 0.002 PHE E 191 TRP 0.016 0.002 TRP B 290 HIS 0.005 0.001 HIS E 97 Details of bonding type rmsd covalent geometry : bond 0.00521 (23203) covalent geometry : angle 0.61609 (31402) hydrogen bonds : bond 0.05191 ( 1000) hydrogen bonds : angle 4.93019 ( 2817) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 555 time to evaluate : 0.719 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: A 68 GLU cc_start: 0.6325 (mt-10) cc_final: 0.3937 (tt0) REVERT: A 127 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7600 (mm-30) REVERT: A 202 MET cc_start: 0.7495 (mmm) cc_final: 0.7260 (tmm) REVERT: A 283 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8109 (tt) REVERT: B 155 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8400 (tp) REVERT: B 159 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8372 (tt) REVERT: D 16 GLN cc_start: 0.8101 (tp40) cc_final: 0.7657 (tm-30) REVERT: D 68 GLU cc_start: 0.7840 (pm20) cc_final: 0.7430 (pm20) REVERT: D 243 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.8178 (ttm170) REVERT: E 86 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7643 (mm-30) REVERT: E 154 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8243 (tt0) REVERT: E 321 LYS cc_start: 0.7613 (mmtt) cc_final: 0.7398 (mmtt) REVERT: F 158 GLU cc_start: 0.7778 (mp0) cc_final: 0.7520 (mm-30) REVERT: F 202 MET cc_start: 0.7029 (mmt) cc_final: 0.6531 (mmt) REVERT: F 245 LYS cc_start: 0.8608 (ttmm) cc_final: 0.8371 (tttp) REVERT: F 280 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.8017 (ttmm) REVERT: G 16 GLN cc_start: 0.8196 (tp-100) cc_final: 0.7841 (tp-100) REVERT: G 118 GLN cc_start: 0.8250 (mt0) cc_final: 0.7941 (mt0) REVERT: G 273 GLU cc_start: 0.7218 (mt-10) cc_final: 0.6951 (mt-10) REVERT: H 10 LEU cc_start: 0.8025 (mt) cc_final: 0.7621 (mt) REVERT: H 63 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7482 (tt0) REVERT: H 213 ASN cc_start: 0.8565 (m110) cc_final: 0.8277 (m110) REVERT: H 233 GLU cc_start: 0.8214 (pp20) cc_final: 0.7824 (pp20) REVERT: I 110 ASP cc_start: 0.7941 (m-30) cc_final: 0.7555 (m-30) REVERT: I 141 ASN cc_start: 0.8412 (m-40) cc_final: 0.8196 (m-40) REVERT: I 151 ASP cc_start: 0.7198 (t0) cc_final: 0.6792 (t0) REVERT: I 159 LYS cc_start: 0.8471 (tttt) cc_final: 0.8046 (tttt) REVERT: I 171 ASN cc_start: 0.8006 (t0) cc_final: 0.7753 (t0) outliers start: 66 outliers final: 40 residues processed: 582 average time/residue: 0.8974 time to fit residues: 598.0757 Evaluate side-chains 589 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 541 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 184 GLN Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 116 CYS Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 243 ARG Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 152 LYS Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 170 MET Chi-restraints excluded: chain F residue 280 LYS Chi-restraints excluded: chain G residue 27 MET Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 279 VAL Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 242 THR Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 187 THR Chi-restraints excluded: chain J residue 121 LYS Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain J residue 197 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 101 optimal weight: 2.9990 chunk 237 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 274 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 271 optimal weight: 0.0870 chunk 280 optimal weight: 7.9990 chunk 259 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 overall best weight: 1.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 173 GLN ** F 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 194 GLN G 213 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.132649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.107766 restraints weight = 95995.267| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.83 r_work: 0.3228 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 23203 Z= 0.217 Angle : 0.613 7.284 31402 Z= 0.328 Chirality : 0.044 0.164 3591 Planarity : 0.005 0.098 3940 Dihedral : 14.079 163.186 3527 Min Nonbonded Distance : 1.695 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.61 % Allowed : 21.33 % Favored : 76.06 % 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: -0.32 (0.15), residues: 2892 helix: 1.27 (0.15), residues: 1123 sheet: -0.15 (0.23), residues: 500 loop : -1.64 (0.16), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 134 TYR 0.011 0.001 TYR C 65 PHE 0.018 0.002 PHE G 270 TRP 0.016 0.002 TRP B 290 HIS 0.005 0.001 HIS E 97 Details of bonding type rmsd covalent geometry : bond 0.00500 (23203) covalent geometry : angle 0.61283 (31402) hydrogen bonds : bond 0.05066 ( 1000) hydrogen bonds : angle 4.86774 ( 2817) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 546 time to evaluate : 0.757 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: A 68 GLU cc_start: 0.6366 (mt-10) cc_final: 0.4002 (pm20) REVERT: A 127 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7597 (mm-30) REVERT: A 202 MET cc_start: 0.7516 (mmm) cc_final: 0.7270 (tmm) REVERT: A 283 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8132 (tt) REVERT: B 155 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8399 (tp) REVERT: B 159 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8371 (tt) REVERT: D 16 GLN cc_start: 0.8084 (tp40) cc_final: 0.7646 (tm-30) REVERT: D 243 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.8164 (ttm170) REVERT: E 86 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7619 (mm-30) REVERT: F 158 GLU cc_start: 0.7752 (mp0) cc_final: 0.7547 (mm-30) REVERT: F 202 MET cc_start: 0.7005 (mmt) cc_final: 0.6514 (mmt) REVERT: G 16 GLN cc_start: 0.8202 (tp-100) cc_final: 0.7841 (tp-100) REVERT: G 118 GLN cc_start: 0.8257 (mt0) cc_final: 0.7982 (mt0) REVERT: H 10 LEU cc_start: 0.8020 (mt) cc_final: 0.7622 (mt) REVERT: H 63 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7432 (tt0) REVERT: H 123 GLU cc_start: 0.5579 (OUTLIER) cc_final: 0.5048 (mt-10) REVERT: H 213 ASN cc_start: 0.8559 (m110) cc_final: 0.8263 (m110) REVERT: H 233 GLU cc_start: 0.8220 (pp20) cc_final: 0.7816 (pp20) REVERT: I 110 ASP cc_start: 0.7943 (m-30) cc_final: 0.7542 (m-30) REVERT: I 141 ASN cc_start: 0.8412 (m-40) cc_final: 0.8200 (m-40) REVERT: I 151 ASP cc_start: 0.7209 (t0) cc_final: 0.6817 (t0) REVERT: I 159 LYS cc_start: 0.8389 (tttt) cc_final: 0.7952 (tttt) REVERT: I 171 ASN cc_start: 0.7960 (t0) cc_final: 0.7730 (t0) REVERT: J 110 ASP cc_start: 0.7729 (m-30) cc_final: 0.7453 (m-30) outliers start: 60 outliers final: 41 residues processed: 571 average time/residue: 0.8918 time to fit residues: 582.9977 Evaluate side-chains 595 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 547 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LYS Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 116 CYS Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 243 ARG Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 152 LYS Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 170 MET Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 279 VAL Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 123 GLU Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 242 THR Chi-restraints excluded: chain H residue 275 VAL Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 187 THR Chi-restraints excluded: chain J residue 121 LYS Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain J residue 197 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 70 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 265 optimal weight: 0.6980 chunk 162 optimal weight: 4.9990 chunk 267 optimal weight: 4.9990 chunk 195 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 245 optimal weight: 2.9990 chunk 272 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 173 GLN ** F 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 198 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.133584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.108679 restraints weight = 96476.568| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.83 r_work: 0.3239 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 23203 Z= 0.127 Angle : 0.574 7.197 31402 Z= 0.305 Chirality : 0.042 0.154 3591 Planarity : 0.005 0.108 3940 Dihedral : 13.803 158.958 3527 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.09 % Allowed : 22.15 % Favored : 75.76 % 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: -0.06 (0.15), residues: 2892 helix: 1.56 (0.15), residues: 1123 sheet: -0.16 (0.23), residues: 514 loop : -1.52 (0.16), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 134 TYR 0.021 0.001 TYR A 293 PHE 0.009 0.001 PHE E 217 TRP 0.014 0.001 TRP F 308 HIS 0.002 0.001 HIS I 93 Details of bonding type rmsd covalent geometry : bond 0.00292 (23203) covalent geometry : angle 0.57440 (31402) hydrogen bonds : bond 0.04162 ( 1000) hydrogen bonds : angle 4.65641 ( 2817) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 563 time to evaluate : 0.731 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: A 68 GLU cc_start: 0.6126 (mt-10) cc_final: 0.4084 (tt0) REVERT: A 127 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7579 (mm-30) REVERT: A 202 MET cc_start: 0.7446 (mmm) cc_final: 0.7212 (tmm) REVERT: A 283 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8110 (tt) REVERT: B 155 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8355 (tp) REVERT: C 271 TYR cc_start: 0.8126 (m-80) cc_final: 0.7686 (m-80) REVERT: D 16 GLN cc_start: 0.8103 (tp40) cc_final: 0.7659 (tm-30) REVERT: D 38 GLU cc_start: 0.7906 (tt0) cc_final: 0.7657 (tt0) REVERT: D 48 ASP cc_start: 0.7935 (m-30) cc_final: 0.7668 (m-30) REVERT: D 68 GLU cc_start: 0.7867 (pm20) cc_final: 0.7463 (pm20) REVERT: D 243 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.8113 (ttm170) REVERT: E 86 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7565 (mm-30) REVERT: E 154 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8189 (tt0) REVERT: F 158 GLU cc_start: 0.7673 (mp0) cc_final: 0.7435 (mm-30) REVERT: F 202 MET cc_start: 0.7001 (mmt) cc_final: 0.6529 (mmt) REVERT: F 245 LYS cc_start: 0.8548 (ttmm) cc_final: 0.8317 (ttmm) REVERT: G 16 GLN cc_start: 0.8229 (tp-100) cc_final: 0.7830 (tp-100) REVERT: G 118 GLN cc_start: 0.8229 (mt0) cc_final: 0.7980 (mt0) REVERT: G 281 GLU cc_start: 0.7522 (mm-30) cc_final: 0.7061 (mm-30) REVERT: H 10 LEU cc_start: 0.8001 (mt) cc_final: 0.7566 (mt) REVERT: H 63 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7430 (tt0) REVERT: H 213 ASN cc_start: 0.8531 (m110) cc_final: 0.8240 (m110) REVERT: H 233 GLU cc_start: 0.8174 (pp20) cc_final: 0.7712 (pp20) REVERT: I 110 ASP cc_start: 0.7953 (m-30) cc_final: 0.7558 (m-30) REVERT: I 141 ASN cc_start: 0.8393 (m-40) cc_final: 0.8174 (m-40) REVERT: I 159 LYS cc_start: 0.8361 (tttt) cc_final: 0.7924 (tttt) REVERT: I 171 ASN cc_start: 0.7926 (t0) cc_final: 0.7685 (t0) outliers start: 48 outliers final: 34 residues processed: 584 average time/residue: 0.8872 time to fit residues: 592.6984 Evaluate side-chains 592 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 552 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 116 CYS Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 243 ARG Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 152 LYS Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 297 LYS Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 170 MET Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 279 VAL Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 242 THR Chi-restraints excluded: chain I residue 127 ASP Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 187 THR Chi-restraints excluded: chain J residue 121 LYS Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain J residue 197 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 97 optimal weight: 3.9990 chunk 261 optimal weight: 50.0000 chunk 252 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 266 optimal weight: 3.9990 chunk 262 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 chunk 276 optimal weight: 3.9990 chunk 190 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN D 205 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.130814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.105952 restraints weight = 96272.676| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.82 r_work: 0.3231 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23203 Z= 0.170 Angle : 0.596 6.906 31402 Z= 0.315 Chirality : 0.043 0.158 3591 Planarity : 0.005 0.115 3940 Dihedral : 13.829 159.177 3527 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.13 % Allowed : 22.63 % Favored : 75.24 % 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: -0.08 (0.15), residues: 2892 helix: 1.56 (0.15), residues: 1123 sheet: -0.17 (0.23), residues: 514 loop : -1.54 (0.16), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG G 134 TYR 0.012 0.001 TYR A 293 PHE 0.023 0.001 PHE G 270 TRP 0.014 0.002 TRP F 308 HIS 0.004 0.001 HIS E 97 Details of bonding type rmsd covalent geometry : bond 0.00394 (23203) covalent geometry : angle 0.59589 (31402) hydrogen bonds : bond 0.04466 ( 1000) hydrogen bonds : angle 4.67156 ( 2817) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 548 time to evaluate : 0.793 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: A 68 GLU cc_start: 0.6291 (mt-10) cc_final: 0.3966 (tt0) REVERT: A 127 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7580 (mm-30) REVERT: A 202 MET cc_start: 0.7489 (mmm) cc_final: 0.7071 (tpp) REVERT: A 283 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8152 (tt) REVERT: B 155 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8388 (tp) REVERT: D 16 GLN cc_start: 0.8115 (tp40) cc_final: 0.7682 (tm-30) REVERT: D 38 GLU cc_start: 0.7886 (tt0) cc_final: 0.7656 (tt0) REVERT: D 48 ASP cc_start: 0.7975 (m-30) cc_final: 0.7728 (m-30) REVERT: D 68 GLU cc_start: 0.7860 (pm20) cc_final: 0.7461 (pm20) REVERT: D 243 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.8129 (ttm170) REVERT: E 86 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7574 (mm-30) REVERT: E 154 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8198 (tt0) REVERT: F 202 MET cc_start: 0.7018 (mmt) cc_final: 0.6559 (mmt) REVERT: G 16 GLN cc_start: 0.8203 (tp-100) cc_final: 0.7850 (tp-100) REVERT: G 118 GLN cc_start: 0.8254 (mt0) cc_final: 0.7976 (mt0) REVERT: G 281 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7140 (mm-30) REVERT: H 10 LEU cc_start: 0.8041 (mt) cc_final: 0.7621 (mt) REVERT: H 63 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7446 (tt0) REVERT: H 213 ASN cc_start: 0.8575 (m110) cc_final: 0.8276 (m110) REVERT: H 233 GLU cc_start: 0.8189 (pp20) cc_final: 0.7741 (pp20) REVERT: I 110 ASP cc_start: 0.7934 (m-30) cc_final: 0.7542 (m-30) REVERT: I 141 ASN cc_start: 0.8405 (m-40) cc_final: 0.8185 (m-40) REVERT: I 159 LYS cc_start: 0.8375 (tttt) cc_final: 0.7948 (tttt) REVERT: I 171 ASN cc_start: 0.8097 (t0) cc_final: 0.7872 (t0) REVERT: I 184 GLN cc_start: 0.8318 (mt0) cc_final: 0.8074 (pt0) REVERT: J 110 ASP cc_start: 0.7767 (m-30) cc_final: 0.7446 (m-30) outliers start: 49 outliers final: 34 residues processed: 571 average time/residue: 0.8708 time to fit residues: 570.9173 Evaluate side-chains 580 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 540 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 127 GLU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 116 CYS Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 243 ARG Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 152 LYS Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 170 MET Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 42 THR Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 279 VAL Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain H residue 242 THR Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 187 THR Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain J residue 197 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 26 optimal weight: 3.9990 chunk 60 optimal weight: 0.0970 chunk 169 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 271 optimal weight: 0.6980 chunk 34 optimal weight: 0.0170 chunk 118 optimal weight: 0.4980 chunk 249 optimal weight: 0.5980 chunk 283 optimal weight: 3.9990 chunk 225 optimal weight: 0.7980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 205 ASN D 213 ASN F 118 GLN F 257 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.135128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.110084 restraints weight = 95950.265| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.85 r_work: 0.3265 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 23203 Z= 0.110 Angle : 0.577 7.624 31402 Z= 0.301 Chirality : 0.042 0.149 3591 Planarity : 0.005 0.116 3940 Dihedral : 13.458 154.239 3527 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.30 % Allowed : 23.72 % Favored : 74.98 % 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: 0.24 (0.15), residues: 2892 helix: 1.84 (0.15), residues: 1124 sheet: 0.18 (0.23), residues: 494 loop : -1.45 (0.16), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG G 134 TYR 0.022 0.001 TYR A 293 PHE 0.036 0.001 PHE C 270 TRP 0.023 0.002 TRP A 308 HIS 0.002 0.001 HIS F 163 Details of bonding type rmsd covalent geometry : bond 0.00256 (23203) covalent geometry : angle 0.57654 (31402) hydrogen bonds : bond 0.03588 ( 1000) hydrogen bonds : angle 4.46300 ( 2817) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5784 Ramachandran restraints generated. 2892 Oldfield, 0 Emsley, 2892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 564 time to evaluate : 0.698 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: A 18 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7515 (mt-10) REVERT: A 68 GLU cc_start: 0.5934 (mt-10) cc_final: 0.4120 (tt0) REVERT: A 202 MET cc_start: 0.7447 (mmm) cc_final: 0.7228 (tmm) REVERT: A 283 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8108 (tt) REVERT: B 155 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8360 (tp) REVERT: C 271 TYR cc_start: 0.8119 (m-80) cc_final: 0.7678 (m-80) REVERT: D 16 GLN cc_start: 0.8133 (tp40) cc_final: 0.7669 (tm-30) REVERT: D 38 GLU cc_start: 0.7867 (tt0) cc_final: 0.7627 (tt0) REVERT: D 48 ASP cc_start: 0.7977 (m-30) cc_final: 0.7720 (m-30) REVERT: D 68 GLU cc_start: 0.7862 (pm20) cc_final: 0.7466 (pm20) REVERT: D 243 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.8121 (ttm170) REVERT: E 321 LYS cc_start: 0.7544 (mmtt) cc_final: 0.7286 (mmtt) REVERT: F 202 MET cc_start: 0.7041 (mmt) cc_final: 0.6535 (mmt) REVERT: F 245 LYS cc_start: 0.8550 (ttmm) cc_final: 0.8327 (tttp) REVERT: G 16 GLN cc_start: 0.8204 (tp-100) cc_final: 0.7933 (tp-100) REVERT: G 118 GLN cc_start: 0.8202 (mt0) cc_final: 0.7984 (mt0) REVERT: G 281 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7106 (mm-30) REVERT: H 26 ILE cc_start: 0.7489 (mt) cc_final: 0.7284 (mm) REVERT: H 63 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7462 (tt0) REVERT: H 213 ASN cc_start: 0.8483 (m110) cc_final: 0.8205 (m110) REVERT: H 233 GLU cc_start: 0.8111 (pp20) cc_final: 0.7738 (pp20) REVERT: I 110 ASP cc_start: 0.7922 (m-30) cc_final: 0.7576 (m-30) REVERT: I 141 ASN cc_start: 0.8380 (m-40) cc_final: 0.8164 (m-40) REVERT: I 159 LYS cc_start: 0.8358 (tttt) cc_final: 0.7936 (tttt) REVERT: I 171 ASN cc_start: 0.8063 (t0) cc_final: 0.7833 (t0) REVERT: I 184 GLN cc_start: 0.8296 (mt0) cc_final: 0.8030 (pt0) outliers start: 30 outliers final: 21 residues processed: 577 average time/residue: 0.8922 time to fit residues: 590.7550 Evaluate side-chains 578 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 553 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 GLU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 170 MET Chi-restraints excluded: chain D residue 183 LYS Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 243 ARG Chi-restraints excluded: chain E residue 152 LYS Chi-restraints excluded: chain F residue 170 MET Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 279 VAL Chi-restraints excluded: chain H residue 63 GLU Chi-restraints excluded: chain H residue 231 VAL Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain J residue 127 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 100 optimal weight: 1.9990 chunk 269 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 245 optimal weight: 0.2980 chunk 51 optimal weight: 0.9980 chunk 95 optimal weight: 0.5980 chunk 32 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 256 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 205 ASN D 213 ASN F 257 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.132426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.108003 restraints weight = 98561.744| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.82 r_work: 0.3252 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23203 Z= 0.140 Angle : 0.578 7.309 31402 Z= 0.303 Chirality : 0.042 0.153 3591 Planarity : 0.005 0.115 3940 Dihedral : 13.464 154.721 3527 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.22 % Allowed : 24.11 % Favored : 74.67 % 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: 0.25 (0.15), residues: 2892 helix: 1.87 (0.15), residues: 1124 sheet: 0.08 (0.23), residues: 501 loop : -1.42 (0.16), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG G 134 TYR 0.014 0.001 TYR A 103 PHE 0.017 0.001 PHE C 270 TRP 0.020 0.002 TRP A 308 HIS 0.003 0.001 HIS E 97 Details of bonding type rmsd covalent geometry : bond 0.00325 (23203) covalent geometry : angle 0.57802 (31402) hydrogen bonds : bond 0.03914 ( 1000) hydrogen bonds : angle 4.49312 ( 2817) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14797.97 seconds wall clock time: 249 minutes 34.49 seconds (14974.49 seconds total)