Starting phenix.real_space_refine on Tue Aug 26 07:41:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jp0_61691/08_2025/9jp0_61691.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jp0_61691/08_2025/9jp0_61691.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jp0_61691/08_2025/9jp0_61691.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jp0_61691/08_2025/9jp0_61691.map" model { file = "/net/cci-nas-00/data/ceres_data/9jp0_61691/08_2025/9jp0_61691.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jp0_61691/08_2025/9jp0_61691.cif" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 11338 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 177 5.16 5 C 16300 2.51 5 N 4149 2.21 5 O 4696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s 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: 25322 Number of models: 1 Model: "" Number of chains: 10 Chain: "E" Number of atoms: 2531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2531 Classifications: {'peptide': 312} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 302} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "B" Number of atoms: 2538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2538 Classifications: {'peptide': 312} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 302} Chain: "C" Number of atoms: 2535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2535 Classifications: {'peptide': 312} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 302} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "F" Number of atoms: 2534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2534 Classifications: {'peptide': 312} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 302} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 2538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2538 Classifications: {'peptide': 312} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 302} Chain: "H" Number of atoms: 2522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2522 Classifications: {'peptide': 312} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 302} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 2538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2538 Classifications: {'peptide': 312} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 302} Chain: "A" Number of atoms: 2538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2538 Classifications: {'peptide': 312} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 302} Chain: "I" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2514 Classifications: {'peptide': 312} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 9, 'TRANS': 302} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "J" Number of atoms: 2534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2534 Classifications: {'peptide': 312} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 302} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 6.08, per 1000 atoms: 0.24 Number of scatterers: 25322 At special positions: 0 Unit cell: (132.48, 129.72, 169.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 177 16.00 O 4696 8.00 N 4149 7.00 C 16300 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.02 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5940 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 45 sheets defined 26.3% alpha, 26.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'E' and resid 62 through 67 Processing helix chain 'E' and resid 69 through 82 Processing helix chain 'E' and resid 83 through 88 removed outlier: 3.531A pdb=" N PHE E 87 " --> pdb=" O ASN E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 109 removed outlier: 3.884A pdb=" N ALA E 106 " --> pdb=" O LEU E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 132 removed outlier: 4.017A pdb=" N TYR E 125 " --> pdb=" O SER E 121 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS E 128 " --> pdb=" O ASP E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 182 Processing helix chain 'E' and resid 206 through 213 removed outlier: 4.094A pdb=" N ASP E 210 " --> pdb=" O ARG E 206 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N TYR E 211 " --> pdb=" O GLN E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 217 Processing helix chain 'E' and resid 224 through 226 No H-bonds generated for 'chain 'E' and resid 224 through 226' Processing helix chain 'E' and resid 227 through 234 Processing helix chain 'E' and resid 241 through 245 removed outlier: 3.505A pdb=" N GLN E 244 " --> pdb=" O ASP E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 260 removed outlier: 4.126A pdb=" N VAL E 260 " --> pdb=" O ILE E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 265 removed outlier: 3.683A pdb=" N ASP E 264 " --> pdb=" O LYS E 261 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU E 265 " --> pdb=" O VAL E 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 261 through 265' Processing helix chain 'B' and resid 62 through 67 removed outlier: 4.027A pdb=" N LEU B 67 " --> pdb=" O HIS B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 81 removed outlier: 4.040A pdb=" N LEU B 74 " --> pdb=" O GLU B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 Processing helix chain 'B' and resid 122 through 133 removed outlier: 4.246A pdb=" N LYS B 128 " --> pdb=" O ASP B 124 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN B 133 " --> pdb=" O ILE B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 183 removed outlier: 3.651A pdb=" N LYS B 183 " --> pdb=" O TYR B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 213 Processing helix chain 'B' and resid 225 through 234 removed outlier: 4.076A pdb=" N ASP B 229 " --> pdb=" O SER B 225 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL B 230 " --> pdb=" O CYS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 245 removed outlier: 3.541A pdb=" N GLN B 244 " --> pdb=" O ASP B 241 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU B 245 " --> pdb=" O PRO B 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 241 through 245' Processing helix chain 'C' and resid 69 through 82 removed outlier: 3.554A pdb=" N LEU C 74 " --> pdb=" O GLU C 70 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR C 75 " --> pdb=" O VAL C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 88 removed outlier: 3.626A pdb=" N PHE C 87 " --> pdb=" O ASN C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 108 Processing helix chain 'C' and resid 124 through 132 Processing helix chain 'C' and resid 133 through 135 No H-bonds generated for 'chain 'C' and resid 133 through 135' Processing helix chain 'C' and resid 165 through 169 Processing helix chain 'C' and resid 173 through 184 Processing helix chain 'C' and resid 206 through 213 Processing helix chain 'C' and resid 214 through 217 Processing helix chain 'C' and resid 225 through 234 removed outlier: 3.969A pdb=" N ASP C 229 " --> pdb=" O SER C 225 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL C 230 " --> pdb=" O CYS C 226 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU C 234 " --> pdb=" O VAL C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 245 Processing helix chain 'C' and resid 258 through 260 No H-bonds generated for 'chain 'C' and resid 258 through 260' Processing helix chain 'F' and resid 62 through 67 removed outlier: 3.749A pdb=" N LEU F 67 " --> pdb=" O HIS F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 83 removed outlier: 3.599A pdb=" N THR F 73 " --> pdb=" O ASP F 69 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR F 75 " --> pdb=" O VAL F 71 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN F 83 " --> pdb=" O SER F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 88 removed outlier: 3.994A pdb=" N LYS F 88 " --> pdb=" O HIS F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 108 Processing helix chain 'F' and resid 121 through 133 removed outlier: 4.294A pdb=" N TYR F 125 " --> pdb=" O SER F 121 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS F 128 " --> pdb=" O ASP F 124 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN F 133 " --> pdb=" O ILE F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 149 removed outlier: 3.908A pdb=" N VAL F 149 " --> pdb=" O VAL F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 169 Processing helix chain 'F' and resid 173 through 185 removed outlier: 3.808A pdb=" N LEU F 185 " --> pdb=" O ARG F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 213 Processing helix chain 'F' and resid 218 through 222 Processing helix chain 'F' and resid 227 through 232 Processing helix chain 'F' and resid 261 through 266 removed outlier: 4.010A pdb=" N THR F 266 " --> pdb=" O GLU F 263 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 67 Processing helix chain 'G' and resid 73 through 83 Processing helix chain 'G' and resid 121 through 133 removed outlier: 4.209A pdb=" N TYR G 125 " --> pdb=" O SER G 121 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS G 128 " --> pdb=" O ASP G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 149 removed outlier: 3.692A pdb=" N VAL G 149 " --> pdb=" O VAL G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 169 removed outlier: 3.505A pdb=" N PHE G 169 " --> pdb=" O TYR G 166 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 184 Processing helix chain 'G' and resid 206 through 213 Processing helix chain 'G' and resid 214 through 218 Processing helix chain 'G' and resid 225 through 234 removed outlier: 3.908A pdb=" N ASP G 229 " --> pdb=" O SER G 225 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N VAL G 230 " --> pdb=" O CYS G 226 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU G 234 " --> pdb=" O VAL G 230 " (cutoff:3.500A) Processing helix chain 'G' and resid 241 through 245 Processing helix chain 'G' and resid 261 through 266 removed outlier: 3.685A pdb=" N THR G 266 " --> pdb=" O GLU G 263 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 67 Processing helix chain 'H' and resid 71 through 82 removed outlier: 3.513A pdb=" N THR H 75 " --> pdb=" O VAL H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 110 removed outlier: 3.971A pdb=" N MET H 104 " --> pdb=" O GLY H 100 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE H 105 " --> pdb=" O ILE H 101 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA H 109 " --> pdb=" O PHE H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 133 removed outlier: 4.000A pdb=" N LYS H 128 " --> pdb=" O ASP H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 165 through 169 Processing helix chain 'H' and resid 173 through 184 Processing helix chain 'H' and resid 208 through 213 removed outlier: 3.968A pdb=" N LYS H 212 " --> pdb=" O TYR H 208 " (cutoff:3.500A) Processing helix chain 'H' and resid 225 through 233 removed outlier: 3.695A pdb=" N ILE H 232 " --> pdb=" O LYS H 228 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LYS H 233 " --> pdb=" O ASP H 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 241 through 245 removed outlier: 3.852A pdb=" N GLN H 244 " --> pdb=" O ASP H 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 82 removed outlier: 3.634A pdb=" N PHE D 81 " --> pdb=" O ARG D 77 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N HIS D 82 " --> pdb=" O ASN D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 88 removed outlier: 3.655A pdb=" N LEU D 86 " --> pdb=" O ASN D 83 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LYS D 88 " --> pdb=" O HIS D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 108 Processing helix chain 'D' and resid 121 through 133 removed outlier: 4.037A pdb=" N TYR D 125 " --> pdb=" O SER D 121 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LYS D 128 " --> pdb=" O ASP D 124 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN D 133 " --> pdb=" O ILE D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 149 removed outlier: 3.797A pdb=" N VAL D 149 " --> pdb=" O VAL D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 169 removed outlier: 3.572A pdb=" N PHE D 169 " --> pdb=" O TYR D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 184 Processing helix chain 'D' and resid 208 through 213 Processing helix chain 'D' and resid 224 through 232 removed outlier: 4.155A pdb=" N LYS D 228 " --> pdb=" O MET D 224 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASP D 229 " --> pdb=" O SER D 225 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N VAL D 230 " --> pdb=" O CYS D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 260 No H-bonds generated for 'chain 'D' and resid 258 through 260' Processing helix chain 'A' and resid 71 through 82 removed outlier: 3.598A pdb=" N THR A 75 " --> pdb=" O VAL A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 108 removed outlier: 3.639A pdb=" N PHE A 105 " --> pdb=" O ILE A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 133 removed outlier: 4.320A pdb=" N LYS A 128 " --> pdb=" O ASP A 124 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASN A 133 " --> pdb=" O ILE A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 169 removed outlier: 3.524A pdb=" N PHE A 169 " --> pdb=" O TYR A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 184 Processing helix chain 'A' and resid 206 through 213 removed outlier: 4.014A pdb=" N ASP A 210 " --> pdb=" O ARG A 206 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR A 211 " --> pdb=" O GLN A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 231 removed outlier: 3.757A pdb=" N LYS A 228 " --> pdb=" O MET A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 245 removed outlier: 3.947A pdb=" N LEU A 245 " --> pdb=" O PRO A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 266 removed outlier: 3.941A pdb=" N THR A 266 " --> pdb=" O GLU A 263 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 82 removed outlier: 3.569A pdb=" N SER I 79 " --> pdb=" O THR I 75 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET I 80 " --> pdb=" O TYR I 76 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE I 81 " --> pdb=" O ARG I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 100 Processing helix chain 'I' and resid 101 through 108 removed outlier: 4.176A pdb=" N PHE I 105 " --> pdb=" O ILE I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 133 removed outlier: 4.163A pdb=" N TYR I 125 " --> pdb=" O SER I 121 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS I 128 " --> pdb=" O ASP I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 165 through 169 removed outlier: 3.760A pdb=" N PHE I 169 " --> pdb=" O TYR I 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 173 through 185 removed outlier: 3.589A pdb=" N LEU I 178 " --> pdb=" O LEU I 174 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR I 179 " --> pdb=" O ASN I 175 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU I 185 " --> pdb=" O ARG I 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 208 through 213 Processing helix chain 'I' and resid 218 through 222 Processing helix chain 'I' and resid 224 through 234 removed outlier: 4.369A pdb=" N VAL I 230 " --> pdb=" O CYS I 226 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 67 removed outlier: 3.545A pdb=" N MET J 66 " --> pdb=" O ILE J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 82 removed outlier: 3.646A pdb=" N THR J 75 " --> pdb=" O VAL J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 108 removed outlier: 3.526A pdb=" N LYS J 108 " --> pdb=" O MET J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 133 removed outlier: 4.450A pdb=" N TYR J 125 " --> pdb=" O SER J 121 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN J 133 " --> pdb=" O ILE J 129 " (cutoff:3.500A) Processing helix chain 'J' and resid 165 through 169 Processing helix chain 'J' and resid 173 through 183 removed outlier: 3.663A pdb=" N LYS J 183 " --> pdb=" O TYR J 179 " (cutoff:3.500A) Processing helix chain 'J' and resid 213 through 218 removed outlier: 3.828A pdb=" N TRP J 216 " --> pdb=" O ILE J 213 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU J 217 " --> pdb=" O HIS J 214 " (cutoff:3.500A) Processing helix chain 'J' and resid 226 through 234 removed outlier: 4.321A pdb=" N VAL J 230 " --> pdb=" O CYS J 226 " (cutoff:3.500A) Processing helix chain 'J' and resid 241 through 245 removed outlier: 3.662A pdb=" N GLN J 244 " --> pdb=" O ASP J 241 " (cutoff:3.500A) Processing helix chain 'J' and resid 261 through 266 removed outlier: 3.631A pdb=" N THR J 266 " --> pdb=" O GLU J 263 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 139 through 143 removed outlier: 6.471A pdb=" N VAL E 114 " --> pdb=" O THR E 140 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ILE E 142 " --> pdb=" O VAL E 114 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLY E 116 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL E 92 " --> pdb=" O ILE E 115 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N ILE E 117 " --> pdb=" O VAL E 92 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ASP E 94 " --> pdb=" O ILE E 117 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N VAL E 91 " --> pdb=" O VAL E 156 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL E 156 " --> pdb=" O ALA E 186 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ASP E 188 " --> pdb=" O VAL E 156 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ILE E 158 " --> pdb=" O ASP E 188 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N LEU E 190 " --> pdb=" O ILE E 158 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE E 160 " --> pdb=" O LEU E 190 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 236 through 237 removed outlier: 12.540A pdb=" N PHE E 317 " --> pdb=" O TYR E 287 " (cutoff:3.500A) removed outlier: 11.838A pdb=" N TYR E 287 " --> pdb=" O PHE E 317 " (cutoff:3.500A) removed outlier: 12.529A pdb=" N MET E 319 " --> pdb=" O VAL E 285 " (cutoff:3.500A) removed outlier: 12.536A pdb=" N VAL E 285 " --> pdb=" O MET E 319 " (cutoff:3.500A) removed outlier: 11.085A pdb=" N ASP E 321 " --> pdb=" O ALA E 283 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ALA E 283 " --> pdb=" O ASP E 321 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP E 279 " --> pdb=" O VAL E 325 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LYS E 253 " --> pdb=" O LEU E 198 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL E 200 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU E 251 " --> pdb=" O VAL E 200 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 267 through 274 removed outlier: 4.101A pdb=" N PHE E 267 " --> pdb=" O MET E 337 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N MET E 337 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY E 333 " --> pdb=" O PHE E 271 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR E 334 " --> pdb=" O ASP E 352 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG E 338 " --> pdb=" O ASP E 348 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP E 348 " --> pdb=" O ARG E 338 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU E 347 " --> pdb=" O MET E 370 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET E 370 " --> pdb=" O LEU E 347 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 291 through 292 removed outlier: 4.512A pdb=" N THR E 299 " --> pdb=" O PHE E 292 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 139 through 143 removed outlier: 6.049A pdb=" N VAL B 114 " --> pdb=" O THR B 140 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N ILE B 142 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N GLY B 116 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE B 115 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP B 94 " --> pdb=" O ILE B 115 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE B 117 " --> pdb=" O ASP B 94 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU B 93 " --> pdb=" O ILE B 160 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL B 156 " --> pdb=" O ALA B 186 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N ASP B 188 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ILE B 158 " --> pdb=" O ASP B 188 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N LEU B 190 " --> pdb=" O ILE B 158 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE B 160 " --> pdb=" O LEU B 190 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 251 through 256 removed outlier: 6.674A pdb=" N LEU B 198 " --> pdb=" O ILE B 252 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLU B 254 " --> pdb=" O ALA B 196 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ALA B 196 " --> pdb=" O GLU B 254 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ARG B 195 " --> pdb=" O GLU B 291 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLU B 291 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR B 197 " --> pdb=" O ASN B 289 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN B 289 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N THR B 299 " --> pdb=" O PHE B 292 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 236 through 237 Processing sheet with id=AA8, first strand: chain 'B' and resid 268 through 270 removed outlier: 3.841A pdb=" N SER B 269 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR B 334 " --> pdb=" O ASP B 352 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LYS B 356 " --> pdb=" O GLU B 330 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N GLU B 330 " --> pdb=" O LYS B 356 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 268 through 270 removed outlier: 3.841A pdb=" N SER B 269 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR B 334 " --> pdb=" O ASP B 352 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU B 347 " --> pdb=" O MET B 370 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS B 364 " --> pdb=" O LEU B 353 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 139 through 143 removed outlier: 6.615A pdb=" N VAL C 114 " --> pdb=" O THR C 140 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE C 142 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLY C 116 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE C 115 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE C 117 " --> pdb=" O ASP C 94 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE C 158 " --> pdb=" O VAL C 91 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 236 through 237 removed outlier: 3.997A pdb=" N THR C 315 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA C 286 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA C 283 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N VAL C 200 " --> pdb=" O LEU C 251 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU C 251 " --> pdb=" O VAL C 200 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 267 through 274 removed outlier: 3.806A pdb=" N PHE C 267 " --> pdb=" O MET C 337 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N MET C 337 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR C 334 " --> pdb=" O ASP C 352 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE C 351 " --> pdb=" O THR C 366 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE C 355 " --> pdb=" O LEU C 362 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU C 362 " --> pdb=" O PHE C 355 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 139 through 143 removed outlier: 5.790A pdb=" N LEU F 93 " --> pdb=" O ILE F 160 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 236 through 238 removed outlier: 3.636A pdb=" N GLN F 314 " --> pdb=" O ASP F 238 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N THR F 315 " --> pdb=" O ALA F 286 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA F 286 " --> pdb=" O THR F 315 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA F 283 " --> pdb=" O ILE F 203 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N TYR F 199 " --> pdb=" O TYR F 287 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASN F 289 " --> pdb=" O THR F 197 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR F 197 " --> pdb=" O ASN F 289 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS F 253 " --> pdb=" O LEU F 198 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL F 200 " --> pdb=" O LEU F 251 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LEU F 251 " --> pdb=" O VAL F 200 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 236 through 238 removed outlier: 3.636A pdb=" N GLN F 314 " --> pdb=" O ASP F 238 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N THR F 315 " --> pdb=" O ALA F 286 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA F 286 " --> pdb=" O THR F 315 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 273 through 274 removed outlier: 3.560A pdb=" N LEU F 273 " --> pdb=" O ILE F 331 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N GLU F 330 " --> pdb=" O LYS F 356 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N LYS F 356 " --> pdb=" O GLU F 330 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE F 332 " --> pdb=" O ASP F 354 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 139 through 143 removed outlier: 6.425A pdb=" N VAL G 114 " --> pdb=" O THR G 140 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N ILE G 142 " --> pdb=" O VAL G 114 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLY G 116 " --> pdb=" O ILE G 142 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL G 92 " --> pdb=" O ILE G 115 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N ILE G 117 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE G 158 " --> pdb=" O VAL G 91 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 236 through 238 removed outlier: 14.106A pdb=" N THR G 315 " --> pdb=" O ASN G 289 " (cutoff:3.500A) removed outlier: 12.683A pdb=" N ASN G 289 " --> pdb=" O THR G 315 " (cutoff:3.500A) removed outlier: 12.314A pdb=" N PHE G 317 " --> pdb=" O TYR G 287 " (cutoff:3.500A) removed outlier: 11.701A pdb=" N TYR G 287 " --> pdb=" O PHE G 317 " (cutoff:3.500A) removed outlier: 12.079A pdb=" N MET G 319 " --> pdb=" O VAL G 285 " (cutoff:3.500A) removed outlier: 12.287A pdb=" N VAL G 285 " --> pdb=" O MET G 319 " (cutoff:3.500A) removed outlier: 10.650A pdb=" N ASP G 321 " --> pdb=" O ALA G 283 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ALA G 283 " --> pdb=" O ASP G 321 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA G 283 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU G 198 " --> pdb=" O LYS G 253 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS G 253 " --> pdb=" O LEU G 198 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL G 200 " --> pdb=" O LEU G 251 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU G 251 " --> pdb=" O VAL G 200 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 236 through 238 removed outlier: 14.106A pdb=" N THR G 315 " --> pdb=" O ASN G 289 " (cutoff:3.500A) removed outlier: 12.683A pdb=" N ASN G 289 " --> pdb=" O THR G 315 " (cutoff:3.500A) removed outlier: 12.314A pdb=" N PHE G 317 " --> pdb=" O TYR G 287 " (cutoff:3.500A) removed outlier: 11.701A pdb=" N TYR G 287 " --> pdb=" O PHE G 317 " (cutoff:3.500A) removed outlier: 12.079A pdb=" N MET G 319 " --> pdb=" O VAL G 285 " (cutoff:3.500A) removed outlier: 12.287A pdb=" N VAL G 285 " --> pdb=" O MET G 319 " (cutoff:3.500A) removed outlier: 10.650A pdb=" N ASP G 321 " --> pdb=" O ALA G 283 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ALA G 283 " --> pdb=" O ASP G 321 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N THR G 299 " --> pdb=" O PHE G 292 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 267 through 273 removed outlier: 3.891A pdb=" N PHE G 267 " --> pdb=" O MET G 337 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET G 337 " --> pdb=" O PHE G 267 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER G 269 " --> pdb=" O ILE G 335 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE G 335 " --> pdb=" O SER G 269 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY G 333 " --> pdb=" O PHE G 271 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE G 332 " --> pdb=" O ASP G 354 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR G 334 " --> pdb=" O ASP G 352 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE G 351 " --> pdb=" O THR G 366 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N CYS G 364 " --> pdb=" O LEU G 353 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N PHE G 355 " --> pdb=" O LEU G 362 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU G 362 " --> pdb=" O PHE G 355 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 91 through 95 removed outlier: 6.241A pdb=" N VAL H 92 " --> pdb=" O ILE H 115 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ILE H 117 " --> pdb=" O VAL H 92 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ASP H 94 " --> pdb=" O ILE H 117 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE H 142 " --> pdb=" O VAL H 114 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLY H 116 " --> pdb=" O ILE H 142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'H' and resid 197 through 203 removed outlier: 3.886A pdb=" N THR H 197 " --> pdb=" O ASN H 289 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA H 283 " --> pdb=" O ILE H 203 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE H 301 " --> pdb=" O ILE H 290 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 197 through 203 removed outlier: 3.886A pdb=" N THR H 197 " --> pdb=" O ASN H 289 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA H 283 " --> pdb=" O ILE H 203 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR H 315 " --> pdb=" O ALA H 286 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 267 through 270 removed outlier: 3.752A pdb=" N PHE H 267 " --> pdb=" O MET H 337 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET H 337 " --> pdb=" O PHE H 267 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER H 269 " --> pdb=" O ILE H 335 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE H 335 " --> pdb=" O SER H 269 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU H 347 " --> pdb=" O MET H 370 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET H 370 " --> pdb=" O LEU H 347 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 279 through 281 Processing sheet with id=AC8, first strand: chain 'H' and resid 353 through 355 Processing sheet with id=AC9, first strand: chain 'D' and resid 139 through 143 removed outlier: 6.259A pdb=" N VAL D 114 " --> pdb=" O THR D 140 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ILE D 142 " --> pdb=" O VAL D 114 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLY D 116 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL D 92 " --> pdb=" O ILE D 115 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N ILE D 117 " --> pdb=" O VAL D 92 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ASP D 94 " --> pdb=" O ILE D 117 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N VAL D 91 " --> pdb=" O ILE D 158 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ASP D 157 " --> pdb=" O ASP D 188 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU D 190 " --> pdb=" O ASP D 157 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 236 through 237 removed outlier: 3.854A pdb=" N THR D 315 " --> pdb=" O ALA D 286 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN D 289 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU D 291 " --> pdb=" O ARG D 195 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ARG D 195 " --> pdb=" O GLU D 291 " (cutoff:3.500A) removed outlier: 11.231A pdb=" N ALA D 196 " --> pdb=" O ILE D 252 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ILE D 252 " --> pdb=" O ALA D 196 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU D 198 " --> pdb=" O CYS D 250 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N CYS D 250 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N VAL D 200 " --> pdb=" O ASN D 248 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ASN D 248 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA D 202 " --> pdb=" O VAL D 246 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 236 through 237 removed outlier: 3.854A pdb=" N THR D 315 " --> pdb=" O ALA D 286 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N THR D 299 " --> pdb=" O PHE D 292 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 332 through 334 removed outlier: 3.971A pdb=" N PHE D 332 " --> pdb=" O ASP D 354 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP D 354 " --> pdb=" O PHE D 332 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 332 through 334 removed outlier: 3.971A pdb=" N PHE D 332 " --> pdb=" O ASP D 354 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP D 354 " --> pdb=" O PHE D 332 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU D 347 " --> pdb=" O MET D 370 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 139 through 143 removed outlier: 6.814A pdb=" N VAL A 114 " --> pdb=" O THR A 140 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N ILE A 142 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLY A 116 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL A 92 " --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ILE A 117 " --> pdb=" O VAL A 92 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ASP A 94 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL A 91 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N ILE A 160 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU A 93 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE A 159 " --> pdb=" O LEU A 190 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'A' and resid 199 through 203 removed outlier: 3.676A pdb=" N ALA A 283 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 10.473A pdb=" N TYR A 280 " --> pdb=" O ASP A 321 " (cutoff:3.500A) removed outlier: 10.624A pdb=" N ASP A 321 " --> pdb=" O TYR A 280 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N HIS A 282 " --> pdb=" O MET A 319 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA A 286 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR A 315 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 268 through 270 removed outlier: 4.045A pdb=" N SER A 269 " --> pdb=" O ILE A 335 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE A 335 " --> pdb=" O SER A 269 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 268 through 270 removed outlier: 4.045A pdb=" N SER A 269 " --> pdb=" O ILE A 335 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE A 335 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR A 334 " --> pdb=" O ASP A 352 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 289 through 292 removed outlier: 3.531A pdb=" N ILE A 290 " --> pdb=" O PHE A 301 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE A 301 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N THR A 299 " --> pdb=" O PHE A 292 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 140 through 143 removed outlier: 3.787A pdb=" N GLU I 118 " --> pdb=" O ILE I 142 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL I 92 " --> pdb=" O ILE I 115 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ILE I 117 " --> pdb=" O VAL I 92 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASP I 94 " --> pdb=" O ILE I 117 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N LEU I 93 " --> pdb=" O ILE I 160 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 236 through 238 removed outlier: 3.685A pdb=" N GLN I 314 " --> pdb=" O ASP I 238 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR I 315 " --> pdb=" O ALA I 286 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ALA I 196 " --> pdb=" O GLU I 254 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLU I 254 " --> pdb=" O ALA I 196 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU I 198 " --> pdb=" O ILE I 252 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL I 200 " --> pdb=" O CYS I 250 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N CYS I 250 " --> pdb=" O VAL I 200 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 236 through 238 removed outlier: 3.685A pdb=" N GLN I 314 " --> pdb=" O ASP I 238 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR I 315 " --> pdb=" O ALA I 286 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR I 299 " --> pdb=" O PHE I 292 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 273 through 274 removed outlier: 7.292A pdb=" N GLU I 330 " --> pdb=" O LYS I 356 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N LYS I 356 " --> pdb=" O GLU I 330 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N PHE I 332 " --> pdb=" O ASP I 354 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP I 354 " --> pdb=" O PHE I 332 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP I 352 " --> pdb=" O THR I 334 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU I 347 " --> pdb=" O MET I 370 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N MET I 370 " --> pdb=" O LEU I 347 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE I 349 " --> pdb=" O TYR I 368 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR I 368 " --> pdb=" O PHE I 349 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE I 351 " --> pdb=" O THR I 366 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 92 through 94 removed outlier: 4.196A pdb=" N ILE J 117 " --> pdb=" O ASP J 94 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ILE J 142 " --> pdb=" O VAL J 114 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N GLY J 116 " --> pdb=" O ILE J 142 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 156 through 158 removed outlier: 7.707A pdb=" N VAL J 156 " --> pdb=" O ALA J 186 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ASP J 188 " --> pdb=" O VAL J 156 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ILE J 158 " --> pdb=" O ASP J 188 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LEU J 190 " --> pdb=" O ILE J 158 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'J' and resid 193 through 195 removed outlier: 3.654A pdb=" N ARG J 195 " --> pdb=" O GLU J 291 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU J 291 " --> pdb=" O ARG J 195 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'J' and resid 199 through 203 removed outlier: 3.601A pdb=" N ALA J 283 " --> pdb=" O ILE J 203 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP J 279 " --> pdb=" O VAL J 325 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA J 283 " --> pdb=" O ASP J 321 " (cutoff:3.500A) removed outlier: 10.977A pdb=" N ASP J 321 " --> pdb=" O ALA J 283 " (cutoff:3.500A) removed outlier: 12.248A pdb=" N VAL J 285 " --> pdb=" O MET J 319 " (cutoff:3.500A) removed outlier: 12.037A pdb=" N MET J 319 " --> pdb=" O VAL J 285 " (cutoff:3.500A) removed outlier: 11.831A pdb=" N TYR J 287 " --> pdb=" O PHE J 317 " (cutoff:3.500A) removed outlier: 12.438A pdb=" N PHE J 317 " --> pdb=" O TYR J 287 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 267 through 274 removed outlier: 3.925A pdb=" N PHE J 267 " --> pdb=" O MET J 337 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET J 337 " --> pdb=" O PHE J 267 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLY J 333 " --> pdb=" O PHE J 271 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR J 334 " --> pdb=" O ASP J 352 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP J 352 " --> pdb=" O THR J 334 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY J 336 " --> pdb=" O THR J 350 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR J 350 " --> pdb=" O GLY J 336 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU J 347 " --> pdb=" O MET J 370 " (cutoff:3.500A) 682 hydrogen bonds defined for protein. 1809 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.10 Time building geometry restraints manager: 2.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5634 1.33 - 1.45: 5715 1.45 - 1.57: 14288 1.57 - 1.70: 0 1.70 - 1.82: 264 Bond restraints: 25901 Sorted by residual: bond pdb=" N GLN D 314 " pdb=" CA GLN D 314 " ideal model delta sigma weight residual 1.455 1.499 -0.044 1.27e-02 6.20e+03 1.22e+01 bond pdb=" N VAL I 156 " pdb=" CA VAL I 156 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.15e-02 7.56e+03 1.21e+01 bond pdb=" N VAL J 153 " pdb=" CA VAL J 153 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.11e-02 8.12e+03 1.20e+01 bond pdb=" N ILE I 158 " pdb=" CA ILE I 158 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.15e-02 7.56e+03 1.16e+01 bond pdb=" N VAL G 149 " pdb=" CA VAL G 149 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.15e-02 7.56e+03 1.15e+01 ... (remaining 25896 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 34037 1.83 - 3.67: 897 3.67 - 5.50: 112 5.50 - 7.33: 22 7.33 - 9.17: 6 Bond angle restraints: 35074 Sorted by residual: angle pdb=" N SER I 97 " pdb=" CA SER I 97 " pdb=" C SER I 97 " ideal model delta sigma weight residual 113.20 107.13 6.07 1.21e+00 6.83e-01 2.52e+01 angle pdb=" O ASN J 340 " pdb=" C ASN J 340 " pdb=" N ALA J 341 " ideal model delta sigma weight residual 120.83 124.50 -3.67 7.40e-01 1.83e+00 2.45e+01 angle pdb=" N LYS B 68 " pdb=" CA LYS B 68 " pdb=" C LYS B 68 " ideal model delta sigma weight residual 113.23 107.28 5.95 1.22e+00 6.72e-01 2.38e+01 angle pdb=" C GLY I 100 " pdb=" N ILE I 101 " pdb=" CA ILE I 101 " ideal model delta sigma weight residual 122.77 117.73 5.04 1.05e+00 9.07e-01 2.30e+01 angle pdb=" CA GLY G 189 " pdb=" C GLY G 189 " pdb=" O GLY G 189 " ideal model delta sigma weight residual 122.76 117.83 4.93 1.12e+00 7.97e-01 1.94e+01 ... (remaining 35069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 13376 17.38 - 34.76: 1579 34.76 - 52.14: 411 52.14 - 69.53: 63 69.53 - 86.91: 12 Dihedral angle restraints: 15441 sinusoidal: 6231 harmonic: 9210 Sorted by residual: dihedral pdb=" CA ASP G 69 " pdb=" CB ASP G 69 " pdb=" CG ASP G 69 " pdb=" OD1 ASP G 69 " ideal model delta sinusoidal sigma weight residual -30.00 -88.89 58.89 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CA ASP H 188 " pdb=" CB ASP H 188 " pdb=" CG ASP H 188 " pdb=" OD1 ASP H 188 " ideal model delta sinusoidal sigma weight residual -30.00 -87.94 57.94 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA ASP J 256 " pdb=" CB ASP J 256 " pdb=" CG ASP J 256 " pdb=" OD1 ASP J 256 " ideal model delta sinusoidal sigma weight residual -30.00 -87.04 57.04 1 2.00e+01 2.50e-03 1.09e+01 ... (remaining 15438 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3032 0.051 - 0.101: 639 0.101 - 0.152: 219 0.152 - 0.203: 37 0.203 - 0.253: 2 Chirality restraints: 3929 Sorted by residual: chirality pdb=" CA LYS H 228 " pdb=" N LYS H 228 " pdb=" C LYS H 228 " pdb=" CB LYS H 228 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA ILE J 142 " pdb=" N ILE J 142 " pdb=" C ILE J 142 " pdb=" CB ILE J 142 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA LEU I 178 " pdb=" N LEU I 178 " pdb=" C LEU I 178 " pdb=" CB LEU I 178 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.96e-01 ... (remaining 3926 not shown) Planarity restraints: 4405 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET I 337 " 0.018 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C MET I 337 " -0.064 2.00e-02 2.50e+03 pdb=" O MET I 337 " 0.024 2.00e-02 2.50e+03 pdb=" N ARG I 338 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 186 " 0.044 5.00e-02 4.00e+02 6.72e-02 7.23e+00 pdb=" N PRO C 187 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO C 187 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 187 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 186 " 0.038 5.00e-02 4.00e+02 5.68e-02 5.15e+00 pdb=" N PRO D 187 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO D 187 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 187 " 0.032 5.00e-02 4.00e+02 ... (remaining 4402 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4479 2.77 - 3.30: 23153 3.30 - 3.84: 39096 3.84 - 4.37: 43569 4.37 - 4.90: 76806 Nonbonded interactions: 187103 Sorted by model distance: nonbonded pdb=" O PHE J 288 " pdb=" OG1 THR J 303 " model vdw 2.241 3.040 nonbonded pdb=" OG1 THR E 73 " pdb=" OH TYR D 220 " model vdw 2.257 3.040 nonbonded pdb=" O PHE G 288 " pdb=" OG1 THR G 303 " model vdw 2.261 3.040 nonbonded pdb=" OG SER B 304 " pdb=" OG SER B 307 " model vdw 2.274 3.040 nonbonded pdb=" O PHE B 288 " pdb=" OG1 THR B 303 " model vdw 2.281 3.040 ... (remaining 187098 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 60 through 67 or (resid 68 and (name N or name CA or name \ C or name O or name CB )) or resid 69 through 71 or (resid 72 and (name N or nam \ e CA or name C or name O or name CB )) or resid 73 through 89 or (resid 90 and ( \ name N or name CA or name C or name O or name CB )) or resid 91 through 103 or ( \ resid 104 and (name N or name CA or name C or name O or name CB )) or resid 105 \ through 111 or (resid 112 and (name N or name CA or name C or name O or name CB \ )) or resid 113 through 144 or (resid 145 and (name N or name CA or name C or na \ me O or name CB )) or resid 146 through 262 or (resid 263 and (name N or name CA \ or name C or name O or name CB )) or resid 264 through 272 or (resid 273 and (n \ ame N or name CA or name C or name O or name CB )) or resid 274 through 312 or ( \ resid 313 and (name N or name CA or name C or name O or name CB )) or resid 314 \ through 336 or (resid 337 and (name N or name CA or name C or name O or name CB \ )) or resid 338 through 341 or (resid 342 and (name N or name CA or name C or na \ me O or name CB )) or resid 343 through 348 or (resid 349 and (name N or name CA \ or name C or name O or name CB )) or resid 350 through 360 or (resid 361 and (n \ ame N or name CA or name C or name O or name CB )) or resid 362 through 371)) selection = (chain 'B' and (resid 60 through 67 or (resid 68 and (name N or name CA or name \ C or name O or name CB )) or resid 69 through 71 or (resid 72 and (name N or nam \ e CA or name C or name O or name CB )) or resid 73 through 89 or (resid 90 and ( \ name N or name CA or name C or name O or name CB )) or resid 91 through 103 or ( \ resid 104 and (name N or name CA or name C or name O or name CB )) or resid 105 \ through 111 or (resid 112 and (name N or name CA or name C or name O or name CB \ )) or resid 113 through 144 or (resid 145 and (name N or name CA or name C or na \ me O or name CB )) or resid 146 through 262 or (resid 263 and (name N or name CA \ or name C or name O or name CB )) or resid 264 through 272 or (resid 273 and (n \ ame N or name CA or name C or name O or name CB )) or resid 274 through 312 or ( \ resid 313 and (name N or name CA or name C or name O or name CB )) or resid 314 \ through 336 or (resid 337 and (name N or name CA or name C or name O or name CB \ )) or resid 338 through 341 or (resid 342 and (name N or name CA or name C or na \ me O or name CB )) or resid 343 through 348 or (resid 349 and (name N or name CA \ or name C or name O or name CB )) or resid 350 through 360 or (resid 361 and (n \ ame N or name CA or name C or name O or name CB )) or resid 362 through 371)) selection = (chain 'C' and (resid 60 through 67 or (resid 68 and (name N or name CA or name \ C or name O or name CB )) or resid 69 through 71 or (resid 72 and (name N or nam \ e CA or name C or name O or name CB )) or resid 73 through 89 or (resid 90 and ( \ name N or name CA or name C or name O or name CB )) or resid 91 through 111 or ( \ resid 112 and (name N or name CA or name C or name O or name CB )) or resid 113 \ through 144 or (resid 145 and (name N or name CA or name C or name O or name CB \ )) or resid 146 through 262 or (resid 263 and (name N or name CA or name C or na \ me O or name CB )) or resid 264 through 272 or (resid 273 and (name N or name CA \ or name C or name O or name CB )) or resid 274 through 312 or (resid 313 and (n \ ame N or name CA or name C or name O or name CB )) or resid 314 through 336 or ( \ resid 337 and (name N or name CA or name C or name O or name CB )) or resid 338 \ through 341 or (resid 342 and (name N or name CA or name C or name O or name CB \ )) or resid 343 through 348 or (resid 349 and (name N or name CA or name C or na \ me O or name CB )) or resid 350 through 360 or (resid 361 and (name N or name CA \ or name C or name O or name CB )) or resid 362 through 371)) selection = (chain 'D' and (resid 60 through 67 or (resid 68 and (name N or name CA or name \ C or name O or name CB )) or resid 69 through 71 or (resid 72 and (name N or nam \ e CA or name C or name O or name CB )) or resid 73 through 89 or (resid 90 and ( \ name N or name CA or name C or name O or name CB )) or resid 91 through 103 or ( \ resid 104 and (name N or name CA or name C or name O or name CB )) or resid 105 \ through 111 or (resid 112 and (name N or name CA or name C or name O or name CB \ )) or resid 113 through 144 or (resid 145 and (name N or name CA or name C or na \ me O or name CB )) or resid 146 through 262 or (resid 263 and (name N or name CA \ or name C or name O or name CB )) or resid 264 through 272 or (resid 273 and (n \ ame N or name CA or name C or name O or name CB )) or resid 274 through 312 or ( \ resid 313 and (name N or name CA or name C or name O or name CB )) or resid 314 \ through 336 or (resid 337 and (name N or name CA or name C or name O or name CB \ )) or resid 338 through 341 or (resid 342 and (name N or name CA or name C or na \ me O or name CB )) or resid 343 through 348 or (resid 349 and (name N or name CA \ or name C or name O or name CB )) or resid 350 through 360 or (resid 361 and (n \ ame N or name CA or name C or name O or name CB )) or resid 362 through 371)) selection = (chain 'E' and (resid 60 through 67 or (resid 68 and (name N or name CA or name \ C or name O or name CB )) or resid 69 through 71 or (resid 72 and (name N or nam \ e CA or name C or name O or name CB )) or resid 73 through 89 or (resid 90 and ( \ name N or name CA or name C or name O or name CB )) or resid 91 through 111 or ( \ resid 112 and (name N or name CA or name C or name O or name CB )) or resid 113 \ through 144 or (resid 145 and (name N or name CA or name C or name O or name CB \ )) or resid 146 through 262 or (resid 263 and (name N or name CA or name C or na \ me O or name CB )) or resid 264 through 272 or (resid 273 and (name N or name CA \ or name C or name O or name CB )) or resid 274 through 312 or (resid 313 and (n \ ame N or name CA or name C or name O or name CB )) or resid 314 through 336 or ( \ resid 337 and (name N or name CA or name C or name O or name CB )) or resid 338 \ through 348 or (resid 349 and (name N or name CA or name C or name O or name CB \ )) or resid 350 through 360 or (resid 361 and (name N or name CA or name C or na \ me O or name CB )) or resid 362 through 371)) selection = (chain 'F' and (resid 60 through 67 or (resid 68 and (name N or name CA or name \ C or name O or name CB )) or resid 69 through 71 or (resid 72 and (name N or nam \ e CA or name C or name O or name CB )) or resid 73 through 89 or (resid 90 and ( \ name N or name CA or name C or name O or name CB )) or resid 91 through 103 or ( \ resid 104 and (name N or name CA or name C or name O or name CB )) or resid 105 \ through 111 or (resid 112 and (name N or name CA or name C or name O or name CB \ )) or resid 113 through 262 or (resid 263 and (name N or name CA or name C or na \ me O or name CB )) or resid 264 through 272 or (resid 273 and (name N or name CA \ or name C or name O or name CB )) or resid 274 through 312 or (resid 313 and (n \ ame N or name CA or name C or name O or name CB )) or resid 314 through 336 or ( \ resid 337 and (name N or name CA or name C or name O or name CB )) or resid 338 \ through 341 or (resid 342 and (name N or name CA or name C or name O or name CB \ )) or resid 343 through 348 or (resid 349 and (name N or name CA or name C or na \ me O or name CB )) or resid 350 through 360 or (resid 361 and (name N or name CA \ or name C or name O or name CB )) or resid 362 through 371)) selection = (chain 'G' and (resid 60 through 67 or (resid 68 and (name N or name CA or name \ C or name O or name CB )) or resid 69 through 71 or (resid 72 and (name N or nam \ e CA or name C or name O or name CB )) or resid 73 through 89 or (resid 90 and ( \ name N or name CA or name C or name O or name CB )) or resid 91 through 103 or ( \ resid 104 and (name N or name CA or name C or name O or name CB )) or resid 105 \ through 111 or (resid 112 and (name N or name CA or name C or name O or name CB \ )) or resid 113 through 144 or (resid 145 and (name N or name CA or name C or na \ me O or name CB )) or resid 146 through 262 or (resid 263 and (name N or name CA \ or name C or name O or name CB )) or resid 264 through 272 or (resid 273 and (n \ ame N or name CA or name C or name O or name CB )) or resid 274 through 312 or ( \ resid 313 and (name N or name CA or name C or name O or name CB )) or resid 314 \ through 336 or (resid 337 and (name N or name CA or name C or name O or name CB \ )) or resid 338 through 341 or (resid 342 and (name N or name CA or name C or na \ me O or name CB )) or resid 343 through 348 or (resid 349 and (name N or name CA \ or name C or name O or name CB )) or resid 350 through 360 or (resid 361 and (n \ ame N or name CA or name C or name O or name CB )) or resid 362 through 371)) selection = (chain 'H' and (resid 60 through 67 or (resid 68 and (name N or name CA or name \ C or name O or name CB )) or resid 69 through 71 or (resid 72 and (name N or nam \ e CA or name C or name O or name CB )) or resid 73 through 89 or (resid 90 and ( \ name N or name CA or name C or name O or name CB )) or resid 91 through 103 or ( \ resid 104 and (name N or name CA or name C or name O or name CB )) or resid 105 \ through 111 or (resid 112 and (name N or name CA or name C or name O or name CB \ )) or resid 113 through 144 or (resid 145 and (name N or name CA or name C or na \ me O or name CB )) or resid 146 through 262 or (resid 263 and (name N or name CA \ or name C or name O or name CB )) or resid 264 through 312 or (resid 313 and (n \ ame N or name CA or name C or name O or name CB )) or resid 314 through 341 or ( \ resid 342 and (name N or name CA or name C or name O or name CB )) or resid 343 \ through 371)) selection = (chain 'I' and (resid 60 through 103 or (resid 104 and (name N or name CA or nam \ e C or name O or name CB )) or resid 105 through 144 or (resid 145 and (name N o \ r name CA or name C or name O or name CB )) or resid 146 through 272 or (resid 2 \ 73 and (name N or name CA or name C or name O or name CB )) or resid 274 through \ 312 or (resid 313 and (name N or name CA or name C or name O or name CB )) or r \ esid 314 through 336 or (resid 337 and (name N or name CA or name C or name O or \ name CB )) or resid 338 through 341 or (resid 342 and (name N or name CA or nam \ e C or name O or name CB )) or resid 343 through 348 or (resid 349 and (name N o \ r name CA or name C or name O or name CB )) or resid 350 through 360 or (resid 3 \ 61 and (name N or name CA or name C or name O or name CB )) or resid 362 through \ 371)) selection = (chain 'J' and (resid 60 through 67 or (resid 68 and (name N or name CA or name \ C or name O or name CB )) or resid 69 through 71 or (resid 72 and (name N or nam \ e CA or name C or name O or name CB )) or resid 73 through 89 or (resid 90 and ( \ name N or name CA or name C or name O or name CB )) or resid 91 through 103 or ( \ resid 104 and (name N or name CA or name C or name O or name CB )) or resid 105 \ through 111 or (resid 112 and (name N or name CA or name C or name O or name CB \ )) or resid 113 through 144 or (resid 145 and (name N or name CA or name C or na \ me O or name CB )) or resid 146 through 262 or (resid 263 and (name N or name CA \ or name C or name O or name CB )) or resid 264 through 272 or (resid 273 and (n \ ame N or name CA or name C or name O or name CB )) or resid 274 through 336 or ( \ resid 337 and (name N or name CA or name C or name O or name CB )) or resid 338 \ through 341 or (resid 342 and (name N or name CA or name C or name O or name CB \ )) or resid 343 through 348 or (resid 349 and (name N or name CA or name C or na \ me O or name CB )) or resid 350 through 360 or (resid 361 and (name N or name CA \ or name C or name O or name CB )) or resid 362 through 371)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.210 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 25901 Z= 0.282 Angle : 0.645 9.166 35074 Z= 0.413 Chirality : 0.049 0.253 3929 Planarity : 0.003 0.067 4405 Dihedral : 15.730 86.908 9501 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.21 % Allowed : 25.41 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.16), residues: 3100 helix: -1.17 (0.20), residues: 720 sheet: -0.64 (0.17), residues: 1070 loop : -1.19 (0.18), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 298 TYR 0.016 0.001 TYR B 179 PHE 0.018 0.001 PHE D 301 TRP 0.030 0.001 TRP A 163 HIS 0.013 0.001 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00398 (25901) covalent geometry : angle 0.64450 (35074) hydrogen bonds : bond 0.26107 ( 646) hydrogen bonds : angle 8.96586 ( 1809) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 456 time to evaluate : 1.038 Fit side-chains revert: symmetry clash REVERT: G 151 LEU cc_start: 0.8048 (pt) cc_final: 0.7842 (mt) REVERT: D 342 LYS cc_start: 0.8297 (tttt) cc_final: 0.8097 (tttm) REVERT: I 301 PHE cc_start: 0.7880 (p90) cc_final: 0.7593 (p90) REVERT: I 346 ASP cc_start: 0.6614 (m-30) cc_final: 0.5585 (p0) REVERT: I 347 LEU cc_start: 0.6235 (tt) cc_final: 0.5465 (tt) outliers start: 6 outliers final: 1 residues processed: 458 average time/residue: 0.1638 time to fit residues: 120.7604 Evaluate side-chains 392 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 391 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 95 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 30.0000 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 20.0000 chunk 298 optimal weight: 6.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 82 HIS B 63 HIS ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 296 HIS H 311 HIS A 311 HIS I 214 HIS I 311 HIS ** J 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.124264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.109360 restraints weight = 57854.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.111915 restraints weight = 29574.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.113588 restraints weight = 18107.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.114726 restraints weight = 12569.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.115486 restraints weight = 9592.546| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 25901 Z= 0.233 Angle : 0.723 9.019 35074 Z= 0.388 Chirality : 0.051 0.215 3929 Planarity : 0.005 0.067 4405 Dihedral : 4.689 25.081 3419 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.29 % Favored : 92.68 % Rotamer: Outliers : 5.17 % Allowed : 21.88 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.12 (0.15), residues: 3100 helix: -1.70 (0.18), residues: 750 sheet: -1.04 (0.16), residues: 1060 loop : -1.34 (0.18), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 338 TYR 0.021 0.002 TYR C 199 PHE 0.026 0.003 PHE G 349 TRP 0.031 0.002 TRP I 216 HIS 0.013 0.002 HIS J 311 Details of bonding type rmsd covalent geometry : bond 0.00532 (25901) covalent geometry : angle 0.72347 (35074) hydrogen bonds : bond 0.05024 ( 646) hydrogen bonds : angle 6.06419 ( 1809) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 410 time to evaluate : 0.699 Fit side-chains revert: symmetry clash REVERT: E 350 THR cc_start: 0.8761 (m) cc_final: 0.8516 (t) REVERT: B 370 MET cc_start: 0.7533 (ttm) cc_final: 0.7317 (mtp) REVERT: C 86 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8630 (tt) REVERT: C 157 ASP cc_start: 0.6759 (OUTLIER) cc_final: 0.6167 (p0) REVERT: C 329 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.6900 (mp0) REVERT: F 90 LYS cc_start: 0.7920 (mmtp) cc_final: 0.7656 (mmtp) REVERT: F 238 ASP cc_start: 0.7382 (p0) cc_final: 0.7003 (m-30) REVERT: G 302 SER cc_start: 0.8151 (t) cc_final: 0.7268 (p) REVERT: H 70 GLU cc_start: 0.8105 (tt0) cc_final: 0.7870 (tt0) REVERT: H 90 LYS cc_start: 0.8437 (mmtp) cc_final: 0.8211 (mmtp) REVERT: H 371 ARG cc_start: 0.3371 (ptm160) cc_final: 0.2398 (ptm-80) REVERT: D 104 MET cc_start: 0.7369 (mpp) cc_final: 0.7163 (mpp) REVERT: D 173 MET cc_start: 0.7304 (mmm) cc_final: 0.6944 (mmm) REVERT: D 342 LYS cc_start: 0.8461 (tttt) cc_final: 0.8210 (tttm) REVERT: I 346 ASP cc_start: 0.6750 (m-30) cc_final: 0.6265 (p0) REVERT: J 94 ASP cc_start: 0.8364 (t0) cc_final: 0.8146 (t0) REVERT: J 245 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8315 (mp) outliers start: 145 outliers final: 97 residues processed: 519 average time/residue: 0.1325 time to fit residues: 113.1677 Evaluate side-chains 463 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 362 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 161 SER Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 260 VAL Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 157 ASP Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 227 ILE Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 237 VAL Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 310 THR Chi-restraints excluded: chain F residue 325 VAL Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 117 ILE Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 246 VAL Chi-restraints excluded: chain G residue 295 CYS Chi-restraints excluded: chain G residue 334 THR Chi-restraints excluded: chain G residue 335 ILE Chi-restraints excluded: chain G residue 337 MET Chi-restraints excluded: chain G residue 354 ASP Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 226 CYS Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 246 VAL Chi-restraints excluded: chain H residue 272 CYS Chi-restraints excluded: chain H residue 276 LYS Chi-restraints excluded: chain H residue 281 VAL Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 226 CYS Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 310 THR Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain I residue 70 GLU Chi-restraints excluded: chain I residue 92 VAL Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 157 ASP Chi-restraints excluded: chain I residue 160 ILE Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 285 VAL Chi-restraints excluded: chain I residue 304 SER Chi-restraints excluded: chain I residue 310 THR Chi-restraints excluded: chain I residue 325 VAL Chi-restraints excluded: chain I residue 366 THR Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain J residue 240 VAL Chi-restraints excluded: chain J residue 245 LEU Chi-restraints excluded: chain J residue 272 CYS Chi-restraints excluded: chain J residue 309 TYR Chi-restraints excluded: chain J residue 334 THR Chi-restraints excluded: chain J residue 340 ASN Chi-restraints excluded: chain J residue 350 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 123 optimal weight: 6.9990 chunk 257 optimal weight: 20.0000 chunk 279 optimal weight: 8.9990 chunk 69 optimal weight: 9.9990 chunk 186 optimal weight: 0.9990 chunk 291 optimal weight: 20.0000 chunk 241 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 111 optimal weight: 5.9990 chunk 286 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 78 ASN B 63 HIS ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 HIS ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 HIS F 85 HIS G 311 HIS ** H 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 ASN D 63 HIS J 311 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.122794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.107975 restraints weight = 58202.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.110513 restraints weight = 29938.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.112166 restraints weight = 18290.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.113266 restraints weight = 12712.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.114035 restraints weight = 9731.784| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25901 Z= 0.171 Angle : 0.614 12.682 35074 Z= 0.326 Chirality : 0.047 0.175 3929 Planarity : 0.004 0.059 4405 Dihedral : 4.433 23.958 3419 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 5.10 % Allowed : 23.63 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.08 (0.15), residues: 3100 helix: -1.55 (0.19), residues: 740 sheet: -1.07 (0.16), residues: 1010 loop : -1.35 (0.18), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 195 TYR 0.018 0.001 TYR C 199 PHE 0.018 0.002 PHE B 105 TRP 0.017 0.001 TRP I 216 HIS 0.010 0.001 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00393 (25901) covalent geometry : angle 0.61447 (35074) hydrogen bonds : bond 0.04386 ( 646) hydrogen bonds : angle 5.77251 ( 1809) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 380 time to evaluate : 0.933 Fit side-chains REVERT: E 350 THR cc_start: 0.8773 (m) cc_final: 0.8565 (t) REVERT: B 370 MET cc_start: 0.7445 (ttm) cc_final: 0.7230 (mtp) REVERT: C 64 GLU cc_start: 0.9145 (OUTLIER) cc_final: 0.7974 (mp0) REVERT: C 157 ASP cc_start: 0.6718 (p0) cc_final: 0.6236 (p0) REVERT: F 90 LYS cc_start: 0.8001 (mmtp) cc_final: 0.7634 (mmtp) REVERT: F 238 ASP cc_start: 0.7275 (p0) cc_final: 0.6735 (m-30) REVERT: F 279 ASP cc_start: 0.7072 (m-30) cc_final: 0.6851 (m-30) REVERT: F 342 LYS cc_start: 0.7747 (pttt) cc_final: 0.6959 (ttpt) REVERT: H 244 GLN cc_start: 0.7807 (pm20) cc_final: 0.7545 (pm20) REVERT: A 104 MET cc_start: 0.5626 (ttt) cc_final: 0.4364 (mmt) REVERT: I 173 MET cc_start: 0.7860 (mmm) cc_final: 0.7313 (mmm) REVERT: I 346 ASP cc_start: 0.7284 (m-30) cc_final: 0.6424 (p0) REVERT: J 370 MET cc_start: 0.7002 (ttt) cc_final: 0.6792 (tmm) outliers start: 143 outliers final: 105 residues processed: 485 average time/residue: 0.1446 time to fit residues: 114.6564 Evaluate side-chains 458 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 352 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 260 VAL Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 310 THR Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 117 ILE Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 279 ASP Chi-restraints excluded: chain G residue 334 THR Chi-restraints excluded: chain G residue 335 ILE Chi-restraints excluded: chain G residue 337 MET Chi-restraints excluded: chain G residue 354 ASP Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 246 VAL Chi-restraints excluded: chain H residue 272 CYS Chi-restraints excluded: chain H residue 276 LYS Chi-restraints excluded: chain H residue 281 VAL Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain H residue 350 THR Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 310 THR Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 157 ASP Chi-restraints excluded: chain I residue 160 ILE Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 241 ASP Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 285 VAL Chi-restraints excluded: chain I residue 291 GLU Chi-restraints excluded: chain I residue 304 SER Chi-restraints excluded: chain I residue 310 THR Chi-restraints excluded: chain I residue 325 VAL Chi-restraints excluded: chain I residue 334 THR Chi-restraints excluded: chain I residue 366 THR Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 174 LEU Chi-restraints excluded: chain J residue 255 VAL Chi-restraints excluded: chain J residue 260 VAL Chi-restraints excluded: chain J residue 272 CYS Chi-restraints excluded: chain J residue 309 TYR Chi-restraints excluded: chain J residue 334 THR Chi-restraints excluded: chain J residue 337 MET Chi-restraints excluded: chain J residue 340 ASN Chi-restraints excluded: chain J residue 366 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 166 optimal weight: 20.0000 chunk 157 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 274 optimal weight: 0.0980 chunk 63 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 284 optimal weight: 20.0000 chunk 86 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 HIS ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 HIS ** G 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS H 289 ASN D 63 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.122853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.107921 restraints weight = 57710.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.110428 restraints weight = 29412.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.112056 restraints weight = 18045.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.113159 restraints weight = 12665.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.113893 restraints weight = 9659.946| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25901 Z= 0.121 Angle : 0.566 11.775 35074 Z= 0.297 Chirality : 0.045 0.168 3929 Planarity : 0.004 0.051 4405 Dihedral : 4.275 22.017 3419 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 4.95 % Allowed : 24.48 % Favored : 70.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.15 (0.15), residues: 3100 helix: -1.67 (0.18), residues: 800 sheet: -1.08 (0.16), residues: 1010 loop : -1.34 (0.18), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 298 TYR 0.018 0.001 TYR C 179 PHE 0.017 0.001 PHE C 267 TRP 0.019 0.001 TRP A 163 HIS 0.010 0.001 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00277 (25901) covalent geometry : angle 0.56626 (35074) hydrogen bonds : bond 0.03500 ( 646) hydrogen bonds : angle 5.49987 ( 1809) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 367 time to evaluate : 1.023 Fit side-chains REVERT: E 350 THR cc_start: 0.8756 (m) cc_final: 0.8544 (t) REVERT: B 104 MET cc_start: 0.6806 (mpp) cc_final: 0.6456 (mpp) REVERT: B 209 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.7849 (tptp) REVERT: C 64 GLU cc_start: 0.9144 (OUTLIER) cc_final: 0.8028 (mp0) REVERT: C 86 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8511 (tt) REVERT: C 157 ASP cc_start: 0.6656 (p0) cc_final: 0.6171 (p0) REVERT: C 329 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.6844 (mp0) REVERT: F 90 LYS cc_start: 0.7957 (mmtp) cc_final: 0.7577 (mmtp) REVERT: F 178 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7867 (pp) REVERT: F 238 ASP cc_start: 0.7171 (p0) cc_final: 0.6625 (m-30) REVERT: F 279 ASP cc_start: 0.7055 (m-30) cc_final: 0.6833 (m-30) REVERT: F 342 LYS cc_start: 0.7612 (pttt) cc_final: 0.6833 (ttpt) REVERT: G 302 SER cc_start: 0.8342 (t) cc_final: 0.7485 (p) REVERT: H 70 GLU cc_start: 0.8108 (tt0) cc_final: 0.7762 (tt0) REVERT: H 244 GLN cc_start: 0.7732 (pm20) cc_final: 0.7516 (pm20) REVERT: H 323 LEU cc_start: 0.6907 (OUTLIER) cc_final: 0.6702 (tt) REVERT: D 185 LEU cc_start: 0.7080 (OUTLIER) cc_final: 0.6591 (mm) REVERT: D 194 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.8046 (p0) REVERT: A 104 MET cc_start: 0.5508 (ttt) cc_final: 0.4286 (mmt) REVERT: I 75 THR cc_start: 0.8308 (OUTLIER) cc_final: 0.8102 (p) REVERT: I 173 MET cc_start: 0.7825 (mmm) cc_final: 0.7284 (mmm) REVERT: I 238 ASP cc_start: 0.6232 (m-30) cc_final: 0.5986 (m-30) REVERT: I 346 ASP cc_start: 0.7592 (m-30) cc_final: 0.6483 (p0) outliers start: 139 outliers final: 95 residues processed: 471 average time/residue: 0.1510 time to fit residues: 117.8758 Evaluate side-chains 454 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 350 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 260 VAL Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 167 CYS Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 310 THR Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 117 ILE Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 279 ASP Chi-restraints excluded: chain G residue 334 THR Chi-restraints excluded: chain G residue 335 ILE Chi-restraints excluded: chain G residue 337 MET Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 226 CYS Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 246 VAL Chi-restraints excluded: chain H residue 281 VAL Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain H residue 350 THR Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 194 ASP Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain A residue 103 CYS Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain I residue 160 ILE Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 226 CYS Chi-restraints excluded: chain I residue 244 GLN Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 285 VAL Chi-restraints excluded: chain I residue 291 GLU Chi-restraints excluded: chain I residue 304 SER Chi-restraints excluded: chain I residue 310 THR Chi-restraints excluded: chain I residue 334 THR Chi-restraints excluded: chain I residue 366 THR Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain J residue 260 VAL Chi-restraints excluded: chain J residue 309 TYR Chi-restraints excluded: chain J residue 334 THR Chi-restraints excluded: chain J residue 337 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 110 optimal weight: 20.0000 chunk 53 optimal weight: 7.9990 chunk 247 optimal weight: 6.9990 chunk 285 optimal weight: 20.0000 chunk 90 optimal weight: 3.9990 chunk 168 optimal weight: 9.9990 chunk 253 optimal weight: 5.9990 chunk 255 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 42 optimal weight: 8.9990 chunk 131 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 HIS B 82 HIS ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 HIS F 133 ASN F 296 HIS ** G 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 ASN D 214 HIS J 83 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.118932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.103980 restraints weight = 58183.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.106436 restraints weight = 29769.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.108052 restraints weight = 18317.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.109142 restraints weight = 12810.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.109882 restraints weight = 9849.030| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 25901 Z= 0.193 Angle : 0.651 12.612 35074 Z= 0.345 Chirality : 0.048 0.198 3929 Planarity : 0.005 0.048 4405 Dihedral : 4.784 27.286 3418 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 6.56 % Allowed : 23.59 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.43 (0.15), residues: 3100 helix: -1.78 (0.18), residues: 800 sheet: -1.32 (0.16), residues: 1000 loop : -1.52 (0.17), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 298 TYR 0.017 0.002 TYR C 199 PHE 0.020 0.002 PHE B 105 TRP 0.022 0.002 TRP H 312 HIS 0.006 0.001 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00449 (25901) covalent geometry : angle 0.65072 (35074) hydrogen bonds : bond 0.04272 ( 646) hydrogen bonds : angle 5.71334 ( 1809) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 364 time to evaluate : 0.971 Fit side-chains REVERT: E 350 THR cc_start: 0.8773 (m) cc_final: 0.8550 (t) REVERT: B 209 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8014 (tptp) REVERT: B 358 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7852 (tt0) REVERT: C 64 GLU cc_start: 0.9131 (OUTLIER) cc_final: 0.8045 (mp0) REVERT: C 86 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8692 (tt) REVERT: C 238 ASP cc_start: 0.7068 (OUTLIER) cc_final: 0.6658 (m-30) REVERT: C 329 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.6777 (mp0) REVERT: F 178 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7927 (pp) REVERT: F 238 ASP cc_start: 0.7247 (p0) cc_final: 0.6725 (m-30) REVERT: F 272 CYS cc_start: 0.7710 (m) cc_final: 0.7340 (t) REVERT: F 279 ASP cc_start: 0.7039 (m-30) cc_final: 0.6814 (m-30) REVERT: F 342 LYS cc_start: 0.7562 (pttt) cc_final: 0.6765 (ttpt) REVERT: H 70 GLU cc_start: 0.8175 (tt0) cc_final: 0.7790 (tt0) REVERT: H 244 GLN cc_start: 0.7838 (pm20) cc_final: 0.7557 (pm20) REVERT: H 323 LEU cc_start: 0.7046 (OUTLIER) cc_final: 0.6798 (tt) REVERT: D 160 ILE cc_start: 0.7607 (OUTLIER) cc_final: 0.7368 (pt) REVERT: A 80 MET cc_start: 0.7564 (tpp) cc_final: 0.7053 (ttm) REVERT: A 104 MET cc_start: 0.5587 (ttt) cc_final: 0.4435 (mmt) REVERT: A 337 MET cc_start: 0.7176 (pmm) cc_final: 0.6921 (pmm) REVERT: I 75 THR cc_start: 0.8394 (OUTLIER) cc_final: 0.8153 (p) REVERT: I 157 ASP cc_start: 0.6150 (OUTLIER) cc_final: 0.5097 (t0) REVERT: I 346 ASP cc_start: 0.7798 (m-30) cc_final: 0.6688 (p0) outliers start: 184 outliers final: 130 residues processed: 515 average time/residue: 0.1303 time to fit residues: 111.8579 Evaluate side-chains 484 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 343 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 260 VAL Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 167 CYS Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 358 GLN Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 364 CYS Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 310 THR Chi-restraints excluded: chain F residue 315 THR Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 137 HIS Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain G residue 279 ASP Chi-restraints excluded: chain G residue 334 THR Chi-restraints excluded: chain G residue 335 ILE Chi-restraints excluded: chain G residue 337 MET Chi-restraints excluded: chain G residue 354 ASP Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 208 TYR Chi-restraints excluded: chain H residue 226 CYS Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 246 VAL Chi-restraints excluded: chain H residue 272 CYS Chi-restraints excluded: chain H residue 276 LYS Chi-restraints excluded: chain H residue 281 VAL Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain H residue 350 THR Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 226 CYS Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 310 THR Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain I residue 70 GLU Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 157 ASP Chi-restraints excluded: chain I residue 160 ILE Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 226 CYS Chi-restraints excluded: chain I residue 244 GLN Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 285 VAL Chi-restraints excluded: chain I residue 291 GLU Chi-restraints excluded: chain I residue 304 SER Chi-restraints excluded: chain I residue 310 THR Chi-restraints excluded: chain I residue 325 VAL Chi-restraints excluded: chain I residue 334 THR Chi-restraints excluded: chain I residue 366 THR Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 105 PHE Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain J residue 153 VAL Chi-restraints excluded: chain J residue 174 LEU Chi-restraints excluded: chain J residue 255 VAL Chi-restraints excluded: chain J residue 260 VAL Chi-restraints excluded: chain J residue 293 THR Chi-restraints excluded: chain J residue 309 TYR Chi-restraints excluded: chain J residue 334 THR Chi-restraints excluded: chain J residue 337 MET Chi-restraints excluded: chain J residue 350 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 257 optimal weight: 7.9990 chunk 114 optimal weight: 6.9990 chunk 119 optimal weight: 0.0970 chunk 116 optimal weight: 20.0000 chunk 88 optimal weight: 9.9990 chunk 136 optimal weight: 10.0000 chunk 197 optimal weight: 4.9990 chunk 188 optimal weight: 9.9990 chunk 278 optimal weight: 20.0000 chunk 227 optimal weight: 0.8980 chunk 23 optimal weight: 0.0570 overall best weight: 2.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 HIS B 82 HIS C 137 HIS F 63 HIS ** G 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 ASN D 214 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.121527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.106706 restraints weight = 58094.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.109196 restraints weight = 29453.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.110835 restraints weight = 18073.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.111949 restraints weight = 12567.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.112704 restraints weight = 9580.838| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25901 Z= 0.111 Angle : 0.572 14.211 35074 Z= 0.300 Chirality : 0.045 0.159 3929 Planarity : 0.004 0.047 4405 Dihedral : 4.402 25.149 3418 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 4.99 % Allowed : 25.34 % Favored : 69.67 % 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: -2.21 (0.15), residues: 3100 helix: -1.62 (0.18), residues: 800 sheet: -1.20 (0.16), residues: 1000 loop : -1.37 (0.18), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 298 TYR 0.018 0.001 TYR C 179 PHE 0.019 0.001 PHE C 267 TRP 0.034 0.001 TRP A 163 HIS 0.005 0.001 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00251 (25901) covalent geometry : angle 0.57176 (35074) hydrogen bonds : bond 0.03257 ( 646) hydrogen bonds : angle 5.36686 ( 1809) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 369 time to evaluate : 0.916 Fit side-chains REVERT: E 350 THR cc_start: 0.8795 (m) cc_final: 0.8563 (t) REVERT: B 151 LEU cc_start: 0.6855 (OUTLIER) cc_final: 0.6017 (mp) REVERT: C 86 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8586 (tt) REVERT: C 329 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.6904 (mp0) REVERT: F 178 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7893 (pp) REVERT: F 238 ASP cc_start: 0.7163 (p0) cc_final: 0.6622 (m-30) REVERT: F 272 CYS cc_start: 0.7651 (m) cc_final: 0.7267 (t) REVERT: F 279 ASP cc_start: 0.6990 (m-30) cc_final: 0.6756 (m-30) REVERT: F 342 LYS cc_start: 0.7567 (pttt) cc_final: 0.6865 (ttpt) REVERT: G 66 MET cc_start: 0.8157 (ttp) cc_final: 0.7905 (ttt) REVERT: G 329 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7374 (mp0) REVERT: H 244 GLN cc_start: 0.7845 (pm20) cc_final: 0.7522 (pm20) REVERT: H 323 LEU cc_start: 0.6959 (OUTLIER) cc_final: 0.6722 (tt) REVERT: A 104 MET cc_start: 0.5450 (ttt) cc_final: 0.4409 (mmt) REVERT: A 337 MET cc_start: 0.7047 (pmm) cc_final: 0.6823 (pmm) REVERT: I 75 THR cc_start: 0.8310 (m) cc_final: 0.8105 (p) REVERT: I 346 ASP cc_start: 0.7768 (m-30) cc_final: 0.6670 (p0) REVERT: J 224 MET cc_start: 0.7181 (ptt) cc_final: 0.6944 (mtm) REVERT: J 370 MET cc_start: 0.7052 (ttt) cc_final: 0.6802 (tmm) outliers start: 140 outliers final: 106 residues processed: 481 average time/residue: 0.1397 time to fit residues: 110.9741 Evaluate side-chains 462 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 350 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 148 GLU Chi-restraints excluded: chain E residue 260 VAL Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 364 CYS Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 310 THR Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 117 ILE Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain G residue 329 GLU Chi-restraints excluded: chain G residue 334 THR Chi-restraints excluded: chain G residue 335 ILE Chi-restraints excluded: chain G residue 354 ASP Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 208 TYR Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 254 GLU Chi-restraints excluded: chain H residue 276 LYS Chi-restraints excluded: chain H residue 281 VAL Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain I residue 70 GLU Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 160 ILE Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 226 CYS Chi-restraints excluded: chain I residue 244 GLN Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 291 GLU Chi-restraints excluded: chain I residue 310 THR Chi-restraints excluded: chain I residue 325 VAL Chi-restraints excluded: chain I residue 334 THR Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 103 CYS Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain J residue 293 THR Chi-restraints excluded: chain J residue 309 TYR Chi-restraints excluded: chain J residue 334 THR Chi-restraints excluded: chain J residue 337 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 228 optimal weight: 4.9990 chunk 296 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 165 optimal weight: 0.9990 chunk 86 optimal weight: 0.4980 chunk 199 optimal weight: 5.9990 chunk 151 optimal weight: 8.9990 chunk 281 optimal weight: 0.7980 chunk 107 optimal weight: 7.9990 chunk 185 optimal weight: 9.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 HIS F 63 HIS ** G 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.122278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.107506 restraints weight = 57821.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.110019 restraints weight = 29266.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.111656 restraints weight = 17910.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.112763 restraints weight = 12449.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.113510 restraints weight = 9481.375| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 25901 Z= 0.105 Angle : 0.562 13.977 35074 Z= 0.293 Chirality : 0.045 0.160 3929 Planarity : 0.004 0.047 4405 Dihedral : 4.224 23.469 3418 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 5.24 % Allowed : 25.16 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.11 (0.15), residues: 3100 helix: -1.56 (0.18), residues: 800 sheet: -1.12 (0.17), residues: 1000 loop : -1.31 (0.18), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 298 TYR 0.019 0.001 TYR A 179 PHE 0.024 0.001 PHE I 192 TRP 0.023 0.001 TRP A 163 HIS 0.006 0.001 HIS C 137 Details of bonding type rmsd covalent geometry : bond 0.00240 (25901) covalent geometry : angle 0.56191 (35074) hydrogen bonds : bond 0.03039 ( 646) hydrogen bonds : angle 5.19563 ( 1809) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 371 time to evaluate : 1.069 Fit side-chains revert: symmetry clash REVERT: E 350 THR cc_start: 0.8769 (m) cc_final: 0.8523 (t) REVERT: B 151 LEU cc_start: 0.6839 (OUTLIER) cc_final: 0.6013 (mp) REVERT: B 358 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7701 (tt0) REVERT: C 86 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8588 (tt) REVERT: C 329 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.6967 (mp0) REVERT: F 178 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7898 (pp) REVERT: F 238 ASP cc_start: 0.7112 (p0) cc_final: 0.6584 (m-30) REVERT: F 272 CYS cc_start: 0.7634 (m) cc_final: 0.7282 (t) REVERT: F 279 ASP cc_start: 0.6931 (m-30) cc_final: 0.6700 (m-30) REVERT: F 342 LYS cc_start: 0.7549 (pttt) cc_final: 0.6820 (ttpt) REVERT: F 356 LYS cc_start: 0.7774 (tptt) cc_final: 0.7183 (pttp) REVERT: G 66 MET cc_start: 0.8146 (ttp) cc_final: 0.7853 (ttt) REVERT: G 329 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7335 (mp0) REVERT: H 244 GLN cc_start: 0.7848 (pm20) cc_final: 0.7509 (pm20) REVERT: H 323 LEU cc_start: 0.6976 (OUTLIER) cc_final: 0.6744 (tt) REVERT: D 185 LEU cc_start: 0.7103 (OUTLIER) cc_final: 0.6452 (mm) REVERT: A 104 MET cc_start: 0.5305 (ttt) cc_final: 0.4285 (mmm) REVERT: A 337 MET cc_start: 0.6967 (pmm) cc_final: 0.6734 (pmm) REVERT: I 346 ASP cc_start: 0.7734 (m-30) cc_final: 0.6641 (p0) REVERT: J 370 MET cc_start: 0.7124 (ttt) cc_final: 0.6865 (tmm) outliers start: 147 outliers final: 117 residues processed: 488 average time/residue: 0.1519 time to fit residues: 122.0700 Evaluate side-chains 478 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 353 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 148 GLU Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 260 VAL Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 167 CYS Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 358 GLN Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 364 CYS Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 310 THR Chi-restraints excluded: chain F residue 315 THR Chi-restraints excluded: chain F residue 337 MET Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 117 ILE Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain G residue 329 GLU Chi-restraints excluded: chain G residue 334 THR Chi-restraints excluded: chain G residue 335 ILE Chi-restraints excluded: chain G residue 354 ASP Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 208 TYR Chi-restraints excluded: chain H residue 276 LYS Chi-restraints excluded: chain H residue 281 VAL Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 331 ILE Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain H residue 350 THR Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain I residue 70 GLU Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 160 ILE Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 226 CYS Chi-restraints excluded: chain I residue 244 GLN Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 285 VAL Chi-restraints excluded: chain I residue 291 GLU Chi-restraints excluded: chain I residue 310 THR Chi-restraints excluded: chain I residue 334 THR Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 103 CYS Chi-restraints excluded: chain J residue 105 PHE Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain J residue 237 VAL Chi-restraints excluded: chain J residue 260 VAL Chi-restraints excluded: chain J residue 293 THR Chi-restraints excluded: chain J residue 309 TYR Chi-restraints excluded: chain J residue 334 THR Chi-restraints excluded: chain J residue 337 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 241 optimal weight: 0.0170 chunk 309 optimal weight: 0.0270 chunk 170 optimal weight: 30.0000 chunk 207 optimal weight: 5.9990 chunk 237 optimal weight: 20.0000 chunk 178 optimal weight: 5.9990 chunk 305 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 96 optimal weight: 0.3980 chunk 68 optimal weight: 3.9990 overall best weight: 2.0880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 HIS F 63 HIS ** G 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.122531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.107716 restraints weight = 57338.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.110261 restraints weight = 29207.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.111920 restraints weight = 17815.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.113038 restraints weight = 12327.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.113795 restraints weight = 9381.829| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.4591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 25901 Z= 0.104 Angle : 0.572 14.362 35074 Z= 0.296 Chirality : 0.045 0.159 3929 Planarity : 0.004 0.047 4405 Dihedral : 4.160 22.394 3418 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 4.99 % Allowed : 25.84 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.07 (0.15), residues: 3100 helix: -1.52 (0.18), residues: 800 sheet: -1.08 (0.17), residues: 1000 loop : -1.30 (0.18), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 84 TYR 0.017 0.001 TYR C 179 PHE 0.021 0.001 PHE C 267 TRP 0.038 0.001 TRP A 163 HIS 0.005 0.001 HIS C 137 Details of bonding type rmsd covalent geometry : bond 0.00237 (25901) covalent geometry : angle 0.57230 (35074) hydrogen bonds : bond 0.02953 ( 646) hydrogen bonds : angle 5.13871 ( 1809) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 375 time to evaluate : 1.191 Fit side-chains revert: symmetry clash REVERT: E 350 THR cc_start: 0.8795 (m) cc_final: 0.8530 (t) REVERT: B 151 LEU cc_start: 0.6807 (OUTLIER) cc_final: 0.5962 (mp) REVERT: C 86 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8576 (tt) REVERT: C 329 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.6996 (mp0) REVERT: F 178 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7900 (pp) REVERT: F 238 ASP cc_start: 0.7090 (p0) cc_final: 0.6564 (m-30) REVERT: F 272 CYS cc_start: 0.7624 (m) cc_final: 0.7261 (t) REVERT: F 279 ASP cc_start: 0.6960 (m-30) cc_final: 0.6754 (m-30) REVERT: F 342 LYS cc_start: 0.7594 (pttt) cc_final: 0.6876 (ttpt) REVERT: F 356 LYS cc_start: 0.7715 (tptt) cc_final: 0.7096 (pttp) REVERT: G 66 MET cc_start: 0.8155 (ttp) cc_final: 0.7860 (ttt) REVERT: G 329 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7331 (mp0) REVERT: H 244 GLN cc_start: 0.7866 (pm20) cc_final: 0.7516 (pm20) REVERT: H 323 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6710 (tt) REVERT: D 185 LEU cc_start: 0.7060 (OUTLIER) cc_final: 0.6548 (mm) REVERT: A 104 MET cc_start: 0.5246 (ttt) cc_final: 0.4280 (mmm) REVERT: A 337 MET cc_start: 0.6940 (pmm) cc_final: 0.6729 (pmm) REVERT: I 346 ASP cc_start: 0.7731 (m-30) cc_final: 0.6637 (p0) REVERT: J 370 MET cc_start: 0.7199 (ttt) cc_final: 0.6898 (tmm) outliers start: 140 outliers final: 120 residues processed: 489 average time/residue: 0.1522 time to fit residues: 122.8396 Evaluate side-chains 485 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 358 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 148 GLU Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 225 SER Chi-restraints excluded: chain E residue 260 VAL Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 359 LEU Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 364 CYS Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 310 THR Chi-restraints excluded: chain F residue 315 THR Chi-restraints excluded: chain F residue 337 MET Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 117 ILE Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain G residue 329 GLU Chi-restraints excluded: chain G residue 334 THR Chi-restraints excluded: chain G residue 335 ILE Chi-restraints excluded: chain G residue 354 ASP Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 208 TYR Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 276 LYS Chi-restraints excluded: chain H residue 281 VAL Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 331 ILE Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain H residue 350 THR Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain I residue 70 GLU Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 160 ILE Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 226 CYS Chi-restraints excluded: chain I residue 244 GLN Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 285 VAL Chi-restraints excluded: chain I residue 291 GLU Chi-restraints excluded: chain I residue 310 THR Chi-restraints excluded: chain I residue 334 THR Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 103 CYS Chi-restraints excluded: chain J residue 105 PHE Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain J residue 237 VAL Chi-restraints excluded: chain J residue 260 VAL Chi-restraints excluded: chain J residue 293 THR Chi-restraints excluded: chain J residue 309 TYR Chi-restraints excluded: chain J residue 334 THR Chi-restraints excluded: chain J residue 337 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 215 optimal weight: 30.0000 chunk 300 optimal weight: 6.9990 chunk 282 optimal weight: 20.0000 chunk 52 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 291 optimal weight: 2.9990 chunk 271 optimal weight: 20.0000 chunk 223 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 HIS F 63 HIS ** G 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.119370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.104508 restraints weight = 58279.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.106976 restraints weight = 29774.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.108606 restraints weight = 18311.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.109696 restraints weight = 12763.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.110448 restraints weight = 9796.820| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25901 Z= 0.166 Angle : 0.641 14.467 35074 Z= 0.335 Chirality : 0.047 0.179 3929 Planarity : 0.004 0.045 4405 Dihedral : 4.557 28.331 3418 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 5.27 % Allowed : 25.69 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.26 (0.15), residues: 3100 helix: -1.59 (0.18), residues: 800 sheet: -1.23 (0.16), residues: 1000 loop : -1.45 (0.18), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 298 TYR 0.017 0.001 TYR D 179 PHE 0.016 0.002 PHE B 105 TRP 0.032 0.002 TRP A 163 HIS 0.006 0.001 HIS C 137 Details of bonding type rmsd covalent geometry : bond 0.00390 (25901) covalent geometry : angle 0.64142 (35074) hydrogen bonds : bond 0.03723 ( 646) hydrogen bonds : angle 5.40995 ( 1809) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 351 time to evaluate : 1.003 Fit side-chains REVERT: E 350 THR cc_start: 0.8815 (m) cc_final: 0.8567 (t) REVERT: B 151 LEU cc_start: 0.6848 (OUTLIER) cc_final: 0.6019 (mp) REVERT: B 358 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.7842 (tt0) REVERT: C 64 GLU cc_start: 0.9110 (OUTLIER) cc_final: 0.8022 (mp0) REVERT: C 86 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8639 (tt) REVERT: C 238 ASP cc_start: 0.7134 (OUTLIER) cc_final: 0.6706 (m-30) REVERT: C 329 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.6890 (mp0) REVERT: F 178 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.7986 (pp) REVERT: F 238 ASP cc_start: 0.7228 (p0) cc_final: 0.6681 (m-30) REVERT: F 272 CYS cc_start: 0.7653 (m) cc_final: 0.7372 (t) REVERT: F 279 ASP cc_start: 0.6975 (m-30) cc_final: 0.6760 (m-30) REVERT: F 342 LYS cc_start: 0.7575 (pttt) cc_final: 0.7015 (mtmt) REVERT: F 356 LYS cc_start: 0.7821 (tptt) cc_final: 0.7183 (pttp) REVERT: G 66 MET cc_start: 0.8135 (ttp) cc_final: 0.7857 (ttt) REVERT: G 104 MET cc_start: 0.7034 (ttt) cc_final: 0.6830 (ptm) REVERT: H 244 GLN cc_start: 0.7864 (pm20) cc_final: 0.7483 (pm20) REVERT: H 323 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6760 (tt) REVERT: A 104 MET cc_start: 0.5238 (ttt) cc_final: 0.4243 (mmm) REVERT: A 337 MET cc_start: 0.7015 (pmm) cc_final: 0.6759 (pmm) REVERT: I 346 ASP cc_start: 0.7796 (m-30) cc_final: 0.6679 (p0) outliers start: 148 outliers final: 124 residues processed: 474 average time/residue: 0.1386 time to fit residues: 108.7315 Evaluate side-chains 475 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 343 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 225 SER Chi-restraints excluded: chain E residue 260 VAL Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 167 CYS Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain B residue 347 LEU Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 358 GLN Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 364 CYS Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 310 THR Chi-restraints excluded: chain F residue 315 THR Chi-restraints excluded: chain F residue 337 MET Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 117 ILE Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain G residue 334 THR Chi-restraints excluded: chain G residue 335 ILE Chi-restraints excluded: chain G residue 354 ASP Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 208 TYR Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 254 GLU Chi-restraints excluded: chain H residue 276 LYS Chi-restraints excluded: chain H residue 281 VAL Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 331 ILE Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain H residue 350 THR Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain I residue 70 GLU Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 160 ILE Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 226 CYS Chi-restraints excluded: chain I residue 244 GLN Chi-restraints excluded: chain I residue 250 CYS Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 285 VAL Chi-restraints excluded: chain I residue 291 GLU Chi-restraints excluded: chain I residue 310 THR Chi-restraints excluded: chain I residue 334 THR Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 105 PHE Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain J residue 237 VAL Chi-restraints excluded: chain J residue 255 VAL Chi-restraints excluded: chain J residue 260 VAL Chi-restraints excluded: chain J residue 293 THR Chi-restraints excluded: chain J residue 309 TYR Chi-restraints excluded: chain J residue 334 THR Chi-restraints excluded: chain J residue 337 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 31 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 chunk 179 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 185 optimal weight: 10.0000 chunk 216 optimal weight: 20.0000 chunk 21 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 121 optimal weight: 0.3980 chunk 116 optimal weight: 0.7980 chunk 7 optimal weight: 0.3980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 HIS F 63 HIS ** G 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.121910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.107117 restraints weight = 57906.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.109642 restraints weight = 29435.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.111294 restraints weight = 17995.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.112398 restraints weight = 12486.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.113163 restraints weight = 9527.825| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 25901 Z= 0.108 Angle : 0.597 14.704 35074 Z= 0.308 Chirality : 0.045 0.161 3929 Planarity : 0.004 0.046 4405 Dihedral : 4.311 29.091 3418 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 4.78 % Allowed : 26.30 % Favored : 68.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.11 (0.15), residues: 3100 helix: -1.48 (0.18), residues: 800 sheet: -1.14 (0.17), residues: 1000 loop : -1.36 (0.18), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 298 TYR 0.018 0.001 TYR G 309 PHE 0.021 0.001 PHE C 267 TRP 0.030 0.001 TRP A 163 HIS 0.005 0.001 HIS C 137 Details of bonding type rmsd covalent geometry : bond 0.00246 (25901) covalent geometry : angle 0.59715 (35074) hydrogen bonds : bond 0.03035 ( 646) hydrogen bonds : angle 5.17899 ( 1809) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 362 time to evaluate : 1.039 Fit side-chains REVERT: E 350 THR cc_start: 0.8761 (m) cc_final: 0.8492 (t) REVERT: B 151 LEU cc_start: 0.6805 (OUTLIER) cc_final: 0.5971 (mp) REVERT: C 86 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8603 (tt) REVERT: C 238 ASP cc_start: 0.7167 (OUTLIER) cc_final: 0.6666 (m-30) REVERT: C 329 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7102 (mp0) REVERT: F 178 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7964 (pp) REVERT: F 238 ASP cc_start: 0.7115 (p0) cc_final: 0.6572 (m-30) REVERT: F 272 CYS cc_start: 0.7601 (m) cc_final: 0.7279 (t) REVERT: F 279 ASP cc_start: 0.6936 (m-30) cc_final: 0.6719 (m-30) REVERT: F 342 LYS cc_start: 0.7512 (pttt) cc_final: 0.6989 (ttpt) REVERT: F 356 LYS cc_start: 0.7777 (tptt) cc_final: 0.7155 (pttp) REVERT: G 66 MET cc_start: 0.8153 (ttp) cc_final: 0.7866 (ttt) REVERT: G 329 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7304 (mp0) REVERT: H 70 GLU cc_start: 0.8139 (tt0) cc_final: 0.7838 (tt0) REVERT: H 244 GLN cc_start: 0.7861 (pm20) cc_final: 0.7482 (pm20) REVERT: H 323 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6740 (tt) REVERT: A 90 LYS cc_start: 0.8780 (mmtt) cc_final: 0.7822 (mttt) REVERT: A 104 MET cc_start: 0.5357 (ttt) cc_final: 0.4367 (mmm) REVERT: I 346 ASP cc_start: 0.7740 (m-30) cc_final: 0.6613 (p0) REVERT: J 370 MET cc_start: 0.7001 (ttt) cc_final: 0.6766 (tmm) outliers start: 134 outliers final: 117 residues processed: 468 average time/residue: 0.1465 time to fit residues: 113.7352 Evaluate side-chains 478 residues out of total 2820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 354 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 225 SER Chi-restraints excluded: chain E residue 260 VAL Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 229 ASP Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 200 VAL Chi-restraints excluded: chain C residue 227 ILE Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 329 GLU Chi-restraints excluded: chain C residue 331 ILE Chi-restraints excluded: chain C residue 364 CYS Chi-restraints excluded: chain F residue 86 LEU Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 156 VAL Chi-restraints excluded: chain F residue 159 ILE Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 260 VAL Chi-restraints excluded: chain F residue 310 THR Chi-restraints excluded: chain F residue 315 THR Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 87 PHE Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 105 PHE Chi-restraints excluded: chain G residue 117 ILE Chi-restraints excluded: chain G residue 172 SER Chi-restraints excluded: chain G residue 200 VAL Chi-restraints excluded: chain G residue 260 VAL Chi-restraints excluded: chain G residue 329 GLU Chi-restraints excluded: chain G residue 334 THR Chi-restraints excluded: chain G residue 335 ILE Chi-restraints excluded: chain G residue 354 ASP Chi-restraints excluded: chain H residue 62 ILE Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 208 TYR Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 276 LYS Chi-restraints excluded: chain H residue 281 VAL Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 331 ILE Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain H residue 350 THR Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 156 VAL Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 280 TYR Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain I residue 70 GLU Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 115 ILE Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 160 ILE Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 226 CYS Chi-restraints excluded: chain I residue 244 GLN Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 285 VAL Chi-restraints excluded: chain I residue 291 GLU Chi-restraints excluded: chain I residue 310 THR Chi-restraints excluded: chain I residue 334 THR Chi-restraints excluded: chain I residue 353 LEU Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 105 PHE Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain J residue 237 VAL Chi-restraints excluded: chain J residue 255 VAL Chi-restraints excluded: chain J residue 260 VAL Chi-restraints excluded: chain J residue 293 THR Chi-restraints excluded: chain J residue 309 TYR Chi-restraints excluded: chain J residue 334 THR Chi-restraints excluded: chain J residue 337 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 109 optimal weight: 7.9990 chunk 281 optimal weight: 2.9990 chunk 213 optimal weight: 10.0000 chunk 305 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 chunk 268 optimal weight: 8.9990 chunk 51 optimal weight: 9.9990 chunk 157 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 14 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 63 HIS F 63 HIS ** G 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.118431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.103540 restraints weight = 57953.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.106017 restraints weight = 29757.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.107635 restraints weight = 18300.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.108735 restraints weight = 12804.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.109413 restraints weight = 9830.053| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.5075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 25901 Z= 0.193 Angle : 0.679 14.800 35074 Z= 0.353 Chirality : 0.048 0.189 3929 Planarity : 0.004 0.048 4405 Dihedral : 4.707 31.803 3418 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 5.02 % Allowed : 26.27 % Favored : 68.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.36 (0.15), residues: 3100 helix: -1.60 (0.18), residues: 790 sheet: -1.29 (0.16), residues: 1000 loop : -1.57 (0.17), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 298 TYR 0.018 0.001 TYR G 309 PHE 0.018 0.002 PHE B 105 TRP 0.028 0.002 TRP A 163 HIS 0.006 0.001 HIS C 137 Details of bonding type rmsd covalent geometry : bond 0.00452 (25901) covalent geometry : angle 0.67856 (35074) hydrogen bonds : bond 0.03953 ( 646) hydrogen bonds : angle 5.50023 ( 1809) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3902.21 seconds wall clock time: 68 minutes 29.66 seconds (4109.66 seconds total)