Starting phenix.real_space_refine on Sun Aug 24 17:52:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bhd_44541/08_2025/9bhd_44541.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bhd_44541/08_2025/9bhd_44541.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bhd_44541/08_2025/9bhd_44541.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bhd_44541/08_2025/9bhd_44541.map" model { file = "/net/cci-nas-00/data/ceres_data/9bhd_44541/08_2025/9bhd_44541.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bhd_44541/08_2025/9bhd_44541.cif" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 160 5.16 5 C 13944 2.51 5 N 3552 2.21 5 O 4064 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 144 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: 21720 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2689 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 320} Chain: "B" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2689 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 320} Chain: "C" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2689 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 320} Chain: "D" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2689 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 320} Chain: "E" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2689 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 320} Chain: "F" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2689 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 320} Chain: "G" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2689 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 320} Chain: "H" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2689 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 320} Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "C" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "D" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "E" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "F" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "G" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "H" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Time building chain proxies: 4.21, per 1000 atoms: 0.19 Number of scatterers: 21720 At special positions: 0 Unit cell: (153.55, 103.75, 117.03, 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 160 16.00 O 4064 8.00 N 3552 7.00 C 13944 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: 1.92 Conformation dependent library (CDL) restraints added in 850.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5056 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 32 sheets defined 36.4% alpha, 37.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 43 through 47 Processing helix chain 'A' and resid 49 through 58 removed outlier: 3.853A pdb=" N TYR A 53 " --> pdb=" O LYS A 50 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N SER A 56 " --> pdb=" O TYR A 53 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N TYR A 57 " --> pdb=" O PHE A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 69 removed outlier: 4.295A pdb=" N HIS A 63 " --> pdb=" O HIS A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 82 Processing helix chain 'A' and resid 83 through 88 removed outlier: 3.839A pdb=" N PHE A 87 " --> pdb=" O ASN A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 109 Processing helix chain 'A' and resid 121 through 133 removed outlier: 4.119A pdb=" N TYR A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 169 Processing helix chain 'A' and resid 172 through 184 removed outlier: 4.298A pdb=" N THR A 176 " --> pdb=" O SER A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 213 Processing helix chain 'A' and resid 214 through 218 Processing helix chain 'A' and resid 224 through 232 removed outlier: 4.065A pdb=" N VAL A 230 " --> pdb=" O CYS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 245 Processing helix chain 'A' and resid 261 through 265 Processing helix chain 'B' and resid 43 through 47 Processing helix chain 'B' and resid 49 through 58 removed outlier: 3.852A pdb=" N TYR B 53 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N SER B 56 " --> pdb=" O TYR B 53 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N TYR B 57 " --> pdb=" O PHE B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 69 removed outlier: 4.296A pdb=" N HIS B 63 " --> pdb=" O HIS B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 82 Processing helix chain 'B' and resid 83 through 88 removed outlier: 3.839A pdb=" N PHE B 87 " --> pdb=" O ASN B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 109 Processing helix chain 'B' and resid 121 through 133 removed outlier: 4.118A pdb=" N TYR B 125 " --> pdb=" O SER B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 169 Processing helix chain 'B' and resid 172 through 184 removed outlier: 4.298A pdb=" N THR B 176 " --> pdb=" O SER B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 213 Processing helix chain 'B' and resid 214 through 218 Processing helix chain 'B' and resid 224 through 232 removed outlier: 4.064A pdb=" N VAL B 230 " --> pdb=" O CYS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 245 Processing helix chain 'B' and resid 261 through 265 Processing helix chain 'C' and resid 43 through 47 Processing helix chain 'C' and resid 49 through 58 removed outlier: 3.853A pdb=" N TYR C 53 " --> pdb=" O LYS C 50 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N SER C 56 " --> pdb=" O TYR C 53 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N TYR C 57 " --> pdb=" O PHE C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 69 removed outlier: 4.296A pdb=" N HIS C 63 " --> pdb=" O HIS C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 82 Processing helix chain 'C' and resid 83 through 88 removed outlier: 3.839A pdb=" N PHE C 87 " --> pdb=" O ASN C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 109 Processing helix chain 'C' and resid 121 through 133 removed outlier: 4.118A pdb=" N TYR C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 169 Processing helix chain 'C' and resid 172 through 184 removed outlier: 4.298A pdb=" N THR C 176 " --> pdb=" O SER C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 213 Processing helix chain 'C' and resid 214 through 218 Processing helix chain 'C' and resid 224 through 232 removed outlier: 4.065A pdb=" N VAL C 230 " --> pdb=" O CYS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 245 Processing helix chain 'C' and resid 261 through 265 Processing helix chain 'D' and resid 43 through 47 Processing helix chain 'D' and resid 49 through 58 removed outlier: 3.853A pdb=" N TYR D 53 " --> pdb=" O LYS D 50 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N SER D 56 " --> pdb=" O TYR D 53 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N TYR D 57 " --> pdb=" O PHE D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 69 removed outlier: 4.296A pdb=" N HIS D 63 " --> pdb=" O HIS D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 82 Processing helix chain 'D' and resid 83 through 88 removed outlier: 3.839A pdb=" N PHE D 87 " --> pdb=" O ASN D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 109 Processing helix chain 'D' and resid 121 through 133 removed outlier: 4.118A pdb=" N TYR D 125 " --> pdb=" O SER D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 169 Processing helix chain 'D' and resid 172 through 184 removed outlier: 4.298A pdb=" N THR D 176 " --> pdb=" O SER D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 213 Processing helix chain 'D' and resid 214 through 218 Processing helix chain 'D' and resid 224 through 232 removed outlier: 4.064A pdb=" N VAL D 230 " --> pdb=" O CYS D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 245 Processing helix chain 'D' and resid 261 through 265 Processing helix chain 'E' and resid 43 through 47 Processing helix chain 'E' and resid 49 through 58 removed outlier: 3.852A pdb=" N TYR E 53 " --> pdb=" O LYS E 50 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N SER E 56 " --> pdb=" O TYR E 53 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N TYR E 57 " --> pdb=" O PHE E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 69 removed outlier: 4.296A pdb=" N HIS E 63 " --> pdb=" O HIS E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 82 Processing helix chain 'E' and resid 83 through 88 removed outlier: 3.839A pdb=" N PHE E 87 " --> pdb=" O ASN E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 109 Processing helix chain 'E' and resid 121 through 133 removed outlier: 4.118A pdb=" N TYR E 125 " --> pdb=" O SER E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 169 Processing helix chain 'E' and resid 172 through 184 removed outlier: 4.298A pdb=" N THR E 176 " --> pdb=" O SER E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 213 Processing helix chain 'E' and resid 214 through 218 Processing helix chain 'E' and resid 224 through 232 removed outlier: 4.064A pdb=" N VAL E 230 " --> pdb=" O CYS E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 245 Processing helix chain 'E' and resid 261 through 265 Processing helix chain 'F' and resid 43 through 47 Processing helix chain 'F' and resid 49 through 58 removed outlier: 3.852A pdb=" N TYR F 53 " --> pdb=" O LYS F 50 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N SER F 56 " --> pdb=" O TYR F 53 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N TYR F 57 " --> pdb=" O PHE F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 69 removed outlier: 4.295A pdb=" N HIS F 63 " --> pdb=" O HIS F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 82 Processing helix chain 'F' and resid 83 through 88 removed outlier: 3.839A pdb=" N PHE F 87 " --> pdb=" O ASN F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 109 Processing helix chain 'F' and resid 121 through 133 removed outlier: 4.118A pdb=" N TYR F 125 " --> pdb=" O SER F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 169 Processing helix chain 'F' and resid 172 through 184 removed outlier: 4.298A pdb=" N THR F 176 " --> pdb=" O SER F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 213 Processing helix chain 'F' and resid 214 through 218 Processing helix chain 'F' and resid 224 through 232 removed outlier: 4.064A pdb=" N VAL F 230 " --> pdb=" O CYS F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 245 Processing helix chain 'F' and resid 261 through 265 Processing helix chain 'G' and resid 43 through 47 Processing helix chain 'G' and resid 49 through 58 removed outlier: 3.852A pdb=" N TYR G 53 " --> pdb=" O LYS G 50 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N SER G 56 " --> pdb=" O TYR G 53 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N TYR G 57 " --> pdb=" O PHE G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 69 removed outlier: 4.296A pdb=" N HIS G 63 " --> pdb=" O HIS G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 82 Processing helix chain 'G' and resid 83 through 88 removed outlier: 3.839A pdb=" N PHE G 87 " --> pdb=" O ASN G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 109 Processing helix chain 'G' and resid 121 through 133 removed outlier: 4.118A pdb=" N TYR G 125 " --> pdb=" O SER G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 169 Processing helix chain 'G' and resid 172 through 184 removed outlier: 4.298A pdb=" N THR G 176 " --> pdb=" O SER G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 213 Processing helix chain 'G' and resid 214 through 218 Processing helix chain 'G' and resid 224 through 232 removed outlier: 4.065A pdb=" N VAL G 230 " --> pdb=" O CYS G 226 " (cutoff:3.500A) Processing helix chain 'G' and resid 241 through 245 Processing helix chain 'G' and resid 261 through 265 Processing helix chain 'H' and resid 43 through 47 Processing helix chain 'H' and resid 49 through 58 removed outlier: 3.853A pdb=" N TYR H 53 " --> pdb=" O LYS H 50 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N SER H 56 " --> pdb=" O TYR H 53 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N TYR H 57 " --> pdb=" O PHE H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 69 removed outlier: 4.295A pdb=" N HIS H 63 " --> pdb=" O HIS H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 82 Processing helix chain 'H' and resid 83 through 88 removed outlier: 3.839A pdb=" N PHE H 87 " --> pdb=" O ASN H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 109 Processing helix chain 'H' and resid 121 through 133 removed outlier: 4.118A pdb=" N TYR H 125 " --> pdb=" O SER H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 165 through 169 Processing helix chain 'H' and resid 172 through 184 removed outlier: 4.298A pdb=" N THR H 176 " --> pdb=" O SER H 172 " (cutoff:3.500A) Processing helix chain 'H' and resid 205 through 213 Processing helix chain 'H' and resid 214 through 218 Processing helix chain 'H' and resid 224 through 232 removed outlier: 4.065A pdb=" N VAL H 230 " --> pdb=" O CYS H 226 " (cutoff:3.500A) Processing helix chain 'H' and resid 241 through 245 Processing helix chain 'H' and resid 261 through 265 Processing sheet with id=AA1, first strand: chain 'A' and resid 139 through 143 removed outlier: 6.410A pdb=" N VAL A 114 " --> pdb=" O THR A 140 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ILE A 142 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLY A 116 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL A 91 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ILE A 160 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU A 93 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ASP A 157 " --> pdb=" O ASP A 188 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 236 through 237 removed outlier: 7.916A pdb=" N HIS A 282 " --> pdb=" O MET A 319 " (cutoff:3.500A) removed outlier: 11.083A pdb=" N ASP A 321 " --> pdb=" O TYR A 280 " (cutoff:3.500A) removed outlier: 10.459A pdb=" N TYR A 280 " --> pdb=" O ASP A 321 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA A 196 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLU A 254 " --> pdb=" O ALA A 196 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU A 198 " --> pdb=" O ILE A 252 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 236 through 237 removed outlier: 7.916A pdb=" N HIS A 282 " --> pdb=" O MET A 319 " (cutoff:3.500A) removed outlier: 11.083A pdb=" N ASP A 321 " --> pdb=" O TYR A 280 " (cutoff:3.500A) removed outlier: 10.459A pdb=" N TYR A 280 " --> pdb=" O ASP A 321 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR A 299 " --> pdb=" O PHE A 292 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 267 through 274 removed outlier: 6.506A pdb=" N GLU A 330 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LYS A 356 " --> pdb=" O GLU A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 139 through 143 removed outlier: 6.410A pdb=" N VAL B 114 " --> pdb=" O THR B 140 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ILE B 142 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLY B 116 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL B 91 " --> pdb=" O ILE B 158 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ILE B 160 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU B 93 " --> pdb=" O ILE B 160 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ASP B 157 " --> pdb=" O ASP B 188 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 236 through 237 removed outlier: 7.916A pdb=" N HIS B 282 " --> pdb=" O MET B 319 " (cutoff:3.500A) removed outlier: 11.084A pdb=" N ASP B 321 " --> pdb=" O TYR B 280 " (cutoff:3.500A) removed outlier: 10.459A pdb=" N TYR B 280 " --> pdb=" O ASP B 321 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA B 196 " --> pdb=" O GLU B 254 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLU B 254 " --> pdb=" O ALA B 196 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU B 198 " --> pdb=" O ILE B 252 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 236 through 237 removed outlier: 7.916A pdb=" N HIS B 282 " --> pdb=" O MET B 319 " (cutoff:3.500A) removed outlier: 11.084A pdb=" N ASP B 321 " --> pdb=" O TYR B 280 " (cutoff:3.500A) removed outlier: 10.459A pdb=" N TYR B 280 " --> pdb=" O ASP B 321 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR B 299 " --> pdb=" O PHE B 292 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 267 through 274 removed outlier: 6.506A pdb=" N GLU B 330 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LYS B 356 " --> pdb=" O GLU B 330 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 139 through 143 removed outlier: 6.410A pdb=" N VAL C 114 " --> pdb=" O THR C 140 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ILE C 142 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLY C 116 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL C 91 " --> pdb=" O ILE C 158 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ILE C 160 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU C 93 " --> pdb=" O ILE C 160 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ASP C 157 " --> pdb=" O ASP C 188 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 236 through 237 removed outlier: 7.916A pdb=" N HIS C 282 " --> pdb=" O MET C 319 " (cutoff:3.500A) removed outlier: 11.083A pdb=" N ASP C 321 " --> pdb=" O TYR C 280 " (cutoff:3.500A) removed outlier: 10.460A pdb=" N TYR C 280 " --> pdb=" O ASP C 321 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA C 196 " --> pdb=" O GLU C 254 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLU C 254 " --> pdb=" O ALA C 196 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU C 198 " --> pdb=" O ILE C 252 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 236 through 237 removed outlier: 7.916A pdb=" N HIS C 282 " --> pdb=" O MET C 319 " (cutoff:3.500A) removed outlier: 11.083A pdb=" N ASP C 321 " --> pdb=" O TYR C 280 " (cutoff:3.500A) removed outlier: 10.460A pdb=" N TYR C 280 " --> pdb=" O ASP C 321 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR C 299 " --> pdb=" O PHE C 292 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 267 through 274 removed outlier: 6.506A pdb=" N GLU C 330 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N LYS C 356 " --> pdb=" O GLU C 330 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 139 through 143 removed outlier: 6.411A pdb=" N VAL D 114 " --> pdb=" O THR D 140 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ILE D 142 " --> pdb=" O VAL D 114 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLY D 116 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL D 91 " --> pdb=" O ILE D 158 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ILE D 160 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU D 93 " --> pdb=" O ILE D 160 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ASP D 157 " --> pdb=" O ASP D 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 236 through 237 removed outlier: 7.916A pdb=" N HIS D 282 " --> pdb=" O MET D 319 " (cutoff:3.500A) removed outlier: 11.084A pdb=" N ASP D 321 " --> pdb=" O TYR D 280 " (cutoff:3.500A) removed outlier: 10.459A pdb=" N TYR D 280 " --> pdb=" O ASP D 321 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA D 196 " --> pdb=" O GLU D 254 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLU D 254 " --> pdb=" O ALA D 196 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU D 198 " --> pdb=" O ILE D 252 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 236 through 237 removed outlier: 7.916A pdb=" N HIS D 282 " --> pdb=" O MET D 319 " (cutoff:3.500A) removed outlier: 11.084A pdb=" N ASP D 321 " --> pdb=" O TYR D 280 " (cutoff:3.500A) removed outlier: 10.459A pdb=" N TYR D 280 " --> pdb=" O ASP D 321 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR D 299 " --> pdb=" O PHE D 292 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 267 through 274 removed outlier: 6.506A pdb=" N GLU D 330 " --> pdb=" O LYS D 356 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LYS D 356 " --> pdb=" O GLU D 330 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 139 through 143 removed outlier: 6.410A pdb=" N VAL E 114 " --> pdb=" O THR E 140 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ILE E 142 " --> pdb=" O VAL E 114 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLY E 116 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL E 91 " --> pdb=" O ILE E 158 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N ILE E 160 " --> pdb=" O VAL E 91 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU E 93 " --> pdb=" O ILE E 160 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ASP E 157 " --> pdb=" O ASP E 188 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 236 through 237 removed outlier: 7.916A pdb=" N HIS E 282 " --> pdb=" O MET E 319 " (cutoff:3.500A) removed outlier: 11.084A pdb=" N ASP E 321 " --> pdb=" O TYR E 280 " (cutoff:3.500A) removed outlier: 10.459A pdb=" N TYR E 280 " --> pdb=" O ASP E 321 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA E 196 " --> pdb=" O GLU E 254 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLU E 254 " --> pdb=" O ALA E 196 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU E 198 " --> pdb=" O ILE E 252 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 236 through 237 removed outlier: 7.916A pdb=" N HIS E 282 " --> pdb=" O MET E 319 " (cutoff:3.500A) removed outlier: 11.084A pdb=" N ASP E 321 " --> pdb=" O TYR E 280 " (cutoff:3.500A) removed outlier: 10.459A pdb=" N TYR E 280 " --> pdb=" O ASP E 321 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR E 299 " --> pdb=" O PHE E 292 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 267 through 274 removed outlier: 6.506A pdb=" N GLU E 330 " --> pdb=" O LYS E 356 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LYS E 356 " --> pdb=" O GLU E 330 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 139 through 143 removed outlier: 6.410A pdb=" N VAL F 114 " --> pdb=" O THR F 140 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ILE F 142 " --> pdb=" O VAL F 114 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLY F 116 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL F 91 " --> pdb=" O ILE F 158 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ILE F 160 " --> pdb=" O VAL F 91 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU F 93 " --> pdb=" O ILE F 160 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ASP F 157 " --> pdb=" O ASP F 188 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 236 through 237 removed outlier: 7.916A pdb=" N HIS F 282 " --> pdb=" O MET F 319 " (cutoff:3.500A) removed outlier: 11.084A pdb=" N ASP F 321 " --> pdb=" O TYR F 280 " (cutoff:3.500A) removed outlier: 10.459A pdb=" N TYR F 280 " --> pdb=" O ASP F 321 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA F 196 " --> pdb=" O GLU F 254 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLU F 254 " --> pdb=" O ALA F 196 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU F 198 " --> pdb=" O ILE F 252 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 236 through 237 removed outlier: 7.916A pdb=" N HIS F 282 " --> pdb=" O MET F 319 " (cutoff:3.500A) removed outlier: 11.084A pdb=" N ASP F 321 " --> pdb=" O TYR F 280 " (cutoff:3.500A) removed outlier: 10.459A pdb=" N TYR F 280 " --> pdb=" O ASP F 321 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR F 299 " --> pdb=" O PHE F 292 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 267 through 274 removed outlier: 6.506A pdb=" N GLU F 330 " --> pdb=" O LYS F 356 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LYS F 356 " --> pdb=" O GLU F 330 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 139 through 143 removed outlier: 6.410A pdb=" N VAL G 114 " --> pdb=" O THR G 140 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ILE G 142 " --> pdb=" O VAL G 114 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLY G 116 " --> pdb=" O ILE G 142 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL G 91 " --> pdb=" O ILE G 158 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ILE G 160 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU G 93 " --> pdb=" O ILE G 160 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ASP G 157 " --> pdb=" O ASP G 188 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 236 through 237 removed outlier: 7.915A pdb=" N HIS G 282 " --> pdb=" O MET G 319 " (cutoff:3.500A) removed outlier: 11.084A pdb=" N ASP G 321 " --> pdb=" O TYR G 280 " (cutoff:3.500A) removed outlier: 10.459A pdb=" N TYR G 280 " --> pdb=" O ASP G 321 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA G 196 " --> pdb=" O GLU G 254 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLU G 254 " --> pdb=" O ALA G 196 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU G 198 " --> pdb=" O ILE G 252 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 236 through 237 removed outlier: 7.915A pdb=" N HIS G 282 " --> pdb=" O MET G 319 " (cutoff:3.500A) removed outlier: 11.084A pdb=" N ASP G 321 " --> pdb=" O TYR G 280 " (cutoff:3.500A) removed outlier: 10.459A pdb=" N TYR G 280 " --> pdb=" O ASP G 321 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR G 299 " --> pdb=" O PHE G 292 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 267 through 274 removed outlier: 6.506A pdb=" N GLU G 330 " --> pdb=" O LYS G 356 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LYS G 356 " --> pdb=" O GLU G 330 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 139 through 143 removed outlier: 6.410A pdb=" N VAL H 114 " --> pdb=" O THR H 140 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ILE H 142 " --> pdb=" O VAL H 114 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLY H 116 " --> pdb=" O ILE H 142 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL H 91 " --> pdb=" O ILE H 158 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ILE H 160 " --> pdb=" O VAL H 91 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU H 93 " --> pdb=" O ILE H 160 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ASP H 157 " --> pdb=" O ASP H 188 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 236 through 237 removed outlier: 7.915A pdb=" N HIS H 282 " --> pdb=" O MET H 319 " (cutoff:3.500A) removed outlier: 11.084A pdb=" N ASP H 321 " --> pdb=" O TYR H 280 " (cutoff:3.500A) removed outlier: 10.458A pdb=" N TYR H 280 " --> pdb=" O ASP H 321 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA H 196 " --> pdb=" O GLU H 254 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLU H 254 " --> pdb=" O ALA H 196 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU H 198 " --> pdb=" O ILE H 252 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 236 through 237 removed outlier: 7.915A pdb=" N HIS H 282 " --> pdb=" O MET H 319 " (cutoff:3.500A) removed outlier: 11.084A pdb=" N ASP H 321 " --> pdb=" O TYR H 280 " (cutoff:3.500A) removed outlier: 10.458A pdb=" N TYR H 280 " --> pdb=" O ASP H 321 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR H 299 " --> pdb=" O PHE H 292 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 267 through 274 removed outlier: 6.507A pdb=" N GLU H 330 " --> pdb=" O LYS H 356 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LYS H 356 " --> pdb=" O GLU H 330 " (cutoff:3.500A) 1008 hydrogen bonds defined for protein. 2496 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: 3.70 Time building geometry restraints manager: 2.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6834 1.34 - 1.45: 4147 1.45 - 1.57: 11019 1.57 - 1.69: 0 1.69 - 1.81: 248 Bond restraints: 22248 Sorted by residual: bond pdb=" C LYS H 233 " pdb=" N GLU H 234 " ideal model delta sigma weight residual 1.331 1.290 0.041 1.63e-02 3.76e+03 6.43e+00 bond pdb=" C LYS E 233 " pdb=" N GLU E 234 " ideal model delta sigma weight residual 1.331 1.290 0.041 1.63e-02 3.76e+03 6.28e+00 bond pdb=" C8 SAH F 401 " pdb=" N7 SAH F 401 " ideal model delta sigma weight residual 1.299 1.349 -0.050 2.00e-02 2.50e+03 6.28e+00 bond pdb=" C8 SAH H 401 " pdb=" N7 SAH H 401 " ideal model delta sigma weight residual 1.299 1.349 -0.050 2.00e-02 2.50e+03 6.28e+00 bond pdb=" C8 SAH G 401 " pdb=" N7 SAH G 401 " ideal model delta sigma weight residual 1.299 1.349 -0.050 2.00e-02 2.50e+03 6.23e+00 ... (remaining 22243 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 29474 2.40 - 4.80: 564 4.80 - 7.20: 66 7.20 - 9.60: 24 9.60 - 12.00: 8 Bond angle restraints: 30136 Sorted by residual: angle pdb=" CG SAH A 401 " pdb=" SD SAH A 401 " pdb=" C5' SAH A 401 " ideal model delta sigma weight residual 101.77 89.77 12.00 3.00e+00 1.11e-01 1.60e+01 angle pdb=" CG SAH G 401 " pdb=" SD SAH G 401 " pdb=" C5' SAH G 401 " ideal model delta sigma weight residual 101.77 89.78 11.99 3.00e+00 1.11e-01 1.60e+01 angle pdb=" CG SAH F 401 " pdb=" SD SAH F 401 " pdb=" C5' SAH F 401 " ideal model delta sigma weight residual 101.77 89.78 11.99 3.00e+00 1.11e-01 1.60e+01 angle pdb=" CG SAH B 401 " pdb=" SD SAH B 401 " pdb=" C5' SAH B 401 " ideal model delta sigma weight residual 101.77 89.78 11.99 3.00e+00 1.11e-01 1.60e+01 angle pdb=" CG SAH C 401 " pdb=" SD SAH C 401 " pdb=" C5' SAH C 401 " ideal model delta sigma weight residual 101.77 89.78 11.99 3.00e+00 1.11e-01 1.60e+01 ... (remaining 30131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.99: 11697 13.99 - 27.98: 1087 27.98 - 41.98: 304 41.98 - 55.97: 32 55.97 - 69.96: 32 Dihedral angle restraints: 13152 sinusoidal: 5312 harmonic: 7840 Sorted by residual: dihedral pdb=" CA TRP D 312 " pdb=" C TRP D 312 " pdb=" N LYS D 313 " pdb=" CA LYS D 313 " ideal model delta harmonic sigma weight residual -180.00 -143.11 -36.89 0 5.00e+00 4.00e-02 5.44e+01 dihedral pdb=" CA TRP F 312 " pdb=" C TRP F 312 " pdb=" N LYS F 313 " pdb=" CA LYS F 313 " ideal model delta harmonic sigma weight residual -180.00 -143.14 -36.86 0 5.00e+00 4.00e-02 5.43e+01 dihedral pdb=" CA TRP A 312 " pdb=" C TRP A 312 " pdb=" N LYS A 313 " pdb=" CA LYS A 313 " ideal model delta harmonic sigma weight residual -180.00 -143.15 -36.85 0 5.00e+00 4.00e-02 5.43e+01 ... (remaining 13149 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1679 0.033 - 0.067: 1030 0.067 - 0.100: 461 0.100 - 0.133: 126 0.133 - 0.167: 40 Chirality restraints: 3336 Sorted by residual: chirality pdb=" CA PHE B 222 " pdb=" N PHE B 222 " pdb=" C PHE B 222 " pdb=" CB PHE B 222 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.95e-01 chirality pdb=" CA PHE H 222 " pdb=" N PHE H 222 " pdb=" C PHE H 222 " pdb=" CB PHE H 222 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.94e-01 chirality pdb=" CA PHE A 222 " pdb=" N PHE A 222 " pdb=" C PHE A 222 " pdb=" CB PHE A 222 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.91e-01 ... (remaining 3333 not shown) Planarity restraints: 3768 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 317 " -0.012 2.00e-02 2.50e+03 1.18e-02 2.45e+00 pdb=" CG PHE C 317 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE C 317 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE C 317 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE C 317 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE C 317 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE C 317 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 317 " 0.011 2.00e-02 2.50e+03 1.18e-02 2.43e+00 pdb=" CG PHE G 317 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE G 317 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE G 317 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE G 317 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE G 317 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE G 317 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 317 " -0.012 2.00e-02 2.50e+03 1.18e-02 2.42e+00 pdb=" CG PHE D 317 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE D 317 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE D 317 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE D 317 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE D 317 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE D 317 " -0.004 2.00e-02 2.50e+03 ... (remaining 3765 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 297 2.64 - 3.21: 20128 3.21 - 3.77: 32462 3.77 - 4.34: 48333 4.34 - 4.90: 79036 Nonbonded interactions: 180256 Sorted by model distance: nonbonded pdb=" O HIS B 82 " pdb=" OH TYR D 280 " model vdw 2.077 3.040 nonbonded pdb=" OE1 GLU F 217 " pdb=" OG SER F 225 " model vdw 2.218 3.040 nonbonded pdb=" OE1 GLU D 217 " pdb=" OG SER D 225 " model vdw 2.218 3.040 nonbonded pdb=" OE1 GLU C 217 " pdb=" OG SER C 225 " model vdw 2.218 3.040 nonbonded pdb=" OE1 GLU G 217 " pdb=" OG SER G 225 " model vdw 2.218 3.040 ... (remaining 180251 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 18.180 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.050 22248 Z= 0.414 Angle : 0.855 12.002 30136 Z= 0.458 Chirality : 0.051 0.167 3336 Planarity : 0.004 0.034 3768 Dihedral : 12.400 69.960 8096 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.17), residues: 2624 helix: -0.95 (0.20), residues: 624 sheet: 0.29 (0.19), residues: 808 loop : 0.47 (0.18), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 195 TYR 0.024 0.002 TYR F 52 PHE 0.027 0.003 PHE C 317 TRP 0.015 0.002 TRP A 184 HIS 0.005 0.001 HIS E 282 Details of bonding type rmsd covalent geometry : bond 0.00932 (22248) covalent geometry : angle 0.85529 (30136) hydrogen bonds : bond 0.16512 ( 952) hydrogen bonds : angle 7.04047 ( 2496) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 487 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LEU cc_start: 0.8788 (mt) cc_final: 0.8440 (tt) REVERT: A 104 MET cc_start: 0.6323 (ttp) cc_final: 0.6120 (tmm) REVERT: A 143 LYS cc_start: 0.6380 (tttm) cc_final: 0.5630 (tttt) REVERT: A 159 ILE cc_start: 0.8314 (mt) cc_final: 0.8022 (mm) REVERT: A 160 ILE cc_start: 0.8439 (mt) cc_final: 0.7952 (tt) REVERT: B 76 TYR cc_start: 0.6654 (m-80) cc_final: 0.6349 (m-80) REVERT: B 114 VAL cc_start: 0.8002 (t) cc_final: 0.7793 (t) REVERT: B 139 VAL cc_start: 0.7748 (t) cc_final: 0.7283 (m) REVERT: B 169 PHE cc_start: 0.6786 (m-80) cc_final: 0.6393 (t80) REVERT: B 235 PRO cc_start: 0.6148 (Cg_exo) cc_final: 0.5832 (Cg_endo) REVERT: B 239 VAL cc_start: 0.8753 (t) cc_final: 0.8380 (p) REVERT: B 244 GLN cc_start: 0.8343 (mt0) cc_final: 0.7032 (mm110) REVERT: B 273 LEU cc_start: 0.8085 (mt) cc_final: 0.7322 (mt) REVERT: B 312 TRP cc_start: 0.7381 (m-90) cc_final: 0.7143 (m-10) REVERT: E 211 TYR cc_start: 0.7577 (t80) cc_final: 0.7291 (t80) REVERT: F 211 TYR cc_start: 0.8050 (t80) cc_final: 0.7678 (t80) REVERT: F 224 MET cc_start: 0.8045 (mtt) cc_final: 0.7839 (mtt) REVERT: F 371 ARG cc_start: 0.7105 (ptt180) cc_final: 0.6789 (ptt180) REVERT: G 167 CYS cc_start: 0.6247 (t) cc_final: 0.5862 (t) REVERT: G 170 TYR cc_start: 0.6045 (t80) cc_final: 0.5755 (t80) REVERT: G 179 TYR cc_start: 0.6943 (t80) cc_final: 0.6473 (m-10) REVERT: G 273 LEU cc_start: 0.7185 (mt) cc_final: 0.6891 (mt) REVERT: G 343 ASN cc_start: 0.3015 (t0) cc_final: 0.2645 (m-40) REVERT: G 349 PHE cc_start: 0.5184 (m-10) cc_final: 0.4639 (m-10) REVERT: H 47 MET cc_start: 0.0140 (ptt) cc_final: -0.0729 (mmm) REVERT: H 70 GLU cc_start: 0.8328 (tt0) cc_final: 0.8113 (tp30) REVERT: H 104 MET cc_start: 0.6854 (ttp) cc_final: 0.6649 (tmm) REVERT: H 105 PHE cc_start: 0.7239 (m-10) cc_final: 0.7038 (m-80) REVERT: H 134 LYS cc_start: 0.7810 (mtmt) cc_final: 0.7497 (mmmt) REVERT: H 143 LYS cc_start: 0.6365 (tttm) cc_final: 0.5901 (tttt) REVERT: H 159 ILE cc_start: 0.8456 (mt) cc_final: 0.8137 (mm) REVERT: H 160 ILE cc_start: 0.8572 (mt) cc_final: 0.8198 (tt) REVERT: H 296 HIS cc_start: 0.6963 (t-90) cc_final: 0.6760 (t70) outliers start: 0 outliers final: 0 residues processed: 487 average time/residue: 0.1481 time to fit residues: 109.1979 Evaluate side-chains 270 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 40.0000 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 HIS ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 ASN ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 ASN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 ASN D 274 GLN E 274 GLN F 175 ASN F 274 GLN ** G 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 HIS ** H 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.162355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.124903 restraints weight = 35536.919| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 2.72 r_work: 0.3567 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22248 Z= 0.139 Angle : 0.592 9.906 30136 Z= 0.321 Chirality : 0.046 0.164 3336 Planarity : 0.004 0.049 3768 Dihedral : 5.937 45.712 2920 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.34 % Allowed : 8.22 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.17), residues: 2624 helix: -0.11 (0.21), residues: 656 sheet: 0.17 (0.20), residues: 728 loop : 0.79 (0.19), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 181 TYR 0.023 0.002 TYR C 208 PHE 0.032 0.002 PHE A 105 TRP 0.027 0.002 TRP H 184 HIS 0.014 0.001 HIS A 82 Details of bonding type rmsd covalent geometry : bond 0.00312 (22248) covalent geometry : angle 0.59158 (30136) hydrogen bonds : bond 0.03965 ( 952) hydrogen bonds : angle 5.27298 ( 2496) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 339 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.6740 (ttp) cc_final: 0.6504 (ttt) REVERT: A 143 LYS cc_start: 0.6161 (tttm) cc_final: 0.5406 (tttt) REVERT: A 159 ILE cc_start: 0.8516 (mt) cc_final: 0.8226 (mm) REVERT: A 160 ILE cc_start: 0.8353 (mt) cc_final: 0.7930 (tt) REVERT: A 224 MET cc_start: 0.8464 (mmm) cc_final: 0.8169 (mmm) REVERT: B 47 MET cc_start: -0.0851 (ptt) cc_final: -0.1300 (ptp) REVERT: B 244 GLN cc_start: 0.7689 (mt0) cc_final: 0.7377 (mm110) REVERT: D 211 TYR cc_start: 0.8112 (t80) cc_final: 0.7496 (t80) REVERT: E 211 TYR cc_start: 0.7943 (t80) cc_final: 0.7557 (t80) REVERT: E 326 LYS cc_start: 0.7901 (mtpp) cc_final: 0.7659 (mtmm) REVERT: G 74 LEU cc_start: 0.7691 (mt) cc_final: 0.7215 (mt) REVERT: G 167 CYS cc_start: 0.6303 (t) cc_final: 0.5886 (t) REVERT: G 169 PHE cc_start: 0.6350 (m-80) cc_final: 0.5643 (t80) REVERT: G 173 MET cc_start: 0.4125 (tpp) cc_final: 0.3368 (tpp) REVERT: G 179 TYR cc_start: 0.6861 (t80) cc_final: 0.6352 (m-10) REVERT: G 203 ILE cc_start: 0.7801 (pt) cc_final: 0.7553 (mp) REVERT: G 216 TRP cc_start: 0.7807 (m100) cc_final: 0.7473 (m100) REVERT: G 220 TYR cc_start: 0.5854 (m-80) cc_final: 0.5391 (m-10) REVERT: G 224 MET cc_start: 0.7091 (mtt) cc_final: 0.6589 (mtt) REVERT: G 238 ASP cc_start: 0.6891 (m-30) cc_final: 0.6644 (p0) REVERT: G 241 ASP cc_start: 0.7428 (t0) cc_final: 0.7049 (t0) REVERT: G 244 GLN cc_start: 0.7843 (mt0) cc_final: 0.7575 (mm-40) REVERT: G 253 LYS cc_start: 0.7404 (tptt) cc_final: 0.7136 (mmtt) REVERT: G 273 LEU cc_start: 0.7546 (mt) cc_final: 0.7201 (mt) REVERT: G 274 GLN cc_start: 0.7973 (tp40) cc_final: 0.7731 (tp40) REVERT: G 315 THR cc_start: 0.5691 (m) cc_final: 0.5388 (p) REVERT: G 343 ASN cc_start: 0.3681 (t0) cc_final: 0.3307 (m-40) REVERT: G 346 ASP cc_start: 0.6343 (m-30) cc_final: 0.5634 (m-30) REVERT: G 370 MET cc_start: 0.6435 (mtp) cc_final: 0.5805 (mtp) REVERT: G 371 ARG cc_start: 0.6810 (OUTLIER) cc_final: 0.6455 (ptp90) REVERT: H 47 MET cc_start: 0.0588 (ptt) cc_final: -0.0669 (mmm) REVERT: H 53 TYR cc_start: 0.4415 (t80) cc_final: 0.3750 (m-80) REVERT: H 64 GLU cc_start: 0.8458 (tt0) cc_final: 0.8068 (tp30) REVERT: H 70 GLU cc_start: 0.8426 (tt0) cc_final: 0.8109 (tp30) REVERT: H 143 LYS cc_start: 0.6229 (tttm) cc_final: 0.5424 (tttt) REVERT: H 160 ILE cc_start: 0.8507 (mt) cc_final: 0.8086 (tt) REVERT: H 224 MET cc_start: 0.8551 (mmm) cc_final: 0.8301 (mmm) REVERT: H 279 ASP cc_start: 0.8671 (OUTLIER) cc_final: 0.8408 (m-30) REVERT: H 321 ASP cc_start: 0.8429 (p0) cc_final: 0.8206 (p0) outliers start: 32 outliers final: 16 residues processed: 359 average time/residue: 0.1302 time to fit residues: 74.0396 Evaluate side-chains 273 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 255 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 371 ARG Chi-restraints excluded: chain D residue 226 CYS Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 226 CYS Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 327 THR Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain G residue 371 ARG Chi-restraints excluded: chain H residue 279 ASP Chi-restraints excluded: chain H residue 334 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 256 optimal weight: 10.0000 chunk 158 optimal weight: 5.9990 chunk 37 optimal weight: 0.0980 chunk 228 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 115 optimal weight: 0.9990 chunk 239 optimal weight: 7.9990 chunk 79 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 190 optimal weight: 0.1980 chunk 237 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 GLN D 274 GLN ** G 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.161168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.124179 restraints weight = 35687.548| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.70 r_work: 0.3557 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22248 Z= 0.120 Angle : 0.544 8.597 30136 Z= 0.295 Chirality : 0.044 0.160 3336 Planarity : 0.004 0.038 3768 Dihedral : 5.746 57.850 2920 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.72 % Allowed : 11.58 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.17), residues: 2624 helix: 0.26 (0.21), residues: 648 sheet: 0.48 (0.20), residues: 736 loop : 0.71 (0.19), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 371 TYR 0.020 0.001 TYR B 211 PHE 0.017 0.002 PHE G 169 TRP 0.033 0.002 TRP G 312 HIS 0.013 0.001 HIS A 82 Details of bonding type rmsd covalent geometry : bond 0.00272 (22248) covalent geometry : angle 0.54388 (30136) hydrogen bonds : bond 0.03584 ( 952) hydrogen bonds : angle 5.02530 ( 2496) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 299 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 LYS cc_start: 0.8391 (mmmt) cc_final: 0.8121 (mmtt) REVERT: A 125 TYR cc_start: 0.6936 (m-80) cc_final: 0.6637 (m-80) REVERT: A 160 ILE cc_start: 0.8487 (mt) cc_final: 0.8159 (tt) REVERT: A 224 MET cc_start: 0.8042 (mmm) cc_final: 0.7823 (mpp) REVERT: A 279 ASP cc_start: 0.8718 (OUTLIER) cc_final: 0.8398 (m-30) REVERT: B 65 GLU cc_start: 0.7682 (tt0) cc_final: 0.7284 (tm-30) REVERT: B 315 THR cc_start: 0.6220 (m) cc_final: 0.6008 (p) REVERT: C 104 MET cc_start: 0.7152 (tmm) cc_final: 0.6434 (tmt) REVERT: C 151 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8296 (mt) REVERT: C 173 MET cc_start: 0.7339 (ttt) cc_final: 0.7110 (ttt) REVERT: D 149 VAL cc_start: 0.8558 (t) cc_final: 0.8279 (m) REVERT: D 211 TYR cc_start: 0.8144 (t80) cc_final: 0.7586 (t80) REVERT: D 319 MET cc_start: 0.7224 (mmm) cc_final: 0.7021 (mtt) REVERT: E 211 TYR cc_start: 0.7939 (t80) cc_final: 0.7576 (t80) REVERT: E 224 MET cc_start: 0.7122 (OUTLIER) cc_final: 0.6686 (mtt) REVERT: F 151 LEU cc_start: 0.8168 (mt) cc_final: 0.7944 (tp) REVERT: G 65 GLU cc_start: 0.7918 (tt0) cc_final: 0.7712 (tm-30) REVERT: G 74 LEU cc_start: 0.7812 (mt) cc_final: 0.7431 (mt) REVERT: G 169 PHE cc_start: 0.6432 (m-80) cc_final: 0.5554 (t80) REVERT: G 179 TYR cc_start: 0.6823 (t80) cc_final: 0.6120 (m-10) REVERT: G 216 TRP cc_start: 0.7778 (m100) cc_final: 0.7433 (m100) REVERT: G 220 TYR cc_start: 0.6034 (m-80) cc_final: 0.5497 (m-10) REVERT: G 224 MET cc_start: 0.7244 (mtt) cc_final: 0.6773 (mtt) REVERT: G 241 ASP cc_start: 0.7563 (t0) cc_final: 0.7175 (t0) REVERT: G 253 LYS cc_start: 0.7043 (tptt) cc_final: 0.6781 (mmtt) REVERT: G 343 ASN cc_start: 0.3719 (t0) cc_final: 0.3353 (m-40) REVERT: G 346 ASP cc_start: 0.5820 (m-30) cc_final: 0.5273 (m-30) REVERT: H 47 MET cc_start: 0.0546 (ptt) cc_final: -0.0664 (mmm) REVERT: H 53 TYR cc_start: 0.4364 (t80) cc_final: 0.3672 (m-80) REVERT: H 64 GLU cc_start: 0.8450 (tt0) cc_final: 0.8028 (tp30) REVERT: H 70 GLU cc_start: 0.8473 (tt0) cc_final: 0.8257 (tp30) REVERT: H 74 LEU cc_start: 0.8635 (mt) cc_final: 0.8182 (tt) REVERT: H 143 LYS cc_start: 0.6024 (tttm) cc_final: 0.5358 (tttt) REVERT: H 160 ILE cc_start: 0.8520 (mt) cc_final: 0.8223 (tt) REVERT: H 224 MET cc_start: 0.8462 (mmm) cc_final: 0.8053 (mpp) REVERT: H 279 ASP cc_start: 0.8714 (OUTLIER) cc_final: 0.8510 (m-30) outliers start: 41 outliers final: 21 residues processed: 326 average time/residue: 0.1262 time to fit residues: 66.8038 Evaluate side-chains 276 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 251 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain D residue 226 CYS Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain E residue 224 MET Chi-restraints excluded: chain E residue 226 CYS Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain G residue 351 ILE Chi-restraints excluded: chain G residue 364 CYS Chi-restraints excluded: chain G residue 371 ARG Chi-restraints excluded: chain H residue 279 ASP Chi-restraints excluded: chain H residue 296 HIS Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain H residue 358 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 94 optimal weight: 6.9990 chunk 226 optimal weight: 6.9990 chunk 247 optimal weight: 0.2980 chunk 157 optimal weight: 4.9990 chunk 235 optimal weight: 0.9990 chunk 146 optimal weight: 0.9980 chunk 203 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 163 optimal weight: 4.9990 chunk 127 optimal weight: 0.9980 chunk 10 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 ASN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 GLN ** G 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 175 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 = 0.4207 r_free = 0.4207 target = 0.161060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.124507 restraints weight = 35305.424| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.57 r_work: 0.3554 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 22248 Z= 0.109 Angle : 0.521 9.764 30136 Z= 0.281 Chirality : 0.044 0.161 3336 Planarity : 0.003 0.037 3768 Dihedral : 5.582 59.252 2920 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.64 % Allowed : 13.63 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.17), residues: 2624 helix: 0.41 (0.21), residues: 640 sheet: 0.53 (0.20), residues: 736 loop : 0.68 (0.19), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 84 TYR 0.022 0.001 TYR G 53 PHE 0.031 0.001 PHE A 60 TRP 0.029 0.001 TRP G 312 HIS 0.003 0.001 HIS G 282 Details of bonding type rmsd covalent geometry : bond 0.00243 (22248) covalent geometry : angle 0.52139 (30136) hydrogen bonds : bond 0.03361 ( 952) hydrogen bonds : angle 4.85913 ( 2496) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 273 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 TYR cc_start: 0.6977 (m-80) cc_final: 0.6733 (m-80) REVERT: A 160 ILE cc_start: 0.8487 (mt) cc_final: 0.8190 (tt) REVERT: A 279 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.8224 (m-30) REVERT: B 47 MET cc_start: -0.1293 (ptt) cc_final: -0.1617 (ptp) REVERT: B 65 GLU cc_start: 0.7558 (tt0) cc_final: 0.7212 (tm-30) REVERT: B 224 MET cc_start: 0.7394 (mtp) cc_final: 0.6942 (mtp) REVERT: B 371 ARG cc_start: 0.6092 (ttp-110) cc_final: 0.5682 (ptt-90) REVERT: C 151 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8309 (mt) REVERT: D 149 VAL cc_start: 0.8562 (t) cc_final: 0.8303 (m) REVERT: D 211 TYR cc_start: 0.7924 (t80) cc_final: 0.7441 (t80) REVERT: D 224 MET cc_start: 0.7295 (mtt) cc_final: 0.6951 (mtt) REVERT: E 162 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7909 (tm-30) REVERT: E 211 TYR cc_start: 0.7788 (t80) cc_final: 0.7403 (t80) REVERT: E 224 MET cc_start: 0.7067 (mtp) cc_final: 0.6762 (mtt) REVERT: F 151 LEU cc_start: 0.8142 (mt) cc_final: 0.7924 (tp) REVERT: G 74 LEU cc_start: 0.7830 (mt) cc_final: 0.7581 (mt) REVERT: G 179 TYR cc_start: 0.6695 (t80) cc_final: 0.5971 (m-10) REVERT: G 220 TYR cc_start: 0.6151 (m-80) cc_final: 0.5766 (m-10) REVERT: G 244 GLN cc_start: 0.7904 (mm-40) cc_final: 0.6868 (mm110) REVERT: G 343 ASN cc_start: 0.3594 (t0) cc_final: 0.3346 (m-40) REVERT: G 346 ASP cc_start: 0.5646 (m-30) cc_final: 0.5162 (m-30) REVERT: H 53 TYR cc_start: 0.4230 (t80) cc_final: 0.3488 (m-80) REVERT: H 74 LEU cc_start: 0.8654 (mt) cc_final: 0.8136 (tt) REVERT: H 143 LYS cc_start: 0.5944 (tttm) cc_final: 0.5324 (tttt) REVERT: H 160 ILE cc_start: 0.8491 (mt) cc_final: 0.8233 (tt) REVERT: H 224 MET cc_start: 0.8258 (mmm) cc_final: 0.7795 (mpp) outliers start: 39 outliers final: 21 residues processed: 298 average time/residue: 0.1293 time to fit residues: 63.0868 Evaluate side-chains 262 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 239 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain D residue 226 CYS Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 226 CYS Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain G residue 351 ILE Chi-restraints excluded: chain G residue 364 CYS Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 296 HIS Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain H residue 358 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 32 optimal weight: 7.9990 chunk 262 optimal weight: 0.8980 chunk 207 optimal weight: 4.9990 chunk 181 optimal weight: 0.7980 chunk 62 optimal weight: 20.0000 chunk 170 optimal weight: 4.9990 chunk 186 optimal weight: 3.9990 chunk 199 optimal weight: 9.9990 chunk 252 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 HIS ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 HIS ** G 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 175 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 = 0.4124 r_free = 0.4124 target = 0.153898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.117682 restraints weight = 35608.835| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.66 r_work: 0.3437 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 22248 Z= 0.259 Angle : 0.666 14.327 30136 Z= 0.355 Chirality : 0.049 0.162 3336 Planarity : 0.004 0.040 3768 Dihedral : 6.041 55.711 2920 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.22 % Allowed : 15.06 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.17), residues: 2624 helix: -0.17 (0.21), residues: 632 sheet: 0.31 (0.20), residues: 720 loop : 0.39 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 84 TYR 0.021 0.002 TYR B 211 PHE 0.024 0.002 PHE H 60 TRP 0.027 0.002 TRP G 312 HIS 0.006 0.001 HIS F 282 Details of bonding type rmsd covalent geometry : bond 0.00611 (22248) covalent geometry : angle 0.66620 (30136) hydrogen bonds : bond 0.04371 ( 952) hydrogen bonds : angle 5.27086 ( 2496) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 246 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 TYR cc_start: 0.7142 (m-80) cc_final: 0.6911 (m-80) REVERT: A 160 ILE cc_start: 0.8663 (mt) cc_final: 0.8367 (tt) REVERT: A 314 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8087 (mp10) REVERT: B 211 TYR cc_start: 0.8505 (t80) cc_final: 0.8200 (t80) REVERT: B 319 MET cc_start: 0.6358 (tpp) cc_final: 0.5642 (tpt) REVERT: B 346 ASP cc_start: 0.6067 (m-30) cc_final: 0.5270 (t0) REVERT: B 371 ARG cc_start: 0.6763 (ttp-110) cc_final: 0.6239 (ttp-110) REVERT: D 60 PHE cc_start: 0.8024 (OUTLIER) cc_final: 0.7654 (p90) REVERT: D 211 TYR cc_start: 0.7799 (t80) cc_final: 0.7214 (t80) REVERT: D 314 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.7576 (mp10) REVERT: E 104 MET cc_start: 0.6262 (ttt) cc_final: 0.5519 (mtp) REVERT: E 211 TYR cc_start: 0.7773 (t80) cc_final: 0.7228 (t80) REVERT: E 238 ASP cc_start: 0.7996 (t0) cc_final: 0.7737 (t0) REVERT: E 314 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.7611 (mp10) REVERT: E 326 LYS cc_start: 0.7973 (mtpp) cc_final: 0.7694 (mtmm) REVERT: G 74 LEU cc_start: 0.7514 (mt) cc_final: 0.7140 (mt) REVERT: G 76 TYR cc_start: 0.7378 (m-80) cc_final: 0.7171 (m-80) REVERT: G 169 PHE cc_start: 0.6810 (m-80) cc_final: 0.5896 (t80) REVERT: G 179 TYR cc_start: 0.6647 (t80) cc_final: 0.5876 (m-10) REVERT: G 343 ASN cc_start: 0.3438 (t0) cc_final: 0.3175 (m-40) REVERT: H 53 TYR cc_start: 0.3990 (t80) cc_final: 0.3400 (m-80) REVERT: H 74 LEU cc_start: 0.8635 (mt) cc_final: 0.8259 (tt) REVERT: H 105 PHE cc_start: 0.6873 (m-80) cc_final: 0.5985 (m-80) REVERT: H 125 TYR cc_start: 0.6757 (m-80) cc_final: 0.6463 (m-80) REVERT: H 143 LYS cc_start: 0.6072 (tttm) cc_final: 0.5437 (tttt) outliers start: 53 outliers final: 36 residues processed: 280 average time/residue: 0.1411 time to fit residues: 63.9809 Evaluate side-chains 259 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 219 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain D residue 60 PHE Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 363 SER Chi-restraints excluded: chain G residue 59 HIS Chi-restraints excluded: chain G residue 60 PHE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 157 ASP Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 226 CYS Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain G residue 364 CYS Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 279 ASP Chi-restraints excluded: chain H residue 296 HIS Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain H residue 358 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 77 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 205 optimal weight: 10.0000 chunk 125 optimal weight: 0.7980 chunk 168 optimal weight: 0.2980 chunk 108 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 136 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 HIS ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN ** E 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 214 HIS ** G 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.158583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.122144 restraints weight = 35362.675| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.58 r_work: 0.3528 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22248 Z= 0.113 Angle : 0.543 10.680 30136 Z= 0.292 Chirality : 0.044 0.160 3336 Planarity : 0.003 0.039 3768 Dihedral : 5.583 54.160 2920 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.89 % Allowed : 16.11 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.17), residues: 2624 helix: 0.33 (0.21), residues: 632 sheet: 0.32 (0.20), residues: 736 loop : 0.44 (0.19), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 371 TYR 0.016 0.001 TYR B 211 PHE 0.013 0.001 PHE C 222 TRP 0.027 0.001 TRP G 184 HIS 0.004 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00252 (22248) covalent geometry : angle 0.54343 (30136) hydrogen bonds : bond 0.03445 ( 952) hydrogen bonds : angle 4.87742 ( 2496) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 254 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ASP cc_start: 0.7917 (t0) cc_final: 0.7678 (t0) REVERT: A 125 TYR cc_start: 0.7219 (m-80) cc_final: 0.6933 (m-80) REVERT: A 160 ILE cc_start: 0.8596 (mt) cc_final: 0.8382 (tt) REVERT: A 173 MET cc_start: 0.8618 (mtt) cc_final: 0.8405 (mtt) REVERT: A 279 ASP cc_start: 0.8721 (OUTLIER) cc_final: 0.8494 (m-30) REVERT: A 314 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8346 (mm-40) REVERT: A 319 MET cc_start: 0.7778 (mmm) cc_final: 0.7463 (mtt) REVERT: B 65 GLU cc_start: 0.7701 (tt0) cc_final: 0.7341 (tm-30) REVERT: B 66 MET cc_start: 0.6176 (OUTLIER) cc_final: 0.5873 (mtp) REVERT: B 108 LYS cc_start: 0.7462 (tppt) cc_final: 0.7234 (tttm) REVERT: B 211 TYR cc_start: 0.8522 (t80) cc_final: 0.8190 (t80) REVERT: B 346 ASP cc_start: 0.6286 (m-30) cc_final: 0.5738 (m-30) REVERT: B 371 ARG cc_start: 0.6513 (ttp-110) cc_final: 0.6306 (ttp-110) REVERT: D 211 TYR cc_start: 0.8007 (t80) cc_final: 0.7411 (t80) REVERT: D 314 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.7584 (mp10) REVERT: E 211 TYR cc_start: 0.7918 (t80) cc_final: 0.7454 (t80) REVERT: E 224 MET cc_start: 0.7427 (mtp) cc_final: 0.7167 (mtt) REVERT: E 314 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.7598 (mp10) REVERT: G 65 GLU cc_start: 0.7882 (tt0) cc_final: 0.7574 (tm-30) REVERT: G 66 MET cc_start: 0.6669 (mtt) cc_final: 0.6431 (mtp) REVERT: G 74 LEU cc_start: 0.7727 (mt) cc_final: 0.7502 (mt) REVERT: G 157 ASP cc_start: 0.5652 (m-30) cc_final: 0.5433 (t0) REVERT: G 169 PHE cc_start: 0.6788 (m-80) cc_final: 0.5885 (t80) REVERT: G 179 TYR cc_start: 0.6421 (t80) cc_final: 0.5673 (m-10) REVERT: G 211 TYR cc_start: 0.8586 (t80) cc_final: 0.8375 (t80) REVERT: G 224 MET cc_start: 0.7340 (mmp) cc_final: 0.5531 (mtt) REVERT: G 343 ASN cc_start: 0.3615 (t0) cc_final: 0.3326 (m-40) REVERT: H 47 MET cc_start: 0.0459 (ptt) cc_final: 0.0086 (ppp) REVERT: H 53 TYR cc_start: 0.3973 (t80) cc_final: 0.3389 (m-80) REVERT: H 74 LEU cc_start: 0.8627 (mt) cc_final: 0.8238 (tt) REVERT: H 105 PHE cc_start: 0.6899 (m-80) cc_final: 0.5981 (m-80) REVERT: H 125 TYR cc_start: 0.6787 (m-80) cc_final: 0.6497 (m-80) REVERT: H 224 MET cc_start: 0.8201 (mmm) cc_final: 0.7794 (mpp) REVERT: H 314 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8245 (mm-40) outliers start: 45 outliers final: 25 residues processed: 286 average time/residue: 0.1474 time to fit residues: 68.1348 Evaluate side-chains 253 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 222 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 295 CYS Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 363 SER Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain G residue 351 ILE Chi-restraints excluded: chain G residue 364 CYS Chi-restraints excluded: chain H residue 279 ASP Chi-restraints excluded: chain H residue 296 HIS Chi-restraints excluded: chain H residue 314 GLN Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain H residue 358 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 201 optimal weight: 10.0000 chunk 223 optimal weight: 0.0770 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 205 optimal weight: 6.9990 chunk 231 optimal weight: 0.6980 chunk 105 optimal weight: 0.6980 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 HIS ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 244 GLN ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 244 GLN ** G 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 HIS ** H 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.158391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.122388 restraints weight = 35441.722| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.57 r_work: 0.3529 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22248 Z= 0.120 Angle : 0.545 8.896 30136 Z= 0.292 Chirality : 0.044 0.161 3336 Planarity : 0.003 0.038 3768 Dihedral : 5.469 58.136 2920 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.97 % Allowed : 16.32 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.17), residues: 2624 helix: 0.33 (0.21), residues: 640 sheet: 0.37 (0.20), residues: 736 loop : 0.51 (0.19), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 371 TYR 0.015 0.001 TYR B 211 PHE 0.017 0.001 PHE B 271 TRP 0.034 0.001 TRP G 312 HIS 0.007 0.001 HIS G 311 Details of bonding type rmsd covalent geometry : bond 0.00270 (22248) covalent geometry : angle 0.54481 (30136) hydrogen bonds : bond 0.03447 ( 952) hydrogen bonds : angle 4.81962 ( 2496) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 234 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 LYS cc_start: 0.8102 (mmtt) cc_final: 0.7146 (mttp) REVERT: A 125 TYR cc_start: 0.7200 (m-80) cc_final: 0.6910 (m-80) REVERT: A 160 ILE cc_start: 0.8496 (mt) cc_final: 0.8191 (tt) REVERT: A 173 MET cc_start: 0.8399 (mtt) cc_final: 0.8119 (mtt) REVERT: A 224 MET cc_start: 0.8085 (mmm) cc_final: 0.6752 (mpp) REVERT: A 279 ASP cc_start: 0.8529 (OUTLIER) cc_final: 0.8301 (m-30) REVERT: A 319 MET cc_start: 0.7646 (mmm) cc_final: 0.7384 (mtt) REVERT: B 53 TYR cc_start: 0.4698 (t80) cc_final: 0.4137 (m-10) REVERT: B 65 GLU cc_start: 0.7535 (tt0) cc_final: 0.7249 (tm-30) REVERT: B 66 MET cc_start: 0.6106 (OUTLIER) cc_final: 0.5775 (mtp) REVERT: B 103 CYS cc_start: 0.7432 (OUTLIER) cc_final: 0.6836 (m) REVERT: B 211 TYR cc_start: 0.8454 (t80) cc_final: 0.8104 (t80) REVERT: B 346 ASP cc_start: 0.6253 (m-30) cc_final: 0.5756 (m-30) REVERT: B 371 ARG cc_start: 0.6483 (ttp-110) cc_final: 0.6267 (ttp-110) REVERT: C 104 MET cc_start: 0.7609 (OUTLIER) cc_final: 0.7357 (tmm) REVERT: D 211 TYR cc_start: 0.7806 (t80) cc_final: 0.7224 (t80) REVERT: D 224 MET cc_start: 0.7118 (mtt) cc_final: 0.6877 (mtt) REVERT: D 314 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.7407 (mp10) REVERT: E 211 TYR cc_start: 0.7759 (t80) cc_final: 0.7331 (t80) REVERT: E 314 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.7448 (mp10) REVERT: E 326 LYS cc_start: 0.7902 (mtpp) cc_final: 0.7669 (mtmt) REVERT: G 66 MET cc_start: 0.6479 (mtt) cc_final: 0.6124 (mtm) REVERT: G 70 GLU cc_start: 0.7849 (tp30) cc_final: 0.7517 (tp30) REVERT: G 74 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7230 (mt) REVERT: G 169 PHE cc_start: 0.6780 (m-80) cc_final: 0.5937 (t80) REVERT: G 179 TYR cc_start: 0.6376 (t80) cc_final: 0.5794 (m-10) REVERT: G 371 ARG cc_start: 0.6521 (ptp90) cc_final: 0.5807 (ptp90) REVERT: H 47 MET cc_start: 0.0536 (ptt) cc_final: 0.0146 (ppp) REVERT: H 53 TYR cc_start: 0.4093 (t80) cc_final: 0.3391 (m-80) REVERT: H 63 HIS cc_start: 0.8250 (OUTLIER) cc_final: 0.7841 (m90) REVERT: H 74 LEU cc_start: 0.8604 (mt) cc_final: 0.8169 (tt) REVERT: H 105 PHE cc_start: 0.6924 (m-80) cc_final: 0.5989 (m-80) REVERT: H 125 TYR cc_start: 0.6861 (m-80) cc_final: 0.6598 (m-80) REVERT: H 222 PHE cc_start: 0.8079 (OUTLIER) cc_final: 0.7407 (p90) REVERT: H 224 MET cc_start: 0.8231 (mmm) cc_final: 0.7749 (mpp) REVERT: H 314 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.8054 (mm-40) outliers start: 47 outliers final: 26 residues processed: 269 average time/residue: 0.1448 time to fit residues: 63.7543 Evaluate side-chains 253 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 217 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 295 CYS Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain D residue 226 CYS Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 226 CYS Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 363 SER Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 226 CYS Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain G residue 351 ILE Chi-restraints excluded: chain G residue 364 CYS Chi-restraints excluded: chain H residue 63 HIS Chi-restraints excluded: chain H residue 222 PHE Chi-restraints excluded: chain H residue 296 HIS Chi-restraints excluded: chain H residue 314 GLN Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain H residue 358 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 63 optimal weight: 5.9990 chunk 207 optimal weight: 6.9990 chunk 216 optimal weight: 8.9990 chunk 72 optimal weight: 0.8980 chunk 34 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 218 optimal weight: 1.9990 chunk 4 optimal weight: 0.3980 chunk 196 optimal weight: 0.6980 chunk 170 optimal weight: 5.9990 chunk 122 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 HIS ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 GLN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 HIS ** H 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.158093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.121825 restraints weight = 34842.350| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 2.53 r_work: 0.3516 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.4791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22248 Z= 0.122 Angle : 0.543 8.631 30136 Z= 0.290 Chirality : 0.044 0.159 3336 Planarity : 0.003 0.038 3768 Dihedral : 5.451 58.436 2920 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.22 % Allowed : 16.90 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.17), residues: 2624 helix: 0.23 (0.21), residues: 648 sheet: 0.40 (0.20), residues: 736 loop : 0.46 (0.19), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 338 TYR 0.022 0.001 TYR E 179 PHE 0.012 0.001 PHE C 222 TRP 0.024 0.001 TRP G 184 HIS 0.005 0.001 HIS H 63 Details of bonding type rmsd covalent geometry : bond 0.00275 (22248) covalent geometry : angle 0.54323 (30136) hydrogen bonds : bond 0.03450 ( 952) hydrogen bonds : angle 4.82684 ( 2496) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 236 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 TYR cc_start: 0.7192 (m-80) cc_final: 0.6872 (m-80) REVERT: A 160 ILE cc_start: 0.8735 (mt) cc_final: 0.8378 (tt) REVERT: A 279 ASP cc_start: 0.8522 (OUTLIER) cc_final: 0.8304 (m-30) REVERT: A 314 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8152 (mm-40) REVERT: A 319 MET cc_start: 0.7669 (mmm) cc_final: 0.7131 (mtt) REVERT: B 53 TYR cc_start: 0.4649 (t80) cc_final: 0.4145 (m-10) REVERT: B 65 GLU cc_start: 0.7557 (tt0) cc_final: 0.7256 (tm-30) REVERT: B 66 MET cc_start: 0.6092 (OUTLIER) cc_final: 0.5757 (mtp) REVERT: B 103 CYS cc_start: 0.7304 (OUTLIER) cc_final: 0.6691 (m) REVERT: B 149 VAL cc_start: 0.8469 (OUTLIER) cc_final: 0.8201 (m) REVERT: B 319 MET cc_start: 0.6096 (tpp) cc_final: 0.5737 (mtt) REVERT: B 346 ASP cc_start: 0.6316 (m-30) cc_final: 0.5791 (m-30) REVERT: C 104 MET cc_start: 0.7624 (OUTLIER) cc_final: 0.7412 (tmm) REVERT: D 211 TYR cc_start: 0.7790 (t80) cc_final: 0.7283 (t80) REVERT: D 314 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.7435 (mp10) REVERT: E 211 TYR cc_start: 0.7751 (t80) cc_final: 0.7358 (t80) REVERT: E 314 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.7463 (mp10) REVERT: E 326 LYS cc_start: 0.7999 (mtpp) cc_final: 0.7711 (mtmt) REVERT: F 314 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.7664 (mp10) REVERT: G 70 GLU cc_start: 0.7867 (tp30) cc_final: 0.7608 (tp30) REVERT: G 74 LEU cc_start: 0.7548 (mt) cc_final: 0.7323 (mt) REVERT: G 169 PHE cc_start: 0.6822 (m-80) cc_final: 0.6017 (t80) REVERT: G 179 TYR cc_start: 0.6307 (t80) cc_final: 0.5711 (m-10) REVERT: G 371 ARG cc_start: 0.6448 (ptp90) cc_final: 0.5759 (ptp90) REVERT: H 47 MET cc_start: 0.0365 (ptt) cc_final: -0.0006 (ppp) REVERT: H 53 TYR cc_start: 0.4191 (t80) cc_final: 0.3433 (m-80) REVERT: H 74 LEU cc_start: 0.8567 (mt) cc_final: 0.8153 (tt) REVERT: H 105 PHE cc_start: 0.6867 (m-80) cc_final: 0.5931 (m-80) REVERT: H 125 TYR cc_start: 0.6786 (m-80) cc_final: 0.6545 (m-80) REVERT: H 222 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.7380 (p90) REVERT: H 224 MET cc_start: 0.8223 (mmm) cc_final: 0.7760 (mpp) REVERT: H 314 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.8067 (mm-40) outliers start: 53 outliers final: 27 residues processed: 276 average time/residue: 0.1401 time to fit residues: 64.0787 Evaluate side-chains 258 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 220 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 295 CYS Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 226 CYS Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 363 SER Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain G residue 53 TYR Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 226 CYS Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain G residue 351 ILE Chi-restraints excluded: chain G residue 364 CYS Chi-restraints excluded: chain H residue 222 PHE Chi-restraints excluded: chain H residue 314 GLN Chi-restraints excluded: chain H residue 334 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 216 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 chunk 210 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 chunk 106 optimal weight: 0.0970 chunk 233 optimal weight: 8.9990 chunk 250 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 HIS ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.155391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.118952 restraints weight = 34831.776| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.65 r_work: 0.3491 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.4891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 22248 Z= 0.214 Angle : 0.621 9.236 30136 Z= 0.331 Chirality : 0.046 0.160 3336 Planarity : 0.004 0.046 3768 Dihedral : 5.786 57.244 2920 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.31 % Allowed : 16.95 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.17), residues: 2624 helix: 0.02 (0.21), residues: 648 sheet: 0.25 (0.20), residues: 736 loop : 0.25 (0.19), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 371 TYR 0.020 0.002 TYR E 179 PHE 0.018 0.002 PHE C 222 TRP 0.028 0.002 TRP A 184 HIS 0.004 0.001 HIS G 63 Details of bonding type rmsd covalent geometry : bond 0.00503 (22248) covalent geometry : angle 0.62141 (30136) hydrogen bonds : bond 0.03991 ( 952) hydrogen bonds : angle 5.08256 ( 2496) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 223 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 TYR cc_start: 0.7060 (m-80) cc_final: 0.6707 (m-80) REVERT: A 160 ILE cc_start: 0.8715 (mt) cc_final: 0.8507 (tt) REVERT: A 279 ASP cc_start: 0.8664 (OUTLIER) cc_final: 0.8395 (m-30) REVERT: A 314 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.8432 (mm-40) REVERT: A 319 MET cc_start: 0.8071 (mmm) cc_final: 0.7644 (mtt) REVERT: B 53 TYR cc_start: 0.4572 (t80) cc_final: 0.4065 (m-10) REVERT: B 65 GLU cc_start: 0.7733 (tt0) cc_final: 0.7396 (tm-30) REVERT: B 66 MET cc_start: 0.6265 (OUTLIER) cc_final: 0.5879 (mtp) REVERT: B 103 CYS cc_start: 0.7575 (OUTLIER) cc_final: 0.6972 (m) REVERT: B 319 MET cc_start: 0.6100 (tpp) cc_final: 0.5666 (mtt) REVERT: B 346 ASP cc_start: 0.6700 (m-30) cc_final: 0.6142 (m-30) REVERT: C 314 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.7819 (mp10) REVERT: D 60 PHE cc_start: 0.8085 (p90) cc_final: 0.7839 (p90) REVERT: D 211 TYR cc_start: 0.8041 (t80) cc_final: 0.7443 (t80) REVERT: D 224 MET cc_start: 0.7187 (mtt) cc_final: 0.6964 (mtt) REVERT: D 314 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.7749 (mp10) REVERT: E 104 MET cc_start: 0.7606 (tmm) cc_final: 0.6507 (mtp) REVERT: E 211 TYR cc_start: 0.8008 (t80) cc_final: 0.7458 (t80) REVERT: E 224 MET cc_start: 0.7478 (mtt) cc_final: 0.7135 (mtt) REVERT: E 314 GLN cc_start: 0.9045 (OUTLIER) cc_final: 0.7798 (mp10) REVERT: E 326 LYS cc_start: 0.8343 (mtpp) cc_final: 0.7899 (mtmt) REVERT: F 314 GLN cc_start: 0.8704 (OUTLIER) cc_final: 0.7822 (mp10) REVERT: G 74 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.7079 (mt) REVERT: G 169 PHE cc_start: 0.6960 (m-80) cc_final: 0.6395 (t80) REVERT: G 179 TYR cc_start: 0.6357 (t80) cc_final: 0.5687 (m-10) REVERT: G 371 ARG cc_start: 0.6523 (ptp90) cc_final: 0.5793 (ptp90) REVERT: H 47 MET cc_start: 0.0350 (ptt) cc_final: -0.0108 (ppp) REVERT: H 53 TYR cc_start: 0.4202 (t80) cc_final: 0.3417 (m-80) REVERT: H 74 LEU cc_start: 0.8643 (mt) cc_final: 0.8229 (tt) REVERT: H 105 PHE cc_start: 0.6887 (m-80) cc_final: 0.5903 (m-80) REVERT: H 125 TYR cc_start: 0.6833 (m-80) cc_final: 0.6602 (m-80) REVERT: H 222 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7492 (p90) REVERT: H 314 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8262 (mm-40) outliers start: 55 outliers final: 34 residues processed: 264 average time/residue: 0.1457 time to fit residues: 63.5846 Evaluate side-chains 254 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 209 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 295 CYS Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain D residue 226 CYS Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 226 CYS Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 363 SER Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain G residue 53 TYR Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 226 CYS Chi-restraints excluded: chain G residue 351 ILE Chi-restraints excluded: chain G residue 364 CYS Chi-restraints excluded: chain H residue 222 PHE Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 279 ASP Chi-restraints excluded: chain H residue 296 HIS Chi-restraints excluded: chain H residue 314 GLN Chi-restraints excluded: chain H residue 334 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 199 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 133 optimal weight: 4.9990 chunk 195 optimal weight: 3.9990 chunk 241 optimal weight: 0.2980 chunk 152 optimal weight: 0.9990 chunk 146 optimal weight: 0.0370 chunk 180 optimal weight: 0.6980 chunk 184 optimal weight: 0.0570 chunk 21 optimal weight: 1.9990 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 HIS ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.161240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.125911 restraints weight = 34788.288| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.35 r_work: 0.3601 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3462 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.5123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 22248 Z= 0.099 Angle : 0.542 8.357 30136 Z= 0.290 Chirality : 0.043 0.159 3336 Planarity : 0.003 0.042 3768 Dihedral : 5.436 59.570 2920 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.55 % Allowed : 17.95 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.17), residues: 2624 helix: 0.20 (0.21), residues: 648 sheet: 0.41 (0.20), residues: 752 loop : 0.47 (0.19), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 371 TYR 0.019 0.001 TYR E 179 PHE 0.012 0.001 PHE E 271 TRP 0.024 0.001 TRP G 184 HIS 0.003 0.001 HIS G 63 Details of bonding type rmsd covalent geometry : bond 0.00211 (22248) covalent geometry : angle 0.54195 (30136) hydrogen bonds : bond 0.03236 ( 952) hydrogen bonds : angle 4.82434 ( 2496) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 237 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 TYR cc_start: 0.7049 (m-80) cc_final: 0.6740 (m-80) REVERT: A 314 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.8259 (mm-40) REVERT: A 319 MET cc_start: 0.7751 (mmm) cc_final: 0.7317 (mtt) REVERT: B 53 TYR cc_start: 0.4251 (t80) cc_final: 0.3839 (m-80) REVERT: B 65 GLU cc_start: 0.7568 (tt0) cc_final: 0.7335 (tm-30) REVERT: B 66 MET cc_start: 0.6029 (OUTLIER) cc_final: 0.5746 (mtp) REVERT: B 103 CYS cc_start: 0.7208 (OUTLIER) cc_final: 0.6687 (m) REVERT: B 149 VAL cc_start: 0.8411 (OUTLIER) cc_final: 0.8132 (m) REVERT: B 319 MET cc_start: 0.5996 (tpp) cc_final: 0.5728 (mtt) REVERT: B 346 ASP cc_start: 0.6623 (m-30) cc_final: 0.6121 (m-30) REVERT: C 104 MET cc_start: 0.7775 (tmm) cc_final: 0.7559 (tmm) REVERT: C 354 ASP cc_start: 0.8563 (m-30) cc_final: 0.8308 (m-30) REVERT: D 149 VAL cc_start: 0.8757 (t) cc_final: 0.8457 (m) REVERT: D 211 TYR cc_start: 0.7994 (t80) cc_final: 0.7492 (t80) REVERT: D 276 LYS cc_start: 0.7245 (mtmm) cc_final: 0.7009 (ptpt) REVERT: E 104 MET cc_start: 0.7314 (tmm) cc_final: 0.6528 (mtp) REVERT: E 211 TYR cc_start: 0.7947 (t80) cc_final: 0.7517 (t80) REVERT: E 224 MET cc_start: 0.7405 (mtt) cc_final: 0.7035 (mtt) REVERT: E 314 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.7508 (mp10) REVERT: E 326 LYS cc_start: 0.8205 (mtpp) cc_final: 0.7773 (mtmt) REVERT: F 314 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.7902 (mp10) REVERT: G 54 PHE cc_start: 0.6196 (m-10) cc_final: 0.5942 (t80) REVERT: G 70 GLU cc_start: 0.7997 (tp30) cc_final: 0.7707 (tp30) REVERT: G 169 PHE cc_start: 0.6787 (m-80) cc_final: 0.6002 (t80) REVERT: G 179 TYR cc_start: 0.6229 (t80) cc_final: 0.5609 (m-10) REVERT: G 246 VAL cc_start: 0.6978 (t) cc_final: 0.6755 (t) REVERT: G 371 ARG cc_start: 0.6391 (ptp90) cc_final: 0.5708 (ptp90) REVERT: H 47 MET cc_start: 0.0200 (ptt) cc_final: -0.0084 (ppp) REVERT: H 53 TYR cc_start: 0.4302 (t80) cc_final: 0.3473 (m-80) REVERT: H 74 LEU cc_start: 0.8577 (mt) cc_final: 0.8161 (tt) REVERT: H 314 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8191 (mm-40) outliers start: 37 outliers final: 20 residues processed: 264 average time/residue: 0.1445 time to fit residues: 62.9279 Evaluate side-chains 251 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 224 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 295 CYS Chi-restraints excluded: chain D residue 226 CYS Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain E residue 226 CYS Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain G residue 53 TYR Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 224 MET Chi-restraints excluded: chain G residue 351 ILE Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 296 HIS Chi-restraints excluded: chain H residue 314 GLN Chi-restraints excluded: chain H residue 334 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 13 optimal weight: 6.9990 chunk 224 optimal weight: 1.9990 chunk 243 optimal weight: 3.9990 chunk 172 optimal weight: 0.5980 chunk 166 optimal weight: 5.9990 chunk 239 optimal weight: 6.9990 chunk 132 optimal weight: 30.0000 chunk 130 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 HIS ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.158507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.122146 restraints weight = 35567.077| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.47 r_work: 0.3514 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.5134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22248 Z= 0.177 Angle : 0.597 9.042 30136 Z= 0.318 Chirality : 0.045 0.158 3336 Planarity : 0.004 0.041 3768 Dihedral : 5.565 59.479 2920 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.47 % Allowed : 17.66 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.17), residues: 2624 helix: 0.14 (0.21), residues: 648 sheet: 0.31 (0.20), residues: 744 loop : 0.33 (0.19), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 371 TYR 0.019 0.001 TYR E 179 PHE 0.016 0.002 PHE D 271 TRP 0.032 0.002 TRP H 184 HIS 0.004 0.001 HIS F 282 Details of bonding type rmsd covalent geometry : bond 0.00415 (22248) covalent geometry : angle 0.59696 (30136) hydrogen bonds : bond 0.03798 ( 952) hydrogen bonds : angle 4.97358 ( 2496) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5539.85 seconds wall clock time: 95 minutes 55.37 seconds (5755.37 seconds total)