Starting phenix.real_space_refine on Sun Aug 24 17:52:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z7h_39814/08_2025/8z7h_39814.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z7h_39814/08_2025/8z7h_39814.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8z7h_39814/08_2025/8z7h_39814.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z7h_39814/08_2025/8z7h_39814.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8z7h_39814/08_2025/8z7h_39814.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z7h_39814/08_2025/8z7h_39814.map" } resolution = 3.56 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: 5.14, per 1000 atoms: 0.24 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: 2.09 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 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: 0.80 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: 3.68 Time building geometry restraints manager: 2.74 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: 0.04 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 20.590 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 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 : 0.766 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: 0.8731 (mt) cc_final: 0.8363 (tt) REVERT: A 87 PHE cc_start: 0.7881 (m-80) cc_final: 0.7670 (m-10) REVERT: A 104 MET cc_start: 0.6506 (ttp) cc_final: 0.6243 (tmm) REVERT: A 143 LYS cc_start: 0.6221 (tttm) cc_final: 0.5487 (tttt) REVERT: A 159 ILE cc_start: 0.8202 (mt) cc_final: 0.7932 (mm) REVERT: A 160 ILE cc_start: 0.8536 (mt) cc_final: 0.7983 (tt) REVERT: B 76 TYR cc_start: 0.6678 (m-80) cc_final: 0.6273 (m-80) REVERT: B 114 VAL cc_start: 0.8113 (t) cc_final: 0.7862 (t) REVERT: B 139 VAL cc_start: 0.7994 (t) cc_final: 0.7458 (m) REVERT: B 169 PHE cc_start: 0.6905 (m-80) cc_final: 0.6451 (t80) REVERT: B 235 PRO cc_start: 0.6106 (Cg_exo) cc_final: 0.5704 (Cg_endo) REVERT: B 239 VAL cc_start: 0.8659 (t) cc_final: 0.8231 (p) REVERT: B 244 GLN cc_start: 0.8261 (mt0) cc_final: 0.6953 (mm110) REVERT: B 273 LEU cc_start: 0.8173 (mt) cc_final: 0.7525 (mt) REVERT: B 312 TRP cc_start: 0.7381 (m-90) cc_final: 0.7128 (m-10) REVERT: E 211 TYR cc_start: 0.7813 (t80) cc_final: 0.7449 (t80) REVERT: E 272 CYS cc_start: 0.6583 (t) cc_final: 0.6273 (t) REVERT: F 211 TYR cc_start: 0.8420 (t80) cc_final: 0.8006 (t80) REVERT: F 224 MET cc_start: 0.8018 (mtt) cc_final: 0.7803 (mtt) REVERT: F 371 ARG cc_start: 0.7030 (ptt180) cc_final: 0.6812 (ptt180) REVERT: G 167 CYS cc_start: 0.6381 (t) cc_final: 0.6020 (t) REVERT: G 170 TYR cc_start: 0.6250 (t80) cc_final: 0.5867 (t80) REVERT: G 179 TYR cc_start: 0.6978 (t80) cc_final: 0.6499 (m-10) REVERT: G 273 LEU cc_start: 0.7242 (mt) cc_final: 0.6967 (mt) REVERT: G 343 ASN cc_start: 0.2764 (t0) cc_final: 0.2464 (m-40) REVERT: G 349 PHE cc_start: 0.5397 (m-10) cc_final: 0.4760 (m-10) REVERT: H 47 MET cc_start: 0.0322 (ptt) cc_final: -0.0632 (mmm) REVERT: H 104 MET cc_start: 0.6990 (ttp) cc_final: 0.6744 (tmm) REVERT: H 105 PHE cc_start: 0.7280 (m-10) cc_final: 0.7022 (m-80) REVERT: H 134 LYS cc_start: 0.7876 (mtmt) cc_final: 0.7534 (mmmt) REVERT: H 143 LYS cc_start: 0.6228 (tttm) cc_final: 0.5790 (tttt) REVERT: H 159 ILE cc_start: 0.8357 (mt) cc_final: 0.8061 (mm) REVERT: H 160 ILE cc_start: 0.8668 (mt) cc_final: 0.8236 (tt) REVERT: H 296 HIS cc_start: 0.6991 (t-90) cc_final: 0.6717 (t70) outliers start: 0 outliers final: 0 residues processed: 487 average time/residue: 0.1546 time to fit residues: 113.8916 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 : 0.853 ------------------------------------------------------------------------------- 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: 0.8980 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: 2.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.4063 r_free = 0.4063 target = 0.156255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.118868 restraints weight = 34879.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.118085 restraints weight = 26584.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.119161 restraints weight = 23349.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.119473 restraints weight = 17933.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.119713 restraints weight = 16144.360| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22248 Z= 0.141 Angle : 0.592 9.654 30136 Z= 0.322 Chirality : 0.046 0.165 3336 Planarity : 0.004 0.050 3768 Dihedral : 5.942 45.759 2920 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.26 % Allowed : 8.14 % Favored : 90.60 % 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: 0.45 (0.17), residues: 2624 helix: -0.04 (0.21), residues: 648 sheet: 0.17 (0.20), residues: 728 loop : 0.82 (0.19), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 298 TYR 0.023 0.002 TYR C 208 PHE 0.033 0.002 PHE A 105 TRP 0.028 0.002 TRP H 184 HIS 0.013 0.001 HIS A 82 Details of bonding type rmsd covalent geometry : bond 0.00317 (22248) covalent geometry : angle 0.59240 (30136) hydrogen bonds : bond 0.04058 ( 952) hydrogen bonds : angle 5.29129 ( 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 361 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 331 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 PHE cc_start: 0.7661 (m-80) cc_final: 0.7082 (m-80) REVERT: A 104 MET cc_start: 0.7132 (ttp) cc_final: 0.6749 (ttt) REVERT: A 143 LYS cc_start: 0.5826 (tttm) cc_final: 0.5150 (tttt) REVERT: A 160 ILE cc_start: 0.8271 (mt) cc_final: 0.8003 (tt) REVERT: A 224 MET cc_start: 0.8406 (mmm) cc_final: 0.8147 (mmm) REVERT: B 47 MET cc_start: -0.0541 (ptt) cc_final: -0.0854 (ptp) REVERT: D 195 ARG cc_start: 0.8021 (ttp80) cc_final: 0.7777 (ttt-90) REVERT: D 211 TYR cc_start: 0.7800 (t80) cc_final: 0.7239 (t80) REVERT: E 211 TYR cc_start: 0.7744 (t80) cc_final: 0.7399 (t80) REVERT: G 74 LEU cc_start: 0.7451 (mt) cc_final: 0.6828 (mt) REVERT: G 167 CYS cc_start: 0.6092 (t) cc_final: 0.5815 (t) REVERT: G 169 PHE cc_start: 0.6352 (m-80) cc_final: 0.5668 (t80) REVERT: G 173 MET cc_start: 0.4273 (tpp) cc_final: 0.3578 (tpp) REVERT: G 203 ILE cc_start: 0.8044 (pt) cc_final: 0.7812 (mp) REVERT: G 273 LEU cc_start: 0.7475 (mt) cc_final: 0.7182 (mt) REVERT: G 346 ASP cc_start: 0.5973 (m-30) cc_final: 0.5731 (m-30) REVERT: G 370 MET cc_start: 0.6489 (mtp) cc_final: 0.6081 (mtp) REVERT: G 371 ARG cc_start: 0.6898 (OUTLIER) cc_final: 0.6545 (ptp90) REVERT: H 47 MET cc_start: 0.0601 (ptt) cc_final: -0.0687 (mmm) REVERT: H 53 TYR cc_start: 0.4318 (t80) cc_final: 0.3706 (m-80) REVERT: H 63 HIS cc_start: 0.8630 (OUTLIER) cc_final: 0.8014 (m90) REVERT: H 87 PHE cc_start: 0.7364 (m-10) cc_final: 0.7048 (m-10) REVERT: H 143 LYS cc_start: 0.6005 (tttm) cc_final: 0.5123 (mttt) REVERT: H 160 ILE cc_start: 0.8478 (mt) cc_final: 0.8186 (tt) REVERT: H 224 MET cc_start: 0.8365 (mmm) cc_final: 0.8137 (mmm) REVERT: H 279 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7821 (m-30) outliers start: 30 outliers final: 14 residues processed: 350 average time/residue: 0.1360 time to fit residues: 74.4922 Evaluate side-chains 267 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 250 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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 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 371 ARG Chi-restraints excluded: chain H residue 63 HIS 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: 7.9990 chunk 158 optimal weight: 5.9990 chunk 37 optimal weight: 0.0870 chunk 228 optimal weight: 4.9990 chunk 14 optimal weight: 0.0070 chunk 115 optimal weight: 0.8980 chunk 239 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 190 optimal weight: 0.2980 chunk 237 optimal weight: 2.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.155442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.119671 restraints weight = 35058.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.118034 restraints weight = 29670.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.119339 restraints weight = 25874.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.119712 restraints weight = 18387.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.119980 restraints weight = 17295.626| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22248 Z= 0.115 Angle : 0.540 9.102 30136 Z= 0.294 Chirality : 0.044 0.159 3336 Planarity : 0.004 0.038 3768 Dihedral : 5.731 55.409 2920 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.68 % Allowed : 11.49 % Favored : 86.83 % 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: 0.20 (0.21), residues: 656 sheet: 0.52 (0.20), residues: 736 loop : 0.71 (0.19), residues: 1232 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 0.031 0.002 TRP G 312 HIS 0.017 0.001 HIS H 63 Details of bonding type rmsd covalent geometry : bond 0.00253 (22248) covalent geometry : angle 0.54040 (30136) hydrogen bonds : bond 0.03581 ( 952) hydrogen bonds : angle 5.03091 ( 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 333 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 293 time to evaluate : 0.796 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 74 LEU cc_start: 0.8702 (mt) cc_final: 0.8306 (tt) REVERT: A 87 PHE cc_start: 0.7717 (m-80) cc_final: 0.7514 (m-10) REVERT: A 160 ILE cc_start: 0.8306 (mt) cc_final: 0.7999 (tt) REVERT: A 279 ASP cc_start: 0.8163 (OUTLIER) cc_final: 0.7818 (m-30) REVERT: B 66 MET cc_start: 0.6065 (mtm) cc_final: 0.5831 (mtp) REVERT: B 222 PHE cc_start: 0.5840 (m-80) cc_final: 0.5562 (m-80) REVERT: C 104 MET cc_start: 0.6995 (tmm) cc_final: 0.6254 (tmt) REVERT: D 195 ARG cc_start: 0.7974 (ttp80) cc_final: 0.7734 (ttt-90) REVERT: D 211 TYR cc_start: 0.7847 (t80) cc_final: 0.7335 (t80) REVERT: D 224 MET cc_start: 0.7505 (OUTLIER) cc_final: 0.7117 (mtt) REVERT: E 162 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7520 (tm-30) REVERT: E 211 TYR cc_start: 0.7720 (t80) cc_final: 0.7419 (t80) REVERT: F 151 LEU cc_start: 0.8162 (mt) cc_final: 0.7868 (tp) REVERT: G 53 TYR cc_start: 0.4915 (t80) cc_final: 0.4310 (m-80) REVERT: G 74 LEU cc_start: 0.7357 (mt) cc_final: 0.6997 (mt) REVERT: G 169 PHE cc_start: 0.6214 (m-80) cc_final: 0.5535 (t80) REVERT: G 244 GLN cc_start: 0.8066 (mm110) cc_final: 0.7155 (mm110) REVERT: G 346 ASP cc_start: 0.5830 (m-30) cc_final: 0.5523 (m-30) REVERT: H 47 MET cc_start: 0.0446 (ptt) cc_final: -0.0692 (mmm) REVERT: H 67 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8517 (mm) REVERT: H 143 LYS cc_start: 0.5763 (tttm) cc_final: 0.5136 (tttt) REVERT: H 160 ILE cc_start: 0.8335 (mt) cc_final: 0.8121 (tt) REVERT: H 224 MET cc_start: 0.8331 (mmm) cc_final: 0.8020 (mpp) REVERT: H 279 ASP cc_start: 0.8130 (OUTLIER) cc_final: 0.7897 (m-30) outliers start: 40 outliers final: 19 residues processed: 321 average time/residue: 0.1264 time to fit residues: 65.9343 Evaluate side-chains 265 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 242 time to evaluate : 0.752 ------------------------------------------------------------------------------- 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 79 SER Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain D residue 224 MET Chi-restraints excluded: chain D residue 226 CYS Chi-restraints excluded: chain D residue 272 CYS 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 371 ARG Chi-restraints excluded: chain H residue 67 LEU 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: 20.0000 chunk 247 optimal weight: 0.0470 chunk 157 optimal weight: 4.9990 chunk 235 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 203 optimal weight: 0.7980 chunk 107 optimal weight: 0.5980 chunk 163 optimal weight: 4.9990 chunk 127 optimal weight: 0.0470 chunk 10 optimal weight: 0.9980 overall best weight: 0.4976 ------------------------------------------------------------------------------- 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 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 GLN G 59 HIS ** 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 = 0.4065 r_free = 0.4065 target = 0.155953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.119973 restraints weight = 34853.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.118556 restraints weight = 28002.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.120111 restraints weight = 25619.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.120237 restraints weight = 18405.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.120554 restraints weight = 16700.438| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 22248 Z= 0.102 Angle : 0.520 9.129 30136 Z= 0.281 Chirality : 0.044 0.160 3336 Planarity : 0.003 0.038 3768 Dihedral : 5.581 59.260 2920 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.72 % Allowed : 13.05 % Favored : 85.23 % 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: 0.69 (0.17), residues: 2624 helix: 0.39 (0.21), residues: 648 sheet: 0.53 (0.20), residues: 736 loop : 0.66 (0.19), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 371 TYR 0.036 0.001 TYR H 53 PHE 0.015 0.001 PHE C 222 TRP 0.029 0.001 TRP G 312 HIS 0.005 0.001 HIS G 311 Details of bonding type rmsd covalent geometry : bond 0.00224 (22248) covalent geometry : angle 0.52017 (30136) hydrogen bonds : bond 0.03309 ( 952) hydrogen bonds : angle 4.84667 ( 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 319 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 278 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8450 (mm) REVERT: A 74 LEU cc_start: 0.8647 (mt) cc_final: 0.8196 (tt) REVERT: A 125 TYR cc_start: 0.6560 (m-80) cc_final: 0.6205 (t80) REVERT: A 160 ILE cc_start: 0.8433 (mt) cc_final: 0.8199 (tt) REVERT: A 279 ASP cc_start: 0.8153 (OUTLIER) cc_final: 0.7840 (m-30) REVERT: B 371 ARG cc_start: 0.6316 (ttp-110) cc_final: 0.5677 (ptt90) REVERT: C 151 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8443 (mt) REVERT: D 195 ARG cc_start: 0.7921 (ttp80) cc_final: 0.7621 (ttt-90) REVERT: D 211 TYR cc_start: 0.7818 (t80) cc_final: 0.7376 (t80) REVERT: D 224 MET cc_start: 0.7411 (mtp) cc_final: 0.7047 (mtt) REVERT: D 279 ASP cc_start: 0.7290 (t0) cc_final: 0.7021 (m-30) REVERT: E 162 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7544 (tm-30) REVERT: E 211 TYR cc_start: 0.7743 (t80) cc_final: 0.7402 (t80) REVERT: E 224 MET cc_start: 0.7597 (mtp) cc_final: 0.7052 (mtt) REVERT: F 151 LEU cc_start: 0.8136 (mt) cc_final: 0.7842 (tp) REVERT: F 224 MET cc_start: 0.8028 (mtt) cc_final: 0.7683 (mtt) REVERT: G 53 TYR cc_start: 0.4587 (t80) cc_final: 0.4184 (m-10) REVERT: G 74 LEU cc_start: 0.7457 (mt) cc_final: 0.7207 (mt) REVERT: G 169 PHE cc_start: 0.6318 (m-80) cc_final: 0.5672 (t80) REVERT: G 346 ASP cc_start: 0.5764 (m-30) cc_final: 0.5398 (m-30) REVERT: H 47 MET cc_start: 0.0441 (ptt) cc_final: -0.0758 (mmm) REVERT: H 74 LEU cc_start: 0.8614 (mt) cc_final: 0.8121 (tt) REVERT: H 143 LYS cc_start: 0.5691 (tttm) cc_final: 0.4979 (tttt) REVERT: H 224 MET cc_start: 0.8319 (mmm) cc_final: 0.7977 (mpp) REVERT: H 279 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.7949 (m-30) outliers start: 41 outliers final: 14 residues processed: 304 average time/residue: 0.1298 time to fit residues: 63.9699 Evaluate side-chains 257 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 239 time to evaluate : 0.764 ------------------------------------------------------------------------------- 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 334 THR Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain D residue 226 CYS Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain E residue 226 CYS Chi-restraints excluded: chain G residue 159 ILE 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 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: 4.9990 chunk 262 optimal weight: 3.9990 chunk 207 optimal weight: 0.3980 chunk 181 optimal weight: 0.6980 chunk 62 optimal weight: 9.9990 chunk 170 optimal weight: 4.9990 chunk 186 optimal weight: 1.9990 chunk 199 optimal weight: 9.9990 chunk 252 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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 133 ASN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 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 = 0.3992 r_free = 0.3992 target = 0.149637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.114466 restraints weight = 34875.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.112077 restraints weight = 29187.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.113576 restraints weight = 28132.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.114151 restraints weight = 18759.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.114416 restraints weight = 17271.784| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 22248 Z= 0.201 Angle : 0.619 14.361 30136 Z= 0.330 Chirality : 0.046 0.176 3336 Planarity : 0.004 0.036 3768 Dihedral : 5.758 59.923 2920 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.06 % Allowed : 14.47 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.17), residues: 2624 helix: 0.14 (0.21), residues: 648 sheet: 0.38 (0.20), residues: 736 loop : 0.41 (0.19), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 371 TYR 0.018 0.002 TYR B 211 PHE 0.031 0.002 PHE H 60 TRP 0.031 0.002 TRP G 312 HIS 0.005 0.001 HIS F 282 Details of bonding type rmsd covalent geometry : bond 0.00469 (22248) covalent geometry : angle 0.61943 (30136) hydrogen bonds : bond 0.03980 ( 952) hydrogen bonds : angle 5.05513 ( 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 301 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 252 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8402 (mm) REVERT: A 74 LEU cc_start: 0.8643 (mt) cc_final: 0.8226 (tt) REVERT: A 160 ILE cc_start: 0.8628 (mt) cc_final: 0.8360 (tt) REVERT: B 346 ASP cc_start: 0.5910 (m-30) cc_final: 0.5655 (m-30) REVERT: C 80 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8547 (mtm) REVERT: D 211 TYR cc_start: 0.7702 (t80) cc_final: 0.7173 (t80) REVERT: D 224 MET cc_start: 0.7640 (mtp) cc_final: 0.7193 (mtt) REVERT: D 314 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.7460 (mp10) REVERT: E 104 MET cc_start: 0.5691 (ttt) cc_final: 0.4985 (mtp) REVERT: E 211 TYR cc_start: 0.7691 (t80) cc_final: 0.7265 (t80) REVERT: E 314 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.7579 (mp10) REVERT: F 224 MET cc_start: 0.8544 (mtt) cc_final: 0.8271 (mtt) REVERT: G 53 TYR cc_start: 0.4749 (t80) cc_final: 0.4366 (t80) REVERT: G 70 GLU cc_start: 0.7539 (tp30) cc_final: 0.7313 (tp30) REVERT: G 74 LEU cc_start: 0.7309 (mt) cc_final: 0.7022 (mt) REVERT: G 76 TYR cc_start: 0.7111 (m-80) cc_final: 0.6893 (m-80) REVERT: G 169 PHE cc_start: 0.6579 (m-80) cc_final: 0.5960 (t80) REVERT: G 346 ASP cc_start: 0.5807 (m-30) cc_final: 0.5473 (m-30) REVERT: H 53 TYR cc_start: 0.4026 (t80) cc_final: 0.3415 (m-80) REVERT: H 74 LEU cc_start: 0.8641 (mt) cc_final: 0.8202 (tt) REVERT: H 104 MET cc_start: 0.6580 (ttt) cc_final: 0.6294 (tmm) REVERT: H 105 PHE cc_start: 0.7299 (m-80) cc_final: 0.6258 (m-80) REVERT: H 143 LYS cc_start: 0.5867 (tttm) cc_final: 0.5139 (tttt) REVERT: H 279 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.7927 (m-30) outliers start: 49 outliers final: 30 residues processed: 284 average time/residue: 0.1385 time to fit residues: 63.7277 Evaluate side-chains 255 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 220 time to evaluate : 0.648 ------------------------------------------------------------------------------- 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 279 ASP Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 295 CYS Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 151 LEU 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 60 PHE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 157 ASP 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 160 ILE Chi-restraints excluded: chain H residue 161 SER 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: 4.9990 chunk 12 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 205 optimal weight: 9.9990 chunk 125 optimal weight: 0.7980 chunk 168 optimal weight: 0.6980 chunk 108 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 136 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.152838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.116754 restraints weight = 34973.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.115703 restraints weight = 26816.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.116797 restraints weight = 24131.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.117178 restraints weight = 17830.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.117382 restraints weight = 16698.762| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22248 Z= 0.120 Angle : 0.552 11.561 30136 Z= 0.296 Chirality : 0.044 0.158 3336 Planarity : 0.003 0.037 3768 Dihedral : 5.499 58.811 2920 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.55 % Allowed : 15.69 % Favored : 82.76 % 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: 0.28 (0.17), residues: 2624 helix: 0.04 (0.20), residues: 688 sheet: 0.39 (0.20), residues: 736 loop : 0.35 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 371 TYR 0.015 0.001 TYR E 179 PHE 0.029 0.001 PHE A 60 TRP 0.028 0.001 TRP G 184 HIS 0.003 0.001 HIS G 282 Details of bonding type rmsd covalent geometry : bond 0.00269 (22248) covalent geometry : angle 0.55244 (30136) hydrogen bonds : bond 0.03418 ( 952) hydrogen bonds : angle 4.83990 ( 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 288 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 251 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8409 (mm) REVERT: A 74 LEU cc_start: 0.8608 (mt) cc_final: 0.8170 (tt) REVERT: A 125 TYR cc_start: 0.6637 (m-80) cc_final: 0.6348 (t80) REVERT: A 279 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7906 (m-30) REVERT: A 314 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8181 (mm-40) REVERT: C 80 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8382 (mtm) REVERT: D 211 TYR cc_start: 0.7754 (t80) cc_final: 0.7204 (t80) REVERT: D 224 MET cc_start: 0.7499 (OUTLIER) cc_final: 0.6957 (mtt) REVERT: E 104 MET cc_start: 0.5816 (ttt) cc_final: 0.5025 (mtp) REVERT: E 195 ARG cc_start: 0.8019 (ttp80) cc_final: 0.7799 (ttt-90) REVERT: E 211 TYR cc_start: 0.7713 (t80) cc_final: 0.7270 (t80) REVERT: E 224 MET cc_start: 0.7650 (OUTLIER) cc_final: 0.7155 (mtt) REVERT: F 104 MET cc_start: 0.7094 (ttp) cc_final: 0.6889 (ttt) REVERT: G 53 TYR cc_start: 0.4654 (t80) cc_final: 0.4090 (m-80) REVERT: G 74 LEU cc_start: 0.7372 (mt) cc_final: 0.7028 (mt) REVERT: G 169 PHE cc_start: 0.6516 (m-80) cc_final: 0.5943 (t80) REVERT: G 203 ILE cc_start: 0.7976 (pt) cc_final: 0.7370 (mt) REVERT: G 312 TRP cc_start: 0.7253 (m100) cc_final: 0.6946 (m100) REVERT: G 346 ASP cc_start: 0.5850 (m-30) cc_final: 0.5439 (m-30) REVERT: H 74 LEU cc_start: 0.8607 (mt) cc_final: 0.8130 (tt) REVERT: H 104 MET cc_start: 0.6518 (ttt) cc_final: 0.6211 (tmm) REVERT: H 279 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7958 (m-30) REVERT: H 314 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.8144 (mm-40) outliers start: 37 outliers final: 22 residues processed: 275 average time/residue: 0.1353 time to fit residues: 59.9906 Evaluate side-chains 254 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 224 time to evaluate : 0.739 ------------------------------------------------------------------------------- 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 A residue 358 GLN Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain D residue 224 MET 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 154 GLU Chi-restraints excluded: chain E residue 224 MET Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 363 SER Chi-restraints excluded: chain G residue 79 SER 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 160 ILE 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: 2.9990 chunk 25 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 201 optimal weight: 6.9990 chunk 223 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 8.9990 chunk 205 optimal weight: 9.9990 chunk 231 optimal weight: 20.0000 chunk 105 optimal weight: 0.9980 overall best weight: 2.9986 ------------------------------------------------------------------------------- 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 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 = 0.3955 r_free = 0.3955 target = 0.146936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.111694 restraints weight = 35462.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.109530 restraints weight = 29068.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.110995 restraints weight = 29110.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.111428 restraints weight = 19927.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.111739 restraints weight = 18368.588| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.4690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 22248 Z= 0.276 Angle : 0.685 14.036 30136 Z= 0.365 Chirality : 0.049 0.167 3336 Planarity : 0.004 0.038 3768 Dihedral : 5.973 56.952 2920 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.35 % Allowed : 15.44 % Favored : 82.21 % 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: 0.05 (0.17), residues: 2624 helix: -0.23 (0.20), residues: 656 sheet: 0.27 (0.20), residues: 720 loop : 0.24 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 369 TYR 0.016 0.002 TYR D 53 PHE 0.024 0.002 PHE A 60 TRP 0.031 0.002 TRP G 216 HIS 0.007 0.001 HIS G 311 Details of bonding type rmsd covalent geometry : bond 0.00650 (22248) covalent geometry : angle 0.68524 (30136) hydrogen bonds : bond 0.04393 ( 952) hydrogen bonds : angle 5.30559 ( 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 297 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 241 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LEU cc_start: 0.8704 (mt) cc_final: 0.8281 (tt) REVERT: A 173 MET cc_start: 0.7825 (mtt) cc_final: 0.7574 (mtt) REVERT: A 314 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8163 (mm-40) REVERT: B 285 VAL cc_start: 0.8267 (t) cc_final: 0.8038 (t) REVERT: B 346 ASP cc_start: 0.6387 (m-30) cc_final: 0.5920 (t0) REVERT: D 60 PHE cc_start: 0.7883 (OUTLIER) cc_final: 0.7533 (p90) REVERT: D 211 TYR cc_start: 0.7710 (t80) cc_final: 0.7129 (t80) REVERT: D 224 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.7316 (mtt) REVERT: D 314 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.7598 (mp10) REVERT: E 104 MET cc_start: 0.6326 (ttt) cc_final: 0.5907 (mtp) REVERT: E 211 TYR cc_start: 0.7696 (t80) cc_final: 0.7170 (t80) REVERT: E 224 MET cc_start: 0.7890 (OUTLIER) cc_final: 0.7203 (mtt) REVERT: E 238 ASP cc_start: 0.7420 (t0) cc_final: 0.7079 (t0) REVERT: E 314 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.7602 (mp10) REVERT: F 104 MET cc_start: 0.7478 (ttp) cc_final: 0.7141 (ttt) REVERT: G 53 TYR cc_start: 0.4630 (t80) cc_final: 0.4213 (m-10) REVERT: G 74 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.6821 (mt) REVERT: G 280 TYR cc_start: 0.6403 (m-80) cc_final: 0.6111 (m-80) REVERT: H 74 LEU cc_start: 0.8698 (mt) cc_final: 0.8214 (tt) REVERT: H 104 MET cc_start: 0.6490 (ttt) cc_final: 0.6158 (tmm) REVERT: H 222 PHE cc_start: 0.8209 (OUTLIER) cc_final: 0.7511 (p90) REVERT: H 314 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.8118 (mm-40) outliers start: 56 outliers final: 39 residues processed: 277 average time/residue: 0.1310 time to fit residues: 58.4032 Evaluate side-chains 265 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 217 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 160 ILE 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 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 295 CYS Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain D residue 60 PHE Chi-restraints excluded: chain D residue 224 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 346 ASP Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain E residue 154 GLU 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 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 74 LEU Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 228 LYS Chi-restraints excluded: chain G residue 271 PHE Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain G residue 364 CYS Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 161 SER Chi-restraints excluded: chain H residue 222 PHE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 63 optimal weight: 9.9990 chunk 207 optimal weight: 0.9980 chunk 216 optimal weight: 10.0000 chunk 72 optimal weight: 0.5980 chunk 34 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 218 optimal weight: 7.9990 chunk 4 optimal weight: 0.9980 chunk 196 optimal weight: 0.7980 chunk 170 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4021 r_free = 0.4021 target = 0.152510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.117161 restraints weight = 34976.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.114788 restraints weight = 28321.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.116182 restraints weight = 26946.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.116558 restraints weight = 19548.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.116714 restraints weight = 18757.091| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.4881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22248 Z= 0.122 Angle : 0.571 13.147 30136 Z= 0.305 Chirality : 0.044 0.160 3336 Planarity : 0.003 0.039 3768 Dihedral : 5.551 55.755 2920 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.89 % Allowed : 16.69 % Favored : 81.42 % 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: 0.04 (0.17), residues: 2624 helix: -0.15 (0.20), residues: 696 sheet: 0.35 (0.20), residues: 696 loop : 0.13 (0.18), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 371 TYR 0.030 0.001 TYR B 53 PHE 0.028 0.001 PHE A 60 TRP 0.041 0.002 TRP G 312 HIS 0.004 0.001 HIS G 311 Details of bonding type rmsd covalent geometry : bond 0.00275 (22248) covalent geometry : angle 0.57057 (30136) hydrogen bonds : bond 0.03502 ( 952) hydrogen bonds : angle 4.96152 ( 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 281 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 236 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.0795 (ppp) cc_final: 0.0551 (ppp) REVERT: A 74 LEU cc_start: 0.8616 (mt) cc_final: 0.8139 (tt) REVERT: A 279 ASP cc_start: 0.8155 (OUTLIER) cc_final: 0.7921 (m-30) REVERT: A 314 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8187 (mm-40) REVERT: B 149 VAL cc_start: 0.8633 (OUTLIER) cc_final: 0.8337 (m) REVERT: B 235 PRO cc_start: 0.6044 (Cg_exo) cc_final: 0.5838 (Cg_endo) REVERT: B 285 VAL cc_start: 0.8146 (t) cc_final: 0.7872 (t) REVERT: B 346 ASP cc_start: 0.6402 (m-30) cc_final: 0.5879 (t0) REVERT: C 224 MET cc_start: 0.8356 (mtt) cc_final: 0.7916 (mtt) REVERT: D 211 TYR cc_start: 0.7665 (t80) cc_final: 0.7158 (t80) REVERT: D 224 MET cc_start: 0.7437 (OUTLIER) cc_final: 0.7026 (mtt) REVERT: D 314 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.7326 (mp10) REVERT: E 104 MET cc_start: 0.6148 (ttt) cc_final: 0.5808 (mtp) REVERT: E 211 TYR cc_start: 0.7679 (t80) cc_final: 0.7201 (t80) REVERT: E 224 MET cc_start: 0.7649 (OUTLIER) cc_final: 0.6753 (mtt) REVERT: E 314 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.7353 (mp10) REVERT: F 224 MET cc_start: 0.8348 (mtt) cc_final: 0.8030 (mtt) REVERT: F 314 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.7506 (mp10) REVERT: G 53 TYR cc_start: 0.4337 (t80) cc_final: 0.4003 (m-10) REVERT: G 70 GLU cc_start: 0.7489 (tp30) cc_final: 0.6971 (tp30) REVERT: H 74 LEU cc_start: 0.8615 (mt) cc_final: 0.8116 (tt) REVERT: H 104 MET cc_start: 0.6338 (ttt) cc_final: 0.6110 (tmm) REVERT: H 314 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.8136 (mm-40) outliers start: 45 outliers final: 22 residues processed: 266 average time/residue: 0.1211 time to fit residues: 52.4750 Evaluate side-chains 246 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 215 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 160 ILE 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 114 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 295 CYS Chi-restraints excluded: chain D residue 224 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 224 MET 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 79 SER Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 364 CYS Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain H residue 160 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 216 optimal weight: 6.9990 chunk 148 optimal weight: 7.9990 chunk 210 optimal weight: 2.9990 chunk 175 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 233 optimal weight: 5.9990 chunk 250 optimal weight: 0.0030 chunk 201 optimal weight: 0.9980 chunk 127 optimal weight: 0.5980 chunk 121 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- 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 207 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.153507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.117935 restraints weight = 34982.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.115816 restraints weight = 28368.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.117249 restraints weight = 26226.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.117557 restraints weight = 19201.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.117934 restraints weight = 18538.792| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.5046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22248 Z= 0.114 Angle : 0.567 13.513 30136 Z= 0.300 Chirality : 0.044 0.158 3336 Planarity : 0.003 0.041 3768 Dihedral : 5.407 59.506 2920 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.01 % Allowed : 16.40 % Favored : 81.59 % 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: 0.19 (0.17), residues: 2624 helix: -0.09 (0.20), residues: 696 sheet: 0.45 (0.20), residues: 712 loop : 0.25 (0.19), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 195 TYR 0.017 0.001 TYR B 53 PHE 0.026 0.001 PHE A 60 TRP 0.025 0.002 TRP G 184 HIS 0.002 0.001 HIS G 63 Details of bonding type rmsd covalent geometry : bond 0.00255 (22248) covalent geometry : angle 0.56661 (30136) hydrogen bonds : bond 0.03400 ( 952) hydrogen bonds : angle 4.86417 ( 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 277 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 229 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LEU cc_start: 0.8574 (mt) cc_final: 0.8075 (tt) REVERT: A 279 ASP cc_start: 0.8130 (OUTLIER) cc_final: 0.7888 (m-30) REVERT: A 314 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.8150 (mm-40) REVERT: B 149 VAL cc_start: 0.8666 (OUTLIER) cc_final: 0.8396 (m) REVERT: B 285 VAL cc_start: 0.8255 (t) cc_final: 0.8013 (t) REVERT: B 346 ASP cc_start: 0.6298 (m-30) cc_final: 0.5775 (t0) REVERT: C 104 MET cc_start: 0.7054 (tmm) cc_final: 0.6815 (tmm) REVERT: C 314 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.7585 (mp10) REVERT: D 211 TYR cc_start: 0.7768 (t80) cc_final: 0.7203 (t80) REVERT: D 224 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.7161 (mtt) REVERT: D 314 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.7345 (mp10) REVERT: E 211 TYR cc_start: 0.7656 (t80) cc_final: 0.7184 (t80) REVERT: E 224 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.6857 (mtt) REVERT: E 314 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.7341 (mp10) REVERT: F 224 MET cc_start: 0.8328 (mtt) cc_final: 0.8026 (mtt) REVERT: F 314 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7600 (mp10) REVERT: G 53 TYR cc_start: 0.4190 (t80) cc_final: 0.3948 (m-10) REVERT: G 169 PHE cc_start: 0.6261 (OUTLIER) cc_final: 0.6056 (m-80) REVERT: G 371 ARG cc_start: 0.6256 (ptp90) cc_final: 0.5838 (ptp90) REVERT: H 66 MET cc_start: 0.7017 (mpp) cc_final: 0.6785 (mpt) REVERT: H 74 LEU cc_start: 0.8548 (mt) cc_final: 0.8015 (tt) REVERT: H 104 MET cc_start: 0.6301 (ttt) cc_final: 0.6060 (tmm) REVERT: H 222 PHE cc_start: 0.8025 (OUTLIER) cc_final: 0.7345 (p90) REVERT: H 314 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.8129 (mm-40) outliers start: 48 outliers final: 25 residues processed: 259 average time/residue: 0.1104 time to fit residues: 47.0480 Evaluate side-chains 254 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 217 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 160 ILE 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 74 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 295 CYS Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain D residue 224 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 224 MET 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 74 LEU Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 169 PHE Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain G residue 364 CYS Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain H residue 160 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 199 optimal weight: 7.9990 chunk 78 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 195 optimal weight: 4.9990 chunk 241 optimal weight: 7.9990 chunk 152 optimal weight: 0.0980 chunk 146 optimal weight: 1.9990 chunk 180 optimal weight: 0.6980 chunk 184 optimal weight: 0.5980 chunk 21 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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** ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 207 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.153223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.117751 restraints weight = 34861.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.115766 restraints weight = 28653.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.117122 restraints weight = 27371.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.117485 restraints weight = 19661.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.117623 restraints weight = 19080.336| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.5168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22248 Z= 0.117 Angle : 0.557 10.003 30136 Z= 0.296 Chirality : 0.044 0.161 3336 Planarity : 0.003 0.044 3768 Dihedral : 5.366 59.857 2920 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.80 % Allowed : 16.69 % Favored : 81.50 % 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: 0.25 (0.17), residues: 2624 helix: -0.03 (0.20), residues: 696 sheet: 0.48 (0.20), residues: 712 loop : 0.29 (0.19), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 195 TYR 0.015 0.001 TYR B 53 PHE 0.026 0.001 PHE A 60 TRP 0.027 0.001 TRP A 184 HIS 0.005 0.001 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00266 (22248) covalent geometry : angle 0.55708 (30136) hydrogen bonds : bond 0.03412 ( 952) hydrogen bonds : angle 4.84503 ( 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 268 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 225 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LEU cc_start: 0.8512 (mt) cc_final: 0.7998 (tt) REVERT: A 279 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7891 (m-30) REVERT: A 314 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.8160 (mm-40) REVERT: B 53 TYR cc_start: 0.4105 (t80) cc_final: 0.3705 (m-80) REVERT: B 149 VAL cc_start: 0.8631 (OUTLIER) cc_final: 0.8344 (m) REVERT: B 285 VAL cc_start: 0.8259 (t) cc_final: 0.8034 (t) REVERT: B 346 ASP cc_start: 0.6276 (m-30) cc_final: 0.5784 (t0) REVERT: C 314 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7561 (mp10) REVERT: D 104 MET cc_start: 0.7167 (tmm) cc_final: 0.6123 (mtp) REVERT: D 211 TYR cc_start: 0.7695 (t80) cc_final: 0.7190 (t80) REVERT: D 224 MET cc_start: 0.7588 (OUTLIER) cc_final: 0.7188 (mtt) REVERT: D 238 ASP cc_start: 0.7717 (p0) cc_final: 0.7513 (p0) REVERT: D 314 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.7312 (mp10) REVERT: E 211 TYR cc_start: 0.7626 (t80) cc_final: 0.7313 (t80) REVERT: E 276 LYS cc_start: 0.7033 (mtmm) cc_final: 0.6635 (ptpp) REVERT: E 314 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.7411 (mp10) REVERT: F 224 MET cc_start: 0.8226 (mtt) cc_final: 0.7917 (mtt) REVERT: F 314 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7543 (mp10) REVERT: G 169 PHE cc_start: 0.6275 (OUTLIER) cc_final: 0.6061 (m-80) REVERT: G 371 ARG cc_start: 0.6180 (ptp90) cc_final: 0.5787 (ptp90) REVERT: H 66 MET cc_start: 0.7046 (mpp) cc_final: 0.6790 (mpt) REVERT: H 67 LEU cc_start: 0.8651 (mm) cc_final: 0.8440 (mm) REVERT: H 74 LEU cc_start: 0.8511 (mt) cc_final: 0.7970 (tt) REVERT: H 104 MET cc_start: 0.6363 (ttt) cc_final: 0.6090 (tmm) REVERT: H 222 PHE cc_start: 0.7875 (OUTLIER) cc_final: 0.7322 (p90) REVERT: H 314 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.8112 (mm-40) outliers start: 43 outliers final: 25 residues processed: 254 average time/residue: 0.1459 time to fit residues: 60.8242 Evaluate side-chains 249 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 213 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 160 ILE 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 74 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 295 CYS Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain D residue 224 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 81 PHE 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 74 LEU Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 169 PHE Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain G residue 364 CYS Chi-restraints excluded: chain H residue 87 PHE Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 222 PHE 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 13 optimal weight: 5.9990 chunk 224 optimal weight: 0.9990 chunk 243 optimal weight: 0.5980 chunk 172 optimal weight: 0.6980 chunk 166 optimal weight: 7.9990 chunk 239 optimal weight: 0.8980 chunk 132 optimal weight: 40.0000 chunk 130 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 181 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 133 ASN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 282 HIS ** 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 = 0.4041 r_free = 0.4041 target = 0.153944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.118183 restraints weight = 34981.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.116372 restraints weight = 28178.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.117666 restraints weight = 25690.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.118014 restraints weight = 18986.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.118195 restraints weight = 18205.330| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.5275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22248 Z= 0.111 Angle : 0.548 9.812 30136 Z= 0.291 Chirality : 0.044 0.156 3336 Planarity : 0.003 0.043 3768 Dihedral : 5.307 59.941 2920 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.59 % Allowed : 17.07 % Favored : 81.33 % 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: 0.31 (0.17), residues: 2624 helix: 0.02 (0.20), residues: 696 sheet: 0.53 (0.20), residues: 712 loop : 0.32 (0.19), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 195 TYR 0.021 0.001 TYR G 211 PHE 0.027 0.001 PHE A 60 TRP 0.024 0.001 TRP G 184 HIS 0.003 0.001 HIS B 63 Details of bonding type rmsd covalent geometry : bond 0.00247 (22248) covalent geometry : angle 0.54758 (30136) hydrogen bonds : bond 0.03344 ( 952) hydrogen bonds : angle 4.81896 ( 2496) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2890.68 seconds wall clock time: 51 minutes 19.43 seconds (3079.43 seconds total)