Starting phenix.real_space_refine on Wed Jun 18 22:44:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z7h_39814/06_2025/8z7h_39814.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z7h_39814/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8z7h_39814/06_2025/8z7h_39814.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z7h_39814/06_2025/8z7h_39814.map" model { file = "/net/cci-nas-00/data/ceres_data/8z7h_39814/06_2025/8z7h_39814.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z7h_39814/06_2025/8z7h_39814.cif" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 12.41, per 1000 atoms: 0.57 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: 4.77 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 2.88 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: 7.61 Time building geometry restraints manager: 5.80 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: 0.18 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' 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: 3.350 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: 0.790 Check model and map are aligned: 0.140 Set scattering table: 0.200 Process input model: 47.120 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.090 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.100 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.015 0.002 TRP A 184 HIS 0.005 0.001 HIS E 282 PHE 0.027 0.003 PHE C 317 TYR 0.024 0.002 TYR F 52 ARG 0.004 0.001 ARG D 195 Details of bonding type rmsd hydrogen bonds : bond 0.16512 ( 952) hydrogen bonds : angle 7.04047 ( 2496) covalent geometry : bond 0.00932 (22248) covalent geometry : angle 0.85529 (30136) *********************** 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 : 2.562 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: 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: 0.6244 (tmm) REVERT: A 143 LYS cc_start: 0.6221 (tttm) cc_final: 0.5492 (tttt) REVERT: A 159 ILE cc_start: 0.8202 (mt) cc_final: 0.7930 (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: 0.6274 (m-80) REVERT: B 114 VAL cc_start: 0.8113 (t) cc_final: 0.7860 (t) REVERT: B 139 VAL cc_start: 0.7994 (t) cc_final: 0.7455 (m) REVERT: B 169 PHE cc_start: 0.6905 (m-80) cc_final: 0.6450 (t80) REVERT: B 235 PRO cc_start: 0.6106 (Cg_exo) cc_final: 0.5703 (Cg_endo) REVERT: B 239 VAL cc_start: 0.8659 (t) cc_final: 0.8230 (p) REVERT: B 244 GLN cc_start: 0.8261 (mt0) cc_final: 0.6952 (mm110) REVERT: B 273 LEU cc_start: 0.8173 (mt) cc_final: 0.7530 (mt) REVERT: B 312 TRP cc_start: 0.7381 (m-90) cc_final: 0.7129 (m-10) REVERT: E 211 TYR cc_start: 0.7813 (t80) cc_final: 0.7446 (t80) REVERT: E 272 CYS cc_start: 0.6583 (t) cc_final: 0.6272 (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: 0.7806 (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: 0.6018 (t) REVERT: G 170 TYR cc_start: 0.6250 (t80) cc_final: 0.5864 (t80) REVERT: G 179 TYR cc_start: 0.6978 (t80) cc_final: 0.6693 (m-10) REVERT: G 273 LEU cc_start: 0.7242 (mt) cc_final: 0.6968 (mt) REVERT: G 343 ASN cc_start: 0.2764 (t0) cc_final: 0.2462 (m-40) REVERT: G 349 PHE cc_start: 0.5397 (m-10) cc_final: 0.4767 (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: 0.6743 (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: 0.7533 (mmmt) REVERT: H 143 LYS cc_start: 0.6228 (tttm) cc_final: 0.5792 (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: 0.8234 (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: 0.3834 time to fit residues: 281.8296 Evaluate side-chains 268 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 2.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 4.9990 chunk 200 optimal weight: 0.4980 chunk 111 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 206 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 154 optimal weight: 0.0980 chunk 239 optimal weight: 5.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 244 GLN ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.157586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.120370 restraints weight = 34849.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.119554 restraints weight = 26605.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.120659 restraints weight = 22867.374| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22248 Z= 0.128 Angle : 0.581 9.419 30136 Z= 0.316 Chirality : 0.046 0.167 3336 Planarity : 0.004 0.049 3768 Dihedral : 5.876 45.684 2920 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.30 % Allowed : 7.89 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.17), residues: 2624 helix: 0.02 (0.21), residues: 648 sheet: 0.22 (0.20), residues: 728 loop : 0.86 (0.19), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP G 312 HIS 0.014 0.001 HIS A 82 PHE 0.035 0.002 PHE A 105 TYR 0.023 0.002 TYR C 208 ARG 0.004 0.001 ARG G 371 Details of bonding type rmsd hydrogen bonds : bond 0.03821 ( 952) hydrogen bonds : angle 5.24974 ( 2496) covalent geometry : bond 0.00278 (22248) covalent geometry : angle 0.58058 (30136) *********************** 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 377 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 346 time to evaluate : 2.643 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: A 87 PHE cc_start: 0.7611 (m-80) cc_final: 0.7082 (m-80) REVERT: A 104 MET cc_start: 0.7149 (ttp) cc_final: 0.6793 (ttt) REVERT: A 143 LYS cc_start: 0.5773 (tttm) cc_final: 0.5031 (ttmt) REVERT: A 160 ILE cc_start: 0.8249 (mt) cc_final: 0.7974 (tt) REVERT: A 224 MET cc_start: 0.8394 (mmm) cc_final: 0.8146 (mmm) REVERT: B 47 MET cc_start: -0.0724 (ptt) cc_final: -0.0935 (ptt) REVERT: D 195 ARG cc_start: 0.7984 (ttp80) cc_final: 0.7743 (ttt-90) REVERT: D 211 TYR cc_start: 0.7792 (t80) cc_final: 0.7221 (t80) REVERT: E 211 TYR cc_start: 0.7727 (t80) cc_final: 0.7431 (t80) REVERT: F 151 LEU cc_start: 0.8051 (mt) cc_final: 0.7662 (tp) REVERT: F 224 MET cc_start: 0.8074 (mtt) cc_final: 0.7739 (mtt) REVERT: G 74 LEU cc_start: 0.7564 (mt) cc_final: 0.6933 (mt) REVERT: G 167 CYS cc_start: 0.6093 (t) cc_final: 0.5851 (t) REVERT: G 169 PHE cc_start: 0.6292 (m-80) cc_final: 0.5596 (t80) REVERT: G 173 MET cc_start: 0.4475 (tpp) cc_final: 0.3722 (tpp) REVERT: G 179 TYR cc_start: 0.6990 (t80) cc_final: 0.6659 (m-10) REVERT: G 203 ILE cc_start: 0.7995 (pt) cc_final: 0.7780 (mp) REVERT: G 273 LEU cc_start: 0.7464 (mt) cc_final: 0.7178 (mt) REVERT: G 346 ASP cc_start: 0.5975 (m-30) cc_final: 0.5718 (m-30) REVERT: G 370 MET cc_start: 0.6498 (mtp) cc_final: 0.5739 (mtp) REVERT: G 371 ARG cc_start: 0.6921 (OUTLIER) cc_final: 0.6552 (ptp90) REVERT: H 47 MET cc_start: 0.0526 (ptt) cc_final: -0.0599 (mmm) REVERT: H 53 TYR cc_start: 0.4252 (t80) cc_final: 0.3673 (m-80) REVERT: H 62 ILE cc_start: 0.8617 (tp) cc_final: 0.8412 (mt) REVERT: H 143 LYS cc_start: 0.5915 (tttm) cc_final: 0.5144 (tttt) REVERT: H 160 ILE cc_start: 0.8437 (mt) cc_final: 0.8144 (tt) REVERT: H 224 MET cc_start: 0.8350 (mmm) cc_final: 0.8131 (mmm) REVERT: H 279 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7800 (m-30) outliers start: 31 outliers final: 14 residues processed: 365 average time/residue: 0.3224 time to fit residues: 184.1527 Evaluate side-chains 267 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 251 time to evaluate : 2.433 ------------------------------------------------------------------------------- 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 370 MET 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 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 167 optimal weight: 3.9990 chunk 22 optimal weight: 8.9990 chunk 218 optimal weight: 9.9990 chunk 209 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 20 optimal weight: 0.0570 chunk 89 optimal weight: 0.8980 chunk 153 optimal weight: 0.0020 chunk 56 optimal weight: 0.9980 overall best weight: 0.9908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.153839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.117823 restraints weight = 34431.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.116404 restraints weight = 26741.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.117691 restraints weight = 24860.000| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22248 Z= 0.133 Angle : 0.553 8.583 30136 Z= 0.300 Chirality : 0.045 0.170 3336 Planarity : 0.004 0.037 3768 Dihedral : 5.776 58.212 2920 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.85 % Allowed : 11.87 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.17), residues: 2624 helix: 0.13 (0.21), residues: 656 sheet: 0.48 (0.20), residues: 736 loop : 0.68 (0.19), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP G 312 HIS 0.014 0.001 HIS A 82 PHE 0.020 0.002 PHE H 87 TYR 0.018 0.001 TYR B 211 ARG 0.003 0.000 ARG B 371 Details of bonding type rmsd hydrogen bonds : bond 0.03694 ( 952) hydrogen bonds : angle 5.05741 ( 2496) covalent geometry : bond 0.00304 (22248) covalent geometry : angle 0.55311 (30136) *********************** 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 336 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 292 time to evaluate : 2.557 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: A 74 LEU cc_start: 0.8693 (mt) cc_final: 0.8309 (tt) REVERT: A 105 PHE cc_start: 0.7164 (m-80) cc_final: 0.6698 (m-80) REVERT: A 160 ILE cc_start: 0.8355 (mt) cc_final: 0.8042 (tt) REVERT: A 279 ASP cc_start: 0.8136 (OUTLIER) cc_final: 0.7807 (m-30) REVERT: B 312 TRP cc_start: 0.7725 (m-90) cc_final: 0.7468 (m-10) REVERT: C 104 MET cc_start: 0.7145 (tmm) cc_final: 0.6394 (tmt) REVERT: C 151 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8487 (mt) REVERT: C 173 MET cc_start: 0.7211 (ttt) cc_final: 0.6895 (ttt) REVERT: D 149 VAL cc_start: 0.8533 (t) cc_final: 0.8290 (m) REVERT: D 195 ARG cc_start: 0.8058 (ttp80) cc_final: 0.7806 (ttt-90) REVERT: D 211 TYR cc_start: 0.7866 (t80) cc_final: 0.7318 (t80) REVERT: D 224 MET cc_start: 0.7552 (OUTLIER) cc_final: 0.7149 (mtt) REVERT: D 279 ASP cc_start: 0.7392 (t0) cc_final: 0.7159 (t0) REVERT: E 162 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7604 (tm-30) REVERT: E 211 TYR cc_start: 0.7715 (t80) cc_final: 0.7317 (t80) REVERT: E 224 MET cc_start: 0.7399 (mtp) cc_final: 0.6788 (mtt) REVERT: F 80 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8415 (mtm) REVERT: G 74 LEU cc_start: 0.7397 (mt) cc_final: 0.7094 (mt) REVERT: G 169 PHE cc_start: 0.6266 (m-80) cc_final: 0.5559 (t80) REVERT: G 179 TYR cc_start: 0.6931 (t80) cc_final: 0.6394 (m-10) REVERT: G 346 ASP cc_start: 0.5779 (m-30) cc_final: 0.5457 (m-30) REVERT: H 47 MET cc_start: 0.0442 (ptt) cc_final: -0.0947 (mmm) REVERT: H 53 TYR cc_start: 0.4202 (t80) cc_final: 0.3644 (m-80) REVERT: H 74 LEU cc_start: 0.8680 (mt) cc_final: 0.8227 (tt) REVERT: H 105 PHE cc_start: 0.7454 (m-80) cc_final: 0.6901 (m-80) REVERT: H 143 LYS cc_start: 0.5731 (tttm) cc_final: 0.5092 (tttt) REVERT: H 224 MET cc_start: 0.8301 (mmm) cc_final: 0.8016 (mpp) REVERT: H 279 ASP cc_start: 0.8169 (OUTLIER) cc_final: 0.7944 (m-30) outliers start: 44 outliers final: 26 residues processed: 319 average time/residue: 0.3090 time to fit residues: 158.2882 Evaluate side-chains 274 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 243 time to evaluate : 2.291 ------------------------------------------------------------------------------- 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 103 CYS Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 224 MET Chi-restraints excluded: chain D residue 226 CYS Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain E residue 226 CYS Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain G residue 351 ILE Chi-restraints excluded: chain G residue 364 CYS Chi-restraints excluded: chain G residue 371 ARG Chi-restraints excluded: chain H residue 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 225 optimal weight: 0.0470 chunk 175 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 207 optimal weight: 7.9990 chunk 257 optimal weight: 0.2980 chunk 24 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 196 optimal weight: 4.9990 chunk 253 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 209 optimal weight: 8.9990 overall best weight: 1.6684 ------------------------------------------------------------------------------- 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** D 274 GLN G 59 HIS ** G 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.150739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.115250 restraints weight = 35129.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.112095 restraints weight = 29107.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.113660 restraints weight = 27434.095| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 22248 Z= 0.174 Angle : 0.573 9.742 30136 Z= 0.309 Chirality : 0.045 0.161 3336 Planarity : 0.004 0.037 3768 Dihedral : 5.762 57.185 2920 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.22 % Allowed : 13.38 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.17), residues: 2624 helix: 0.08 (0.21), residues: 656 sheet: 0.48 (0.21), residues: 680 loop : 0.53 (0.18), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP G 312 HIS 0.004 0.001 HIS F 282 PHE 0.028 0.002 PHE H 60 TYR 0.023 0.002 TYR G 53 ARG 0.003 0.000 ARG G 371 Details of bonding type rmsd hydrogen bonds : bond 0.03822 ( 952) hydrogen bonds : angle 5.06487 ( 2496) covalent geometry : bond 0.00403 (22248) covalent geometry : angle 0.57330 (30136) *********************** 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 323 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 270 time to evaluate : 2.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LEU cc_start: 0.8668 (mt) cc_final: 0.8237 (tt) REVERT: A 160 ILE cc_start: 0.8561 (mt) cc_final: 0.8264 (tt) REVERT: A 279 ASP cc_start: 0.8141 (OUTLIER) cc_final: 0.7829 (m-30) REVERT: B 371 ARG cc_start: 0.6612 (ttp-110) cc_final: 0.5586 (ptt-90) REVERT: D 211 TYR cc_start: 0.7790 (t80) cc_final: 0.7225 (t80) REVERT: D 224 MET cc_start: 0.7601 (mtp) cc_final: 0.7173 (mtt) REVERT: E 211 TYR cc_start: 0.7771 (t80) cc_final: 0.7284 (t80) REVERT: E 224 MET cc_start: 0.7682 (OUTLIER) cc_final: 0.6741 (mtt) REVERT: F 151 LEU cc_start: 0.8339 (mt) cc_final: 0.8118 (tp) REVERT: F 224 MET cc_start: 0.8475 (mtt) cc_final: 0.8174 (mtt) REVERT: G 74 LEU cc_start: 0.7284 (mt) cc_final: 0.7018 (mt) REVERT: G 169 PHE cc_start: 0.6558 (m-80) cc_final: 0.5920 (t80) REVERT: G 179 TYR cc_start: 0.6752 (t80) cc_final: 0.6169 (m-10) REVERT: G 346 ASP cc_start: 0.5802 (m-30) cc_final: 0.5477 (m-30) REVERT: H 47 MET cc_start: 0.0689 (ptt) cc_final: -0.0734 (mmm) REVERT: H 53 TYR cc_start: 0.4169 (t80) cc_final: 0.3508 (m-80) REVERT: H 74 LEU cc_start: 0.8683 (mt) cc_final: 0.8221 (tt) REVERT: H 105 PHE cc_start: 0.7451 (m-80) cc_final: 0.6674 (m-80) REVERT: H 143 LYS cc_start: 0.5832 (tttm) cc_final: 0.5220 (tttt) REVERT: H 224 MET cc_start: 0.8387 (mmm) cc_final: 0.8118 (mmm) REVERT: H 279 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7934 (m-30) outliers start: 53 outliers final: 32 residues processed: 305 average time/residue: 0.2973 time to fit residues: 147.3227 Evaluate side-chains 269 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 234 time to evaluate : 2.472 ------------------------------------------------------------------------------- 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 60 PHE Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 295 CYS Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 226 CYS Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 274 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 334 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain G residue 351 ILE Chi-restraints excluded: chain G residue 364 CYS Chi-restraints excluded: chain H residue 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 244 optimal weight: 7.9990 chunk 160 optimal weight: 6.9990 chunk 207 optimal weight: 6.9990 chunk 254 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 201 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 chunk 248 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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** B 340 ASN ** 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 = 0.3977 r_free = 0.3977 target = 0.148723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.113316 restraints weight = 35226.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.111415 restraints weight = 29079.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.112776 restraints weight = 27157.135| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 22248 Z= 0.209 Angle : 0.622 12.952 30136 Z= 0.332 Chirality : 0.046 0.163 3336 Planarity : 0.004 0.037 3768 Dihedral : 5.862 58.535 2920 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.39 % Allowed : 14.85 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.17), residues: 2624 helix: -0.04 (0.21), residues: 648 sheet: 0.33 (0.21), residues: 680 loop : 0.29 (0.18), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP H 184 HIS 0.005 0.001 HIS C 282 PHE 0.029 0.002 PHE A 60 TYR 0.015 0.002 TYR D 53 ARG 0.003 0.001 ARG B 369 Details of bonding type rmsd hydrogen bonds : bond 0.04028 ( 952) hydrogen bonds : angle 5.13903 ( 2496) covalent geometry : bond 0.00492 (22248) covalent geometry : angle 0.62154 (30136) *********************** 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 306 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 249 time to evaluate : 2.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LEU cc_start: 0.8665 (mt) cc_final: 0.8263 (tt) REVERT: A 125 TYR cc_start: 0.6674 (m-80) cc_final: 0.6398 (t80) REVERT: A 160 ILE cc_start: 0.8656 (mt) cc_final: 0.8383 (tt) REVERT: A 279 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7872 (m-30) REVERT: A 314 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8132 (mp10) REVERT: A 319 MET cc_start: 0.7903 (mmm) cc_final: 0.7560 (mtt) REVERT: B 370 MET cc_start: 0.7318 (mtp) cc_final: 0.7025 (ttp) REVERT: B 371 ARG cc_start: 0.6621 (ttp-110) cc_final: 0.4741 (tpp-160) REVERT: C 224 MET cc_start: 0.8580 (mtt) cc_final: 0.8361 (mtt) REVERT: D 60 PHE cc_start: 0.7900 (OUTLIER) cc_final: 0.7636 (p90) REVERT: D 211 TYR cc_start: 0.7746 (t80) cc_final: 0.7205 (t80) REVERT: D 224 MET cc_start: 0.7692 (mtp) cc_final: 0.7226 (mtt) REVERT: D 314 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.7500 (mp10) REVERT: E 211 TYR cc_start: 0.7736 (t80) cc_final: 0.7215 (t80) REVERT: E 224 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7166 (mtt) REVERT: E 314 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.7527 (mp10) REVERT: F 151 LEU cc_start: 0.8545 (mt) cc_final: 0.8343 (tp) REVERT: G 74 LEU cc_start: 0.7283 (mt) cc_final: 0.7020 (mt) REVERT: G 169 PHE cc_start: 0.6748 (m-80) cc_final: 0.6435 (t80) REVERT: G 179 TYR cc_start: 0.6697 (t80) cc_final: 0.6222 (m-10) REVERT: H 53 TYR cc_start: 0.4008 (t80) cc_final: 0.3469 (m-80) REVERT: H 74 LEU cc_start: 0.8699 (mt) cc_final: 0.8243 (tt) REVERT: H 105 PHE cc_start: 0.7472 (m-80) cc_final: 0.6630 (m-80) REVERT: H 143 LYS cc_start: 0.5925 (tttm) cc_final: 0.5297 (tttt) REVERT: H 279 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7966 (m-30) REVERT: H 314 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.8102 (mp10) outliers start: 57 outliers final: 37 residues processed: 284 average time/residue: 0.3045 time to fit residues: 139.3439 Evaluate side-chains 266 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 221 time to evaluate : 2.318 ------------------------------------------------------------------------------- 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 285 VAL Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 295 CYS Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain D residue 60 PHE Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain E residue 81 PHE Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 224 MET Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain G residue 60 PHE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain G residue 351 ILE Chi-restraints excluded: chain G residue 364 CYS Chi-restraints excluded: chain H residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 44 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 156 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 150 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 164 optimal weight: 6.9990 chunk 180 optimal weight: 0.9980 chunk 262 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 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 = 0.3995 r_free = 0.3995 target = 0.150091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.114678 restraints weight = 35041.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.112193 restraints weight = 28712.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.113652 restraints weight = 26167.056| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22248 Z= 0.153 Angle : 0.575 10.906 30136 Z= 0.309 Chirality : 0.045 0.166 3336 Planarity : 0.004 0.037 3768 Dihedral : 5.689 58.177 2920 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.47 % Allowed : 15.60 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.17), residues: 2624 helix: -0.03 (0.21), residues: 656 sheet: 0.25 (0.20), residues: 736 loop : 0.34 (0.19), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 184 HIS 0.003 0.001 HIS G 282 PHE 0.035 0.002 PHE H 87 TYR 0.020 0.001 TYR B 211 ARG 0.002 0.000 ARG A 338 Details of bonding type rmsd hydrogen bonds : bond 0.03719 ( 952) hydrogen bonds : angle 5.01202 ( 2496) covalent geometry : bond 0.00357 (22248) covalent geometry : angle 0.57542 (30136) *********************** 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 304 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 245 time to evaluate : 2.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.0925 (ppp) cc_final: 0.0667 (ppp) REVERT: A 74 LEU cc_start: 0.8670 (mt) cc_final: 0.8233 (tt) REVERT: A 160 ILE cc_start: 0.8584 (mt) cc_final: 0.8381 (tt) REVERT: A 279 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7897 (m-30) REVERT: A 314 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8172 (mp10) REVERT: A 319 MET cc_start: 0.7827 (mmm) cc_final: 0.7498 (mtt) REVERT: D 211 TYR cc_start: 0.7726 (t80) cc_final: 0.7163 (t80) REVERT: D 224 MET cc_start: 0.7630 (OUTLIER) cc_final: 0.7178 (mtt) REVERT: D 314 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.7432 (mp10) REVERT: E 211 TYR cc_start: 0.7692 (t80) cc_final: 0.7091 (t80) REVERT: E 224 MET cc_start: 0.7716 (OUTLIER) cc_final: 0.7186 (mtt) REVERT: E 314 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.7463 (mp10) REVERT: F 80 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8363 (mtm) REVERT: F 151 LEU cc_start: 0.8471 (mt) cc_final: 0.8266 (tp) REVERT: G 70 GLU cc_start: 0.7565 (tp30) cc_final: 0.7361 (tp30) REVERT: G 74 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.6908 (mt) REVERT: G 169 PHE cc_start: 0.6784 (m-80) cc_final: 0.6339 (t80) REVERT: G 179 TYR cc_start: 0.6467 (t80) cc_final: 0.6072 (m-10) REVERT: H 53 TYR cc_start: 0.4119 (t80) cc_final: 0.3424 (m-80) REVERT: H 74 LEU cc_start: 0.8705 (mt) cc_final: 0.8234 (tt) REVERT: H 105 PHE cc_start: 0.7303 (m-80) cc_final: 0.6517 (m-80) REVERT: H 224 MET cc_start: 0.8192 (mmm) cc_final: 0.7864 (mpp) REVERT: H 314 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8144 (mp10) outliers start: 59 outliers final: 36 residues processed: 285 average time/residue: 0.3066 time to fit residues: 140.6819 Evaluate side-chains 262 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 217 time to evaluate : 2.344 ------------------------------------------------------------------------------- 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 285 VAL 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 79 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 295 CYS Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 149 VAL 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 325 VAL 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 226 CYS Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain G residue 351 ILE Chi-restraints excluded: chain G residue 364 CYS Chi-restraints excluded: chain H residue 103 CYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 0.7980 chunk 107 optimal weight: 0.1980 chunk 109 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 259 optimal weight: 2.9990 chunk 255 optimal weight: 4.9990 chunk 215 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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** B 340 ASN C 244 GLN F 244 GLN ** G 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 HIS ** H 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.149453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.114016 restraints weight = 35100.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.111761 restraints weight = 29621.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.113275 restraints weight = 28653.459| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 22248 Z= 0.198 Angle : 0.610 10.119 30136 Z= 0.327 Chirality : 0.046 0.164 3336 Planarity : 0.004 0.040 3768 Dihedral : 5.816 56.677 2920 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.81 % Allowed : 16.02 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.17), residues: 2624 helix: -0.14 (0.20), residues: 656 sheet: 0.28 (0.21), residues: 680 loop : 0.23 (0.18), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 184 HIS 0.005 0.001 HIS G 311 PHE 0.027 0.002 PHE A 60 TYR 0.019 0.002 TYR B 53 ARG 0.008 0.000 ARG B 371 Details of bonding type rmsd hydrogen bonds : bond 0.03958 ( 952) hydrogen bonds : angle 5.12316 ( 2496) covalent geometry : bond 0.00466 (22248) covalent geometry : angle 0.60961 (30136) *********************** 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 296 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 229 time to evaluate : 2.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LEU cc_start: 0.8673 (mt) cc_final: 0.8212 (tt) REVERT: A 82 HIS cc_start: 0.7508 (OUTLIER) cc_final: 0.6922 (m170) REVERT: A 279 ASP cc_start: 0.8165 (OUTLIER) cc_final: 0.7864 (m-30) REVERT: A 314 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8160 (mp10) REVERT: A 319 MET cc_start: 0.7824 (mmm) cc_final: 0.7566 (mtt) REVERT: B 149 VAL cc_start: 0.8691 (OUTLIER) cc_final: 0.8352 (m) REVERT: B 371 ARG cc_start: 0.6336 (ttp-110) cc_final: 0.5995 (ttp-110) REVERT: D 60 PHE cc_start: 0.7832 (OUTLIER) cc_final: 0.7606 (p90) REVERT: D 211 TYR cc_start: 0.7685 (t80) cc_final: 0.7089 (t80) REVERT: D 224 MET cc_start: 0.7659 (OUTLIER) cc_final: 0.7195 (mtt) REVERT: D 314 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.7535 (mp10) REVERT: E 211 TYR cc_start: 0.7665 (t80) cc_final: 0.7080 (t80) REVERT: E 224 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.6960 (mtt) REVERT: E 238 ASP cc_start: 0.7296 (t0) cc_final: 0.6970 (t0) REVERT: E 314 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.7560 (mp10) REVERT: F 80 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8485 (mtm) REVERT: G 169 PHE cc_start: 0.6909 (m-80) cc_final: 0.6640 (t80) REVERT: G 179 TYR cc_start: 0.6532 (t80) cc_final: 0.6215 (m-10) REVERT: G 371 ARG cc_start: 0.6259 (ptp90) cc_final: 0.5741 (ptp90) REVERT: H 53 TYR cc_start: 0.4333 (t80) cc_final: 0.3424 (m-80) REVERT: H 74 LEU cc_start: 0.8707 (mt) cc_final: 0.8248 (tt) REVERT: H 105 PHE cc_start: 0.7239 (m-80) cc_final: 0.6434 (m-80) REVERT: H 224 MET cc_start: 0.8192 (mmm) cc_final: 0.7820 (mpp) REVERT: H 314 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.8119 (mp10) REVERT: H 319 MET cc_start: 0.7853 (mmm) cc_final: 0.7561 (mtt) outliers start: 67 outliers final: 42 residues processed: 279 average time/residue: 0.3106 time to fit residues: 140.2606 Evaluate side-chains 263 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 210 time to evaluate : 2.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 HIS Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 285 VAL 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 B residue 60 PHE Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 295 CYS Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain D residue 60 PHE Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 149 VAL 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 325 VAL Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain E residue 140 THR 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 F residue 80 MET Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 188 ASP Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 151 LEU 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 80 MET Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 279 ASP Chi-restraints excluded: chain H residue 296 HIS Chi-restraints excluded: chain H residue 314 GLN Chi-restraints excluded: chain H residue 334 THR 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 25 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 184 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 143 optimal weight: 0.3980 chunk 145 optimal weight: 2.9990 chunk 256 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 168 optimal weight: 0.8980 chunk 1 optimal weight: 8.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 HIS ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 GLN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 133 ASN ** 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 = 0.4016 r_free = 0.4016 target = 0.151941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.116285 restraints weight = 34901.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.114373 restraints weight = 27622.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.115637 restraints weight = 25537.802| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 22248 Z= 0.127 Angle : 0.559 9.958 30136 Z= 0.301 Chirality : 0.044 0.165 3336 Planarity : 0.003 0.041 3768 Dihedral : 5.583 56.930 2920 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.43 % Allowed : 16.69 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.17), residues: 2624 helix: -0.16 (0.20), residues: 696 sheet: 0.25 (0.19), residues: 752 loop : 0.20 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 312 HIS 0.003 0.001 HIS G 63 PHE 0.025 0.001 PHE A 60 TYR 0.019 0.001 TYR B 211 ARG 0.002 0.000 ARG A 338 Details of bonding type rmsd hydrogen bonds : bond 0.03539 ( 952) hydrogen bonds : angle 4.97341 ( 2496) covalent geometry : bond 0.00291 (22248) covalent geometry : angle 0.55856 (30136) *********************** 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 293 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 235 time to evaluate : 2.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LEU cc_start: 0.8620 (mt) cc_final: 0.8132 (tt) REVERT: A 82 HIS cc_start: 0.7597 (OUTLIER) cc_final: 0.7051 (m170) REVERT: A 279 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7916 (m-30) REVERT: A 319 MET cc_start: 0.7765 (mmm) cc_final: 0.7195 (mtt) REVERT: B 103 CYS cc_start: 0.7037 (OUTLIER) cc_final: 0.6689 (m) REVERT: B 149 VAL cc_start: 0.8612 (OUTLIER) cc_final: 0.8303 (m) REVERT: C 104 MET cc_start: 0.7697 (tmm) cc_final: 0.7401 (tmm) REVERT: D 95 VAL cc_start: 0.9160 (OUTLIER) cc_final: 0.8944 (m) REVERT: D 211 TYR cc_start: 0.7661 (t80) cc_final: 0.7110 (t80) REVERT: D 224 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.7020 (mtt) REVERT: D 314 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.7322 (mp10) REVERT: E 211 TYR cc_start: 0.7663 (t80) cc_final: 0.7129 (t80) REVERT: E 224 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.6703 (mtt) REVERT: E 314 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.7415 (mp10) REVERT: F 224 MET cc_start: 0.8373 (mtt) cc_final: 0.8029 (mtt) REVERT: G 169 PHE cc_start: 0.6908 (m-80) cc_final: 0.6611 (t80) REVERT: G 179 TYR cc_start: 0.6341 (t80) cc_final: 0.5916 (m-10) REVERT: G 246 VAL cc_start: 0.7700 (t) cc_final: 0.7446 (t) REVERT: G 371 ARG cc_start: 0.6329 (ptp90) cc_final: 0.5784 (ptp90) REVERT: H 53 TYR cc_start: 0.4187 (t80) cc_final: 0.3380 (m-80) REVERT: H 74 LEU cc_start: 0.8694 (mt) cc_final: 0.8194 (tt) REVERT: H 224 MET cc_start: 0.8059 (mmm) cc_final: 0.7850 (mmm) REVERT: H 314 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8157 (mp10) outliers start: 58 outliers final: 34 residues processed: 273 average time/residue: 0.3075 time to fit residues: 134.2648 Evaluate side-chains 256 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 212 time to evaluate : 2.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 82 HIS 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 285 VAL Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 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 207 GLN Chi-restraints excluded: chain B residue 295 CYS Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 224 MET Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 325 VAL 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 224 MET Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain G residue 53 TYR Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 351 ILE Chi-restraints excluded: chain G residue 364 CYS Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 296 HIS Chi-restraints excluded: chain H residue 314 GLN Chi-restraints excluded: chain H residue 334 THR 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 187 optimal weight: 4.9990 chunk 225 optimal weight: 7.9990 chunk 221 optimal weight: 7.9990 chunk 129 optimal weight: 6.9990 chunk 168 optimal weight: 1.9990 chunk 249 optimal weight: 0.8980 chunk 250 optimal weight: 0.0070 chunk 52 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 261 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 HIS ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 GLN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.152257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.116471 restraints weight = 34986.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.114182 restraints weight = 28527.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.115547 restraints weight = 26957.541| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22248 Z= 0.167 Angle : 0.591 9.760 30136 Z= 0.317 Chirality : 0.045 0.164 3336 Planarity : 0.004 0.064 3768 Dihedral : 5.652 57.861 2920 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.27 % Allowed : 16.74 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.17), residues: 2624 helix: -0.19 (0.20), residues: 696 sheet: 0.18 (0.19), residues: 752 loop : 0.16 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 184 HIS 0.004 0.001 HIS G 63 PHE 0.037 0.002 PHE D 222 TYR 0.020 0.001 TYR E 179 ARG 0.003 0.000 ARG B 206 Details of bonding type rmsd hydrogen bonds : bond 0.03764 ( 952) hydrogen bonds : angle 5.06519 ( 2496) covalent geometry : bond 0.00389 (22248) covalent geometry : angle 0.59128 (30136) *********************** 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: 54 poor density : 223 time to evaluate : 2.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LEU cc_start: 0.8647 (mt) cc_final: 0.8156 (tt) REVERT: A 279 ASP cc_start: 0.8134 (OUTLIER) cc_final: 0.7839 (m-30) REVERT: B 103 CYS cc_start: 0.7061 (OUTLIER) cc_final: 0.6792 (m) REVERT: B 149 VAL cc_start: 0.8610 (OUTLIER) cc_final: 0.8329 (m) REVERT: B 244 GLN cc_start: 0.7829 (tp-100) cc_final: 0.7501 (tp-100) REVERT: B 371 ARG cc_start: 0.6214 (ttp-110) cc_final: 0.5997 (ttp-110) REVERT: D 211 TYR cc_start: 0.7653 (t80) cc_final: 0.7094 (t80) REVERT: D 224 MET cc_start: 0.7635 (OUTLIER) cc_final: 0.7123 (mtt) REVERT: D 314 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.7530 (mp10) REVERT: E 104 MET cc_start: 0.7065 (tmm) cc_final: 0.5898 (mtp) REVERT: E 211 TYR cc_start: 0.7637 (t80) cc_final: 0.7070 (t80) REVERT: E 224 MET cc_start: 0.7672 (OUTLIER) cc_final: 0.7140 (mtt) REVERT: E 314 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.7544 (mp10) REVERT: F 104 MET cc_start: 0.7031 (ttp) cc_final: 0.6781 (ttt) REVERT: G 70 GLU cc_start: 0.7535 (tp30) cc_final: 0.7155 (tp30) REVERT: G 179 TYR cc_start: 0.6293 (t80) cc_final: 0.5967 (m-10) REVERT: G 371 ARG cc_start: 0.6284 (ptp90) cc_final: 0.5682 (ptp90) REVERT: H 53 TYR cc_start: 0.4252 (t80) cc_final: 0.3416 (m-80) REVERT: H 74 LEU cc_start: 0.8692 (mt) cc_final: 0.8210 (tt) REVERT: H 143 LYS cc_start: 0.5976 (tttm) cc_final: 0.5297 (tttt) REVERT: H 224 MET cc_start: 0.8128 (mmm) cc_final: 0.7811 (mpp) REVERT: H 319 MET cc_start: 0.7806 (mmm) cc_final: 0.7552 (mtt) outliers start: 54 outliers final: 39 residues processed: 260 average time/residue: 0.2946 time to fit residues: 124.9781 Evaluate side-chains 254 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 208 time to evaluate : 2.597 ------------------------------------------------------------------------------- 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 285 VAL Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 295 CYS Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain D residue 95 VAL 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 325 VAL 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 226 CYS Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain G residue 53 TYR Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 158 ILE Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 351 ILE Chi-restraints excluded: chain G residue 364 CYS Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 279 ASP Chi-restraints excluded: chain H residue 296 HIS Chi-restraints excluded: chain H residue 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 74 optimal weight: 0.6980 chunk 67 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 262 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 223 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 225 optimal weight: 7.9990 chunk 196 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 HIS ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 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 = 0.4041 r_free = 0.4041 target = 0.153989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.118092 restraints weight = 35151.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.116496 restraints weight = 28870.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.117787 restraints weight = 25786.053| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.5130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22248 Z= 0.125 Angle : 0.568 9.765 30136 Z= 0.303 Chirality : 0.044 0.203 3336 Planarity : 0.004 0.057 3768 Dihedral : 5.530 58.984 2920 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.14 % Allowed : 17.20 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.17), residues: 2624 helix: -0.07 (0.20), residues: 696 sheet: 0.35 (0.20), residues: 704 loop : 0.15 (0.19), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 184 HIS 0.004 0.001 HIS G 63 PHE 0.036 0.001 PHE D 222 TYR 0.020 0.001 TYR E 179 ARG 0.003 0.000 ARG A 338 Details of bonding type rmsd hydrogen bonds : bond 0.03534 ( 952) hydrogen bonds : angle 4.97575 ( 2496) covalent geometry : bond 0.00282 (22248) covalent geometry : angle 0.56788 (30136) ********************** 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 279 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 228 time to evaluate : 2.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LEU cc_start: 0.8550 (mt) cc_final: 0.8075 (tt) REVERT: A 279 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7893 (m-30) REVERT: B 103 CYS cc_start: 0.6947 (OUTLIER) cc_final: 0.6719 (m) REVERT: B 149 VAL cc_start: 0.8623 (OUTLIER) cc_final: 0.8362 (m) REVERT: B 244 GLN cc_start: 0.7895 (tp-100) cc_final: 0.7659 (tp-100) REVERT: B 371 ARG cc_start: 0.6226 (ttp-110) cc_final: 0.5976 (ttp-110) REVERT: D 211 TYR cc_start: 0.7676 (t80) cc_final: 0.7154 (t80) REVERT: D 224 MET cc_start: 0.7505 (OUTLIER) cc_final: 0.6997 (mtt) REVERT: D 314 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.7370 (mp10) REVERT: E 104 MET cc_start: 0.6808 (tmm) cc_final: 0.6025 (mtm) REVERT: E 211 TYR cc_start: 0.7603 (t80) cc_final: 0.7120 (t80) REVERT: E 224 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.6748 (mtt) REVERT: E 276 LYS cc_start: 0.7195 (mtmm) cc_final: 0.6711 (ptpp) REVERT: E 314 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.7436 (mp10) REVERT: G 179 TYR cc_start: 0.6186 (t80) cc_final: 0.5889 (m-10) REVERT: G 292 PHE cc_start: 0.5308 (OUTLIER) cc_final: 0.4217 (m-80) REVERT: G 371 ARG cc_start: 0.6314 (ptp90) cc_final: 0.5700 (ptp90) REVERT: H 53 TYR cc_start: 0.4263 (t80) cc_final: 0.3476 (m-80) REVERT: H 74 LEU cc_start: 0.8622 (mt) cc_final: 0.8131 (tt) REVERT: H 143 LYS cc_start: 0.5941 (tttm) cc_final: 0.5263 (tttt) REVERT: H 224 MET cc_start: 0.8036 (mmm) cc_final: 0.7764 (mpp) REVERT: H 314 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.8145 (mp10) REVERT: H 319 MET cc_start: 0.7724 (mmm) cc_final: 0.7415 (mtt) outliers start: 51 outliers final: 37 residues processed: 264 average time/residue: 0.3106 time to fit residues: 133.5537 Evaluate side-chains 258 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 212 time to evaluate : 2.432 ------------------------------------------------------------------------------- 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 285 VAL Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 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 B residue 337 MET Chi-restraints excluded: chain C residue 366 THR 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 325 VAL 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 226 CYS Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain G residue 53 TYR Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 292 PHE Chi-restraints excluded: chain G residue 351 ILE Chi-restraints excluded: chain G residue 364 CYS Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 296 HIS Chi-restraints excluded: chain H residue 314 GLN Chi-restraints excluded: chain H residue 334 THR 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 178 optimal weight: 4.9990 chunk 200 optimal weight: 3.9990 chunk 262 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 156 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 197 optimal weight: 0.9990 chunk 202 optimal weight: 6.9990 chunk 251 optimal weight: 1.9990 chunk 192 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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** F 59 HIS G 207 GLN 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 = 0.4038 r_free = 0.4038 target = 0.153736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.117810 restraints weight = 34973.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.116428 restraints weight = 27992.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.117605 restraints weight = 26207.966| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.5210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22248 Z= 0.137 Angle : 0.578 9.973 30136 Z= 0.307 Chirality : 0.044 0.167 3336 Planarity : 0.004 0.054 3768 Dihedral : 5.529 59.456 2920 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.35 % Allowed : 16.99 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.17), residues: 2624 helix: -0.06 (0.20), residues: 696 sheet: 0.33 (0.20), residues: 704 loop : 0.15 (0.19), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 184 HIS 0.004 0.001 HIS G 63 PHE 0.036 0.001 PHE D 222 TYR 0.020 0.001 TYR B 211 ARG 0.002 0.000 ARG A 338 Details of bonding type rmsd hydrogen bonds : bond 0.03556 ( 952) hydrogen bonds : angle 4.99675 ( 2496) covalent geometry : bond 0.00315 (22248) covalent geometry : angle 0.57824 (30136) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6063.34 seconds wall clock time: 106 minutes 55.67 seconds (6415.67 seconds total)