Starting phenix.real_space_refine on Wed May 21 18:09:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z7h_39814/05_2025/8z7h_39814.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z7h_39814/05_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_39814/05_2025/8z7h_39814.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z7h_39814/05_2025/8z7h_39814.map" model { file = "/net/cci-nas-00/data/ceres_data/8z7h_39814/05_2025/8z7h_39814.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z7h_39814/05_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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 12.90, per 1000 atoms: 0.59 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: 5.77 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: 3.35 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: 7.75 Time building geometry restraints manager: 6.69 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: 0.19 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: 3.570 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: 0.750 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 50.340 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.600 ------------------------------------------------------------------------------- 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 : 2.437 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: 0.3688 time to fit residues: 269.3375 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 : 2.456 ------------------------------------------------------------------------------- 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 = 0.157610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.120371 restraints weight = 34844.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.119579 restraints weight = 26531.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.120680 restraints weight = 22803.373| |-----------------------------------------------------------------------------| 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 45.685 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 5.24975 ( 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 : 2.488 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: 0.7612 (m-80) cc_final: 0.7084 (m-80) REVERT: A 104 MET cc_start: 0.7149 (ttp) cc_final: 0.6795 (ttt) REVERT: A 143 LYS cc_start: 0.5774 (tttm) cc_final: 0.5030 (ttmt) REVERT: A 160 ILE cc_start: 0.8248 (mt) cc_final: 0.7973 (tt) REVERT: A 224 MET cc_start: 0.8393 (mmm) cc_final: 0.8146 (mmm) REVERT: B 47 MET cc_start: -0.0725 (ptt) cc_final: -0.0938 (ptt) REVERT: D 195 ARG cc_start: 0.7982 (ttp80) cc_final: 0.7741 (ttt-90) REVERT: D 211 TYR cc_start: 0.7792 (t80) cc_final: 0.7222 (t80) REVERT: E 211 TYR cc_start: 0.7724 (t80) cc_final: 0.7429 (t80) REVERT: F 151 LEU cc_start: 0.8052 (mt) cc_final: 0.7663 (tp) REVERT: F 224 MET cc_start: 0.8074 (mtt) cc_final: 0.7740 (mtt) REVERT: G 74 LEU cc_start: 0.7566 (mt) cc_final: 0.6934 (mt) REVERT: G 167 CYS cc_start: 0.6094 (t) cc_final: 0.5853 (t) REVERT: G 169 PHE cc_start: 0.6294 (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: 0.6991 (t80) cc_final: 0.6658 (m-10) REVERT: G 203 ILE cc_start: 0.7994 (pt) cc_final: 0.7781 (mp) REVERT: G 273 LEU cc_start: 0.7464 (mt) cc_final: 0.7178 (mt) REVERT: G 346 ASP cc_start: 0.5977 (m-30) cc_final: 0.5719 (m-30) REVERT: G 370 MET cc_start: 0.6501 (mtp) cc_final: 0.5737 (mtp) REVERT: G 371 ARG cc_start: 0.6920 (OUTLIER) cc_final: 0.6555 (ptp90) REVERT: H 47 MET cc_start: 0.0517 (ptt) cc_final: -0.0607 (mmm) REVERT: H 53 TYR cc_start: 0.4256 (t80) cc_final: 0.3676 (m-80) REVERT: H 62 ILE cc_start: 0.8617 (tp) cc_final: 0.8412 (mt) REVERT: H 143 LYS cc_start: 0.5916 (tttm) cc_final: 0.5145 (tttt) REVERT: H 160 ILE cc_start: 0.8436 (mt) cc_final: 0.8142 (tt) REVERT: H 224 MET cc_start: 0.8350 (mmm) cc_final: 0.8131 (mmm) REVERT: H 279 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7801 (m-30) outliers start: 31 outliers final: 14 residues processed: 365 average time/residue: 0.3219 time to fit residues: 183.6002 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 : 2.427 ------------------------------------------------------------------------------- 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: 10.0000 chunk 209 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 20 optimal weight: 0.0000 chunk 89 optimal weight: 2.9990 chunk 153 optimal weight: 0.0980 chunk 56 optimal weight: 4.9990 overall best weight: 2.0190 ------------------------------------------------------------------------------- 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 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 = 0.4000 r_free = 0.4000 target = 0.150532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.114587 restraints weight = 34552.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.111722 restraints weight = 28406.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.113103 restraints weight = 27216.396| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 22248 Z= 0.204 Angle : 0.611 9.591 30136 Z= 0.331 Chirality : 0.047 0.175 3336 Planarity : 0.004 0.037 3768 Dihedral : 5.983 51.549 2920 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.22 % Allowed : 12.16 % Favored : 85.61 % 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: 0.35 (0.17), residues: 2624 helix: -0.10 (0.21), residues: 656 sheet: 0.40 (0.21), residues: 680 loop : 0.53 (0.18), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP G 312 HIS 0.011 0.001 HIS A 82 PHE 0.027 0.002 PHE H 87 TYR 0.019 0.002 TYR B 211 ARG 0.004 0.001 ARG B 371 Details of bonding type rmsd hydrogen bonds : bond 0.04155 ( 952) hydrogen bonds : angle 5.23756 ( 2496) covalent geometry : bond 0.00478 (22248) covalent geometry : angle 0.61122 (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 325 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 272 time to evaluate : 2.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LEU cc_start: 0.8750 (mt) cc_final: 0.8354 (tt) REVERT: A 90 LYS cc_start: 0.8197 (mmmt) cc_final: 0.7953 (mmtm) REVERT: A 105 PHE cc_start: 0.7172 (m-80) cc_final: 0.6649 (m-80) REVERT: A 160 ILE cc_start: 0.8484 (mt) cc_final: 0.8153 (tt) REVERT: C 104 MET cc_start: 0.7266 (tmm) cc_final: 0.6487 (tmm) REVERT: C 224 MET cc_start: 0.8496 (mtt) cc_final: 0.8260 (mtt) REVERT: D 211 TYR cc_start: 0.7809 (t80) cc_final: 0.7237 (t80) REVERT: D 224 MET cc_start: 0.7668 (OUTLIER) cc_final: 0.7288 (mtt) REVERT: E 211 TYR cc_start: 0.7746 (t80) cc_final: 0.7226 (t80) REVERT: E 224 MET cc_start: 0.7615 (OUTLIER) cc_final: 0.6663 (mtt) REVERT: G 53 TYR cc_start: 0.4944 (t80) cc_final: 0.4277 (m-80) REVERT: G 74 LEU cc_start: 0.7383 (mt) cc_final: 0.6976 (mt) REVERT: G 169 PHE cc_start: 0.6457 (m-80) cc_final: 0.5796 (t80) REVERT: G 173 MET cc_start: 0.5029 (tpp) cc_final: 0.4724 (tpp) REVERT: G 179 TYR cc_start: 0.6911 (t80) cc_final: 0.6358 (m-10) REVERT: G 244 GLN cc_start: 0.7990 (mm-40) cc_final: 0.7768 (mm-40) REVERT: G 346 ASP cc_start: 0.5770 (m-30) cc_final: 0.5464 (m-30) REVERT: H 47 MET cc_start: 0.0687 (ptt) cc_final: -0.0801 (mmm) REVERT: H 74 LEU cc_start: 0.8694 (mt) cc_final: 0.8254 (tt) REVERT: H 105 PHE cc_start: 0.7460 (m-80) cc_final: 0.6813 (m-80) REVERT: H 143 LYS cc_start: 0.5922 (tttm) cc_final: 0.5277 (tttt) REVERT: H 224 MET cc_start: 0.8296 (mmm) cc_final: 0.8093 (mmm) outliers start: 53 outliers final: 34 residues processed: 308 average time/residue: 0.2958 time to fit residues: 145.1920 Evaluate side-chains 269 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 233 time to evaluate : 2.316 ------------------------------------------------------------------------------- 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 115 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 295 CYS 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 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 60 PHE Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 226 CYS Chi-restraints excluded: chain G residue 289 ASN 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: 10.0000 chunk 175 optimal weight: 9.9990 chunk 97 optimal weight: 0.7980 chunk 207 optimal weight: 6.9990 chunk 257 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 196 optimal weight: 0.9980 chunk 253 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 209 optimal weight: 0.0370 overall best weight: 1.3662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 HIS ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 GLN ** G 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 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 = 0.4007 r_free = 0.4007 target = 0.151235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.115456 restraints weight = 35144.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.113821 restraints weight = 29413.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.115133 restraints weight = 25994.309| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22248 Z= 0.150 Angle : 0.556 9.405 30136 Z= 0.300 Chirality : 0.045 0.163 3336 Planarity : 0.004 0.037 3768 Dihedral : 5.721 53.438 2920 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.22 % Allowed : 13.59 % Favored : 84.19 % 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: 0.43 (0.17), residues: 2624 helix: 0.07 (0.21), residues: 656 sheet: 0.57 (0.22), residues: 640 loop : 0.43 (0.18), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H 184 HIS 0.004 0.001 HIS G 282 PHE 0.031 0.002 PHE H 60 TYR 0.037 0.001 TYR H 53 ARG 0.008 0.000 ARG H 84 Details of bonding type rmsd hydrogen bonds : bond 0.03689 ( 952) hydrogen bonds : angle 5.05476 ( 2496) covalent geometry : bond 0.00347 (22248) covalent geometry : angle 0.55629 (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 312 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 259 time to evaluate : 2.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8382 (mm) REVERT: A 74 LEU cc_start: 0.8688 (mt) cc_final: 0.8270 (tt) REVERT: A 160 ILE cc_start: 0.8455 (mt) cc_final: 0.8255 (tt) REVERT: A 279 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7838 (m-30) REVERT: D 195 ARG cc_start: 0.8080 (ttp80) cc_final: 0.7879 (ttt-90) REVERT: D 211 TYR cc_start: 0.7782 (t80) cc_final: 0.7235 (t80) REVERT: D 224 MET cc_start: 0.7537 (mtp) cc_final: 0.7087 (mtt) REVERT: E 211 TYR cc_start: 0.7740 (t80) cc_final: 0.7248 (t80) REVERT: F 151 LEU cc_start: 0.8353 (mt) cc_final: 0.8094 (tp) REVERT: G 74 LEU cc_start: 0.7320 (mt) cc_final: 0.6940 (mt) REVERT: G 169 PHE cc_start: 0.6587 (m-80) cc_final: 0.5998 (t80) REVERT: G 173 MET cc_start: 0.5108 (tpp) cc_final: 0.4877 (tpp) REVERT: G 179 TYR cc_start: 0.6723 (t80) cc_final: 0.6237 (m-10) REVERT: H 74 LEU cc_start: 0.8708 (mt) cc_final: 0.8268 (tt) REVERT: H 105 PHE cc_start: 0.7661 (m-80) cc_final: 0.6989 (m-80) REVERT: H 125 TYR cc_start: 0.6712 (m-80) cc_final: 0.6425 (t80) REVERT: H 143 LYS cc_start: 0.5855 (tttm) cc_final: 0.5229 (tttt) REVERT: H 224 MET cc_start: 0.8270 (mmm) cc_final: 0.7926 (mpp) REVERT: H 279 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7993 (m-30) outliers start: 53 outliers final: 35 residues processed: 294 average time/residue: 0.3025 time to fit residues: 143.2214 Evaluate side-chains 267 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 229 time to evaluate : 2.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 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 197 THR Chi-restraints excluded: chain B residue 295 CYS Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 149 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 334 THR Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 226 CYS Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 363 SER Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain G residue 351 ILE Chi-restraints excluded: chain G residue 364 CYS Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 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: 7.9990 chunk 254 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 201 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 59 HIS ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 ASN ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 HIS ** G 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.148447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.113454 restraints weight = 35027.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.110117 restraints weight = 29946.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.111683 restraints weight = 27886.791| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 22248 Z= 0.211 Angle : 0.611 10.149 30136 Z= 0.330 Chirality : 0.047 0.167 3336 Planarity : 0.004 0.037 3768 Dihedral : 5.960 58.465 2920 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.73 % Allowed : 15.02 % Favored : 82.26 % 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: 0.23 (0.17), residues: 2624 helix: -0.06 (0.21), residues: 648 sheet: 0.29 (0.20), residues: 720 loop : 0.39 (0.18), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP G 312 HIS 0.004 0.001 HIS C 282 PHE 0.024 0.002 PHE F 222 TYR 0.017 0.002 TYR H 53 ARG 0.007 0.001 ARG B 371 Details of bonding type rmsd hydrogen bonds : bond 0.04058 ( 952) hydrogen bonds : angle 5.17704 ( 2496) covalent geometry : bond 0.00496 (22248) covalent geometry : angle 0.61117 (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 312 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 247 time to evaluate : 2.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8392 (mm) REVERT: A 74 LEU cc_start: 0.8669 (mt) cc_final: 0.8274 (tt) REVERT: A 105 PHE cc_start: 0.7407 (m-80) cc_final: 0.6358 (m-80) REVERT: A 125 TYR cc_start: 0.6758 (m-80) cc_final: 0.6381 (t80) REVERT: A 160 ILE cc_start: 0.8557 (mt) cc_final: 0.8336 (tt) REVERT: A 279 ASP cc_start: 0.8160 (OUTLIER) cc_final: 0.7873 (m-30) REVERT: A 314 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8123 (mp10) REVERT: A 319 MET cc_start: 0.7936 (mmm) cc_final: 0.7391 (mtt) REVERT: C 104 MET cc_start: 0.7877 (tmm) cc_final: 0.6904 (tmm) REVERT: D 60 PHE cc_start: 0.7934 (OUTLIER) cc_final: 0.7634 (p90) REVERT: D 211 TYR cc_start: 0.7739 (t80) cc_final: 0.7156 (t80) REVERT: D 224 MET cc_start: 0.7719 (OUTLIER) cc_final: 0.7254 (mtt) REVERT: D 314 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.7596 (mp10) REVERT: E 211 TYR cc_start: 0.7685 (t80) cc_final: 0.7213 (t80) REVERT: E 224 MET cc_start: 0.7729 (mtp) cc_final: 0.7273 (mtt) REVERT: E 238 ASP cc_start: 0.7320 (t0) cc_final: 0.7035 (t0) REVERT: E 314 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.7613 (mp10) REVERT: F 80 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8495 (mtm) REVERT: F 151 LEU cc_start: 0.8558 (mt) cc_final: 0.8329 (tp) REVERT: G 53 TYR cc_start: 0.4756 (t80) cc_final: 0.4074 (m-10) REVERT: G 74 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.7087 (mt) REVERT: G 169 PHE cc_start: 0.6743 (m-80) cc_final: 0.6279 (t80) REVERT: G 173 MET cc_start: 0.5384 (tpp) cc_final: 0.4632 (tpp) REVERT: G 179 TYR cc_start: 0.6665 (t80) cc_final: 0.6129 (m-10) REVERT: H 74 LEU cc_start: 0.8709 (mt) cc_final: 0.8251 (tt) REVERT: H 105 PHE cc_start: 0.7607 (m-80) cc_final: 0.6798 (m-80) REVERT: H 125 TYR cc_start: 0.6896 (m-80) cc_final: 0.6407 (t80) REVERT: H 143 LYS cc_start: 0.5959 (tttm) cc_final: 0.5310 (tttt) REVERT: H 279 ASP cc_start: 0.8185 (OUTLIER) cc_final: 0.7972 (m-30) REVERT: H 314 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.8030 (mp10) REVERT: H 319 MET cc_start: 0.7897 (mmm) cc_final: 0.7667 (mtt) outliers start: 65 outliers final: 43 residues processed: 291 average time/residue: 0.2898 time to fit residues: 135.8931 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 : 2.292 ------------------------------------------------------------------------------- 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 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 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 224 MET Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain E residue 81 PHE Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 363 SER Chi-restraints excluded: chain 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 74 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 157 ASP Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 226 CYS Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain G residue 351 ILE Chi-restraints excluded: chain G residue 364 CYS Chi-restraints excluded: chain H residue 158 ILE Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 161 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 44 optimal weight: 0.8980 chunk 1 optimal weight: 9.9990 chunk 156 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 150 optimal weight: 3.9990 chunk 157 optimal weight: 0.4980 chunk 113 optimal weight: 0.2980 chunk 102 optimal weight: 1.9990 chunk 164 optimal weight: 6.9990 chunk 180 optimal weight: 2.9990 chunk 262 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 HIS ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.153431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.117795 restraints weight = 34873.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.115789 restraints weight = 27521.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.117125 restraints weight = 25656.796| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 22248 Z= 0.111 Angle : 0.541 11.161 30136 Z= 0.292 Chirality : 0.044 0.166 3336 Planarity : 0.003 0.039 3768 Dihedral : 5.594 59.323 2920 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.10 % Allowed : 16.15 % Favored : 81.75 % 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: 0.35 (0.17), residues: 2624 helix: 0.17 (0.21), residues: 648 sheet: 0.34 (0.20), residues: 736 loop : 0.40 (0.19), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP G 312 HIS 0.005 0.001 HIS G 311 PHE 0.033 0.001 PHE A 87 TYR 0.019 0.001 TYR B 211 ARG 0.005 0.000 ARG B 371 Details of bonding type rmsd hydrogen bonds : bond 0.03400 ( 952) hydrogen bonds : angle 4.90240 ( 2496) covalent geometry : bond 0.00246 (22248) covalent geometry : angle 0.54084 (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 311 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 261 time to evaluate : 2.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LEU cc_start: 0.8653 (mt) cc_final: 0.8228 (tt) REVERT: A 82 HIS cc_start: 0.7156 (OUTLIER) cc_final: 0.6555 (m170) REVERT: A 279 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7923 (m-30) REVERT: A 314 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8172 (mp10) REVERT: A 319 MET cc_start: 0.7731 (mmm) cc_final: 0.7277 (mtt) REVERT: C 224 MET cc_start: 0.8249 (mtt) cc_final: 0.7935 (mtt) REVERT: D 211 TYR cc_start: 0.7651 (t80) cc_final: 0.7178 (t80) REVERT: D 224 MET cc_start: 0.7414 (OUTLIER) cc_final: 0.6909 (mtt) REVERT: D 314 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.7411 (mp10) REVERT: E 211 TYR cc_start: 0.7668 (t80) cc_final: 0.7208 (t80) REVERT: E 224 MET cc_start: 0.7516 (mtp) cc_final: 0.7072 (mtt) REVERT: E 314 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.7433 (mp10) REVERT: F 151 LEU cc_start: 0.8375 (mt) cc_final: 0.8108 (tp) REVERT: F 224 MET cc_start: 0.8269 (mtt) cc_final: 0.8012 (mtt) REVERT: G 53 TYR cc_start: 0.4427 (t80) cc_final: 0.3929 (m-80) REVERT: G 169 PHE cc_start: 0.6742 (m-80) cc_final: 0.6309 (t80) REVERT: G 179 TYR cc_start: 0.6459 (t80) cc_final: 0.6056 (m-10) REVERT: H 74 LEU cc_start: 0.8681 (mt) cc_final: 0.8209 (tt) REVERT: H 105 PHE cc_start: 0.7602 (m-80) cc_final: 0.6834 (m-80) REVERT: H 125 TYR cc_start: 0.6956 (m-80) cc_final: 0.6579 (t80) REVERT: H 314 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.8155 (mp10) REVERT: H 319 MET cc_start: 0.7754 (mmm) cc_final: 0.7440 (mtt) outliers start: 50 outliers final: 25 residues processed: 294 average time/residue: 0.3013 time to fit residues: 140.8074 Evaluate side-chains 252 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 220 time to evaluate : 2.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 HIS 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 295 CYS 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 363 SER Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 363 SER 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 332 PHE Chi-restraints excluded: chain G residue 351 ILE Chi-restraints excluded: chain G residue 364 CYS 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: 0.5980 chunk 107 optimal weight: 0.6980 chunk 109 optimal weight: 0.0070 chunk 62 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 259 optimal weight: 4.9990 chunk 255 optimal weight: 2.9990 chunk 215 optimal weight: 8.9990 chunk 55 optimal weight: 6.9990 overall best weight: 1.2602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 HIS ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 244 GLN ** E 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 244 GLN ** G 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 HIS ** H 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.152983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.116928 restraints weight = 34903.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.115562 restraints weight = 27564.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.116687 restraints weight = 27001.150| |-----------------------------------------------------------------------------| r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22248 Z= 0.143 Angle : 0.564 9.434 30136 Z= 0.304 Chirality : 0.044 0.165 3336 Planarity : 0.003 0.039 3768 Dihedral : 5.589 56.682 2920 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.22 % Allowed : 16.19 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.37 (0.17), residues: 2624 helix: 0.08 (0.21), residues: 656 sheet: 0.43 (0.21), residues: 680 loop : 0.43 (0.18), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP G 312 HIS 0.003 0.001 HIS G 63 PHE 0.024 0.001 PHE A 87 TYR 0.015 0.001 TYR D 53 ARG 0.003 0.000 ARG B 371 Details of bonding type rmsd hydrogen bonds : bond 0.03598 ( 952) hydrogen bonds : angle 4.95518 ( 2496) covalent geometry : bond 0.00330 (22248) covalent geometry : angle 0.56377 (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 290 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 237 time to evaluate : 2.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 LEU cc_start: 0.8693 (mt) cc_final: 0.8229 (tt) REVERT: A 82 HIS cc_start: 0.7069 (OUTLIER) cc_final: 0.6473 (m170) REVERT: A 279 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7877 (m-30) REVERT: A 314 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8170 (mp10) REVERT: B 149 VAL cc_start: 0.8648 (OUTLIER) cc_final: 0.8364 (m) REVERT: B 285 VAL cc_start: 0.8102 (t) cc_final: 0.7812 (t) REVERT: C 224 MET cc_start: 0.8397 (mtt) cc_final: 0.8045 (mtt) REVERT: D 211 TYR cc_start: 0.7721 (t80) cc_final: 0.7213 (t80) REVERT: D 224 MET cc_start: 0.7495 (OUTLIER) cc_final: 0.6953 (mtt) REVERT: D 314 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.7558 (mp10) REVERT: E 80 MET cc_start: 0.8963 (ttm) cc_final: 0.8631 (mtp) REVERT: E 211 TYR cc_start: 0.7662 (t80) cc_final: 0.7161 (t80) REVERT: E 224 MET cc_start: 0.7527 (mtp) cc_final: 0.7062 (mtt) REVERT: E 314 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.7562 (mp10) REVERT: F 151 LEU cc_start: 0.8462 (mt) cc_final: 0.8193 (tp) REVERT: G 53 TYR cc_start: 0.4277 (t80) cc_final: 0.4022 (m-10) REVERT: G 169 PHE cc_start: 0.6794 (m-80) cc_final: 0.6438 (t80) REVERT: G 179 TYR cc_start: 0.6504 (t80) cc_final: 0.6159 (m-10) REVERT: G 227 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7805 (mt) REVERT: H 63 HIS cc_start: 0.8296 (OUTLIER) cc_final: 0.7673 (m90) REVERT: H 74 LEU cc_start: 0.8685 (mt) cc_final: 0.8220 (tt) REVERT: H 105 PHE cc_start: 0.7555 (m-80) cc_final: 0.6759 (m-80) REVERT: H 125 TYR cc_start: 0.6890 (m-80) cc_final: 0.6546 (t80) REVERT: H 222 PHE cc_start: 0.8143 (OUTLIER) cc_final: 0.7685 (p90) REVERT: H 319 MET cc_start: 0.7793 (mmm) cc_final: 0.7575 (mtt) outliers start: 53 outliers final: 32 residues processed: 275 average time/residue: 0.3010 time to fit residues: 133.7152 Evaluate side-chains 259 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 217 time to evaluate : 2.547 ------------------------------------------------------------------------------- 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 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 149 VAL Chi-restraints excluded: chain B residue 295 CYS 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 334 THR Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 226 CYS Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 363 SER Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain G residue 115 ILE 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 227 ILE Chi-restraints excluded: chain G residue 351 ILE Chi-restraints excluded: chain G residue 364 CYS Chi-restraints excluded: chain H residue 63 HIS Chi-restraints excluded: chain H residue 222 PHE Chi-restraints excluded: chain H residue 279 ASP 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: 4.9990 chunk 95 optimal weight: 0.5980 chunk 184 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 145 optimal weight: 0.8980 chunk 256 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 chunk 168 optimal weight: 0.6980 chunk 1 optimal weight: 9.9990 chunk 26 optimal weight: 0.0980 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 214 HIS ** G 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.155299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.119807 restraints weight = 34881.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.118142 restraints weight = 28575.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.119691 restraints weight = 26943.926| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22248 Z= 0.108 Angle : 0.544 10.232 30136 Z= 0.291 Chirality : 0.044 0.163 3336 Planarity : 0.003 0.039 3768 Dihedral : 5.423 57.772 2920 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.31 % Allowed : 16.69 % Favored : 81.00 % 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: 0.50 (0.17), residues: 2624 helix: 0.19 (0.21), residues: 648 sheet: 0.55 (0.21), residues: 680 loop : 0.47 (0.18), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 184 HIS 0.011 0.001 HIS H 63 PHE 0.014 0.001 PHE C 222 TYR 0.020 0.001 TYR B 211 ARG 0.003 0.000 ARG A 338 Details of bonding type rmsd hydrogen bonds : bond 0.03324 ( 952) hydrogen bonds : angle 4.83760 ( 2496) covalent geometry : bond 0.00237 (22248) covalent geometry : angle 0.54384 (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 295 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 240 time to evaluate : 2.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LEU cc_start: 0.8665 (mt) cc_final: 0.8186 (tt) REVERT: A 222 PHE cc_start: 0.7978 (OUTLIER) cc_final: 0.7541 (p90) REVERT: A 279 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7921 (m-30) REVERT: A 314 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.8156 (mp10) REVERT: A 319 MET cc_start: 0.7744 (mmm) cc_final: 0.7044 (mtt) REVERT: B 149 VAL cc_start: 0.8647 (OUTLIER) cc_final: 0.8430 (m) REVERT: B 207 GLN cc_start: 0.7464 (OUTLIER) cc_final: 0.6916 (pm20) REVERT: B 285 VAL cc_start: 0.8107 (t) cc_final: 0.7836 (t) REVERT: C 104 MET cc_start: 0.7367 (tmm) cc_final: 0.7133 (tmm) REVERT: C 224 MET cc_start: 0.8203 (mtt) cc_final: 0.7826 (mtt) REVERT: D 211 TYR cc_start: 0.7650 (t80) cc_final: 0.7255 (t80) REVERT: D 224 MET cc_start: 0.7405 (OUTLIER) cc_final: 0.6806 (mtt) REVERT: D 314 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.7345 (mp10) REVERT: E 80 MET cc_start: 0.8960 (ttm) cc_final: 0.8631 (mtp) REVERT: E 211 TYR cc_start: 0.7588 (t80) cc_final: 0.7209 (t80) REVERT: E 224 MET cc_start: 0.7461 (mtp) cc_final: 0.7019 (mtt) REVERT: E 244 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.7342 (mt0) REVERT: E 314 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.7416 (mp10) REVERT: F 151 LEU cc_start: 0.8399 (mt) cc_final: 0.8105 (tp) REVERT: F 314 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.7701 (mp10) REVERT: G 169 PHE cc_start: 0.6751 (m-80) cc_final: 0.6379 (t80) REVERT: G 179 TYR cc_start: 0.6356 (t80) cc_final: 0.6022 (m-10) REVERT: G 227 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7871 (mt) REVERT: H 63 HIS cc_start: 0.8322 (OUTLIER) cc_final: 0.7659 (m90) REVERT: H 74 LEU cc_start: 0.8693 (mt) cc_final: 0.8181 (tt) REVERT: H 105 PHE cc_start: 0.7456 (m-80) cc_final: 0.6641 (m-80) REVERT: H 125 TYR cc_start: 0.6891 (m-80) cc_final: 0.6587 (t80) REVERT: H 222 PHE cc_start: 0.8066 (OUTLIER) cc_final: 0.7672 (p90) REVERT: H 314 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.8151 (mp10) REVERT: H 319 MET cc_start: 0.7693 (mmm) cc_final: 0.7451 (mtt) outliers start: 55 outliers final: 33 residues processed: 280 average time/residue: 0.2860 time to fit residues: 130.8291 Evaluate side-chains 264 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 217 time to evaluate : 2.425 ------------------------------------------------------------------------------- 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 222 PHE 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 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 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 334 THR Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain E residue 244 GLN Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 363 SER Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 366 THR 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 224 MET Chi-restraints excluded: chain G residue 227 ILE Chi-restraints excluded: chain G residue 327 THR Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain G residue 351 ILE Chi-restraints excluded: chain G residue 364 CYS Chi-restraints excluded: chain H residue 63 HIS Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 222 PHE 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: 0.8980 chunk 225 optimal weight: 0.9980 chunk 221 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 168 optimal weight: 0.6980 chunk 249 optimal weight: 1.9990 chunk 250 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 261 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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** H 63 HIS ** H 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.154812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.119624 restraints weight = 34752.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.117651 restraints weight = 29814.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.119213 restraints weight = 28700.638| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.5000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22248 Z= 0.124 Angle : 0.564 12.406 30136 Z= 0.299 Chirality : 0.044 0.160 3336 Planarity : 0.003 0.041 3768 Dihedral : 5.492 59.819 2920 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.39 % Allowed : 16.57 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.49 (0.17), residues: 2624 helix: 0.18 (0.21), residues: 648 sheet: 0.58 (0.21), residues: 680 loop : 0.45 (0.18), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP B 216 HIS 0.008 0.001 HIS H 63 PHE 0.014 0.001 PHE C 222 TYR 0.029 0.001 TYR B 53 ARG 0.004 0.000 ARG B 206 Details of bonding type rmsd hydrogen bonds : bond 0.03434 ( 952) hydrogen bonds : angle 4.89118 ( 2496) covalent geometry : bond 0.00283 (22248) covalent geometry : angle 0.56426 (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 288 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 231 time to evaluate : 2.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LEU cc_start: 0.8660 (mt) cc_final: 0.8166 (tt) REVERT: A 104 MET cc_start: 0.5833 (ttt) cc_final: 0.5548 (tmm) REVERT: A 222 PHE cc_start: 0.7991 (OUTLIER) cc_final: 0.7419 (p90) REVERT: A 279 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7887 (m-30) REVERT: A 314 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8167 (mp10) REVERT: A 319 MET cc_start: 0.7780 (mmm) cc_final: 0.7132 (mtt) REVERT: A 337 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.7397 (mmm) REVERT: B 103 CYS cc_start: 0.6912 (OUTLIER) cc_final: 0.6662 (m) REVERT: B 149 VAL cc_start: 0.8651 (OUTLIER) cc_final: 0.8416 (m) REVERT: B 207 GLN cc_start: 0.7294 (OUTLIER) cc_final: 0.6883 (pm20) REVERT: B 235 PRO cc_start: 0.6070 (Cg_exo) cc_final: 0.5847 (Cg_endo) REVERT: B 285 VAL cc_start: 0.8134 (t) cc_final: 0.7889 (t) REVERT: C 224 MET cc_start: 0.8278 (mtt) cc_final: 0.7933 (mtt) REVERT: C 238 ASP cc_start: 0.7705 (m-30) cc_final: 0.7442 (m-30) REVERT: C 314 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7620 (mp10) REVERT: C 354 ASP cc_start: 0.8035 (m-30) cc_final: 0.7771 (m-30) REVERT: D 211 TYR cc_start: 0.7657 (t80) cc_final: 0.7288 (t80) REVERT: D 224 MET cc_start: 0.7504 (OUTLIER) cc_final: 0.6904 (mtt) REVERT: D 314 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.7472 (mp10) REVERT: E 80 MET cc_start: 0.8963 (ttm) cc_final: 0.8633 (mtp) REVERT: E 211 TYR cc_start: 0.7639 (t80) cc_final: 0.7215 (t80) REVERT: E 224 MET cc_start: 0.7441 (mtp) cc_final: 0.7094 (mtt) REVERT: E 244 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7399 (mt0) REVERT: E 314 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.7516 (mp10) REVERT: F 151 LEU cc_start: 0.8411 (mt) cc_final: 0.8117 (tp) REVERT: F 314 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.7623 (mp10) REVERT: F 319 MET cc_start: 0.8642 (mtp) cc_final: 0.8393 (mtp) REVERT: G 169 PHE cc_start: 0.6740 (m-80) cc_final: 0.6403 (t80) REVERT: G 179 TYR cc_start: 0.6265 (t80) cc_final: 0.6024 (m-10) REVERT: G 227 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7809 (mt) REVERT: G 292 PHE cc_start: 0.5169 (OUTLIER) cc_final: 0.4188 (m-80) REVERT: H 74 LEU cc_start: 0.8664 (mt) cc_final: 0.8171 (tt) REVERT: H 105 PHE cc_start: 0.7428 (m-80) cc_final: 0.6579 (m-80) REVERT: H 125 TYR cc_start: 0.6811 (m-80) cc_final: 0.6557 (t80) REVERT: H 222 PHE cc_start: 0.8144 (OUTLIER) cc_final: 0.7765 (p90) REVERT: H 314 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.8156 (mp10) outliers start: 57 outliers final: 36 residues processed: 272 average time/residue: 0.2864 time to fit residues: 126.9067 Evaluate side-chains 270 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 217 time to evaluate : 2.440 ------------------------------------------------------------------------------- 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 222 PHE 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 337 MET Chi-restraints excluded: chain A residue 358 GLN 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 C residue 314 GLN 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 334 THR Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 226 CYS Chi-restraints excluded: chain E residue 244 GLN Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 363 SER Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 115 ILE 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 224 MET Chi-restraints excluded: chain G residue 227 ILE Chi-restraints excluded: chain G residue 292 PHE Chi-restraints excluded: chain G residue 327 THR 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 222 PHE Chi-restraints excluded: chain H residue 279 ASP 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 74 optimal weight: 0.7980 chunk 67 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 262 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 122 optimal weight: 8.9990 chunk 223 optimal weight: 0.7980 chunk 43 optimal weight: 0.0770 chunk 225 optimal weight: 0.9990 chunk 196 optimal weight: 2.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- 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 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.155554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.119925 restraints weight = 35112.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.118408 restraints weight = 27866.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.119697 restraints weight = 27567.927| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.5138 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= 0.112 Angle : 0.551 9.484 30136 Z= 0.293 Chirality : 0.044 0.161 3336 Planarity : 0.003 0.041 3768 Dihedral : 5.395 59.428 2920 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.39 % Allowed : 16.82 % Favored : 80.79 % 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: 0.50 (0.17), residues: 2624 helix: 0.22 (0.21), residues: 648 sheet: 0.52 (0.20), residues: 736 loop : 0.48 (0.19), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP B 216 HIS 0.004 0.001 HIS G 282 PHE 0.013 0.001 PHE F 222 TYR 0.029 0.001 TYR B 211 ARG 0.007 0.000 ARG B 206 Details of bonding type rmsd hydrogen bonds : bond 0.03301 ( 952) hydrogen bonds : angle 4.84634 ( 2496) covalent geometry : bond 0.00251 (22248) covalent geometry : angle 0.55144 (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 284 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 227 time to evaluate : 2.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LEU cc_start: 0.8616 (mt) cc_final: 0.8122 (tt) REVERT: A 104 MET cc_start: 0.5827 (ttt) cc_final: 0.5581 (tmm) REVERT: A 222 PHE cc_start: 0.7855 (OUTLIER) cc_final: 0.7281 (p90) REVERT: A 279 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7891 (m-30) REVERT: A 314 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.8144 (mp10) REVERT: A 319 MET cc_start: 0.7732 (mmm) cc_final: 0.7113 (mtt) REVERT: A 337 MET cc_start: 0.7623 (OUTLIER) cc_final: 0.7392 (mmm) REVERT: B 103 CYS cc_start: 0.6828 (OUTLIER) cc_final: 0.6575 (m) REVERT: B 149 VAL cc_start: 0.8629 (OUTLIER) cc_final: 0.8403 (m) REVERT: B 207 GLN cc_start: 0.7356 (OUTLIER) cc_final: 0.6833 (pm20) REVERT: B 235 PRO cc_start: 0.6030 (Cg_exo) cc_final: 0.5819 (Cg_endo) REVERT: B 285 VAL cc_start: 0.8114 (t) cc_final: 0.7870 (t) REVERT: C 104 MET cc_start: 0.7316 (tmm) cc_final: 0.7081 (tmm) REVERT: C 224 MET cc_start: 0.8284 (mtt) cc_final: 0.7934 (mtt) REVERT: C 238 ASP cc_start: 0.7669 (m-30) cc_final: 0.7458 (m-30) REVERT: C 314 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.7577 (mp10) REVERT: D 149 VAL cc_start: 0.8772 (t) cc_final: 0.8519 (m) REVERT: D 211 TYR cc_start: 0.7646 (t80) cc_final: 0.7196 (t80) REVERT: D 224 MET cc_start: 0.7433 (OUTLIER) cc_final: 0.6865 (mtt) REVERT: D 314 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.7380 (mp10) REVERT: E 80 MET cc_start: 0.8964 (ttm) cc_final: 0.8617 (mtp) REVERT: E 104 MET cc_start: 0.7867 (tpp) cc_final: 0.7520 (mpp) REVERT: E 211 TYR cc_start: 0.7637 (t80) cc_final: 0.7324 (t80) REVERT: E 224 MET cc_start: 0.7433 (mtp) cc_final: 0.7128 (mtt) REVERT: E 244 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7470 (mt0) REVERT: E 276 LYS cc_start: 0.7051 (mtmm) cc_final: 0.6632 (ptpp) REVERT: E 314 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.7505 (mp10) REVERT: F 151 LEU cc_start: 0.8388 (mt) cc_final: 0.8082 (tp) REVERT: F 314 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.7613 (mp10) REVERT: G 164 MET cc_start: 0.5392 (mtm) cc_final: 0.5104 (mtm) REVERT: G 169 PHE cc_start: 0.6761 (m-80) cc_final: 0.6425 (t80) REVERT: G 179 TYR cc_start: 0.6300 (t80) cc_final: 0.6024 (m-10) REVERT: G 227 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7871 (mt) REVERT: G 292 PHE cc_start: 0.5262 (OUTLIER) cc_final: 0.4181 (m-80) REVERT: G 371 ARG cc_start: 0.6279 (ptp90) cc_final: 0.5825 (ptp90) REVERT: H 74 LEU cc_start: 0.8597 (mt) cc_final: 0.8067 (tt) REVERT: H 105 PHE cc_start: 0.7356 (m-80) cc_final: 0.6485 (m-80) REVERT: H 125 TYR cc_start: 0.6791 (m-80) cc_final: 0.6536 (t80) REVERT: H 314 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.8127 (mp10) outliers start: 57 outliers final: 32 residues processed: 268 average time/residue: 0.3004 time to fit residues: 130.3632 Evaluate side-chains 266 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 218 time to evaluate : 2.758 ------------------------------------------------------------------------------- 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 222 PHE 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 314 GLN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 358 GLN 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 C residue 314 GLN 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 334 THR Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 226 CYS Chi-restraints excluded: chain E residue 244 GLN Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain E residue 363 SER Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 115 ILE 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 224 MET Chi-restraints excluded: chain G residue 227 ILE Chi-restraints excluded: chain G residue 245 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 160 ILE Chi-restraints excluded: chain H residue 314 GLN Chi-restraints excluded: chain H residue 334 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 178 optimal weight: 4.9990 chunk 200 optimal weight: 4.9990 chunk 262 optimal weight: 4.9990 chunk 111 optimal weight: 0.0980 chunk 156 optimal weight: 3.9990 chunk 31 optimal weight: 0.1980 chunk 65 optimal weight: 10.0000 chunk 197 optimal weight: 0.8980 chunk 202 optimal weight: 6.9990 chunk 251 optimal weight: 0.8980 chunk 192 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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** F 59 HIS ** G 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.156368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.120788 restraints weight = 34822.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.119537 restraints weight = 27716.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.120813 restraints weight = 27431.243| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.5246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 22248 Z= 0.104 Angle : 0.541 9.381 30136 Z= 0.288 Chirality : 0.043 0.160 3336 Planarity : 0.003 0.040 3768 Dihedral : 5.310 59.686 2920 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.18 % Allowed : 17.11 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.34 (0.17), residues: 2624 helix: -0.02 (0.20), residues: 696 sheet: 0.56 (0.20), residues: 736 loop : 0.37 (0.19), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP B 216 HIS 0.004 0.001 HIS G 63 PHE 0.013 0.001 PHE F 222 TYR 0.022 0.001 TYR B 53 ARG 0.005 0.000 ARG B 206 Details of bonding type rmsd hydrogen bonds : bond 0.03201 ( 952) hydrogen bonds : angle 4.80310 ( 2496) covalent geometry : bond 0.00229 (22248) covalent geometry : angle 0.54093 (30136) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5923.61 seconds wall clock time: 105 minutes 41.16 seconds (6341.16 seconds total)