Starting phenix.real_space_refine on Wed Jun 18 22:39:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bhd_44541/06_2025/9bhd_44541.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bhd_44541/06_2025/9bhd_44541.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bhd_44541/06_2025/9bhd_44541.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bhd_44541/06_2025/9bhd_44541.map" model { file = "/net/cci-nas-00/data/ceres_data/9bhd_44541/06_2025/9bhd_44541.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bhd_44541/06_2025/9bhd_44541.cif" } resolution = 3.38 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-5710/modules/chem_data/mon_lib" Total number of atoms: 21720 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2689 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 320} Chain: "B" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2689 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 320} Chain: "C" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2689 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 320} Chain: "D" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2689 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 320} Chain: "E" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2689 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 320} Chain: "F" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2689 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 320} Chain: "G" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2689 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 320} Chain: "H" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2689 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 320} Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "C" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "D" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "E" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "F" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "G" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "H" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Time building chain proxies: 14.06, per 1000 atoms: 0.65 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: 5.52 Conformation dependent library (CDL) restraints added in 3.3 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: 3.27 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: 8.62 Time building geometry restraints manager: 6.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6834 1.34 - 1.45: 4147 1.45 - 1.57: 11019 1.57 - 1.69: 0 1.69 - 1.81: 248 Bond restraints: 22248 Sorted by residual: bond pdb=" C LYS H 233 " pdb=" N GLU H 234 " ideal model delta sigma weight residual 1.331 1.290 0.041 1.63e-02 3.76e+03 6.43e+00 bond pdb=" C LYS E 233 " pdb=" N GLU E 234 " ideal model delta sigma weight residual 1.331 1.290 0.041 1.63e-02 3.76e+03 6.28e+00 bond pdb=" C8 SAH F 401 " pdb=" N7 SAH F 401 " ideal model delta sigma weight residual 1.299 1.349 -0.050 2.00e-02 2.50e+03 6.28e+00 bond pdb=" C8 SAH H 401 " pdb=" N7 SAH H 401 " ideal model delta sigma weight residual 1.299 1.349 -0.050 2.00e-02 2.50e+03 6.28e+00 bond pdb=" C8 SAH G 401 " pdb=" N7 SAH G 401 " ideal model delta sigma weight residual 1.299 1.349 -0.050 2.00e-02 2.50e+03 6.23e+00 ... (remaining 22243 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 29474 2.40 - 4.80: 564 4.80 - 7.20: 66 7.20 - 9.60: 24 9.60 - 12.00: 8 Bond angle restraints: 30136 Sorted by residual: angle pdb=" CG SAH A 401 " pdb=" SD SAH A 401 " pdb=" C5' SAH A 401 " ideal model delta sigma weight residual 101.77 89.77 12.00 3.00e+00 1.11e-01 1.60e+01 angle pdb=" CG SAH G 401 " pdb=" SD SAH G 401 " pdb=" C5' SAH G 401 " ideal model delta sigma weight residual 101.77 89.78 11.99 3.00e+00 1.11e-01 1.60e+01 angle pdb=" CG SAH F 401 " pdb=" SD SAH F 401 " pdb=" C5' SAH F 401 " ideal model delta sigma weight residual 101.77 89.78 11.99 3.00e+00 1.11e-01 1.60e+01 angle pdb=" CG SAH B 401 " pdb=" SD SAH B 401 " pdb=" C5' SAH B 401 " ideal model delta sigma weight residual 101.77 89.78 11.99 3.00e+00 1.11e-01 1.60e+01 angle pdb=" CG SAH C 401 " pdb=" SD SAH C 401 " pdb=" C5' SAH C 401 " ideal model delta sigma weight residual 101.77 89.78 11.99 3.00e+00 1.11e-01 1.60e+01 ... (remaining 30131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.99: 11697 13.99 - 27.98: 1087 27.98 - 41.98: 304 41.98 - 55.97: 32 55.97 - 69.96: 32 Dihedral angle restraints: 13152 sinusoidal: 5312 harmonic: 7840 Sorted by residual: dihedral pdb=" CA TRP D 312 " pdb=" C TRP D 312 " pdb=" N LYS D 313 " pdb=" CA LYS D 313 " ideal model delta harmonic sigma weight residual -180.00 -143.11 -36.89 0 5.00e+00 4.00e-02 5.44e+01 dihedral pdb=" CA TRP F 312 " pdb=" C TRP F 312 " pdb=" N LYS F 313 " pdb=" CA LYS F 313 " ideal model delta harmonic sigma weight residual -180.00 -143.14 -36.86 0 5.00e+00 4.00e-02 5.43e+01 dihedral pdb=" CA TRP A 312 " pdb=" C TRP A 312 " pdb=" N LYS A 313 " pdb=" CA LYS A 313 " ideal model delta harmonic sigma weight residual -180.00 -143.15 -36.85 0 5.00e+00 4.00e-02 5.43e+01 ... (remaining 13149 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1679 0.033 - 0.067: 1030 0.067 - 0.100: 461 0.100 - 0.133: 126 0.133 - 0.167: 40 Chirality restraints: 3336 Sorted by residual: chirality pdb=" CA PHE B 222 " pdb=" N PHE B 222 " pdb=" C PHE B 222 " pdb=" CB PHE B 222 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.95e-01 chirality pdb=" CA PHE H 222 " pdb=" N PHE H 222 " pdb=" C PHE H 222 " pdb=" CB PHE H 222 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.94e-01 chirality pdb=" CA PHE A 222 " pdb=" N PHE A 222 " pdb=" C PHE A 222 " pdb=" CB PHE A 222 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.91e-01 ... (remaining 3333 not shown) Planarity restraints: 3768 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 317 " -0.012 2.00e-02 2.50e+03 1.18e-02 2.45e+00 pdb=" CG PHE C 317 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE C 317 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE C 317 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE C 317 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE C 317 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE C 317 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 317 " 0.011 2.00e-02 2.50e+03 1.18e-02 2.43e+00 pdb=" CG PHE G 317 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE G 317 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE G 317 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE G 317 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE G 317 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE G 317 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 317 " -0.012 2.00e-02 2.50e+03 1.18e-02 2.42e+00 pdb=" CG PHE D 317 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE D 317 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE D 317 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE D 317 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE D 317 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE D 317 " -0.004 2.00e-02 2.50e+03 ... (remaining 3765 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 297 2.64 - 3.21: 20128 3.21 - 3.77: 32462 3.77 - 4.34: 48333 4.34 - 4.90: 79036 Nonbonded interactions: 180256 Sorted by model distance: nonbonded pdb=" O HIS B 82 " pdb=" OH TYR D 280 " model vdw 2.077 3.040 nonbonded pdb=" OE1 GLU F 217 " pdb=" OG SER F 225 " model vdw 2.218 3.040 nonbonded pdb=" OE1 GLU D 217 " pdb=" OG SER D 225 " model vdw 2.218 3.040 nonbonded pdb=" OE1 GLU C 217 " pdb=" OG SER C 225 " model vdw 2.218 3.040 nonbonded pdb=" OE1 GLU G 217 " pdb=" OG SER G 225 " model vdw 2.218 3.040 ... (remaining 180251 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.18 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.630 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: 0.940 Check model and map are aligned: 0.180 Set scattering table: 0.250 Process input model: 53.260 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.120 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.050 22248 Z= 0.414 Angle : 0.855 12.002 30136 Z= 0.458 Chirality : 0.051 0.167 3336 Planarity : 0.004 0.034 3768 Dihedral : 12.400 69.960 8096 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z (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 : 2.255 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: 0.8788 (mt) cc_final: 0.8439 (tt) REVERT: A 104 MET cc_start: 0.6323 (ttp) cc_final: 0.6120 (tmm) REVERT: A 143 LYS cc_start: 0.6380 (tttm) cc_final: 0.5629 (tttt) REVERT: A 159 ILE cc_start: 0.8314 (mt) cc_final: 0.8021 (mm) REVERT: A 160 ILE cc_start: 0.8439 (mt) cc_final: 0.7952 (tt) REVERT: B 76 TYR cc_start: 0.6654 (m-80) cc_final: 0.6349 (m-80) REVERT: B 114 VAL cc_start: 0.8002 (t) cc_final: 0.7795 (t) REVERT: B 139 VAL cc_start: 0.7748 (t) cc_final: 0.7285 (m) REVERT: B 169 PHE cc_start: 0.6786 (m-80) cc_final: 0.6393 (t80) REVERT: B 235 PRO cc_start: 0.6148 (Cg_exo) cc_final: 0.5829 (Cg_endo) REVERT: B 239 VAL cc_start: 0.8753 (t) cc_final: 0.8381 (p) REVERT: B 244 GLN cc_start: 0.8343 (mt0) cc_final: 0.7034 (mm110) REVERT: B 273 LEU cc_start: 0.8085 (mt) cc_final: 0.7321 (mt) REVERT: B 312 TRP cc_start: 0.7381 (m-90) cc_final: 0.7143 (m-10) REVERT: E 211 TYR cc_start: 0.7577 (t80) cc_final: 0.7283 (t80) REVERT: F 211 TYR cc_start: 0.8050 (t80) cc_final: 0.7679 (t80) REVERT: F 224 MET cc_start: 0.8045 (mtt) cc_final: 0.7839 (mtt) REVERT: F 371 ARG cc_start: 0.7105 (ptt180) cc_final: 0.6791 (ptt180) REVERT: G 167 CYS cc_start: 0.6247 (t) cc_final: 0.5858 (t) REVERT: G 170 TYR cc_start: 0.6045 (t80) cc_final: 0.5750 (t80) REVERT: G 179 TYR cc_start: 0.6943 (t80) cc_final: 0.6653 (m-10) REVERT: G 273 LEU cc_start: 0.7185 (mt) cc_final: 0.6890 (mt) REVERT: G 343 ASN cc_start: 0.3015 (t0) cc_final: 0.2650 (m-40) REVERT: G 349 PHE cc_start: 0.5184 (m-10) cc_final: 0.4641 (m-10) REVERT: H 47 MET cc_start: 0.0140 (ptt) cc_final: -0.0733 (mmm) REVERT: H 70 GLU cc_start: 0.8328 (tt0) cc_final: 0.8113 (tp30) REVERT: H 104 MET cc_start: 0.6854 (ttp) cc_final: 0.6648 (tmm) REVERT: H 134 LYS cc_start: 0.7810 (mtmt) cc_final: 0.7497 (mmmt) REVERT: H 143 LYS cc_start: 0.6365 (tttm) cc_final: 0.5897 (tttt) REVERT: H 159 ILE cc_start: 0.8456 (mt) cc_final: 0.8135 (mm) REVERT: H 160 ILE cc_start: 0.8572 (mt) cc_final: 0.8198 (tt) REVERT: H 296 HIS cc_start: 0.6963 (t-90) cc_final: 0.6762 (t70) outliers start: 0 outliers final: 0 residues processed: 487 average time/residue: 0.3744 time to fit residues: 275.3165 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 : 2.465 ------------------------------------------------------------------------------- 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 ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 ASN D 274 GLN E 274 GLN F 175 ASN F 274 GLN ** G 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 HIS ** H 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.163379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.126195 restraints weight = 35478.552| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.65 r_work: 0.3570 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22248 Z= 0.127 Angle : 0.584 9.196 30136 Z= 0.317 Chirality : 0.045 0.163 3336 Planarity : 0.004 0.049 3768 Dihedral : 5.857 45.249 2920 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.34 % Allowed : 8.01 % Favored : 90.65 % 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: 0.45 (0.17), residues: 2624 helix: -0.08 (0.21), residues: 656 sheet: 0.20 (0.20), residues: 728 loop : 0.83 (0.19), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP G 312 HIS 0.013 0.001 HIS A 82 PHE 0.032 0.002 PHE A 105 TYR 0.023 0.001 TYR C 208 ARG 0.003 0.001 ARG G 298 Details of bonding type rmsd hydrogen bonds : bond 0.03964 ( 952) hydrogen bonds : angle 5.28401 ( 2496) covalent geometry : bond 0.00278 (22248) covalent geometry : angle 0.58365 (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 378 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 346 time to evaluate : 2.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.6690 (ttp) cc_final: 0.6464 (ttt) REVERT: A 143 LYS cc_start: 0.6080 (tttm) cc_final: 0.5366 (tttt) REVERT: A 160 ILE cc_start: 0.8282 (mt) cc_final: 0.7849 (tt) REVERT: A 211 TYR cc_start: 0.8052 (t80) cc_final: 0.7706 (t80) REVERT: A 224 MET cc_start: 0.8417 (mmm) cc_final: 0.8128 (mmm) REVERT: B 47 MET cc_start: -0.0974 (ptt) cc_final: -0.1209 (ptt) REVERT: B 244 GLN cc_start: 0.7652 (mt0) cc_final: 0.7442 (mm110) REVERT: D 162 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7895 (tm-30) REVERT: D 211 TYR cc_start: 0.7911 (t80) cc_final: 0.7321 (t80) REVERT: E 211 TYR cc_start: 0.7795 (t80) cc_final: 0.7437 (t80) REVERT: E 326 LYS cc_start: 0.7748 (mtpp) cc_final: 0.7497 (mtmm) REVERT: G 74 LEU cc_start: 0.7801 (mt) cc_final: 0.7277 (mt) REVERT: G 167 CYS cc_start: 0.6172 (t) cc_final: 0.5831 (t) REVERT: G 169 PHE cc_start: 0.6268 (m-80) cc_final: 0.5536 (t80) REVERT: G 173 MET cc_start: 0.4309 (tpp) cc_final: 0.3542 (tpp) REVERT: G 179 TYR cc_start: 0.6861 (t80) cc_final: 0.6231 (m-10) REVERT: G 203 ILE cc_start: 0.7788 (pt) cc_final: 0.7532 (mp) REVERT: G 216 TRP cc_start: 0.7733 (m100) cc_final: 0.7362 (m100) REVERT: G 220 TYR cc_start: 0.5919 (m-80) cc_final: 0.5432 (m-10) REVERT: G 224 MET cc_start: 0.7084 (mtt) cc_final: 0.6611 (mtt) REVERT: G 241 ASP cc_start: 0.7425 (t0) cc_final: 0.7056 (t0) REVERT: G 253 LYS cc_start: 0.7304 (tptt) cc_final: 0.7025 (mmtt) REVERT: G 273 LEU cc_start: 0.7459 (mt) cc_final: 0.7099 (mt) REVERT: G 274 GLN cc_start: 0.8005 (tp40) cc_final: 0.7782 (tp40) REVERT: G 315 THR cc_start: 0.5542 (m) cc_final: 0.5288 (p) REVERT: G 319 MET cc_start: 0.5576 (ttm) cc_final: 0.5350 (tpt) REVERT: G 343 ASN cc_start: 0.3592 (t0) cc_final: 0.3274 (m-40) REVERT: G 346 ASP cc_start: 0.6336 (m-30) cc_final: 0.5651 (m-30) REVERT: G 370 MET cc_start: 0.6370 (mtp) cc_final: 0.5351 (mtp) REVERT: G 371 ARG cc_start: 0.6854 (OUTLIER) cc_final: 0.6473 (ptp90) REVERT: H 47 MET cc_start: 0.0578 (ptt) cc_final: -0.0591 (mmm) REVERT: H 53 TYR cc_start: 0.4455 (t80) cc_final: 0.3814 (m-80) REVERT: H 70 GLU cc_start: 0.8384 (tt0) cc_final: 0.8079 (tp30) REVERT: H 105 PHE cc_start: 0.7159 (m-80) cc_final: 0.6691 (m-80) REVERT: H 143 LYS cc_start: 0.6147 (tttm) cc_final: 0.5375 (tttt) REVERT: H 160 ILE cc_start: 0.8428 (mt) cc_final: 0.8007 (tt) REVERT: H 224 MET cc_start: 0.8474 (mmm) cc_final: 0.8220 (mmm) REVERT: H 279 ASP cc_start: 0.8479 (OUTLIER) cc_final: 0.8206 (m-30) REVERT: H 321 ASP cc_start: 0.8247 (p0) cc_final: 0.8045 (p0) outliers start: 32 outliers final: 16 residues processed: 365 average time/residue: 0.3291 time to fit residues: 187.6383 Evaluate side-chains 276 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 258 time to evaluate : 2.483 ------------------------------------------------------------------------------- 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 88 LYS Chi-restraints excluded: chain D residue 226 CYS Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 226 CYS Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 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: 5.9990 chunk 209 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 20 optimal weight: 0.0670 chunk 89 optimal weight: 4.9990 chunk 153 optimal weight: 0.0870 chunk 56 optimal weight: 20.0000 overall best weight: 2.8302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.154277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.118227 restraints weight = 35239.549| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.67 r_work: 0.3440 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 22248 Z= 0.272 Angle : 0.671 9.470 30136 Z= 0.364 Chirality : 0.049 0.180 3336 Planarity : 0.004 0.044 3768 Dihedral : 6.168 52.371 2920 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.60 % Allowed : 12.16 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.17), residues: 2624 helix: -0.17 (0.21), residues: 648 sheet: 0.22 (0.20), residues: 720 loop : 0.52 (0.18), residues: 1256 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 0.021 0.003 PHE G 292 TYR 0.020 0.002 TYR B 211 ARG 0.008 0.001 ARG E 369 Details of bonding type rmsd hydrogen bonds : bond 0.04520 ( 952) hydrogen bonds : angle 5.42131 ( 2496) covalent geometry : bond 0.00634 (22248) covalent geometry : angle 0.67111 (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 335 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 273 time to evaluate : 2.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LEU cc_start: 0.8713 (mt) cc_final: 0.8373 (tt) REVERT: A 90 LYS cc_start: 0.8435 (mmmt) cc_final: 0.8156 (mmtt) REVERT: A 125 TYR cc_start: 0.7002 (m-80) cc_final: 0.6625 (m-80) REVERT: A 160 ILE cc_start: 0.8589 (mt) cc_final: 0.8268 (tt) REVERT: A 211 TYR cc_start: 0.8301 (t80) cc_final: 0.7958 (t80) REVERT: A 319 MET cc_start: 0.8155 (mmm) cc_final: 0.7626 (mtt) REVERT: B 173 MET cc_start: 0.5065 (tpp) cc_final: 0.4723 (tpp) REVERT: B 222 PHE cc_start: 0.7041 (m-80) cc_final: 0.6635 (m-80) REVERT: B 315 THR cc_start: 0.6471 (m) cc_final: 0.6240 (p) REVERT: C 104 MET cc_start: 0.7989 (tmm) cc_final: 0.7141 (tmm) REVERT: C 371 ARG cc_start: 0.7830 (ptt180) cc_final: 0.7572 (ptt180) REVERT: D 60 PHE cc_start: 0.8175 (OUTLIER) cc_final: 0.7911 (p90) REVERT: D 211 TYR cc_start: 0.8074 (t80) cc_final: 0.7490 (t80) REVERT: D 224 MET cc_start: 0.7583 (OUTLIER) cc_final: 0.7332 (mtt) REVERT: E 211 TYR cc_start: 0.8009 (t80) cc_final: 0.7443 (t80) REVERT: E 224 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.6847 (mtt) REVERT: F 371 ARG cc_start: 0.7803 (ptt180) cc_final: 0.7564 (ptt180) REVERT: G 53 TYR cc_start: 0.4961 (t80) cc_final: 0.4214 (m-80) REVERT: G 94 ASP cc_start: 0.4698 (m-30) cc_final: 0.4455 (m-30) REVERT: G 167 CYS cc_start: 0.6410 (t) cc_final: 0.6182 (t) REVERT: G 169 PHE cc_start: 0.6683 (m-80) cc_final: 0.5970 (t80) REVERT: G 173 MET cc_start: 0.4975 (tpp) cc_final: 0.4540 (tpp) REVERT: G 179 TYR cc_start: 0.6777 (t80) cc_final: 0.5972 (m-10) REVERT: G 220 TYR cc_start: 0.5987 (m-80) cc_final: 0.5490 (m-10) REVERT: G 244 GLN cc_start: 0.7950 (mm-40) cc_final: 0.7680 (mm-40) REVERT: G 315 THR cc_start: 0.6191 (m) cc_final: 0.5939 (p) REVERT: G 343 ASN cc_start: 0.3613 (t0) cc_final: 0.3142 (m-40) REVERT: G 346 ASP cc_start: 0.5749 (m-30) cc_final: 0.5209 (m-30) REVERT: G 371 ARG cc_start: 0.6529 (OUTLIER) cc_final: 0.5731 (ptp90) REVERT: H 63 HIS cc_start: 0.8380 (OUTLIER) cc_final: 0.8009 (m90) REVERT: H 70 GLU cc_start: 0.8460 (tt0) cc_final: 0.8235 (tp30) REVERT: H 74 LEU cc_start: 0.8711 (mt) cc_final: 0.8295 (tt) REVERT: H 105 PHE cc_start: 0.7105 (m-80) cc_final: 0.6591 (m-80) REVERT: H 125 TYR cc_start: 0.6934 (m-80) cc_final: 0.6100 (t80) REVERT: H 143 LYS cc_start: 0.6167 (tttm) cc_final: 0.5453 (tttt) REVERT: H 160 ILE cc_start: 0.8599 (mt) cc_final: 0.8321 (tt) REVERT: H 224 MET cc_start: 0.8371 (mmm) cc_final: 0.8155 (mmm) REVERT: H 321 ASP cc_start: 0.8394 (p0) cc_final: 0.8141 (p0) outliers start: 62 outliers final: 38 residues processed: 313 average time/residue: 0.3150 time to fit residues: 157.1756 Evaluate side-chains 276 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 233 time to evaluate : 2.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 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 151 LEU Chi-restraints excluded: chain C residue 349 PHE 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 224 MET 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 95 VAL Chi-restraints excluded: chain E residue 224 MET Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain F residue 188 ASP Chi-restraints excluded: chain G residue 59 HIS 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 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 63 HIS 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 225 optimal weight: 9.9990 chunk 175 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 257 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 196 optimal weight: 1.9990 chunk 253 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 chunk 209 optimal weight: 0.0980 overall best weight: 1.2188 ------------------------------------------------------------------------------- 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 ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.156747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.120204 restraints weight = 35518.002| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.56 r_work: 0.3491 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.4023 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= 0.142 Angle : 0.552 8.353 30136 Z= 0.300 Chirality : 0.045 0.170 3336 Planarity : 0.004 0.037 3768 Dihedral : 5.791 52.280 2920 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.14 % Allowed : 14.68 % Favored : 83.18 % 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: 0.38 (0.17), residues: 2624 helix: 0.13 (0.21), residues: 648 sheet: 0.34 (0.21), residues: 680 loop : 0.47 (0.18), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP G 312 HIS 0.007 0.001 HIS A 82 PHE 0.030 0.002 PHE H 60 TYR 0.014 0.001 TYR D 53 ARG 0.003 0.000 ARG B 371 Details of bonding type rmsd hydrogen bonds : bond 0.03696 ( 952) hydrogen bonds : angle 5.07283 ( 2496) covalent geometry : bond 0.00328 (22248) covalent geometry : angle 0.55247 (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 311 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 260 time to evaluate : 2.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 HIS cc_start: 0.8548 (OUTLIER) cc_final: 0.8311 (m-70) REVERT: A 64 GLU cc_start: 0.8454 (tt0) cc_final: 0.8237 (tm-30) REVERT: A 67 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8417 (mm) REVERT: A 74 LEU cc_start: 0.8628 (mt) cc_final: 0.8280 (tt) REVERT: A 90 LYS cc_start: 0.8488 (mmmt) cc_final: 0.8206 (mmtm) REVERT: A 125 TYR cc_start: 0.7037 (m-80) cc_final: 0.6751 (m-80) REVERT: A 160 ILE cc_start: 0.8572 (mt) cc_final: 0.8302 (tt) REVERT: A 279 ASP cc_start: 0.8755 (OUTLIER) cc_final: 0.8484 (m-30) REVERT: A 319 MET cc_start: 0.7944 (mmm) cc_final: 0.7405 (mtt) REVERT: B 66 MET cc_start: 0.6550 (mtm) cc_final: 0.6310 (mtp) REVERT: B 315 THR cc_start: 0.6335 (m) cc_final: 0.6119 (p) REVERT: B 346 ASP cc_start: 0.6092 (m-30) cc_final: 0.5859 (m-30) REVERT: D 211 TYR cc_start: 0.8054 (t80) cc_final: 0.7425 (t80) REVERT: D 224 MET cc_start: 0.7345 (mtp) cc_final: 0.7135 (mtt) REVERT: D 274 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7677 (mm110) REVERT: E 211 TYR cc_start: 0.7957 (t80) cc_final: 0.7435 (t80) REVERT: E 224 MET cc_start: 0.7450 (mtp) cc_final: 0.7106 (mtt) REVERT: E 326 LYS cc_start: 0.8011 (mtmt) cc_final: 0.7558 (mtmm) REVERT: G 167 CYS cc_start: 0.6404 (t) cc_final: 0.6160 (t) REVERT: G 169 PHE cc_start: 0.6885 (m-80) cc_final: 0.6109 (t80) REVERT: G 173 MET cc_start: 0.4940 (tpp) cc_final: 0.4586 (tpp) REVERT: G 179 TYR cc_start: 0.6610 (t80) cc_final: 0.5798 (m-10) REVERT: G 220 TYR cc_start: 0.6016 (m-80) cc_final: 0.5568 (m-10) REVERT: G 315 THR cc_start: 0.6041 (m) cc_final: 0.5809 (p) REVERT: G 343 ASN cc_start: 0.3498 (t0) cc_final: 0.3122 (m-40) REVERT: H 53 TYR cc_start: 0.4568 (t80) cc_final: 0.3751 (m-80) REVERT: H 70 GLU cc_start: 0.8447 (tt0) cc_final: 0.8218 (tp30) REVERT: H 74 LEU cc_start: 0.8688 (mt) cc_final: 0.8247 (tt) REVERT: H 105 PHE cc_start: 0.7313 (m-80) cc_final: 0.6726 (m-80) REVERT: H 125 TYR cc_start: 0.6925 (m-80) cc_final: 0.6642 (m-80) REVERT: H 143 LYS cc_start: 0.6111 (tttm) cc_final: 0.5424 (tttt) outliers start: 51 outliers final: 32 residues processed: 293 average time/residue: 0.3086 time to fit residues: 145.7867 Evaluate side-chains 264 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 228 time to evaluate : 2.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 HIS 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 284 LEU 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 274 GLN Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 226 CYS Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 226 CYS Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain G residue 351 ILE Chi-restraints excluded: chain G residue 364 CYS 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: 8.9990 chunk 160 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 254 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 201 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 106 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 HIS ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.152755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.116421 restraints weight = 35652.121| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.65 r_work: 0.3422 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.4420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 22248 Z= 0.262 Angle : 0.650 8.839 30136 Z= 0.351 Chirality : 0.048 0.168 3336 Planarity : 0.004 0.037 3768 Dihedral : 6.127 57.534 2920 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.23 % Allowed : 15.10 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.17), residues: 2624 helix: -0.17 (0.21), residues: 648 sheet: 0.10 (0.20), residues: 720 loop : 0.32 (0.19), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP G 312 HIS 0.006 0.001 HIS A 63 PHE 0.024 0.002 PHE H 60 TYR 0.021 0.002 TYR B 211 ARG 0.003 0.001 ARG E 84 Details of bonding type rmsd hydrogen bonds : bond 0.04363 ( 952) hydrogen bonds : angle 5.31324 ( 2496) covalent geometry : bond 0.00616 (22248) covalent geometry : angle 0.64961 (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 323 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 246 time to evaluate : 2.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LEU cc_start: 0.8695 (mt) cc_final: 0.8341 (tt) REVERT: A 125 TYR cc_start: 0.7016 (m-80) cc_final: 0.6665 (m-80) REVERT: A 160 ILE cc_start: 0.8615 (mt) cc_final: 0.8378 (tt) REVERT: A 224 MET cc_start: 0.8200 (mmm) cc_final: 0.7969 (mpp) REVERT: A 314 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8197 (mp10) REVERT: A 319 MET cc_start: 0.8132 (mmm) cc_final: 0.7718 (mtt) REVERT: B 76 TYR cc_start: 0.7511 (m-80) cc_final: 0.7305 (m-80) REVERT: B 346 ASP cc_start: 0.6453 (m-30) cc_final: 0.5922 (m-30) REVERT: D 60 PHE cc_start: 0.8197 (OUTLIER) cc_final: 0.7915 (p90) REVERT: D 211 TYR cc_start: 0.8046 (t80) cc_final: 0.7408 (t80) REVERT: D 224 MET cc_start: 0.7564 (OUTLIER) cc_final: 0.7232 (mtt) REVERT: D 274 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7935 (tp40) REVERT: D 314 GLN cc_start: 0.9062 (OUTLIER) cc_final: 0.7769 (mp10) REVERT: E 211 TYR cc_start: 0.7948 (t80) cc_final: 0.7370 (t80) REVERT: E 224 MET cc_start: 0.7649 (OUTLIER) cc_final: 0.6793 (mtt) REVERT: E 238 ASP cc_start: 0.8524 (t0) cc_final: 0.8311 (m-30) REVERT: E 314 GLN cc_start: 0.9089 (OUTLIER) cc_final: 0.7773 (mp10) REVERT: F 80 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8611 (mtm) REVERT: G 167 CYS cc_start: 0.6469 (t) cc_final: 0.6195 (t) REVERT: G 169 PHE cc_start: 0.7098 (m-80) cc_final: 0.6634 (t80) REVERT: G 173 MET cc_start: 0.5225 (tpp) cc_final: 0.4990 (tpp) REVERT: G 220 TYR cc_start: 0.6159 (m-80) cc_final: 0.5688 (m-10) REVERT: G 271 PHE cc_start: 0.7307 (p90) cc_final: 0.6954 (p90) REVERT: G 343 ASN cc_start: 0.3405 (t0) cc_final: 0.3168 (m-40) REVERT: H 53 TYR cc_start: 0.4521 (t80) cc_final: 0.3631 (m-80) REVERT: H 70 GLU cc_start: 0.8422 (tt0) cc_final: 0.8190 (tp30) REVERT: H 74 LEU cc_start: 0.8748 (mt) cc_final: 0.8323 (tt) REVERT: H 105 PHE cc_start: 0.7293 (m-80) cc_final: 0.6596 (m-80) REVERT: H 125 TYR cc_start: 0.6928 (m-80) cc_final: 0.6441 (m-80) REVERT: H 143 LYS cc_start: 0.6187 (tttm) cc_final: 0.5461 (tttt) REVERT: H 314 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.8160 (mp10) outliers start: 77 outliers final: 51 residues processed: 295 average time/residue: 0.3020 time to fit residues: 144.4029 Evaluate side-chains 283 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 223 time to evaluate : 2.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain 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 349 PHE Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain D residue 60 PHE Chi-restraints excluded: chain D residue 81 PHE Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 224 MET Chi-restraints excluded: chain D residue 226 CYS Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 274 GLN Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 346 ASP Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain E residue 81 PHE Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 224 MET Chi-restraints excluded: chain E residue 226 CYS Chi-restraints excluded: chain E residue 252 ILE Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain F residue 80 MET Chi-restraints excluded: chain G residue 60 PHE Chi-restraints excluded: chain G residue 74 LEU 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 226 CYS Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain G residue 364 CYS Chi-restraints excluded: chain H residue 80 MET 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 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: 0.0980 chunk 1 optimal weight: 5.9990 chunk 156 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 150 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 164 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 262 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 214 HIS ** 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 = 0.4182 r_free = 0.4182 target = 0.159017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.122900 restraints weight = 35545.143| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.56 r_work: 0.3514 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 22248 Z= 0.111 Angle : 0.536 11.647 30136 Z= 0.291 Chirality : 0.044 0.167 3336 Planarity : 0.003 0.040 3768 Dihedral : 5.676 57.367 2920 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.10 % Allowed : 16.57 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.17), residues: 2624 helix: 0.25 (0.21), residues: 640 sheet: 0.26 (0.20), residues: 736 loop : 0.37 (0.19), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 312 HIS 0.004 0.001 HIS G 311 PHE 0.012 0.001 PHE G 292 TYR 0.015 0.001 TYR D 53 ARG 0.003 0.000 ARG B 371 Details of bonding type rmsd hydrogen bonds : bond 0.03451 ( 952) hydrogen bonds : angle 4.94746 ( 2496) covalent geometry : bond 0.00246 (22248) covalent geometry : angle 0.53581 (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 309 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 259 time to evaluate : 2.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 ASP cc_start: 0.7959 (t0) cc_final: 0.7736 (t0) REVERT: A 74 LEU cc_start: 0.8603 (mt) cc_final: 0.8250 (tt) REVERT: A 125 TYR cc_start: 0.6997 (m-80) cc_final: 0.6678 (m-80) REVERT: A 279 ASP cc_start: 0.8713 (OUTLIER) cc_final: 0.8502 (m-30) REVERT: A 314 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8291 (mp10) REVERT: A 319 MET cc_start: 0.7840 (mmm) cc_final: 0.7495 (mtt) REVERT: B 65 GLU cc_start: 0.7685 (tt0) cc_final: 0.7372 (tm-30) REVERT: B 149 VAL cc_start: 0.8384 (OUTLIER) cc_final: 0.8007 (m) REVERT: B 319 MET cc_start: 0.6608 (tpp) cc_final: 0.6332 (mtt) REVERT: B 346 ASP cc_start: 0.6421 (m-30) cc_final: 0.6050 (m-30) REVERT: C 224 MET cc_start: 0.8429 (mtt) cc_final: 0.8216 (mtt) REVERT: D 104 MET cc_start: 0.7847 (ttp) cc_final: 0.7551 (ttp) REVERT: D 162 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8140 (tm-30) REVERT: D 211 TYR cc_start: 0.8044 (t80) cc_final: 0.7467 (t80) REVERT: D 224 MET cc_start: 0.7300 (OUTLIER) cc_final: 0.6876 (mtt) REVERT: D 274 GLN cc_start: 0.8102 (mm-40) cc_final: 0.7879 (tp40) REVERT: D 314 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.7562 (mp10) REVERT: E 162 GLU cc_start: 0.8390 (tm-30) cc_final: 0.8091 (tm-30) REVERT: E 205 ASP cc_start: 0.7272 (OUTLIER) cc_final: 0.6957 (m-30) REVERT: E 211 TYR cc_start: 0.7945 (t80) cc_final: 0.7408 (t80) REVERT: E 224 MET cc_start: 0.7327 (mtp) cc_final: 0.7072 (mtt) REVERT: E 277 ARG cc_start: 0.7474 (mtm180) cc_final: 0.7265 (ptt180) REVERT: E 314 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.7563 (mp10) REVERT: F 104 MET cc_start: 0.7385 (OUTLIER) cc_final: 0.6959 (ttt) REVERT: G 53 TYR cc_start: 0.4839 (t80) cc_final: 0.4000 (m-10) REVERT: G 74 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7102 (mt) REVERT: G 157 ASP cc_start: 0.5723 (m-30) cc_final: 0.5478 (t0) REVERT: G 169 PHE cc_start: 0.6946 (m-80) cc_final: 0.6424 (t80) REVERT: G 173 MET cc_start: 0.5028 (tpp) cc_final: 0.4637 (tpp) REVERT: G 179 TYR cc_start: 0.6356 (t80) cc_final: 0.5647 (m-10) REVERT: G 220 TYR cc_start: 0.6312 (m-80) cc_final: 0.5854 (m-10) REVERT: H 63 HIS cc_start: 0.8202 (m90) cc_final: 0.7953 (m-70) REVERT: H 74 LEU cc_start: 0.8679 (mt) cc_final: 0.8190 (tt) REVERT: H 105 PHE cc_start: 0.7351 (m-80) cc_final: 0.6758 (m-80) REVERT: H 125 TYR cc_start: 0.7035 (m-80) cc_final: 0.6706 (m-80) REVERT: H 224 MET cc_start: 0.8070 (mmm) cc_final: 0.7799 (mpp) REVERT: H 314 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.8256 (mp10) outliers start: 50 outliers final: 26 residues processed: 292 average time/residue: 0.3291 time to fit residues: 154.6250 Evaluate side-chains 265 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 229 time to evaluate : 2.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 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 149 VAL Chi-restraints excluded: chain B residue 284 LEU 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 325 VAL Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain E residue 81 PHE Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 205 ASP 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 F residue 104 MET Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 79 SER Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 351 ILE Chi-restraints excluded: chain G residue 364 CYS Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 279 ASP Chi-restraints excluded: chain H residue 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: 0.6980 chunk 107 optimal weight: 0.6980 chunk 109 optimal weight: 6.9990 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: 5.9990 chunk 255 optimal weight: 0.6980 chunk 215 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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 F 244 GLN ** G 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.157647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.121253 restraints weight = 35690.498| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.45 r_work: 0.3502 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.4761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22248 Z= 0.169 Angle : 0.579 12.273 30136 Z= 0.312 Chirality : 0.045 0.162 3336 Planarity : 0.004 0.039 3768 Dihedral : 5.683 54.135 2920 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.52 % Allowed : 17.11 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.31 (0.17), residues: 2624 helix: 0.13 (0.21), residues: 648 sheet: 0.30 (0.20), residues: 696 loop : 0.38 (0.18), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP H 184 HIS 0.008 0.001 HIS G 311 PHE 0.019 0.002 PHE H 87 TYR 0.020 0.002 TYR B 211 ARG 0.003 0.000 ARG B 371 Details of bonding type rmsd hydrogen bonds : bond 0.03774 ( 952) hydrogen bonds : angle 5.02595 ( 2496) covalent geometry : bond 0.00395 (22248) covalent geometry : angle 0.57864 (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 292 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 232 time to evaluate : 2.323 Fit side-chains revert: symmetry clash REVERT: A 74 LEU cc_start: 0.8693 (mt) cc_final: 0.8319 (tt) REVERT: A 90 LYS cc_start: 0.7732 (mmtm) cc_final: 0.6745 (mttt) REVERT: A 279 ASP cc_start: 0.8627 (OUTLIER) cc_final: 0.8351 (m-30) REVERT: A 314 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8257 (mp10) REVERT: A 319 MET cc_start: 0.8006 (mmm) cc_final: 0.7711 (mtt) REVERT: B 65 GLU cc_start: 0.7669 (tt0) cc_final: 0.7345 (tm-30) REVERT: B 103 CYS cc_start: 0.7782 (OUTLIER) cc_final: 0.7081 (m) REVERT: B 149 VAL cc_start: 0.8453 (OUTLIER) cc_final: 0.8070 (m) REVERT: B 319 MET cc_start: 0.6531 (tpp) cc_final: 0.6281 (mtt) REVERT: B 346 ASP cc_start: 0.6531 (m-30) cc_final: 0.5996 (m-30) REVERT: D 60 PHE cc_start: 0.8107 (OUTLIER) cc_final: 0.7866 (p90) REVERT: D 211 TYR cc_start: 0.8045 (t80) cc_final: 0.7413 (t80) REVERT: D 224 MET cc_start: 0.7463 (OUTLIER) cc_final: 0.6992 (mtt) REVERT: D 254 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.6992 (tp30) REVERT: D 274 GLN cc_start: 0.8133 (mm-40) cc_final: 0.7855 (tp40) REVERT: D 314 GLN cc_start: 0.9033 (OUTLIER) cc_final: 0.7779 (mp10) REVERT: E 80 MET cc_start: 0.9112 (ttm) cc_final: 0.8823 (mtp) REVERT: E 211 TYR cc_start: 0.7963 (t80) cc_final: 0.7449 (t80) REVERT: E 224 MET cc_start: 0.7521 (mtp) cc_final: 0.7227 (mtt) REVERT: E 238 ASP cc_start: 0.8239 (t0) cc_final: 0.8027 (t0) REVERT: E 244 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.7472 (mt0) REVERT: E 314 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.7785 (mp10) REVERT: F 224 MET cc_start: 0.8718 (mtt) cc_final: 0.8320 (mtt) REVERT: G 53 TYR cc_start: 0.4708 (t80) cc_final: 0.4101 (m-10) REVERT: G 74 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.6962 (mt) REVERT: G 169 PHE cc_start: 0.7037 (m-80) cc_final: 0.6600 (t80) REVERT: G 179 TYR cc_start: 0.6376 (t80) cc_final: 0.5750 (m-10) REVERT: H 74 LEU cc_start: 0.8653 (mt) cc_final: 0.8213 (tt) REVERT: H 90 LYS cc_start: 0.8274 (mmmt) cc_final: 0.7578 (mttt) REVERT: H 125 TYR cc_start: 0.7149 (m-80) cc_final: 0.6835 (m-80) REVERT: H 222 PHE cc_start: 0.8227 (OUTLIER) cc_final: 0.7611 (p90) REVERT: H 314 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8208 (mp10) outliers start: 60 outliers final: 35 residues processed: 273 average time/residue: 0.2925 time to fit residues: 129.7542 Evaluate side-chains 260 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 212 time to evaluate : 2.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 295 CYS Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain D residue 60 PHE Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 224 MET Chi-restraints excluded: chain D residue 226 CYS Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 272 CYS Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain D residue 325 VAL Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain E residue 81 PHE Chi-restraints excluded: chain E residue 95 VAL 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 F residue 104 MET Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 79 SER 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 226 CYS Chi-restraints excluded: chain G residue 292 PHE 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 296 HIS Chi-restraints excluded: chain H residue 314 GLN Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain H residue 358 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 25 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 184 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 143 optimal weight: 0.7980 chunk 145 optimal weight: 3.9990 chunk 256 optimal weight: 0.0870 chunk 75 optimal weight: 0.5980 chunk 168 optimal weight: 0.8980 chunk 1 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 HIS ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.161051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.125110 restraints weight = 35562.345| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.49 r_work: 0.3569 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.4927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 22248 Z= 0.108 Angle : 0.545 11.807 30136 Z= 0.293 Chirality : 0.044 0.157 3336 Planarity : 0.003 0.041 3768 Dihedral : 5.457 57.805 2920 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.31 % Allowed : 17.66 % Favored : 80.03 % 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: 0.47 (0.17), residues: 2624 helix: 0.34 (0.21), residues: 640 sheet: 0.35 (0.19), residues: 752 loop : 0.48 (0.19), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 184 HIS 0.003 0.001 HIS G 311 PHE 0.011 0.001 PHE C 222 TYR 0.018 0.001 TYR B 211 ARG 0.002 0.000 ARG B 371 Details of bonding type rmsd hydrogen bonds : bond 0.03385 ( 952) hydrogen bonds : angle 4.86925 ( 2496) covalent geometry : bond 0.00238 (22248) covalent geometry : angle 0.54534 (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 302 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 247 time to evaluate : 2.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: -0.0043 (OUTLIER) cc_final: -0.0333 (ppp) REVERT: A 74 LEU cc_start: 0.8670 (mt) cc_final: 0.8273 (tt) REVERT: A 224 MET cc_start: 0.8162 (mmm) cc_final: 0.7862 (mpp) REVERT: A 314 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8259 (mp10) REVERT: A 319 MET cc_start: 0.7802 (mmm) cc_final: 0.7557 (mtt) REVERT: B 53 TYR cc_start: 0.4603 (t80) cc_final: 0.4125 (m-10) REVERT: B 65 GLU cc_start: 0.7645 (tt0) cc_final: 0.7366 (tm-30) REVERT: B 66 MET cc_start: 0.6121 (OUTLIER) cc_final: 0.5878 (mtp) REVERT: B 103 CYS cc_start: 0.7422 (OUTLIER) cc_final: 0.6932 (m) REVERT: B 149 VAL cc_start: 0.8408 (OUTLIER) cc_final: 0.8073 (m) REVERT: B 346 ASP cc_start: 0.6374 (m-30) cc_final: 0.5864 (m-30) REVERT: D 162 GLU cc_start: 0.8370 (tm-30) cc_final: 0.8145 (tm-30) REVERT: D 211 TYR cc_start: 0.8001 (t80) cc_final: 0.7446 (t80) REVERT: D 224 MET cc_start: 0.7313 (OUTLIER) cc_final: 0.7046 (mtt) REVERT: D 254 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.6914 (tp30) REVERT: D 276 LYS cc_start: 0.7306 (mtmm) cc_final: 0.6997 (ptpt) REVERT: D 314 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.7582 (mp10) REVERT: E 80 MET cc_start: 0.9072 (ttm) cc_final: 0.8811 (mtp) REVERT: E 162 GLU cc_start: 0.8343 (tm-30) cc_final: 0.8062 (tm-30) REVERT: E 211 TYR cc_start: 0.7906 (t80) cc_final: 0.7428 (t80) REVERT: E 224 MET cc_start: 0.7385 (mtp) cc_final: 0.7106 (mtt) REVERT: E 314 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.7567 (mp10) REVERT: F 104 MET cc_start: 0.7262 (OUTLIER) cc_final: 0.6904 (ttt) REVERT: G 53 TYR cc_start: 0.4532 (t80) cc_final: 0.4003 (m-10) REVERT: G 74 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.6976 (mt) REVERT: G 169 PHE cc_start: 0.6936 (m-80) cc_final: 0.6492 (t80) REVERT: G 179 TYR cc_start: 0.6145 (t80) cc_final: 0.5567 (m-10) REVERT: G 246 VAL cc_start: 0.7313 (t) cc_final: 0.7103 (t) REVERT: H 63 HIS cc_start: 0.8109 (m90) cc_final: 0.7882 (m-70) REVERT: H 74 LEU cc_start: 0.8557 (mt) cc_final: 0.8164 (tt) REVERT: H 90 LYS cc_start: 0.8306 (mmmt) cc_final: 0.7666 (mttt) REVERT: H 125 TYR cc_start: 0.7184 (m-80) cc_final: 0.6972 (m-80) REVERT: H 222 PHE cc_start: 0.8152 (OUTLIER) cc_final: 0.7673 (p90) REVERT: H 314 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.8241 (mp10) outliers start: 55 outliers final: 33 residues processed: 285 average time/residue: 0.2925 time to fit residues: 136.6697 Evaluate side-chains 265 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 219 time to evaluate : 2.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 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 66 MET 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 149 VAL Chi-restraints excluded: chain B residue 226 CYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 197 THR 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 254 GLU 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 95 VAL 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 F residue 104 MET Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 79 SER 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 158 ILE Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 226 CYS Chi-restraints excluded: chain G residue 351 ILE Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 222 PHE Chi-restraints excluded: chain H residue 296 HIS Chi-restraints excluded: chain H residue 314 GLN Chi-restraints excluded: chain H residue 334 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 187 optimal weight: 0.9990 chunk 225 optimal weight: 7.9990 chunk 221 optimal weight: 7.9990 chunk 129 optimal weight: 0.9990 chunk 168 optimal weight: 0.7980 chunk 249 optimal weight: 0.2980 chunk 250 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 261 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 HIS ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.159613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.122992 restraints weight = 35058.064| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.43 r_work: 0.3547 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.5054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22248 Z= 0.115 Angle : 0.554 11.987 30136 Z= 0.295 Chirality : 0.044 0.176 3336 Planarity : 0.003 0.042 3768 Dihedral : 5.404 58.125 2920 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.14 % Allowed : 17.66 % Favored : 80.20 % 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: 0.51 (0.17), residues: 2624 helix: 0.33 (0.21), residues: 640 sheet: 0.40 (0.19), residues: 752 loop : 0.51 (0.19), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP H 184 HIS 0.004 0.001 HIS G 63 PHE 0.015 0.001 PHE B 271 TYR 0.017 0.001 TYR B 211 ARG 0.002 0.000 ARG B 371 Details of bonding type rmsd hydrogen bonds : bond 0.03431 ( 952) hydrogen bonds : angle 4.87113 ( 2496) covalent geometry : bond 0.00259 (22248) covalent geometry : angle 0.55382 (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 282 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 231 time to evaluate : 3.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: 0.0001 (OUTLIER) cc_final: -0.0308 (ppp) REVERT: A 74 LEU cc_start: 0.8660 (mt) cc_final: 0.8237 (tt) REVERT: A 90 LYS cc_start: 0.7633 (mmtm) cc_final: 0.6729 (mttt) REVERT: A 224 MET cc_start: 0.8200 (mmm) cc_final: 0.7913 (mpp) REVERT: A 314 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.8267 (mp10) REVERT: A 337 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.7435 (mmm) REVERT: B 53 TYR cc_start: 0.4592 (t80) cc_final: 0.4127 (m-80) REVERT: B 103 CYS cc_start: 0.7437 (OUTLIER) cc_final: 0.6887 (m) REVERT: B 149 VAL cc_start: 0.8450 (OUTLIER) cc_final: 0.8154 (m) REVERT: B 244 GLN cc_start: 0.7733 (tp-100) cc_final: 0.7475 (tp-100) REVERT: B 346 ASP cc_start: 0.6341 (m-30) cc_final: 0.5694 (m-30) REVERT: D 162 GLU cc_start: 0.8420 (tm-30) cc_final: 0.8216 (tm-30) REVERT: D 211 TYR cc_start: 0.7944 (t80) cc_final: 0.7475 (t80) REVERT: D 224 MET cc_start: 0.7318 (OUTLIER) cc_final: 0.7034 (mtt) REVERT: D 276 LYS cc_start: 0.7325 (mtmm) cc_final: 0.7084 (ptpt) REVERT: D 314 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.7714 (mp10) REVERT: E 80 MET cc_start: 0.9061 (ttm) cc_final: 0.8812 (mtp) REVERT: E 211 TYR cc_start: 0.7875 (t80) cc_final: 0.7535 (t80) REVERT: E 224 MET cc_start: 0.7430 (mtp) cc_final: 0.7128 (mtt) REVERT: E 314 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.7757 (mp10) REVERT: F 104 MET cc_start: 0.7312 (ttp) cc_final: 0.6857 (ttt) REVERT: G 53 TYR cc_start: 0.4261 (t80) cc_final: 0.3913 (m-10) REVERT: G 74 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6885 (mt) REVERT: G 169 PHE cc_start: 0.6936 (m-80) cc_final: 0.6475 (t80) REVERT: G 179 TYR cc_start: 0.6150 (t80) cc_final: 0.5571 (m-10) REVERT: G 246 VAL cc_start: 0.7411 (t) cc_final: 0.7123 (t) REVERT: H 74 LEU cc_start: 0.8609 (mt) cc_final: 0.8193 (tt) REVERT: H 90 LYS cc_start: 0.8342 (mmmt) cc_final: 0.7709 (mttt) REVERT: H 222 PHE cc_start: 0.8199 (OUTLIER) cc_final: 0.7334 (p90) REVERT: H 224 MET cc_start: 0.8261 (mmm) cc_final: 0.7720 (mpp) REVERT: H 337 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7555 (mmm) outliers start: 51 outliers final: 34 residues processed: 265 average time/residue: 0.4052 time to fit residues: 178.0747 Evaluate side-chains 264 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 219 time to evaluate : 4.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 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 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 149 VAL Chi-restraints excluded: chain B residue 226 CYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 295 CYS Chi-restraints excluded: chain C residue 197 THR 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 95 VAL Chi-restraints excluded: chain E residue 226 CYS Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain G residue 74 LEU 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 176 THR Chi-restraints excluded: chain G residue 226 CYS Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 351 ILE Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 222 PHE Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 279 ASP Chi-restraints excluded: chain H residue 296 HIS Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain H residue 337 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 74 optimal weight: 0.9980 chunk 67 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 262 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 223 optimal weight: 0.6980 chunk 43 optimal weight: 5.9990 chunk 225 optimal weight: 0.0370 chunk 196 optimal weight: 2.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 HIS ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.160323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.124688 restraints weight = 35407.173| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.43 r_work: 0.3566 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.5182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 22248 Z= 0.112 Angle : 0.556 11.738 30136 Z= 0.296 Chirality : 0.044 0.160 3336 Planarity : 0.003 0.041 3768 Dihedral : 5.361 59.168 2920 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.97 % Allowed : 17.83 % Favored : 80.20 % 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: 0.52 (0.17), residues: 2624 helix: 0.35 (0.21), residues: 640 sheet: 0.49 (0.20), residues: 744 loop : 0.44 (0.19), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 184 HIS 0.004 0.001 HIS G 63 PHE 0.015 0.001 PHE E 317 TYR 0.017 0.001 TYR B 211 ARG 0.007 0.000 ARG B 371 Details of bonding type rmsd hydrogen bonds : bond 0.03388 ( 952) hydrogen bonds : angle 4.85854 ( 2496) covalent geometry : bond 0.00250 (22248) covalent geometry : angle 0.55614 (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 283 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 236 time to evaluate : 3.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 MET cc_start: -0.0338 (OUTLIER) cc_final: -0.0633 (ppp) REVERT: A 74 LEU cc_start: 0.8676 (mt) cc_final: 0.8224 (tt) REVERT: A 90 LYS cc_start: 0.7615 (mmtm) cc_final: 0.6809 (mttt) REVERT: A 224 MET cc_start: 0.8145 (mmm) cc_final: 0.7854 (mpp) REVERT: A 314 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.8214 (mp10) REVERT: A 319 MET cc_start: 0.7776 (mmm) cc_final: 0.7282 (mtt) REVERT: A 337 MET cc_start: 0.7654 (OUTLIER) cc_final: 0.7397 (mmm) REVERT: B 53 TYR cc_start: 0.4328 (t80) cc_final: 0.3939 (m-80) REVERT: B 103 CYS cc_start: 0.7410 (OUTLIER) cc_final: 0.6869 (m) REVERT: B 149 VAL cc_start: 0.8452 (OUTLIER) cc_final: 0.8174 (m) REVERT: B 244 GLN cc_start: 0.7832 (tp-100) cc_final: 0.7586 (tp-100) REVERT: B 319 MET cc_start: 0.6904 (tmm) cc_final: 0.6586 (tpt) REVERT: B 346 ASP cc_start: 0.6378 (m-30) cc_final: 0.5832 (m-30) REVERT: B 371 ARG cc_start: 0.6648 (ttp-110) cc_final: 0.6323 (ttp-110) REVERT: D 207 GLN cc_start: 0.8167 (pm20) cc_final: 0.7961 (pt0) REVERT: D 211 TYR cc_start: 0.7954 (t80) cc_final: 0.7433 (t80) REVERT: D 276 LYS cc_start: 0.7294 (mtmm) cc_final: 0.7063 (ptmt) REVERT: D 314 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.7612 (mp10) REVERT: E 80 MET cc_start: 0.9055 (ttm) cc_final: 0.8774 (mtp) REVERT: E 211 TYR cc_start: 0.7890 (t80) cc_final: 0.7545 (t80) REVERT: E 224 MET cc_start: 0.7300 (mtp) cc_final: 0.7009 (mtt) REVERT: E 244 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7566 (mt0) REVERT: E 314 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.7627 (mp10) REVERT: F 104 MET cc_start: 0.7255 (OUTLIER) cc_final: 0.6822 (ttt) REVERT: G 53 TYR cc_start: 0.4176 (t80) cc_final: 0.3973 (m-10) REVERT: G 74 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.6890 (mt) REVERT: G 169 PHE cc_start: 0.6958 (m-80) cc_final: 0.6517 (t80) REVERT: G 179 TYR cc_start: 0.6163 (t80) cc_final: 0.5560 (m-10) REVERT: G 246 VAL cc_start: 0.7112 (t) cc_final: 0.6889 (t) REVERT: H 74 LEU cc_start: 0.8554 (mt) cc_final: 0.8140 (tt) REVERT: H 90 LYS cc_start: 0.8321 (mmmt) cc_final: 0.7715 (mttt) REVERT: H 136 ASP cc_start: 0.7684 (p0) cc_final: 0.7251 (t0) REVERT: H 222 PHE cc_start: 0.8188 (OUTLIER) cc_final: 0.7413 (p90) REVERT: H 224 MET cc_start: 0.8276 (mmm) cc_final: 0.7738 (mpp) REVERT: H 337 MET cc_start: 0.7723 (OUTLIER) cc_final: 0.7511 (mmm) outliers start: 47 outliers final: 29 residues processed: 269 average time/residue: 0.4380 time to fit residues: 197.3814 Evaluate side-chains 265 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 224 time to evaluate : 8.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 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 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 149 VAL Chi-restraints excluded: chain B residue 226 CYS Chi-restraints excluded: chain B residue 295 CYS Chi-restraints excluded: chain C residue 366 THR 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 95 VAL 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 F residue 104 MET Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 351 ILE Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 222 PHE Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 279 ASP Chi-restraints excluded: chain H residue 296 HIS Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain H residue 337 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 178 optimal weight: 3.9990 chunk 200 optimal weight: 3.9990 chunk 262 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 chunk 156 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 197 optimal weight: 0.7980 chunk 202 optimal weight: 6.9990 chunk 251 optimal weight: 0.1980 chunk 192 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 HIS ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 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 63 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.160333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.124555 restraints weight = 35170.009| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.29 r_work: 0.3577 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.5265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22248 Z= 0.113 Angle : 0.546 8.997 30136 Z= 0.293 Chirality : 0.044 0.160 3336 Planarity : 0.003 0.041 3768 Dihedral : 5.309 59.926 2920 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.97 % Allowed : 17.87 % Favored : 80.16 % 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: 0.54 (0.17), residues: 2624 helix: 0.35 (0.21), residues: 640 sheet: 0.49 (0.20), residues: 744 loop : 0.47 (0.19), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP H 184 HIS 0.004 0.001 HIS G 63 PHE 0.020 0.001 PHE F 222 TYR 0.017 0.001 TYR B 211 ARG 0.004 0.000 ARG B 371 Details of bonding type rmsd hydrogen bonds : bond 0.03357 ( 952) hydrogen bonds : angle 4.84785 ( 2496) covalent geometry : bond 0.00254 (22248) covalent geometry : angle 0.54643 (30136) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12922.02 seconds wall clock time: 227 minutes 59.63 seconds (13679.63 seconds total)