Starting phenix.real_space_refine on Wed May 21 18:06:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bhd_44541/05_2025/9bhd_44541.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bhd_44541/05_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_44541/05_2025/9bhd_44541.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bhd_44541/05_2025/9bhd_44541.map" model { file = "/net/cci-nas-00/data/ceres_data/9bhd_44541/05_2025/9bhd_44541.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bhd_44541/05_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 21720 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2689 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 320} Chain: "B" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2689 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 320} Chain: "C" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2689 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 320} Chain: "D" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2689 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 320} Chain: "E" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2689 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 320} Chain: "F" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2689 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 320} Chain: "G" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2689 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 320} Chain: "H" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2689 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 320} Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "C" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "D" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "E" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "F" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "G" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "H" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Time building chain proxies: 12.63, per 1000 atoms: 0.58 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: 5.63 Conformation dependent library (CDL) restraints added in 3.0 seconds 5248 Ramachandran restraints generated. 2624 Oldfield, 0 Emsley, 2624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5056 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 32 sheets defined 36.4% alpha, 37.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.86 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: 8.08 Time building geometry restraints manager: 6.50 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: 3.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.740 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 49.530 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.260 ------------------------------------------------------------------------------- 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 : 2.706 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: 0.3693 time to fit residues: 271.6025 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 : 2.498 ------------------------------------------------------------------------------- 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 = 0.126196 restraints weight = 35478.557| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.65 r_work: 0.3571 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 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 : 2.369 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: 0.6465 (ttt) REVERT: A 143 LYS cc_start: 0.6082 (tttm) cc_final: 0.5367 (tttt) REVERT: A 160 ILE cc_start: 0.8283 (mt) cc_final: 0.7851 (tt) REVERT: A 211 TYR cc_start: 0.8047 (t80) cc_final: 0.7702 (t80) REVERT: A 224 MET cc_start: 0.8417 (mmm) cc_final: 0.8127 (mmm) REVERT: B 47 MET cc_start: -0.0983 (ptt) cc_final: -0.1215 (ptt) REVERT: B 244 GLN cc_start: 0.7655 (mt0) cc_final: 0.7448 (mm110) REVERT: D 162 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7904 (tm-30) REVERT: D 211 TYR cc_start: 0.7910 (t80) cc_final: 0.7321 (t80) REVERT: E 211 TYR cc_start: 0.7795 (t80) cc_final: 0.7438 (t80) REVERT: E 326 LYS cc_start: 0.7747 (mtpp) cc_final: 0.7496 (mtmm) REVERT: G 74 LEU cc_start: 0.7795 (mt) cc_final: 0.7269 (mt) REVERT: G 167 CYS cc_start: 0.6177 (t) cc_final: 0.5837 (t) REVERT: G 169 PHE cc_start: 0.6269 (m-80) cc_final: 0.5539 (t80) REVERT: G 173 MET cc_start: 0.4311 (tpp) cc_final: 0.3545 (tpp) REVERT: G 179 TYR cc_start: 0.6863 (t80) cc_final: 0.6232 (m-10) REVERT: G 203 ILE cc_start: 0.7793 (pt) cc_final: 0.7534 (mp) REVERT: G 216 TRP cc_start: 0.7731 (m100) cc_final: 0.7363 (m100) REVERT: G 220 TYR cc_start: 0.5923 (m-80) cc_final: 0.5440 (m-10) REVERT: G 224 MET cc_start: 0.7085 (mtt) cc_final: 0.6614 (mtt) REVERT: G 241 ASP cc_start: 0.7428 (t0) cc_final: 0.7059 (t0) REVERT: G 253 LYS cc_start: 0.7307 (tptt) cc_final: 0.7028 (mmtt) REVERT: G 273 LEU cc_start: 0.7462 (mt) cc_final: 0.7101 (mt) REVERT: G 274 GLN cc_start: 0.7999 (tp40) cc_final: 0.7775 (tp40) REVERT: G 315 THR cc_start: 0.5553 (m) cc_final: 0.5300 (p) REVERT: G 319 MET cc_start: 0.5575 (ttm) cc_final: 0.5353 (tpt) REVERT: G 343 ASN cc_start: 0.3580 (t0) cc_final: 0.3269 (m-40) REVERT: G 346 ASP cc_start: 0.6334 (m-30) cc_final: 0.5657 (m-30) REVERT: G 370 MET cc_start: 0.6382 (mtp) cc_final: 0.5358 (mtp) REVERT: G 371 ARG cc_start: 0.6861 (OUTLIER) cc_final: 0.6478 (ptp90) REVERT: H 47 MET cc_start: 0.0572 (ptt) cc_final: -0.0593 (mmm) REVERT: H 53 TYR cc_start: 0.4454 (t80) cc_final: 0.3814 (m-80) REVERT: H 70 GLU cc_start: 0.8375 (tt0) cc_final: 0.8075 (tp30) REVERT: H 105 PHE cc_start: 0.7162 (m-80) cc_final: 0.6694 (m-80) REVERT: H 143 LYS cc_start: 0.6152 (tttm) cc_final: 0.5379 (tttt) REVERT: H 160 ILE cc_start: 0.8430 (mt) cc_final: 0.8009 (tt) REVERT: H 224 MET cc_start: 0.8471 (mmm) cc_final: 0.8217 (mmm) REVERT: H 279 ASP cc_start: 0.8470 (OUTLIER) cc_final: 0.8196 (m-30) REVERT: H 321 ASP cc_start: 0.8255 (p0) cc_final: 0.8052 (p0) outliers start: 32 outliers final: 16 residues processed: 365 average time/residue: 0.3246 time to fit residues: 185.4481 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 : 2.330 ------------------------------------------------------------------------------- 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: 7.9990 chunk 218 optimal weight: 5.9990 chunk 209 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 62 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 153 optimal weight: 0.0980 chunk 56 optimal weight: 20.0000 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4120 r_free = 0.4120 target = 0.153932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.117860 restraints weight = 35265.742| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.65 r_work: 0.3438 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 22248 Z= 0.282 Angle : 0.683 9.604 30136 Z= 0.369 Chirality : 0.049 0.184 3336 Planarity : 0.004 0.047 3768 Dihedral : 6.205 53.624 2920 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.60 % Allowed : 12.25 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.17), residues: 2624 helix: -0.22 (0.21), residues: 648 sheet: 0.19 (0.20), residues: 720 loop : 0.49 (0.18), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP G 312 HIS 0.009 0.001 HIS A 82 PHE 0.023 0.003 PHE F 222 TYR 0.020 0.002 TYR B 211 ARG 0.004 0.001 ARG E 369 Details of bonding type rmsd hydrogen bonds : bond 0.04606 ( 952) hydrogen bonds : angle 5.44296 ( 2496) covalent geometry : bond 0.00665 (22248) covalent geometry : angle 0.68294 (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 : 2.332 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: 0.8714 (mt) cc_final: 0.8372 (tt) REVERT: A 125 TYR cc_start: 0.7010 (m-80) cc_final: 0.6645 (m-80) REVERT: A 160 ILE cc_start: 0.8550 (mt) cc_final: 0.8245 (tt) REVERT: A 211 TYR cc_start: 0.8313 (t80) cc_final: 0.7959 (t80) REVERT: A 224 MET cc_start: 0.8226 (mmm) cc_final: 0.7853 (mpp) REVERT: A 319 MET cc_start: 0.8165 (mmm) cc_final: 0.7625 (mtt) REVERT: B 173 MET cc_start: 0.5018 (tpp) cc_final: 0.4673 (tpp) REVERT: B 222 PHE cc_start: 0.7046 (m-80) cc_final: 0.6627 (m-80) REVERT: B 315 THR cc_start: 0.6470 (m) cc_final: 0.6244 (p) REVERT: C 104 MET cc_start: 0.8007 (tmm) cc_final: 0.7187 (tmm) REVERT: C 125 TYR cc_start: 0.8203 (m-10) cc_final: 0.7995 (m-10) REVERT: D 60 PHE cc_start: 0.8211 (OUTLIER) cc_final: 0.7941 (p90) REVERT: D 211 TYR cc_start: 0.8093 (t80) cc_final: 0.7495 (t80) REVERT: E 211 TYR cc_start: 0.8019 (t80) cc_final: 0.7445 (t80) REVERT: E 224 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.6853 (mtt) REVERT: F 371 ARG cc_start: 0.7812 (ptt180) cc_final: 0.7582 (ptt180) REVERT: G 53 TYR cc_start: 0.4969 (t80) cc_final: 0.4760 (t80) REVERT: G 74 LEU cc_start: 0.7767 (mt) cc_final: 0.7548 (mm) REVERT: G 94 ASP cc_start: 0.4725 (m-30) cc_final: 0.4478 (m-30) REVERT: G 167 CYS cc_start: 0.6421 (t) cc_final: 0.6220 (t) REVERT: G 169 PHE cc_start: 0.6708 (m-80) cc_final: 0.6000 (t80) REVERT: G 173 MET cc_start: 0.5019 (tpp) cc_final: 0.4585 (tpp) REVERT: G 179 TYR cc_start: 0.6765 (t80) cc_final: 0.5957 (m-10) REVERT: G 220 TYR cc_start: 0.5978 (m-80) cc_final: 0.5497 (m-10) REVERT: G 244 GLN cc_start: 0.7945 (mm-40) cc_final: 0.7682 (mm-40) REVERT: G 315 THR cc_start: 0.6226 (m) cc_final: 0.5963 (p) REVERT: G 343 ASN cc_start: 0.3643 (t0) cc_final: 0.3163 (m-40) REVERT: G 346 ASP cc_start: 0.5784 (m-30) cc_final: 0.5242 (m-30) REVERT: H 53 TYR cc_start: 0.4433 (t80) cc_final: 0.3742 (m-80) REVERT: H 63 HIS cc_start: 0.8397 (OUTLIER) cc_final: 0.8049 (m90) REVERT: H 70 GLU cc_start: 0.8440 (tt0) cc_final: 0.8224 (tp30) REVERT: H 74 LEU cc_start: 0.8704 (mt) cc_final: 0.8290 (tt) REVERT: H 105 PHE cc_start: 0.7131 (m-80) cc_final: 0.6618 (m-80) REVERT: H 125 TYR cc_start: 0.6896 (m-80) cc_final: 0.6076 (t80) REVERT: H 143 LYS cc_start: 0.6210 (tttm) cc_final: 0.5501 (tttt) REVERT: H 160 ILE cc_start: 0.8623 (mt) cc_final: 0.8346 (tt) REVERT: H 224 MET cc_start: 0.8384 (mmm) cc_final: 0.8168 (mmm) REVERT: H 321 ASP cc_start: 0.8402 (p0) cc_final: 0.8149 (p0) outliers start: 62 outliers final: 39 residues processed: 313 average time/residue: 0.3006 time to fit residues: 151.4477 Evaluate side-chains 272 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 230 time to evaluate : 2.249 ------------------------------------------------------------------------------- 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 194 ASP 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 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: 0.6980 chunk 97 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 257 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 196 optimal weight: 1.9990 chunk 253 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 209 optimal weight: 9.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 = 0.4129 r_free = 0.4129 target = 0.154673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.118464 restraints weight = 35605.011| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.64 r_work: 0.3455 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 22248 Z= 0.192 Angle : 0.588 8.859 30136 Z= 0.319 Chirality : 0.046 0.162 3336 Planarity : 0.004 0.037 3768 Dihedral : 5.974 57.919 2920 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.52 % Allowed : 15.18 % Favored : 82.30 % 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: 0.18 (0.17), residues: 2624 helix: -0.05 (0.21), residues: 648 sheet: 0.20 (0.21), residues: 680 loop : 0.36 (0.18), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H 184 HIS 0.006 0.001 HIS A 82 PHE 0.029 0.002 PHE H 60 TYR 0.015 0.002 TYR D 53 ARG 0.003 0.000 ARG B 371 Details of bonding type rmsd hydrogen bonds : bond 0.03979 ( 952) hydrogen bonds : angle 5.19442 ( 2496) covalent geometry : bond 0.00452 (22248) covalent geometry : angle 0.58835 (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 315 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 255 time to evaluate : 2.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.8406 (tt0) cc_final: 0.8182 (tm-30) REVERT: A 74 LEU cc_start: 0.8646 (mt) cc_final: 0.8318 (tt) REVERT: A 90 LYS cc_start: 0.8401 (mmmt) cc_final: 0.8062 (mptt) REVERT: A 125 TYR cc_start: 0.7036 (m-80) cc_final: 0.6749 (m-80) REVERT: A 160 ILE cc_start: 0.8534 (mt) cc_final: 0.8259 (tt) REVERT: A 211 TYR cc_start: 0.8210 (t80) cc_final: 0.7855 (t80) REVERT: A 224 MET cc_start: 0.8116 (OUTLIER) cc_final: 0.7809 (mmm) REVERT: A 279 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.8285 (m-30) REVERT: A 319 MET cc_start: 0.7966 (mmm) cc_final: 0.7372 (mtt) REVERT: B 315 THR cc_start: 0.6316 (m) cc_final: 0.6103 (p) REVERT: B 346 ASP cc_start: 0.6121 (m-30) cc_final: 0.5683 (m-30) REVERT: D 211 TYR cc_start: 0.7838 (t80) cc_final: 0.7254 (t80) REVERT: D 224 MET cc_start: 0.7403 (mtt) cc_final: 0.7098 (mtt) REVERT: D 274 GLN cc_start: 0.7954 (OUTLIER) cc_final: 0.7667 (tp40) REVERT: E 211 TYR cc_start: 0.7779 (t80) cc_final: 0.7233 (t80) REVERT: E 238 ASP cc_start: 0.8057 (t0) cc_final: 0.7821 (m-30) REVERT: E 314 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.7491 (mp10) REVERT: G 76 TYR cc_start: 0.7336 (m-80) cc_final: 0.7111 (m-80) REVERT: G 167 CYS cc_start: 0.6403 (t) cc_final: 0.6149 (t) REVERT: G 169 PHE cc_start: 0.6995 (m-80) cc_final: 0.6183 (t80) REVERT: G 173 MET cc_start: 0.4980 (tpp) cc_final: 0.4595 (tpp) REVERT: G 179 TYR cc_start: 0.6639 (t80) cc_final: 0.5867 (m-10) REVERT: G 220 TYR cc_start: 0.5987 (m-80) cc_final: 0.5559 (m-10) REVERT: G 343 ASN cc_start: 0.3327 (t0) cc_final: 0.3092 (m-40) REVERT: H 47 MET cc_start: 0.0265 (ptt) cc_final: 0.0050 (ppp) REVERT: H 53 TYR cc_start: 0.4364 (t80) cc_final: 0.3702 (m-80) REVERT: H 70 GLU cc_start: 0.8362 (tt0) cc_final: 0.8143 (tp30) REVERT: H 74 LEU cc_start: 0.8692 (mt) cc_final: 0.8260 (tt) REVERT: H 105 PHE cc_start: 0.7340 (m-80) cc_final: 0.6667 (m-80) REVERT: H 125 TYR cc_start: 0.6885 (m-80) cc_final: 0.6620 (m-80) REVERT: H 143 LYS cc_start: 0.6076 (tttm) cc_final: 0.5412 (tttt) REVERT: H 279 ASP cc_start: 0.8603 (OUTLIER) cc_final: 0.8393 (m-30) outliers start: 60 outliers final: 37 residues processed: 294 average time/residue: 0.2964 time to fit residues: 140.6066 Evaluate side-chains 274 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 232 time to evaluate : 2.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 224 MET 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 C residue 366 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 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 81 PHE Chi-restraints excluded: chain E residue 95 VAL 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 G residue 79 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 159 ILE Chi-restraints excluded: chain G residue 226 CYS Chi-restraints excluded: chain G residue 351 ILE Chi-restraints excluded: chain G residue 364 CYS Chi-restraints excluded: chain H residue 161 SER Chi-restraints excluded: chain H residue 279 ASP Chi-restraints excluded: chain H residue 296 HIS Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain H residue 358 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 244 optimal weight: 6.9990 chunk 160 optimal weight: 2.9990 chunk 207 optimal weight: 0.9990 chunk 254 optimal weight: 0.4980 chunk 31 optimal weight: 5.9990 chunk 201 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 134 optimal weight: 0.8980 chunk 248 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 HIS ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4139 r_free = 0.4139 target = 0.155501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.119253 restraints weight = 35333.430| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.56 r_work: 0.3478 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 22248 Z= 0.158 Angle : 0.561 8.823 30136 Z= 0.305 Chirality : 0.045 0.167 3336 Planarity : 0.004 0.039 3768 Dihedral : 5.797 55.577 2920 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.68 % Allowed : 15.18 % Favored : 82.13 % 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: 0.27 (0.17), residues: 2624 helix: 0.12 (0.21), residues: 640 sheet: 0.25 (0.21), residues: 680 loop : 0.36 (0.18), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 312 HIS 0.004 0.001 HIS G 311 PHE 0.024 0.002 PHE H 60 TYR 0.020 0.001 TYR B 211 ARG 0.002 0.000 ARG A 338 Details of bonding type rmsd hydrogen bonds : bond 0.03743 ( 952) hydrogen bonds : angle 5.03952 ( 2496) covalent geometry : bond 0.00367 (22248) covalent geometry : angle 0.56124 (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 320 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 256 time to evaluate : 2.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.8447 (tt0) cc_final: 0.8209 (tm-30) REVERT: A 74 LEU cc_start: 0.8630 (mt) cc_final: 0.8294 (tt) REVERT: A 125 TYR cc_start: 0.6998 (m-80) cc_final: 0.6688 (m-80) REVERT: A 160 ILE cc_start: 0.8564 (mt) cc_final: 0.8337 (tt) REVERT: A 279 ASP cc_start: 0.8738 (OUTLIER) cc_final: 0.8456 (m-30) REVERT: A 314 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.8280 (mp10) REVERT: A 319 MET cc_start: 0.8004 (mmm) cc_final: 0.7583 (mtt) REVERT: B 65 GLU cc_start: 0.7785 (tt0) cc_final: 0.7394 (tm-30) REVERT: B 315 THR cc_start: 0.6358 (m) cc_final: 0.6145 (p) REVERT: B 346 ASP cc_start: 0.6389 (m-30) cc_final: 0.5881 (m-30) REVERT: D 211 TYR cc_start: 0.8063 (t80) cc_final: 0.7457 (t80) REVERT: D 274 GLN cc_start: 0.8139 (OUTLIER) cc_final: 0.7923 (tp40) REVERT: D 314 GLN cc_start: 0.9024 (OUTLIER) cc_final: 0.7691 (mp10) REVERT: E 211 TYR cc_start: 0.7968 (t80) cc_final: 0.7419 (t80) REVERT: E 224 MET cc_start: 0.7527 (mtp) cc_final: 0.7215 (mtt) REVERT: G 53 TYR cc_start: 0.4982 (t80) cc_final: 0.4097 (m-10) REVERT: G 169 PHE cc_start: 0.6847 (m-80) cc_final: 0.6261 (t80) REVERT: G 220 TYR cc_start: 0.6186 (m-80) cc_final: 0.5719 (m-10) REVERT: G 271 PHE cc_start: 0.6959 (p90) cc_final: 0.6741 (p90) REVERT: G 343 ASN cc_start: 0.3430 (t0) cc_final: 0.3206 (m-40) REVERT: H 47 MET cc_start: 0.0172 (ptt) cc_final: -0.0121 (ppp) REVERT: H 70 GLU cc_start: 0.8440 (tt0) cc_final: 0.8214 (tp30) REVERT: H 74 LEU cc_start: 0.8703 (mt) cc_final: 0.8265 (tt) REVERT: H 80 MET cc_start: 0.8098 (tpp) cc_final: 0.7546 (tpp) REVERT: H 105 PHE cc_start: 0.7225 (m-80) cc_final: 0.6467 (m-80) REVERT: H 125 TYR cc_start: 0.6920 (m-80) cc_final: 0.6572 (m-80) REVERT: H 143 LYS cc_start: 0.6172 (tttm) cc_final: 0.5444 (tttt) REVERT: H 224 MET cc_start: 0.8236 (mmm) cc_final: 0.7821 (mpp) REVERT: H 314 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8251 (mp10) outliers start: 64 outliers final: 38 residues processed: 298 average time/residue: 0.2947 time to fit residues: 142.3196 Evaluate side-chains 270 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 227 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 295 CYS Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain D residue 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 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 154 GLU Chi-restraints excluded: chain E residue 226 CYS Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain G residue 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 158 ILE Chi-restraints excluded: chain G residue 226 CYS Chi-restraints excluded: chain G residue 351 ILE Chi-restraints excluded: chain G residue 364 CYS Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 245 LEU 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: 0.5980 chunk 1 optimal weight: 0.5980 chunk 156 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 150 optimal weight: 4.9990 chunk 157 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 164 optimal weight: 7.9990 chunk 180 optimal weight: 0.6980 chunk 262 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 HIS ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 244 GLN F 244 GLN G 214 HIS ** G 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.161458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.125094 restraints weight = 35670.127| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.66 r_work: 0.3575 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.4585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22248 Z= 0.110 Angle : 0.535 11.157 30136 Z= 0.290 Chirality : 0.044 0.163 3336 Planarity : 0.003 0.040 3768 Dihedral : 5.590 58.459 2920 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.01 % Allowed : 16.61 % Favored : 81.38 % 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: 0.44 (0.17), residues: 2624 helix: 0.33 (0.21), residues: 640 sheet: 0.31 (0.20), residues: 736 loop : 0.47 (0.19), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP G 312 HIS 0.004 0.001 HIS G 311 PHE 0.021 0.001 PHE C 222 TYR 0.017 0.001 TYR D 208 ARG 0.004 0.000 ARG B 371 Details of bonding type rmsd hydrogen bonds : bond 0.03402 ( 952) hydrogen bonds : angle 4.85834 ( 2496) covalent geometry : bond 0.00243 (22248) covalent geometry : angle 0.53520 (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 303 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 255 time to evaluate : 2.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.8420 (tt0) cc_final: 0.8192 (tm-30) REVERT: A 67 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8372 (mm) REVERT: A 74 LEU cc_start: 0.8630 (mt) cc_final: 0.8250 (tt) REVERT: A 90 LYS cc_start: 0.8491 (mmmt) cc_final: 0.7729 (mttt) REVERT: A 125 TYR cc_start: 0.7013 (m-80) cc_final: 0.6722 (m-80) REVERT: A 160 ILE cc_start: 0.8547 (mt) cc_final: 0.8315 (tt) REVERT: A 224 MET cc_start: 0.7949 (mmm) cc_final: 0.6721 (mpp) REVERT: A 279 ASP cc_start: 0.8594 (OUTLIER) cc_final: 0.8390 (m-30) REVERT: A 314 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8290 (mp10) REVERT: A 319 MET cc_start: 0.7845 (mmm) cc_final: 0.7541 (mtt) REVERT: B 65 GLU cc_start: 0.7578 (tt0) cc_final: 0.7286 (tm-30) REVERT: B 66 MET cc_start: 0.6123 (OUTLIER) cc_final: 0.5837 (mtp) REVERT: B 149 VAL cc_start: 0.8352 (OUTLIER) cc_final: 0.7978 (m) REVERT: B 346 ASP cc_start: 0.6256 (m-30) cc_final: 0.5921 (m-30) REVERT: D 162 GLU cc_start: 0.8388 (tm-30) cc_final: 0.8108 (tm-30) REVERT: D 211 TYR cc_start: 0.8104 (t80) cc_final: 0.7544 (t80) REVERT: D 274 GLN cc_start: 0.8089 (mm-40) cc_final: 0.7876 (tp40) REVERT: D 314 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.7616 (mp10) REVERT: E 162 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8073 (tm-30) REVERT: E 211 TYR cc_start: 0.7949 (t80) cc_final: 0.7397 (t80) REVERT: E 224 MET cc_start: 0.7453 (OUTLIER) cc_final: 0.7151 (mtt) REVERT: E 277 ARG cc_start: 0.7443 (mtm180) cc_final: 0.7234 (ptt180) REVERT: E 314 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.7586 (mp10) REVERT: G 53 TYR cc_start: 0.4832 (t80) cc_final: 0.4124 (m-10) REVERT: G 70 GLU cc_start: 0.7749 (tp30) cc_final: 0.7439 (tp30) REVERT: G 157 ASP cc_start: 0.5569 (m-30) cc_final: 0.5366 (t0) REVERT: G 169 PHE cc_start: 0.6861 (m-80) cc_final: 0.6284 (t80) REVERT: G 179 TYR cc_start: 0.6406 (t80) cc_final: 0.5671 (m-10) REVERT: G 220 TYR cc_start: 0.6330 (m-80) cc_final: 0.5896 (m-10) REVERT: H 47 MET cc_start: 0.0094 (ptt) cc_final: -0.0156 (ppp) REVERT: H 63 HIS cc_start: 0.8128 (m90) cc_final: 0.7889 (m-70) REVERT: H 70 GLU cc_start: 0.8437 (tt0) cc_final: 0.8234 (tp30) REVERT: H 74 LEU cc_start: 0.8680 (mt) cc_final: 0.8195 (tt) REVERT: H 90 LYS cc_start: 0.8198 (mmmt) cc_final: 0.7521 (mttt) REVERT: H 125 TYR cc_start: 0.6946 (m-80) cc_final: 0.6610 (m-80) REVERT: H 224 MET cc_start: 0.8186 (mmm) cc_final: 0.7831 (mpp) REVERT: H 314 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.8219 (mp10) outliers start: 48 outliers final: 27 residues processed: 287 average time/residue: 0.2905 time to fit residues: 135.0728 Evaluate side-chains 263 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 227 time to evaluate : 2.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain B residue 66 MET Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 295 CYS Chi-restraints excluded: chain D residue 95 VAL 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 363 SER Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 224 MET Chi-restraints excluded: chain E residue 226 CYS Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain G residue 59 HIS 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 327 THR Chi-restraints excluded: chain G residue 351 ILE Chi-restraints excluded: chain G residue 364 CYS Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 279 ASP Chi-restraints excluded: chain H residue 314 GLN Chi-restraints excluded: chain H residue 334 THR 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: 0.5980 chunk 109 optimal weight: 0.0670 chunk 62 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 93 optimal weight: 0.8980 chunk 259 optimal weight: 5.9990 chunk 255 optimal weight: 0.9990 chunk 215 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 HIS B 207 GLN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.159989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.123067 restraints weight = 34843.796| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.56 r_work: 0.3584 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.4775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 22248 Z= 0.108 Angle : 0.538 10.455 30136 Z= 0.290 Chirality : 0.044 0.161 3336 Planarity : 0.003 0.040 3768 Dihedral : 5.434 55.432 2920 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.18 % Allowed : 16.86 % Favored : 80.96 % 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: 0.52 (0.17), residues: 2624 helix: 0.34 (0.21), residues: 640 sheet: 0.39 (0.20), residues: 736 loop : 0.53 (0.19), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP G 312 HIS 0.004 0.000 HIS G 311 PHE 0.021 0.001 PHE C 222 TYR 0.021 0.001 TYR B 211 ARG 0.005 0.000 ARG B 72 Details of bonding type rmsd hydrogen bonds : bond 0.03371 ( 952) hydrogen bonds : angle 4.83494 ( 2496) covalent geometry : bond 0.00239 (22248) covalent geometry : angle 0.53830 (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 303 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 251 time to evaluate : 2.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 LEU cc_start: 0.8617 (mt) cc_final: 0.8224 (tt) REVERT: A 90 LYS cc_start: 0.8480 (mmmt) cc_final: 0.7724 (mttt) REVERT: A 160 ILE cc_start: 0.8471 (mt) cc_final: 0.8224 (tt) REVERT: A 224 MET cc_start: 0.8043 (mmm) cc_final: 0.6805 (mpp) REVERT: A 279 ASP cc_start: 0.8628 (OUTLIER) cc_final: 0.8417 (m-30) REVERT: A 314 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8275 (mp10) REVERT: A 319 MET cc_start: 0.7789 (mmm) cc_final: 0.7542 (mtt) REVERT: A 337 MET cc_start: 0.7712 (OUTLIER) cc_final: 0.7431 (mmm) REVERT: B 103 CYS cc_start: 0.7513 (OUTLIER) cc_final: 0.7059 (m) REVERT: B 149 VAL cc_start: 0.8401 (OUTLIER) cc_final: 0.8078 (m) REVERT: B 207 GLN cc_start: 0.7554 (OUTLIER) cc_final: 0.7050 (pm20) REVERT: B 346 ASP cc_start: 0.6254 (m-30) cc_final: 0.5723 (m-30) REVERT: C 354 ASP cc_start: 0.8575 (m-30) cc_final: 0.8352 (m-30) REVERT: D 162 GLU cc_start: 0.8389 (tm-30) cc_final: 0.8173 (tm-30) REVERT: D 211 TYR cc_start: 0.8099 (t80) cc_final: 0.7566 (t80) REVERT: D 224 MET cc_start: 0.7159 (mtt) cc_final: 0.6822 (mtt) REVERT: D 274 GLN cc_start: 0.7981 (mm-40) cc_final: 0.7758 (tp40) REVERT: D 276 LYS cc_start: 0.7338 (mtmm) cc_final: 0.6973 (ptmt) REVERT: D 314 GLN cc_start: 0.8969 (OUTLIER) cc_final: 0.7678 (mp10) REVERT: E 162 GLU cc_start: 0.8367 (tm-30) cc_final: 0.8143 (tm-30) REVERT: E 211 TYR cc_start: 0.7973 (t80) cc_final: 0.7496 (t80) REVERT: E 224 MET cc_start: 0.7453 (mtp) cc_final: 0.7139 (mtt) REVERT: E 243 LYS cc_start: 0.8508 (mtmm) cc_final: 0.8258 (pttm) REVERT: E 314 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.7585 (mp10) REVERT: G 53 TYR cc_start: 0.4489 (t80) cc_final: 0.3998 (m-10) REVERT: G 74 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.6834 (mt) REVERT: G 169 PHE cc_start: 0.6877 (m-80) cc_final: 0.6320 (t80) REVERT: G 179 TYR cc_start: 0.6290 (t80) cc_final: 0.5595 (m-10) REVERT: G 220 TYR cc_start: 0.6388 (m-80) cc_final: 0.5958 (m-10) REVERT: G 271 PHE cc_start: 0.7207 (p90) cc_final: 0.6902 (p90) REVERT: H 47 MET cc_start: 0.0008 (ptt) cc_final: -0.0274 (ppp) REVERT: H 74 LEU cc_start: 0.8650 (mt) cc_final: 0.8171 (tt) REVERT: H 90 LYS cc_start: 0.8293 (mmmt) cc_final: 0.7619 (mttt) REVERT: H 125 TYR cc_start: 0.6897 (m-80) cc_final: 0.6553 (m-80) REVERT: H 222 PHE cc_start: 0.8116 (OUTLIER) cc_final: 0.7456 (p90) REVERT: H 224 MET cc_start: 0.8290 (mmm) cc_final: 0.7852 (mpp) REVERT: H 314 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8237 (mp10) REVERT: H 337 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.7537 (mmm) outliers start: 52 outliers final: 31 residues processed: 284 average time/residue: 0.3002 time to fit residues: 137.9415 Evaluate side-chains 268 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 225 time to evaluate : 2.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 207 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 295 CYS Chi-restraints excluded: chain B residue 370 MET Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain D residue 95 VAL 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 363 SER Chi-restraints excluded: chain E residue 226 CYS Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 314 GLN Chi-restraints excluded: chain E residue 334 THR Chi-restraints excluded: chain G residue 59 HIS Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 115 ILE Chi-restraints excluded: chain G residue 151 LEU Chi-restraints excluded: chain G residue 176 THR Chi-restraints excluded: chain G residue 226 CYS Chi-restraints excluded: chain G residue 351 ILE Chi-restraints excluded: chain G residue 364 CYS Chi-restraints excluded: chain H residue 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 314 GLN Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain H residue 337 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 25 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 143 optimal weight: 0.0670 chunk 145 optimal weight: 4.9990 chunk 256 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 168 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 overall best weight: 0.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 HIS ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 GLN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.159929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.123823 restraints weight = 35045.098| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.69 r_work: 0.3545 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.4862 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= 0.125 Angle : 0.546 8.939 30136 Z= 0.293 Chirality : 0.044 0.197 3336 Planarity : 0.003 0.041 3768 Dihedral : 5.391 57.145 2920 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.27 % Allowed : 16.99 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.17), residues: 2624 helix: 0.31 (0.21), residues: 640 sheet: 0.39 (0.20), residues: 736 loop : 0.53 (0.19), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 184 HIS 0.003 0.001 HIS G 63 PHE 0.027 0.001 PHE C 222 TYR 0.021 0.001 TYR B 170 ARG 0.005 0.000 ARG B 206 Details of bonding type rmsd hydrogen bonds : bond 0.03411 ( 952) hydrogen bonds : angle 4.84275 ( 2496) covalent geometry : bond 0.00288 (22248) covalent geometry : angle 0.54553 (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 292 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 238 time to evaluate : 2.619 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 LEU cc_start: 0.8614 (mt) cc_final: 0.8193 (tt) REVERT: A 90 LYS cc_start: 0.8461 (mmmt) cc_final: 0.7725 (mttt) REVERT: A 160 ILE cc_start: 0.8542 (mt) cc_final: 0.8337 (tt) REVERT: A 224 MET cc_start: 0.8252 (mmm) cc_final: 0.7827 (mpp) REVERT: A 279 ASP cc_start: 0.8626 (OUTLIER) cc_final: 0.8402 (m-30) REVERT: A 314 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8268 (mp10) REVERT: A 319 MET cc_start: 0.7885 (mmm) cc_final: 0.7343 (mtt) REVERT: B 53 TYR cc_start: 0.4588 (t80) cc_final: 0.4117 (m-10) REVERT: B 103 CYS cc_start: 0.7497 (OUTLIER) cc_final: 0.6948 (m) REVERT: B 149 VAL cc_start: 0.8470 (OUTLIER) cc_final: 0.8172 (m) REVERT: B 207 GLN cc_start: 0.7456 (OUTLIER) cc_final: 0.7011 (pm20) REVERT: B 346 ASP cc_start: 0.6171 (m-30) cc_final: 0.5568 (m-30) REVERT: B 371 ARG cc_start: 0.6594 (ttp-110) cc_final: 0.6364 (ttp-110) REVERT: C 354 ASP cc_start: 0.8590 (m-30) cc_final: 0.8357 (m-30) REVERT: D 211 TYR cc_start: 0.8068 (t80) cc_final: 0.7520 (t80) REVERT: D 224 MET cc_start: 0.7201 (mtt) cc_final: 0.6918 (mtt) REVERT: D 276 LYS cc_start: 0.7312 (mtmm) cc_final: 0.6994 (ptmt) REVERT: D 314 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.7653 (mp10) REVERT: E 80 MET cc_start: 0.9097 (ttm) cc_final: 0.8861 (mtp) REVERT: E 211 TYR cc_start: 0.8039 (t80) cc_final: 0.7462 (t80) REVERT: E 224 MET cc_start: 0.7440 (mtp) cc_final: 0.7143 (mtt) REVERT: E 244 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7437 (mt0) REVERT: E 314 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.7621 (mp10) REVERT: G 53 TYR cc_start: 0.4347 (t80) cc_final: 0.3946 (m-10) REVERT: G 66 MET cc_start: 0.6577 (mtt) cc_final: 0.6377 (mtm) REVERT: G 74 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.6990 (mt) REVERT: G 169 PHE cc_start: 0.6924 (m-80) cc_final: 0.6406 (t80) REVERT: G 179 TYR cc_start: 0.6246 (t80) cc_final: 0.5601 (m-10) REVERT: G 271 PHE cc_start: 0.7383 (p90) cc_final: 0.7061 (p90) REVERT: G 292 PHE cc_start: 0.5553 (OUTLIER) cc_final: 0.4559 (m-80) REVERT: H 47 MET cc_start: -0.0001 (ptt) cc_final: -0.0338 (ppp) REVERT: H 63 HIS cc_start: 0.8134 (OUTLIER) cc_final: 0.7762 (m90) REVERT: H 74 LEU cc_start: 0.8579 (mt) cc_final: 0.8151 (tt) REVERT: H 90 LYS cc_start: 0.8247 (mmmt) cc_final: 0.7607 (mttt) REVERT: H 125 TYR cc_start: 0.6931 (m-80) cc_final: 0.6648 (m-80) REVERT: H 222 PHE cc_start: 0.8121 (OUTLIER) cc_final: 0.7694 (p90) REVERT: H 314 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.8233 (mp10) outliers start: 54 outliers final: 37 residues processed: 274 average time/residue: 0.2897 time to fit residues: 130.7175 Evaluate side-chains 278 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 228 time to evaluate : 2.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 207 GLN Chi-restraints excluded: chain B residue 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 95 VAL 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 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 366 THR Chi-restraints excluded: chain G residue 59 HIS Chi-restraints excluded: chain G residue 60 PHE Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 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 292 PHE Chi-restraints excluded: chain G residue 351 ILE Chi-restraints excluded: chain G residue 364 CYS Chi-restraints excluded: chain H residue 63 HIS Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 222 PHE Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 279 ASP Chi-restraints excluded: chain H residue 296 HIS Chi-restraints excluded: chain H residue 314 GLN Chi-restraints excluded: chain H residue 334 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 187 optimal weight: 4.9990 chunk 225 optimal weight: 8.9990 chunk 221 optimal weight: 8.9990 chunk 129 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 249 optimal weight: 4.9990 chunk 250 optimal weight: 1.9990 chunk 52 optimal weight: 0.0970 chunk 64 optimal weight: 1.9990 chunk 261 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 HIS ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 GLN ** G 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 HIS ** H 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.160277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.124020 restraints weight = 35564.458| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.49 r_work: 0.3534 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.4963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22248 Z= 0.142 Angle : 0.559 9.007 30136 Z= 0.301 Chirality : 0.044 0.159 3336 Planarity : 0.004 0.040 3768 Dihedral : 5.414 57.365 2920 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.35 % Allowed : 17.11 % Favored : 80.54 % 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: 0.51 (0.17), residues: 2624 helix: 0.29 (0.21), residues: 640 sheet: 0.48 (0.21), residues: 680 loop : 0.47 (0.18), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP H 184 HIS 0.017 0.001 HIS H 63 PHE 0.019 0.001 PHE C 222 TYR 0.020 0.001 TYR D 208 ARG 0.004 0.000 ARG B 371 Details of bonding type rmsd hydrogen bonds : bond 0.03560 ( 952) hydrogen bonds : angle 4.91710 ( 2496) covalent geometry : bond 0.00327 (22248) covalent geometry : angle 0.55861 (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 285 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 229 time to evaluate : 2.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LEU cc_start: 0.8649 (mt) cc_final: 0.8197 (tt) REVERT: A 90 LYS cc_start: 0.8463 (mmmt) cc_final: 0.7732 (mttt) REVERT: A 224 MET cc_start: 0.8280 (mmm) cc_final: 0.7851 (mpp) REVERT: A 279 ASP cc_start: 0.8614 (OUTLIER) cc_final: 0.8378 (m-30) REVERT: A 314 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.8274 (mp10) REVERT: A 319 MET cc_start: 0.7906 (mmm) cc_final: 0.7433 (mtt) REVERT: A 337 MET cc_start: 0.7686 (OUTLIER) cc_final: 0.7435 (mmm) REVERT: B 53 TYR cc_start: 0.4549 (t80) cc_final: 0.4133 (m-10) REVERT: B 103 CYS cc_start: 0.7410 (OUTLIER) cc_final: 0.6822 (m) REVERT: B 149 VAL cc_start: 0.8467 (OUTLIER) cc_final: 0.8178 (m) REVERT: B 207 GLN cc_start: 0.7439 (OUTLIER) cc_final: 0.7131 (pm20) REVERT: B 346 ASP cc_start: 0.6103 (m-30) cc_final: 0.5468 (m-30) REVERT: B 371 ARG cc_start: 0.6666 (ttp-110) cc_final: 0.6363 (ttp-110) REVERT: C 354 ASP cc_start: 0.8581 (m-30) cc_final: 0.8330 (m-30) REVERT: D 211 TYR cc_start: 0.8048 (t80) cc_final: 0.7499 (t80) REVERT: D 224 MET cc_start: 0.7215 (mtt) cc_final: 0.6959 (mtt) REVERT: D 276 LYS cc_start: 0.7356 (mtmm) cc_final: 0.7055 (ptmt) REVERT: D 314 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.7709 (mp10) REVERT: E 211 TYR cc_start: 0.7991 (t80) cc_final: 0.7498 (t80) REVERT: E 224 MET cc_start: 0.7466 (mtp) cc_final: 0.7133 (mtt) REVERT: E 244 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7289 (mt0) REVERT: E 314 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.7666 (mp10) REVERT: F 314 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.7756 (mp10) REVERT: G 53 TYR cc_start: 0.4276 (t80) cc_final: 0.3990 (m-10) REVERT: G 74 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.7000 (mt) REVERT: G 169 PHE cc_start: 0.6990 (m-80) cc_final: 0.6543 (t80) REVERT: G 179 TYR cc_start: 0.6175 (t80) cc_final: 0.5587 (m-10) REVERT: G 271 PHE cc_start: 0.7374 (p90) cc_final: 0.7069 (p90) REVERT: G 292 PHE cc_start: 0.5538 (OUTLIER) cc_final: 0.4418 (m-80) REVERT: H 47 MET cc_start: -0.0129 (ptt) cc_final: -0.0456 (ppp) REVERT: H 63 HIS cc_start: 0.8240 (OUTLIER) cc_final: 0.7838 (m90) REVERT: H 74 LEU cc_start: 0.8554 (mt) cc_final: 0.8151 (tt) REVERT: H 90 LYS cc_start: 0.8255 (mmmt) cc_final: 0.7643 (mttt) REVERT: H 125 TYR cc_start: 0.6983 (m-80) cc_final: 0.6733 (m-80) REVERT: H 222 PHE cc_start: 0.8201 (OUTLIER) cc_final: 0.7738 (p90) REVERT: H 314 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.8221 (mp10) REVERT: H 337 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.7533 (mmm) outliers start: 56 outliers final: 37 residues processed: 268 average time/residue: 0.2967 time to fit residues: 128.0988 Evaluate side-chains 277 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 224 time to evaluate : 2.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 296 HIS Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 337 MET Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 207 GLN 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 88 LYS Chi-restraints excluded: chain D residue 95 VAL 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 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 197 THR Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain G residue 59 HIS Chi-restraints excluded: chain G residue 60 PHE Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 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 292 PHE Chi-restraints excluded: chain G residue 351 ILE Chi-restraints excluded: chain G residue 364 CYS Chi-restraints excluded: chain H residue 63 HIS Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 222 PHE Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 279 ASP Chi-restraints excluded: chain H residue 296 HIS Chi-restraints excluded: chain H residue 314 GLN Chi-restraints excluded: chain H residue 334 THR Chi-restraints excluded: chain H residue 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: 4.9990 chunk 39 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 262 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 223 optimal weight: 0.5980 chunk 43 optimal weight: 5.9990 chunk 225 optimal weight: 4.9990 chunk 196 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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** D 274 GLN G 59 HIS ** G 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 HIS H 63 HIS ** H 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.156730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.120724 restraints weight = 35556.504| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.41 r_work: 0.3500 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 22248 Z= 0.193 Angle : 0.601 9.306 30136 Z= 0.322 Chirality : 0.046 0.157 3336 Planarity : 0.004 0.040 3768 Dihedral : 5.564 56.044 2920 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.52 % Allowed : 16.99 % Favored : 80.49 % 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: 0.24 (0.17), residues: 2624 helix: 0.06 (0.21), residues: 648 sheet: 0.37 (0.21), residues: 672 loop : 0.27 (0.18), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP H 184 HIS 0.010 0.001 HIS H 63 PHE 0.023 0.002 PHE C 222 TYR 0.020 0.002 TYR D 208 ARG 0.003 0.000 ARG E 195 Details of bonding type rmsd hydrogen bonds : bond 0.03875 ( 952) hydrogen bonds : angle 5.10796 ( 2496) covalent geometry : bond 0.00455 (22248) covalent geometry : angle 0.60081 (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 300 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 240 time to evaluate : 2.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 LEU cc_start: 0.8711 (mt) cc_final: 0.8249 (tt) REVERT: A 90 LYS cc_start: 0.8467 (mmmt) cc_final: 0.7747 (mttt) REVERT: A 279 ASP cc_start: 0.8643 (OUTLIER) cc_final: 0.8367 (m-30) REVERT: A 314 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8256 (mp10) REVERT: A 319 MET cc_start: 0.8104 (mmm) cc_final: 0.7639 (mtt) REVERT: B 53 TYR cc_start: 0.4586 (t80) cc_final: 0.4152 (m-10) REVERT: B 103 CYS cc_start: 0.7532 (OUTLIER) cc_final: 0.6898 (m) REVERT: B 149 VAL cc_start: 0.8416 (OUTLIER) cc_final: 0.8127 (m) REVERT: B 207 GLN cc_start: 0.7345 (OUTLIER) cc_final: 0.7010 (pm20) REVERT: B 279 ASP cc_start: 0.5552 (m-30) cc_final: 0.5334 (m-30) REVERT: B 346 ASP cc_start: 0.6185 (m-30) cc_final: 0.5544 (m-30) REVERT: B 371 ARG cc_start: 0.6686 (ttp-110) cc_final: 0.6383 (ttp-110) REVERT: D 211 TYR cc_start: 0.8054 (t80) cc_final: 0.7482 (t80) REVERT: D 224 MET cc_start: 0.7293 (mtt) cc_final: 0.7034 (mtt) REVERT: D 254 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.6947 (tp30) REVERT: D 274 GLN cc_start: 0.7954 (OUTLIER) cc_final: 0.7728 (tp40) REVERT: D 276 LYS cc_start: 0.7446 (mtmm) cc_final: 0.7105 (ptmt) REVERT: D 314 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.7781 (mp10) REVERT: E 211 TYR cc_start: 0.7961 (t80) cc_final: 0.7458 (t80) REVERT: E 224 MET cc_start: 0.7512 (mtp) cc_final: 0.7287 (mtt) REVERT: E 244 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7488 (mt0) REVERT: E 314 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.7653 (mp10) REVERT: E 326 LYS cc_start: 0.8256 (mtmt) cc_final: 0.8021 (mmmt) REVERT: F 314 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.7792 (mp10) REVERT: G 74 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.6976 (mt) REVERT: G 169 PHE cc_start: 0.6969 (m-80) cc_final: 0.6710 (t80) REVERT: G 179 TYR cc_start: 0.6230 (t80) cc_final: 0.5590 (m-10) REVERT: G 371 ARG cc_start: 0.6315 (ptp90) cc_final: 0.5634 (ptp90) REVERT: H 47 MET cc_start: -0.0105 (ptt) cc_final: -0.0337 (ppp) REVERT: H 74 LEU cc_start: 0.8571 (mt) cc_final: 0.8161 (tt) REVERT: H 90 LYS cc_start: 0.8281 (mmmt) cc_final: 0.7620 (mttt) REVERT: H 125 TYR cc_start: 0.7059 (m-80) cc_final: 0.6806 (m-80) REVERT: H 136 ASP cc_start: 0.7645 (p0) cc_final: 0.7202 (t0) REVERT: H 222 PHE cc_start: 0.8270 (OUTLIER) cc_final: 0.7571 (p90) REVERT: H 314 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.8182 (mp10) outliers start: 60 outliers final: 37 residues processed: 280 average time/residue: 0.3090 time to fit residues: 138.8006 Evaluate side-chains 273 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 222 time to evaluate : 2.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 279 ASP Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 207 GLN Chi-restraints excluded: chain B residue 295 CYS Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain C residue 222 PHE Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 95 VAL 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 274 GLN 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 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 197 THR Chi-restraints excluded: chain F residue 314 GLN Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain G residue 59 HIS Chi-restraints excluded: chain G residue 60 PHE Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 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 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 245 LEU Chi-restraints excluded: chain H residue 279 ASP Chi-restraints excluded: chain H residue 296 HIS Chi-restraints excluded: chain H residue 314 GLN Chi-restraints excluded: chain H residue 334 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 178 optimal weight: 0.9990 chunk 200 optimal weight: 0.9980 chunk 262 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 197 optimal weight: 0.9990 chunk 202 optimal weight: 6.9990 chunk 251 optimal weight: 3.9990 chunk 192 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 274 GLN ** E 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 HIS ** H 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.156843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.120469 restraints weight = 35243.732| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.49 r_work: 0.3491 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.5087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.120 22248 Z= 0.195 Angle : 0.782 59.187 30136 Z= 0.445 Chirality : 0.045 0.204 3336 Planarity : 0.005 0.155 3768 Dihedral : 5.567 56.001 2920 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.39 % Allowed : 17.49 % Favored : 80.12 % Cbeta Deviations : 0.08 % 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: 0.24 (0.17), residues: 2624 helix: 0.07 (0.21), residues: 648 sheet: 0.37 (0.21), residues: 672 loop : 0.27 (0.18), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 184 HIS 0.154 0.002 HIS G 59 PHE 0.013 0.002 PHE E 222 TYR 0.017 0.001 TYR D 53 ARG 0.003 0.000 ARG E 195 Details of bonding type rmsd hydrogen bonds : bond 0.03841 ( 952) hydrogen bonds : angle 5.10443 ( 2496) covalent geometry : bond 0.00437 (22248) covalent geometry : angle 0.78177 (30136) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11626.03 seconds wall clock time: 202 minutes 11.98 seconds (12131.98 seconds total)