Starting phenix.real_space_refine on Thu Sep 18 11:11:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bh4_44532/09_2025/9bh4_44532.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bh4_44532/09_2025/9bh4_44532.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bh4_44532/09_2025/9bh4_44532.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bh4_44532/09_2025/9bh4_44532.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bh4_44532/09_2025/9bh4_44532.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bh4_44532/09_2025/9bh4_44532.map" } resolution = 2.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.107 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 120 5.16 5 C 10458 2.51 5 N 2664 2.21 5 O 3048 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16290 Number of models: 1 Model: "" Number of chains: 2 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: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 2.90, per 1000 atoms: 0.18 Number of scatterers: 16290 At special positions: 0 Unit cell: (125.33, 150.23, 109.56, 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 120 16.00 O 3048 8.00 N 2664 7.00 C 10458 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: 1.37 Conformation dependent library (CDL) restraints added in 746.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3792 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 24 sheets defined 34.8% alpha, 37.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 48 through 55 removed outlier: 3.887A pdb=" N TYR A 53 " --> pdb=" O SER A 49 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE A 54 " --> pdb=" O LYS A 50 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP A 55 " --> pdb=" O ASP A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 59 through 68 removed outlier: 4.139A 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: 3.676A 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: 4.248A 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: 4.128A 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: 3.651A 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 262 through 266 Processing helix chain 'B' and resid 48 through 55 removed outlier: 3.886A pdb=" N TYR B 53 " --> pdb=" O SER B 49 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE B 54 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP B 55 " --> pdb=" O ASP B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 58 No H-bonds generated for 'chain 'B' and resid 56 through 58' Processing helix chain 'B' and resid 59 through 68 removed outlier: 4.139A 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: 3.676A 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: 4.248A 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: 4.128A 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: 3.651A 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 262 through 266 Processing helix chain 'C' and resid 48 through 55 removed outlier: 3.887A pdb=" N TYR C 53 " --> pdb=" O SER C 49 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE C 54 " --> pdb=" O LYS C 50 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP C 55 " --> pdb=" O ASP C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 58 No H-bonds generated for 'chain 'C' and resid 56 through 58' Processing helix chain 'C' and resid 59 through 68 removed outlier: 4.138A 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: 3.676A 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: 4.247A 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: 4.128A 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: 3.651A 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 262 through 266 Processing helix chain 'D' and resid 48 through 55 removed outlier: 3.887A pdb=" N TYR D 53 " --> pdb=" O SER D 49 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP D 55 " --> pdb=" O ASP D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 58 No H-bonds generated for 'chain 'D' and resid 56 through 58' Processing helix chain 'D' and resid 59 through 68 removed outlier: 4.139A 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: 3.677A 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: 4.247A 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: 4.129A 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: 3.651A 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 262 through 266 Processing helix chain 'E' and resid 48 through 55 removed outlier: 3.887A pdb=" N TYR E 53 " --> pdb=" O SER E 49 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE E 54 " --> pdb=" O LYS E 50 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP E 55 " --> pdb=" O ASP E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 58 No H-bonds generated for 'chain 'E' and resid 56 through 58' Processing helix chain 'E' and resid 59 through 68 removed outlier: 4.139A 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: 3.676A 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: 4.247A 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: 4.128A 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: 3.651A 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 262 through 266 Processing helix chain 'F' and resid 48 through 55 removed outlier: 3.887A pdb=" N TYR F 53 " --> pdb=" O SER F 49 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE F 54 " --> pdb=" O LYS F 50 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP F 55 " --> pdb=" O ASP F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 58 No H-bonds generated for 'chain 'F' and resid 56 through 58' Processing helix chain 'F' and resid 59 through 68 removed outlier: 4.139A 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: 3.676A 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: 4.247A 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: 4.128A 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: 3.651A 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 262 through 266 Processing sheet with id=AA1, first strand: chain 'A' and resid 139 through 143 removed outlier: 6.480A pdb=" N VAL A 114 " --> pdb=" O THR A 140 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ILE A 142 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLY A 116 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL A 91 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ILE A 160 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU A 93 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 7.653A 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: 7.827A pdb=" N HIS A 282 " --> pdb=" O MET A 319 " (cutoff:3.500A) removed outlier: 11.221A pdb=" N ASP A 321 " --> pdb=" O TYR A 280 " (cutoff:3.500A) removed outlier: 10.414A pdb=" N TYR A 280 " --> pdb=" O ASP A 321 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ALA A 196 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLU A 254 " --> pdb=" O ALA A 196 " (cutoff:3.500A) removed outlier: 6.532A 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: 7.827A pdb=" N HIS A 282 " --> pdb=" O MET A 319 " (cutoff:3.500A) removed outlier: 11.221A pdb=" N ASP A 321 " --> pdb=" O TYR A 280 " (cutoff:3.500A) removed outlier: 10.414A pdb=" N TYR A 280 " --> pdb=" O ASP A 321 " (cutoff:3.500A) removed outlier: 4.322A 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: 5.952A pdb=" N GLU A 330 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 4.997A 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: 6.480A pdb=" N VAL B 114 " --> pdb=" O THR B 140 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ILE B 142 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLY B 116 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL B 91 " --> pdb=" O ILE B 158 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ILE B 160 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU B 93 " --> pdb=" O ILE B 160 " (cutoff:3.500A) removed outlier: 7.652A 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: 7.828A pdb=" N HIS B 282 " --> pdb=" O MET B 319 " (cutoff:3.500A) removed outlier: 11.221A pdb=" N ASP B 321 " --> pdb=" O TYR B 280 " (cutoff:3.500A) removed outlier: 10.415A pdb=" N TYR B 280 " --> pdb=" O ASP B 321 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ALA B 196 " --> pdb=" O GLU B 254 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLU B 254 " --> pdb=" O ALA B 196 " (cutoff:3.500A) removed outlier: 6.532A 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: 7.828A pdb=" N HIS B 282 " --> pdb=" O MET B 319 " (cutoff:3.500A) removed outlier: 11.221A pdb=" N ASP B 321 " --> pdb=" O TYR B 280 " (cutoff:3.500A) removed outlier: 10.415A pdb=" N TYR B 280 " --> pdb=" O ASP B 321 " (cutoff:3.500A) removed outlier: 4.321A 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: 5.952A pdb=" N GLU B 330 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 4.996A 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: 6.480A pdb=" N VAL C 114 " --> pdb=" O THR C 140 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ILE C 142 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLY C 116 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL C 91 " --> pdb=" O ILE C 158 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ILE C 160 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU C 93 " --> pdb=" O ILE C 160 " (cutoff:3.500A) removed outlier: 7.651A 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: 7.827A pdb=" N HIS C 282 " --> pdb=" O MET C 319 " (cutoff:3.500A) removed outlier: 11.221A pdb=" N ASP C 321 " --> pdb=" O TYR C 280 " (cutoff:3.500A) removed outlier: 10.415A pdb=" N TYR C 280 " --> pdb=" O ASP C 321 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ALA C 196 " --> pdb=" O GLU C 254 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLU C 254 " --> pdb=" O ALA C 196 " (cutoff:3.500A) removed outlier: 6.532A 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: 7.827A pdb=" N HIS C 282 " --> pdb=" O MET C 319 " (cutoff:3.500A) removed outlier: 11.221A pdb=" N ASP C 321 " --> pdb=" O TYR C 280 " (cutoff:3.500A) removed outlier: 10.415A pdb=" N TYR C 280 " --> pdb=" O ASP C 321 " (cutoff:3.500A) removed outlier: 4.322A 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: 5.951A pdb=" N GLU C 330 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 4.997A 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: 6.480A pdb=" N VAL D 114 " --> pdb=" O THR D 140 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ILE D 142 " --> pdb=" O VAL D 114 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N GLY D 116 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL D 91 " --> pdb=" O ILE D 158 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ILE D 160 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU D 93 " --> pdb=" O ILE D 160 " (cutoff:3.500A) removed outlier: 7.652A 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: 7.827A pdb=" N HIS D 282 " --> pdb=" O MET D 319 " (cutoff:3.500A) removed outlier: 11.221A pdb=" N ASP D 321 " --> pdb=" O TYR D 280 " (cutoff:3.500A) removed outlier: 10.415A pdb=" N TYR D 280 " --> pdb=" O ASP D 321 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ALA D 196 " --> pdb=" O GLU D 254 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLU D 254 " --> pdb=" O ALA D 196 " (cutoff:3.500A) removed outlier: 6.532A 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: 7.827A pdb=" N HIS D 282 " --> pdb=" O MET D 319 " (cutoff:3.500A) removed outlier: 11.221A pdb=" N ASP D 321 " --> pdb=" O TYR D 280 " (cutoff:3.500A) removed outlier: 10.415A pdb=" N TYR D 280 " --> pdb=" O ASP D 321 " (cutoff:3.500A) removed outlier: 4.322A 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: 5.952A pdb=" N GLU D 330 " --> pdb=" O LYS D 356 " (cutoff:3.500A) removed outlier: 4.997A 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: 6.481A pdb=" N VAL E 114 " --> pdb=" O THR E 140 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N ILE E 142 " --> pdb=" O VAL E 114 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLY E 116 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL E 91 " --> pdb=" O ILE E 158 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ILE E 160 " --> pdb=" O VAL E 91 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU E 93 " --> pdb=" O ILE E 160 " (cutoff:3.500A) removed outlier: 7.652A 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: 7.827A pdb=" N HIS E 282 " --> pdb=" O MET E 319 " (cutoff:3.500A) removed outlier: 11.221A pdb=" N ASP E 321 " --> pdb=" O TYR E 280 " (cutoff:3.500A) removed outlier: 10.416A pdb=" N TYR E 280 " --> pdb=" O ASP E 321 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ALA E 196 " --> pdb=" O GLU E 254 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLU E 254 " --> pdb=" O ALA E 196 " (cutoff:3.500A) removed outlier: 6.532A 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: 7.827A pdb=" N HIS E 282 " --> pdb=" O MET E 319 " (cutoff:3.500A) removed outlier: 11.221A pdb=" N ASP E 321 " --> pdb=" O TYR E 280 " (cutoff:3.500A) removed outlier: 10.416A pdb=" N TYR E 280 " --> pdb=" O ASP E 321 " (cutoff:3.500A) removed outlier: 4.322A 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: 5.952A pdb=" N GLU E 330 " --> pdb=" O LYS E 356 " (cutoff:3.500A) removed outlier: 4.997A 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: 6.480A pdb=" N VAL F 114 " --> pdb=" O THR F 140 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ILE F 142 " --> pdb=" O VAL F 114 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLY F 116 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL F 91 " --> pdb=" O ILE F 158 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ILE F 160 " --> pdb=" O VAL F 91 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU F 93 " --> pdb=" O ILE F 160 " (cutoff:3.500A) removed outlier: 7.652A 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: 7.827A pdb=" N HIS F 282 " --> pdb=" O MET F 319 " (cutoff:3.500A) removed outlier: 11.221A pdb=" N ASP F 321 " --> pdb=" O TYR F 280 " (cutoff:3.500A) removed outlier: 10.415A pdb=" N TYR F 280 " --> pdb=" O ASP F 321 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ALA F 196 " --> pdb=" O GLU F 254 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLU F 254 " --> pdb=" O ALA F 196 " (cutoff:3.500A) removed outlier: 6.532A 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: 7.827A pdb=" N HIS F 282 " --> pdb=" O MET F 319 " (cutoff:3.500A) removed outlier: 11.221A pdb=" N ASP F 321 " --> pdb=" O TYR F 280 " (cutoff:3.500A) removed outlier: 10.415A pdb=" N TYR F 280 " --> pdb=" O ASP F 321 " (cutoff:3.500A) removed outlier: 4.321A 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: 5.952A pdb=" N GLU F 330 " --> pdb=" O LYS F 356 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LYS F 356 " --> pdb=" O GLU F 330 " (cutoff:3.500A) 720 hydrogen bonds defined for protein. 1872 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.26 Time building geometry restraints manager: 1.73 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: 5124 1.34 - 1.46: 3564 1.46 - 1.58: 7812 1.58 - 1.70: 0 1.70 - 1.81: 186 Bond restraints: 16686 Sorted by residual: bond pdb=" C2 SAH E 401 " pdb=" N3 SAH E 401 " ideal model delta sigma weight residual 1.322 1.378 -0.056 2.00e-02 2.50e+03 7.85e+00 bond pdb=" C2 SAH F 401 " pdb=" N3 SAH F 401 " ideal model delta sigma weight residual 1.322 1.378 -0.056 2.00e-02 2.50e+03 7.80e+00 bond pdb=" C2 SAH B 401 " pdb=" N3 SAH B 401 " ideal model delta sigma weight residual 1.322 1.378 -0.056 2.00e-02 2.50e+03 7.77e+00 bond pdb=" C2 SAH C 401 " pdb=" N3 SAH C 401 " ideal model delta sigma weight residual 1.322 1.377 -0.055 2.00e-02 2.50e+03 7.70e+00 bond pdb=" C2 SAH A 401 " pdb=" N3 SAH A 401 " ideal model delta sigma weight residual 1.322 1.377 -0.055 2.00e-02 2.50e+03 7.62e+00 ... (remaining 16681 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 22203 2.26 - 4.53: 335 4.53 - 6.79: 34 6.79 - 9.05: 24 9.05 - 11.31: 6 Bond angle restraints: 22602 Sorted by residual: angle pdb=" C CYS E 167 " pdb=" N LEU E 168 " pdb=" CA LEU E 168 " ideal model delta sigma weight residual 121.54 128.99 -7.45 1.91e+00 2.74e-01 1.52e+01 angle pdb=" C CYS C 167 " pdb=" N LEU C 168 " pdb=" CA LEU C 168 " ideal model delta sigma weight residual 121.54 128.94 -7.40 1.91e+00 2.74e-01 1.50e+01 angle pdb=" C CYS D 167 " pdb=" N LEU D 168 " pdb=" CA LEU D 168 " ideal model delta sigma weight residual 121.54 128.94 -7.40 1.91e+00 2.74e-01 1.50e+01 angle pdb=" C CYS F 167 " pdb=" N LEU F 168 " pdb=" CA LEU F 168 " ideal model delta sigma weight residual 121.54 128.93 -7.39 1.91e+00 2.74e-01 1.50e+01 angle pdb=" C CYS B 167 " pdb=" N LEU B 168 " pdb=" CA LEU B 168 " ideal model delta sigma weight residual 121.54 128.90 -7.36 1.91e+00 2.74e-01 1.48e+01 ... (remaining 22597 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.14: 8910 14.14 - 28.29: 744 28.29 - 42.43: 174 42.43 - 56.58: 18 56.58 - 70.72: 18 Dihedral angle restraints: 9864 sinusoidal: 3984 harmonic: 5880 Sorted by residual: dihedral pdb=" CA TRP E 312 " pdb=" C TRP E 312 " pdb=" N LYS E 313 " pdb=" CA LYS E 313 " ideal model delta harmonic sigma weight residual -180.00 -138.82 -41.18 0 5.00e+00 4.00e-02 6.78e+01 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 -138.85 -41.15 0 5.00e+00 4.00e-02 6.77e+01 dihedral pdb=" CA TRP B 312 " pdb=" C TRP B 312 " pdb=" N LYS B 313 " pdb=" CA LYS B 313 " ideal model delta harmonic sigma weight residual -180.00 -138.86 -41.14 0 5.00e+00 4.00e-02 6.77e+01 ... (remaining 9861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1368 0.028 - 0.056: 654 0.056 - 0.083: 252 0.083 - 0.111: 182 0.111 - 0.139: 46 Chirality restraints: 2502 Sorted by residual: chirality pdb=" CA ILE A 331 " pdb=" N ILE A 331 " pdb=" C ILE A 331 " pdb=" CB ILE A 331 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.83e-01 chirality pdb=" CA ILE D 331 " pdb=" N ILE D 331 " pdb=" C ILE D 331 " pdb=" CB ILE D 331 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.67e-01 chirality pdb=" CA ILE C 331 " pdb=" N ILE C 331 " pdb=" C ILE C 331 " pdb=" CB ILE C 331 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.62e-01 ... (remaining 2499 not shown) Planarity restraints: 2826 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 313 " -0.009 2.00e-02 2.50e+03 1.80e-02 3.24e+00 pdb=" C LYS C 313 " 0.031 2.00e-02 2.50e+03 pdb=" O LYS C 313 " -0.011 2.00e-02 2.50e+03 pdb=" N GLN C 314 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 313 " -0.009 2.00e-02 2.50e+03 1.80e-02 3.23e+00 pdb=" C LYS E 313 " 0.031 2.00e-02 2.50e+03 pdb=" O LYS E 313 " -0.011 2.00e-02 2.50e+03 pdb=" N GLN E 314 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 313 " -0.009 2.00e-02 2.50e+03 1.79e-02 3.22e+00 pdb=" C LYS D 313 " 0.031 2.00e-02 2.50e+03 pdb=" O LYS D 313 " -0.011 2.00e-02 2.50e+03 pdb=" N GLN D 314 " -0.011 2.00e-02 2.50e+03 ... (remaining 2823 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3660 2.78 - 3.31: 14933 3.31 - 3.84: 27801 3.84 - 4.37: 36754 4.37 - 4.90: 58428 Nonbonded interactions: 141576 Sorted by model distance: nonbonded pdb=" OD2 ASP E 194 " pdb=" OG1 THR E 293 " model vdw 2.254 3.040 nonbonded pdb=" OD2 ASP F 194 " pdb=" OG1 THR F 293 " model vdw 2.255 3.040 nonbonded pdb=" OD2 ASP C 194 " pdb=" OG1 THR C 293 " model vdw 2.255 3.040 nonbonded pdb=" OD2 ASP D 194 " pdb=" OG1 THR D 293 " model vdw 2.255 3.040 nonbonded pdb=" OD2 ASP B 194 " pdb=" OG1 THR B 293 " model vdw 2.255 3.040 ... (remaining 141571 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 6.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 16.050 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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:9.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 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 : 0.004 0.056 16686 Z= 0.203 Angle : 0.748 11.313 22602 Z= 0.406 Chirality : 0.044 0.139 2502 Planarity : 0.004 0.034 2826 Dihedral : 11.486 70.725 6072 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.18), residues: 1968 helix: -1.30 (0.21), residues: 528 sheet: 1.28 (0.22), residues: 552 loop : 0.47 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 371 TYR 0.024 0.001 TYR E 52 PHE 0.011 0.001 PHE D 292 TRP 0.010 0.001 TRP D 312 HIS 0.004 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00405 (16686) covalent geometry : angle 0.74750 (22602) hydrogen bonds : bond 0.15061 ( 678) hydrogen bonds : angle 5.88418 ( 1872) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 0.725 Fit side-chains REVERT: A 294 ARG cc_start: 0.6950 (mmt90) cc_final: 0.6520 (mmm160) REVERT: A 337 MET cc_start: 0.7725 (ttm) cc_final: 0.7460 (ttp) REVERT: B 272 CYS cc_start: 0.7084 (t) cc_final: 0.6719 (t) REVERT: B 332 PHE cc_start: 0.8502 (m-80) cc_final: 0.7991 (m-10) REVERT: B 345 ARG cc_start: 0.6778 (mtt-85) cc_final: 0.5784 (mtp180) REVERT: E 272 CYS cc_start: 0.7072 (t) cc_final: 0.6717 (t) REVERT: E 332 PHE cc_start: 0.8501 (m-80) cc_final: 0.8104 (m-10) REVERT: E 345 ARG cc_start: 0.6757 (mtt-85) cc_final: 0.5822 (mtp180) REVERT: F 145 LYS cc_start: 0.7546 (mmmt) cc_final: 0.7333 (mtmt) REVERT: F 243 LYS cc_start: 0.7782 (ptpt) cc_final: 0.7399 (mmtm) REVERT: F 294 ARG cc_start: 0.7023 (mmt90) cc_final: 0.6610 (mmm160) REVERT: F 337 MET cc_start: 0.7669 (ttm) cc_final: 0.7417 (ttp) REVERT: F 356 LYS cc_start: 0.7932 (mppt) cc_final: 0.7615 (mptt) outliers start: 0 outliers final: 2 residues processed: 349 average time/residue: 0.7818 time to fit residues: 297.1887 Evaluate side-chains 248 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 246 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 236 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS A 358 GLN B 314 GLN B 343 ASN ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 GLN C 340 ASN D 59 HIS ** D 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 GLN E 314 GLN E 343 ASN F 59 HIS F 358 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.151823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.124568 restraints weight = 18508.231| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.53 r_work: 0.3363 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 16686 Z= 0.163 Angle : 0.560 7.694 22602 Z= 0.306 Chirality : 0.045 0.143 2502 Planarity : 0.004 0.036 2826 Dihedral : 5.653 44.574 2194 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.24 % Allowed : 9.51 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.19), residues: 1968 helix: -0.62 (0.21), residues: 552 sheet: 1.25 (0.23), residues: 540 loop : 0.74 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 369 TYR 0.016 0.001 TYR B 53 PHE 0.016 0.002 PHE B 292 TRP 0.018 0.002 TRP D 312 HIS 0.003 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00365 (16686) covalent geometry : angle 0.55957 (22602) hydrogen bonds : bond 0.04942 ( 678) hydrogen bonds : angle 4.97486 ( 1872) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 255 time to evaluate : 0.712 Fit side-chains REVERT: A 88 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7469 (mptp) REVERT: A 243 LYS cc_start: 0.8030 (mmtt) cc_final: 0.7695 (pttp) REVERT: A 294 ARG cc_start: 0.7240 (mmt90) cc_final: 0.6714 (mmm160) REVERT: A 337 MET cc_start: 0.8401 (ttm) cc_final: 0.8060 (ttp) REVERT: A 354 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7970 (t0) REVERT: B 131 LYS cc_start: 0.8431 (ttmt) cc_final: 0.8165 (ttpm) REVERT: B 272 CYS cc_start: 0.7815 (t) cc_final: 0.7470 (t) REVERT: B 332 PHE cc_start: 0.8690 (m-80) cc_final: 0.8138 (m-10) REVERT: B 345 ARG cc_start: 0.6806 (mtt-85) cc_final: 0.5679 (mtp180) REVERT: C 131 LYS cc_start: 0.8599 (tmtt) cc_final: 0.8398 (ttpp) REVERT: E 70 GLU cc_start: 0.8508 (tp30) cc_final: 0.8242 (tt0) REVERT: E 131 LYS cc_start: 0.8382 (ttmt) cc_final: 0.8124 (ttpm) REVERT: E 272 CYS cc_start: 0.7838 (t) cc_final: 0.7438 (t) REVERT: E 329 GLU cc_start: 0.7321 (mt-10) cc_final: 0.7120 (mm-30) REVERT: E 332 PHE cc_start: 0.8640 (m-80) cc_final: 0.8078 (m-10) REVERT: E 345 ARG cc_start: 0.6780 (mtt-85) cc_final: 0.5710 (mtp180) REVERT: E 369 ARG cc_start: 0.8055 (mmm-85) cc_final: 0.7424 (mtp85) REVERT: F 243 LYS cc_start: 0.8016 (ptpt) cc_final: 0.7646 (mmtt) REVERT: F 294 ARG cc_start: 0.7200 (mmt90) cc_final: 0.6679 (mmm160) REVERT: F 337 MET cc_start: 0.8357 (ttm) cc_final: 0.8024 (ttp) REVERT: F 356 LYS cc_start: 0.8089 (mppt) cc_final: 0.7777 (mptt) outliers start: 40 outliers final: 14 residues processed: 273 average time/residue: 0.8070 time to fit residues: 239.3590 Evaluate side-chains 250 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 234 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain A residue 369 ARG Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 369 ARG Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 207 GLN Chi-restraints excluded: chain F residue 272 CYS Chi-restraints excluded: chain F residue 274 GLN Chi-restraints excluded: chain F residue 354 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 95 optimal weight: 0.2980 chunk 105 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 170 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 152 optimal weight: 7.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS A 358 GLN B 175 ASN C 59 HIS ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 GLN C 358 GLN D 59 HIS ** D 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 GLN D 358 GLN E 175 ASN F 59 HIS F 358 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.146637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.119325 restraints weight = 18630.969| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.51 r_work: 0.3316 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 16686 Z= 0.269 Angle : 0.639 7.244 22602 Z= 0.348 Chirality : 0.049 0.158 2502 Planarity : 0.005 0.049 2826 Dihedral : 5.935 46.157 2190 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.18 % Favored : 97.71 % Rotamer: Outliers : 3.30 % Allowed : 10.79 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.34 (0.19), residues: 1968 helix: -0.82 (0.21), residues: 564 sheet: 1.35 (0.22), residues: 600 loop : 0.33 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 369 TYR 0.016 0.002 TYR B 53 PHE 0.019 0.002 PHE B 292 TRP 0.018 0.002 TRP D 312 HIS 0.004 0.001 HIS D 59 Details of bonding type rmsd covalent geometry : bond 0.00629 (16686) covalent geometry : angle 0.63923 (22602) hydrogen bonds : bond 0.05645 ( 678) hydrogen bonds : angle 5.17005 ( 1872) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 230 time to evaluate : 0.746 Fit side-chains REVERT: A 88 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7295 (mptp) REVERT: A 243 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7707 (pttp) REVERT: A 294 ARG cc_start: 0.7298 (mmt90) cc_final: 0.6805 (mmm160) REVERT: A 337 MET cc_start: 0.8517 (ttm) cc_final: 0.8126 (ttp) REVERT: A 369 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7394 (tpp-160) REVERT: B 131 LYS cc_start: 0.8512 (ttmt) cc_final: 0.8285 (ttpm) REVERT: B 345 ARG cc_start: 0.6798 (mtt-85) cc_final: 0.5730 (mtp180) REVERT: C 131 LYS cc_start: 0.8797 (tmtt) cc_final: 0.8582 (ttpp) REVERT: D 131 LYS cc_start: 0.8782 (tmtt) cc_final: 0.8555 (ttpp) REVERT: D 369 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8230 (mmm160) REVERT: E 70 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8262 (tt0) REVERT: E 131 LYS cc_start: 0.8534 (ttmt) cc_final: 0.8307 (ttpm) REVERT: E 345 ARG cc_start: 0.6943 (mtt-85) cc_final: 0.5837 (mtp180) REVERT: F 88 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7475 (mptp) REVERT: F 294 ARG cc_start: 0.7270 (mmt90) cc_final: 0.6764 (mmm160) REVERT: F 337 MET cc_start: 0.8459 (ttm) cc_final: 0.8082 (ttp) REVERT: F 356 LYS cc_start: 0.8029 (mppt) cc_final: 0.7808 (mptt) outliers start: 59 outliers final: 19 residues processed: 256 average time/residue: 0.8125 time to fit residues: 226.0354 Evaluate side-chains 246 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 221 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain A residue 369 ARG Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 369 ARG Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain E residue 173 MET Chi-restraints excluded: chain E residue 356 LYS Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 148 GLU Chi-restraints excluded: chain F residue 207 GLN Chi-restraints excluded: chain F residue 272 CYS Chi-restraints excluded: chain F residue 274 GLN Chi-restraints excluded: chain F residue 354 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 143 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 175 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 118 optimal weight: 0.6980 chunk 195 optimal weight: 0.8980 chunk 126 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS A 278 ASN A 358 GLN C 59 HIS ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 GLN D 59 HIS ** D 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 GLN F 59 HIS ** F 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 358 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.147639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.118871 restraints weight = 18547.391| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.71 r_work: 0.3265 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16686 Z= 0.116 Angle : 0.494 6.339 22602 Z= 0.273 Chirality : 0.043 0.154 2502 Planarity : 0.003 0.032 2826 Dihedral : 5.272 40.980 2190 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.52 % Allowed : 12.81 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.19), residues: 1968 helix: -0.41 (0.22), residues: 564 sheet: 1.11 (0.22), residues: 582 loop : 0.42 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 369 TYR 0.014 0.001 TYR C 53 PHE 0.012 0.001 PHE B 292 TRP 0.013 0.001 TRP E 312 HIS 0.004 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00249 (16686) covalent geometry : angle 0.49403 (22602) hydrogen bonds : bond 0.04236 ( 678) hydrogen bonds : angle 4.85214 ( 1872) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 240 time to evaluate : 0.687 Fit side-chains REVERT: A 52 TYR cc_start: 0.5361 (OUTLIER) cc_final: 0.2599 (m-10) REVERT: A 88 LYS cc_start: 0.7694 (OUTLIER) cc_final: 0.7219 (mptp) REVERT: A 243 LYS cc_start: 0.8027 (mmtt) cc_final: 0.7397 (pttm) REVERT: A 291 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7580 (mp0) REVERT: A 294 ARG cc_start: 0.7212 (mmt90) cc_final: 0.6716 (mmm160) REVERT: A 337 MET cc_start: 0.8519 (ttm) cc_final: 0.8040 (ttp) REVERT: B 131 LYS cc_start: 0.8499 (ttmt) cc_final: 0.8228 (ttpm) REVERT: B 332 PHE cc_start: 0.8434 (m-80) cc_final: 0.8117 (m-10) REVERT: B 345 ARG cc_start: 0.6797 (mtt-85) cc_final: 0.5682 (mtp180) REVERT: C 131 LYS cc_start: 0.8765 (tmtt) cc_final: 0.8475 (ttpp) REVERT: D 131 LYS cc_start: 0.8773 (tmtt) cc_final: 0.8451 (ttpp) REVERT: E 70 GLU cc_start: 0.8521 (tp30) cc_final: 0.8220 (tt0) REVERT: E 131 LYS cc_start: 0.8510 (ttmt) cc_final: 0.8245 (ttpm) REVERT: E 332 PHE cc_start: 0.8392 (m-80) cc_final: 0.8033 (m-10) REVERT: E 345 ARG cc_start: 0.6805 (mtt-85) cc_final: 0.5699 (mtp180) REVERT: F 52 TYR cc_start: 0.5191 (OUTLIER) cc_final: 0.2601 (m-10) REVERT: F 88 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7414 (mptp) REVERT: F 294 ARG cc_start: 0.7183 (mmt90) cc_final: 0.6703 (mmm160) REVERT: F 337 MET cc_start: 0.8547 (ttm) cc_final: 0.8068 (ttp) REVERT: F 356 LYS cc_start: 0.8086 (mppt) cc_final: 0.7767 (mptt) outliers start: 45 outliers final: 20 residues processed: 261 average time/residue: 0.7482 time to fit residues: 212.4010 Evaluate side-chains 253 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 229 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 207 GLN Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 369 ARG Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 356 LYS Chi-restraints excluded: chain F residue 52 TYR Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 207 GLN Chi-restraints excluded: chain F residue 272 CYS Chi-restraints excluded: chain F residue 274 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 166 optimal weight: 0.3980 chunk 163 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 149 optimal weight: 4.9990 chunk 53 optimal weight: 0.0370 chunk 89 optimal weight: 0.9990 chunk 85 optimal weight: 0.4980 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 overall best weight: 0.5460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS A 278 ASN A 358 GLN C 59 HIS ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 GLN D 59 HIS ** D 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 GLN F 59 HIS F 278 ASN F 358 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.148568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.119686 restraints weight = 18251.369| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.60 r_work: 0.3273 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16686 Z= 0.103 Angle : 0.470 5.906 22602 Z= 0.260 Chirality : 0.043 0.165 2502 Planarity : 0.003 0.032 2826 Dihedral : 5.003 40.517 2190 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.40 % Allowed : 14.15 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.19), residues: 1968 helix: -0.30 (0.23), residues: 552 sheet: 1.09 (0.23), residues: 582 loop : 0.37 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 369 TYR 0.013 0.001 TYR C 53 PHE 0.012 0.001 PHE B 292 TRP 0.014 0.001 TRP B 312 HIS 0.003 0.001 HIS D 59 Details of bonding type rmsd covalent geometry : bond 0.00218 (16686) covalent geometry : angle 0.47029 (22602) hydrogen bonds : bond 0.03888 ( 678) hydrogen bonds : angle 4.71985 ( 1872) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 232 time to evaluate : 0.805 Fit side-chains REVERT: A 52 TYR cc_start: 0.5288 (OUTLIER) cc_final: 0.2525 (m-10) REVERT: A 62 ILE cc_start: 0.8543 (tt) cc_final: 0.8331 (tp) REVERT: A 88 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.7240 (mptp) REVERT: A 243 LYS cc_start: 0.7884 (mmtt) cc_final: 0.7401 (pttp) REVERT: A 291 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7494 (mp0) REVERT: A 294 ARG cc_start: 0.7126 (mmt90) cc_final: 0.6664 (mmm160) REVERT: A 337 MET cc_start: 0.8504 (ttm) cc_final: 0.8013 (ttp) REVERT: B 131 LYS cc_start: 0.8479 (ttmt) cc_final: 0.8192 (ttpm) REVERT: B 294 ARG cc_start: 0.7936 (mmt90) cc_final: 0.7713 (mmt90) REVERT: B 332 PHE cc_start: 0.8364 (m-80) cc_final: 0.8112 (m-10) REVERT: B 345 ARG cc_start: 0.6791 (mtt-85) cc_final: 0.5664 (mtp180) REVERT: C 131 LYS cc_start: 0.8738 (tmtt) cc_final: 0.8419 (ttpp) REVERT: C 154 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7545 (tm-30) REVERT: C 369 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.8027 (mmm160) REVERT: D 131 LYS cc_start: 0.8723 (tmtt) cc_final: 0.8401 (ttpp) REVERT: E 70 GLU cc_start: 0.8501 (tp30) cc_final: 0.8128 (tt0) REVERT: E 131 LYS cc_start: 0.8541 (ttmt) cc_final: 0.8255 (ttpm) REVERT: E 294 ARG cc_start: 0.7910 (mmt90) cc_final: 0.7693 (mmt90) REVERT: E 332 PHE cc_start: 0.8340 (m-80) cc_final: 0.8025 (m-10) REVERT: E 345 ARG cc_start: 0.6746 (mtt-85) cc_final: 0.5633 (mtp180) REVERT: F 52 TYR cc_start: 0.5320 (OUTLIER) cc_final: 0.2584 (m-10) REVERT: F 55 ASP cc_start: 0.6235 (OUTLIER) cc_final: 0.5888 (t70) REVERT: F 88 LYS cc_start: 0.7700 (OUTLIER) cc_final: 0.7261 (mptp) REVERT: F 291 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7441 (mp0) REVERT: F 294 ARG cc_start: 0.7128 (mmt90) cc_final: 0.6674 (mmm160) REVERT: F 337 MET cc_start: 0.8512 (ttm) cc_final: 0.8015 (ttp) REVERT: F 356 LYS cc_start: 0.8071 (mppt) cc_final: 0.7711 (mptt) outliers start: 43 outliers final: 20 residues processed: 250 average time/residue: 0.7894 time to fit residues: 214.5127 Evaluate side-chains 255 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 228 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 154 GLU Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 207 GLN Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 369 ARG Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 356 LYS Chi-restraints excluded: chain F residue 52 TYR Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 207 GLN Chi-restraints excluded: chain F residue 272 CYS Chi-restraints excluded: chain F residue 274 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 96 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 131 optimal weight: 0.9990 chunk 103 optimal weight: 0.2980 chunk 157 optimal weight: 0.9980 chunk 196 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS A 358 GLN B 343 ASN C 59 HIS ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 HIS ** D 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 HIS F 278 ASN F 358 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.142942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.114205 restraints weight = 18314.496| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.57 r_work: 0.3202 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 16686 Z= 0.248 Angle : 0.606 6.388 22602 Z= 0.331 Chirality : 0.048 0.160 2502 Planarity : 0.004 0.038 2826 Dihedral : 5.669 43.446 2190 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.19 % Allowed : 13.81 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.19), residues: 1968 helix: -0.63 (0.22), residues: 564 sheet: 1.11 (0.22), residues: 570 loop : 0.20 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 345 TYR 0.014 0.002 TYR B 53 PHE 0.018 0.002 PHE E 292 TRP 0.016 0.002 TRP E 312 HIS 0.004 0.001 HIS C 311 Details of bonding type rmsd covalent geometry : bond 0.00578 (16686) covalent geometry : angle 0.60604 (22602) hydrogen bonds : bond 0.05281 ( 678) hydrogen bonds : angle 5.08771 ( 1872) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 234 time to evaluate : 0.743 Fit side-chains REVERT: A 52 TYR cc_start: 0.5573 (OUTLIER) cc_final: 0.3084 (m-10) REVERT: A 88 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.7255 (mptp) REVERT: A 243 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7496 (pttm) REVERT: A 294 ARG cc_start: 0.7032 (mmt90) cc_final: 0.6659 (mmm160) REVERT: A 337 MET cc_start: 0.8541 (ttm) cc_final: 0.8059 (ttp) REVERT: B 131 LYS cc_start: 0.8557 (ttmt) cc_final: 0.8290 (ttpm) REVERT: B 332 PHE cc_start: 0.8515 (m-80) cc_final: 0.8013 (m-10) REVERT: B 345 ARG cc_start: 0.6895 (mtt-85) cc_final: 0.5766 (mtp180) REVERT: C 131 LYS cc_start: 0.8843 (tmtt) cc_final: 0.8546 (ttpp) REVERT: C 369 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8129 (mmm160) REVERT: D 131 LYS cc_start: 0.8822 (tmtt) cc_final: 0.8511 (ttpp) REVERT: D 369 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.8090 (mmm160) REVERT: E 47 MET cc_start: 0.7279 (mtt) cc_final: 0.6918 (ttm) REVERT: E 70 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8241 (tt0) REVERT: E 131 LYS cc_start: 0.8569 (ttmt) cc_final: 0.8305 (ttpm) REVERT: E 206 ARG cc_start: 0.7023 (ttp-110) cc_final: 0.6753 (ttp80) REVERT: E 332 PHE cc_start: 0.8509 (m-80) cc_final: 0.8015 (m-10) REVERT: E 345 ARG cc_start: 0.6847 (mtt-85) cc_final: 0.5735 (mtp180) REVERT: F 52 TYR cc_start: 0.5632 (OUTLIER) cc_final: 0.3076 (m-10) REVERT: F 88 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7316 (mptp) REVERT: F 294 ARG cc_start: 0.7013 (mmt90) cc_final: 0.6736 (mmm160) REVERT: F 337 MET cc_start: 0.8598 (ttm) cc_final: 0.8113 (ttp) REVERT: F 356 LYS cc_start: 0.8064 (mppt) cc_final: 0.7753 (mptt) outliers start: 57 outliers final: 26 residues processed: 258 average time/residue: 0.8050 time to fit residues: 225.3868 Evaluate side-chains 256 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 222 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 243 LYS Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain C residue 72 ARG Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 207 GLN Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 369 ARG Chi-restraints excluded: chain D residue 72 ARG Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 369 ARG Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 356 LYS Chi-restraints excluded: chain F residue 52 TYR Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 207 GLN Chi-restraints excluded: chain F residue 272 CYS Chi-restraints excluded: chain F residue 274 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 28 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 139 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 166 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 11 optimal weight: 0.1980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS A 358 GLN C 59 HIS ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 HIS ** D 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 GLN F 59 HIS F 358 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.145556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.116694 restraints weight = 18134.386| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.61 r_work: 0.3249 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16686 Z= 0.154 Angle : 0.532 5.857 22602 Z= 0.295 Chirality : 0.044 0.159 2502 Planarity : 0.004 0.032 2826 Dihedral : 5.398 41.709 2190 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.85 % Allowed : 14.88 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.19), residues: 1968 helix: -0.58 (0.22), residues: 570 sheet: 1.08 (0.23), residues: 570 loop : 0.12 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 345 TYR 0.013 0.001 TYR E 53 PHE 0.014 0.002 PHE E 292 TRP 0.016 0.001 TRP E 312 HIS 0.004 0.001 HIS D 59 Details of bonding type rmsd covalent geometry : bond 0.00345 (16686) covalent geometry : angle 0.53238 (22602) hydrogen bonds : bond 0.04536 ( 678) hydrogen bonds : angle 4.95278 ( 1872) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 229 time to evaluate : 0.653 Fit side-chains REVERT: A 52 TYR cc_start: 0.5430 (OUTLIER) cc_final: 0.2843 (m-10) REVERT: A 88 LYS cc_start: 0.7688 (OUTLIER) cc_final: 0.7304 (mptp) REVERT: A 243 LYS cc_start: 0.7900 (mmtt) cc_final: 0.7439 (pttm) REVERT: A 294 ARG cc_start: 0.7003 (mmt90) cc_final: 0.6704 (mmm160) REVERT: A 337 MET cc_start: 0.8566 (ttm) cc_final: 0.8070 (ttp) REVERT: B 47 MET cc_start: 0.7313 (mtt) cc_final: 0.6951 (ttm) REVERT: B 131 LYS cc_start: 0.8526 (ttmt) cc_final: 0.8249 (ttpm) REVERT: B 206 ARG cc_start: 0.6969 (ttp-110) cc_final: 0.6688 (ttp80) REVERT: B 332 PHE cc_start: 0.8423 (m-80) cc_final: 0.7979 (m-10) REVERT: B 345 ARG cc_start: 0.6876 (mtt-85) cc_final: 0.5727 (mtp180) REVERT: C 131 LYS cc_start: 0.8805 (tmtt) cc_final: 0.8494 (ttpp) REVERT: C 352 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7960 (m-30) REVERT: C 369 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.8083 (mmm160) REVERT: D 131 LYS cc_start: 0.8808 (tmtt) cc_final: 0.8485 (ttpp) REVERT: D 352 ASP cc_start: 0.8213 (OUTLIER) cc_final: 0.8000 (m-30) REVERT: D 369 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8063 (mmm160) REVERT: E 47 MET cc_start: 0.7259 (mtt) cc_final: 0.6873 (ttm) REVERT: E 70 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8210 (tt0) REVERT: E 131 LYS cc_start: 0.8532 (ttmt) cc_final: 0.8278 (ttpm) REVERT: E 206 ARG cc_start: 0.7063 (ttp-110) cc_final: 0.6804 (ttp80) REVERT: E 332 PHE cc_start: 0.8409 (m-80) cc_final: 0.7968 (m-10) REVERT: E 345 ARG cc_start: 0.6783 (mtt-85) cc_final: 0.5681 (mtp180) REVERT: F 88 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7341 (mptp) REVERT: F 337 MET cc_start: 0.8549 (ttm) cc_final: 0.8049 (ttp) REVERT: F 356 LYS cc_start: 0.8060 (mppt) cc_final: 0.7703 (mptt) outliers start: 51 outliers final: 25 residues processed: 251 average time/residue: 0.7900 time to fit residues: 215.0554 Evaluate side-chains 252 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 219 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 207 GLN Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 352 ASP Chi-restraints excluded: chain C residue 369 ARG Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 352 ASP Chi-restraints excluded: chain D residue 369 ARG Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 356 LYS Chi-restraints excluded: chain F residue 52 TYR Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 207 GLN Chi-restraints excluded: chain F residue 272 CYS Chi-restraints excluded: chain F residue 274 GLN Chi-restraints excluded: chain F residue 320 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 0.6980 chunk 152 optimal weight: 0.9980 chunk 98 optimal weight: 0.0000 chunk 64 optimal weight: 9.9990 chunk 160 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 169 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS A 358 GLN C 59 HIS ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 HIS ** D 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 HIS F 358 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.148784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.120765 restraints weight = 18207.460| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.57 r_work: 0.3281 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16686 Z= 0.107 Angle : 0.489 6.103 22602 Z= 0.270 Chirality : 0.043 0.155 2502 Planarity : 0.003 0.041 2826 Dihedral : 4.998 39.734 2190 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.18 % Allowed : 15.83 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.19), residues: 1968 helix: -0.28 (0.23), residues: 552 sheet: 0.98 (0.23), residues: 582 loop : 0.26 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 294 TYR 0.011 0.001 TYR C 53 PHE 0.013 0.001 PHE F 292 TRP 0.015 0.001 TRP D 312 HIS 0.003 0.001 HIS D 59 Details of bonding type rmsd covalent geometry : bond 0.00230 (16686) covalent geometry : angle 0.48888 (22602) hydrogen bonds : bond 0.03841 ( 678) hydrogen bonds : angle 4.75456 ( 1872) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 233 time to evaluate : 0.736 Fit side-chains revert: symmetry clash REVERT: A 47 MET cc_start: 0.5791 (mtp) cc_final: 0.5454 (mtp) REVERT: A 52 TYR cc_start: 0.5393 (OUTLIER) cc_final: 0.3185 (m-80) REVERT: A 62 ILE cc_start: 0.8565 (tt) cc_final: 0.8359 (tp) REVERT: A 112 ARG cc_start: 0.8254 (ttp80) cc_final: 0.7875 (ttp80) REVERT: A 243 LYS cc_start: 0.7867 (mmtt) cc_final: 0.7449 (pttm) REVERT: A 291 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7457 (mp0) REVERT: A 337 MET cc_start: 0.8503 (ttm) cc_final: 0.8012 (ttp) REVERT: B 47 MET cc_start: 0.7242 (mtt) cc_final: 0.6863 (ttm) REVERT: B 131 LYS cc_start: 0.8497 (ttmt) cc_final: 0.8216 (ttpm) REVERT: B 206 ARG cc_start: 0.6958 (ttp-110) cc_final: 0.6660 (ttp80) REVERT: B 332 PHE cc_start: 0.8374 (m-80) cc_final: 0.8135 (m-10) REVERT: B 345 ARG cc_start: 0.6823 (mtt-85) cc_final: 0.5686 (mtp180) REVERT: C 131 LYS cc_start: 0.8725 (tmtt) cc_final: 0.8413 (ttpp) REVERT: C 298 ARG cc_start: 0.7437 (tmt170) cc_final: 0.6995 (ttp80) REVERT: C 369 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.8050 (mmm160) REVERT: D 131 LYS cc_start: 0.8769 (tmtt) cc_final: 0.8436 (ttpp) REVERT: D 298 ARG cc_start: 0.7430 (tmt170) cc_final: 0.6979 (ttp80) REVERT: D 369 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.8026 (mmm160) REVERT: E 47 MET cc_start: 0.7186 (mtt) cc_final: 0.6773 (ttm) REVERT: E 70 GLU cc_start: 0.8488 (tp30) cc_final: 0.8118 (tt0) REVERT: E 131 LYS cc_start: 0.8554 (ttmt) cc_final: 0.8289 (ttpm) REVERT: E 206 ARG cc_start: 0.7048 (ttp-110) cc_final: 0.6782 (ttp80) REVERT: E 332 PHE cc_start: 0.8347 (m-80) cc_final: 0.8055 (m-10) REVERT: E 345 ARG cc_start: 0.6743 (mtt-85) cc_final: 0.5650 (mtp180) REVERT: F 52 TYR cc_start: 0.5650 (OUTLIER) cc_final: 0.3401 (m-80) REVERT: F 55 ASP cc_start: 0.6305 (OUTLIER) cc_final: 0.5885 (t70) REVERT: F 62 ILE cc_start: 0.8572 (tt) cc_final: 0.8368 (tp) REVERT: F 88 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7306 (mptp) REVERT: F 171 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7457 (mm-30) REVERT: F 291 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7480 (mp0) REVERT: F 337 MET cc_start: 0.8481 (ttm) cc_final: 0.7992 (ttp) REVERT: F 356 LYS cc_start: 0.8030 (mppt) cc_final: 0.7684 (mptt) outliers start: 39 outliers final: 22 residues processed: 245 average time/residue: 0.8107 time to fit residues: 215.7980 Evaluate side-chains 253 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 225 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 207 GLN Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 369 ARG Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 369 ARG Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 356 LYS Chi-restraints excluded: chain F residue 52 TYR Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 207 GLN Chi-restraints excluded: chain F residue 272 CYS Chi-restraints excluded: chain F residue 274 GLN Chi-restraints excluded: chain F residue 320 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 103 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS C 59 HIS ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 HIS ** D 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 GLN F 59 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.144794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.115860 restraints weight = 18063.000| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.62 r_work: 0.3222 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16686 Z= 0.186 Angle : 0.567 7.414 22602 Z= 0.312 Chirality : 0.045 0.157 2502 Planarity : 0.004 0.085 2826 Dihedral : 5.391 42.167 2190 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.13 % Allowed : 16.00 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.19), residues: 1968 helix: -0.34 (0.23), residues: 546 sheet: 1.03 (0.23), residues: 570 loop : 0.27 (0.21), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG F 294 TYR 0.012 0.001 TYR E 53 PHE 0.016 0.002 PHE E 292 TRP 0.016 0.002 TRP E 312 HIS 0.004 0.001 HIS D 59 Details of bonding type rmsd covalent geometry : bond 0.00426 (16686) covalent geometry : angle 0.56699 (22602) hydrogen bonds : bond 0.04778 ( 678) hydrogen bonds : angle 4.95652 ( 1872) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 226 time to evaluate : 0.763 Fit side-chains REVERT: A 52 TYR cc_start: 0.5682 (OUTLIER) cc_final: 0.3037 (m-10) REVERT: A 243 LYS cc_start: 0.7900 (mmtt) cc_final: 0.7424 (pttm) REVERT: A 337 MET cc_start: 0.8556 (ttm) cc_final: 0.8064 (ttp) REVERT: B 47 MET cc_start: 0.7294 (mtt) cc_final: 0.6963 (ttm) REVERT: B 131 LYS cc_start: 0.8538 (ttmt) cc_final: 0.8258 (ttpm) REVERT: B 206 ARG cc_start: 0.7004 (ttp-110) cc_final: 0.6713 (ttp80) REVERT: B 332 PHE cc_start: 0.8448 (m-80) cc_final: 0.8016 (m-10) REVERT: B 337 MET cc_start: 0.8484 (ttm) cc_final: 0.8124 (ttm) REVERT: B 345 ARG cc_start: 0.6846 (mtt-85) cc_final: 0.5705 (mtp180) REVERT: C 131 LYS cc_start: 0.8830 (tmtt) cc_final: 0.8504 (ttpp) REVERT: C 352 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7976 (m-30) REVERT: C 369 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8076 (mmm160) REVERT: D 131 LYS cc_start: 0.8827 (tmtt) cc_final: 0.8503 (ttpp) REVERT: D 352 ASP cc_start: 0.8239 (OUTLIER) cc_final: 0.8026 (m-30) REVERT: D 369 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.8049 (mmm160) REVERT: E 47 MET cc_start: 0.7214 (mtt) cc_final: 0.6849 (ttm) REVERT: E 70 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8188 (tt0) REVERT: E 131 LYS cc_start: 0.8552 (ttmt) cc_final: 0.8286 (ttpm) REVERT: E 206 ARG cc_start: 0.7071 (ttp-110) cc_final: 0.6822 (ttp80) REVERT: E 332 PHE cc_start: 0.8426 (m-80) cc_final: 0.7974 (m-10) REVERT: E 337 MET cc_start: 0.8449 (ttm) cc_final: 0.8035 (ttm) REVERT: E 345 ARG cc_start: 0.6793 (mtt-85) cc_final: 0.5669 (mtp180) REVERT: F 88 LYS cc_start: 0.7815 (OUTLIER) cc_final: 0.7324 (mptp) REVERT: F 171 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7379 (mt-10) REVERT: F 337 MET cc_start: 0.8571 (ttm) cc_final: 0.8074 (ttp) REVERT: F 356 LYS cc_start: 0.8112 (mppt) cc_final: 0.7721 (mptt) outliers start: 38 outliers final: 25 residues processed: 240 average time/residue: 0.8051 time to fit residues: 209.9272 Evaluate side-chains 258 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 226 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 MET Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 207 GLN Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 352 ASP Chi-restraints excluded: chain C residue 369 ARG Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 352 ASP Chi-restraints excluded: chain D residue 369 ARG Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 356 LYS Chi-restraints excluded: chain F residue 52 TYR Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 207 GLN Chi-restraints excluded: chain F residue 272 CYS Chi-restraints excluded: chain F residue 274 GLN Chi-restraints excluded: chain F residue 320 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 41 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 197 optimal weight: 7.9990 chunk 107 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS C 59 HIS ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 HIS ** D 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.144780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.115757 restraints weight = 18155.520| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.63 r_work: 0.3218 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16686 Z= 0.186 Angle : 0.573 7.903 22602 Z= 0.315 Chirality : 0.045 0.154 2502 Planarity : 0.005 0.092 2826 Dihedral : 5.445 42.685 2190 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.90 % Allowed : 16.28 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.19), residues: 1968 helix: -0.53 (0.22), residues: 564 sheet: 1.00 (0.23), residues: 570 loop : 0.16 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 294 TYR 0.012 0.001 TYR B 53 PHE 0.016 0.002 PHE E 292 TRP 0.015 0.002 TRP E 312 HIS 0.005 0.001 HIS D 59 Details of bonding type rmsd covalent geometry : bond 0.00427 (16686) covalent geometry : angle 0.57292 (22602) hydrogen bonds : bond 0.04788 ( 678) hydrogen bonds : angle 5.00194 ( 1872) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3936 Ramachandran restraints generated. 1968 Oldfield, 0 Emsley, 1968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 221 time to evaluate : 0.697 Fit side-chains REVERT: A 47 MET cc_start: 0.5929 (mtp) cc_final: 0.5593 (OUTLIER) REVERT: A 52 TYR cc_start: 0.5894 (OUTLIER) cc_final: 0.3584 (m-80) REVERT: A 243 LYS cc_start: 0.7907 (mmtt) cc_final: 0.7428 (pttm) REVERT: A 294 ARG cc_start: 0.7401 (mmm160) cc_final: 0.7161 (mmt90) REVERT: A 337 MET cc_start: 0.8588 (ttm) cc_final: 0.8092 (ttp) REVERT: B 47 MET cc_start: 0.7277 (mtt) cc_final: 0.6955 (ttm) REVERT: B 131 LYS cc_start: 0.8536 (ttmt) cc_final: 0.8261 (ttpm) REVERT: B 206 ARG cc_start: 0.6976 (ttp-110) cc_final: 0.6698 (ttp80) REVERT: B 332 PHE cc_start: 0.8457 (m-80) cc_final: 0.8027 (m-10) REVERT: B 337 MET cc_start: 0.8465 (ttm) cc_final: 0.8118 (ttm) REVERT: B 345 ARG cc_start: 0.6851 (mtt-85) cc_final: 0.5695 (mtp180) REVERT: C 131 LYS cc_start: 0.8822 (tmtt) cc_final: 0.8500 (ttpp) REVERT: C 352 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7997 (m-30) REVERT: C 369 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.8075 (mmm160) REVERT: D 131 LYS cc_start: 0.8795 (tmtt) cc_final: 0.8480 (ttpp) REVERT: D 352 ASP cc_start: 0.8239 (OUTLIER) cc_final: 0.8033 (m-30) REVERT: D 369 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.8049 (mmm160) REVERT: E 47 MET cc_start: 0.7186 (mtt) cc_final: 0.6823 (ttm) REVERT: E 70 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8222 (tt0) REVERT: E 131 LYS cc_start: 0.8551 (ttmt) cc_final: 0.8283 (ttpm) REVERT: E 206 ARG cc_start: 0.7063 (ttp-110) cc_final: 0.6811 (ttp80) REVERT: E 332 PHE cc_start: 0.8464 (m-80) cc_final: 0.7998 (m-10) REVERT: E 337 MET cc_start: 0.8449 (ttm) cc_final: 0.8043 (ttm) REVERT: E 345 ARG cc_start: 0.6809 (mtt-85) cc_final: 0.5682 (mtp180) REVERT: F 171 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7428 (mt-10) REVERT: F 337 MET cc_start: 0.8578 (ttm) cc_final: 0.8080 (ttp) REVERT: F 356 LYS cc_start: 0.8060 (mppt) cc_final: 0.7735 (mptt) outliers start: 34 outliers final: 24 residues processed: 234 average time/residue: 0.8008 time to fit residues: 203.6131 Evaluate side-chains 247 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 218 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 207 GLN Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 352 ASP Chi-restraints excluded: chain C residue 369 ARG Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 352 ASP Chi-restraints excluded: chain D residue 369 ARG Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 207 GLN Chi-restraints excluded: chain F residue 272 CYS Chi-restraints excluded: chain F residue 274 GLN Chi-restraints excluded: chain F residue 320 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 94 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 119 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 115 optimal weight: 0.7980 chunk 50 optimal weight: 0.0980 chunk 187 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 138 optimal weight: 0.6980 chunk 147 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS A 358 GLN C 59 HIS ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 HIS ** D 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 59 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 = 0.3730 r_free = 0.3730 target = 0.148208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.119215 restraints weight = 18135.513| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.59 r_work: 0.3271 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16686 Z= 0.111 Angle : 0.506 7.787 22602 Z= 0.278 Chirality : 0.043 0.154 2502 Planarity : 0.004 0.084 2826 Dihedral : 4.975 37.607 2190 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.51 % Allowed : 16.67 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.19), residues: 1968 helix: -0.31 (0.23), residues: 552 sheet: 0.91 (0.23), residues: 582 loop : 0.28 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG A 294 TYR 0.010 0.001 TYR C 53 PHE 0.011 0.001 PHE E 292 TRP 0.015 0.001 TRP D 312 HIS 0.004 0.001 HIS D 59 Details of bonding type rmsd covalent geometry : bond 0.00242 (16686) covalent geometry : angle 0.50574 (22602) hydrogen bonds : bond 0.03889 ( 678) hydrogen bonds : angle 4.79448 ( 1872) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7484.85 seconds wall clock time: 128 minutes 14.46 seconds (7694.46 seconds total)