Starting phenix.real_space_refine on Sat May 17 23:54:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bh4_44532/05_2025/9bh4_44532.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bh4_44532/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9bh4_44532/05_2025/9bh4_44532.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bh4_44532/05_2025/9bh4_44532.map" model { file = "/net/cci-nas-00/data/ceres_data/9bh4_44532/05_2025/9bh4_44532.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bh4_44532/05_2025/9bh4_44532.cif" } resolution = 2.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: C, B, E, D, F Time building chain proxies: 7.47, per 1000 atoms: 0.46 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: 3.89 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 2.00 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: 6.48 Time building geometry restraints manager: 4.59 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: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' 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: 3.850 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: 0.720 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 36.330 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.660 ------------------------------------------------------------------------------- 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 : 8.77 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.18), 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 TRP 0.010 0.001 TRP D 312 HIS 0.004 0.001 HIS B 311 PHE 0.011 0.001 PHE D 292 TYR 0.024 0.001 TYR E 52 ARG 0.007 0.001 ARG F 371 Details of bonding type rmsd hydrogen bonds : bond 0.15061 ( 678) hydrogen bonds : angle 5.88418 ( 1872) covalent geometry : bond 0.00405 (16686) covalent geometry : angle 0.74750 (22602) *********************** 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 : 1.915 Fit side-chains REVERT: A 243 LYS cc_start: 0.7748 (ptpt) cc_final: 0.7341 (mmtt) 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: 0.6718 (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: 0.7400 (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: 1.4361 time to fit residues: 547.6959 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 : 1.788 ------------------------------------------------------------------------------- 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 167 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 155 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 179 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 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 175 ASN E 314 GLN E 343 ASN F 59 HIS F 358 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.147979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.120644 restraints weight = 18496.297| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.53 r_work: 0.3331 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 16686 Z= 0.240 Angle : 0.633 7.852 22602 Z= 0.345 Chirality : 0.048 0.144 2502 Planarity : 0.005 0.054 2826 Dihedral : 6.079 47.787 2194 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.78 % Favored : 98.12 % Rotamer: Outliers : 2.74 % Allowed : 9.17 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.19), residues: 1968 helix: -0.95 (0.20), residues: 576 sheet: 1.45 (0.22), residues: 600 loop : 0.49 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 312 HIS 0.003 0.001 HIS D 59 PHE 0.018 0.002 PHE E 292 TYR 0.017 0.002 TYR B 53 ARG 0.004 0.001 ARG B 369 Details of bonding type rmsd hydrogen bonds : bond 0.05704 ( 678) hydrogen bonds : angle 5.16288 ( 1872) covalent geometry : bond 0.00556 (16686) covalent geometry : angle 0.63291 (22602) *********************** 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: 49 poor density : 246 time to evaluate : 1.762 Fit side-chains REVERT: A 88 LYS cc_start: 0.7833 (OUTLIER) cc_final: 0.7452 (mptp) REVERT: A 294 ARG cc_start: 0.7190 (mmt90) cc_final: 0.6690 (mmm160) REVERT: A 337 MET cc_start: 0.8449 (ttm) cc_final: 0.8093 (ttp) REVERT: A 369 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7307 (tpp-160) REVERT: B 131 LYS cc_start: 0.8479 (ttmt) cc_final: 0.8253 (ttpm) REVERT: B 272 CYS cc_start: 0.7872 (t) cc_final: 0.7515 (t) REVERT: B 332 PHE cc_start: 0.8726 (m-80) cc_final: 0.8121 (m-10) REVERT: B 345 ARG cc_start: 0.6820 (mtt-85) cc_final: 0.5735 (mtp180) REVERT: B 356 LYS cc_start: 0.6947 (mppt) cc_final: 0.6618 (mppt) REVERT: D 369 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8188 (mmm160) REVERT: E 70 GLU cc_start: 0.8523 (tp30) cc_final: 0.8278 (tt0) REVERT: E 131 LYS cc_start: 0.8446 (ttmt) cc_final: 0.8210 (ttpm) REVERT: E 272 CYS cc_start: 0.7868 (t) cc_final: 0.7526 (t) REVERT: E 332 PHE cc_start: 0.8697 (m-80) cc_final: 0.8109 (m-10) REVERT: E 345 ARG cc_start: 0.6832 (mtt-85) cc_final: 0.5759 (mtp180) REVERT: F 243 LYS cc_start: 0.8125 (ptpt) cc_final: 0.7723 (mmtt) REVERT: F 294 ARG cc_start: 0.7192 (mmt90) cc_final: 0.6692 (mmm160) REVERT: F 337 MET cc_start: 0.8393 (ttm) cc_final: 0.8058 (ttp) REVERT: F 356 LYS cc_start: 0.8072 (mppt) cc_final: 0.7776 (mptt) outliers start: 49 outliers final: 18 residues processed: 268 average time/residue: 1.5524 time to fit residues: 454.1628 Evaluate side-chains 254 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 233 time to evaluate : 1.795 ------------------------------------------------------------------------------- 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 369 ARG Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 207 GLN Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 369 ARG Chi-restraints excluded: chain E residue 173 MET 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 354 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 45 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 177 optimal weight: 0.5980 chunk 136 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 143 optimal weight: 0.9980 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 C 358 GLN D 59 HIS ** D 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 GLN D 358 GLN F 59 HIS F 358 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.145836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.117487 restraints weight = 18262.972| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.60 r_work: 0.3266 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16686 Z= 0.196 Angle : 0.571 7.057 22602 Z= 0.313 Chirality : 0.046 0.159 2502 Planarity : 0.004 0.037 2826 Dihedral : 5.827 45.051 2194 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.96 % Allowed : 10.79 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.19), residues: 1968 helix: -0.73 (0.21), residues: 576 sheet: 1.29 (0.23), residues: 570 loop : 0.32 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 312 HIS 0.004 0.001 HIS B 59 PHE 0.016 0.002 PHE B 292 TYR 0.015 0.001 TYR B 53 ARG 0.004 0.001 ARG E 369 Details of bonding type rmsd hydrogen bonds : bond 0.05074 ( 678) hydrogen bonds : angle 5.03389 ( 1872) covalent geometry : bond 0.00448 (16686) covalent geometry : angle 0.57114 (22602) *********************** 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 288 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 235 time to evaluate : 2.052 Fit side-chains REVERT: A 88 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.7206 (mptp) REVERT: A 294 ARG cc_start: 0.7260 (mmt90) cc_final: 0.6737 (mmm160) REVERT: A 337 MET cc_start: 0.8460 (ttm) cc_final: 0.8048 (ttp) REVERT: A 369 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7481 (tpp-160) REVERT: B 131 LYS cc_start: 0.8507 (ttmt) cc_final: 0.8244 (ttpm) REVERT: B 272 CYS cc_start: 0.7849 (t) cc_final: 0.7485 (t) REVERT: B 329 GLU cc_start: 0.7337 (mt-10) cc_final: 0.7121 (mm-30) REVERT: B 332 PHE cc_start: 0.8726 (m-80) cc_final: 0.8101 (m-10) REVERT: B 337 MET cc_start: 0.8400 (ttm) cc_final: 0.8016 (ttm) REVERT: B 345 ARG cc_start: 0.6742 (mtt-85) cc_final: 0.5656 (mtp180) REVERT: D 131 LYS cc_start: 0.8794 (tmtt) cc_final: 0.8497 (ttpp) REVERT: D 369 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8204 (mmm160) REVERT: E 70 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8264 (tt0) REVERT: E 131 LYS cc_start: 0.8527 (ttmt) cc_final: 0.8273 (ttpm) REVERT: E 272 CYS cc_start: 0.7826 (t) cc_final: 0.7464 (t) REVERT: E 332 PHE cc_start: 0.8702 (m-80) cc_final: 0.8084 (m-10) REVERT: E 337 MET cc_start: 0.8496 (ttm) cc_final: 0.7980 (ttm) REVERT: E 345 ARG cc_start: 0.6824 (mtt-85) cc_final: 0.5716 (mtp180) REVERT: F 88 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7380 (mptp) REVERT: F 294 ARG cc_start: 0.7254 (mmt90) cc_final: 0.6725 (mmm160) REVERT: F 337 MET cc_start: 0.8444 (ttm) cc_final: 0.8034 (ttp) REVERT: F 345 ARG cc_start: 0.7363 (mtt180) cc_final: 0.7126 (mtt180) REVERT: F 356 LYS cc_start: 0.8082 (mppt) cc_final: 0.7814 (mptt) outliers start: 53 outliers final: 20 residues processed: 261 average time/residue: 1.4557 time to fit residues: 415.3594 Evaluate side-chains 248 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 223 time to evaluate : 1.824 ------------------------------------------------------------------------------- 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 A residue 369 ARG Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 207 GLN Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 207 GLN 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 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 46 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 188 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 140 optimal weight: 0.9980 chunk 179 optimal weight: 0.4980 chunk 151 optimal weight: 0.0470 chunk 32 optimal weight: 7.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.147798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.119236 restraints weight = 18211.854| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.57 r_work: 0.3284 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2356 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= 0.111 Angle : 0.483 6.224 22602 Z= 0.267 Chirality : 0.043 0.152 2502 Planarity : 0.003 0.032 2826 Dihedral : 5.202 40.950 2190 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.63 % Allowed : 12.47 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.19), residues: 1968 helix: -0.36 (0.22), residues: 564 sheet: 1.13 (0.23), residues: 582 loop : 0.42 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 312 HIS 0.004 0.001 HIS E 59 PHE 0.012 0.001 PHE E 292 TYR 0.014 0.001 TYR C 53 ARG 0.003 0.000 ARG B 369 Details of bonding type rmsd hydrogen bonds : bond 0.04109 ( 678) hydrogen bonds : angle 4.80888 ( 1872) covalent geometry : bond 0.00237 (16686) covalent geometry : angle 0.48280 (22602) *********************** 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 279 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 232 time to evaluate : 1.914 Fit side-chains REVERT: A 52 TYR cc_start: 0.5279 (OUTLIER) cc_final: 0.2744 (m-10) REVERT: A 88 LYS cc_start: 0.7676 (OUTLIER) cc_final: 0.7198 (mptp) REVERT: A 291 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7478 (mp0) REVERT: A 294 ARG cc_start: 0.7187 (mmt90) cc_final: 0.6673 (mmm160) REVERT: A 337 MET cc_start: 0.8486 (ttm) cc_final: 0.7997 (ttp) REVERT: B 131 LYS cc_start: 0.8458 (ttmt) cc_final: 0.8185 (ttpm) REVERT: B 272 CYS cc_start: 0.7745 (t) cc_final: 0.7377 (t) REVERT: B 332 PHE cc_start: 0.8679 (m-80) cc_final: 0.8033 (m-10) REVERT: B 337 MET cc_start: 0.8311 (ttm) cc_final: 0.7995 (ttm) REVERT: B 345 ARG cc_start: 0.6781 (mtt-85) cc_final: 0.5652 (mtp180) REVERT: D 131 LYS cc_start: 0.8724 (tmtt) cc_final: 0.8416 (ttpp) REVERT: E 70 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8178 (tt0) REVERT: E 131 LYS cc_start: 0.8489 (ttmt) cc_final: 0.8216 (ttpm) REVERT: E 272 CYS cc_start: 0.7723 (t) cc_final: 0.7289 (t) REVERT: E 332 PHE cc_start: 0.8662 (m-80) cc_final: 0.8039 (m-10) REVERT: E 337 MET cc_start: 0.8413 (ttm) cc_final: 0.7905 (ttm) REVERT: E 345 ARG cc_start: 0.6780 (mtt-85) cc_final: 0.5672 (mtp180) REVERT: F 52 TYR cc_start: 0.5257 (OUTLIER) cc_final: 0.2435 (m-10) REVERT: F 88 LYS cc_start: 0.7752 (OUTLIER) cc_final: 0.7360 (mptp) REVERT: F 294 ARG cc_start: 0.7212 (mmt90) cc_final: 0.6683 (mmm160) REVERT: F 337 MET cc_start: 0.8523 (ttm) cc_final: 0.8037 (ttp) REVERT: F 356 LYS cc_start: 0.8032 (mppt) cc_final: 0.7722 (mptt) outliers start: 47 outliers final: 18 residues processed: 251 average time/residue: 1.4885 time to fit residues: 408.0643 Evaluate side-chains 243 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 220 time to evaluate : 1.798 ------------------------------------------------------------------------------- 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 C residue 140 THR Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 298 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 298 ARG Chi-restraints excluded: chain D residue 369 ARG Chi-restraints excluded: chain E residue 70 GLU 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 141 optimal weight: 2.9990 chunk 187 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 143 optimal weight: 0.9990 chunk 157 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 103 optimal weight: 0.0670 overall best weight: 0.9922 ------------------------------------------------------------------------------- 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 274 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 = 0.3712 r_free = 0.3712 target = 0.146735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.117816 restraints weight = 18312.552| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.60 r_work: 0.3242 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16686 Z= 0.135 Angle : 0.503 6.020 22602 Z= 0.278 Chirality : 0.044 0.150 2502 Planarity : 0.004 0.031 2826 Dihedral : 5.252 40.466 2190 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.63 % Allowed : 13.26 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.19), residues: 1968 helix: -0.36 (0.23), residues: 552 sheet: 1.08 (0.22), residues: 582 loop : 0.31 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 312 HIS 0.003 0.001 HIS F 59 PHE 0.014 0.002 PHE E 292 TYR 0.014 0.001 TYR C 53 ARG 0.003 0.000 ARG A 345 Details of bonding type rmsd hydrogen bonds : bond 0.04356 ( 678) hydrogen bonds : angle 4.83446 ( 1872) covalent geometry : bond 0.00301 (16686) covalent geometry : angle 0.50302 (22602) *********************** 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 282 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 235 time to evaluate : 1.944 Fit side-chains REVERT: A 88 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.7238 (mptp) REVERT: A 243 LYS cc_start: 0.8011 (pttp) cc_final: 0.7493 (mmtt) REVERT: A 291 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7543 (mp0) REVERT: A 294 ARG cc_start: 0.7063 (mmt90) cc_final: 0.6647 (mmm160) REVERT: A 337 MET cc_start: 0.8518 (ttm) cc_final: 0.8021 (ttp) REVERT: A 369 ARG cc_start: 0.7713 (tpp-160) cc_final: 0.7216 (mpp-170) REVERT: B 131 LYS cc_start: 0.8513 (ttmt) cc_final: 0.8240 (ttpm) REVERT: B 272 CYS cc_start: 0.7768 (t) cc_final: 0.7423 (t) REVERT: B 332 PHE cc_start: 0.8693 (m-80) cc_final: 0.8035 (m-10) REVERT: B 337 MET cc_start: 0.8352 (ttm) cc_final: 0.8003 (ttm) REVERT: B 345 ARG cc_start: 0.6820 (mtt-85) cc_final: 0.5686 (mtp180) REVERT: C 154 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7536 (tm-30) REVERT: C 369 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8074 (mmm160) REVERT: D 131 LYS cc_start: 0.8795 (tmtt) cc_final: 0.8455 (ttpp) REVERT: E 70 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8164 (tt0) REVERT: E 131 LYS cc_start: 0.8542 (ttmt) cc_final: 0.8260 (ttpm) REVERT: E 272 CYS cc_start: 0.7759 (t) cc_final: 0.7431 (t) REVERT: E 332 PHE cc_start: 0.8684 (m-80) cc_final: 0.8060 (m-10) REVERT: E 337 MET cc_start: 0.8412 (ttm) cc_final: 0.8025 (ttm) REVERT: E 345 ARG cc_start: 0.6771 (mtt-85) cc_final: 0.5647 (mtp180) REVERT: F 52 TYR cc_start: 0.5387 (OUTLIER) cc_final: 0.2612 (m-10) REVERT: F 88 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7332 (mptp) REVERT: F 294 ARG cc_start: 0.7081 (mmt90) cc_final: 0.6663 (mmm160) REVERT: F 337 MET cc_start: 0.8562 (ttm) cc_final: 0.8079 (ttp) REVERT: F 356 LYS cc_start: 0.8059 (mppt) cc_final: 0.7689 (mptt) outliers start: 47 outliers final: 26 residues processed: 255 average time/residue: 1.5156 time to fit residues: 421.4274 Evaluate side-chains 251 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 219 time to evaluate : 2.020 ------------------------------------------------------------------------------- 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 A residue 358 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 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 298 ARG 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 298 ARG 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 122 optimal weight: 2.9990 chunk 135 optimal weight: 0.7980 chunk 115 optimal weight: 0.6980 chunk 43 optimal weight: 0.0770 chunk 51 optimal weight: 0.5980 chunk 110 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 192 optimal weight: 0.8980 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 278 ASN F 358 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.148619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.120004 restraints weight = 18245.472| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.59 r_work: 0.3276 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16686 Z= 0.106 Angle : 0.473 5.758 22602 Z= 0.262 Chirality : 0.043 0.147 2502 Planarity : 0.003 0.031 2826 Dihedral : 4.994 39.360 2190 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.57 % Allowed : 14.15 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.19), residues: 1968 helix: -0.25 (0.23), residues: 552 sheet: 1.05 (0.23), residues: 582 loop : 0.31 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 312 HIS 0.003 0.001 HIS F 59 PHE 0.012 0.001 PHE E 292 TYR 0.013 0.001 TYR C 53 ARG 0.003 0.000 ARG A 345 Details of bonding type rmsd hydrogen bonds : bond 0.03913 ( 678) hydrogen bonds : angle 4.71669 ( 1872) covalent geometry : bond 0.00227 (16686) covalent geometry : angle 0.47274 (22602) *********************** 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 286 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 240 time to evaluate : 1.820 Fit side-chains REVERT: A 88 LYS cc_start: 0.7647 (OUTLIER) cc_final: 0.7251 (mptp) REVERT: A 291 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7489 (mp0) REVERT: A 294 ARG cc_start: 0.7043 (mmt90) cc_final: 0.6660 (mmm160) REVERT: A 337 MET cc_start: 0.8481 (ttm) cc_final: 0.7982 (ttp) REVERT: B 131 LYS cc_start: 0.8532 (ttmt) cc_final: 0.8255 (ttpm) REVERT: B 272 CYS cc_start: 0.7721 (t) cc_final: 0.7363 (t) REVERT: B 332 PHE cc_start: 0.8619 (m-80) cc_final: 0.7936 (m-10) REVERT: B 337 MET cc_start: 0.8316 (ttm) cc_final: 0.7865 (ttm) REVERT: B 345 ARG cc_start: 0.6799 (mtt-85) cc_final: 0.5666 (mtp180) REVERT: C 369 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.8058 (mmm160) REVERT: D 131 LYS cc_start: 0.8719 (tmtt) cc_final: 0.8399 (ttpp) REVERT: D 154 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7526 (tm-30) REVERT: E 70 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8108 (tt0) REVERT: E 131 LYS cc_start: 0.8561 (ttmt) cc_final: 0.8294 (ttpm) REVERT: E 272 CYS cc_start: 0.7696 (t) cc_final: 0.7340 (t) REVERT: E 332 PHE cc_start: 0.8617 (m-80) cc_final: 0.7927 (m-10) REVERT: E 337 MET cc_start: 0.8340 (ttm) cc_final: 0.7849 (ttm) REVERT: E 345 ARG cc_start: 0.6726 (mtt-85) cc_final: 0.5634 (mtp180) REVERT: F 52 TYR cc_start: 0.5374 (OUTLIER) cc_final: 0.2572 (m-10) REVERT: F 55 ASP cc_start: 0.6274 (OUTLIER) cc_final: 0.5960 (t70) REVERT: F 62 ILE cc_start: 0.8538 (tt) cc_final: 0.8322 (tp) REVERT: F 88 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.7266 (mptp) REVERT: F 291 GLU cc_start: 0.8023 (tt0) cc_final: 0.7454 (mp0) REVERT: F 294 ARG cc_start: 0.7031 (mmt90) cc_final: 0.6651 (mmm160) REVERT: F 337 MET cc_start: 0.8545 (ttm) cc_final: 0.8055 (ttp) REVERT: F 356 LYS cc_start: 0.8054 (mppt) cc_final: 0.7701 (mptt) outliers start: 46 outliers final: 20 residues processed: 254 average time/residue: 1.5080 time to fit residues: 417.6925 Evaluate side-chains 251 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 224 time to evaluate : 1.840 ------------------------------------------------------------------------------- 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 B residue 80 MET Chi-restraints excluded: chain B residue 138 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 369 ARG Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 154 GLU 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 70 GLU Chi-restraints excluded: chain E residue 230 VAL 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 148 GLU Chi-restraints excluded: chain F residue 207 GLN Chi-restraints excluded: chain F residue 274 GLN Chi-restraints excluded: chain F residue 320 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 172 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 145 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 278 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.142597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.113709 restraints weight = 18312.934| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.59 r_work: 0.3191 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 16686 Z= 0.275 Angle : 0.629 6.320 22602 Z= 0.344 Chirality : 0.049 0.140 2502 Planarity : 0.005 0.039 2826 Dihedral : 5.749 43.931 2190 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.96 % Allowed : 14.26 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.19), residues: 1968 helix: -0.68 (0.22), residues: 564 sheet: 1.13 (0.23), residues: 564 loop : 0.14 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 312 HIS 0.004 0.001 HIS C 311 PHE 0.019 0.002 PHE B 292 TYR 0.015 0.002 TYR D 52 ARG 0.006 0.001 ARG A 345 Details of bonding type rmsd hydrogen bonds : bond 0.05480 ( 678) hydrogen bonds : angle 5.13819 ( 1872) covalent geometry : bond 0.00642 (16686) covalent geometry : angle 0.62943 (22602) *********************** 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 271 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 218 time to evaluate : 2.051 Fit side-chains REVERT: A 52 TYR cc_start: 0.5350 (OUTLIER) cc_final: 0.2566 (m-10) REVERT: A 88 LYS cc_start: 0.7679 (OUTLIER) cc_final: 0.7261 (mptp) REVERT: A 294 ARG cc_start: 0.7001 (mmt90) cc_final: 0.6749 (mmm160) REVERT: A 337 MET cc_start: 0.8593 (ttm) cc_final: 0.8104 (ttp) REVERT: A 369 ARG cc_start: 0.7738 (OUTLIER) cc_final: 0.7192 (mpp-170) REVERT: B 131 LYS cc_start: 0.8570 (ttmt) cc_final: 0.8300 (ttpm) REVERT: B 206 ARG cc_start: 0.6995 (ttp-110) cc_final: 0.6723 (ttp80) REVERT: B 337 MET cc_start: 0.8497 (ttm) cc_final: 0.8011 (ttm) REVERT: B 345 ARG cc_start: 0.6919 (mtt-85) cc_final: 0.5794 (mtp180) REVERT: D 131 LYS cc_start: 0.8836 (tmtt) cc_final: 0.8534 (ttpp) REVERT: E 47 MET cc_start: 0.7295 (mtt) cc_final: 0.6947 (ttm) REVERT: E 70 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8274 (tt0) REVERT: E 131 LYS cc_start: 0.8575 (ttmt) cc_final: 0.8304 (ttpm) REVERT: E 206 ARG cc_start: 0.7025 (ttp-110) cc_final: 0.6746 (ttp80) REVERT: E 337 MET cc_start: 0.8474 (ttm) cc_final: 0.8029 (ttm) REVERT: E 345 ARG cc_start: 0.6855 (mtt-85) cc_final: 0.5728 (mtp180) REVERT: F 52 TYR cc_start: 0.5532 (OUTLIER) cc_final: 0.2916 (m-10) REVERT: F 55 ASP cc_start: 0.6565 (OUTLIER) cc_final: 0.5837 (t70) REVERT: F 88 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7316 (mptp) REVERT: F 337 MET cc_start: 0.8624 (ttm) cc_final: 0.8134 (ttp) REVERT: F 356 LYS cc_start: 0.8061 (mppt) cc_final: 0.7735 (mptt) outliers start: 53 outliers final: 27 residues processed: 244 average time/residue: 1.4893 time to fit residues: 398.0891 Evaluate side-chains 248 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 214 time to evaluate : 1.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 74 LEU 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 356 LYS Chi-restraints excluded: chain A residue 369 ARG Chi-restraints excluded: chain B residue 89 ASP 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 140 THR Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 236 LEU 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 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 55 ASP 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 145 LYS 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 0 optimal weight: 20.0000 chunk 150 optimal weight: 5.9990 chunk 127 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 184 optimal weight: 4.9990 chunk 193 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 chunk 178 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.144702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.115700 restraints weight = 18107.826| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.63 r_work: 0.3214 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16686 Z= 0.184 Angle : 0.559 5.908 22602 Z= 0.308 Chirality : 0.045 0.142 2502 Planarity : 0.004 0.050 2826 Dihedral : 5.539 43.276 2190 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.35 % Allowed : 15.55 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.19), residues: 1968 helix: -0.63 (0.22), residues: 564 sheet: 1.03 (0.22), residues: 570 loop : 0.16 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 312 HIS 0.004 0.001 HIS C 59 PHE 0.016 0.002 PHE B 292 TYR 0.013 0.001 TYR E 53 ARG 0.011 0.001 ARG F 294 Details of bonding type rmsd hydrogen bonds : bond 0.04835 ( 678) hydrogen bonds : angle 5.03529 ( 1872) covalent geometry : bond 0.00421 (16686) covalent geometry : angle 0.55856 (22602) *********************** 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 256 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 214 time to evaluate : 1.924 Fit side-chains REVERT: A 52 TYR cc_start: 0.5546 (OUTLIER) cc_final: 0.3020 (m-80) REVERT: A 337 MET cc_start: 0.8574 (ttm) cc_final: 0.8079 (ttp) REVERT: A 369 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.7001 (mpp-170) REVERT: B 47 MET cc_start: 0.7315 (mtt) cc_final: 0.6951 (ttm) REVERT: B 131 LYS cc_start: 0.8533 (ttmt) cc_final: 0.8260 (ttpm) REVERT: B 206 ARG cc_start: 0.7039 (ttp-110) cc_final: 0.6774 (ttp80) REVERT: B 332 PHE cc_start: 0.8498 (m-80) cc_final: 0.8013 (m-10) REVERT: B 337 MET cc_start: 0.8488 (ttm) cc_final: 0.8021 (ttm) REVERT: B 345 ARG cc_start: 0.6902 (mtt-85) cc_final: 0.5767 (mtp180) REVERT: C 352 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7985 (m-30) REVERT: D 131 LYS cc_start: 0.8798 (tmtt) cc_final: 0.8485 (ttpp) REVERT: E 47 MET cc_start: 0.7303 (mtt) cc_final: 0.6942 (ttm) REVERT: E 70 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8248 (tt0) REVERT: E 131 LYS cc_start: 0.8540 (ttmt) cc_final: 0.8277 (ttpm) REVERT: E 206 ARG cc_start: 0.7028 (ttp-110) cc_final: 0.6759 (ttp80) REVERT: E 332 PHE cc_start: 0.8485 (m-80) cc_final: 0.8004 (m-10) REVERT: E 337 MET cc_start: 0.8458 (ttm) cc_final: 0.8050 (ttm) REVERT: E 345 ARG cc_start: 0.6835 (mtt-85) cc_final: 0.5677 (mtp180) REVERT: F 52 TYR cc_start: 0.5694 (OUTLIER) cc_final: 0.3031 (m-10) REVERT: F 88 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7337 (mptp) REVERT: F 337 MET cc_start: 0.8580 (ttm) cc_final: 0.8088 (ttp) REVERT: F 356 LYS cc_start: 0.8096 (mppt) cc_final: 0.7754 (mptt) outliers start: 42 outliers final: 24 residues processed: 235 average time/residue: 1.4690 time to fit residues: 378.3584 Evaluate side-chains 236 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 206 time to evaluate : 1.736 ------------------------------------------------------------------------------- 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 A residue 356 LYS Chi-restraints excluded: chain A residue 369 ARG 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 236 LEU Chi-restraints excluded: chain C residue 352 ASP Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 236 LEU 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 145 LYS 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 93 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 167 optimal weight: 0.9980 chunk 138 optimal weight: 4.9990 chunk 164 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 133 optimal weight: 7.9990 chunk 185 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.146594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.117725 restraints weight = 18168.421| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.63 r_work: 0.3241 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16686 Z= 0.131 Angle : 0.518 7.661 22602 Z= 0.285 Chirality : 0.043 0.145 2502 Planarity : 0.004 0.083 2826 Dihedral : 5.236 40.308 2190 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.07 % Allowed : 16.00 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.19), residues: 1968 helix: -0.41 (0.23), residues: 552 sheet: 1.00 (0.23), residues: 570 loop : 0.23 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 312 HIS 0.004 0.001 HIS D 59 PHE 0.014 0.001 PHE E 292 TYR 0.011 0.001 TYR D 53 ARG 0.018 0.000 ARG F 294 Details of bonding type rmsd hydrogen bonds : bond 0.04266 ( 678) hydrogen bonds : angle 4.89704 ( 1872) covalent geometry : bond 0.00292 (16686) covalent geometry : angle 0.51780 (22602) *********************** 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 252 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 215 time to evaluate : 1.962 Fit side-chains REVERT: A 337 MET cc_start: 0.8534 (ttm) cc_final: 0.8050 (ttp) REVERT: B 47 MET cc_start: 0.7328 (mtt) cc_final: 0.6955 (ttm) REVERT: B 131 LYS cc_start: 0.8519 (ttmt) cc_final: 0.8239 (ttpm) REVERT: B 206 ARG cc_start: 0.7071 (ttp-110) cc_final: 0.6795 (ttp80) REVERT: B 332 PHE cc_start: 0.8398 (m-80) cc_final: 0.8135 (m-10) REVERT: B 337 MET cc_start: 0.8446 (ttm) cc_final: 0.7970 (ttm) REVERT: B 345 ARG cc_start: 0.6883 (mtt-85) cc_final: 0.5728 (mtp180) REVERT: C 298 ARG cc_start: 0.7488 (tmt170) cc_final: 0.7037 (ttp80) REVERT: C 344 ASN cc_start: 0.8067 (m-40) cc_final: 0.7798 (m110) REVERT: D 131 LYS cc_start: 0.8813 (tmtt) cc_final: 0.8475 (ttpp) REVERT: D 298 ARG cc_start: 0.7481 (tmt170) cc_final: 0.7030 (ttp80) REVERT: E 47 MET cc_start: 0.7238 (mtt) cc_final: 0.6843 (ttm) REVERT: E 70 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8199 (tt0) REVERT: E 131 LYS cc_start: 0.8525 (ttmt) cc_final: 0.8265 (ttpm) REVERT: E 206 ARG cc_start: 0.7082 (ttp-110) cc_final: 0.6804 (ttp80) REVERT: E 332 PHE cc_start: 0.8389 (m-80) cc_final: 0.8069 (m-10) REVERT: E 337 MET cc_start: 0.8405 (ttm) cc_final: 0.7950 (ttm) REVERT: E 345 ARG cc_start: 0.6801 (mtt-85) cc_final: 0.5677 (mtp180) REVERT: F 52 TYR cc_start: 0.5710 (OUTLIER) cc_final: 0.3358 (m-80) REVERT: F 88 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7328 (mptp) REVERT: F 337 MET cc_start: 0.8547 (ttm) cc_final: 0.8050 (ttp) REVERT: F 356 LYS cc_start: 0.8062 (mppt) cc_final: 0.7823 (mptt) outliers start: 37 outliers final: 24 residues processed: 231 average time/residue: 1.4796 time to fit residues: 378.3340 Evaluate side-chains 241 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 214 time to evaluate : 2.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 356 LYS Chi-restraints excluded: chain A residue 360 CYS 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 236 LEU 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 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 145 LYS 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 182 optimal weight: 1.9990 chunk 19 optimal weight: 0.0020 chunk 164 optimal weight: 1.9990 chunk 192 optimal weight: 0.6980 chunk 191 optimal weight: 0.8980 chunk 160 optimal weight: 0.9980 chunk 141 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 183 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.148076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.119361 restraints weight = 18176.075| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.61 r_work: 0.3261 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16686 Z= 0.115 Angle : 0.508 8.063 22602 Z= 0.279 Chirality : 0.043 0.146 2502 Planarity : 0.004 0.086 2826 Dihedral : 5.025 38.380 2190 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.62 % Allowed : 16.72 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.19), residues: 1968 helix: -0.33 (0.23), residues: 552 sheet: 0.90 (0.22), residues: 582 loop : 0.27 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 312 HIS 0.004 0.001 HIS D 59 PHE 0.012 0.001 PHE E 292 TYR 0.011 0.001 TYR D 53 ARG 0.021 0.000 ARG A 294 Details of bonding type rmsd hydrogen bonds : bond 0.03966 ( 678) hydrogen bonds : angle 4.78809 ( 1872) covalent geometry : bond 0.00255 (16686) covalent geometry : angle 0.50765 (22602) ********************** 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: 29 poor density : 226 time to evaluate : 1.897 Fit side-chains REVERT: A 112 ARG cc_start: 0.8243 (ttp80) cc_final: 0.7861 (ttp80) REVERT: A 291 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7477 (mp0) REVERT: A 294 ARG cc_start: 0.7401 (mmm160) cc_final: 0.6968 (mmp80) REVERT: A 337 MET cc_start: 0.8509 (ttm) cc_final: 0.8001 (ttp) REVERT: B 47 MET cc_start: 0.7276 (mtt) cc_final: 0.6913 (ttm) REVERT: B 131 LYS cc_start: 0.8487 (ttmt) cc_final: 0.8195 (ttpm) REVERT: B 206 ARG cc_start: 0.7062 (ttp-110) cc_final: 0.6777 (ttp80) REVERT: B 332 PHE cc_start: 0.8357 (m-80) cc_final: 0.8157 (m-10) REVERT: B 337 MET cc_start: 0.8411 (ttm) cc_final: 0.7945 (ttm) REVERT: B 345 ARG cc_start: 0.6881 (mtt-85) cc_final: 0.5717 (mtp180) REVERT: C 298 ARG cc_start: 0.7426 (tmt170) cc_final: 0.6977 (ttp80) REVERT: C 344 ASN cc_start: 0.8060 (m-40) cc_final: 0.7786 (m110) REVERT: D 131 LYS cc_start: 0.8768 (tmtt) cc_final: 0.8428 (ttpp) REVERT: D 298 ARG cc_start: 0.7415 (tmt170) cc_final: 0.6972 (ttp80) REVERT: D 344 ASN cc_start: 0.8073 (m-40) cc_final: 0.7801 (m110) REVERT: E 47 MET cc_start: 0.7184 (mtt) cc_final: 0.6794 (ttm) REVERT: E 70 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8113 (tt0) REVERT: E 131 LYS cc_start: 0.8568 (ttmt) cc_final: 0.8308 (ttpm) REVERT: E 206 ARG cc_start: 0.7096 (ttp-110) cc_final: 0.6813 (ttp80) REVERT: E 332 PHE cc_start: 0.8333 (m-80) cc_final: 0.8074 (m-10) REVERT: E 337 MET cc_start: 0.8357 (ttm) cc_final: 0.7934 (ttm) REVERT: E 345 ARG cc_start: 0.6790 (mtt-85) cc_final: 0.5679 (mtp180) REVERT: F 52 TYR cc_start: 0.5686 (OUTLIER) cc_final: 0.3318 (m-80) REVERT: F 62 ILE cc_start: 0.8556 (tt) cc_final: 0.8344 (tp) REVERT: F 88 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7277 (mptp) REVERT: F 112 ARG cc_start: 0.8261 (ttp80) cc_final: 0.7888 (ttp80) REVERT: F 291 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7482 (mp0) REVERT: F 337 MET cc_start: 0.8518 (ttm) cc_final: 0.8025 (ttp) REVERT: F 356 LYS cc_start: 0.7998 (mppt) cc_final: 0.7776 (mptt) outliers start: 29 outliers final: 23 residues processed: 237 average time/residue: 1.4532 time to fit residues: 377.3269 Evaluate side-chains 248 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 222 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 356 LYS Chi-restraints excluded: chain A residue 360 CYS Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 236 LEU 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 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 145 LYS 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 169 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 156 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 151 optimal weight: 0.3980 chunk 102 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.147271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.118288 restraints weight = 18115.753| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.60 r_work: 0.3251 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16686 Z= 0.129 Angle : 0.520 7.930 22602 Z= 0.286 Chirality : 0.043 0.165 2502 Planarity : 0.004 0.083 2826 Dihedral : 5.080 45.411 2190 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.73 % Allowed : 16.55 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.19), residues: 1968 helix: -0.32 (0.23), residues: 516 sheet: 0.88 (0.22), residues: 582 loop : 0.19 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 312 HIS 0.004 0.001 HIS D 59 PHE 0.013 0.001 PHE E 292 TYR 0.011 0.001 TYR B 53 ARG 0.019 0.000 ARG F 294 Details of bonding type rmsd hydrogen bonds : bond 0.04131 ( 678) hydrogen bonds : angle 4.80605 ( 1872) covalent geometry : bond 0.00286 (16686) covalent geometry : angle 0.51987 (22602) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13562.38 seconds wall clock time: 233 minutes 49.75 seconds (14029.75 seconds total)