Starting phenix.real_space_refine on Sat Jun 14 15:45:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bh4_44532/06_2025/9bh4_44532.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bh4_44532/06_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_44532/06_2025/9bh4_44532.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bh4_44532/06_2025/9bh4_44532.map" model { file = "/net/cci-nas-00/data/ceres_data/9bh4_44532/06_2025/9bh4_44532.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bh4_44532/06_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-5710/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: 7.65, per 1000 atoms: 0.47 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: 4.02 Conformation dependent library (CDL) restraints added in 2.2 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: 2.47 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: 5.75 Time building geometry restraints manager: 4.82 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: 3.390 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: 0.730 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 37.490 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 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:12.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.760 ------------------------------------------------------------------------------- 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 : 1.904 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: 1.4695 time to fit residues: 561.4894 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 : 1.920 ------------------------------------------------------------------------------- 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: 0.3330 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 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 : 1.746 Fit side-chains REVERT: A 88 LYS cc_start: 0.7833 (OUTLIER) cc_final: 0.7452 (mptp) REVERT: A 294 ARG cc_start: 0.7188 (mmt90) cc_final: 0.6690 (mmm160) REVERT: A 337 MET cc_start: 0.8446 (ttm) cc_final: 0.8093 (ttp) REVERT: A 369 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7308 (tpp-160) REVERT: B 131 LYS cc_start: 0.8477 (ttmt) cc_final: 0.8253 (ttpm) REVERT: B 272 CYS cc_start: 0.7875 (t) cc_final: 0.7518 (t) REVERT: B 332 PHE cc_start: 0.8727 (m-80) cc_final: 0.8124 (m-10) REVERT: B 345 ARG cc_start: 0.6821 (mtt-85) cc_final: 0.5739 (mtp180) REVERT: B 356 LYS cc_start: 0.6951 (mppt) cc_final: 0.6624 (mppt) REVERT: D 369 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8187 (mmm160) REVERT: E 70 GLU cc_start: 0.8525 (tp30) cc_final: 0.8280 (tt0) REVERT: E 131 LYS cc_start: 0.8443 (ttmt) cc_final: 0.8209 (ttpm) REVERT: E 272 CYS cc_start: 0.7867 (t) cc_final: 0.7524 (t) REVERT: E 332 PHE cc_start: 0.8699 (m-80) cc_final: 0.8111 (m-10) REVERT: E 345 ARG cc_start: 0.6831 (mtt-85) cc_final: 0.5763 (mtp180) REVERT: F 243 LYS cc_start: 0.8127 (ptpt) cc_final: 0.7721 (mmtt) REVERT: F 294 ARG cc_start: 0.7189 (mmt90) cc_final: 0.6692 (mmm160) REVERT: F 337 MET cc_start: 0.8392 (ttm) cc_final: 0.8057 (ttp) REVERT: F 356 LYS cc_start: 0.8071 (mppt) cc_final: 0.7774 (mptt) outliers start: 49 outliers final: 18 residues processed: 268 average time/residue: 1.5069 time to fit residues: 441.5396 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 : 1.806 ------------------------------------------------------------------------------- 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: 0.0980 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: 1.0982 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.147526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.119323 restraints weight = 18298.013| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.59 r_work: 0.3292 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16686 Z= 0.146 Angle : 0.525 6.868 22602 Z= 0.289 Chirality : 0.044 0.159 2502 Planarity : 0.004 0.032 2826 Dihedral : 5.524 42.398 2194 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.80 % Allowed : 10.57 % Favored : 86.63 % 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: 0.37 (0.19), residues: 1968 helix: -0.62 (0.21), residues: 576 sheet: 1.09 (0.23), residues: 552 loop : 0.52 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 312 HIS 0.003 0.001 HIS B 59 PHE 0.014 0.002 PHE E 292 TYR 0.014 0.001 TYR B 53 ARG 0.004 0.000 ARG B 369 Details of bonding type rmsd hydrogen bonds : bond 0.04592 ( 678) hydrogen bonds : angle 4.90561 ( 1872) covalent geometry : bond 0.00324 (16686) covalent geometry : angle 0.52507 (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 286 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 236 time to evaluate : 1.753 Fit side-chains REVERT: A 88 LYS cc_start: 0.7750 (OUTLIER) cc_final: 0.7235 (mptp) REVERT: A 294 ARG cc_start: 0.7227 (mmt90) cc_final: 0.6719 (mmm160) REVERT: A 337 MET cc_start: 0.8509 (ttm) cc_final: 0.8031 (ttp) REVERT: A 369 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7221 (mpp-170) REVERT: B 131 LYS cc_start: 0.8473 (ttmt) cc_final: 0.8211 (ttpm) REVERT: B 272 CYS cc_start: 0.7813 (t) cc_final: 0.7454 (t) REVERT: B 329 GLU cc_start: 0.7317 (mt-10) cc_final: 0.7116 (mm-30) REVERT: B 332 PHE cc_start: 0.8704 (m-80) cc_final: 0.8085 (m-10) REVERT: B 337 MET cc_start: 0.8427 (ttm) cc_final: 0.8048 (ttm) REVERT: B 345 ARG cc_start: 0.6689 (mtt-85) cc_final: 0.5615 (mtp180) REVERT: D 131 LYS cc_start: 0.8740 (tmtt) cc_final: 0.8455 (ttpp) REVERT: E 70 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8223 (tt0) REVERT: E 131 LYS cc_start: 0.8463 (ttmt) cc_final: 0.8221 (ttpm) REVERT: E 272 CYS cc_start: 0.7792 (t) cc_final: 0.7430 (t) REVERT: E 332 PHE cc_start: 0.8675 (m-80) cc_final: 0.8052 (m-10) REVERT: E 337 MET cc_start: 0.8481 (ttm) cc_final: 0.7964 (ttm) REVERT: E 345 ARG cc_start: 0.6776 (mtt-85) cc_final: 0.5678 (mtp180) REVERT: F 88 LYS cc_start: 0.7815 (OUTLIER) cc_final: 0.7446 (mptp) REVERT: F 243 LYS cc_start: 0.8217 (ptpt) cc_final: 0.7758 (mmtt) REVERT: F 294 ARG cc_start: 0.7275 (mmt90) cc_final: 0.6739 (mmm160) REVERT: F 337 MET cc_start: 0.8428 (ttm) cc_final: 0.7985 (ttp) REVERT: F 345 ARG cc_start: 0.7329 (mtt180) cc_final: 0.7096 (mtt180) REVERT: F 356 LYS cc_start: 0.8107 (mppt) cc_final: 0.7821 (mptt) outliers start: 50 outliers final: 21 residues processed: 261 average time/residue: 1.5065 time to fit residues: 429.8569 Evaluate side-chains 247 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 222 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 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 C residue 140 THR Chi-restraints excluded: chain C residue 298 ARG Chi-restraints excluded: chain C residue 352 ASP Chi-restraints excluded: chain D residue 140 THR 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 E residue 230 VAL 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 320 GLU 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: 1.9990 chunk 72 optimal weight: 1.9990 chunk 188 optimal weight: 5.9990 chunk 153 optimal weight: 0.0020 chunk 38 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 chunk 179 optimal weight: 6.9990 chunk 151 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 111 optimal weight: 0.9980 overall best weight: 1.1992 ------------------------------------------------------------------------------- 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 358 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.146032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.117119 restraints weight = 18174.252| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.58 r_work: 0.3236 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16686 Z= 0.153 Angle : 0.525 6.442 22602 Z= 0.290 Chirality : 0.044 0.154 2502 Planarity : 0.004 0.031 2826 Dihedral : 5.412 42.163 2190 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.74 % Allowed : 12.08 % Favored : 85.18 % 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: 0.30 (0.19), residues: 1968 helix: -0.58 (0.22), residues: 570 sheet: 1.21 (0.23), residues: 570 loop : 0.22 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 312 HIS 0.004 0.001 HIS E 59 PHE 0.015 0.002 PHE E 292 TYR 0.014 0.001 TYR B 53 ARG 0.003 0.000 ARG E 369 Details of bonding type rmsd hydrogen bonds : bond 0.04606 ( 678) hydrogen bonds : angle 4.90358 ( 1872) covalent geometry : bond 0.00345 (16686) covalent geometry : angle 0.52467 (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 283 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 234 time to evaluate : 1.774 Fit side-chains REVERT: A 52 TYR cc_start: 0.5407 (OUTLIER) cc_final: 0.2709 (m-10) REVERT: A 88 LYS cc_start: 0.7662 (OUTLIER) cc_final: 0.7181 (mptp) REVERT: A 294 ARG cc_start: 0.7217 (mmt90) cc_final: 0.6707 (mmm160) REVERT: A 337 MET cc_start: 0.8506 (ttm) cc_final: 0.8017 (ttp) REVERT: A 369 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7220 (mpp-170) REVERT: B 131 LYS cc_start: 0.8500 (ttmt) cc_final: 0.8216 (ttpm) REVERT: B 272 CYS cc_start: 0.7765 (t) cc_final: 0.7401 (t) REVERT: B 332 PHE cc_start: 0.8694 (m-80) cc_final: 0.8015 (m-10) REVERT: B 337 MET cc_start: 0.8394 (ttm) cc_final: 0.8040 (ttm) REVERT: B 345 ARG cc_start: 0.6767 (mtt-85) cc_final: 0.5662 (mtp180) REVERT: D 131 LYS cc_start: 0.8795 (tmtt) cc_final: 0.8485 (ttpp) REVERT: E 70 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8209 (tt0) REVERT: E 131 LYS cc_start: 0.8530 (ttmt) cc_final: 0.8263 (ttpm) REVERT: E 272 CYS cc_start: 0.7746 (t) cc_final: 0.7401 (t) REVERT: E 332 PHE cc_start: 0.8678 (m-80) cc_final: 0.8003 (m-10) REVERT: E 337 MET cc_start: 0.8439 (ttm) cc_final: 0.8056 (ttm) REVERT: E 345 ARG cc_start: 0.6797 (mtt-85) cc_final: 0.5665 (mtp180) REVERT: F 52 TYR cc_start: 0.5229 (OUTLIER) cc_final: 0.2519 (m-10) REVERT: F 88 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7324 (mptp) REVERT: F 171 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7336 (mm-30) REVERT: F 294 ARG cc_start: 0.7197 (mmt90) cc_final: 0.6697 (mmm160) REVERT: F 337 MET cc_start: 0.8567 (ttm) cc_final: 0.8072 (ttp) REVERT: F 345 ARG cc_start: 0.7372 (mtt180) cc_final: 0.7095 (mtt180) REVERT: F 356 LYS cc_start: 0.8041 (mppt) cc_final: 0.7721 (mptt) outliers start: 49 outliers final: 24 residues processed: 256 average time/residue: 1.5115 time to fit residues: 422.2316 Evaluate side-chains 250 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 220 time to evaluate : 1.806 ------------------------------------------------------------------------------- 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 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 298 ARG 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 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 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 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 320 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 141 optimal weight: 3.9990 chunk 187 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 157 optimal weight: 0.0770 chunk 71 optimal weight: 3.9990 chunk 152 optimal weight: 0.9990 chunk 99 optimal weight: 0.0970 chunk 103 optimal weight: 0.5980 overall best weight: 0.5540 ------------------------------------------------------------------------------- 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 358 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.148708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.120154 restraints weight = 18363.422| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.59 r_work: 0.3275 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2461 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= 0.101 Angle : 0.469 5.802 22602 Z= 0.259 Chirality : 0.043 0.150 2502 Planarity : 0.003 0.031 2826 Dihedral : 5.002 39.576 2190 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.52 % Allowed : 13.26 % Favored : 84.23 % 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: 0.48 (0.19), residues: 1968 helix: -0.26 (0.23), residues: 552 sheet: 1.08 (0.23), residues: 582 loop : 0.37 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 312 HIS 0.003 0.001 HIS E 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 0.03896 ( 678) hydrogen bonds : angle 4.71201 ( 1872) covalent geometry : bond 0.00213 (16686) covalent geometry : angle 0.46893 (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: 45 poor density : 237 time to evaluate : 1.847 Fit side-chains REVERT: A 52 TYR cc_start: 0.5362 (OUTLIER) cc_final: 0.2612 (m-10) REVERT: A 88 LYS cc_start: 0.7647 (OUTLIER) cc_final: 0.7248 (mptp) REVERT: A 291 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7482 (mp0) REVERT: A 294 ARG cc_start: 0.7110 (mmt90) cc_final: 0.6657 (mmm160) REVERT: A 337 MET cc_start: 0.8498 (ttm) cc_final: 0.8005 (ttp) REVERT: B 131 LYS cc_start: 0.8462 (ttmt) cc_final: 0.8175 (ttpm) REVERT: B 272 CYS cc_start: 0.7738 (t) cc_final: 0.7410 (t) REVERT: B 294 ARG cc_start: 0.7915 (mmt90) cc_final: 0.7699 (mmt90) REVERT: B 332 PHE cc_start: 0.8678 (m-80) cc_final: 0.8050 (m-10) REVERT: B 337 MET cc_start: 0.8301 (ttm) cc_final: 0.7841 (ttm) REVERT: B 345 ARG cc_start: 0.6819 (mtt-85) cc_final: 0.5659 (mtp180) REVERT: B 356 LYS cc_start: 0.6802 (mppt) cc_final: 0.6472 (mptt) REVERT: C 154 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7492 (tm-30) REVERT: C 369 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.8069 (mmm160) REVERT: D 131 LYS cc_start: 0.8723 (tmtt) cc_final: 0.8395 (ttpp) REVERT: E 70 GLU cc_start: 0.8492 (tp30) cc_final: 0.8114 (tt0) REVERT: E 131 LYS cc_start: 0.8545 (ttmt) cc_final: 0.8254 (ttpm) REVERT: E 272 CYS cc_start: 0.7674 (t) cc_final: 0.7262 (t) REVERT: E 332 PHE cc_start: 0.8649 (m-80) cc_final: 0.7992 (m-10) REVERT: E 337 MET cc_start: 0.8355 (ttm) cc_final: 0.7847 (ttm) REVERT: E 345 ARG cc_start: 0.6764 (mtt-85) cc_final: 0.5645 (mtp180) REVERT: F 52 TYR cc_start: 0.5276 (OUTLIER) cc_final: 0.2578 (m-10) REVERT: F 55 ASP cc_start: 0.6236 (OUTLIER) cc_final: 0.5871 (t70) REVERT: F 88 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7266 (mptp) REVERT: F 291 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7470 (mp0) REVERT: F 294 ARG cc_start: 0.7132 (mmt90) cc_final: 0.6672 (mmm160) REVERT: F 337 MET cc_start: 0.8532 (ttm) cc_final: 0.8043 (ttp) REVERT: F 356 LYS cc_start: 0.8044 (mppt) cc_final: 0.7694 (mptt) outliers start: 45 outliers final: 21 residues processed: 256 average time/residue: 1.5432 time to fit residues: 431.3371 Evaluate side-chains 253 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 225 time to evaluate : 1.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 88 LYS Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 272 CYS Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 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 352 ASP Chi-restraints excluded: chain C residue 369 ARG Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain 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 145 LYS Chi-restraints excluded: chain F residue 207 GLN Chi-restraints excluded: chain F residue 272 CYS Chi-restraints excluded: chain F residue 274 GLN Chi-restraints excluded: chain F residue 320 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 122 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 110 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 192 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS A 358 GLN B 343 ASN ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 HIS ** D 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 HIS F 358 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.147631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.118903 restraints weight = 18266.000| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.58 r_work: 0.3262 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16686 Z= 0.122 Angle : 0.487 5.752 22602 Z= 0.270 Chirality : 0.043 0.172 2502 Planarity : 0.003 0.030 2826 Dihedral : 5.043 39.793 2190 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.80 % Allowed : 13.87 % Favored : 83.33 % 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: -0.27 (0.23), residues: 552 sheet: 1.03 (0.22), residues: 582 loop : 0.34 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 312 HIS 0.003 0.001 HIS E 59 PHE 0.013 0.001 PHE E 292 TYR 0.013 0.001 TYR C 53 ARG 0.004 0.000 ARG A 345 Details of bonding type rmsd hydrogen bonds : bond 0.04126 ( 678) hydrogen bonds : angle 4.74572 ( 1872) covalent geometry : bond 0.00270 (16686) covalent geometry : angle 0.48708 (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 279 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 229 time to evaluate : 1.784 Fit side-chains REVERT: A 47 MET cc_start: 0.5786 (mtm) cc_final: 0.5530 (mtp) REVERT: A 52 TYR cc_start: 0.5117 (OUTLIER) cc_final: 0.2558 (m-10) REVERT: A 88 LYS cc_start: 0.7644 (OUTLIER) cc_final: 0.7243 (mptp) REVERT: A 243 LYS cc_start: 0.8014 (pttp) cc_final: 0.7450 (mmtt) REVERT: A 291 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7523 (mp0) REVERT: A 294 ARG cc_start: 0.7050 (mmt90) cc_final: 0.6650 (mmm160) REVERT: A 337 MET cc_start: 0.8502 (ttm) cc_final: 0.8021 (ttp) REVERT: B 131 LYS cc_start: 0.8489 (ttmt) cc_final: 0.8220 (ttpm) REVERT: B 272 CYS cc_start: 0.7721 (t) cc_final: 0.7379 (t) REVERT: B 332 PHE cc_start: 0.8635 (m-80) cc_final: 0.7964 (m-10) REVERT: B 337 MET cc_start: 0.8333 (ttm) cc_final: 0.7894 (ttm) REVERT: B 345 ARG cc_start: 0.6831 (mtt-85) cc_final: 0.5659 (mtp180) REVERT: B 356 LYS cc_start: 0.6800 (OUTLIER) cc_final: 0.6463 (mptt) REVERT: C 154 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7508 (tm-30) REVERT: C 369 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8074 (mmm160) REVERT: D 131 LYS cc_start: 0.8744 (tmtt) cc_final: 0.8425 (ttpp) REVERT: E 70 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8150 (tt0) REVERT: E 131 LYS cc_start: 0.8526 (ttmt) cc_final: 0.8248 (ttpm) REVERT: E 272 CYS cc_start: 0.7672 (t) cc_final: 0.7330 (t) REVERT: E 332 PHE cc_start: 0.8667 (m-80) cc_final: 0.7985 (m-10) REVERT: E 337 MET cc_start: 0.8363 (ttm) cc_final: 0.7874 (ttm) REVERT: E 345 ARG cc_start: 0.6742 (mtt-85) cc_final: 0.5641 (mtp180) REVERT: F 47 MET cc_start: 0.5740 (mtm) cc_final: 0.5473 (mtp) REVERT: F 52 TYR cc_start: 0.5135 (OUTLIER) cc_final: 0.2548 (m-10) REVERT: F 88 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.7263 (mptp) REVERT: F 291 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7482 (mp0) REVERT: F 294 ARG cc_start: 0.7052 (mmt90) cc_final: 0.6664 (mmm160) REVERT: F 337 MET cc_start: 0.8538 (ttm) cc_final: 0.8062 (ttp) REVERT: F 356 LYS cc_start: 0.8076 (mppt) cc_final: 0.7705 (mptt) outliers start: 50 outliers final: 24 residues processed: 250 average time/residue: 1.5017 time to fit residues: 410.7892 Evaluate side-chains 255 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 223 time to evaluate : 2.025 ------------------------------------------------------------------------------- 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 A residue 369 ARG 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 154 GLU Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 207 GLN Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 369 ARG Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 356 LYS Chi-restraints excluded: chain F residue 52 TYR Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 207 GLN Chi-restraints excluded: chain F residue 272 CYS Chi-restraints excluded: chain F residue 274 GLN Chi-restraints excluded: chain F residue 320 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 172 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 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: A 59 HIS A 358 GLN ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 HIS ** D 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 GLN F 59 HIS F 278 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.143124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.114063 restraints weight = 18142.130| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.60 r_work: 0.3187 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 16686 Z= 0.278 Angle : 0.632 6.404 22602 Z= 0.346 Chirality : 0.049 0.167 2502 Planarity : 0.005 0.041 2826 Dihedral : 5.798 44.266 2190 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.85 % Allowed : 14.49 % Favored : 82.66 % 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: 0.16 (0.19), residues: 1968 helix: -0.68 (0.22), residues: 564 sheet: 1.11 (0.22), residues: 564 loop : 0.14 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 312 HIS 0.004 0.001 HIS C 311 PHE 0.020 0.002 PHE E 292 TYR 0.017 0.002 TYR C 52 ARG 0.006 0.001 ARG D 72 Details of bonding type rmsd hydrogen bonds : bond 0.05547 ( 678) hydrogen bonds : angle 5.15328 ( 1872) covalent geometry : bond 0.00649 (16686) covalent geometry : angle 0.63191 (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 275 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 224 time to evaluate : 1.965 Fit side-chains REVERT: A 52 TYR cc_start: 0.5467 (OUTLIER) cc_final: 0.2889 (m-10) REVERT: A 88 LYS cc_start: 0.7663 (OUTLIER) cc_final: 0.7249 (mptp) REVERT: A 294 ARG cc_start: 0.7008 (mmt90) cc_final: 0.6736 (mmm160) REVERT: A 337 MET cc_start: 0.8567 (ttm) cc_final: 0.8083 (ttp) REVERT: A 369 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.7253 (tpp-160) REVERT: B 131 LYS cc_start: 0.8560 (ttmt) cc_final: 0.8287 (ttpm) REVERT: B 206 ARG cc_start: 0.6946 (ttp-110) cc_final: 0.6658 (ttp80) REVERT: B 337 MET cc_start: 0.8420 (ttm) cc_final: 0.8008 (ttm) REVERT: B 345 ARG cc_start: 0.6897 (mtt-85) cc_final: 0.5781 (mtp180) REVERT: D 131 LYS cc_start: 0.8837 (tmtt) cc_final: 0.8526 (ttpp) REVERT: E 47 MET cc_start: 0.7282 (mtt) cc_final: 0.6931 (ttm) REVERT: E 70 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.8255 (tt0) REVERT: E 131 LYS cc_start: 0.8581 (ttmt) cc_final: 0.8306 (ttpm) REVERT: E 206 ARG cc_start: 0.6986 (ttp-110) cc_final: 0.6709 (ttp80) REVERT: E 337 MET cc_start: 0.8489 (ttm) cc_final: 0.8034 (ttm) REVERT: E 345 ARG cc_start: 0.6852 (mtt-85) cc_final: 0.5713 (mtp180) REVERT: F 52 TYR cc_start: 0.5489 (OUTLIER) cc_final: 0.2924 (m-10) REVERT: F 88 LYS cc_start: 0.7732 (OUTLIER) cc_final: 0.7382 (mptp) REVERT: F 337 MET cc_start: 0.8620 (ttm) cc_final: 0.8134 (ttp) REVERT: F 356 LYS cc_start: 0.8054 (mppt) cc_final: 0.7728 (mptt) outliers start: 51 outliers final: 26 residues processed: 249 average time/residue: 1.5050 time to fit residues: 410.5065 Evaluate side-chains 248 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 216 time to evaluate : 1.771 ------------------------------------------------------------------------------- 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 356 LYS Chi-restraints excluded: chain A residue 358 GLN 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 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 207 GLN Chi-restraints excluded: chain F residue 272 CYS Chi-restraints excluded: chain F residue 274 GLN Chi-restraints excluded: chain F residue 320 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 0 optimal weight: 20.0000 chunk 150 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 184 optimal weight: 0.9990 chunk 193 optimal weight: 4.9990 chunk 99 optimal weight: 9.9990 chunk 178 optimal weight: 4.9990 chunk 190 optimal weight: 0.0670 overall best weight: 0.9322 ------------------------------------------------------------------------------- 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 ** 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.146560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.117892 restraints weight = 18113.334| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.60 r_work: 0.3245 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16686 Z= 0.132 Angle : 0.511 5.614 22602 Z= 0.283 Chirality : 0.044 0.163 2502 Planarity : 0.004 0.047 2826 Dihedral : 5.274 40.526 2190 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.24 % Allowed : 15.60 % Favored : 82.16 % 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: -0.56 (0.22), residues: 570 sheet: 1.01 (0.23), residues: 570 loop : 0.14 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 312 HIS 0.004 0.001 HIS F 59 PHE 0.013 0.001 PHE E 292 TYR 0.012 0.001 TYR C 53 ARG 0.013 0.000 ARG F 294 Details of bonding type rmsd hydrogen bonds : bond 0.04276 ( 678) hydrogen bonds : angle 4.89084 ( 1872) covalent geometry : bond 0.00294 (16686) covalent geometry : angle 0.51110 (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 264 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 224 time to evaluate : 1.867 Fit side-chains REVERT: A 52 TYR cc_start: 0.5528 (OUTLIER) cc_final: 0.2836 (m-10) REVERT: A 337 MET cc_start: 0.8538 (ttm) cc_final: 0.8047 (ttp) REVERT: A 345 ARG cc_start: 0.7227 (mtt180) cc_final: 0.7017 (mmt180) REVERT: A 369 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7103 (tpp-160) REVERT: B 47 MET cc_start: 0.7292 (mtt) cc_final: 0.6960 (ttm) REVERT: B 131 LYS cc_start: 0.8509 (ttmt) cc_final: 0.8232 (ttpm) REVERT: B 206 ARG cc_start: 0.6973 (ttp-110) cc_final: 0.6672 (ttp80) REVERT: B 332 PHE cc_start: 0.8424 (m-80) cc_final: 0.8090 (m-10) REVERT: B 337 MET cc_start: 0.8379 (ttm) cc_final: 0.7960 (ttm) REVERT: B 345 ARG cc_start: 0.6856 (mtt-85) cc_final: 0.5704 (mtp180) REVERT: D 131 LYS cc_start: 0.8803 (tmtt) cc_final: 0.8454 (ttpp) REVERT: E 47 MET cc_start: 0.7272 (mtt) cc_final: 0.6906 (ttm) REVERT: E 70 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8204 (tt0) REVERT: E 131 LYS cc_start: 0.8523 (ttmt) cc_final: 0.8267 (ttpm) REVERT: E 206 ARG cc_start: 0.7076 (ttp-110) cc_final: 0.6800 (ttp80) REVERT: E 332 PHE cc_start: 0.8406 (m-80) cc_final: 0.8080 (m-10) REVERT: E 337 MET cc_start: 0.8405 (ttm) cc_final: 0.7938 (ttm) REVERT: E 345 ARG cc_start: 0.6797 (mtt-85) cc_final: 0.5672 (mtp180) REVERT: F 52 TYR cc_start: 0.5554 (OUTLIER) cc_final: 0.2885 (m-10) REVERT: F 88 LYS cc_start: 0.7791 (OUTLIER) cc_final: 0.7339 (mptp) REVERT: F 337 MET cc_start: 0.8558 (ttm) cc_final: 0.8054 (ttp) REVERT: F 356 LYS cc_start: 0.8073 (mppt) cc_final: 0.7753 (mptt) outliers start: 40 outliers final: 23 residues processed: 240 average time/residue: 1.4724 time to fit residues: 386.9686 Evaluate side-chains 242 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 214 time to evaluate : 1.885 ------------------------------------------------------------------------------- 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 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 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 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 89 ASP Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 356 LYS Chi-restraints excluded: chain F residue 52 TYR Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 207 GLN Chi-restraints excluded: chain F residue 272 CYS Chi-restraints excluded: chain F residue 274 GLN Chi-restraints excluded: chain F residue 320 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 93 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 167 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 164 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 133 optimal weight: 8.9990 chunk 185 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.145849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.116796 restraints weight = 18126.317| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.59 r_work: 0.3232 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16686 Z= 0.153 Angle : 0.543 7.621 22602 Z= 0.299 Chirality : 0.044 0.167 2502 Planarity : 0.004 0.085 2826 Dihedral : 5.320 41.531 2190 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.18 % Allowed : 16.00 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.19), residues: 1968 helix: -0.41 (0.23), residues: 552 sheet: 0.99 (0.23), residues: 570 loop : 0.16 (0.21), residues: 846 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 0.014 0.002 PHE E 292 TYR 0.012 0.001 TYR E 53 ARG 0.018 0.001 ARG F 294 Details of bonding type rmsd hydrogen bonds : bond 0.04471 ( 678) hydrogen bonds : angle 4.92639 ( 1872) covalent geometry : bond 0.00346 (16686) covalent geometry : angle 0.54272 (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 253 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 214 time to evaluate : 1.770 Fit side-chains REVERT: A 52 TYR cc_start: 0.5634 (OUTLIER) cc_final: 0.2814 (m-10) REVERT: A 243 LYS cc_start: 0.8121 (pttp) cc_final: 0.7895 (pptt) REVERT: A 337 MET cc_start: 0.8550 (ttm) cc_final: 0.8063 (ttp) REVERT: A 345 ARG cc_start: 0.7268 (mtt180) cc_final: 0.7044 (mmt180) REVERT: A 369 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7159 (tpp-160) REVERT: B 47 MET cc_start: 0.7305 (mtt) cc_final: 0.6938 (ttm) REVERT: B 131 LYS cc_start: 0.8521 (ttmt) cc_final: 0.8239 (ttpm) REVERT: B 206 ARG cc_start: 0.6985 (ttp-110) cc_final: 0.6683 (ttp80) REVERT: B 332 PHE cc_start: 0.8422 (m-80) cc_final: 0.8092 (m-10) REVERT: B 337 MET cc_start: 0.8418 (ttm) cc_final: 0.7996 (ttm) REVERT: B 345 ARG cc_start: 0.6852 (mtt-85) cc_final: 0.5695 (mtp180) REVERT: C 352 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7977 (m-30) REVERT: D 131 LYS cc_start: 0.8815 (tmtt) cc_final: 0.8475 (ttpp) REVERT: D 352 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.8021 (m-30) REVERT: E 47 MET cc_start: 0.7258 (mtt) cc_final: 0.6898 (ttm) REVERT: E 70 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8191 (tt0) REVERT: E 131 LYS cc_start: 0.8548 (ttmt) cc_final: 0.8280 (ttpm) REVERT: E 206 ARG cc_start: 0.7070 (ttp-110) cc_final: 0.6795 (ttp80) REVERT: E 332 PHE cc_start: 0.8412 (m-80) cc_final: 0.8084 (m-10) REVERT: E 337 MET cc_start: 0.8417 (ttm) cc_final: 0.7949 (ttm) REVERT: E 345 ARG cc_start: 0.6818 (mtt-85) cc_final: 0.5654 (mtp180) REVERT: F 52 TYR cc_start: 0.5590 (OUTLIER) cc_final: 0.3263 (m-80) REVERT: F 88 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7363 (mptp) REVERT: F 337 MET cc_start: 0.8586 (ttm) cc_final: 0.8098 (ttp) REVERT: F 356 LYS cc_start: 0.8069 (mppt) cc_final: 0.7750 (mptt) outliers start: 39 outliers final: 23 residues processed: 228 average time/residue: 1.5534 time to fit residues: 389.1967 Evaluate side-chains 242 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 212 time to evaluate : 1.825 ------------------------------------------------------------------------------- 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 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 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 207 GLN Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 352 ASP Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain E residue 89 ASP Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 356 LYS Chi-restraints excluded: chain F residue 52 TYR Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 207 GLN Chi-restraints excluded: chain F residue 272 CYS Chi-restraints excluded: chain F residue 274 GLN Chi-restraints excluded: chain F residue 320 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 182 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 164 optimal weight: 9.9990 chunk 192 optimal weight: 0.9990 chunk 191 optimal weight: 0.8980 chunk 160 optimal weight: 2.9990 chunk 141 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 183 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 HIS C 59 HIS ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 HIS ** D 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 HIS ** F 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.147159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.118200 restraints weight = 18149.885| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.59 r_work: 0.3254 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16686 Z= 0.131 Angle : 0.524 8.037 22602 Z= 0.288 Chirality : 0.044 0.165 2502 Planarity : 0.004 0.088 2826 Dihedral : 5.132 39.289 2190 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.79 % Allowed : 16.61 % Favored : 81.60 % 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: 0.26 (0.19), residues: 1968 helix: -0.34 (0.23), residues: 552 sheet: 0.97 (0.23), residues: 570 loop : 0.15 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 312 HIS 0.004 0.001 HIS D 59 PHE 0.013 0.001 PHE E 292 TYR 0.011 0.001 TYR C 53 ARG 0.020 0.001 ARG A 294 Details of bonding type rmsd hydrogen bonds : bond 0.04182 ( 678) hydrogen bonds : angle 4.85230 ( 1872) covalent geometry : bond 0.00292 (16686) covalent geometry : angle 0.52420 (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 251 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 219 time to evaluate : 2.260 Fit side-chains REVERT: A 291 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7517 (mp0) REVERT: A 294 ARG cc_start: 0.7400 (mmm160) cc_final: 0.6948 (mmp80) REVERT: A 337 MET cc_start: 0.8538 (ttm) cc_final: 0.8045 (ttp) REVERT: A 345 ARG cc_start: 0.7269 (mtt180) cc_final: 0.7032 (mmt180) REVERT: A 369 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7152 (tpp-160) REVERT: B 47 MET cc_start: 0.7322 (mtt) cc_final: 0.6965 (ttm) REVERT: B 131 LYS cc_start: 0.8503 (ttmt) cc_final: 0.8223 (ttpm) REVERT: B 206 ARG cc_start: 0.7000 (ttp-110) cc_final: 0.6698 (ttp80) REVERT: B 332 PHE cc_start: 0.8402 (m-80) cc_final: 0.8105 (m-10) REVERT: B 337 MET cc_start: 0.8358 (ttm) cc_final: 0.7935 (ttm) REVERT: B 345 ARG cc_start: 0.6845 (mtt-85) cc_final: 0.5698 (mtp180) REVERT: C 298 ARG cc_start: 0.7440 (tmt170) cc_final: 0.6994 (ttp80) REVERT: D 131 LYS cc_start: 0.8777 (tmtt) cc_final: 0.8449 (ttpp) REVERT: D 298 ARG cc_start: 0.7438 (tmt170) cc_final: 0.6998 (ttp80) REVERT: E 47 MET cc_start: 0.7262 (mtt) cc_final: 0.6861 (ttm) REVERT: E 70 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8150 (tt0) REVERT: E 131 LYS cc_start: 0.8523 (ttmt) cc_final: 0.8259 (ttpm) REVERT: E 206 ARG cc_start: 0.7068 (ttp-110) cc_final: 0.6785 (ttp80) REVERT: E 332 PHE cc_start: 0.8379 (m-80) cc_final: 0.8076 (m-10) REVERT: E 337 MET cc_start: 0.8373 (ttm) cc_final: 0.7927 (ttm) REVERT: E 345 ARG cc_start: 0.6782 (mtt-85) cc_final: 0.5669 (mtp180) REVERT: F 52 TYR cc_start: 0.5686 (OUTLIER) cc_final: 0.3320 (m-80) REVERT: F 88 LYS cc_start: 0.7790 (OUTLIER) cc_final: 0.7268 (mptp) REVERT: F 337 MET cc_start: 0.8563 (ttm) cc_final: 0.8068 (ttp) REVERT: F 356 LYS cc_start: 0.8017 (mppt) cc_final: 0.7787 (mptt) outliers start: 32 outliers final: 22 residues processed: 231 average time/residue: 1.7649 time to fit residues: 444.7523 Evaluate side-chains 236 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 210 time to evaluate : 2.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 89 ASP Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 356 LYS Chi-restraints excluded: chain F residue 52 TYR Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 207 GLN Chi-restraints excluded: chain F residue 272 CYS Chi-restraints excluded: chain F residue 274 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 169 optimal weight: 0.5980 chunk 123 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 156 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 147 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 278 ASN C 59 HIS ** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 HIS ** D 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 HIS ** F 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.147093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.118128 restraints weight = 18067.882| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.59 r_work: 0.3252 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2783 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= 0.132 Angle : 0.525 7.875 22602 Z= 0.289 Chirality : 0.044 0.164 2502 Planarity : 0.004 0.085 2826 Dihedral : 5.101 39.821 2190 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.51 % Allowed : 16.83 % 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: 0.26 (0.19), residues: 1968 helix: -0.35 (0.23), residues: 552 sheet: 0.95 (0.23), residues: 570 loop : 0.16 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 312 HIS 0.003 0.001 HIS D 59 PHE 0.013 0.001 PHE E 292 TYR 0.011 0.001 TYR C 53 ARG 0.019 0.001 ARG F 294 Details of bonding type rmsd hydrogen bonds : bond 0.04187 ( 678) hydrogen bonds : angle 4.84753 ( 1872) covalent geometry : bond 0.00295 (16686) covalent geometry : angle 0.52549 (22602) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14676.61 seconds wall clock time: 252 minutes 36.88 seconds (15156.88 seconds total)