Starting phenix.real_space_refine on Mon Sep 14 15:39:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pbs_13301/09_2026/7pbs_13301_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pbs_13301/09_2026/7pbs_13301.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7pbs_13301/09_2026/7pbs_13301_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pbs_13301/09_2026/7pbs_13301_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pbs_13301/09_2026/7pbs_13301.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pbs_13301/09_2026/7pbs_13301.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 7 Type Number sf(0) Gaussians P 47 5.49 5 Mg 5 5.21 5 S 102 5.16 5 C 9900 2.51 5 N 2683 2.21 5 O 3152 1.98 5 H 15439 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31328 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "B" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "C" Number of atoms: 4895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 4895 Classifications: {'peptide': 309} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 294} Chain breaks: 1 Chain: "D" Number of atoms: 4934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 4934 Classifications: {'peptide': 313} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 298} Chain: "E" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "F" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "G" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 719 Classifications: {'peptide': 48} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "U" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 479 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "V" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 474 Classifications: {'DNA': 15} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.75, per 1000 atoms: 0.18 Number of scatterers: 31328 At special positions: 0 Unit cell: (123.2, 137.5, 107.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 102 16.00 P 47 15.00 Mg 5 11.99 O 3152 8.00 N 2683 7.00 C 9900 6.00 H 15439 1.00 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: 2.97 Conformation dependent library (CDL) restraints added in 884.6 milliseconds 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3526 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 21 sheets defined 60.1% alpha, 11.4% beta 12 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 5.12 Creating SS restraints... Processing helix chain 'A' and resid 31 through 49 removed outlier: 3.617A pdb=" N ILE A 40 " --> pdb=" O ASP A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.559A pdb=" N PHE A 70 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 88 No H-bonds generated for 'chain 'A' and resid 86 through 88' Processing helix chain 'A' and resid 90 through 100 removed outlier: 3.654A pdb=" N LEU A 94 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 115 Processing helix chain 'A' and resid 116 through 130 removed outlier: 4.413A pdb=" N VAL A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 123 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N SER A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU A 128 " --> pdb=" O TYR A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 164 Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 182 through 198 removed outlier: 3.590A pdb=" N GLU A 188 " --> pdb=" O PRO A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 212 Processing helix chain 'A' and resid 216 through 234 Processing helix chain 'A' and resid 240 through 252 removed outlier: 3.612A pdb=" N ASP A 245 " --> pdb=" O ASP A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 274 Processing helix chain 'A' and resid 279 through 288 Processing helix chain 'A' and resid 290 through 298 Processing helix chain 'A' and resid 298 through 305 removed outlier: 3.783A pdb=" N LEU A 302 " --> pdb=" O TYR A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 326 Processing helix chain 'B' and resid 31 through 49 removed outlier: 3.585A pdb=" N ILE B 40 " --> pdb=" O ASP B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 77 removed outlier: 3.522A pdb=" N PHE B 70 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 90 through 100 removed outlier: 3.605A pdb=" N LEU B 94 " --> pdb=" O LYS B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 115 removed outlier: 3.565A pdb=" N MET B 115 " --> pdb=" O ILE B 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 112 through 115' Processing helix chain 'B' and resid 116 through 130 removed outlier: 3.524A pdb=" N GLU B 121 " --> pdb=" O MET B 117 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VAL B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU B 123 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N SER B 125 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA B 126 " --> pdb=" O VAL B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 142 Processing helix chain 'B' and resid 160 through 164 Processing helix chain 'B' and resid 165 through 170 Processing helix chain 'B' and resid 182 through 197 Processing helix chain 'B' and resid 202 through 211 Processing helix chain 'B' and resid 216 through 232 Processing helix chain 'B' and resid 240 through 252 Processing helix chain 'B' and resid 259 through 273 removed outlier: 3.515A pdb=" N TYR B 273 " --> pdb=" O MET B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 287 removed outlier: 3.505A pdb=" N ASN B 286 " --> pdb=" O THR B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 297 Processing helix chain 'B' and resid 298 through 305 removed outlier: 3.670A pdb=" N LEU B 302 " --> pdb=" O TYR B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 326 Processing helix chain 'C' and resid 31 through 49 Processing helix chain 'C' and resid 64 through 77 Processing helix chain 'C' and resid 90 through 100 removed outlier: 3.539A pdb=" N LEU C 94 " --> pdb=" O LYS C 90 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP C 100 " --> pdb=" O ALA C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 115 Processing helix chain 'C' and resid 116 through 129 removed outlier: 4.137A pdb=" N VAL C 122 " --> pdb=" O ALA C 118 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER C 125 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA C 126 " --> pdb=" O VAL C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 164 Processing helix chain 'C' and resid 165 through 170 removed outlier: 3.519A pdb=" N ALA C 170 " --> pdb=" O ASN C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 Processing helix chain 'C' and resid 202 through 213 removed outlier: 3.787A pdb=" N ARG C 212 " --> pdb=" O GLU C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 235 Processing helix chain 'C' and resid 240 through 252 removed outlier: 3.691A pdb=" N ASP C 245 " --> pdb=" O ASP C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 273 Processing helix chain 'C' and resid 279 through 288 Processing helix chain 'C' and resid 290 through 298 Processing helix chain 'C' and resid 298 through 305 removed outlier: 3.780A pdb=" N LEU C 302 " --> pdb=" O TYR C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 326 Processing helix chain 'D' and resid 31 through 47 Processing helix chain 'D' and resid 64 through 77 Processing helix chain 'D' and resid 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'D' and resid 90 through 100 removed outlier: 3.720A pdb=" N LEU D 94 " --> pdb=" O LYS D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 115 Processing helix chain 'D' and resid 116 through 130 removed outlier: 4.435A pdb=" N VAL D 122 " --> pdb=" O ALA D 118 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N SER D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA D 126 " --> pdb=" O VAL D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 172 removed outlier: 3.593A pdb=" N ARG D 171 " --> pdb=" O PRO D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 197 removed outlier: 3.667A pdb=" N GLU D 188 " --> pdb=" O PRO D 184 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE D 197 " --> pdb=" O THR D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 212 removed outlier: 3.578A pdb=" N ARG D 212 " --> pdb=" O GLU D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 234 Processing helix chain 'D' and resid 240 through 251 Processing helix chain 'D' and resid 259 through 274 removed outlier: 3.575A pdb=" N GLY D 274 " --> pdb=" O ILE D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 288 removed outlier: 3.512A pdb=" N ASN D 286 " --> pdb=" O THR D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 297 Processing helix chain 'D' and resid 298 through 305 removed outlier: 3.557A pdb=" N LEU D 302 " --> pdb=" O TYR D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 326 Processing helix chain 'E' and resid 31 through 48 removed outlier: 3.532A pdb=" N ILE E 40 " --> pdb=" O ASP E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 77 Processing helix chain 'E' and resid 86 through 88 No H-bonds generated for 'chain 'E' and resid 86 through 88' Processing helix chain 'E' and resid 90 through 100 removed outlier: 3.544A pdb=" N LEU E 94 " --> pdb=" O LYS E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 115 removed outlier: 3.658A pdb=" N MET E 115 " --> pdb=" O ILE E 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 112 through 115' Processing helix chain 'E' and resid 116 through 130 removed outlier: 3.743A pdb=" N GLU E 121 " --> pdb=" O MET E 117 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL E 122 " --> pdb=" O ALA E 118 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU E 123 " --> pdb=" O VAL E 119 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER E 125 " --> pdb=" O GLU E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 170 Processing helix chain 'E' and resid 182 through 197 removed outlier: 3.816A pdb=" N GLU E 188 " --> pdb=" O PRO E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 213 Processing helix chain 'E' and resid 216 through 235 removed outlier: 3.736A pdb=" N ASP E 229 " --> pdb=" O LYS E 225 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE E 233 " --> pdb=" O ASP E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 251 Processing helix chain 'E' and resid 259 through 274 Processing helix chain 'E' and resid 279 through 287 removed outlier: 3.746A pdb=" N ASN E 286 " --> pdb=" O THR E 282 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE E 287 " --> pdb=" O LEU E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 298 Processing helix chain 'E' and resid 298 through 305 Processing helix chain 'E' and resid 318 through 326 Processing helix chain 'F' and resid 31 through 48 removed outlier: 3.712A pdb=" N GLN F 37 " --> pdb=" O LYS F 33 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE F 40 " --> pdb=" O ASP F 36 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG F 48 " --> pdb=" O ALA F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 77 Processing helix chain 'F' and resid 86 through 88 No H-bonds generated for 'chain 'F' and resid 86 through 88' Processing helix chain 'F' and resid 90 through 100 removed outlier: 3.713A pdb=" N LEU F 94 " --> pdb=" O LYS F 90 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP F 100 " --> pdb=" O ALA F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 115 Processing helix chain 'F' and resid 116 through 130 removed outlier: 4.483A pdb=" N VAL F 122 " --> pdb=" O ALA F 118 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU F 123 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR F 124 " --> pdb=" O GLU F 120 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N SER F 125 " --> pdb=" O GLU F 121 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA F 126 " --> pdb=" O VAL F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 142 Processing helix chain 'F' and resid 160 through 164 Processing helix chain 'F' and resid 165 through 170 Processing helix chain 'F' and resid 182 through 197 removed outlier: 3.542A pdb=" N PHE F 197 " --> pdb=" O THR F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 213 Processing helix chain 'F' and resid 216 through 234 Processing helix chain 'F' and resid 240 through 251 Processing helix chain 'F' and resid 259 through 273 Processing helix chain 'F' and resid 279 through 288 removed outlier: 3.669A pdb=" N VAL F 285 " --> pdb=" O GLY F 281 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN F 286 " --> pdb=" O THR F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 297 Processing helix chain 'F' and resid 298 through 305 Processing helix chain 'F' and resid 318 through 326 Processing helix chain 'G' and resid 157 through 170 Processing helix chain 'G' and resid 173 through 183 Processing helix chain 'G' and resid 190 through 202 Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 84 removed outlier: 6.528A pdb=" N LYS A 81 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ASP A 110 " --> pdb=" O LYS A 81 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N THR A 83 " --> pdb=" O ASP A 110 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU A 107 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N ALA A 157 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ILE A 109 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU A 56 " --> pdb=" O GLY A 176 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 131 through 137 Processing sheet with id=AA3, first strand: chain 'A' and resid 200 through 201 removed outlier: 7.008A pdb=" N THR A 200 " --> pdb=" O ILE A 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 308 through 311 Processing sheet with id=AA5, first strand: chain 'B' and resid 80 through 84 removed outlier: 6.408A pdb=" N LYS B 81 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ASP B 110 " --> pdb=" O LYS B 81 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N THR B 83 " --> pdb=" O ASP B 110 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU B 107 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N ALA B 157 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE B 109 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU B 56 " --> pdb=" O GLY B 176 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 131 through 136 Processing sheet with id=AA7, first strand: chain 'B' and resid 308 through 311 Processing sheet with id=AA8, first strand: chain 'C' and resid 80 through 84 removed outlier: 6.349A pdb=" N LEU C 107 " --> pdb=" O VAL C 155 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N ALA C 157 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE C 109 " --> pdb=" O ALA C 157 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 131 through 136 Processing sheet with id=AB1, first strand: chain 'C' and resid 308 through 311 Processing sheet with id=AB2, first strand: chain 'D' and resid 80 through 84 removed outlier: 6.441A pdb=" N LYS D 81 " --> pdb=" O PHE D 108 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ASP D 110 " --> pdb=" O LYS D 81 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N THR D 83 " --> pdb=" O ASP D 110 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU D 107 " --> pdb=" O VAL D 155 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ALA D 157 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE D 109 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N THR D 55 " --> pdb=" O GLY D 156 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N THR D 158 " --> pdb=" O THR D 55 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LEU D 57 " --> pdb=" O THR D 158 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 131 through 136 Processing sheet with id=AB4, first strand: chain 'D' and resid 308 through 311 Processing sheet with id=AB5, first strand: chain 'E' and resid 80 through 84 removed outlier: 6.340A pdb=" N LYS E 81 " --> pdb=" O PHE E 108 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ASP E 110 " --> pdb=" O LYS E 81 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N THR E 83 " --> pdb=" O ASP E 110 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU E 107 " --> pdb=" O VAL E 155 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ALA E 157 " --> pdb=" O LEU E 107 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE E 109 " --> pdb=" O ALA E 157 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU E 56 " --> pdb=" O GLY E 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 131 through 136 Processing sheet with id=AB7, first strand: chain 'E' and resid 200 through 201 removed outlier: 7.189A pdb=" N THR E 200 " --> pdb=" O ILE E 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'E' and resid 308 through 311 Processing sheet with id=AB9, first strand: chain 'F' and resid 80 through 84 removed outlier: 6.507A pdb=" N LYS F 81 " --> pdb=" O PHE F 108 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ASP F 110 " --> pdb=" O LYS F 81 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N THR F 83 " --> pdb=" O ASP F 110 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU F 107 " --> pdb=" O VAL F 155 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ALA F 157 " --> pdb=" O LEU F 107 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ILE F 109 " --> pdb=" O ALA F 157 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 131 through 136 Processing sheet with id=AC2, first strand: chain 'F' and resid 200 through 201 removed outlier: 7.085A pdb=" N THR F 200 " --> pdb=" O ILE F 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'F' and resid 308 through 311 775 hydrogen bonds defined for protein. 2226 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 25 hydrogen bonds 50 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 6.93 Time building geometry restraints manager: 4.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.05: 15439 1.05 - 1.28: 2655 1.28 - 1.50: 6782 1.50 - 1.72: 6592 1.72 - 1.94: 199 Bond restraints: 31667 Sorted by residual: bond pdb=" O3B AGS A 401 " pdb=" PB AGS A 401 " ideal model delta sigma weight residual 1.673 1.569 0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" O3B AGS B 401 " pdb=" PB AGS B 401 " ideal model delta sigma weight residual 1.673 1.570 0.103 2.00e-02 2.50e+03 2.67e+01 bond pdb=" N THR D 19 " pdb=" H1 THR D 19 " ideal model delta sigma weight residual 0.960 0.859 0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" O3B AGS D 401 " pdb=" PB AGS D 401 " ideal model delta sigma weight residual 1.673 1.573 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" N THR E 19 " pdb=" H1 THR E 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.52e+01 ... (remaining 31662 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 56768 2.28 - 4.57: 479 4.57 - 6.85: 38 6.85 - 9.13: 25 9.13 - 11.41: 11 Bond angle restraints: 57321 Sorted by residual: angle pdb=" O4' DC V 6 " pdb=" C1' DC V 6 " pdb=" N1 DC V 6 " ideal model delta sigma weight residual 108.00 111.24 -3.24 7.00e-01 2.04e+00 2.14e+01 angle pdb=" N3 DT V 4 " pdb=" C4 DT V 4 " pdb=" O4 DT V 4 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 angle pdb=" N3 DT V 7 " pdb=" C4 DT V 7 " pdb=" O4 DT V 7 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 angle pdb=" N3 DT V 14 " pdb=" C4 DT V 14 " pdb=" O4 DT V 14 " ideal model delta sigma weight residual 119.90 122.30 -2.40 6.00e-01 2.78e+00 1.59e+01 angle pdb=" N3 DT U 6 " pdb=" C4 DT U 6 " pdb=" O4 DT U 6 " ideal model delta sigma weight residual 119.90 122.29 -2.39 6.00e-01 2.78e+00 1.59e+01 ... (remaining 57316 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.42: 14120 31.42 - 62.84: 611 62.84 - 94.26: 57 94.26 - 125.68: 0 125.68 - 157.10: 1 Dihedral angle restraints: 14789 sinusoidal: 8520 harmonic: 6269 Sorted by residual: dihedral pdb=" O2A ADP E 600 " pdb=" O3A ADP E 600 " pdb=" PA ADP E 600 " pdb=" PB ADP E 600 " ideal model delta sinusoidal sigma weight residual -60.00 97.10 -157.10 1 2.00e+01 2.50e-03 4.61e+01 dihedral pdb=" C1' ADP E 600 " pdb=" C4' ADP E 600 " pdb=" O4' ADP E 600 " pdb=" C5' ADP E 600 " ideal model delta sinusoidal sigma weight residual -150.00 -90.39 -59.61 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CA ASP D 133 " pdb=" CB ASP D 133 " pdb=" CG ASP D 133 " pdb=" OD1 ASP D 133 " ideal model delta sinusoidal sigma weight residual -30.00 -86.49 56.49 1 2.00e+01 2.50e-03 1.08e+01 ... (remaining 14786 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 2251 0.085 - 0.170: 223 0.170 - 0.254: 9 0.254 - 0.339: 4 0.339 - 0.424: 1 Chirality restraints: 2488 Sorted by residual: chirality pdb=" P DT V 4 " pdb=" OP1 DT V 4 " pdb=" OP2 DT V 4 " pdb=" O5' DT V 4 " both_signs ideal model delta sigma weight residual True 2.34 -2.76 -0.42 2.00e-01 2.50e+01 4.49e+00 chirality pdb=" C3' AGS C 401 " pdb=" C2' AGS C 401 " pdb=" C4' AGS C 401 " pdb=" O3' AGS C 401 " both_signs ideal model delta sigma weight residual False -2.37 -2.64 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C3' AGS F 401 " pdb=" C2' AGS F 401 " pdb=" C4' AGS F 401 " pdb=" O3' AGS F 401 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 2485 not shown) Planarity restraints: 4586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 218 " 0.145 9.50e-02 1.11e+02 6.91e-02 5.71e+01 pdb=" NE ARG E 218 " 0.037 2.00e-02 2.50e+03 pdb=" CZ ARG E 218 " -0.029 2.00e-02 2.50e+03 pdb=" NH1 ARG E 218 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG E 218 " -0.099 2.00e-02 2.50e+03 pdb="HH11 ARG E 218 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG E 218 " -0.013 2.00e-02 2.50e+03 pdb="HH21 ARG E 218 " -0.006 2.00e-02 2.50e+03 pdb="HH22 ARG E 218 " 0.099 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 160 " 0.312 9.50e-02 1.11e+02 1.13e-01 5.48e+01 pdb=" NE ARG E 160 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG E 160 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG E 160 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG E 160 " -0.091 2.00e-02 2.50e+03 pdb="HH11 ARG E 160 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG E 160 " -0.004 2.00e-02 2.50e+03 pdb="HH21 ARG E 160 " -0.004 2.00e-02 2.50e+03 pdb="HH22 ARG E 160 " 0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 192 " -0.168 9.50e-02 1.11e+02 7.21e-02 4.99e+01 pdb=" NE ARG C 192 " -0.001 2.00e-02 2.50e+03 pdb=" CZ ARG C 192 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG C 192 " -0.043 2.00e-02 2.50e+03 pdb=" NH2 ARG C 192 " 0.083 2.00e-02 2.50e+03 pdb="HH11 ARG C 192 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG C 192 " 0.053 2.00e-02 2.50e+03 pdb="HH21 ARG C 192 " 0.004 2.00e-02 2.50e+03 pdb="HH22 ARG C 192 " -0.084 2.00e-02 2.50e+03 ... (remaining 4583 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.13: 760 2.13 - 2.75: 56501 2.75 - 3.37: 84017 3.37 - 3.98: 108550 3.98 - 4.60: 175860 Nonbonded interactions: 425688 Sorted by model distance: nonbonded pdb=" OE2 GLU D 120 " pdb=" HG SER D 165 " model vdw 1.516 2.450 nonbonded pdb=" HZ3 LYS E 81 " pdb=" O ASP E 100 " model vdw 1.525 2.450 nonbonded pdb=" O ALA B 138 " pdb=" HG1 THR B 141 " model vdw 1.534 2.450 nonbonded pdb=" HZ3 LYS D 46 " pdb=" O GLU D 75 " model vdw 1.538 2.450 nonbonded pdb=" HG1 THR A 311 " pdb=" O GLY A 314 " model vdw 1.568 2.450 ... (remaining 425683 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'B' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'C' and resid 19 through 330) selection = (chain 'D' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'E' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'F' and (resid 19 through 136 or resid 141 through 330)) } 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: 3.070 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: 0.220 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 33.220 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.050 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 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 : 0.006 0.104 16228 Z= 0.320 Angle : 0.827 11.413 22105 Z= 0.466 Chirality : 0.050 0.424 2488 Planarity : 0.011 0.137 2739 Dihedral : 15.479 157.097 6377 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 0.25 % Allowed : 1.37 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.18), residues: 1902 helix: -0.48 (0.15), residues: 1018 sheet: 0.80 (0.30), residues: 309 loop : 0.47 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.003 ARG C 114 TYR 0.025 0.005 TYR E 273 PHE 0.020 0.003 PHE A 25 HIS 0.012 0.003 HIS B 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00626 / 0.32 (16228) covalent geometry : angle 0.82725 / 0.47 (22105) hydrogen bonds : bond 0.24351 / 16.05 ( 800) hydrogen bonds : angle 8.57410 / 6.15 ( 2276) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 420 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.7757 (mtpt) cc_final: 0.7428 (mttt) REVERT: A 43 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7476 (mt-10) REVERT: A 131 TYR cc_start: 0.8742 (p90) cc_final: 0.7984 (p90) REVERT: A 160 ARG cc_start: 0.8019 (ptp90) cc_final: 0.7771 (ptp-170) REVERT: A 234 MET cc_start: 0.7411 (ptp) cc_final: 0.7066 (ptp) REVERT: A 252 ASP cc_start: 0.7867 (t0) cc_final: 0.7416 (t0) REVERT: A 292 GLU cc_start: 0.7277 (mt-10) cc_final: 0.6966 (tt0) REVERT: A 309 MET cc_start: 0.7326 (ttm) cc_final: 0.7124 (ttt) REVERT: A 325 MET cc_start: 0.7672 (mmm) cc_final: 0.7250 (mmt) REVERT: B 49 ASP cc_start: 0.7720 (t0) cc_final: 0.7439 (t0) REVERT: B 102 GLU cc_start: 0.7541 (mm-30) cc_final: 0.6946 (mt-10) REVERT: B 178 MET cc_start: 0.8658 (mmm) cc_final: 0.7603 (mmt) REVERT: B 199 MET cc_start: 0.7852 (mmp) cc_final: 0.7278 (tpt) REVERT: B 234 MET cc_start: 0.8341 (mmp) cc_final: 0.8123 (mmm) REVERT: C 47 LEU cc_start: 0.8037 (tp) cc_final: 0.7701 (mt) REVERT: C 260 TYR cc_start: 0.7683 (t80) cc_final: 0.7359 (t80) REVERT: D 78 VAL cc_start: 0.7517 (t) cc_final: 0.7270 (p) REVERT: D 264 LYS cc_start: 0.7838 (tttt) cc_final: 0.7482 (ttpt) REVERT: D 292 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7162 (mp0) REVERT: D 309 MET cc_start: 0.7813 (mtp) cc_final: 0.7579 (mtp) REVERT: D 330 THR cc_start: 0.6052 (m) cc_final: 0.5665 (p) REVERT: E 76 MET cc_start: 0.8489 (mmm) cc_final: 0.7798 (mmt) REVERT: E 89 GLU cc_start: 0.7131 (mt-10) cc_final: 0.6160 (mm-30) REVERT: E 111 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7734 (mt-10) REVERT: E 125 SER cc_start: 0.7697 (m) cc_final: 0.7494 (t) REVERT: E 143 ARG cc_start: 0.6340 (mtm180) cc_final: 0.6012 (mtm110) REVERT: E 179 GLU cc_start: 0.7682 (pt0) cc_final: 0.7455 (pt0) REVERT: E 242 LYS cc_start: 0.7315 (pttm) cc_final: 0.6655 (tppt) REVERT: E 267 ARG cc_start: 0.7120 (ttm-80) cc_final: 0.6663 (ttp-110) REVERT: E 299 GLU cc_start: 0.7020 (mt-10) cc_final: 0.6124 (mt-10) REVERT: E 301 TYR cc_start: 0.7101 (t80) cc_final: 0.6824 (t80) REVERT: F 102 GLU cc_start: 0.7187 (mt-10) cc_final: 0.6767 (mp0) REVERT: F 125 SER cc_start: 0.8456 (m) cc_final: 0.8214 (p) REVERT: F 143 ARG cc_start: 0.7562 (ptt90) cc_final: 0.7229 (ptt-90) REVERT: F 144 SER cc_start: 0.8630 (p) cc_final: 0.8350 (t) REVERT: F 199 MET cc_start: 0.7222 (tpp) cc_final: 0.6662 (tpp) REVERT: F 267 ARG cc_start: 0.6547 (ttm170) cc_final: 0.5890 (ttp80) REVERT: F 286 ASN cc_start: 0.7162 (m-40) cc_final: 0.6900 (m110) outliers start: 4 outliers final: 1 residues processed: 421 average time/residue: 0.3453 time to fit residues: 206.3196 Evaluate side-chains 275 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 274 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 280 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.3980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 246 GLN D 232 GLN D 286 ASN E 166 ASN F 23 GLN F 113 HIS F 232 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.123485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.094861 restraints weight = 66001.611| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.94 r_work: 0.2840 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16228 Z= 0.174 Angle : 0.642 7.638 22105 Z= 0.353 Chirality : 0.043 0.173 2488 Planarity : 0.006 0.072 2739 Dihedral : 14.815 140.681 2653 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 0.87 % Allowed : 5.61 % Favored : 93.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.19), residues: 1902 helix: 0.47 (0.16), residues: 1046 sheet: 1.26 (0.31), residues: 272 loop : 0.37 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 291 TYR 0.011 0.001 TYR E 273 PHE 0.011 0.001 PHE D 172 HIS 0.004 0.001 HIS D 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.17 (16228) covalent geometry : angle 0.64184 / 0.35 (22105) hydrogen bonds : bond 0.07527 / 5.06 ( 800) hydrogen bonds : angle 6.14553 / 4.39 ( 2276) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 265 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 TYR cc_start: 0.9049 (p90) cc_final: 0.8749 (p90) REVERT: A 160 ARG cc_start: 0.8554 (ptp90) cc_final: 0.8270 (ptp-170) REVERT: A 234 MET cc_start: 0.8083 (ptp) cc_final: 0.7658 (ptp) REVERT: A 252 ASP cc_start: 0.7992 (t0) cc_final: 0.7405 (t0) REVERT: A 309 MET cc_start: 0.8014 (ttm) cc_final: 0.7805 (ttt) REVERT: A 325 MET cc_start: 0.7707 (mmm) cc_final: 0.7351 (mmt) REVERT: B 49 ASP cc_start: 0.8326 (t0) cc_final: 0.8034 (t0) REVERT: B 102 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7269 (mt-10) REVERT: B 178 MET cc_start: 0.8945 (mmm) cc_final: 0.8066 (mmt) REVERT: B 199 MET cc_start: 0.8174 (mmp) cc_final: 0.7572 (tpt) REVERT: C 260 TYR cc_start: 0.7840 (t80) cc_final: 0.7577 (t80) REVERT: D 78 VAL cc_start: 0.7718 (t) cc_final: 0.7473 (p) REVERT: D 117 MET cc_start: 0.6830 (ttm) cc_final: 0.6517 (mtp) REVERT: D 272 MET cc_start: 0.8801 (mmm) cc_final: 0.8540 (mmm) REVERT: D 292 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7749 (mp0) REVERT: D 330 THR cc_start: 0.6166 (m) cc_final: 0.5825 (p) REVERT: E 89 GLU cc_start: 0.6978 (mt-10) cc_final: 0.6236 (mm-30) REVERT: E 135 MET cc_start: 0.5800 (mmm) cc_final: 0.5399 (mmm) REVERT: E 143 ARG cc_start: 0.6217 (mtm180) cc_final: 0.5627 (mtm110) REVERT: E 255 HIS cc_start: 0.6762 (p-80) cc_final: 0.6061 (m90) REVERT: E 267 ARG cc_start: 0.7416 (ttm-80) cc_final: 0.6816 (ttp-110) REVERT: E 301 TYR cc_start: 0.7277 (t80) cc_final: 0.6902 (t80) REVERT: F 102 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7168 (mp0) REVERT: F 143 ARG cc_start: 0.7855 (ptt90) cc_final: 0.7476 (ptt-90) REVERT: F 144 SER cc_start: 0.8756 (p) cc_final: 0.8482 (t) REVERT: F 195 GLU cc_start: 0.7371 (tp30) cc_final: 0.7068 (tm-30) REVERT: F 267 ARG cc_start: 0.6650 (ttm170) cc_final: 0.6008 (ttp80) outliers start: 14 outliers final: 11 residues processed: 273 average time/residue: 0.3079 time to fit residues: 123.0790 Evaluate side-chains 252 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 241 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain E residue 292 GLU Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 280 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 39 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 134 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 174 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 117 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 146 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.121859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.091323 restraints weight = 66403.510| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.98 r_work: 0.2823 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16228 Z= 0.167 Angle : 0.571 6.128 22105 Z= 0.309 Chirality : 0.041 0.155 2488 Planarity : 0.005 0.063 2739 Dihedral : 14.215 142.734 2653 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.87 % Allowed : 6.30 % Favored : 92.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.19), residues: 1902 helix: 0.67 (0.16), residues: 1047 sheet: 1.05 (0.31), residues: 272 loop : 0.31 (0.24), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 160 TYR 0.011 0.001 TYR E 298 PHE 0.007 0.001 PHE E 58 HIS 0.004 0.001 HIS B 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (16228) covalent geometry : angle 0.57134 / 0.31 (22105) hydrogen bonds : bond 0.06477 / 4.40 ( 800) hydrogen bonds : angle 5.58895 / 3.98 ( 2276) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 245 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 ARG cc_start: 0.8602 (ptp90) cc_final: 0.8221 (ptp-170) REVERT: A 234 MET cc_start: 0.8202 (ptp) cc_final: 0.7778 (ptp) REVERT: A 252 ASP cc_start: 0.7893 (t0) cc_final: 0.7324 (t0) REVERT: A 291 ARG cc_start: 0.7629 (tpp80) cc_final: 0.7175 (ttt-90) REVERT: B 49 ASP cc_start: 0.8306 (t0) cc_final: 0.8093 (t0) REVERT: B 102 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7296 (mt-10) REVERT: B 128 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7219 (tt0) REVERT: B 199 MET cc_start: 0.8216 (mmp) cc_final: 0.7523 (tpt) REVERT: C 260 TYR cc_start: 0.7888 (t80) cc_final: 0.7574 (t80) REVERT: D 78 VAL cc_start: 0.7814 (t) cc_final: 0.7551 (p) REVERT: D 117 MET cc_start: 0.6837 (ttm) cc_final: 0.6614 (mtp) REVERT: D 272 MET cc_start: 0.8851 (mmm) cc_final: 0.8611 (mmm) REVERT: D 292 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7784 (mp0) REVERT: D 330 THR cc_start: 0.6270 (m) cc_final: 0.5896 (p) REVERT: E 89 GLU cc_start: 0.7007 (mt-10) cc_final: 0.6259 (mm-30) REVERT: E 143 ARG cc_start: 0.6403 (mtm180) cc_final: 0.6073 (mtm110) REVERT: E 255 HIS cc_start: 0.6882 (p-80) cc_final: 0.6253 (m90) REVERT: E 267 ARG cc_start: 0.7503 (ttm-80) cc_final: 0.6936 (ttp-110) REVERT: E 301 TYR cc_start: 0.7459 (t80) cc_final: 0.7027 (t80) REVERT: F 102 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7263 (mp0) REVERT: F 143 ARG cc_start: 0.7923 (ptt90) cc_final: 0.7635 (ptt-90) outliers start: 14 outliers final: 10 residues processed: 252 average time/residue: 0.3331 time to fit residues: 121.2246 Evaluate side-chains 243 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 232 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 280 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 182 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 150 optimal weight: 0.7980 chunk 163 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 324 HIS ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.122981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.092543 restraints weight = 65535.744| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.96 r_work: 0.2827 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16228 Z= 0.155 Angle : 0.551 6.432 22105 Z= 0.296 Chirality : 0.041 0.315 2488 Planarity : 0.005 0.056 2739 Dihedral : 13.984 143.947 2653 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.19 % Allowed : 6.86 % Favored : 91.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.19), residues: 1902 helix: 0.79 (0.16), residues: 1049 sheet: 0.87 (0.30), residues: 272 loop : 0.21 (0.24), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 48 TYR 0.018 0.001 TYR A 322 PHE 0.007 0.001 PHE C 152 HIS 0.008 0.001 HIS A 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (16228) covalent geometry : angle 0.55050 / 0.30 (22105) hydrogen bonds : bond 0.05507 / 3.74 ( 800) hydrogen bonds : angle 5.25931 / 3.75 ( 2276) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 243 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 ARG cc_start: 0.8588 (ptp90) cc_final: 0.8264 (ptp-170) REVERT: A 234 MET cc_start: 0.8061 (ptp) cc_final: 0.7509 (ptp) REVERT: A 252 ASP cc_start: 0.7905 (t0) cc_final: 0.7407 (t0) REVERT: A 291 ARG cc_start: 0.7563 (tpp80) cc_final: 0.7219 (ttt90) REVERT: A 325 MET cc_start: 0.7783 (mmp) cc_final: 0.7392 (mmp) REVERT: B 102 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7488 (mt-10) REVERT: B 128 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7205 (tt0) REVERT: B 199 MET cc_start: 0.8251 (mmp) cc_final: 0.7539 (tpt) REVERT: D 78 VAL cc_start: 0.7806 (t) cc_final: 0.7553 (p) REVERT: D 130 TYR cc_start: 0.5624 (m-80) cc_final: 0.5321 (m-80) REVERT: D 272 MET cc_start: 0.8820 (mmm) cc_final: 0.8555 (mmm) REVERT: D 292 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7812 (mp0) REVERT: D 330 THR cc_start: 0.6284 (m) cc_final: 0.5918 (p) REVERT: E 89 GLU cc_start: 0.6846 (mt-10) cc_final: 0.6085 (mm-30) REVERT: E 143 ARG cc_start: 0.6412 (mtm180) cc_final: 0.6078 (mtm110) REVERT: E 255 HIS cc_start: 0.6894 (p-80) cc_final: 0.6266 (m90) REVERT: E 267 ARG cc_start: 0.7456 (ttm-80) cc_final: 0.6900 (ttp-110) REVERT: E 301 TYR cc_start: 0.7437 (t80) cc_final: 0.7144 (t80) REVERT: F 102 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7292 (mp0) REVERT: F 143 ARG cc_start: 0.7940 (ptt90) cc_final: 0.7657 (ptt-90) outliers start: 19 outliers final: 12 residues processed: 252 average time/residue: 0.3180 time to fit residues: 116.5679 Evaluate side-chains 249 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 236 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 313 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 136 optimal weight: 0.0870 chunk 126 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 96 optimal weight: 0.0970 chunk 95 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 324 HIS D 286 ASN ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.122945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.092528 restraints weight = 65820.600| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 1.96 r_work: 0.2830 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16228 Z= 0.133 Angle : 0.517 6.222 22105 Z= 0.277 Chirality : 0.040 0.154 2488 Planarity : 0.005 0.049 2739 Dihedral : 13.825 144.910 2653 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.12 % Allowed : 7.17 % Favored : 91.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.19), residues: 1902 helix: 1.00 (0.16), residues: 1050 sheet: 0.82 (0.30), residues: 274 loop : 0.16 (0.24), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 48 TYR 0.010 0.001 TYR D 131 PHE 0.006 0.001 PHE C 307 HIS 0.004 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (16228) covalent geometry : angle 0.51722 / 0.28 (22105) hydrogen bonds : bond 0.04882 / 3.32 ( 800) hydrogen bonds : angle 5.02056 / 3.57 ( 2276) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 249 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 ARG cc_start: 0.8522 (ptp90) cc_final: 0.8168 (ptp-170) REVERT: A 234 MET cc_start: 0.8028 (ptp) cc_final: 0.7515 (ptp) REVERT: A 252 ASP cc_start: 0.7939 (t0) cc_final: 0.7486 (t0) REVERT: A 291 ARG cc_start: 0.7618 (tpp80) cc_final: 0.7322 (ttt90) REVERT: B 102 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7498 (mt-10) REVERT: B 128 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.7038 (tt0) REVERT: B 199 MET cc_start: 0.8319 (mmp) cc_final: 0.7604 (tpt) REVERT: D 78 VAL cc_start: 0.7872 (t) cc_final: 0.7591 (p) REVERT: D 272 MET cc_start: 0.8799 (mmm) cc_final: 0.8555 (mmm) REVERT: D 292 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7896 (mp0) REVERT: E 89 GLU cc_start: 0.6994 (mt-10) cc_final: 0.6240 (mm-30) REVERT: E 101 LEU cc_start: 0.7743 (mt) cc_final: 0.7505 (mt) REVERT: E 143 ARG cc_start: 0.6430 (mtm180) cc_final: 0.6089 (mtm110) REVERT: E 255 HIS cc_start: 0.6912 (p-80) cc_final: 0.6225 (m90) REVERT: E 267 ARG cc_start: 0.7470 (ttm-80) cc_final: 0.6862 (ttp-110) REVERT: E 301 TYR cc_start: 0.7505 (t80) cc_final: 0.7180 (t80) REVERT: E 309 MET cc_start: 0.4534 (ptt) cc_final: 0.4282 (ptt) REVERT: F 102 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7164 (mp0) REVERT: F 121 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8540 (mm-30) outliers start: 18 outliers final: 15 residues processed: 255 average time/residue: 0.3212 time to fit residues: 119.1545 Evaluate side-chains 248 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 232 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 313 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 19 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 182 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 chunk 154 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 324 HIS ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.121731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.091133 restraints weight = 65800.431| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 1.98 r_work: 0.2816 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16228 Z= 0.152 Angle : 0.527 6.223 22105 Z= 0.284 Chirality : 0.040 0.162 2488 Planarity : 0.005 0.047 2739 Dihedral : 13.855 147.110 2653 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.06 % Allowed : 7.74 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.19), residues: 1902 helix: 1.04 (0.16), residues: 1049 sheet: 0.76 (0.30), residues: 274 loop : 0.13 (0.24), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 228 TYR 0.009 0.001 TYR D 131 PHE 0.007 0.001 PHE A 152 HIS 0.003 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (16228) covalent geometry : angle 0.52739 / 0.28 (22105) hydrogen bonds : bond 0.04961 / 3.39 ( 800) hydrogen bonds : angle 4.98274 / 3.54 ( 2276) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 237 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 ARG cc_start: 0.8527 (ptp90) cc_final: 0.8167 (ptp-170) REVERT: A 234 MET cc_start: 0.8012 (ptp) cc_final: 0.7476 (ptp) REVERT: A 252 ASP cc_start: 0.7838 (t0) cc_final: 0.7401 (t0) REVERT: A 291 ARG cc_start: 0.7649 (tpp80) cc_final: 0.7349 (ttt90) REVERT: B 102 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7540 (mt-10) REVERT: B 128 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7111 (tt0) REVERT: B 199 MET cc_start: 0.8349 (mmp) cc_final: 0.7618 (tpt) REVERT: D 78 VAL cc_start: 0.7905 (t) cc_final: 0.7623 (p) REVERT: D 272 MET cc_start: 0.8791 (mmm) cc_final: 0.8488 (mmm) REVERT: D 292 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7958 (mp0) REVERT: E 89 GLU cc_start: 0.6983 (mt-10) cc_final: 0.6229 (mm-30) REVERT: E 143 ARG cc_start: 0.6482 (mtm180) cc_final: 0.6141 (mtm110) REVERT: E 255 HIS cc_start: 0.6964 (p-80) cc_final: 0.6243 (m90) REVERT: E 267 ARG cc_start: 0.7475 (ttm-80) cc_final: 0.6872 (ttp-110) REVERT: E 301 TYR cc_start: 0.7513 (t80) cc_final: 0.7198 (t80) REVERT: E 309 MET cc_start: 0.4511 (ptt) cc_final: 0.4255 (ptt) REVERT: F 102 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7165 (mp0) REVERT: F 121 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8536 (mm-30) outliers start: 17 outliers final: 15 residues processed: 244 average time/residue: 0.3194 time to fit residues: 114.0290 Evaluate side-chains 247 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 231 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 MET Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 313 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 79 optimal weight: 0.5980 chunk 173 optimal weight: 0.9980 chunk 174 optimal weight: 0.5980 chunk 169 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 176 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.122975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.092171 restraints weight = 65924.847| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.00 r_work: 0.2813 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16228 Z= 0.133 Angle : 0.511 5.989 22105 Z= 0.274 Chirality : 0.040 0.157 2488 Planarity : 0.005 0.044 2739 Dihedral : 13.840 148.342 2653 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.25 % Allowed : 7.92 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.19), residues: 1902 helix: 1.16 (0.16), residues: 1046 sheet: 0.73 (0.30), residues: 274 loop : 0.14 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 312 TYR 0.011 0.001 TYR A 322 PHE 0.007 0.001 PHE B 58 HIS 0.005 0.001 HIS B 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (16228) covalent geometry : angle 0.51149 / 0.27 (22105) hydrogen bonds : bond 0.04678 / 3.17 ( 800) hydrogen bonds : angle 4.89084 / 3.48 ( 2276) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 235 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 ARG cc_start: 0.8516 (ptp90) cc_final: 0.8142 (ptp-170) REVERT: A 234 MET cc_start: 0.8004 (ptp) cc_final: 0.7470 (ptp) REVERT: A 252 ASP cc_start: 0.7863 (t0) cc_final: 0.7326 (t0) REVERT: A 291 ARG cc_start: 0.7595 (tpp80) cc_final: 0.7308 (ttt90) REVERT: B 102 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7518 (mt-10) REVERT: B 128 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.7103 (tt0) REVERT: B 199 MET cc_start: 0.8419 (mmp) cc_final: 0.7674 (tpt) REVERT: B 242 LYS cc_start: 0.7987 (tppt) cc_final: 0.7495 (tppt) REVERT: D 78 VAL cc_start: 0.7904 (t) cc_final: 0.7618 (p) REVERT: D 272 MET cc_start: 0.8793 (mmm) cc_final: 0.8482 (mmm) REVERT: D 292 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7934 (mp0) REVERT: E 89 GLU cc_start: 0.7006 (mt-10) cc_final: 0.6249 (mm-30) REVERT: E 101 LEU cc_start: 0.7677 (mt) cc_final: 0.7467 (mt) REVERT: E 143 ARG cc_start: 0.6477 (mtm180) cc_final: 0.6128 (mtm110) REVERT: E 255 HIS cc_start: 0.7002 (p-80) cc_final: 0.6264 (m90) REVERT: E 260 TYR cc_start: 0.7193 (t80) cc_final: 0.6787 (t80) REVERT: E 267 ARG cc_start: 0.7470 (ttm-80) cc_final: 0.6896 (ttp-110) REVERT: E 301 TYR cc_start: 0.7490 (t80) cc_final: 0.7185 (t80) REVERT: E 309 MET cc_start: 0.4514 (ptt) cc_final: 0.4258 (ptt) REVERT: F 47 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8383 (mp) REVERT: F 102 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7175 (mp0) outliers start: 20 outliers final: 15 residues processed: 244 average time/residue: 0.3209 time to fit residues: 114.2615 Evaluate side-chains 251 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 234 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 313 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 96 optimal weight: 1.9990 chunk 184 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 186 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 179 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 13 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 56.9633 > 50:) overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 286 ASN ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.123627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.092758 restraints weight = 65834.755| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.01 r_work: 0.2877 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16228 Z= 0.137 Angle : 0.509 8.605 22105 Z= 0.271 Chirality : 0.040 0.147 2488 Planarity : 0.005 0.042 2739 Dihedral : 13.815 150.684 2653 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.06 % Allowed : 8.73 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.19), residues: 1902 helix: 1.24 (0.16), residues: 1046 sheet: 0.59 (0.30), residues: 264 loop : 0.08 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 312 TYR 0.016 0.001 TYR A 322 PHE 0.007 0.001 PHE B 58 HIS 0.004 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (16228) covalent geometry : angle 0.50912 / 0.27 (22105) hydrogen bonds : bond 0.04535 / 3.05 ( 800) hydrogen bonds : angle 4.80612 / 3.41 ( 2276) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 237 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: A 160 ARG cc_start: 0.8509 (ptp90) cc_final: 0.8118 (ptp-170) REVERT: A 234 MET cc_start: 0.8043 (ptp) cc_final: 0.7543 (ptp) REVERT: A 252 ASP cc_start: 0.7838 (t0) cc_final: 0.7315 (t0) REVERT: A 291 ARG cc_start: 0.7605 (tpp80) cc_final: 0.7322 (ttt90) REVERT: B 102 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7503 (mt-10) REVERT: B 128 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.7021 (tt0) REVERT: B 199 MET cc_start: 0.8411 (mmp) cc_final: 0.7675 (tpt) REVERT: D 78 VAL cc_start: 0.7886 (t) cc_final: 0.7603 (p) REVERT: D 272 MET cc_start: 0.8744 (mmm) cc_final: 0.8440 (mmm) REVERT: D 292 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7887 (mp0) REVERT: E 89 GLU cc_start: 0.6997 (mt-10) cc_final: 0.6232 (mm-30) REVERT: E 101 LEU cc_start: 0.7676 (mt) cc_final: 0.7446 (mt) REVERT: E 143 ARG cc_start: 0.6481 (mtm180) cc_final: 0.6129 (mtm110) REVERT: E 255 HIS cc_start: 0.7030 (p-80) cc_final: 0.6288 (m90) REVERT: E 260 TYR cc_start: 0.7174 (t80) cc_final: 0.6792 (t80) REVERT: E 267 ARG cc_start: 0.7493 (ttm-80) cc_final: 0.6902 (ttp-110) REVERT: E 301 TYR cc_start: 0.7505 (t80) cc_final: 0.7240 (t80) REVERT: E 309 MET cc_start: 0.4506 (ptt) cc_final: 0.4268 (ptt) REVERT: F 47 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8397 (mp) REVERT: F 102 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7185 (mp0) outliers start: 17 outliers final: 13 residues processed: 243 average time/residue: 0.3330 time to fit residues: 117.2964 Evaluate side-chains 247 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 232 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 313 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 26 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 122 optimal weight: 0.8980 chunk 176 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 187 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 79 ASN D 286 ASN ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.122940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.092459 restraints weight = 65537.309| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.97 r_work: 0.2866 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16228 Z= 0.137 Angle : 0.509 7.263 22105 Z= 0.273 Chirality : 0.040 0.141 2488 Planarity : 0.005 0.042 2739 Dihedral : 13.811 151.570 2653 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.00 % Allowed : 8.92 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.19), residues: 1902 helix: 1.25 (0.16), residues: 1046 sheet: 0.58 (0.30), residues: 264 loop : 0.08 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 312 TYR 0.012 0.001 TYR D 131 PHE 0.006 0.001 PHE A 152 HIS 0.004 0.001 HIS D 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (16228) covalent geometry : angle 0.50913 / 0.27 (22105) hydrogen bonds : bond 0.04531 / 3.06 ( 800) hydrogen bonds : angle 4.79175 / 3.40 ( 2276) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 236 time to evaluate : 0.849 Fit side-chains revert: symmetry clash REVERT: A 100 ASP cc_start: 0.8218 (m-30) cc_final: 0.7928 (t70) REVERT: A 111 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7683 (mp0) REVERT: A 160 ARG cc_start: 0.8499 (ptp90) cc_final: 0.8100 (ptp-170) REVERT: A 234 MET cc_start: 0.8026 (ptp) cc_final: 0.7530 (ptp) REVERT: A 252 ASP cc_start: 0.7853 (t0) cc_final: 0.7306 (t0) REVERT: A 291 ARG cc_start: 0.7546 (tpp80) cc_final: 0.7243 (ttt90) REVERT: B 102 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7503 (mt-10) REVERT: B 128 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.7007 (tt0) REVERT: B 199 MET cc_start: 0.8414 (mmp) cc_final: 0.7658 (tpt) REVERT: B 242 LYS cc_start: 0.7928 (tppt) cc_final: 0.7448 (tppt) REVERT: D 78 VAL cc_start: 0.7892 (t) cc_final: 0.7605 (p) REVERT: D 272 MET cc_start: 0.8765 (mmm) cc_final: 0.8472 (mmm) REVERT: D 292 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7890 (mp0) REVERT: E 84 SER cc_start: 0.8320 (p) cc_final: 0.8073 (t) REVERT: E 89 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6242 (mm-30) REVERT: E 101 LEU cc_start: 0.7685 (mt) cc_final: 0.7456 (mt) REVERT: E 143 ARG cc_start: 0.6491 (mtm180) cc_final: 0.6143 (mtm110) REVERT: E 255 HIS cc_start: 0.7050 (p-80) cc_final: 0.6302 (m90) REVERT: E 260 TYR cc_start: 0.7183 (t80) cc_final: 0.6807 (t80) REVERT: E 267 ARG cc_start: 0.7511 (ttm-80) cc_final: 0.6927 (ttp-110) REVERT: E 301 TYR cc_start: 0.7501 (t80) cc_final: 0.7236 (t80) REVERT: E 309 MET cc_start: 0.4516 (ptt) cc_final: 0.4279 (ptt) REVERT: F 47 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8396 (mp) REVERT: F 102 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7177 (mp0) outliers start: 16 outliers final: 12 residues processed: 243 average time/residue: 0.3050 time to fit residues: 108.0057 Evaluate side-chains 247 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 233 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 272 MET Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 313 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 31 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 146 HIS D 286 ASN ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.122449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.091928 restraints weight = 65793.589| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 1.96 r_work: 0.2864 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16228 Z= 0.138 Angle : 0.506 7.484 22105 Z= 0.270 Chirality : 0.040 0.141 2488 Planarity : 0.005 0.041 2739 Dihedral : 13.827 153.409 2653 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.87 % Allowed : 9.05 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.19), residues: 1902 helix: 1.28 (0.16), residues: 1046 sheet: 0.54 (0.30), residues: 264 loop : 0.06 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 312 TYR 0.012 0.001 TYR A 322 PHE 0.007 0.001 PHE A 152 HIS 0.003 0.001 HIS B 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (16228) covalent geometry : angle 0.50621 / 0.27 (22105) hydrogen bonds : bond 0.04511 / 3.03 ( 800) hydrogen bonds : angle 4.77414 / 3.39 ( 2276) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 235 time to evaluate : 0.756 Fit side-chains revert: symmetry clash REVERT: A 100 ASP cc_start: 0.8212 (m-30) cc_final: 0.7928 (t70) REVERT: A 111 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7667 (mp0) REVERT: A 160 ARG cc_start: 0.8504 (ptp90) cc_final: 0.8116 (ptp-170) REVERT: A 234 MET cc_start: 0.8087 (ptp) cc_final: 0.7556 (ptp) REVERT: A 252 ASP cc_start: 0.7843 (t0) cc_final: 0.7294 (t0) REVERT: A 291 ARG cc_start: 0.7629 (tpp80) cc_final: 0.7332 (ttt90) REVERT: B 102 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7507 (mt-10) REVERT: B 128 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6984 (tt0) REVERT: B 199 MET cc_start: 0.8379 (mmp) cc_final: 0.7639 (tpt) REVERT: B 242 LYS cc_start: 0.7919 (tppt) cc_final: 0.7441 (tppt) REVERT: D 78 VAL cc_start: 0.7922 (t) cc_final: 0.7628 (p) REVERT: D 272 MET cc_start: 0.8741 (mmm) cc_final: 0.8440 (mmm) REVERT: D 292 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7887 (mp0) REVERT: E 84 SER cc_start: 0.8306 (p) cc_final: 0.8075 (t) REVERT: E 89 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6404 (mm-30) REVERT: E 101 LEU cc_start: 0.7687 (mt) cc_final: 0.7457 (mt) REVERT: E 143 ARG cc_start: 0.6551 (mtm180) cc_final: 0.6207 (mtm110) REVERT: E 240 ASP cc_start: 0.7056 (m-30) cc_final: 0.6283 (t70) REVERT: E 255 HIS cc_start: 0.7155 (p-80) cc_final: 0.6322 (m90) REVERT: E 260 TYR cc_start: 0.7177 (t80) cc_final: 0.6789 (t80) REVERT: E 267 ARG cc_start: 0.7503 (ttm-80) cc_final: 0.6927 (ttp-110) REVERT: E 301 TYR cc_start: 0.7500 (t80) cc_final: 0.7231 (t80) REVERT: E 309 MET cc_start: 0.4670 (ptt) cc_final: 0.4462 (ptt) REVERT: F 102 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7250 (mp0) outliers start: 14 outliers final: 13 residues processed: 240 average time/residue: 0.3037 time to fit residues: 105.9797 Evaluate side-chains 248 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 234 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain D residue 115 MET Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 272 MET Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 313 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 134 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 177 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 163 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 154 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.122890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.092405 restraints weight = 65771.966| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.96 r_work: 0.2872 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.294 16228 Z= 0.210 Angle : 0.716 59.199 22105 Z= 0.426 Chirality : 0.040 0.139 2488 Planarity : 0.005 0.041 2739 Dihedral : 13.828 153.415 2653 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.94 % Allowed : 9.05 % Favored : 90.02 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.19), residues: 1902 helix: 1.27 (0.16), residues: 1046 sheet: 0.54 (0.30), residues: 264 loop : 0.06 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 315 TYR 0.011 0.001 TYR A 322 PHE 0.006 0.001 PHE A 152 HIS 0.003 0.001 HIS B 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.21 (16228) covalent geometry : angle 0.71628 / 0.43 (22105) hydrogen bonds : bond 0.04509 / 3.03 ( 800) hydrogen bonds : angle 4.77362 / 3.39 ( 2276) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7774.62 seconds wall clock time: 132 minutes 15.35 seconds (7935.35 seconds total)