Starting phenix.real_space_refine on Fri Mar 6 13:58:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pbs_13301/03_2026/7pbs_13301_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pbs_13301/03_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_13301/03_2026/7pbs_13301_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pbs_13301/03_2026/7pbs_13301_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pbs_13301/03_2026/7pbs_13301.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pbs_13301/03_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-dev-5986/lib/python3.9/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: 4.99, per 1000 atoms: 0.16 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: 2.74 Conformation dependent library (CDL) restraints added in 787.1 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: 4.90 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: 6.39 Time building geometry restraints manager: 3.73 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=" 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=" 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 bond pdb=" N THR C 19 " pdb=" H1 THR C 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" N THR B 19 " pdb=" H1 THR B 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" N THR F 19 " pdb=" H1 THR F 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.50e+01 ... (remaining 31662 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 56778 2.16 - 4.31: 516 4.31 - 6.47: 22 6.47 - 8.63: 3 8.63 - 10.78: 2 Bond angle restraints: 57321 Sorted by residual: angle pdb=" N PHE B 197 " pdb=" CA PHE B 197 " pdb=" C PHE B 197 " ideal model delta sigma weight residual 110.48 104.85 5.63 1.48e+00 4.57e-01 1.45e+01 angle pdb=" N ILE E 233 " pdb=" CA ILE E 233 " pdb=" C ILE E 233 " ideal model delta sigma weight residual 111.62 108.75 2.87 7.90e-01 1.60e+00 1.32e+01 angle pdb=" OP1 DT V 4 " pdb=" P DT V 4 " pdb=" OP2 DT V 4 " ideal model delta sigma weight residual 120.00 109.22 10.78 3.00e+00 1.11e-01 1.29e+01 angle pdb=" O3' DT V 3 " pdb=" P DT V 4 " pdb=" OP1 DT V 4 " ideal model delta sigma weight residual 108.00 118.12 -10.12 3.00e+00 1.11e-01 1.14e+01 angle pdb=" N LEU D 251 " pdb=" CA LEU D 251 " pdb=" C LEU D 251 " ideal model delta sigma weight residual 110.20 105.10 5.10 1.58e+00 4.01e-01 1.04e+01 ... (remaining 57316 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.75: 14162 34.75 - 69.50: 515 69.50 - 104.25: 16 104.25 - 139.00: 3 139.00 - 173.75: 3 Dihedral angle restraints: 14699 sinusoidal: 8430 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=" O1A AGS F 401 " pdb=" O3A AGS F 401 " pdb=" PA AGS F 401 " pdb=" PB AGS F 401 " ideal model delta sinusoidal sigma weight residual -67.73 106.02 -173.75 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1A AGS D 401 " pdb=" O3A AGS D 401 " pdb=" PA AGS D 401 " pdb=" PB AGS D 401 " ideal model delta sinusoidal sigma weight residual -67.73 76.82 -144.55 1 3.00e+01 1.11e-03 1.94e+01 ... (remaining 14696 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2269 0.083 - 0.166: 228 0.166 - 0.248: 0 0.248 - 0.331: 0 0.331 - 0.414: 1 Chirality restraints: 2498 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 2.35 -2.76 -0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" CA PRO C 300 " pdb=" N PRO C 300 " pdb=" C PRO C 300 " pdb=" CB PRO C 300 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.23e-01 chirality pdb=" C3' DA U 10 " pdb=" C4' DA U 10 " pdb=" O3' DA U 10 " pdb=" C2' DA U 10 " both_signs ideal model delta sigma weight residual False -2.66 -2.51 -0.15 2.00e-01 2.50e+01 5.88e-01 ... (remaining 2495 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: 2.960 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: 0.160 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 30.350 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 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 : 0.005 0.041 16228 Z= 0.220 Angle : 0.715 10.783 22105 Z= 0.415 Chirality : 0.046 0.414 2498 Planarity : 0.011 0.137 2739 Dihedral : 14.970 173.751 6287 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 covalent geometry : bond 0.00515 (16228) covalent geometry : angle 0.71476 (22105) hydrogen bonds : bond 0.24351 ( 800) hydrogen bonds : angle 8.57410 ( 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 : 0.711 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: 0.7067 (ptp) REVERT: A 252 ASP cc_start: 0.7867 (t0) cc_final: 0.7416 (t0) REVERT: A 282 THR cc_start: 0.8514 (m) cc_final: 0.8033 (p) REVERT: A 292 GLU cc_start: 0.7277 (mt-10) cc_final: 0.6967 (tt0) REVERT: A 309 MET cc_start: 0.7326 (ttm) cc_final: 0.7122 (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: 0.8124 (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: 0.7360 (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: 0.7580 (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: 0.7456 (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: 0.3427 time to fit residues: 199.6974 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 : 0.823 ------------------------------------------------------------------------------- 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: 0.9990 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: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3431 r_free = 0.3431 target = 0.123231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.094513 restraints weight = 66144.893| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 1.91 r_work: 0.2834 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16228 Z= 0.176 Angle : 0.610 7.120 22105 Z= 0.335 Chirality : 0.042 0.160 2498 Planarity : 0.006 0.064 2739 Dihedral : 15.079 159.750 2563 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Rotamer: Outliers : 0.81 % Allowed : 5.86 % Favored : 93.33 % 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: 0.74 (0.19), residues: 1902 helix: 0.52 (0.16), residues: 1046 sheet: 1.20 (0.31), residues: 272 loop : 0.39 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 218 TYR 0.009 0.001 TYR E 131 PHE 0.008 0.001 PHE A 152 HIS 0.004 0.001 HIS D 54 Details of bonding type rmsd covalent geometry : bond 0.00384 (16228) covalent geometry : angle 0.60961 (22105) hydrogen bonds : bond 0.06923 ( 800) hydrogen bonds : angle 5.93102 ( 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 280 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 267 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 TYR cc_start: 0.9061 (p90) cc_final: 0.8498 (p90) REVERT: A 160 ARG cc_start: 0.8562 (ptp90) cc_final: 0.8257 (ptp-170) REVERT: A 234 MET cc_start: 0.8094 (ptp) cc_final: 0.7719 (ptp) REVERT: A 252 ASP cc_start: 0.8018 (t0) cc_final: 0.7415 (t0) REVERT: A 282 THR cc_start: 0.8317 (m) cc_final: 0.8084 (p) REVERT: B 49 ASP cc_start: 0.8325 (t0) cc_final: 0.8103 (t0) REVERT: B 102 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7283 (mt-10) REVERT: B 199 MET cc_start: 0.8178 (mmp) cc_final: 0.7482 (tpt) REVERT: C 260 TYR cc_start: 0.7834 (t80) cc_final: 0.7534 (t80) REVERT: D 78 VAL cc_start: 0.7726 (t) cc_final: 0.7476 (p) REVERT: D 117 MET cc_start: 0.6894 (ttm) cc_final: 0.6664 (mtp) REVERT: D 272 MET cc_start: 0.8836 (mmm) cc_final: 0.8567 (mmm) REVERT: D 292 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7748 (mp0) REVERT: D 330 THR cc_start: 0.6229 (m) cc_final: 0.5851 (p) REVERT: E 84 SER cc_start: 0.8490 (p) cc_final: 0.8189 (t) REVERT: E 89 GLU cc_start: 0.6968 (mt-10) cc_final: 0.6237 (mm-30) REVERT: E 143 ARG cc_start: 0.6380 (mtm180) cc_final: 0.5985 (mtm110) REVERT: E 255 HIS cc_start: 0.6796 (p-80) cc_final: 0.6081 (m90) REVERT: E 267 ARG cc_start: 0.7316 (ttm-80) cc_final: 0.6694 (ttp-110) REVERT: E 301 TYR cc_start: 0.7331 (t80) cc_final: 0.7045 (t80) REVERT: F 102 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7255 (mp0) REVERT: F 143 ARG cc_start: 0.7870 (ptt90) cc_final: 0.7553 (ptt-90) REVERT: F 144 SER cc_start: 0.8751 (p) cc_final: 0.8477 (t) REVERT: F 267 ARG cc_start: 0.6679 (ttm170) cc_final: 0.6035 (ttp80) REVERT: F 309 MET cc_start: 0.7408 (tpp) cc_final: 0.6731 (ttm) outliers start: 13 outliers final: 10 residues processed: 274 average time/residue: 0.3163 time to fit residues: 123.8705 Evaluate side-chains 254 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 244 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 125 SER Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 183 LEU 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: 0.9980 chunk 5 optimal weight: 0.9990 chunk 134 optimal weight: 0.6980 chunk 139 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 66 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN A 324 HIS B 146 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.123121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.092484 restraints weight = 66444.796| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 1.99 r_work: 0.2814 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16228 Z= 0.146 Angle : 0.533 6.032 22105 Z= 0.289 Chirality : 0.040 0.148 2498 Planarity : 0.005 0.057 2739 Dihedral : 15.101 160.542 2563 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.00 % Allowed : 6.05 % Favored : 92.95 % 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: 0.93 (0.19), residues: 1902 helix: 0.79 (0.16), residues: 1050 sheet: 1.00 (0.31), residues: 272 loop : 0.39 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 48 TYR 0.012 0.001 TYR E 298 PHE 0.006 0.001 PHE E 58 HIS 0.007 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00328 (16228) covalent geometry : angle 0.53274 (22105) hydrogen bonds : bond 0.05463 ( 800) hydrogen bonds : angle 5.30318 ( 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 275 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 259 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 TYR cc_start: 0.9057 (p90) cc_final: 0.8578 (p90) REVERT: A 160 ARG cc_start: 0.8560 (ptp90) cc_final: 0.8240 (ptp-170) REVERT: A 234 MET cc_start: 0.8027 (ptp) cc_final: 0.7471 (ptp) REVERT: A 252 ASP cc_start: 0.7940 (t0) cc_final: 0.7398 (t0) REVERT: A 325 MET cc_start: 0.7697 (mmp) cc_final: 0.7368 (mmp) REVERT: B 102 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7395 (mt-10) REVERT: B 128 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7173 (tt0) REVERT: B 199 MET cc_start: 0.8217 (mmp) cc_final: 0.7517 (tpt) REVERT: D 78 VAL cc_start: 0.7727 (t) cc_final: 0.7483 (p) REVERT: D 130 TYR cc_start: 0.5633 (m-80) cc_final: 0.5357 (m-80) REVERT: D 272 MET cc_start: 0.8843 (mmm) cc_final: 0.8566 (mmm) REVERT: D 292 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7764 (mp0) REVERT: D 330 THR cc_start: 0.6313 (m) cc_final: 0.5936 (p) REVERT: E 84 SER cc_start: 0.8405 (p) cc_final: 0.8093 (t) REVERT: E 89 GLU cc_start: 0.6832 (mt-10) cc_final: 0.6071 (mm-30) REVERT: E 143 ARG cc_start: 0.6396 (mtm180) cc_final: 0.6064 (mtm110) REVERT: E 234 MET cc_start: 0.6779 (mpp) cc_final: 0.6521 (mpp) REVERT: E 255 HIS cc_start: 0.6881 (p-80) cc_final: 0.6252 (m90) REVERT: E 267 ARG cc_start: 0.7435 (ttm-80) cc_final: 0.6847 (ttp-110) REVERT: E 301 TYR cc_start: 0.7471 (t80) cc_final: 0.7102 (t80) REVERT: F 102 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7249 (mp0) REVERT: F 143 ARG cc_start: 0.7915 (ptt90) cc_final: 0.7612 (ptt-90) outliers start: 16 outliers final: 11 residues processed: 268 average time/residue: 0.3300 time to fit residues: 124.6667 Evaluate side-chains 251 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 239 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 132 ILE 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: 0.6980 chunk 106 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 150 optimal weight: 3.9990 chunk 163 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 HIS D 286 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.121924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.091662 restraints weight = 65844.929| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 1.94 r_work: 0.2863 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16228 Z= 0.180 Angle : 0.548 5.947 22105 Z= 0.297 Chirality : 0.041 0.175 2498 Planarity : 0.005 0.052 2739 Dihedral : 15.142 164.545 2563 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.25 % Allowed : 7.17 % Favored : 91.58 % 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: 0.82 (0.19), residues: 1902 helix: 0.83 (0.16), residues: 1050 sheet: 0.78 (0.30), residues: 274 loop : 0.14 (0.24), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 160 TYR 0.022 0.001 TYR A 329 PHE 0.008 0.001 PHE B 152 HIS 0.004 0.001 HIS B 146 Details of bonding type rmsd covalent geometry : bond 0.00421 (16228) covalent geometry : angle 0.54846 (22105) hydrogen bonds : bond 0.05344 ( 800) hydrogen bonds : angle 5.11711 ( 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 265 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 245 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.8226 (m-30) cc_final: 0.7897 (t70) REVERT: A 160 ARG cc_start: 0.8556 (ptp90) cc_final: 0.8219 (ptp-170) REVERT: A 234 MET cc_start: 0.8148 (ptp) cc_final: 0.7585 (ptp) REVERT: A 252 ASP cc_start: 0.7911 (t0) cc_final: 0.7469 (t0) REVERT: B 102 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7530 (mt-10) REVERT: B 128 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7163 (tt0) REVERT: B 199 MET cc_start: 0.8305 (mmp) cc_final: 0.7563 (tpt) REVERT: B 242 LYS cc_start: 0.8064 (tppt) cc_final: 0.7559 (tppt) REVERT: D 78 VAL cc_start: 0.7869 (t) cc_final: 0.7584 (p) REVERT: D 272 MET cc_start: 0.8781 (mmm) cc_final: 0.8536 (mmm) REVERT: D 292 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7849 (mp0) REVERT: D 330 THR cc_start: 0.6644 (m) cc_final: 0.6290 (p) REVERT: E 84 SER cc_start: 0.8445 (p) cc_final: 0.8168 (t) REVERT: E 89 GLU cc_start: 0.6841 (mt-10) cc_final: 0.6079 (mm-30) REVERT: E 143 ARG cc_start: 0.6434 (mtm180) cc_final: 0.6094 (mtm110) REVERT: E 255 HIS cc_start: 0.6964 (p-80) cc_final: 0.6222 (m90) REVERT: E 260 TYR cc_start: 0.7178 (t80) cc_final: 0.6765 (t80) REVERT: E 267 ARG cc_start: 0.7414 (ttm-80) cc_final: 0.6859 (ttp-110) REVERT: E 301 TYR cc_start: 0.7484 (t80) cc_final: 0.7217 (t80) REVERT: F 102 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7278 (mp0) outliers start: 20 outliers final: 14 residues processed: 255 average time/residue: 0.3191 time to fit residues: 115.9833 Evaluate side-chains 242 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 227 time to evaluate : 0.777 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 136 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 108 optimal weight: 0.4980 chunk 96 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 116 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.123172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.092469 restraints weight = 66209.925| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.99 r_work: 0.2865 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16228 Z= 0.139 Angle : 0.516 5.912 22105 Z= 0.278 Chirality : 0.040 0.141 2498 Planarity : 0.005 0.046 2739 Dihedral : 15.111 163.673 2563 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.06 % Allowed : 7.67 % Favored : 91.27 % 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: 0.95 (0.19), residues: 1902 helix: 0.98 (0.16), residues: 1049 sheet: 0.76 (0.30), residues: 274 loop : 0.14 (0.24), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 160 TYR 0.010 0.001 TYR D 131 PHE 0.006 0.001 PHE B 58 HIS 0.003 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00317 (16228) covalent geometry : angle 0.51555 (22105) hydrogen bonds : bond 0.04855 ( 800) hydrogen bonds : angle 4.97262 ( 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 258 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 241 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.8220 (m-30) cc_final: 0.7895 (t70) REVERT: A 160 ARG cc_start: 0.8540 (ptp90) cc_final: 0.8191 (ptp-170) REVERT: A 234 MET cc_start: 0.7998 (ptp) cc_final: 0.7471 (ptp) REVERT: A 252 ASP cc_start: 0.7847 (t0) cc_final: 0.7299 (t0) REVERT: B 102 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7531 (mt-10) REVERT: B 128 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7105 (tt0) REVERT: B 199 MET cc_start: 0.8334 (mmp) cc_final: 0.7579 (tpt) REVERT: B 242 LYS cc_start: 0.7959 (tppt) cc_final: 0.7546 (tppt) REVERT: D 78 VAL cc_start: 0.7912 (t) cc_final: 0.7631 (p) REVERT: D 272 MET cc_start: 0.8796 (mmm) cc_final: 0.8484 (mmm) REVERT: D 292 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7857 (mp0) REVERT: E 84 SER cc_start: 0.8446 (p) cc_final: 0.8239 (t) REVERT: E 89 GLU cc_start: 0.6989 (mt-10) cc_final: 0.6254 (mm-30) REVERT: E 143 ARG cc_start: 0.6486 (mtm180) cc_final: 0.6147 (mtm110) REVERT: E 255 HIS cc_start: 0.6908 (p-80) cc_final: 0.6195 (m90) REVERT: E 260 TYR cc_start: 0.7197 (t80) cc_final: 0.6794 (t80) REVERT: E 267 ARG cc_start: 0.7445 (ttm-80) cc_final: 0.6919 (ttp-110) REVERT: E 301 TYR cc_start: 0.7486 (t80) cc_final: 0.7188 (t80) REVERT: E 309 MET cc_start: 0.4536 (ptt) cc_final: 0.4264 (ptt) REVERT: F 102 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7296 (mp0) outliers start: 17 outliers final: 13 residues processed: 248 average time/residue: 0.3083 time to fit residues: 109.7438 Evaluate side-chains 250 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 236 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 41 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 182 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 154 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS D 286 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.122030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.091838 restraints weight = 65740.912| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.95 r_work: 0.2862 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16228 Z= 0.157 Angle : 0.522 5.912 22105 Z= 0.281 Chirality : 0.040 0.143 2498 Planarity : 0.005 0.045 2739 Dihedral : 15.131 166.055 2563 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.31 % Allowed : 8.48 % 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: 0.95 (0.19), residues: 1902 helix: 1.07 (0.16), residues: 1046 sheet: 0.62 (0.30), residues: 264 loop : 0.05 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 160 TYR 0.010 0.001 TYR E 298 PHE 0.007 0.001 PHE A 152 HIS 0.004 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00365 (16228) covalent geometry : angle 0.52152 (22105) hydrogen bonds : bond 0.04828 ( 800) hydrogen bonds : angle 4.90206 ( 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 257 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 236 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.8215 (m-30) cc_final: 0.7903 (t70) REVERT: A 160 ARG cc_start: 0.8520 (ptp90) cc_final: 0.8176 (ptp-170) REVERT: A 234 MET cc_start: 0.8116 (ptp) cc_final: 0.7610 (ptp) REVERT: A 252 ASP cc_start: 0.7868 (t0) cc_final: 0.7356 (t0) REVERT: B 102 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7474 (mt-10) REVERT: B 128 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.7126 (tt0) REVERT: B 199 MET cc_start: 0.8417 (mmp) cc_final: 0.7646 (tpt) REVERT: B 242 LYS cc_start: 0.8009 (tppt) cc_final: 0.7605 (tppt) REVERT: D 78 VAL cc_start: 0.7905 (t) cc_final: 0.7624 (p) REVERT: D 272 MET cc_start: 0.8787 (mmm) cc_final: 0.8483 (mmm) REVERT: D 292 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7876 (mp0) REVERT: E 89 GLU cc_start: 0.7008 (mt-10) cc_final: 0.6265 (mm-30) REVERT: E 101 LEU cc_start: 0.7748 (mt) cc_final: 0.7538 (mt) REVERT: E 143 ARG cc_start: 0.6466 (mtm180) cc_final: 0.6113 (mtm110) REVERT: E 255 HIS cc_start: 0.6980 (p-80) cc_final: 0.6240 (m90) REVERT: E 260 TYR cc_start: 0.7205 (t80) cc_final: 0.6803 (t80) REVERT: E 267 ARG cc_start: 0.7440 (ttm-80) cc_final: 0.6934 (ttp-110) REVERT: E 301 TYR cc_start: 0.7526 (t80) cc_final: 0.7257 (t80) REVERT: E 309 MET cc_start: 0.4669 (ptt) cc_final: 0.4436 (ptt) REVERT: F 102 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7315 (mp0) outliers start: 21 outliers final: 17 residues processed: 246 average time/residue: 0.3104 time to fit residues: 109.5900 Evaluate side-chains 249 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 231 time to evaluate : 0.770 ------------------------------------------------------------------------------- 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 144 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 D residue 330 THR Chi-restraints excluded: chain E residue 149 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 79 optimal weight: 0.3980 chunk 173 optimal weight: 1.9990 chunk 174 optimal weight: 0.9990 chunk 169 optimal weight: 0.9990 chunk 111 optimal weight: 0.5980 chunk 176 optimal weight: 0.0570 chunk 156 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 18 optimal weight: 0.0980 chunk 16 optimal weight: 0.5980 overall best weight: 0.3498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3450 r_free = 0.3450 target = 0.124387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.093679 restraints weight = 66007.775| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.00 r_work: 0.2864 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16228 Z= 0.103 Angle : 0.483 6.159 22105 Z= 0.259 Chirality : 0.039 0.196 2498 Planarity : 0.004 0.036 2739 Dihedral : 15.041 163.146 2563 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 1.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % 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: 1.25 (0.19), residues: 1902 helix: 1.29 (0.16), residues: 1046 sheet: 0.70 (0.29), residues: 274 loop : 0.24 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 291 TYR 0.012 0.001 TYR D 131 PHE 0.005 0.001 PHE C 58 HIS 0.003 0.001 HIS F 146 Details of bonding type rmsd covalent geometry : bond 0.00223 (16228) covalent geometry : angle 0.48273 (22105) hydrogen bonds : bond 0.04165 ( 800) hydrogen bonds : angle 4.73877 ( 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 251 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 235 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.8190 (m-30) cc_final: 0.7920 (t70) REVERT: A 111 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7661 (mp0) REVERT: A 160 ARG cc_start: 0.8519 (ptp90) cc_final: 0.8119 (ptp-170) REVERT: A 234 MET cc_start: 0.7996 (ptp) cc_final: 0.7550 (ptp) REVERT: A 252 ASP cc_start: 0.7970 (t0) cc_final: 0.7446 (t0) REVERT: B 102 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7492 (mt-10) REVERT: B 128 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.6980 (tt0) REVERT: B 199 MET cc_start: 0.8378 (mmp) cc_final: 0.7612 (tpt) REVERT: B 242 LYS cc_start: 0.7982 (tppt) cc_final: 0.7585 (tppt) REVERT: D 78 VAL cc_start: 0.7834 (t) cc_final: 0.7543 (p) REVERT: D 292 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7883 (mp0) REVERT: E 89 GLU cc_start: 0.7004 (mt-10) cc_final: 0.6246 (mm-30) REVERT: E 101 LEU cc_start: 0.7663 (mt) cc_final: 0.7414 (mt) REVERT: E 143 ARG cc_start: 0.6479 (mtm180) cc_final: 0.6125 (mtm110) REVERT: E 255 HIS cc_start: 0.6927 (p-80) cc_final: 0.6220 (m90) REVERT: E 260 TYR cc_start: 0.7172 (t80) cc_final: 0.6801 (t80) REVERT: E 267 ARG cc_start: 0.7305 (ttm-80) cc_final: 0.6921 (ttp-110) REVERT: E 301 TYR cc_start: 0.7507 (t80) cc_final: 0.7255 (t80) REVERT: E 309 MET cc_start: 0.4512 (ptt) cc_final: 0.4262 (ptt) REVERT: F 47 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8380 (mp) REVERT: F 102 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7304 (mp0) outliers start: 16 outliers final: 11 residues processed: 242 average time/residue: 0.3203 time to fit residues: 111.0741 Evaluate side-chains 243 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 230 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 144 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 D residue 115 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 96 optimal weight: 1.9990 chunk 184 optimal weight: 0.9980 chunk 49 optimal weight: 0.4980 chunk 186 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 179 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3439 r_free = 0.3439 target = 0.123544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.095291 restraints weight = 65776.452| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.87 r_work: 0.2843 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3549 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= 0.137 Angle : 0.499 5.921 22105 Z= 0.268 Chirality : 0.040 0.151 2498 Planarity : 0.005 0.040 2739 Dihedral : 15.059 166.207 2563 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.94 % Allowed : 9.17 % Favored : 89.89 % 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: 1.21 (0.19), residues: 1902 helix: 1.33 (0.17), residues: 1046 sheet: 0.55 (0.30), residues: 264 loop : 0.16 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 312 TYR 0.010 0.001 TYR D 131 PHE 0.007 0.001 PHE A 152 HIS 0.003 0.001 HIS F 146 Details of bonding type rmsd covalent geometry : bond 0.00318 (16228) covalent geometry : angle 0.49874 (22105) hydrogen bonds : bond 0.04413 ( 800) hydrogen bonds : angle 4.72983 ( 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 248 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 233 time to evaluate : 0.838 Fit side-chains revert: symmetry clash REVERT: A 100 ASP cc_start: 0.8248 (m-30) cc_final: 0.7949 (t70) REVERT: A 111 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7655 (mp0) REVERT: A 160 ARG cc_start: 0.8503 (ptp90) cc_final: 0.8112 (ptp-170) REVERT: A 234 MET cc_start: 0.8003 (ptp) cc_final: 0.7527 (ptp) REVERT: A 252 ASP cc_start: 0.7907 (t0) cc_final: 0.7380 (t0) REVERT: B 102 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7457 (mt-10) REVERT: B 128 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6945 (tt0) REVERT: B 199 MET cc_start: 0.8377 (mmp) cc_final: 0.7600 (tpt) REVERT: B 242 LYS cc_start: 0.7961 (tppt) cc_final: 0.7542 (tppt) REVERT: D 78 VAL cc_start: 0.7874 (t) cc_final: 0.7598 (p) REVERT: D 292 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7909 (mp0) REVERT: E 89 GLU cc_start: 0.7196 (mt-10) cc_final: 0.6428 (mm-30) REVERT: E 101 LEU cc_start: 0.7660 (mt) cc_final: 0.7404 (mt) REVERT: E 143 ARG cc_start: 0.6469 (mtm180) cc_final: 0.6104 (mtm110) REVERT: E 240 ASP cc_start: 0.7061 (m-30) cc_final: 0.6295 (t70) REVERT: E 255 HIS cc_start: 0.6940 (p-80) cc_final: 0.6218 (m90) REVERT: E 260 TYR cc_start: 0.7189 (t80) cc_final: 0.6824 (t80) REVERT: E 267 ARG cc_start: 0.7268 (ttm-80) cc_final: 0.6901 (ttp-110) REVERT: E 301 TYR cc_start: 0.7498 (t80) cc_final: 0.7252 (t80) REVERT: E 309 MET cc_start: 0.4694 (ptt) cc_final: 0.4474 (ptt) REVERT: F 47 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8384 (mp) REVERT: F 102 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7407 (mp0) outliers start: 15 outliers final: 10 residues processed: 240 average time/residue: 0.3124 time to fit residues: 107.0529 Evaluate side-chains 244 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 232 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 144 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 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 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: 0.8980 chunk 62 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 187 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3440 r_free = 0.3440 target = 0.123708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.092792 restraints weight = 66089.808| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.00 r_work: 0.2844 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3615 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= 0.134 Angle : 0.496 6.659 22105 Z= 0.266 Chirality : 0.039 0.137 2498 Planarity : 0.005 0.039 2739 Dihedral : 15.065 166.059 2563 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.94 % Allowed : 9.23 % Favored : 89.83 % 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: 1.22 (0.19), residues: 1902 helix: 1.35 (0.16), residues: 1046 sheet: 0.52 (0.30), residues: 264 loop : 0.15 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 310 TYR 0.010 0.001 TYR D 131 PHE 0.007 0.001 PHE B 58 HIS 0.003 0.001 HIS F 146 Details of bonding type rmsd covalent geometry : bond 0.00308 (16228) covalent geometry : angle 0.49604 (22105) hydrogen bonds : bond 0.04343 ( 800) hydrogen bonds : angle 4.70625 ( 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 251 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 236 time to evaluate : 0.814 Fit side-chains revert: symmetry clash REVERT: A 100 ASP cc_start: 0.8257 (m-30) cc_final: 0.7969 (t70) REVERT: A 111 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7687 (mp0) REVERT: A 160 ARG cc_start: 0.8515 (ptp90) cc_final: 0.8132 (ptp-170) REVERT: A 234 MET cc_start: 0.8122 (ptp) cc_final: 0.7618 (ptp) REVERT: A 252 ASP cc_start: 0.7922 (t0) cc_final: 0.7366 (t0) REVERT: B 102 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7502 (mt-10) REVERT: B 128 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6916 (tt0) REVERT: B 199 MET cc_start: 0.8375 (mmp) cc_final: 0.7563 (tpt) REVERT: B 242 LYS cc_start: 0.7967 (tppt) cc_final: 0.7559 (tppt) REVERT: D 78 VAL cc_start: 0.7859 (t) cc_final: 0.7567 (p) REVERT: D 272 MET cc_start: 0.8806 (mmm) cc_final: 0.8508 (mmm) REVERT: D 292 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7935 (mp0) REVERT: E 89 GLU cc_start: 0.7198 (mt-10) cc_final: 0.6450 (mm-30) REVERT: E 101 LEU cc_start: 0.7696 (mt) cc_final: 0.7430 (mt) REVERT: E 143 ARG cc_start: 0.6512 (mtm180) cc_final: 0.6163 (mtm110) REVERT: E 240 ASP cc_start: 0.7065 (m-30) cc_final: 0.6318 (t70) REVERT: E 255 HIS cc_start: 0.6954 (p-80) cc_final: 0.6241 (m90) REVERT: E 260 TYR cc_start: 0.7206 (t80) cc_final: 0.6822 (t80) REVERT: E 267 ARG cc_start: 0.7204 (ttm-80) cc_final: 0.6837 (ttp-110) REVERT: E 301 TYR cc_start: 0.7511 (t80) cc_final: 0.7268 (t80) REVERT: E 309 MET cc_start: 0.4691 (ptt) cc_final: 0.4447 (ptt) REVERT: F 47 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8386 (mp) REVERT: F 102 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7422 (mp0) REVERT: F 309 MET cc_start: 0.7538 (tpp) cc_final: 0.7029 (ttm) outliers start: 15 outliers final: 8 residues processed: 243 average time/residue: 0.3175 time to fit residues: 110.8748 Evaluate side-chains 245 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 235 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain C residue 125 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 31 optimal weight: 0.3980 chunk 142 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 164 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 36 optimal weight: 0.1980 chunk 5 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.123639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.092759 restraints weight = 66107.684| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.02 r_work: 0.2898 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3683 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= 0.122 Angle : 0.485 6.343 22105 Z= 0.260 Chirality : 0.039 0.136 2498 Planarity : 0.005 0.038 2739 Dihedral : 15.042 166.062 2563 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.75 % Allowed : 9.61 % Favored : 89.64 % 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: 1.33 (0.19), residues: 1902 helix: 1.43 (0.17), residues: 1049 sheet: 0.51 (0.30), residues: 264 loop : 0.24 (0.24), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 312 TYR 0.011 0.001 TYR D 131 PHE 0.005 0.001 PHE B 58 HIS 0.003 0.001 HIS F 146 Details of bonding type rmsd covalent geometry : bond 0.00278 (16228) covalent geometry : angle 0.48537 (22105) hydrogen bonds : bond 0.04115 ( 800) hydrogen bonds : angle 4.64667 ( 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 250 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 238 time to evaluate : 0.816 Fit side-chains revert: symmetry clash REVERT: A 100 ASP cc_start: 0.8252 (m-30) cc_final: 0.7971 (t70) REVERT: A 111 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7683 (mp0) REVERT: A 160 ARG cc_start: 0.8494 (ptp90) cc_final: 0.8113 (ptp-170) REVERT: A 234 MET cc_start: 0.8088 (ptp) cc_final: 0.7647 (ptp) REVERT: A 252 ASP cc_start: 0.7934 (t0) cc_final: 0.7356 (t0) REVERT: B 102 GLU cc_start: 0.8372 (mm-30) cc_final: 0.7578 (mt-10) REVERT: B 128 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6839 (tt0) REVERT: B 199 MET cc_start: 0.8262 (mmp) cc_final: 0.7522 (tpt) REVERT: B 242 LYS cc_start: 0.7951 (tppt) cc_final: 0.7542 (tppt) REVERT: D 78 VAL cc_start: 0.7808 (t) cc_final: 0.7518 (p) REVERT: D 272 MET cc_start: 0.8793 (mmm) cc_final: 0.8503 (mmm) REVERT: D 292 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7942 (mp0) REVERT: E 89 GLU cc_start: 0.7190 (mt-10) cc_final: 0.6441 (mm-30) REVERT: E 101 LEU cc_start: 0.7692 (mt) cc_final: 0.7422 (mt) REVERT: E 143 ARG cc_start: 0.6562 (mtm180) cc_final: 0.6214 (mtm110) REVERT: E 240 ASP cc_start: 0.7047 (m-30) cc_final: 0.6313 (t70) REVERT: E 255 HIS cc_start: 0.7009 (p-80) cc_final: 0.6275 (m90) REVERT: E 260 TYR cc_start: 0.7192 (t80) cc_final: 0.6819 (t80) REVERT: E 267 ARG cc_start: 0.7202 (ttm-80) cc_final: 0.6838 (ttp-110) REVERT: E 301 TYR cc_start: 0.7496 (t80) cc_final: 0.7252 (t80) REVERT: F 47 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8364 (mp) REVERT: F 102 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7332 (mp0) REVERT: F 143 ARG cc_start: 0.7839 (ptp-170) cc_final: 0.7479 (ptp-170) REVERT: F 195 GLU cc_start: 0.7379 (tp30) cc_final: 0.7075 (tp30) REVERT: F 309 MET cc_start: 0.7550 (tpp) cc_final: 0.7034 (ttm) outliers start: 12 outliers final: 10 residues processed: 244 average time/residue: 0.3185 time to fit residues: 110.8416 Evaluate side-chains 245 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 233 time to evaluate : 0.825 ------------------------------------------------------------------------------- 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 144 SER Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 236 ASP 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 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: 3.9990 chunk 30 optimal weight: 0.3980 chunk 89 optimal weight: 0.9990 chunk 177 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 163 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 35 optimal weight: 0.0870 chunk 154 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.123790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.092968 restraints weight = 66137.558| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.01 r_work: 0.2880 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3721 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= 0.119 Angle : 0.485 6.585 22105 Z= 0.259 Chirality : 0.039 0.206 2498 Planarity : 0.005 0.037 2739 Dihedral : 15.033 166.176 2563 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.81 % Allowed : 9.54 % Favored : 89.64 % 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: 1.39 (0.19), residues: 1902 helix: 1.48 (0.17), residues: 1049 sheet: 0.53 (0.30), residues: 264 loop : 0.27 (0.24), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 114 TYR 0.014 0.001 TYR A 260 PHE 0.005 0.001 PHE A 152 HIS 0.003 0.001 HIS F 146 Details of bonding type rmsd covalent geometry : bond 0.00271 (16228) covalent geometry : angle 0.48457 (22105) hydrogen bonds : bond 0.04058 ( 800) hydrogen bonds : angle 4.62397 ( 2276) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7497.60 seconds wall clock time: 127 minutes 26.85 seconds (7646.85 seconds total)