Starting phenix.real_space_refine on Fri Jun 5 01:29:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5bkk_9407/06_2026/5bkk_9407.cif Found real_map, /net/cci-nas-00/data/ceres_data/5bkk_9407/06_2026/5bkk_9407.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5bkk_9407/06_2026/5bkk_9407.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5bkk_9407/06_2026/5bkk_9407.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5bkk_9407/06_2026/5bkk_9407.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5bkk_9407/06_2026/5bkk_9407.map" } resolution = 3.5 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= 0.005 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: 5 Type Number sf(0) Gaussians K 3 8.98 5 S 68 5.16 5 C 10617 2.51 5 N 2897 2.21 5 O 3246 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 124 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16831 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2467 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Chain: "B" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1725 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "C" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2464 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1725 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "E" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2464 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1725 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "G" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2464 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 307} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1725 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 56 Unusual residues: {' K': 1, 'PGW': 1, 'YQ4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' K': 1, 'PGW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PGW:plan-1': 1, 'PGW:plan-2': 1, 'PGW:plan-3': 1} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 4.27, per 1000 atoms: 0.25 Number of scatterers: 16831 At special positions: 0 Unit cell: (147.96, 147.96, 119.464, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 3 19.00 S 68 16.00 O 3246 8.00 N 2897 7.00 C 10617 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 842.1 milliseconds 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3952 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 16 sheets defined 47.7% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'A' and resid 21 through 42 removed outlier: 3.530A pdb=" N PHE A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 58 Processing helix chain 'A' and resid 69 through 107 removed outlier: 4.158A pdb=" N VAL A 77 " --> pdb=" O MET A 73 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR A 78 " --> pdb=" O TYR A 74 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET A 107 " --> pdb=" O GLN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 129 Processing helix chain 'A' and resid 145 through 155 removed outlier: 3.993A pdb=" N ARG A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG A 154 " --> pdb=" O LYS A 150 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER A 155 " --> pdb=" O LYS A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 176 removed outlier: 4.378A pdb=" N GLU A 171 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS A 172 " --> pdb=" O ASP A 169 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL A 175 " --> pdb=" O LYS A 172 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ARG A 176 " --> pdb=" O ALA A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 202 removed outlier: 3.537A pdb=" N THR A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE A 192 " --> pdb=" O ASP A 188 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N HIS A 193 " --> pdb=" O SER A 189 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 224 Processing helix chain 'A' and resid 230 through 239 Processing helix chain 'A' and resid 247 through 256 removed outlier: 3.587A pdb=" N PHE A 251 " --> pdb=" O TYR A 247 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 284 Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 323 through 332 removed outlier: 3.659A pdb=" N GLU A 328 " --> pdb=" O PRO A 324 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN A 332 " --> pdb=" O GLU A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 129 Processing helix chain 'B' and resid 147 through 155 removed outlier: 4.290A pdb=" N LYS B 151 " --> pdb=" O ASN B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 171 removed outlier: 3.540A pdb=" N GLU B 171 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 199 removed outlier: 3.742A pdb=" N HIS B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 230 through 238 Processing helix chain 'B' and resid 248 through 256 removed outlier: 3.561A pdb=" N ASP B 254 " --> pdb=" O MET B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 335 removed outlier: 3.721A pdb=" N GLU B 328 " --> pdb=" O PRO B 324 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG B 329 " --> pdb=" O GLU B 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 42 removed outlier: 3.954A pdb=" N PHE C 40 " --> pdb=" O ALA C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 58 removed outlier: 3.652A pdb=" N ALA C 58 " --> pdb=" O PHE C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 107 removed outlier: 4.121A pdb=" N MET C 107 " --> pdb=" O GLN C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 129 Processing helix chain 'C' and resid 130 through 132 No H-bonds generated for 'chain 'C' and resid 130 through 132' Processing helix chain 'C' and resid 145 through 154 removed outlier: 3.649A pdb=" N ARG C 149 " --> pdb=" O ASP C 145 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS C 150 " --> pdb=" O GLU C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 171 Processing helix chain 'C' and resid 188 through 202 removed outlier: 3.581A pdb=" N ILE C 192 " --> pdb=" O ASP C 188 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS C 200 " --> pdb=" O LEU C 196 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE C 201 " --> pdb=" O GLY C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 215 No H-bonds generated for 'chain 'C' and resid 213 through 215' Processing helix chain 'C' and resid 216 through 224 removed outlier: 3.522A pdb=" N ARG C 221 " --> pdb=" O ILE C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 240 removed outlier: 3.649A pdb=" N SER C 240 " --> pdb=" O GLY C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 256 removed outlier: 3.571A pdb=" N PHE C 251 " --> pdb=" O TYR C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 284 Processing helix chain 'C' and resid 284 through 289 Processing helix chain 'C' and resid 323 through 328 removed outlier: 3.625A pdb=" N GLU C 328 " --> pdb=" O PRO C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 334 Processing helix chain 'D' and resid 124 through 129 Processing helix chain 'D' and resid 130 through 133 removed outlier: 3.885A pdb=" N GLU D 133 " --> pdb=" O CYS D 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 130 through 133' Processing helix chain 'D' and resid 147 through 155 removed outlier: 4.329A pdb=" N LYS D 151 " --> pdb=" O ASN D 147 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER D 155 " --> pdb=" O LYS D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 171 Processing helix chain 'D' and resid 188 through 200 removed outlier: 3.504A pdb=" N LYS D 200 " --> pdb=" O LEU D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 224 removed outlier: 3.924A pdb=" N MET D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 241 removed outlier: 3.643A pdb=" N SER D 240 " --> pdb=" O GLY D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 256 removed outlier: 3.501A pdb=" N PHE D 251 " --> pdb=" O TYR D 247 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP D 254 " --> pdb=" O MET D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 284 Processing helix chain 'D' and resid 284 through 290 removed outlier: 3.647A pdb=" N THR D 289 " --> pdb=" O ILE D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 335 removed outlier: 3.793A pdb=" N GLU D 328 " --> pdb=" O PRO D 324 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG D 329 " --> pdb=" O GLU D 325 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER D 335 " --> pdb=" O LYS D 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 43 removed outlier: 4.165A pdb=" N ILE E 41 " --> pdb=" O GLY E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 58 removed outlier: 3.605A pdb=" N ALA E 58 " --> pdb=" O PHE E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 107 removed outlier: 3.864A pdb=" N MET E 107 " --> pdb=" O GLN E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 128 Processing helix chain 'E' and resid 130 through 134 Processing helix chain 'E' and resid 146 through 155 removed outlier: 3.940A pdb=" N LYS E 150 " --> pdb=" O GLU E 146 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS E 151 " --> pdb=" O ASN E 147 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER E 155 " --> pdb=" O LYS E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 171 Processing helix chain 'E' and resid 174 through 178 removed outlier: 3.663A pdb=" N ALA E 178 " --> pdb=" O VAL E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 202 removed outlier: 3.722A pdb=" N HIS E 193 " --> pdb=" O SER E 189 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE E 201 " --> pdb=" O GLY E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 224 removed outlier: 3.571A pdb=" N ARG E 221 " --> pdb=" O ILE E 217 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 240 removed outlier: 3.655A pdb=" N SER E 240 " --> pdb=" O GLY E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 256 removed outlier: 3.561A pdb=" N ASP E 254 " --> pdb=" O MET E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 284 Processing helix chain 'E' and resid 284 through 290 removed outlier: 3.612A pdb=" N VAL E 288 " --> pdb=" O ASP E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 329 removed outlier: 3.871A pdb=" N GLU E 328 " --> pdb=" O PRO E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 329 through 334 Processing helix chain 'F' and resid 124 through 129 Processing helix chain 'F' and resid 130 through 134 removed outlier: 3.851A pdb=" N GLU F 133 " --> pdb=" O CYS F 130 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU F 134 " --> pdb=" O LEU F 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 130 through 134' Processing helix chain 'F' and resid 147 through 155 removed outlier: 4.108A pdb=" N LYS F 151 " --> pdb=" O ASN F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 171 removed outlier: 3.913A pdb=" N GLU F 171 " --> pdb=" O VAL F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 202 removed outlier: 3.725A pdb=" N ILE F 192 " --> pdb=" O ASP F 188 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS F 200 " --> pdb=" O LEU F 196 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE F 201 " --> pdb=" O GLY F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 224 Processing helix chain 'F' and resid 230 through 241 removed outlier: 3.661A pdb=" N MET F 239 " --> pdb=" O SER F 235 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER F 240 " --> pdb=" O GLY F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 256 removed outlier: 3.607A pdb=" N PHE F 251 " --> pdb=" O TYR F 247 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP F 254 " --> pdb=" O MET F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 335 removed outlier: 3.949A pdb=" N GLU F 328 " --> pdb=" O PRO F 324 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG F 329 " --> pdb=" O GLU F 325 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER F 335 " --> pdb=" O LYS F 331 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 42 removed outlier: 3.592A pdb=" N LEU G 25 " --> pdb=" O THR G 21 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE G 40 " --> pdb=" O ALA G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 58 removed outlier: 3.888A pdb=" N ALA G 58 " --> pdb=" O PHE G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 105 Processing helix chain 'G' and resid 124 through 129 Processing helix chain 'G' and resid 145 through 155 removed outlier: 3.629A pdb=" N LYS G 150 " --> pdb=" O GLU G 146 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER G 155 " --> pdb=" O LYS G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 170 through 174 Processing helix chain 'G' and resid 187 through 200 removed outlier: 3.567A pdb=" N THR G 191 " --> pdb=" O SER G 187 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS G 193 " --> pdb=" O SER G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 215 No H-bonds generated for 'chain 'G' and resid 213 through 215' Processing helix chain 'G' and resid 216 through 224 removed outlier: 3.565A pdb=" N ARG G 221 " --> pdb=" O ILE G 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 230 through 238 Processing helix chain 'G' and resid 247 through 256 removed outlier: 3.696A pdb=" N PHE G 251 " --> pdb=" O TYR G 247 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 284 Processing helix chain 'G' and resid 284 through 289 Processing helix chain 'G' and resid 323 through 334 removed outlier: 3.803A pdb=" N ARG G 329 " --> pdb=" O GLU G 325 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU G 330 " --> pdb=" O GLU G 326 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 131 Processing helix chain 'H' and resid 147 through 156 removed outlier: 4.161A pdb=" N LYS H 151 " --> pdb=" O ASN H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 171 Processing helix chain 'H' and resid 188 through 202 removed outlier: 3.695A pdb=" N ILE H 192 " --> pdb=" O ASP H 188 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE H 201 " --> pdb=" O GLY H 197 " (cutoff:3.500A) Processing helix chain 'H' and resid 213 through 215 No H-bonds generated for 'chain 'H' and resid 213 through 215' Processing helix chain 'H' and resid 216 through 224 Processing helix chain 'H' and resid 230 through 241 removed outlier: 3.655A pdb=" N SER H 240 " --> pdb=" O GLY H 236 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 256 removed outlier: 3.688A pdb=" N PHE H 251 " --> pdb=" O TYR H 247 " (cutoff:3.500A) Processing helix chain 'H' and resid 279 through 283 removed outlier: 3.510A pdb=" N ASP H 282 " --> pdb=" O SER H 279 " (cutoff:3.500A) Processing helix chain 'H' and resid 323 through 332 removed outlier: 3.663A pdb=" N GLU H 328 " --> pdb=" O PRO H 324 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG H 329 " --> pdb=" O GLU H 325 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 161 removed outlier: 6.876A pdb=" N VAL A 139 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N VAL A 160 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL A 141 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N HIS A 117 " --> pdb=" O ARG A 179 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N VAL A 181 " --> pdb=" O HIS A 117 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL A 119 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL A 183 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N CYS A 121 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ARG A 206 " --> pdb=" O ARG A 179 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 263 through 268 removed outlier: 6.919A pdb=" N ILE A 321 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ILE A 293 " --> pdb=" O ILE A 321 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 158 through 161 removed outlier: 6.293A pdb=" N VAL B 139 " --> pdb=" O ASN B 158 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL B 160 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL B 141 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL B 118 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N LEU B 142 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE B 120 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL B 119 " --> pdb=" O ALA B 180 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE B 229 " --> pdb=" O ALA B 209 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 263 through 268 removed outlier: 3.528A pdb=" N GLY B 295 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE B 321 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ILE B 293 " --> pdb=" O ILE B 321 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 158 through 161 removed outlier: 6.505A pdb=" N VAL C 118 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N LEU C 142 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE C 120 " --> pdb=" O LEU C 142 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL C 119 " --> pdb=" O ILE C 182 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE C 207 " --> pdb=" O GLN C 227 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ILE C 229 " --> pdb=" O ILE C 207 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ALA C 209 " --> pdb=" O ILE C 229 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 263 through 267 removed outlier: 3.666A pdb=" N ILE C 317 " --> pdb=" O GLY C 297 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ILE C 321 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N ILE C 293 " --> pdb=" O ILE C 321 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 158 through 161 removed outlier: 6.633A pdb=" N VAL D 139 " --> pdb=" O ASN D 158 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL D 160 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N VAL D 141 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL D 118 " --> pdb=" O PHE D 140 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N LEU D 142 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE D 120 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL D 119 " --> pdb=" O ILE D 182 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 263 through 268 removed outlier: 3.524A pdb=" N GLY D 295 " --> pdb=" O LEU D 319 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ILE D 321 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ILE D 293 " --> pdb=" O ILE D 321 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 158 through 161 removed outlier: 6.497A pdb=" N VAL E 139 " --> pdb=" O ASN E 158 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N VAL E 160 " --> pdb=" O VAL E 139 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL E 141 " --> pdb=" O VAL E 160 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL E 118 " --> pdb=" O PHE E 140 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LEU E 142 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE E 120 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL E 119 " --> pdb=" O ILE E 182 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE E 207 " --> pdb=" O GLN E 227 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ILE E 229 " --> pdb=" O ILE E 207 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ALA E 209 " --> pdb=" O ILE E 229 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 265 through 268 removed outlier: 3.853A pdb=" N ILE E 317 " --> pdb=" O GLY E 297 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY E 295 " --> pdb=" O LEU E 319 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ILE E 321 " --> pdb=" O ILE E 293 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ILE E 293 " --> pdb=" O ILE E 321 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL E 296 " --> pdb=" O ILE E 303 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 158 through 161 removed outlier: 6.231A pdb=" N VAL F 139 " --> pdb=" O ASN F 158 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL F 160 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL F 141 " --> pdb=" O VAL F 160 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL F 118 " --> pdb=" O PHE F 140 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N LEU F 142 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE F 120 " --> pdb=" O LEU F 142 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ILE F 207 " --> pdb=" O GLN F 227 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N ILE F 229 " --> pdb=" O ILE F 207 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ALA F 209 " --> pdb=" O ILE F 229 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 263 through 268 removed outlier: 6.981A pdb=" N ILE F 321 " --> pdb=" O ILE F 293 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ILE F 293 " --> pdb=" O ILE F 321 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 158 through 161 removed outlier: 6.631A pdb=" N VAL G 139 " --> pdb=" O ASN G 158 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N VAL G 160 " --> pdb=" O VAL G 139 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N VAL G 141 " --> pdb=" O VAL G 160 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL G 118 " --> pdb=" O PHE G 140 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LEU G 142 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE G 120 " --> pdb=" O LEU G 142 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL G 119 " --> pdb=" O ILE G 182 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 263 through 268 removed outlier: 7.117A pdb=" N ILE G 321 " --> pdb=" O ILE G 293 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ILE G 293 " --> pdb=" O ILE G 321 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 158 through 161 removed outlier: 6.369A pdb=" N VAL H 139 " --> pdb=" O ASN H 158 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL H 160 " --> pdb=" O VAL H 139 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL H 141 " --> pdb=" O VAL H 160 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL H 118 " --> pdb=" O PHE H 140 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LEU H 142 " --> pdb=" O VAL H 118 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE H 120 " --> pdb=" O LEU H 142 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL H 181 " --> pdb=" O ILE H 208 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 263 through 268 removed outlier: 6.998A pdb=" N ILE H 321 " --> pdb=" O ILE H 293 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ILE H 293 " --> pdb=" O ILE H 321 " (cutoff:3.500A) 692 hydrogen bonds defined for protein. 1977 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.18 Time building geometry restraints manager: 1.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5596 1.34 - 1.46: 2021 1.46 - 1.57: 9335 1.57 - 1.69: 3 1.69 - 1.81: 112 Bond restraints: 17067 Sorted by residual: bond pdb=" C1 PGW A 401 " pdb=" O01 PGW A 401 " ideal model delta sigma weight residual 1.332 1.455 -0.123 2.00e-02 2.50e+03 3.78e+01 bond pdb=" C19 PGW A 401 " pdb=" O03 PGW A 401 " ideal model delta sigma weight residual 1.332 1.454 -0.122 2.00e-02 2.50e+03 3.70e+01 bond pdb=" C11 YQ4 A 403 " pdb=" C12 YQ4 A 403 " ideal model delta sigma weight residual 1.473 1.587 -0.114 2.00e-02 2.50e+03 3.22e+01 bond pdb=" C01 YQ4 A 403 " pdb=" O01 YQ4 A 403 " ideal model delta sigma weight residual 1.464 1.388 0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C12 YQ4 A 403 " pdb=" N01 YQ4 A 403 " ideal model delta sigma weight residual 1.580 1.524 0.056 2.00e-02 2.50e+03 7.81e+00 ... (remaining 17062 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 22464 1.87 - 3.73: 529 3.73 - 5.60: 56 5.60 - 7.46: 18 7.46 - 9.33: 6 Bond angle restraints: 23073 Sorted by residual: angle pdb=" N LEU H 275 " pdb=" CA LEU H 275 " pdb=" C LEU H 275 " ideal model delta sigma weight residual 112.41 118.31 -5.90 1.30e+00 5.92e-01 2.06e+01 angle pdb=" C SER C 273 " pdb=" N LYS C 274 " pdb=" CA LYS C 274 " ideal model delta sigma weight residual 121.54 129.94 -8.40 1.91e+00 2.74e-01 1.94e+01 angle pdb=" N VAL G 60 " pdb=" CA VAL G 60 " pdb=" C VAL G 60 " ideal model delta sigma weight residual 111.67 107.96 3.71 9.50e-01 1.11e+00 1.53e+01 angle pdb=" C SER D 273 " pdb=" N LYS D 274 " pdb=" CA LYS D 274 " ideal model delta sigma weight residual 121.54 127.89 -6.35 1.91e+00 2.74e-01 1.11e+01 angle pdb=" CA GLU F 259 " pdb=" CB GLU F 259 " pdb=" CG GLU F 259 " ideal model delta sigma weight residual 114.10 120.64 -6.54 2.00e+00 2.50e-01 1.07e+01 ... (remaining 23068 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.80: 10108 32.80 - 65.61: 251 65.61 - 98.41: 29 98.41 - 131.22: 2 131.22 - 164.02: 1 Dihedral angle restraints: 10391 sinusoidal: 4239 harmonic: 6152 Sorted by residual: dihedral pdb=" CA SER D 273 " pdb=" C SER D 273 " pdb=" N LYS D 274 " pdb=" CA LYS D 274 " ideal model delta harmonic sigma weight residual 180.00 156.38 23.62 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA ASP D 284 " pdb=" C ASP D 284 " pdb=" N ILE D 285 " pdb=" CA ILE D 285 " ideal model delta harmonic sigma weight residual -180.00 -156.81 -23.19 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" C01 PGW A 401 " pdb=" C19 PGW A 401 " pdb=" O03 PGW A 401 " pdb=" O04 PGW A 401 " ideal model delta sinusoidal sigma weight residual 9.00 173.02 -164.02 1 3.00e+01 1.11e-03 2.09e+01 ... (remaining 10388 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2032 0.057 - 0.113: 540 0.113 - 0.170: 105 0.170 - 0.227: 8 0.227 - 0.283: 2 Chirality restraints: 2687 Sorted by residual: chirality pdb=" CB ILE H 334 " pdb=" CA ILE H 334 " pdb=" CG1 ILE H 334 " pdb=" CG2 ILE H 334 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CB ILE F 317 " pdb=" CA ILE F 317 " pdb=" CG1 ILE F 317 " pdb=" CG2 ILE F 317 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CB ILE F 285 " pdb=" CA ILE F 285 " pdb=" CG1 ILE F 285 " pdb=" CG2 ILE F 285 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 2684 not shown) Planarity restraints: 2993 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 69 " -0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO C 70 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 70 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 70 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS H 274 " -0.010 2.00e-02 2.50e+03 2.04e-02 4.18e+00 pdb=" C LYS H 274 " 0.035 2.00e-02 2.50e+03 pdb=" O LYS H 274 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU H 275 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 267 " -0.033 5.00e-02 4.00e+02 4.94e-02 3.91e+00 pdb=" N PRO A 268 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 268 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 268 " -0.027 5.00e-02 4.00e+02 ... (remaining 2990 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.82: 5086 2.82 - 3.40: 17299 3.40 - 3.98: 31528 3.98 - 4.56: 44027 4.56 - 5.14: 67739 Nonbonded interactions: 165679 Sorted by model distance: nonbonded pdb=" O VAL G 60 " pdb=" K K G 402 " model vdw 2.242 2.850 nonbonded pdb=" OG SER F 279 " pdb=" O ARG F 308 " model vdw 2.273 3.040 nonbonded pdb=" OG SER E 126 " pdb=" OD2 ASP E 184 " model vdw 2.289 3.040 nonbonded pdb=" OH TYR C 62 " pdb=" OG1 THR E 56 " model vdw 2.298 3.040 nonbonded pdb=" OG SER C 126 " pdb=" OD2 ASP C 184 " model vdw 2.301 3.040 ... (remaining 165674 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 20 through 274 or (resid 275 and (name N or name CA or nam \ e C or name O or name CB )) or resid 276 through 336)) selection = chain 'C' selection = (chain 'E' and resid 20 through 336) selection = (chain 'G' and resid 20 through 336) } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } 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 group one per residue 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: 1.310 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: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.310 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 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 0.123 17067 Z= 0.217 Angle : 0.716 9.325 23073 Z= 0.401 Chirality : 0.053 0.283 2687 Planarity : 0.005 0.051 2993 Dihedral : 14.951 164.021 6439 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.11 % Allowed : 6.16 % Favored : 93.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.88 (0.13), residues: 2140 helix: -3.78 (0.09), residues: 976 sheet: -1.91 (0.26), residues: 316 loop : -2.83 (0.17), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 132 TYR 0.012 0.002 TYR E 33 PHE 0.010 0.001 PHE A 87 TRP 0.008 0.001 TRP C 52 HIS 0.006 0.001 HIS A 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.22 (17067) covalent geometry : angle 0.71614 / 0.40 (23073) hydrogen bonds : bond 0.24416 / 16.10 ( 692) hydrogen bonds : angle 9.01947 / 6.31 ( 1977) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 453 time to evaluate : 0.665 Fit side-chains revert: symmetry clash REVERT: A 28 LEU cc_start: 0.8256 (mm) cc_final: 0.8037 (mm) REVERT: A 114 LYS cc_start: 0.7929 (mmtp) cc_final: 0.7492 (mmmt) REVERT: A 149 ARG cc_start: 0.8089 (ttp80) cc_final: 0.7879 (ttp-170) REVERT: A 200 LYS cc_start: 0.8285 (ttmt) cc_final: 0.8080 (ttmm) REVERT: A 239 MET cc_start: 0.8335 (mtt) cc_final: 0.8107 (mtt) REVERT: B 210 GLU cc_start: 0.7860 (tt0) cc_final: 0.7653 (tt0) REVERT: C 93 ARG cc_start: 0.7624 (mmt180) cc_final: 0.7349 (mmt180) REVERT: D 200 LYS cc_start: 0.7933 (mmtt) cc_final: 0.7724 (mtmt) REVERT: D 239 MET cc_start: 0.7936 (mtt) cc_final: 0.7622 (mtt) REVERT: E 35 THR cc_start: 0.7684 (p) cc_final: 0.7278 (p) REVERT: E 84 ILE cc_start: 0.8979 (mm) cc_final: 0.8562 (mt) REVERT: E 94 LEU cc_start: 0.8554 (tt) cc_final: 0.8299 (tt) REVERT: E 98 LEU cc_start: 0.9036 (tp) cc_final: 0.8706 (tp) REVERT: E 241 ARG cc_start: 0.6840 (mtt180) cc_final: 0.6498 (mtt-85) REVERT: F 125 GLU cc_start: 0.8767 (tp30) cc_final: 0.8404 (tp30) REVERT: F 163 ASP cc_start: 0.8834 (t0) cc_final: 0.8634 (t70) REVERT: G 92 GLU cc_start: 0.7938 (tp30) cc_final: 0.7269 (tp30) REVERT: H 203 GLU cc_start: 0.7069 (mm-30) cc_final: 0.6741 (tp30) REVERT: H 239 MET cc_start: 0.8725 (mtt) cc_final: 0.8511 (mtt) outliers start: 2 outliers final: 0 residues processed: 454 average time/residue: 0.1730 time to fit residues: 109.9405 Evaluate side-chains 343 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.0870 chunk 200 optimal weight: 1.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 0.9980 overall best weight: 0.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS C 332 ASN D 286 HIS E 39 HIS E 158 ASN E 227 GLN F 286 HIS G 219 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.138809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.110392 restraints weight = 21260.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.113369 restraints weight = 12847.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.115336 restraints weight = 9081.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.116438 restraints weight = 7188.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.117349 restraints weight = 6225.235| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17067 Z= 0.129 Angle : 0.507 7.572 23073 Z= 0.271 Chirality : 0.046 0.151 2687 Planarity : 0.004 0.061 2993 Dihedral : 8.021 146.621 2441 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.96 % Allowed : 11.46 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.18 (0.16), residues: 2140 helix: -1.95 (0.13), residues: 998 sheet: -1.75 (0.27), residues: 312 loop : -2.23 (0.19), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 241 TYR 0.020 0.001 TYR F 333 PHE 0.012 0.001 PHE E 75 TRP 0.007 0.001 TRP C 52 HIS 0.005 0.001 HIS E 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (17067) covalent geometry : angle 0.50735 / 0.27 (23073) hydrogen bonds : bond 0.03804 / 2.53 ( 692) hydrogen bonds : angle 5.10171 / 3.54 ( 1977) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 382 time to evaluate : 0.686 Fit side-chains REVERT: A 28 LEU cc_start: 0.8602 (mm) cc_final: 0.8359 (mm) REVERT: A 114 LYS cc_start: 0.7937 (mmtp) cc_final: 0.7431 (mmmt) REVERT: A 210 GLU cc_start: 0.7960 (tt0) cc_final: 0.7705 (tt0) REVERT: A 259 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7475 (mt-10) REVERT: A 313 ARG cc_start: 0.6433 (mmp-170) cc_final: 0.6204 (mmp-170) REVERT: B 153 LEU cc_start: 0.6550 (mm) cc_final: 0.6166 (mm) REVERT: B 169 ASP cc_start: 0.8977 (t70) cc_final: 0.8544 (t0) REVERT: B 210 GLU cc_start: 0.8098 (tt0) cc_final: 0.7853 (tt0) REVERT: C 73 MET cc_start: 0.8173 (mtt) cc_final: 0.7845 (mtm) REVERT: C 93 ARG cc_start: 0.7760 (mmt180) cc_final: 0.7403 (mmt180) REVERT: C 135 ARG cc_start: 0.7175 (mtt90) cc_final: 0.6882 (mtm-85) REVERT: D 154 ARG cc_start: 0.7301 (mtt180) cc_final: 0.7046 (mtm180) REVERT: D 200 LYS cc_start: 0.8208 (mmtt) cc_final: 0.7733 (mtmt) REVERT: D 239 MET cc_start: 0.8099 (mtt) cc_final: 0.7836 (mtt) REVERT: D 266 GLU cc_start: 0.8374 (pm20) cc_final: 0.8131 (mp0) REVERT: E 73 MET cc_start: 0.8114 (mtm) cc_final: 0.7812 (mtm) REVERT: E 84 ILE cc_start: 0.8885 (mm) cc_final: 0.8522 (mt) REVERT: E 169 ASP cc_start: 0.8838 (m-30) cc_final: 0.8589 (m-30) REVERT: E 241 ARG cc_start: 0.7047 (mtt180) cc_final: 0.6570 (mtt-85) REVERT: F 300 ASP cc_start: 0.7717 (m-30) cc_final: 0.7177 (t70) REVERT: F 328 GLU cc_start: 0.6357 (tp30) cc_final: 0.5990 (tp30) REVERT: G 300 ASP cc_start: 0.7300 (OUTLIER) cc_final: 0.6990 (t70) REVERT: H 172 LYS cc_start: 0.8493 (mtpt) cc_final: 0.8285 (ttpt) REVERT: H 203 GLU cc_start: 0.7336 (mm-30) cc_final: 0.6882 (tp30) REVERT: H 218 GLU cc_start: 0.7827 (pt0) cc_final: 0.7535 (pm20) REVERT: H 239 MET cc_start: 0.8644 (mtt) cc_final: 0.8368 (mtt) REVERT: H 250 MET cc_start: 0.8387 (ttm) cc_final: 0.8150 (ttm) outliers start: 36 outliers final: 19 residues processed: 396 average time/residue: 0.1622 time to fit residues: 91.9359 Evaluate side-chains 355 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 335 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 285 ILE Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 300 ASP Chi-restraints excluded: chain H residue 184 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 142 optimal weight: 0.0970 chunk 199 optimal weight: 0.5980 chunk 178 optimal weight: 1.9990 chunk 195 optimal weight: 4.9990 chunk 161 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 100 optimal weight: 0.0470 chunk 78 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.1480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 HIS C 219 GLN E 227 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.137500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.108619 restraints weight = 21491.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.111512 restraints weight = 12975.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.113526 restraints weight = 9240.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.114825 restraints weight = 7326.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.115429 restraints weight = 6311.268| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17067 Z= 0.149 Angle : 0.493 5.226 23073 Z= 0.261 Chirality : 0.046 0.146 2687 Planarity : 0.004 0.053 2993 Dihedral : 7.672 136.430 2441 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.13 % Allowed : 13.69 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.23 (0.17), residues: 2140 helix: -0.98 (0.15), residues: 1004 sheet: -1.62 (0.27), residues: 312 loop : -1.88 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 241 TYR 0.020 0.001 TYR F 333 PHE 0.013 0.001 PHE E 75 TRP 0.007 0.001 TRP C 52 HIS 0.004 0.001 HIS E 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (17067) covalent geometry : angle 0.49346 / 0.26 (23073) hydrogen bonds : bond 0.03492 / 2.34 ( 692) hydrogen bonds : angle 4.64960 / 3.20 ( 1977) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 356 time to evaluate : 0.673 Fit side-chains revert: symmetry clash REVERT: A 28 LEU cc_start: 0.8581 (mm) cc_final: 0.8315 (mm) REVERT: A 114 LYS cc_start: 0.8001 (mmtp) cc_final: 0.7416 (mmmt) REVERT: A 259 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7583 (mt-10) REVERT: A 313 ARG cc_start: 0.6544 (mmp-170) cc_final: 0.6181 (mmp-170) REVERT: B 153 LEU cc_start: 0.6595 (mm) cc_final: 0.6287 (mm) REVERT: B 169 ASP cc_start: 0.8980 (t70) cc_final: 0.8482 (t0) REVERT: B 210 GLU cc_start: 0.8102 (tt0) cc_final: 0.7864 (tt0) REVERT: C 73 MET cc_start: 0.8257 (mtt) cc_final: 0.7923 (mtm) REVERT: C 93 ARG cc_start: 0.7843 (mmt180) cc_final: 0.7479 (mmt180) REVERT: C 135 ARG cc_start: 0.7302 (mtt90) cc_final: 0.7013 (mtm-85) REVERT: D 200 LYS cc_start: 0.8195 (mmtt) cc_final: 0.7777 (mmmm) REVERT: D 266 GLU cc_start: 0.8372 (pm20) cc_final: 0.7662 (mp0) REVERT: E 73 MET cc_start: 0.8240 (mtm) cc_final: 0.7906 (mtm) REVERT: E 84 ILE cc_start: 0.8827 (mm) cc_final: 0.8463 (mt) REVERT: E 169 ASP cc_start: 0.8900 (m-30) cc_final: 0.8670 (m-30) REVERT: E 237 ARG cc_start: 0.7813 (mtt90) cc_final: 0.7586 (mtt90) REVERT: E 241 ARG cc_start: 0.7070 (mtt180) cc_final: 0.6486 (mtt-85) REVERT: F 313 ARG cc_start: 0.7464 (mtt180) cc_final: 0.6926 (mtp85) REVERT: F 328 GLU cc_start: 0.6566 (tp30) cc_final: 0.6155 (tp30) REVERT: G 169 ASP cc_start: 0.8685 (OUTLIER) cc_final: 0.8484 (t70) REVERT: G 248 GLU cc_start: 0.7642 (tt0) cc_final: 0.7260 (tt0) REVERT: G 300 ASP cc_start: 0.7305 (OUTLIER) cc_final: 0.7074 (t70) REVERT: H 172 LYS cc_start: 0.8472 (mtpt) cc_final: 0.8210 (ttpt) REVERT: H 203 GLU cc_start: 0.7330 (mm-30) cc_final: 0.6915 (tp30) REVERT: H 239 MET cc_start: 0.8673 (mtt) cc_final: 0.8431 (mtt) outliers start: 39 outliers final: 30 residues processed: 371 average time/residue: 0.1579 time to fit residues: 84.5871 Evaluate side-chains 363 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 331 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain E residue 46 TRP Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 285 ILE Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 169 ASP Chi-restraints excluded: chain G residue 300 ASP Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain H residue 200 LYS Chi-restraints excluded: chain H residue 245 ASP Chi-restraints excluded: chain H residue 319 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 137 optimal weight: 0.8980 chunk 143 optimal weight: 0.9980 chunk 201 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 123 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.138124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.110874 restraints weight = 21368.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.113780 restraints weight = 12553.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.115078 restraints weight = 9054.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.116450 restraints weight = 6837.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.116604 restraints weight = 6249.400| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17067 Z= 0.123 Angle : 0.474 7.048 23073 Z= 0.249 Chirality : 0.046 0.197 2687 Planarity : 0.003 0.049 2993 Dihedral : 7.305 129.088 2441 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.51 % Allowed : 14.73 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.63 (0.17), residues: 2140 helix: -0.37 (0.16), residues: 1004 sheet: -1.41 (0.28), residues: 308 loop : -1.69 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 176 TYR 0.020 0.001 TYR F 333 PHE 0.011 0.001 PHE E 75 TRP 0.007 0.001 TRP C 52 HIS 0.003 0.001 HIS E 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (17067) covalent geometry : angle 0.47395 / 0.25 (23073) hydrogen bonds : bond 0.03119 / 2.10 ( 692) hydrogen bonds : angle 4.43686 / 3.05 ( 1977) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 352 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: A 28 LEU cc_start: 0.8541 (mm) cc_final: 0.8317 (mm) REVERT: A 114 LYS cc_start: 0.7966 (mmtp) cc_final: 0.7455 (mmmt) REVERT: A 210 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.8043 (tt0) REVERT: B 153 LEU cc_start: 0.6566 (mm) cc_final: 0.6336 (mm) REVERT: B 169 ASP cc_start: 0.8945 (t70) cc_final: 0.8715 (t0) REVERT: B 210 GLU cc_start: 0.8021 (tt0) cc_final: 0.7810 (tt0) REVERT: C 73 MET cc_start: 0.8034 (mtt) cc_final: 0.7775 (mtm) REVERT: C 93 ARG cc_start: 0.7819 (mmt180) cc_final: 0.7447 (mmt180) REVERT: C 313 ARG cc_start: 0.6807 (mmp80) cc_final: 0.6456 (mmp80) REVERT: D 154 ARG cc_start: 0.7178 (mtm180) cc_final: 0.6959 (ttm170) REVERT: D 200 LYS cc_start: 0.8168 (mmtt) cc_final: 0.7756 (mmmm) REVERT: D 266 GLU cc_start: 0.8398 (pm20) cc_final: 0.7842 (mp0) REVERT: E 84 ILE cc_start: 0.8918 (mm) cc_final: 0.8519 (mt) REVERT: E 237 ARG cc_start: 0.7445 (mtt90) cc_final: 0.7217 (mpt-90) REVERT: E 241 ARG cc_start: 0.6800 (mtt180) cc_final: 0.6357 (mtt-85) REVERT: E 250 MET cc_start: 0.8978 (ttm) cc_final: 0.8758 (mtm) REVERT: F 300 ASP cc_start: 0.7616 (m-30) cc_final: 0.7031 (t0) REVERT: F 310 TYR cc_start: 0.7432 (t80) cc_final: 0.7199 (t80) REVERT: F 328 GLU cc_start: 0.6186 (tp30) cc_final: 0.5793 (tp30) REVERT: G 248 GLU cc_start: 0.7639 (tt0) cc_final: 0.7319 (tt0) REVERT: G 300 ASP cc_start: 0.7243 (OUTLIER) cc_final: 0.6954 (t70) REVERT: H 203 GLU cc_start: 0.7155 (mm-30) cc_final: 0.6767 (tp30) REVERT: H 239 MET cc_start: 0.8674 (mtt) cc_final: 0.8441 (mtt) outliers start: 46 outliers final: 33 residues processed: 372 average time/residue: 0.1556 time to fit residues: 83.9482 Evaluate side-chains 368 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 333 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain E residue 46 TRP Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 174 ASN Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain G residue 300 ASP Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain H residue 319 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 72 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 161 optimal weight: 10.0000 chunk 73 optimal weight: 0.5980 chunk 171 optimal weight: 2.9990 chunk 158 optimal weight: 0.7980 chunk 53 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.135204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.107746 restraints weight = 21491.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.111439 restraints weight = 12913.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.112820 restraints weight = 7769.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.113139 restraints weight = 6445.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.113316 restraints weight = 6269.457| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 17067 Z= 0.187 Angle : 0.516 6.428 23073 Z= 0.271 Chirality : 0.047 0.154 2687 Planarity : 0.004 0.050 2993 Dihedral : 7.217 127.549 2441 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.84 % Allowed : 15.55 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.18), residues: 2140 helix: -0.13 (0.16), residues: 1008 sheet: -1.35 (0.28), residues: 308 loop : -1.64 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 154 TYR 0.022 0.001 TYR F 333 PHE 0.018 0.001 PHE G 75 TRP 0.011 0.001 TRP C 52 HIS 0.011 0.001 HIS G 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 (17067) covalent geometry : angle 0.51568 / 0.27 (23073) hydrogen bonds : bond 0.03278 / 2.21 ( 692) hydrogen bonds : angle 4.40148 / 3.04 ( 1977) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 350 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 LEU cc_start: 0.8562 (mm) cc_final: 0.8355 (mm) REVERT: A 114 LYS cc_start: 0.7998 (mmtp) cc_final: 0.7484 (mmmt) REVERT: A 145 ASP cc_start: 0.8041 (m-30) cc_final: 0.7727 (m-30) REVERT: B 153 LEU cc_start: 0.6545 (mm) cc_final: 0.6308 (mm) REVERT: B 169 ASP cc_start: 0.9016 (t70) cc_final: 0.8571 (t0) REVERT: C 301 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.6223 (pm20) REVERT: C 326 GLU cc_start: 0.6878 (mt-10) cc_final: 0.6468 (mt-10) REVERT: D 200 LYS cc_start: 0.8210 (mmtt) cc_final: 0.7836 (mmmm) REVERT: D 215 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8568 (pm20) REVERT: D 266 GLU cc_start: 0.8410 (pm20) cc_final: 0.7846 (mp0) REVERT: D 328 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7859 (mm-30) REVERT: E 84 ILE cc_start: 0.8935 (mm) cc_final: 0.8539 (mt) REVERT: E 241 ARG cc_start: 0.6888 (mtt180) cc_final: 0.6523 (mtt-85) REVERT: E 250 MET cc_start: 0.9034 (ttm) cc_final: 0.8825 (mtm) REVERT: F 241 ARG cc_start: 0.8082 (ttm-80) cc_final: 0.7582 (ttm-80) REVERT: F 300 ASP cc_start: 0.7599 (m-30) cc_final: 0.7020 (t0) REVERT: F 310 TYR cc_start: 0.7270 (t80) cc_final: 0.6940 (t80) REVERT: F 328 GLU cc_start: 0.6149 (tp30) cc_final: 0.5860 (tp30) REVERT: G 44 GLU cc_start: 0.6075 (tp30) cc_final: 0.5861 (tp30) REVERT: G 92 GLU cc_start: 0.8234 (tp30) cc_final: 0.7671 (tp30) REVERT: G 248 GLU cc_start: 0.7655 (tt0) cc_final: 0.7133 (tt0) REVERT: G 300 ASP cc_start: 0.7271 (OUTLIER) cc_final: 0.7062 (t70) REVERT: H 203 GLU cc_start: 0.7151 (mm-30) cc_final: 0.6768 (tp30) REVERT: H 239 MET cc_start: 0.8671 (mtt) cc_final: 0.8444 (mtt) outliers start: 52 outliers final: 40 residues processed: 375 average time/residue: 0.1568 time to fit residues: 85.3223 Evaluate side-chains 370 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 327 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain E residue 46 TRP Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 293 ILE Chi-restraints excluded: chain G residue 300 ASP Chi-restraints excluded: chain H residue 184 ASP Chi-restraints excluded: chain H residue 200 LYS Chi-restraints excluded: chain H residue 319 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 138 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 202 optimal weight: 0.6980 chunk 161 optimal weight: 10.0000 chunk 22 optimal weight: 0.8980 chunk 147 optimal weight: 0.7980 chunk 211 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.136410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.109393 restraints weight = 21354.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.112323 restraints weight = 13442.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.113741 restraints weight = 8668.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.114212 restraints weight = 7003.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.114454 restraints weight = 6728.254| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17067 Z= 0.139 Angle : 0.491 7.962 23073 Z= 0.255 Chirality : 0.046 0.166 2687 Planarity : 0.003 0.048 2993 Dihedral : 7.075 122.862 2441 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.27 % Allowed : 15.82 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.13 (0.18), residues: 2140 helix: 0.11 (0.16), residues: 1020 sheet: -1.23 (0.28), residues: 308 loop : -1.55 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 154 TYR 0.023 0.001 TYR F 333 PHE 0.020 0.001 PHE G 75 TRP 0.009 0.001 TRP C 52 HIS 0.009 0.001 HIS G 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (17067) covalent geometry : angle 0.49146 / 0.26 (23073) hydrogen bonds : bond 0.03037 / 2.05 ( 692) hydrogen bonds : angle 4.30974 / 2.96 ( 1977) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 338 time to evaluate : 0.810 Fit side-chains revert: symmetry clash REVERT: A 114 LYS cc_start: 0.8014 (mmtp) cc_final: 0.7495 (mmmt) REVERT: A 145 ASP cc_start: 0.8016 (m-30) cc_final: 0.7728 (m-30) REVERT: A 210 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7989 (tt0) REVERT: B 169 ASP cc_start: 0.8988 (t70) cc_final: 0.8755 (t0) REVERT: B 215 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8494 (pm20) REVERT: C 73 MET cc_start: 0.8015 (mtt) cc_final: 0.7768 (mtm) REVERT: C 301 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6221 (pm20) REVERT: C 313 ARG cc_start: 0.6841 (mmp80) cc_final: 0.6489 (mmp80) REVERT: D 200 LYS cc_start: 0.8210 (mmtt) cc_final: 0.7844 (mmmm) REVERT: D 266 GLU cc_start: 0.8392 (pm20) cc_final: 0.7855 (mp0) REVERT: D 328 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7841 (mm-30) REVERT: E 84 ILE cc_start: 0.8929 (mm) cc_final: 0.8538 (mt) REVERT: E 241 ARG cc_start: 0.6881 (mtt180) cc_final: 0.6437 (mtt-85) REVERT: F 215 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8229 (pm20) REVERT: F 291 VAL cc_start: 0.8868 (OUTLIER) cc_final: 0.8641 (p) REVERT: F 300 ASP cc_start: 0.7568 (m-30) cc_final: 0.7031 (t0) REVERT: F 310 TYR cc_start: 0.7329 (t80) cc_final: 0.7065 (t80) REVERT: F 328 GLU cc_start: 0.6153 (tp30) cc_final: 0.5789 (tp30) REVERT: G 92 GLU cc_start: 0.8186 (tp30) cc_final: 0.7656 (tp30) REVERT: G 248 GLU cc_start: 0.7626 (tt0) cc_final: 0.7358 (tt0) REVERT: G 276 GLU cc_start: 0.7038 (mm-30) cc_final: 0.6707 (mm-30) REVERT: H 203 GLU cc_start: 0.7112 (mm-30) cc_final: 0.6716 (tp30) REVERT: H 239 MET cc_start: 0.8636 (mtt) cc_final: 0.8412 (mtt) outliers start: 60 outliers final: 45 residues processed: 366 average time/residue: 0.1536 time to fit residues: 82.1091 Evaluate side-chains 372 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 322 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain E residue 46 TRP Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain E residue 313 ARG Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 215 GLU Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 200 LYS Chi-restraints excluded: chain H residue 319 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 96 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 197 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 145 optimal weight: 0.6980 chunk 208 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 200 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.161407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.133268 restraints weight = 20295.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.137572 restraints weight = 10264.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.140005 restraints weight = 6618.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.141765 restraints weight = 5017.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.142628 restraints weight = 4195.369| |-----------------------------------------------------------------------------| r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17067 Z= 0.143 Angle : 0.494 8.662 23073 Z= 0.256 Chirality : 0.046 0.164 2687 Planarity : 0.003 0.048 2993 Dihedral : 6.974 119.880 2441 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.55 % Allowed : 16.04 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.98 (0.18), residues: 2140 helix: 0.22 (0.16), residues: 1026 sheet: -1.18 (0.28), residues: 308 loop : -1.46 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 154 TYR 0.023 0.001 TYR F 333 PHE 0.012 0.001 PHE G 75 TRP 0.007 0.001 TRP C 52 HIS 0.008 0.001 HIS G 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (17067) covalent geometry : angle 0.49403 / 0.26 (23073) hydrogen bonds : bond 0.03011 / 2.03 ( 692) hydrogen bonds : angle 4.27243 / 2.93 ( 1977) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 329 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: A 114 LYS cc_start: 0.8017 (mmtp) cc_final: 0.7448 (mmmt) REVERT: A 145 ASP cc_start: 0.8088 (m-30) cc_final: 0.7789 (m-30) REVERT: A 210 GLU cc_start: 0.8296 (tt0) cc_final: 0.7942 (tt0) REVERT: B 169 ASP cc_start: 0.8972 (t70) cc_final: 0.8654 (t0) REVERT: B 215 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8552 (pm20) REVERT: C 45 SER cc_start: 0.8084 (t) cc_final: 0.7642 (p) REVERT: C 73 MET cc_start: 0.8151 (mtt) cc_final: 0.7869 (mtm) REVERT: C 301 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6185 (pm20) REVERT: C 326 GLU cc_start: 0.6880 (mt-10) cc_final: 0.6500 (mt-10) REVERT: D 200 LYS cc_start: 0.8271 (mmtt) cc_final: 0.7819 (mmmm) REVERT: D 215 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8578 (pm20) REVERT: D 266 GLU cc_start: 0.8384 (pm20) cc_final: 0.7817 (mp0) REVERT: D 328 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7909 (mm-30) REVERT: E 84 ILE cc_start: 0.8811 (mm) cc_final: 0.8440 (mt) REVERT: E 241 ARG cc_start: 0.6914 (mtt180) cc_final: 0.6433 (mtt-85) REVERT: F 215 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8289 (pm20) REVERT: F 291 VAL cc_start: 0.8848 (OUTLIER) cc_final: 0.8622 (p) REVERT: F 300 ASP cc_start: 0.7499 (m-30) cc_final: 0.6965 (t0) REVERT: F 310 TYR cc_start: 0.7250 (t80) cc_final: 0.6978 (t80) REVERT: F 328 GLU cc_start: 0.6250 (tp30) cc_final: 0.5848 (tp30) REVERT: G 92 GLU cc_start: 0.8378 (tp30) cc_final: 0.7674 (tp30) REVERT: G 248 GLU cc_start: 0.7724 (tt0) cc_final: 0.7470 (tt0) REVERT: H 203 GLU cc_start: 0.7216 (mm-30) cc_final: 0.6819 (tp30) REVERT: H 239 MET cc_start: 0.8654 (mtt) cc_final: 0.8440 (mtt) outliers start: 65 outliers final: 48 residues processed: 364 average time/residue: 0.1519 time to fit residues: 80.6250 Evaluate side-chains 367 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 314 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain E residue 46 TRP Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 104 MET Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain E residue 313 ARG Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 215 GLU Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 200 LYS Chi-restraints excluded: chain H residue 319 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 3 optimal weight: 3.9990 chunk 127 optimal weight: 0.7980 chunk 49 optimal weight: 0.0570 chunk 0 optimal weight: 9.9990 chunk 183 optimal weight: 0.7980 chunk 128 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 146 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.160269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.131187 restraints weight = 20540.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.135422 restraints weight = 10515.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.137906 restraints weight = 6873.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.139732 restraints weight = 5272.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.140412 restraints weight = 4401.979| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17067 Z= 0.107 Angle : 0.486 8.659 23073 Z= 0.248 Chirality : 0.046 0.330 2687 Planarity : 0.003 0.042 2993 Dihedral : 6.809 114.703 2441 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.11 % Allowed : 17.08 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.79 (0.18), residues: 2140 helix: 0.36 (0.16), residues: 1034 sheet: -1.10 (0.28), residues: 304 loop : -1.34 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 154 TYR 0.024 0.001 TYR F 333 PHE 0.013 0.001 PHE G 75 TRP 0.007 0.001 TRP G 52 HIS 0.009 0.001 HIS G 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (17067) covalent geometry : angle 0.48619 / 0.25 (23073) hydrogen bonds : bond 0.02857 / 1.94 ( 692) hydrogen bonds : angle 4.22507 / 2.89 ( 1977) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 335 time to evaluate : 0.693 Fit side-chains revert: symmetry clash REVERT: A 114 LYS cc_start: 0.8011 (mmtp) cc_final: 0.7420 (mmmt) REVERT: A 145 ASP cc_start: 0.8079 (m-30) cc_final: 0.7780 (m-30) REVERT: A 210 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7962 (tt0) REVERT: B 169 ASP cc_start: 0.8944 (t70) cc_final: 0.8638 (t0) REVERT: C 45 SER cc_start: 0.8312 (t) cc_final: 0.7939 (p) REVERT: C 73 MET cc_start: 0.8153 (mtt) cc_final: 0.7877 (mtm) REVERT: C 93 ARG cc_start: 0.7430 (mmt180) cc_final: 0.7108 (mmt180) REVERT: C 301 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6200 (pm20) REVERT: C 326 GLU cc_start: 0.6849 (mt-10) cc_final: 0.6472 (mt-10) REVERT: D 200 LYS cc_start: 0.8233 (mmtt) cc_final: 0.7748 (mmmm) REVERT: D 215 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8542 (pm20) REVERT: D 266 GLU cc_start: 0.8383 (pm20) cc_final: 0.7825 (mp0) REVERT: D 298 ARG cc_start: 0.7970 (ttm170) cc_final: 0.7454 (ttt180) REVERT: D 328 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7869 (mm-30) REVERT: E 84 ILE cc_start: 0.8779 (mm) cc_final: 0.8413 (mt) REVERT: E 241 ARG cc_start: 0.6937 (mtt180) cc_final: 0.6476 (mtt-85) REVERT: F 215 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8223 (pm20) REVERT: F 241 ARG cc_start: 0.7960 (ttm-80) cc_final: 0.7636 (ttm-80) REVERT: F 291 VAL cc_start: 0.8827 (OUTLIER) cc_final: 0.8597 (p) REVERT: F 300 ASP cc_start: 0.7470 (m-30) cc_final: 0.6935 (t0) REVERT: F 310 TYR cc_start: 0.7261 (t80) cc_final: 0.7015 (t80) REVERT: G 92 GLU cc_start: 0.8368 (tp30) cc_final: 0.7654 (tp30) REVERT: G 248 GLU cc_start: 0.7770 (tt0) cc_final: 0.7283 (tt0) REVERT: G 274 LYS cc_start: 0.7450 (ptmm) cc_final: 0.7150 (ptpt) REVERT: H 203 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6802 (tp30) outliers start: 57 outliers final: 43 residues processed: 360 average time/residue: 0.1530 time to fit residues: 80.5600 Evaluate side-chains 370 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 322 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain E residue 46 TRP Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain E residue 313 ARG Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 215 GLU Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 293 ILE Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain H residue 145 ASP Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 200 LYS Chi-restraints excluded: chain H residue 319 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 10 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 134 optimal weight: 0.4980 chunk 193 optimal weight: 0.2980 chunk 74 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 180 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 227 GLN ** 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 = 0.3443 r_free = 0.3443 target = 0.138524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.111580 restraints weight = 21195.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.114333 restraints weight = 13518.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.115897 restraints weight = 8641.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.116922 restraints weight = 6921.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.117011 restraints weight = 6413.631| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17067 Z= 0.107 Angle : 0.496 9.322 23073 Z= 0.252 Chirality : 0.046 0.191 2687 Planarity : 0.003 0.044 2993 Dihedral : 6.674 111.065 2441 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.62 % Allowed : 17.84 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.60 (0.18), residues: 2140 helix: 0.55 (0.16), residues: 1024 sheet: -1.03 (0.29), residues: 304 loop : -1.28 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 154 TYR 0.028 0.001 TYR E 333 PHE 0.010 0.001 PHE E 75 TRP 0.006 0.001 TRP C 52 HIS 0.008 0.001 HIS G 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (17067) covalent geometry : angle 0.49600 / 0.25 (23073) hydrogen bonds : bond 0.02823 / 1.91 ( 692) hydrogen bonds : angle 4.16939 / 2.86 ( 1977) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 331 time to evaluate : 0.608 Fit side-chains revert: symmetry clash REVERT: A 114 LYS cc_start: 0.7939 (mmtp) cc_final: 0.7431 (mmmt) REVERT: A 145 ASP cc_start: 0.8011 (m-30) cc_final: 0.7710 (m-30) REVERT: A 210 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7949 (tt0) REVERT: B 169 ASP cc_start: 0.8962 (t70) cc_final: 0.8507 (t0) REVERT: B 254 ASP cc_start: 0.7591 (m-30) cc_final: 0.7355 (m-30) REVERT: C 45 SER cc_start: 0.8161 (t) cc_final: 0.7846 (p) REVERT: C 73 MET cc_start: 0.7965 (mtt) cc_final: 0.7705 (mtm) REVERT: C 93 ARG cc_start: 0.7554 (mmt180) cc_final: 0.7251 (mmt180) REVERT: C 301 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6371 (pm20) REVERT: C 326 GLU cc_start: 0.6843 (mt-10) cc_final: 0.6435 (mt-10) REVERT: D 200 LYS cc_start: 0.8187 (mmtt) cc_final: 0.7774 (mmmm) REVERT: D 215 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8472 (pm20) REVERT: D 266 GLU cc_start: 0.8397 (pm20) cc_final: 0.7912 (mp0) REVERT: D 298 ARG cc_start: 0.8065 (ttm170) cc_final: 0.7647 (ttt180) REVERT: D 328 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7802 (mm-30) REVERT: E 84 ILE cc_start: 0.8905 (mm) cc_final: 0.8527 (mt) REVERT: E 241 ARG cc_start: 0.6869 (mtt180) cc_final: 0.6474 (mtt-85) REVERT: F 215 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8081 (pm20) REVERT: F 291 VAL cc_start: 0.8806 (OUTLIER) cc_final: 0.8574 (p) REVERT: F 300 ASP cc_start: 0.7377 (m-30) cc_final: 0.7035 (t70) REVERT: F 310 TYR cc_start: 0.7265 (t80) cc_final: 0.7026 (t80) REVERT: G 92 GLU cc_start: 0.8152 (tp30) cc_final: 0.7627 (tp30) REVERT: G 248 GLU cc_start: 0.7754 (tt0) cc_final: 0.7278 (tt0) REVERT: G 263 ARG cc_start: 0.8408 (ttp80) cc_final: 0.8201 (ttp80) REVERT: G 274 LYS cc_start: 0.7463 (ptmm) cc_final: 0.7163 (ptpt) REVERT: H 203 GLU cc_start: 0.7071 (mm-30) cc_final: 0.6699 (tp30) outliers start: 48 outliers final: 40 residues processed: 354 average time/residue: 0.1511 time to fit residues: 77.4825 Evaluate side-chains 361 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 316 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain E residue 46 TRP Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 215 GLU Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 293 ILE Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain H residue 145 ASP Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 200 LYS Chi-restraints excluded: chain H residue 319 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 198 optimal weight: 0.8980 chunk 168 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 192 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 125 optimal weight: 0.7980 chunk 146 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 227 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.165059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.136654 restraints weight = 20154.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.140901 restraints weight = 10318.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.143559 restraints weight = 6738.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.144997 restraints weight = 5109.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.145939 restraints weight = 4324.248| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17067 Z= 0.123 Angle : 0.509 8.559 23073 Z= 0.259 Chirality : 0.046 0.178 2687 Planarity : 0.003 0.045 2993 Dihedral : 6.630 108.870 2441 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.56 % Allowed : 18.33 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.58 (0.18), residues: 2140 helix: 0.60 (0.16), residues: 1024 sheet: -0.99 (0.29), residues: 308 loop : -1.33 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 154 TYR 0.025 0.001 TYR E 333 PHE 0.026 0.001 PHE C 75 TRP 0.006 0.001 TRP C 52 HIS 0.009 0.001 HIS G 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (17067) covalent geometry : angle 0.50928 / 0.26 (23073) hydrogen bonds : bond 0.02865 / 1.94 ( 692) hydrogen bonds : angle 4.15599 / 2.84 ( 1977) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 323 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: A 114 LYS cc_start: 0.7950 (mmtp) cc_final: 0.7409 (mmmt) REVERT: A 145 ASP cc_start: 0.8072 (m-30) cc_final: 0.7776 (m-30) REVERT: A 210 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8003 (tt0) REVERT: B 169 ASP cc_start: 0.8945 (t70) cc_final: 0.8454 (t0) REVERT: C 45 SER cc_start: 0.8276 (t) cc_final: 0.7900 (p) REVERT: C 73 MET cc_start: 0.8132 (mtt) cc_final: 0.7845 (mtm) REVERT: C 93 ARG cc_start: 0.7622 (mmt180) cc_final: 0.7241 (mmt180) REVERT: C 301 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.5287 (pm20) REVERT: C 326 GLU cc_start: 0.6852 (mt-10) cc_final: 0.6478 (mt-10) REVERT: D 200 LYS cc_start: 0.8255 (mmtt) cc_final: 0.7758 (mmmm) REVERT: D 215 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8522 (pm20) REVERT: D 247 TYR cc_start: 0.7782 (m-80) cc_final: 0.7399 (m-80) REVERT: D 266 GLU cc_start: 0.8414 (pm20) cc_final: 0.7883 (mp0) REVERT: D 298 ARG cc_start: 0.8093 (ttm170) cc_final: 0.7621 (ttt180) REVERT: D 328 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7875 (mm-30) REVERT: E 84 ILE cc_start: 0.8740 (mm) cc_final: 0.8382 (mt) REVERT: E 241 ARG cc_start: 0.6938 (mtt180) cc_final: 0.6497 (mtt-85) REVERT: F 215 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8160 (pm20) REVERT: F 291 VAL cc_start: 0.8786 (OUTLIER) cc_final: 0.8578 (p) REVERT: F 300 ASP cc_start: 0.7452 (m-30) cc_final: 0.7033 (t70) REVERT: F 310 TYR cc_start: 0.7248 (t80) cc_final: 0.6979 (t80) REVERT: G 92 GLU cc_start: 0.8375 (tp30) cc_final: 0.7690 (tp30) REVERT: G 248 GLU cc_start: 0.7755 (tt0) cc_final: 0.7265 (tt0) REVERT: G 274 LYS cc_start: 0.7444 (ptmm) cc_final: 0.7144 (ptpt) REVERT: H 203 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6808 (tp30) REVERT: H 316 ASP cc_start: 0.7119 (m-30) cc_final: 0.6766 (m-30) outliers start: 47 outliers final: 41 residues processed: 347 average time/residue: 0.1588 time to fit residues: 79.9654 Evaluate side-chains 364 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 318 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 168 SER Chi-restraints excluded: chain B residue 230 SER Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 301 GLU Chi-restraints excluded: chain C residue 318 ILE Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain D residue 215 GLU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain E residue 46 TRP Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 285 ILE Chi-restraints excluded: chain E residue 309 ASP Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 215 GLU Chi-restraints excluded: chain F residue 244 ASP Chi-restraints excluded: chain F residue 291 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 293 ILE Chi-restraints excluded: chain G residue 296 VAL Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain H residue 200 LYS Chi-restraints excluded: chain H residue 319 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 112 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 201 optimal weight: 0.9980 chunk 124 optimal weight: 0.0370 chunk 162 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 186 optimal weight: 5.9990 chunk 138 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 147 optimal weight: 0.4980 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 227 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.138709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.110593 restraints weight = 21192.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.113538 restraints weight = 12682.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.115507 restraints weight = 8921.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.116588 restraints weight = 7105.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.117479 restraints weight = 6170.399| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17067 Z= 0.110 Angle : 0.509 8.397 23073 Z= 0.258 Chirality : 0.046 0.181 2687 Planarity : 0.003 0.045 2993 Dihedral : 6.535 105.428 2441 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.73 % Allowed : 18.28 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.47 (0.18), residues: 2140 helix: 0.74 (0.16), residues: 1016 sheet: -0.95 (0.29), residues: 304 loop : -1.32 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 241 TYR 0.024 0.001 TYR F 333 PHE 0.022 0.001 PHE C 75 TRP 0.006 0.001 TRP C 52 HIS 0.009 0.001 HIS G 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (17067) covalent geometry : angle 0.50881 / 0.26 (23073) hydrogen bonds : bond 0.02788 / 1.89 ( 692) hydrogen bonds : angle 4.11734 / 2.82 ( 1977) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3155.56 seconds wall clock time: 55 minutes 9.60 seconds (3309.60 seconds total)