Starting phenix.real_space_refine on Fri Jul 3 23:47:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5bkk_9407/07_2026/5bkk_9407.cif Found real_map, /net/cci-nas-00/data/ceres_data/5bkk_9407/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/5bkk_9407/07_2026/5bkk_9407.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5bkk_9407/07_2026/5bkk_9407.map" model { file = "/net/cci-nas-00/data/ceres_data/5bkk_9407/07_2026/5bkk_9407.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5bkk_9407/07_2026/5bkk_9407.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/5bkk_9407/07_2026/5bkk_9407.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5bkk_9407/07_2026/5bkk_9407.cif" } 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-6108/lib/python3.11/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: 18 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: 24 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: 4.14, 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: 1.39 Conformation dependent library (CDL) restraints added in 927.2 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: 0.67 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: 2.99 Time building geometry restraints manager: 1.89 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: 10107 32.80 - 65.61: 248 65.61 - 98.41: 29 98.41 - 131.22: 0 131.22 - 164.02: 1 Dihedral angle restraints: 10385 sinusoidal: 4233 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 10382 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: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.920 Find NCS groups from input model: 0.360 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: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 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 : 14.760 164.021 6433 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 : 0.687 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: 0.1699 time to fit residues: 109.0463 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 : 0.575 ------------------------------------------------------------------------------- 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... 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 = 0.138816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.110371 restraints weight = 21253.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.113351 restraints weight = 12872.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.115266 restraints weight = 9088.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.116589 restraints weight = 7231.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.117211 restraints weight = 6204.503| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17067 Z= 0.131 Angle : 0.506 7.550 23073 Z= 0.272 Chirality : 0.046 0.152 2687 Planarity : 0.004 0.061 2993 Dihedral : 7.038 135.206 2435 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.97 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: -1.96 (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 0.006 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 G 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (17067) covalent geometry : angle 0.50606 / 0.27 (23073) hydrogen bonds : bond 0.03837 / 2.55 ( 692) hydrogen bonds : angle 5.11027 / 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 416 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 380 time to evaluate : 0.687 Fit side-chains REVERT: A 28 LEU cc_start: 0.8602 (mm) cc_final: 0.8359 (mm) REVERT: A 114 LYS cc_start: 0.7940 (mmtp) cc_final: 0.7432 (mmmt) REVERT: A 210 GLU cc_start: 0.7960 (tt0) cc_final: 0.7702 (tt0) REVERT: A 259 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7474 (mt-10) REVERT: A 313 ARG cc_start: 0.6435 (mmp-170) cc_final: 0.6203 (mmp-170) REVERT: B 153 LEU cc_start: 0.6547 (mm) cc_final: 0.6164 (mm) REVERT: B 169 ASP cc_start: 0.8974 (t70) cc_final: 0.8548 (t0) REVERT: B 210 GLU cc_start: 0.8098 (tt0) cc_final: 0.7853 (tt0) REVERT: C 73 MET cc_start: 0.8171 (mtt) cc_final: 0.7842 (mtm) REVERT: C 93 ARG cc_start: 0.7761 (mmt180) cc_final: 0.7402 (mmt180) REVERT: C 135 ARG cc_start: 0.7180 (mtt90) cc_final: 0.6885 (mtm-85) REVERT: D 154 ARG cc_start: 0.7299 (mtt180) cc_final: 0.7047 (mtm180) REVERT: D 200 LYS cc_start: 0.8207 (mmtt) cc_final: 0.7731 (mtmt) REVERT: D 239 MET cc_start: 0.8098 (mtt) cc_final: 0.7834 (mtt) REVERT: D 266 GLU cc_start: 0.8374 (pm20) cc_final: 0.8132 (mp0) REVERT: E 73 MET cc_start: 0.8147 (mtm) cc_final: 0.7820 (mtm) REVERT: E 84 ILE cc_start: 0.8883 (mm) cc_final: 0.8520 (mt) REVERT: E 169 ASP cc_start: 0.8835 (m-30) cc_final: 0.8584 (m-30) REVERT: E 241 ARG cc_start: 0.7044 (mtt180) cc_final: 0.6568 (mtt-85) REVERT: F 300 ASP cc_start: 0.7720 (m-30) cc_final: 0.7179 (t70) REVERT: F 328 GLU cc_start: 0.6349 (tp30) cc_final: 0.5982 (tp30) REVERT: G 300 ASP cc_start: 0.7302 (OUTLIER) cc_final: 0.6994 (t70) REVERT: H 172 LYS cc_start: 0.8495 (mtpt) cc_final: 0.8285 (ttpt) REVERT: H 203 GLU cc_start: 0.7336 (mm-30) cc_final: 0.6883 (tp30) REVERT: H 218 GLU cc_start: 0.7824 (pt0) cc_final: 0.7529 (pm20) REVERT: H 239 MET cc_start: 0.8645 (mtt) cc_final: 0.8367 (mtt) REVERT: H 250 MET cc_start: 0.8388 (ttm) cc_final: 0.8155 (ttm) outliers start: 36 outliers final: 19 residues processed: 394 average time/residue: 0.1573 time to fit residues: 89.2882 Evaluate side-chains 357 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 337 time to evaluate : 0.648 ------------------------------------------------------------------------------- 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: 0.5980 chunk 199 optimal weight: 0.6980 chunk 178 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 100 optimal weight: 0.8980 chunk 78 optimal weight: 0.0060 chunk 128 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 219 GLN E 227 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.139313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.110491 restraints weight = 21376.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.113490 restraints weight = 12810.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.115484 restraints weight = 9097.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.116700 restraints weight = 7211.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.117569 restraints weight = 6219.611| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17067 Z= 0.108 Angle : 0.471 5.087 23073 Z= 0.248 Chirality : 0.045 0.146 2687 Planarity : 0.003 0.052 2993 Dihedral : 6.672 130.258 2435 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.80 % Allowed : 13.48 % Favored : 84.72 % 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: -2.14 (0.17), residues: 2140 helix: -0.91 (0.15), residues: 1004 sheet: -1.53 (0.27), residues: 308 loop : -1.85 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 241 TYR 0.019 0.001 TYR F 333 PHE 0.014 0.001 PHE E 75 TRP 0.006 0.001 TRP C 52 HIS 0.005 0.001 HIS E 286 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (17067) covalent geometry : angle 0.47122 / 0.25 (23073) hydrogen bonds : bond 0.03336 / 2.24 ( 692) hydrogen bonds : angle 4.58426 / 3.15 ( 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 403 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 370 time to evaluate : 0.591 Fit side-chains revert: symmetry clash REVERT: A 28 LEU cc_start: 0.8589 (mm) cc_final: 0.8328 (mm) REVERT: A 114 LYS cc_start: 0.7942 (mmtp) cc_final: 0.7385 (mmmt) REVERT: A 151 LYS cc_start: 0.8832 (mttp) cc_final: 0.8416 (mtpt) REVERT: B 153 LEU cc_start: 0.6663 (mm) cc_final: 0.6324 (mm) REVERT: B 169 ASP cc_start: 0.8954 (t70) cc_final: 0.8495 (t0) REVERT: B 210 GLU cc_start: 0.8058 (tt0) cc_final: 0.7713 (tt0) REVERT: C 73 MET cc_start: 0.8233 (mtt) cc_final: 0.7913 (mtm) REVERT: C 93 ARG cc_start: 0.7829 (mmt180) cc_final: 0.7479 (mmt180) REVERT: C 135 ARG cc_start: 0.7215 (mtt90) cc_final: 0.6955 (mtm-85) REVERT: D 200 LYS cc_start: 0.8187 (mmtt) cc_final: 0.7728 (mmmm) REVERT: D 266 GLU cc_start: 0.8349 (pm20) cc_final: 0.7685 (mp0) REVERT: E 73 MET cc_start: 0.8232 (mtm) cc_final: 0.7942 (mtm) REVERT: E 84 ILE cc_start: 0.8803 (mm) cc_final: 0.8422 (mt) REVERT: E 169 ASP cc_start: 0.8873 (m-30) cc_final: 0.8664 (m-30) REVERT: E 241 ARG cc_start: 0.7054 (mtt180) cc_final: 0.6470 (mtt-85) REVERT: F 298 ARG cc_start: 0.7770 (ttm110) cc_final: 0.7475 (ptp-170) REVERT: F 313 ARG cc_start: 0.7434 (mtt180) cc_final: 0.6679 (mtt180) REVERT: F 328 GLU cc_start: 0.6502 (tp30) cc_final: 0.6103 (tp30) REVERT: G 44 GLU cc_start: 0.6408 (tp30) cc_final: 0.6120 (tp30) REVERT: G 73 MET cc_start: 0.7833 (mtm) cc_final: 0.7457 (ttm) REVERT: G 248 GLU cc_start: 0.7698 (tt0) cc_final: 0.7281 (tt0) REVERT: G 300 ASP cc_start: 0.7251 (OUTLIER) cc_final: 0.6992 (t70) REVERT: H 172 LYS cc_start: 0.8466 (mtpt) cc_final: 0.8179 (ttpt) REVERT: H 203 GLU cc_start: 0.7303 (mm-30) cc_final: 0.6887 (tp30) REVERT: H 239 MET cc_start: 0.8691 (mtt) cc_final: 0.8474 (mtt) REVERT: H 250 MET cc_start: 0.8314 (ttm) cc_final: 0.8106 (ttm) outliers start: 33 outliers final: 24 residues processed: 380 average time/residue: 0.1549 time to fit residues: 85.8359 Evaluate side-chains 359 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 334 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU 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 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 208 ILE 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 175 VAL 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 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: 0.6980 chunk 143 optimal weight: 0.9980 chunk 201 optimal weight: 2.9990 chunk 8 optimal weight: 0.3980 chunk 31 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 114 optimal weight: 6.9990 chunk 123 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 46 optimal weight: 0.2980 chunk 79 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.139824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.112776 restraints weight = 21268.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.116446 restraints weight = 12510.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.117597 restraints weight = 7548.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.118433 restraints weight = 6404.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.118502 restraints weight = 6044.852| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17067 Z= 0.098 Angle : 0.459 7.103 23073 Z= 0.241 Chirality : 0.045 0.159 2687 Planarity : 0.003 0.048 2993 Dihedral : 6.282 127.425 2435 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.24 % Allowed : 14.51 % Favored : 83.25 % 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: -1.51 (0.17), residues: 2140 helix: -0.27 (0.16), residues: 1008 sheet: -1.29 (0.28), residues: 308 loop : -1.67 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 154 TYR 0.020 0.001 TYR F 333 PHE 0.011 0.001 PHE E 75 TRP 0.010 0.001 TRP C 52 HIS 0.011 0.001 HIS G 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (17067) covalent geometry : angle 0.45929 / 0.24 (23073) hydrogen bonds : bond 0.02971 / 2.00 ( 692) hydrogen bonds : angle 4.35879 / 2.98 ( 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 395 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 354 time to evaluate : 0.685 Fit side-chains revert: symmetry clash REVERT: A 28 LEU cc_start: 0.8523 (mm) cc_final: 0.8298 (mm) REVERT: A 114 LYS cc_start: 0.7934 (mmtp) cc_final: 0.7415 (mmmt) REVERT: A 151 LYS cc_start: 0.8879 (mttp) cc_final: 0.8516 (mtpt) REVERT: B 153 LEU cc_start: 0.6593 (mm) cc_final: 0.6370 (mm) REVERT: B 210 GLU cc_start: 0.7962 (tt0) cc_final: 0.7733 (tt0) REVERT: C 73 MET cc_start: 0.8018 (mtt) cc_final: 0.7731 (mtm) REVERT: C 93 ARG cc_start: 0.7769 (mmt180) cc_final: 0.7402 (mmt180) REVERT: D 200 LYS cc_start: 0.8158 (mmtt) cc_final: 0.7741 (mmmm) REVERT: D 266 GLU cc_start: 0.8357 (pm20) cc_final: 0.7836 (mp0) REVERT: E 73 MET cc_start: 0.8165 (mtm) cc_final: 0.7924 (mtm) REVERT: E 82 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8688 (mp) REVERT: E 84 ILE cc_start: 0.8895 (mm) cc_final: 0.8471 (mt) REVERT: E 169 ASP cc_start: 0.8748 (m-30) cc_final: 0.8487 (m-30) REVERT: E 241 ARG cc_start: 0.6784 (mtt180) cc_final: 0.6348 (mtt-85) REVERT: E 250 MET cc_start: 0.8956 (ttm) cc_final: 0.8750 (mtm) REVERT: F 300 ASP cc_start: 0.7555 (m-30) cc_final: 0.6984 (t0) REVERT: F 313 ARG cc_start: 0.7250 (mtt180) cc_final: 0.6995 (mtp85) REVERT: F 328 GLU cc_start: 0.6207 (tp30) cc_final: 0.5850 (tp30) REVERT: G 73 MET cc_start: 0.7918 (mtm) cc_final: 0.7580 (ttm) REVERT: G 92 GLU cc_start: 0.8117 (tp30) cc_final: 0.7732 (tp30) REVERT: G 248 GLU cc_start: 0.7603 (tt0) cc_final: 0.7275 (tt0) REVERT: G 263 ARG cc_start: 0.8326 (ttp80) cc_final: 0.8039 (ttp80) REVERT: G 300 ASP cc_start: 0.7148 (OUTLIER) cc_final: 0.6906 (t0) REVERT: H 203 GLU cc_start: 0.7118 (mm-30) cc_final: 0.6730 (tp30) outliers start: 41 outliers final: 26 residues processed: 367 average time/residue: 0.1517 time to fit residues: 81.6501 Evaluate side-chains 356 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 328 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU 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 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 82 LEU 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: 4.9990 chunk 96 optimal weight: 2.9990 chunk 161 optimal weight: 7.9990 chunk 73 optimal weight: 0.3980 chunk 171 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 43 optimal weight: 5.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 253 GLN C 39 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.161952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.133390 restraints weight = 20340.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.137641 restraints weight = 10430.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.140271 restraints weight = 6807.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.141662 restraints weight = 5172.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.142735 restraints weight = 4387.813| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17067 Z= 0.186 Angle : 0.520 6.409 23073 Z= 0.272 Chirality : 0.047 0.170 2687 Planarity : 0.004 0.048 2993 Dihedral : 6.365 130.003 2435 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.84 % Allowed : 15.66 % Favored : 81.51 % 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: -1.33 (0.18), residues: 2140 helix: -0.11 (0.16), residues: 1020 sheet: -1.32 (0.28), residues: 316 loop : -1.56 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 298 TYR 0.022 0.001 TYR F 333 PHE 0.018 0.001 PHE G 75 TRP 0.009 0.001 TRP C 52 HIS 0.007 0.001 HIS A 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.19 (17067) covalent geometry : angle 0.52023 / 0.27 (23073) hydrogen bonds : bond 0.03257 / 2.20 ( 692) hydrogen bonds : angle 4.35519 / 3.00 ( 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 396 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 344 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 LEU cc_start: 0.8590 (mm) cc_final: 0.8371 (mm) REVERT: A 114 LYS cc_start: 0.7992 (mmtp) cc_final: 0.7440 (mmmt) REVERT: A 145 ASP cc_start: 0.8098 (m-30) cc_final: 0.7801 (m-30) REVERT: B 153 LEU cc_start: 0.6649 (mm) cc_final: 0.6432 (mm) REVERT: B 169 ASP cc_start: 0.8985 (t70) cc_final: 0.8445 (t0) REVERT: C 73 MET cc_start: 0.8248 (mtt) cc_final: 0.7958 (mtm) REVERT: C 301 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6138 (pm20) REVERT: C 326 GLU cc_start: 0.6857 (mt-10) cc_final: 0.6431 (mt-10) REVERT: D 200 LYS cc_start: 0.8263 (mmtt) cc_final: 0.7819 (mmmm) REVERT: D 266 GLU cc_start: 0.8442 (pm20) cc_final: 0.7898 (mp0) REVERT: D 328 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7905 (mm-30) REVERT: E 73 MET cc_start: 0.8443 (mtm) cc_final: 0.8065 (mtm) REVERT: E 84 ILE cc_start: 0.8793 (mm) cc_final: 0.8424 (mt) REVERT: E 241 ARG cc_start: 0.6942 (mtt180) cc_final: 0.6418 (mtt-85) REVERT: F 310 TYR cc_start: 0.7369 (t80) cc_final: 0.7055 (t80) REVERT: F 328 GLU cc_start: 0.6233 (tp30) cc_final: 0.5847 (tp30) REVERT: G 92 GLU cc_start: 0.8387 (tp30) cc_final: 0.7692 (tp30) REVERT: G 248 GLU cc_start: 0.7662 (tt0) cc_final: 0.7155 (tt0) REVERT: G 300 ASP cc_start: 0.7322 (OUTLIER) cc_final: 0.7021 (t70) REVERT: H 203 GLU cc_start: 0.7256 (mm-30) cc_final: 0.6869 (tp30) outliers start: 52 outliers final: 41 residues processed: 370 average time/residue: 0.1509 time to fit residues: 82.2266 Evaluate side-chains 367 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 324 time to evaluate : 0.610 ------------------------------------------------------------------------------- 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 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 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 57 ILE Chi-restraints excluded: chain C residue 95 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 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 82 LEU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 285 ILE Chi-restraints excluded: chain E residue 289 THR 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 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 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: 0.8980 chunk 59 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 202 optimal weight: 1.9990 chunk 161 optimal weight: 7.9990 chunk 22 optimal weight: 0.2980 chunk 147 optimal weight: 0.6980 chunk 211 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.137365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.109286 restraints weight = 21265.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.112189 restraints weight = 12725.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.114146 restraints weight = 9020.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.115330 restraints weight = 7132.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.116246 restraints weight = 6153.936| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17067 Z= 0.131 Angle : 0.479 6.131 23073 Z= 0.250 Chirality : 0.046 0.152 2687 Planarity : 0.003 0.047 2993 Dihedral : 6.241 125.368 2435 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.78 % Allowed : 16.42 % Favored : 80.80 % 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: -1.02 (0.18), residues: 2140 helix: 0.16 (0.16), residues: 1024 sheet: -1.16 (0.28), residues: 308 loop : -1.46 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 154 TYR 0.022 0.001 TYR F 333 PHE 0.019 0.001 PHE G 75 TRP 0.008 0.001 TRP C 52 HIS 0.008 0.001 HIS G 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (17067) covalent geometry : angle 0.47903 / 0.25 (23073) hydrogen bonds : bond 0.02991 / 2.03 ( 692) hydrogen bonds : angle 4.26869 / 2.93 ( 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 389 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 338 time to evaluate : 0.674 Fit side-chains revert: symmetry clash REVERT: A 28 LEU cc_start: 0.8559 (mm) cc_final: 0.8350 (mm) REVERT: A 114 LYS cc_start: 0.7996 (mmtp) cc_final: 0.7473 (mmmt) REVERT: A 145 ASP cc_start: 0.8035 (m-30) cc_final: 0.7741 (m-30) REVERT: B 169 ASP cc_start: 0.8935 (t70) cc_final: 0.8484 (t0) REVERT: C 73 MET cc_start: 0.8034 (mtt) cc_final: 0.7780 (mtm) REVERT: C 301 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6183 (pm20) REVERT: C 326 GLU cc_start: 0.6818 (mt-10) cc_final: 0.6371 (mt-10) REVERT: D 200 LYS cc_start: 0.8219 (mmtt) cc_final: 0.7840 (mmmm) REVERT: D 215 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8525 (pm20) REVERT: D 266 GLU cc_start: 0.8401 (pm20) cc_final: 0.7896 (mp0) REVERT: D 328 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7831 (mm-30) REVERT: E 73 MET cc_start: 0.8366 (mtm) cc_final: 0.8031 (mtm) REVERT: E 84 ILE cc_start: 0.8904 (mm) cc_final: 0.8512 (mt) REVERT: E 241 ARG cc_start: 0.6879 (mtt180) cc_final: 0.6425 (mtt-85) REVERT: F 291 VAL cc_start: 0.8837 (OUTLIER) cc_final: 0.8591 (p) REVERT: F 300 ASP cc_start: 0.7625 (m-30) cc_final: 0.7054 (t0) REVERT: F 310 TYR cc_start: 0.7319 (t80) cc_final: 0.6988 (t80) REVERT: F 328 GLU cc_start: 0.6099 (tp30) cc_final: 0.5697 (tp30) REVERT: G 92 GLU cc_start: 0.8214 (tp30) cc_final: 0.7680 (tp30) REVERT: G 248 GLU cc_start: 0.7624 (tt0) cc_final: 0.7320 (tt0) REVERT: G 274 LYS cc_start: 0.7531 (ptmm) cc_final: 0.7152 (ptpt) REVERT: H 184 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7989 (p0) REVERT: H 203 GLU cc_start: 0.7133 (mm-30) cc_final: 0.6747 (tp30) outliers start: 51 outliers final: 39 residues processed: 360 average time/residue: 0.1519 time to fit residues: 80.3763 Evaluate side-chains 362 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 319 time to evaluate : 0.687 ------------------------------------------------------------------------------- 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 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 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 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 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 303 ILE Chi-restraints excluded: chain E residue 46 TRP Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 82 LEU 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 F residue 167 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 293 ILE Chi-restraints excluded: chain G residue 296 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 96 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 197 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 145 optimal weight: 0.7980 chunk 208 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 200 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.134824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.107490 restraints weight = 21460.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.110235 restraints weight = 13488.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.111909 restraints weight = 8632.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.112418 restraints weight = 6827.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.112480 restraints weight = 6507.184| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 17067 Z= 0.201 Angle : 0.529 8.285 23073 Z= 0.275 Chirality : 0.048 0.157 2687 Planarity : 0.004 0.047 2993 Dihedral : 6.383 127.340 2435 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.44 % Allowed : 16.26 % Favored : 80.31 % 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: -1.04 (0.18), residues: 2140 helix: 0.16 (0.16), residues: 1024 sheet: -1.19 (0.28), residues: 308 loop : -1.48 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 154 TYR 0.024 0.001 TYR F 333 PHE 0.012 0.001 PHE G 75 TRP 0.006 0.001 TRP A 46 HIS 0.008 0.001 HIS G 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.20 (17067) covalent geometry : angle 0.52930 / 0.28 (23073) hydrogen bonds : bond 0.03257 / 2.20 ( 692) hydrogen bonds : angle 4.33655 / 2.98 ( 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 400 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 337 time to evaluate : 0.685 Fit side-chains REVERT: A 114 LYS cc_start: 0.8009 (mmtp) cc_final: 0.7483 (mmmt) REVERT: B 169 ASP cc_start: 0.8980 (t70) cc_final: 0.8454 (t0) REVERT: B 215 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8595 (pm20) REVERT: C 301 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6249 (pm20) REVERT: C 326 GLU cc_start: 0.6881 (mt-10) cc_final: 0.6482 (mt-10) REVERT: D 200 LYS cc_start: 0.8238 (mmtt) cc_final: 0.7886 (mmmm) REVERT: D 215 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8595 (pm20) REVERT: D 266 GLU cc_start: 0.8420 (pm20) cc_final: 0.7889 (mp0) REVERT: D 328 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7870 (mm-30) REVERT: E 73 MET cc_start: 0.8416 (mtm) cc_final: 0.8096 (mtm) REVERT: E 82 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8674 (mp) REVERT: E 84 ILE cc_start: 0.8895 (mm) cc_final: 0.8534 (mt) REVERT: E 241 ARG cc_start: 0.6892 (mtt180) cc_final: 0.6424 (mtt-85) REVERT: F 215 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8263 (pm20) REVERT: F 241 ARG cc_start: 0.8005 (ttm-80) cc_final: 0.7600 (ttm-80) REVERT: F 291 VAL cc_start: 0.8858 (OUTLIER) cc_final: 0.8628 (p) REVERT: F 300 ASP cc_start: 0.7613 (m-30) cc_final: 0.7045 (t0) REVERT: F 310 TYR cc_start: 0.7219 (t80) cc_final: 0.6870 (t80) REVERT: F 328 GLU cc_start: 0.6246 (tp30) cc_final: 0.5861 (tp30) REVERT: G 92 GLU cc_start: 0.8271 (tp30) cc_final: 0.7646 (tp30) REVERT: G 274 LYS cc_start: 0.7537 (ptmm) cc_final: 0.7117 (ptpt) REVERT: H 203 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6788 (tp30) outliers start: 63 outliers final: 48 residues processed: 372 average time/residue: 0.1536 time to fit residues: 83.6627 Evaluate side-chains 378 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 324 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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 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 303 ILE 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 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 215 GLU Chi-restraints excluded: chain D residue 278 VAL 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 82 LEU 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 285 ILE 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 3 optimal weight: 2.9990 chunk 127 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 183 optimal weight: 0.7980 chunk 128 optimal weight: 0.9980 chunk 2 optimal weight: 7.9990 chunk 146 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 131 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.158590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.130219 restraints weight = 20441.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.134312 restraints weight = 10409.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.136852 restraints weight = 6778.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.138252 restraints weight = 5152.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.139236 restraints weight = 4364.111| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 17067 Z= 0.117 Angle : 0.489 8.323 23073 Z= 0.252 Chirality : 0.046 0.165 2687 Planarity : 0.003 0.043 2993 Dihedral : 6.186 121.413 2435 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.11 % Allowed : 17.13 % Favored : 79.76 % 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: -0.78 (0.18), residues: 2140 helix: 0.37 (0.16), residues: 1034 sheet: -1.12 (0.28), residues: 304 loop : -1.33 (0.22), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 154 TYR 0.024 0.001 TYR F 333 PHE 0.012 0.001 PHE G 75 TRP 0.007 0.001 TRP G 52 HIS 0.008 0.001 HIS G 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (17067) covalent geometry : angle 0.48941 / 0.25 (23073) hydrogen bonds : bond 0.02919 / 1.98 ( 692) hydrogen bonds : angle 4.25188 / 2.91 ( 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 385 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 328 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: A 114 LYS cc_start: 0.8026 (mmtp) cc_final: 0.7454 (mmmt) REVERT: B 169 ASP cc_start: 0.8989 (t70) cc_final: 0.8660 (t0) REVERT: C 45 SER cc_start: 0.8067 (t) cc_final: 0.7659 (p) REVERT: C 73 MET cc_start: 0.8137 (mtt) cc_final: 0.7860 (mtm) REVERT: C 93 ARG cc_start: 0.7458 (mmt180) cc_final: 0.7125 (mmt180) REVERT: C 301 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6203 (pm20) REVERT: C 326 GLU cc_start: 0.6859 (mt-10) cc_final: 0.6464 (mt-10) REVERT: D 200 LYS cc_start: 0.8266 (mmtt) cc_final: 0.7824 (mmmm) REVERT: D 215 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8570 (pm20) REVERT: D 266 GLU cc_start: 0.8382 (pm20) cc_final: 0.7826 (mp0) REVERT: D 328 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7896 (mm-30) REVERT: E 73 MET cc_start: 0.8423 (mtm) cc_final: 0.8089 (mtm) REVERT: E 84 ILE cc_start: 0.8763 (mm) cc_final: 0.8412 (mt) REVERT: E 241 ARG cc_start: 0.6918 (mtt180) cc_final: 0.6409 (mtt-85) REVERT: F 215 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8241 (pm20) REVERT: F 291 VAL cc_start: 0.8809 (OUTLIER) cc_final: 0.8599 (p) REVERT: F 300 ASP cc_start: 0.7479 (m-30) cc_final: 0.6961 (t0) REVERT: F 310 TYR cc_start: 0.7230 (t80) cc_final: 0.6870 (t80) REVERT: F 328 GLU cc_start: 0.6246 (tp30) cc_final: 0.5812 (tp30) REVERT: G 92 GLU cc_start: 0.8351 (tp30) cc_final: 0.7680 (tp30) REVERT: G 274 LYS cc_start: 0.7577 (ptmm) cc_final: 0.7182 (ptpt) REVERT: H 203 GLU cc_start: 0.7199 (mm-30) cc_final: 0.6802 (tp30) outliers start: 57 outliers final: 42 residues processed: 354 average time/residue: 0.1509 time to fit residues: 78.4727 Evaluate side-chains 365 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 319 time to evaluate : 0.654 ------------------------------------------------------------------------------- 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 260 SER 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 126 SER Chi-restraints excluded: chain B residue 168 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 175 VAL Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 208 ILE 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 303 ILE Chi-restraints excluded: chain E residue 46 TRP Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 208 ILE 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 245 ASP 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: 0.6980 chunk 12 optimal weight: 0.6980 chunk 150 optimal weight: 0.3980 chunk 134 optimal weight: 1.9990 chunk 193 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 24 optimal weight: 0.0000 chunk 32 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 180 optimal weight: 0.5980 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.160444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.132120 restraints weight = 20270.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.136309 restraints weight = 10375.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.138700 restraints weight = 6719.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.140322 restraints weight = 5115.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.141373 restraints weight = 4291.338| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2757 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= 0.099 Angle : 0.491 9.510 23073 Z= 0.250 Chirality : 0.046 0.308 2687 Planarity : 0.003 0.042 2993 Dihedral : 5.984 115.987 2435 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.45 % Allowed : 17.95 % Favored : 79.60 % 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: -0.56 (0.18), residues: 2140 helix: 0.56 (0.16), residues: 1032 sheet: -0.99 (0.29), residues: 304 loop : -1.24 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 154 TYR 0.024 0.001 TYR F 333 PHE 0.010 0.001 PHE G 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 0.00223 / 0.10 (17067) covalent geometry : angle 0.49067 / 0.25 (23073) hydrogen bonds : bond 0.02790 / 1.89 ( 692) hydrogen bonds : angle 4.15874 / 2.83 ( 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 385 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 340 time to evaluate : 0.688 Fit side-chains revert: symmetry clash REVERT: A 114 LYS cc_start: 0.7975 (mmtp) cc_final: 0.7417 (mmmt) REVERT: A 145 ASP cc_start: 0.8074 (m-30) cc_final: 0.7772 (m-30) REVERT: B 169 ASP cc_start: 0.8977 (t70) cc_final: 0.8590 (t0) REVERT: C 45 SER cc_start: 0.8303 (t) cc_final: 0.7928 (p) REVERT: C 73 MET cc_start: 0.8121 (mtt) cc_final: 0.7816 (mtm) REVERT: C 93 ARG cc_start: 0.7545 (mmt180) cc_final: 0.7200 (mmt180) REVERT: C 210 GLU cc_start: 0.8080 (tt0) cc_final: 0.7757 (tt0) REVERT: C 301 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6167 (pm20) REVERT: C 326 GLU cc_start: 0.6843 (mt-10) cc_final: 0.6445 (mt-10) REVERT: D 154 ARG cc_start: 0.7215 (mtm180) cc_final: 0.6769 (ttp-110) REVERT: D 200 LYS cc_start: 0.8236 (mmtt) cc_final: 0.7742 (mmmm) REVERT: D 266 GLU cc_start: 0.8381 (pm20) cc_final: 0.7836 (mp0) REVERT: D 328 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7854 (mm-30) REVERT: E 73 MET cc_start: 0.8408 (mtm) cc_final: 0.8076 (mtm) REVERT: E 82 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8625 (tp) REVERT: E 84 ILE cc_start: 0.8781 (mm) cc_final: 0.8411 (mt) REVERT: E 241 ARG cc_start: 0.6919 (mtt180) cc_final: 0.6414 (mtt-85) REVERT: F 215 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8178 (pm20) REVERT: F 241 ARG cc_start: 0.7847 (ttm-80) cc_final: 0.7495 (ttm-80) REVERT: F 291 VAL cc_start: 0.8802 (OUTLIER) cc_final: 0.8598 (p) REVERT: F 300 ASP cc_start: 0.7453 (m-30) cc_final: 0.7035 (t70) REVERT: F 310 TYR cc_start: 0.7254 (t80) cc_final: 0.6932 (t80) REVERT: G 44 GLU cc_start: 0.6080 (tp30) cc_final: 0.5820 (tp30) REVERT: G 73 MET cc_start: 0.7598 (mtm) cc_final: 0.7135 (ttm) REVERT: G 92 GLU cc_start: 0.8357 (tp30) cc_final: 0.7682 (tp30) REVERT: G 263 ARG cc_start: 0.8417 (ttp80) cc_final: 0.8157 (ttp80) REVERT: H 203 GLU cc_start: 0.7154 (mm-30) cc_final: 0.6763 (tp30) REVERT: H 316 ASP cc_start: 0.7176 (m-30) cc_final: 0.6862 (m-30) outliers start: 45 outliers final: 37 residues processed: 362 average time/residue: 0.1540 time to fit residues: 81.5845 Evaluate side-chains 363 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 322 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 THR 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 293 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 175 VAL Chi-restraints excluded: chain C residue 189 SER 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 82 LEU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 208 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 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: 2.9990 chunk 16 optimal weight: 0.0870 chunk 192 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 146 optimal weight: 0.9980 chunk 112 optimal weight: 0.0060 chunk 71 optimal weight: 0.1980 chunk 90 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 overall best weight: 0.3974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.163031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.134025 restraints weight = 20292.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.138235 restraints weight = 10439.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.140895 restraints weight = 6844.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.142404 restraints weight = 5196.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.143417 restraints weight = 4388.885| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 17067 Z= 0.096 Angle : 0.501 10.611 23073 Z= 0.254 Chirality : 0.046 0.242 2687 Planarity : 0.003 0.042 2993 Dihedral : 5.850 110.577 2435 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.40 % Allowed : 18.71 % Favored : 78.89 % 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: -0.37 (0.18), residues: 2140 helix: 0.77 (0.16), residues: 1024 sheet: -0.91 (0.29), residues: 304 loop : -1.21 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 154 TYR 0.026 0.001 TYR E 333 PHE 0.024 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 0.00215 / 0.10 (17067) covalent geometry : angle 0.50115 / 0.25 (23073) hydrogen bonds : bond 0.02723 / 1.85 ( 692) hydrogen bonds : angle 4.13705 / 2.81 ( 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 374 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 330 time to evaluate : 0.683 Fit side-chains revert: symmetry clash REVERT: A 114 LYS cc_start: 0.7960 (mmtp) cc_final: 0.7372 (mmmt) REVERT: A 145 ASP cc_start: 0.8073 (m-30) cc_final: 0.7774 (m-30) REVERT: B 169 ASP cc_start: 0.8938 (t70) cc_final: 0.8418 (t0) REVERT: C 45 SER cc_start: 0.8312 (t) cc_final: 0.7922 (p) REVERT: C 73 MET cc_start: 0.8228 (mtt) cc_final: 0.7900 (mtm) REVERT: C 93 ARG cc_start: 0.7612 (mmt180) cc_final: 0.7240 (mmt180) REVERT: C 210 GLU cc_start: 0.8093 (tt0) cc_final: 0.7800 (tt0) REVERT: C 301 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6255 (pm20) REVERT: D 154 ARG cc_start: 0.7162 (mtm180) cc_final: 0.6583 (ttp-110) REVERT: D 200 LYS cc_start: 0.8234 (mmtt) cc_final: 0.7736 (mmmm) REVERT: D 215 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8421 (pm20) REVERT: D 266 GLU cc_start: 0.8388 (pm20) cc_final: 0.7856 (mp0) REVERT: D 328 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7932 (mm-30) REVERT: E 73 MET cc_start: 0.8426 (mtm) cc_final: 0.8093 (mtm) REVERT: E 84 ILE cc_start: 0.8764 (mm) cc_final: 0.8414 (mt) REVERT: E 241 ARG cc_start: 0.6917 (mtt180) cc_final: 0.6465 (mtt-85) REVERT: F 241 ARG cc_start: 0.7811 (ttm-80) cc_final: 0.7469 (ttm-80) REVERT: F 291 VAL cc_start: 0.8763 (OUTLIER) cc_final: 0.8546 (p) REVERT: F 298 ARG cc_start: 0.7757 (ptp-110) cc_final: 0.7466 (ttp80) REVERT: F 300 ASP cc_start: 0.7473 (m-30) cc_final: 0.7068 (t70) REVERT: F 310 TYR cc_start: 0.7242 (t80) cc_final: 0.6951 (t80) REVERT: G 44 GLU cc_start: 0.6066 (tp30) cc_final: 0.5788 (tp30) REVERT: G 92 GLU cc_start: 0.8375 (tp30) cc_final: 0.7665 (tp30) REVERT: G 263 ARG cc_start: 0.8472 (ttp80) cc_final: 0.8177 (ttp80) REVERT: H 203 GLU cc_start: 0.7187 (mm-30) cc_final: 0.6796 (tp30) REVERT: H 316 ASP cc_start: 0.7040 (m-30) cc_final: 0.6770 (m-30) outliers start: 44 outliers final: 38 residues processed: 354 average time/residue: 0.1519 time to fit residues: 79.1816 Evaluate side-chains 360 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 319 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 293 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 175 VAL Chi-restraints excluded: chain C residue 189 SER 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 303 ILE Chi-restraints excluded: chain E residue 46 TRP Chi-restraints excluded: chain E residue 57 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 208 ILE 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 245 ASP 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: 0.6980 chunk 105 optimal weight: 5.9990 chunk 201 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 162 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 186 optimal weight: 6.9990 chunk 138 optimal weight: 0.0670 chunk 81 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 147 optimal weight: 0.4980 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 227 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.139131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.111339 restraints weight = 21163.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.114125 restraints weight = 12926.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.116053 restraints weight = 9240.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.117318 restraints weight = 7368.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.117989 restraints weight = 6322.340| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2883 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= 0.119 Angle : 0.512 9.639 23073 Z= 0.258 Chirality : 0.046 0.219 2687 Planarity : 0.003 0.043 2993 Dihedral : 5.847 109.778 2435 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.40 % Allowed : 19.09 % Favored : 78.51 % 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: -0.34 (0.18), residues: 2140 helix: 0.84 (0.16), residues: 1016 sheet: -0.87 (0.29), residues: 304 loop : -1.27 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 154 TYR 0.026 0.001 TYR E 333 PHE 0.020 0.001 PHE C 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 0.00279 / 0.12 (17067) covalent geometry : angle 0.51180 / 0.26 (23073) hydrogen bonds : bond 0.02843 / 1.94 ( 692) hydrogen bonds : angle 4.11396 / 2.81 ( 1977) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3158.59 seconds wall clock time: 55 minutes 30.22 seconds (3330.22 seconds total)