Starting phenix.real_space_refine on Sat Oct 31 08:19:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wk1_66036/10_2026/9wk1_66036_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wk1_66036/10_2026/9wk1_66036.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wk1_66036/10_2026/9wk1_66036_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wk1_66036/10_2026/9wk1_66036_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wk1_66036/10_2026/9wk1_66036.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wk1_66036/10_2026/9wk1_66036.map" } resolution = 2.6 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= 0.003 sd= 0.037 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: 6 Type Number sf(0) Gaussians P 24 5.49 5 S 21 5.16 5 C 12866 2.51 5 N 3769 2.21 5 O 4044 1.98 5 H 20166 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 40890 Number of models: 1 Model: "" Number of chains: 16 Chain: "D" Number of atoms: 5231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5231 Classifications: {'peptide': 338} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 318} Chain breaks: 1 Chain: "A" Number of atoms: 4883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 4883 Classifications: {'peptide': 318} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 18, 'TRANS': 299} Chain breaks: 1 Chain: "B" Number of atoms: 5155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 5155 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 19, 'TRANS': 313} Chain breaks: 2 Chain: "C" Number of atoms: 5034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 5034 Classifications: {'peptide': 325} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 18, 'TRANS': 306} Chain breaks: 3 Chain: "E" Number of atoms: 5287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 5287 Classifications: {'peptide': 343} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 19, 'TRANS': 323} Chain: "F" Number of atoms: 4929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 4929 Classifications: {'peptide': 321} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 18, 'TRANS': 302} Chain breaks: 1 Chain: "G" Number of atoms: 5212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 5212 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 19, 'TRANS': 317} Chain breaks: 1 Chain: "H" Number of atoms: 4775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 4775 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 18, 'TRANS': 292} Chain breaks: 2 Chain: "D" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.24, per 1000 atoms: 0.15 Number of scatterers: 40890 At special positions: 0 Unit cell: (103, 127.72, 130.192, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 21 16.00 P 24 15.00 O 4044 8.00 N 3769 7.00 C 12866 6.00 H 20166 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.69 Conformation dependent library (CDL) restraints added in 1.2 seconds 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4838 Finding SS restraints... Secondary structure from input PDB file: 133 helices and 16 sheets defined 54.7% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'D' and resid 31 through 46 Processing helix chain 'D' and resid 55 through 58 Processing helix chain 'D' and resid 59 through 73 removed outlier: 3.549A pdb=" N ALA D 70 " --> pdb=" O GLY D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 78 removed outlier: 3.513A pdb=" N VAL D 78 " --> pdb=" O ARG D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 114 removed outlier: 3.816A pdb=" N GLU D 107 " --> pdb=" O ARG D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 145 removed outlier: 3.558A pdb=" N THR D 135 " --> pdb=" O GLU D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 172 Processing helix chain 'D' and resid 187 through 191 Processing helix chain 'D' and resid 192 through 200 Processing helix chain 'D' and resid 213 through 217 removed outlier: 4.161A pdb=" N GLY D 217 " --> pdb=" O TRP D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 232 Processing helix chain 'D' and resid 233 through 238 Processing helix chain 'D' and resid 241 through 262 Processing helix chain 'D' and resid 264 through 276 removed outlier: 3.948A pdb=" N HIS D 276 " --> pdb=" O PHE D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 298 Processing helix chain 'D' and resid 304 through 315 Processing helix chain 'D' and resid 322 through 327 Processing helix chain 'D' and resid 330 through 334 Processing helix chain 'D' and resid 335 through 340 removed outlier: 4.198A pdb=" N ARG D 339 " --> pdb=" O GLN D 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 46 Processing helix chain 'A' and resid 55 through 58 Processing helix chain 'A' and resid 59 through 72 Processing helix chain 'A' and resid 73 through 78 removed outlier: 4.489A pdb=" N GLU A 76 " --> pdb=" O GLY A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 114 removed outlier: 3.779A pdb=" N GLU A 107 " --> pdb=" O ARG A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 146 removed outlier: 3.591A pdb=" N THR A 135 " --> pdb=" O GLU A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 172 Processing helix chain 'A' and resid 187 through 191 Processing helix chain 'A' and resid 192 through 200 Processing helix chain 'A' and resid 244 through 261 Processing helix chain 'A' and resid 264 through 276 removed outlier: 3.855A pdb=" N HIS A 276 " --> pdb=" O PHE A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 300 removed outlier: 4.166A pdb=" N ASP A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 315 Processing helix chain 'A' and resid 322 through 327 Processing helix chain 'A' and resid 330 through 335 Processing helix chain 'A' and resid 336 through 340 Processing helix chain 'B' and resid 31 through 46 Processing helix chain 'B' and resid 55 through 58 Processing helix chain 'B' and resid 59 through 73 Processing helix chain 'B' and resid 74 through 78 Processing helix chain 'B' and resid 98 through 114 removed outlier: 3.705A pdb=" N GLU B 107 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 145 removed outlier: 3.503A pdb=" N THR B 135 " --> pdb=" O GLU B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 172 Processing helix chain 'B' and resid 187 through 191 Processing helix chain 'B' and resid 192 through 201 Processing helix chain 'B' and resid 213 through 217 removed outlier: 3.652A pdb=" N SER B 216 " --> pdb=" O GLY B 213 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLY B 217 " --> pdb=" O TRP B 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 213 through 217' Processing helix chain 'B' and resid 241 through 261 Processing helix chain 'B' and resid 264 through 276 removed outlier: 3.973A pdb=" N HIS B 276 " --> pdb=" O PHE B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 300 removed outlier: 4.103A pdb=" N ASP B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 315 Processing helix chain 'B' and resid 322 through 326 Processing helix chain 'B' and resid 330 through 335 Processing helix chain 'B' and resid 336 through 340 removed outlier: 3.832A pdb=" N ARG B 340 " --> pdb=" O ARG B 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 46 Processing helix chain 'C' and resid 55 through 58 Processing helix chain 'C' and resid 59 through 73 Processing helix chain 'C' and resid 74 through 78 Processing helix chain 'C' and resid 98 through 113 removed outlier: 3.789A pdb=" N GLU C 107 " --> pdb=" O ARG C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 145 removed outlier: 3.525A pdb=" N THR C 135 " --> pdb=" O GLU C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 172 Processing helix chain 'C' and resid 187 through 191 Processing helix chain 'C' and resid 192 through 200 Processing helix chain 'C' and resid 242 through 261 Processing helix chain 'C' and resid 264 through 276 removed outlier: 4.005A pdb=" N HIS C 276 " --> pdb=" O PHE C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 300 removed outlier: 4.197A pdb=" N ASP C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 315 Processing helix chain 'C' and resid 322 through 326 Processing helix chain 'C' and resid 330 through 334 Processing helix chain 'C' and resid 335 through 340 removed outlier: 3.939A pdb=" N ARG C 339 " --> pdb=" O GLN C 335 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 46 Processing helix chain 'E' and resid 55 through 58 Processing helix chain 'E' and resid 59 through 73 Processing helix chain 'E' and resid 74 through 78 Processing helix chain 'E' and resid 98 through 113 removed outlier: 3.833A pdb=" N ARG E 104 " --> pdb=" O ARG E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 145 Processing helix chain 'E' and resid 157 through 170 Processing helix chain 'E' and resid 187 through 191 Processing helix chain 'E' and resid 192 through 200 Processing helix chain 'E' and resid 227 through 232 removed outlier: 3.523A pdb=" N TRP E 231 " --> pdb=" O GLN E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 238 Processing helix chain 'E' and resid 241 through 262 Processing helix chain 'E' and resid 264 through 274 Processing helix chain 'E' and resid 288 through 298 Processing helix chain 'E' and resid 304 through 315 Processing helix chain 'E' and resid 322 through 327 Processing helix chain 'E' and resid 330 through 335 Processing helix chain 'F' and resid 31 through 46 Processing helix chain 'F' and resid 59 through 73 Processing helix chain 'F' and resid 74 through 78 Processing helix chain 'F' and resid 98 through 114 Processing helix chain 'F' and resid 131 through 145 Processing helix chain 'F' and resid 157 through 172 Processing helix chain 'F' and resid 187 through 191 Processing helix chain 'F' and resid 192 through 200 Processing helix chain 'F' and resid 213 through 217 removed outlier: 4.303A pdb=" N GLY F 217 " --> pdb=" O TRP F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 262 Processing helix chain 'F' and resid 264 through 276 removed outlier: 3.920A pdb=" N HIS F 276 " --> pdb=" O PHE F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 300 removed outlier: 4.275A pdb=" N ASP F 300 " --> pdb=" O LEU F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 315 Processing helix chain 'F' and resid 322 through 327 removed outlier: 3.556A pdb=" N ILE F 326 " --> pdb=" O SER F 322 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLY F 327 " --> pdb=" O PRO F 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 322 through 327' Processing helix chain 'F' and resid 330 through 335 Processing helix chain 'F' and resid 335 through 340 removed outlier: 4.026A pdb=" N ARG F 339 " --> pdb=" O GLN F 335 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 46 Processing helix chain 'G' and resid 55 through 58 removed outlier: 3.989A pdb=" N ALA G 58 " --> pdb=" O VAL G 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 55 through 58' Processing helix chain 'G' and resid 59 through 73 Processing helix chain 'G' and resid 74 through 78 Processing helix chain 'G' and resid 98 through 114 removed outlier: 3.769A pdb=" N GLU G 107 " --> pdb=" O ARG G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 146 removed outlier: 3.539A pdb=" N THR G 135 " --> pdb=" O GLU G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 157 through 172 Processing helix chain 'G' and resid 187 through 191 Processing helix chain 'G' and resid 192 through 200 Processing helix chain 'G' and resid 213 through 217 removed outlier: 4.241A pdb=" N GLY G 217 " --> pdb=" O TRP G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 232 Processing helix chain 'G' and resid 241 through 261 Processing helix chain 'G' and resid 264 through 276 removed outlier: 3.839A pdb=" N HIS G 276 " --> pdb=" O PHE G 272 " (cutoff:3.500A) Processing helix chain 'G' and resid 288 through 298 Processing helix chain 'G' and resid 304 through 315 Processing helix chain 'G' and resid 322 through 327 Processing helix chain 'G' and resid 330 through 334 Processing helix chain 'G' and resid 335 through 339 Processing helix chain 'H' and resid 31 through 46 Processing helix chain 'H' and resid 55 through 58 Processing helix chain 'H' and resid 59 through 73 Processing helix chain 'H' and resid 74 through 78 Processing helix chain 'H' and resid 98 through 114 Processing helix chain 'H' and resid 131 through 145 Processing helix chain 'H' and resid 157 through 172 Processing helix chain 'H' and resid 188 through 200 removed outlier: 4.308A pdb=" N GLU H 192 " --> pdb=" O HIS H 188 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N LEU H 194 " --> pdb=" O GLU H 190 " (cutoff:3.500A) Proline residue: H 195 - end of helix Processing helix chain 'H' and resid 246 through 261 Processing helix chain 'H' and resid 264 through 276 removed outlier: 3.878A pdb=" N HIS H 276 " --> pdb=" O PHE H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 288 through 299 Processing helix chain 'H' and resid 304 through 315 Processing helix chain 'H' and resid 330 through 335 removed outlier: 3.556A pdb=" N ARG H 334 " --> pdb=" O PRO H 330 " (cutoff:3.500A) Processing helix chain 'H' and resid 336 through 340 removed outlier: 3.731A pdb=" N ARG H 340 " --> pdb=" O ARG H 337 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 5 through 6 Processing sheet with id=AA2, first strand: chain 'D' and resid 17 through 20 removed outlier: 7.633A pdb=" N LEU D 17 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N ASP D 51 " --> pdb=" O LEU D 17 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU D 19 " --> pdb=" O ASP D 51 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU D 80 " --> pdb=" O ILE D 120 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N TYR D 122 " --> pdb=" O LEU D 80 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N SER D 82 " --> pdb=" O TYR D 122 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ASP D 119 " --> pdb=" O TYR D 150 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N GLY D 152 " --> pdb=" O ASP D 119 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N TYR D 121 " --> pdb=" O GLY D 152 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL D 177 " --> pdb=" O TYR D 151 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR D 153 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLU D 178 " --> pdb=" O PHE D 205 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N THR D 18 " --> pdb=" O ILE D 284 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 5 through 6 Processing sheet with id=AA4, first strand: chain 'A' and resid 17 through 20 removed outlier: 7.802A pdb=" N LEU A 17 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N ASP A 51 " --> pdb=" O LEU A 17 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU A 19 " --> pdb=" O ASP A 51 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE A 50 " --> pdb=" O ALA A 81 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU A 80 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N LEU A 118 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N TYR A 151 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N ILE A 120 " --> pdb=" O TYR A 151 " (cutoff:3.500A) removed outlier: 9.588A pdb=" N THR A 153 " --> pdb=" O ILE A 120 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL A 177 " --> pdb=" O TYR A 151 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR A 153 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN A 179 " --> pdb=" O THR A 153 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLU A 178 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N THR A 204 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ILE A 283 " --> pdb=" O THR A 204 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ALA A 206 " --> pdb=" O ILE A 283 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 5 through 6 Processing sheet with id=AA6, first strand: chain 'B' and resid 17 through 20 removed outlier: 5.241A pdb=" N VAL B 49 " --> pdb=" O LEU B 17 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE B 50 " --> pdb=" O ALA B 81 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N LYS B 83 " --> pdb=" O ILE B 50 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU B 80 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N TYR B 122 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N SER B 82 " --> pdb=" O TYR B 122 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N LEU B 118 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N TYR B 151 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N ILE B 120 " --> pdb=" O TYR B 151 " (cutoff:3.500A) removed outlier: 9.551A pdb=" N THR B 153 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N TYR B 122 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL B 177 " --> pdb=" O TYR B 151 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR B 153 " --> pdb=" O VAL B 177 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLU B 178 " --> pdb=" O PHE B 205 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N TRP B 207 " --> pdb=" O GLU B 178 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N THR B 204 " --> pdb=" O SER B 281 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ILE B 283 " --> pdb=" O THR B 204 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA B 206 " --> pdb=" O ILE B 283 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 5 through 6 Processing sheet with id=AA8, first strand: chain 'C' and resid 17 through 20 removed outlier: 5.193A pdb=" N VAL C 49 " --> pdb=" O LEU C 17 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE C 50 " --> pdb=" O ALA C 81 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N LYS C 83 " --> pdb=" O ILE C 50 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU C 80 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N TYR C 122 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N SER C 82 " --> pdb=" O TYR C 122 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ASP C 119 " --> pdb=" O TYR C 150 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N GLY C 152 " --> pdb=" O ASP C 119 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TYR C 121 " --> pdb=" O GLY C 152 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N SER C 154 " --> pdb=" O TYR C 121 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ALA C 123 " --> pdb=" O SER C 154 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL C 177 " --> pdb=" O TYR C 151 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLU C 178 " --> pdb=" O PHE C 205 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 5 through 6 Processing sheet with id=AB1, first strand: chain 'E' and resid 17 through 20 removed outlier: 7.745A pdb=" N LEU E 17 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N ASP E 51 " --> pdb=" O LEU E 17 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU E 19 " --> pdb=" O ASP E 51 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE E 50 " --> pdb=" O ALA E 81 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU E 80 " --> pdb=" O ILE E 120 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ASP E 119 " --> pdb=" O TYR E 150 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N GLY E 152 " --> pdb=" O ASP E 119 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N TYR E 121 " --> pdb=" O GLY E 152 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL E 177 " --> pdb=" O TYR E 151 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N THR E 204 " --> pdb=" O SER E 281 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ILE E 283 " --> pdb=" O THR E 204 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ALA E 206 " --> pdb=" O ILE E 283 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 5 through 6 Processing sheet with id=AB3, first strand: chain 'F' and resid 17 through 20 removed outlier: 5.291A pdb=" N VAL F 49 " --> pdb=" O LEU F 17 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE F 50 " --> pdb=" O ALA F 81 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU F 80 " --> pdb=" O ILE F 120 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ASP F 119 " --> pdb=" O TYR F 150 " (cutoff:3.500A) removed outlier: 8.117A pdb=" N GLY F 152 " --> pdb=" O ASP F 119 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N TYR F 121 " --> pdb=" O GLY F 152 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N SER F 154 " --> pdb=" O TYR F 121 " (cutoff:3.500A) removed outlier: 9.046A pdb=" N VAL F 177 " --> pdb=" O LEU F 149 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N TYR F 151 " --> pdb=" O VAL F 177 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N GLN F 179 " --> pdb=" O TYR F 151 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N THR F 153 " --> pdb=" O GLN F 179 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N THR F 204 " --> pdb=" O SER F 281 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ILE F 283 " --> pdb=" O THR F 204 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ALA F 206 " --> pdb=" O ILE F 283 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N THR F 18 " --> pdb=" O ILE F 284 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 5 through 6 Processing sheet with id=AB5, first strand: chain 'G' and resid 148 through 151 removed outlier: 6.033A pdb=" N ASP G 119 " --> pdb=" O TYR G 150 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU G 80 " --> pdb=" O ILE G 120 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N LEU G 17 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 8.624A pdb=" N ASP G 51 " --> pdb=" O LEU G 17 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU G 19 " --> pdb=" O ASP G 51 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N THR G 18 " --> pdb=" O ILE G 284 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N THR G 204 " --> pdb=" O SER G 281 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ILE G 283 " --> pdb=" O THR G 204 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ALA G 206 " --> pdb=" O ILE G 283 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLU G 178 " --> pdb=" O PHE G 205 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AB7, first strand: chain 'H' and resid 17 through 20 removed outlier: 7.560A pdb=" N LEU H 17 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N ASP H 51 " --> pdb=" O LEU H 17 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU H 19 " --> pdb=" O ASP H 51 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE H 50 " --> pdb=" O ALA H 81 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU H 80 " --> pdb=" O ILE H 120 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ASP H 119 " --> pdb=" O TYR H 150 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N GLY H 152 " --> pdb=" O ASP H 119 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TYR H 121 " --> pdb=" O GLY H 152 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N SER H 154 " --> pdb=" O TYR H 121 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL H 177 " --> pdb=" O TYR H 151 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR H 153 " --> pdb=" O VAL H 177 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLU H 178 " --> pdb=" O PHE H 205 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N THR H 204 " --> pdb=" O SER H 281 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ILE H 283 " --> pdb=" O THR H 204 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ALA H 206 " --> pdb=" O ILE H 283 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N THR H 18 " --> pdb=" O ILE H 284 " (cutoff:3.500A) 952 hydrogen bonds defined for protein. 2628 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: 11.03 Time building geometry restraints manager: 4.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 20166 1.03 - 1.23: 143 1.23 - 1.43: 8718 1.43 - 1.62: 12215 1.62 - 1.82: 82 Bond restraints: 41324 Sorted by residual: bond pdb=" C SER D 208 " pdb=" O SER D 208 " ideal model delta sigma weight residual 1.235 1.220 0.015 4.70e-03 4.53e+04 1.07e+01 bond pdb=" N MET H 2 " pdb=" CA MET H 2 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.90e-02 2.77e+03 4.47e+00 bond pdb=" C SER B 208 " pdb=" O SER B 208 " ideal model delta sigma weight residual 1.235 1.244 -0.009 4.70e-03 4.53e+04 3.79e+00 bond pdb=" CB ARG H 246 " pdb=" CG ARG H 246 " ideal model delta sigma weight residual 1.520 1.576 -0.056 3.00e-02 1.11e+03 3.43e+00 bond pdb=" N MET B 2 " pdb=" CA MET B 2 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 ... (remaining 41319 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 74126 2.23 - 4.46: 370 4.46 - 6.68: 42 6.68 - 8.91: 1 8.91 - 11.14: 1 Bond angle restraints: 74540 Sorted by residual: angle pdb=" N ASN A 85 " pdb=" CA ASN A 85 " pdb=" CB ASN A 85 " ideal model delta sigma weight residual 114.10 109.81 4.29 1.00e+00 1.00e+00 1.84e+01 angle pdb=" N ASN D 85 " pdb=" CA ASN D 85 " pdb=" CB ASN D 85 " ideal model delta sigma weight residual 114.17 109.86 4.31 1.14e+00 7.69e-01 1.43e+01 angle pdb=" CB MET H 2 " pdb=" CG MET H 2 " pdb=" SD MET H 2 " ideal model delta sigma weight residual 112.70 123.84 -11.14 3.00e+00 1.11e-01 1.38e+01 angle pdb=" CA ARG H 246 " pdb=" CB ARG H 246 " pdb=" CG ARG H 246 " ideal model delta sigma weight residual 114.10 120.15 -6.05 2.00e+00 2.50e-01 9.15e+00 angle pdb=" N ASN F 85 " pdb=" CA ASN F 85 " pdb=" CB ASN F 85 " ideal model delta sigma weight residual 114.10 111.21 2.89 1.00e+00 1.00e+00 8.35e+00 ... (remaining 74535 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 17732 17.80 - 35.60: 1306 35.60 - 53.41: 544 53.41 - 71.21: 96 71.21 - 89.01: 18 Dihedral angle restraints: 19696 sinusoidal: 11194 harmonic: 8502 Sorted by residual: dihedral pdb=" CA ARG F 174 " pdb=" C ARG F 174 " pdb=" N PRO F 175 " pdb=" CA PRO F 175 " ideal model delta harmonic sigma weight residual 180.00 162.47 17.53 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA TYR E 122 " pdb=" C TYR E 122 " pdb=" N ALA E 123 " pdb=" CA ALA E 123 " ideal model delta harmonic sigma weight residual 180.00 162.81 17.19 0 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CA ARG A 174 " pdb=" C ARG A 174 " pdb=" N PRO A 175 " pdb=" CA PRO A 175 " ideal model delta harmonic sigma weight residual 180.00 162.96 17.04 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 19693 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2601 0.044 - 0.089: 490 0.089 - 0.133: 176 0.133 - 0.178: 2 0.178 - 0.222: 1 Chirality restraints: 3270 Sorted by residual: chirality pdb=" CB VAL C 71 " pdb=" CA VAL C 71 " pdb=" CG1 VAL C 71 " pdb=" CG2 VAL C 71 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CG LEU G 331 " pdb=" CB LEU G 331 " pdb=" CD1 LEU G 331 " pdb=" CD2 LEU G 331 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.87e-01 chirality pdb=" CG LEU C 193 " pdb=" CB LEU C 193 " pdb=" CD1 LEU C 193 " pdb=" CD2 LEU C 193 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.50e-01 ... (remaining 3267 not shown) Planarity restraints: 6201 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 285 " 0.031 5.00e-02 4.00e+02 4.69e-02 3.51e+00 pdb=" N PRO C 286 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO C 286 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 286 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP F 101 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.27e+00 pdb=" C TRP F 101 " -0.031 2.00e-02 2.50e+03 pdb=" O TRP F 101 " 0.012 2.00e-02 2.50e+03 pdb=" N ILE F 102 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY F 285 " -0.029 5.00e-02 4.00e+02 4.41e-02 3.12e+00 pdb=" N PRO F 286 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO F 286 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO F 286 " -0.025 5.00e-02 4.00e+02 ... (remaining 6198 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.07: 646 2.07 - 2.71: 67507 2.71 - 3.34: 125484 3.34 - 3.97: 160051 3.97 - 4.60: 253197 Nonbonded interactions: 606885 Sorted by model distance: nonbonded pdb=" OE1 GLN E 221 " pdb=" H GLN E 221 " model vdw 1.443 2.450 nonbonded pdb=" OE2 GLU B 163 " pdb=" HE1 TRP E 166 " model vdw 1.457 2.450 nonbonded pdb=" O ALA B 249 " pdb="HE21 GLN B 253 " model vdw 1.509 2.450 nonbonded pdb=" OE1 GLU F 128 " pdb=" H GLU F 128 " model vdw 1.518 2.450 nonbonded pdb=" H ARG F 287 " pdb=" OE1 GLN F 291 " model vdw 1.563 2.450 ... (remaining 606880 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 2 through 217 or resid 245 through 325 or resid 329 throug \ h 401)) selection = (chain 'B' and (resid 2 through 217 or resid 245 through 325 or resid 329 throug \ h 341 or resid 401)) selection = (chain 'C' and (resid 2 through 217 or resid 245 through 325 or resid 329 throug \ h 401)) selection = (chain 'D' and (resid 2 through 217 or resid 245 through 325 or resid 329 throug \ h 341 or resid 401)) selection = (chain 'E' and (resid 2 through 217 or resid 245 through 325 or resid 329 throug \ h 341 or resid 401)) selection = (chain 'F' and (resid 2 through 217 or resid 245 through 325 or resid 329 throug \ h 341 or resid 401)) selection = (chain 'G' and (resid 2 through 217 or resid 245 through 325 or resid 329 throug \ h 341 or resid 401)) selection = (chain 'H' and (resid 2 through 341 or resid 401)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.110 Extract box with map and model: 0.640 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 38.290 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.070 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:8.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 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 : 0.007 0.881 21159 Z= 0.630 Angle : 0.559 11.140 28871 Z= 0.284 Chirality : 0.040 0.222 3270 Planarity : 0.004 0.047 3742 Dihedral : 14.733 89.012 8209 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.56 % Allowed : 12.78 % Favored : 86.67 % 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: 1.31 (0.17), residues: 2588 helix: 2.19 (0.16), residues: 1202 sheet: -1.88 (0.28), residues: 315 loop : 0.35 (0.20), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 337 TYR 0.013 0.001 TYR H 295 PHE 0.013 0.001 PHE B 84 TRP 0.012 0.001 TRP B 207 HIS 0.006 0.001 HIS E 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (21158) covalent geometry : angle 0.55857 / 0.28 (28871) hydrogen bonds : bond 0.14296 / 9.79 ( 952) hydrogen bonds : angle 5.85197 / 4.35 ( 2628) Misc. bond : bond 0.88079 / 41.94 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 145 GLU cc_start: 0.8993 (tt0) cc_final: 0.8752 (tt0) REVERT: D 232 ASN cc_start: 0.9001 (m-40) cc_final: 0.8694 (m-40) REVERT: E 90 LYS cc_start: 0.9289 (tppp) cc_final: 0.8926 (tptp) REVERT: E 319 GLU cc_start: 0.8934 (tt0) cc_final: 0.8289 (tm-30) REVERT: H 253 GLN cc_start: 0.9280 (mm-40) cc_final: 0.8950 (tp-100) REVERT: H 334 ARG cc_start: 0.8911 (mpp80) cc_final: 0.8569 (mpp80) outliers start: 12 outliers final: 9 residues processed: 114 average time/residue: 1.2327 time to fit residues: 161.9212 Evaluate side-chains 104 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 95 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 MET Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain H residue 78 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: [197, 215, 20, 132, 248, 207, 155, 244, 183, 111, 258] chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 258 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 ASN F 23 ASN ** F 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 HIS ** H 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.074072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.055071 restraints weight = 148432.121| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 3.12 r_work: 0.2656 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.0706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 21159 Z= 0.231 Angle : 0.567 9.811 28871 Z= 0.285 Chirality : 0.041 0.172 3270 Planarity : 0.005 0.045 3742 Dihedral : 8.869 70.019 3477 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.30 % Allowed : 11.30 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.17), residues: 2588 helix: 2.33 (0.15), residues: 1231 sheet: -1.84 (0.28), residues: 315 loop : 0.28 (0.20), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 287 TYR 0.008 0.001 TYR E 122 PHE 0.007 0.001 PHE C 272 TRP 0.010 0.001 TRP G 207 HIS 0.006 0.001 HIS E 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.23 (21158) covalent geometry : angle 0.56689 / 0.28 (28871) hydrogen bonds : bond 0.04769 / 3.25 ( 952) hydrogen bonds : angle 4.51366 / 3.31 ( 2628) Misc. bond : bond 0.00397 / 0.19 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 101 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 145 GLU cc_start: 0.8939 (tt0) cc_final: 0.8678 (tt0) REVERT: D 232 ASN cc_start: 0.8956 (m-40) cc_final: 0.8641 (m-40) REVERT: A 335 GLN cc_start: 0.8205 (tp40) cc_final: 0.7877 (tt0) REVERT: B 163 GLU cc_start: 0.9119 (mm-30) cc_final: 0.8919 (tp30) REVERT: E 131 GLU cc_start: 0.8134 (tp30) cc_final: 0.7883 (tp30) REVERT: E 337 ARG cc_start: 0.8049 (tpt170) cc_final: 0.7391 (tpp-160) REVERT: H 253 GLN cc_start: 0.9304 (mm-40) cc_final: 0.8959 (tp-100) REVERT: H 331 LEU cc_start: 0.9066 (pp) cc_final: 0.8797 (pp) REVERT: H 334 ARG cc_start: 0.8923 (mpp80) cc_final: 0.8638 (mpp80) outliers start: 28 outliers final: 15 residues processed: 124 average time/residue: 1.2154 time to fit residues: 174.1789 Evaluate side-chains 108 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 MET Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain H residue 51 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: [69, 82, 187, 23, 238, 246, 24, 190, 2, 112, 206] chunk 69 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 187 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 238 optimal weight: 4.9990 chunk 246 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 190 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 112 optimal weight: 0.0980 chunk 206 optimal weight: 2.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 124 HIS H 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.074454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.055461 restraints weight = 147287.246| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 3.13 r_work: 0.2666 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.0916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21159 Z= 0.148 Angle : 0.516 9.364 28871 Z= 0.257 Chirality : 0.039 0.158 3270 Planarity : 0.004 0.049 3742 Dihedral : 8.462 76.934 3471 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.20 % Allowed : 11.25 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.17), residues: 2588 helix: 2.58 (0.15), residues: 1228 sheet: -1.81 (0.28), residues: 331 loop : 0.35 (0.20), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 287 TYR 0.011 0.001 TYR H 295 PHE 0.006 0.001 PHE G 205 TRP 0.008 0.001 TRP D 101 HIS 0.005 0.000 HIS E 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (21158) covalent geometry : angle 0.51644 / 0.26 (28871) hydrogen bonds : bond 0.03999 / 2.72 ( 952) hydrogen bonds : angle 4.15146 / 3.04 ( 2628) Misc. bond : bond 0.00066 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 145 GLU cc_start: 0.8927 (tt0) cc_final: 0.8580 (tt0) REVERT: D 147 LYS cc_start: 0.9390 (mttm) cc_final: 0.9060 (mttm) REVERT: D 232 ASN cc_start: 0.8941 (m-40) cc_final: 0.8618 (m-40) REVERT: A 90 LYS cc_start: 0.9279 (ttmm) cc_final: 0.9078 (tppp) REVERT: A 335 GLN cc_start: 0.8161 (tp40) cc_final: 0.7826 (tt0) REVERT: B 163 GLU cc_start: 0.9102 (mm-30) cc_final: 0.8852 (tp30) REVERT: C 131 GLU cc_start: 0.8835 (tp30) cc_final: 0.8132 (tt0) REVERT: E 131 GLU cc_start: 0.8047 (tp30) cc_final: 0.7774 (tp30) REVERT: G 193 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9195 (tt) REVERT: H 253 GLN cc_start: 0.9304 (mm-40) cc_final: 0.8944 (tp-100) REVERT: H 331 LEU cc_start: 0.9069 (pp) cc_final: 0.8800 (pp) REVERT: H 334 ARG cc_start: 0.8911 (mpp80) cc_final: 0.8620 (mpp80) outliers start: 26 outliers final: 13 residues processed: 128 average time/residue: 1.2110 time to fit residues: 178.6992 Evaluate side-chains 112 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain H residue 78 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: [45, 137, 124, 167, 83, 19, 225, 30, 179, 109, 65] chunk 45 optimal weight: 3.9990 chunk 137 optimal weight: 0.0770 chunk 124 optimal weight: 1.9990 chunk 167 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 225 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 179 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.073834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.054754 restraints weight = 148678.035| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 3.11 r_work: 0.2655 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.151 21159 Z= 0.176 Angle : 0.518 9.171 28871 Z= 0.258 Chirality : 0.040 0.165 3270 Planarity : 0.005 0.050 3742 Dihedral : 8.354 75.915 3467 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.25 % Allowed : 11.16 % Favored : 87.59 % 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: 1.68 (0.17), residues: 2588 helix: 2.66 (0.15), residues: 1222 sheet: -1.82 (0.27), residues: 341 loop : 0.36 (0.20), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 86 TYR 0.011 0.001 TYR H 295 PHE 0.006 0.001 PHE G 205 TRP 0.009 0.001 TRP G 207 HIS 0.033 0.001 HIS F 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 (21158) covalent geometry : angle 0.51807 / 0.26 (28871) hydrogen bonds : bond 0.03830 / 2.61 ( 952) hydrogen bonds : angle 4.02027 / 2.94 ( 2628) Misc. bond : bond 0.00048 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 145 GLU cc_start: 0.8924 (tt0) cc_final: 0.8526 (tt0) REVERT: D 147 LYS cc_start: 0.9386 (mttm) cc_final: 0.9028 (mttm) REVERT: D 232 ASN cc_start: 0.8938 (m-40) cc_final: 0.8615 (m-40) REVERT: B 163 GLU cc_start: 0.9114 (OUTLIER) cc_final: 0.8780 (tp30) REVERT: C 131 GLU cc_start: 0.8866 (tp30) cc_final: 0.8229 (tt0) REVERT: G 193 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9200 (tt) REVERT: H 253 GLN cc_start: 0.9291 (mm-40) cc_final: 0.8929 (tp-100) REVERT: H 331 LEU cc_start: 0.9085 (pp) cc_final: 0.8816 (pp) REVERT: H 334 ARG cc_start: 0.8878 (mpp80) cc_final: 0.8556 (mpp80) outliers start: 27 outliers final: 16 residues processed: 120 average time/residue: 1.2266 time to fit residues: 170.5001 Evaluate side-chains 111 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 MET Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 311 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: [196, 217, 158, 17, 169, 92, 182, 101, 55, 233, 98] chunk 196 optimal weight: 0.8980 chunk 217 optimal weight: 9.9990 chunk 158 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 169 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 182 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 chunk 233 optimal weight: 0.0980 chunk 98 optimal weight: 3.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 244 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.074101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.055085 restraints weight = 147929.607| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 3.10 r_work: 0.2663 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21159 Z= 0.134 Angle : 0.501 9.149 28871 Z= 0.248 Chirality : 0.039 0.157 3270 Planarity : 0.004 0.053 3742 Dihedral : 8.185 76.992 3467 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.06 % Allowed : 11.44 % Favored : 87.50 % 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: 1.76 (0.17), residues: 2588 helix: 2.75 (0.15), residues: 1223 sheet: -1.81 (0.27), residues: 341 loop : 0.39 (0.20), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 339 TYR 0.012 0.001 TYR H 295 PHE 0.006 0.001 PHE G 205 TRP 0.008 0.001 TRP G 207 HIS 0.005 0.000 HIS E 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (21158) covalent geometry : angle 0.50122 / 0.25 (28871) hydrogen bonds : bond 0.03609 / 2.46 ( 952) hydrogen bonds : angle 3.87695 / 2.84 ( 2628) Misc. bond : bond 0.00058 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 145 GLU cc_start: 0.8934 (tt0) cc_final: 0.8545 (tt0) REVERT: D 147 LYS cc_start: 0.9388 (mttm) cc_final: 0.9027 (mttm) REVERT: D 232 ASN cc_start: 0.8919 (m-40) cc_final: 0.8593 (m-40) REVERT: A 145 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8456 (mt-10) REVERT: B 163 GLU cc_start: 0.9105 (OUTLIER) cc_final: 0.8761 (tp30) REVERT: C 131 GLU cc_start: 0.8870 (tp30) cc_final: 0.8286 (tt0) REVERT: G 193 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9199 (tt) REVERT: H 253 GLN cc_start: 0.9301 (mm-40) cc_final: 0.8890 (tp-100) REVERT: H 331 LEU cc_start: 0.9103 (pp) cc_final: 0.8834 (pp) REVERT: H 334 ARG cc_start: 0.8875 (mpp80) cc_final: 0.8515 (mpp80) outliers start: 23 outliers final: 15 residues processed: 119 average time/residue: 1.1600 time to fit residues: 160.2427 Evaluate side-chains 120 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 MET Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 85 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: [11, 230, 251, 242, 125, 179, 55, 104, 120, 189, 151] chunk 11 optimal weight: 5.9990 chunk 230 optimal weight: 6.9990 chunk 251 optimal weight: 6.9990 chunk 242 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 chunk 179 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 chunk 104 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 189 optimal weight: 1.9990 chunk 151 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.070898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.052003 restraints weight = 151089.167| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 3.08 r_work: 0.2595 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.120 21159 Z= 0.302 Angle : 0.591 9.271 28871 Z= 0.295 Chirality : 0.042 0.181 3270 Planarity : 0.005 0.055 3742 Dihedral : 8.753 73.799 3467 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.39 % Allowed : 11.76 % Favored : 86.85 % 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: 1.42 (0.17), residues: 2588 helix: 2.37 (0.15), residues: 1236 sheet: -1.79 (0.28), residues: 328 loop : 0.21 (0.20), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 339 TYR 0.017 0.001 TYR H 295 PHE 0.009 0.001 PHE G 205 TRP 0.013 0.001 TRP G 207 HIS 0.006 0.001 HIS F 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00690 / 0.30 (21158) covalent geometry : angle 0.59065 / 0.29 (28871) hydrogen bonds : bond 0.04456 / 3.03 ( 952) hydrogen bonds : angle 4.21485 / 3.08 ( 2628) Misc. bond : bond 0.00119 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 96 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 145 GLU cc_start: 0.8929 (tt0) cc_final: 0.8571 (tt0) REVERT: D 147 LYS cc_start: 0.9376 (mttm) cc_final: 0.9042 (mttm) REVERT: D 232 ASN cc_start: 0.8931 (m-40) cc_final: 0.8617 (m-40) REVERT: A 145 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8426 (mt-10) REVERT: B 163 GLU cc_start: 0.9174 (OUTLIER) cc_final: 0.8712 (tp30) REVERT: C 131 GLU cc_start: 0.8916 (tp30) cc_final: 0.8408 (tt0) REVERT: C 145 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8305 (tm-30) REVERT: E 337 ARG cc_start: 0.8078 (tpt170) cc_final: 0.7840 (tpt170) REVERT: G 193 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9194 (tt) REVERT: H 253 GLN cc_start: 0.9318 (mm-40) cc_final: 0.8935 (tp-100) outliers start: 30 outliers final: 18 residues processed: 121 average time/residue: 1.1404 time to fit residues: 161.9843 Evaluate side-chains 113 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 MET Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 85 ASN Chi-restraints excluded: chain H residue 311 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: [67, 23, 40, 238, 257, 69, 81, 160, 179, 99, 174] chunk 67 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 238 optimal weight: 0.9980 chunk 257 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 chunk 179 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 174 optimal weight: 0.0270 overall best weight: 2.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 259 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.072517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.053669 restraints weight = 149058.036| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 3.06 r_work: 0.2626 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21159 Z= 0.145 Angle : 0.516 8.926 28871 Z= 0.255 Chirality : 0.039 0.150 3270 Planarity : 0.004 0.054 3742 Dihedral : 8.307 77.078 3465 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.30 % Allowed : 11.85 % Favored : 86.85 % 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: 1.67 (0.17), residues: 2588 helix: 2.68 (0.15), residues: 1217 sheet: -1.84 (0.27), residues: 338 loop : 0.33 (0.20), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 339 TYR 0.017 0.001 TYR H 295 PHE 0.006 0.001 PHE A 84 TRP 0.009 0.001 TRP E 207 HIS 0.005 0.000 HIS E 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (21158) covalent geometry : angle 0.51609 / 0.26 (28871) hydrogen bonds : bond 0.03748 / 2.56 ( 952) hydrogen bonds : angle 3.87351 / 2.83 ( 2628) Misc. bond : bond 0.00061 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 145 GLU cc_start: 0.8913 (tt0) cc_final: 0.8522 (tt0) REVERT: D 147 LYS cc_start: 0.9388 (mttm) cc_final: 0.9046 (mttm) REVERT: D 232 ASN cc_start: 0.8950 (m-40) cc_final: 0.8637 (m-40) REVERT: A 145 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8352 (mt-10) REVERT: B 163 GLU cc_start: 0.9134 (OUTLIER) cc_final: 0.8703 (tp30) REVERT: C 131 GLU cc_start: 0.8881 (tp30) cc_final: 0.8432 (tt0) REVERT: C 145 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8336 (tm-30) REVERT: H 253 GLN cc_start: 0.9285 (mm-40) cc_final: 0.8881 (tp-100) outliers start: 28 outliers final: 18 residues processed: 126 average time/residue: 1.2197 time to fit residues: 177.7332 Evaluate side-chains 120 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 MET Chi-restraints excluded: chain D residue 85 ASN Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 221 GLN Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 337 ARG Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 85 ASN Chi-restraints excluded: chain H residue 145 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: [174, 198, 27, 112, 55, 166, 51, 116, 34, 146, 33] chunk 174 optimal weight: 5.9990 chunk 198 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3132 r_free = 0.3132 target = 0.070684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.051848 restraints weight = 149790.419| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 3.05 r_work: 0.2598 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 21159 Z= 0.256 Angle : 0.564 8.853 28871 Z= 0.280 Chirality : 0.041 0.168 3270 Planarity : 0.005 0.055 3742 Dihedral : 8.425 73.964 3463 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.16 % Allowed : 12.41 % Favored : 86.44 % 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: 1.56 (0.17), residues: 2588 helix: 2.57 (0.15), residues: 1224 sheet: -1.76 (0.28), residues: 324 loop : 0.21 (0.20), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 339 TYR 0.016 0.001 TYR H 295 PHE 0.007 0.001 PHE G 205 TRP 0.011 0.001 TRP G 207 HIS 0.006 0.001 HIS E 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.26 (21158) covalent geometry : angle 0.56422 / 0.28 (28871) hydrogen bonds : bond 0.04092 / 2.79 ( 952) hydrogen bonds : angle 4.01290 / 2.93 ( 2628) Misc. bond : bond 0.00077 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 145 GLU cc_start: 0.8950 (tt0) cc_final: 0.8572 (tt0) REVERT: D 147 LYS cc_start: 0.9381 (mttm) cc_final: 0.9044 (mttm) REVERT: D 232 ASN cc_start: 0.8958 (m-40) cc_final: 0.8643 (m-40) REVERT: B 163 GLU cc_start: 0.9143 (OUTLIER) cc_final: 0.8701 (tp30) REVERT: C 131 GLU cc_start: 0.8883 (tp30) cc_final: 0.8467 (tt0) REVERT: C 145 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8418 (tm-30) REVERT: H 253 GLN cc_start: 0.9287 (mm-40) cc_final: 0.8900 (tp-100) outliers start: 25 outliers final: 15 residues processed: 119 average time/residue: 1.2376 time to fit residues: 171.0809 Evaluate side-chains 112 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 MET Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 85 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: [206, 130, 86, 27, 78, 117, 248, 38, 9, 209, 138] chunk 206 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 78 optimal weight: 0.0980 chunk 117 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 209 optimal weight: 0.9980 chunk 138 optimal weight: 5.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.072587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.053773 restraints weight = 148767.904| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 3.04 r_work: 0.2631 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 21159 Z= 0.121 Angle : 0.528 9.987 28871 Z= 0.261 Chirality : 0.039 0.135 3270 Planarity : 0.004 0.055 3742 Dihedral : 8.086 77.394 3463 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.02 % Allowed : 12.45 % Favored : 86.53 % 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: 1.77 (0.17), residues: 2588 helix: 2.79 (0.15), residues: 1218 sheet: -1.83 (0.28), residues: 334 loop : 0.35 (0.20), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 144 TYR 0.021 0.001 TYR H 295 PHE 0.006 0.001 PHE B 272 TRP 0.009 0.001 TRP E 207 HIS 0.005 0.000 HIS E 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (21158) covalent geometry : angle 0.52822 / 0.26 (28871) hydrogen bonds : bond 0.03586 / 2.45 ( 952) hydrogen bonds : angle 3.75059 / 2.74 ( 2628) Misc. bond : bond 0.00049 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 145 GLU cc_start: 0.8902 (tt0) cc_final: 0.8475 (tt0) REVERT: D 147 LYS cc_start: 0.9390 (mttm) cc_final: 0.9020 (mttm) REVERT: D 232 ASN cc_start: 0.8954 (m-40) cc_final: 0.8641 (m-40) REVERT: B 163 GLU cc_start: 0.9121 (OUTLIER) cc_final: 0.8698 (tp30) REVERT: C 131 GLU cc_start: 0.8863 (tp30) cc_final: 0.8473 (tt0) REVERT: C 145 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8419 (tm-30) REVERT: H 253 GLN cc_start: 0.9271 (mm-40) cc_final: 0.8878 (tp-100) outliers start: 22 outliers final: 13 residues processed: 119 average time/residue: 1.2414 time to fit residues: 171.0948 Evaluate side-chains 114 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 MET Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 85 ASN Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 85 ASN Chi-restraints excluded: chain H residue 331 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: [125, 112, 134, 219, 117, 205, 210, 24, 160, 12, 240] chunk 125 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 134 optimal weight: 4.9990 chunk 219 optimal weight: 8.9990 chunk 117 optimal weight: 4.9990 chunk 205 optimal weight: 3.9990 chunk 210 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 160 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 240 optimal weight: 5.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 259 ASN G 267 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.071259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.052530 restraints weight = 148477.199| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 3.03 r_work: 0.2612 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 21159 Z= 0.197 Angle : 0.549 9.947 28871 Z= 0.271 Chirality : 0.040 0.159 3270 Planarity : 0.004 0.055 3742 Dihedral : 8.144 74.256 3463 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.93 % Allowed : 12.55 % Favored : 86.53 % 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: 1.72 (0.17), residues: 2588 helix: 2.72 (0.15), residues: 1225 sheet: -1.85 (0.28), residues: 329 loop : 0.32 (0.20), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 287 TYR 0.017 0.001 TYR H 295 PHE 0.007 0.001 PHE G 205 TRP 0.014 0.001 TRP C 228 HIS 0.006 0.001 HIS E 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 (21158) covalent geometry : angle 0.54894 / 0.27 (28871) hydrogen bonds : bond 0.03755 / 2.56 ( 952) hydrogen bonds : angle 3.83480 / 2.80 ( 2628) Misc. bond : bond 0.00063 / 0.03 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5176 Ramachandran restraints generated. 2588 Oldfield, 0 Emsley, 2588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 145 GLU cc_start: 0.8945 (tt0) cc_final: 0.8560 (tt0) REVERT: D 147 LYS cc_start: 0.9384 (mttm) cc_final: 0.9041 (mttm) REVERT: D 232 ASN cc_start: 0.8952 (m-40) cc_final: 0.8636 (m-40) REVERT: B 163 GLU cc_start: 0.9133 (OUTLIER) cc_final: 0.8692 (tp30) REVERT: C 131 GLU cc_start: 0.8861 (tp30) cc_final: 0.8467 (tt0) REVERT: H 253 GLN cc_start: 0.9269 (mm-40) cc_final: 0.8882 (tp-100) outliers start: 20 outliers final: 14 residues processed: 113 average time/residue: 1.2361 time to fit residues: 162.1583 Evaluate side-chains 110 residues out of total 2160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 MET Chi-restraints excluded: chain D residue 281 SER Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 170 SER Chi-restraints excluded: chain F residue 106 VAL Chi-restraints excluded: chain F residue 124 HIS Chi-restraints excluded: chain F residue 170 SER Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 85 ASN Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain H residue 78 VAL Chi-restraints excluded: chain H residue 85 ASN Chi-restraints excluded: chain H residue 331 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 259 random chunks: [167, 73, 89, 196, 78, 170, 24, 120, 113, 121, 195] chunk 167 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 196 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 120 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 195 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.071618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.052895 restraints weight = 149491.868| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 3.05 r_work: 0.2619 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 21159 Z= 0.166 Angle : 0.543 11.096 28871 Z= 0.268 Chirality : 0.040 0.170 3270 Planarity : 0.004 0.055 3742 Dihedral : 8.068 75.125 3463 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.74 % Allowed : 12.87 % Favored : 86.39 % 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: 1.77 (0.17), residues: 2588 helix: 2.80 (0.15), residues: 1218 sheet: -1.82 (0.28), residues: 331 loop : 0.33 (0.20), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 287 TYR 0.017 0.001 TYR H 295 PHE 0.006 0.001 PHE G 205 TRP 0.009 0.001 TRP E 207 HIS 0.006 0.000 HIS E 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (21158) covalent geometry : angle 0.54324 / 0.27 (28871) hydrogen bonds : bond 0.03656 / 2.49 ( 952) hydrogen bonds : angle 3.76893 / 2.75 ( 2628) Misc. bond : bond 0.00059 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8719.42 seconds wall clock time: 148 minutes 36.54 seconds (8916.54 seconds total)