Starting phenix.real_space_refine on Sat Jul 4 08:31:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jpg_61699/07_2026/9jpg_61699.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jpg_61699/07_2026/9jpg_61699.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jpg_61699/07_2026/9jpg_61699.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jpg_61699/07_2026/9jpg_61699.map" model { file = "/net/cci-nas-00/data/ceres_data/9jpg_61699/07_2026/9jpg_61699.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jpg_61699/07_2026/9jpg_61699.cif" } resolution = 3.32 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= 0.001 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 37 5.49 5 S 18 5.16 5 C 11814 2.51 5 N 3487 2.21 5 O 3704 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 93 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19060 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2557 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 22, 'TRANS': 296} Chain breaks: 1 Chain: "B" Number of atoms: 2543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2543 Classifications: {'peptide': 327} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 300} Chain: "C" Number of atoms: 2634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2634 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 327} Chain: "D" Number of atoms: 2634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2634 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 327} Chain: "E" Number of atoms: 2634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2634 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 327} Chain: "F" Number of atoms: 2634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2634 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 327} Chain: "G" Number of atoms: 2634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2634 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 327} Chain: "I" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 790 Classifications: {'RNA': 37} Modifications used: {'p5*END': 1, 'rna2p_pur': 13, 'rna2p_pyr': 8, 'rna3p_pur': 8, 'rna3p_pyr': 8} Link IDs: {'rna2p': 20, 'rna3p': 16} Time building chain proxies: 3.62, per 1000 atoms: 0.19 Number of scatterers: 19060 At special positions: 0 Unit cell: (99.6506, 123.098, 161.618, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 P 37 15.00 O 3704 8.00 N 3487 7.00 C 11814 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 587.8 milliseconds 4660 Ramachandran restraints generated. 2330 Oldfield, 0 Emsley, 2330 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4364 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 27 sheets defined 36.5% alpha, 15.3% beta 0 base pairs and 4 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.942A pdb=" N GLU A 138 " --> pdb=" O GLY A 135 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU A 139 " --> pdb=" O SER A 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 135 through 139' Processing helix chain 'A' and resid 234 through 251 Processing helix chain 'A' and resid 251 through 264 Processing helix chain 'A' and resid 291 through 298 removed outlier: 3.919A pdb=" N SER A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 349 removed outlier: 3.536A pdb=" N ALA A 337 " --> pdb=" O SER A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 379 removed outlier: 4.133A pdb=" N LEU A 379 " --> pdb=" O TYR A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.834A pdb=" N SER A 389 " --> pdb=" O TRP A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 402 removed outlier: 3.920A pdb=" N GLN A 399 " --> pdb=" O HIS A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 409 removed outlier: 3.836A pdb=" N VAL A 407 " --> pdb=" O PRO A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 420 Processing helix chain 'A' and resid 421 through 440 removed outlier: 3.807A pdb=" N GLU A 425 " --> pdb=" O ASP A 421 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASN A 440 " --> pdb=" O ARG A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 472 removed outlier: 3.514A pdb=" N ASP A 470 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG A 472 " --> pdb=" O LEU A 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 53 removed outlier: 4.898A pdb=" N ALA B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N THR B 51 " --> pdb=" O ARG B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 removed outlier: 3.628A pdb=" N ASP B 120 " --> pdb=" O ASP B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 136 removed outlier: 3.579A pdb=" N SER B 135 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA B 136 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 181 removed outlier: 3.914A pdb=" N ARG B 169 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU B 181 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 204 removed outlier: 3.921A pdb=" N THR B 203 " --> pdb=" O ASP B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 217 Processing helix chain 'B' and resid 233 through 238 Processing helix chain 'B' and resid 291 through 295 Processing helix chain 'B' and resid 297 through 301 Processing helix chain 'B' and resid 318 through 324 Processing helix chain 'C' and resid 29 through 33 removed outlier: 3.592A pdb=" N ARG C 33 " --> pdb=" O TRP C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 39 removed outlier: 3.726A pdb=" N TRP C 39 " --> pdb=" O SER C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 62 removed outlier: 3.626A pdb=" N ARG C 62 " --> pdb=" O THR C 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 59 through 62' Processing helix chain 'C' and resid 63 through 72 Processing helix chain 'C' and resid 111 through 129 Processing helix chain 'C' and resid 131 through 144 Processing helix chain 'C' and resid 148 through 152 Processing helix chain 'C' and resid 189 through 204 Processing helix chain 'C' and resid 256 through 265 Processing helix chain 'C' and resid 297 through 301 Processing helix chain 'C' and resid 303 through 315 Processing helix chain 'C' and resid 319 through 333 removed outlier: 3.508A pdb=" N GLY C 333 " --> pdb=" O ASN C 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 39 Processing helix chain 'D' and resid 63 through 73 Processing helix chain 'D' and resid 111 through 129 Processing helix chain 'D' and resid 131 through 144 Processing helix chain 'D' and resid 145 through 152 removed outlier: 6.423A pdb=" N ARG D 150 " --> pdb=" O PHE D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 204 Processing helix chain 'D' and resid 256 through 265 Processing helix chain 'D' and resid 303 through 313 removed outlier: 3.711A pdb=" N LEU D 307 " --> pdb=" O ASP D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 333 Processing helix chain 'E' and resid 35 through 39 Processing helix chain 'E' and resid 58 through 62 removed outlier: 3.511A pdb=" N ASP E 61 " --> pdb=" O LYS E 58 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG E 62 " --> pdb=" O THR E 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 58 through 62' Processing helix chain 'E' and resid 63 through 73 Processing helix chain 'E' and resid 111 through 129 Processing helix chain 'E' and resid 132 through 144 removed outlier: 3.516A pdb=" N ASN E 144 " --> pdb=" O HIS E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 149 Processing helix chain 'E' and resid 189 through 205 removed outlier: 4.001A pdb=" N ASP E 193 " --> pdb=" O ASP E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 265 removed outlier: 3.982A pdb=" N ILE E 260 " --> pdb=" O HIS E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 314 removed outlier: 3.551A pdb=" N ARG E 314 " --> pdb=" O ASN E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 333 removed outlier: 3.539A pdb=" N GLY E 333 " --> pdb=" O ASN E 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 39 removed outlier: 4.010A pdb=" N ARG F 33 " --> pdb=" O TRP F 30 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ASP F 34 " --> pdb=" O ALA F 31 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER F 36 " --> pdb=" O ARG F 33 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N GLN F 37 " --> pdb=" O ASP F 34 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP F 39 " --> pdb=" O SER F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 62 removed outlier: 3.884A pdb=" N ARG F 62 " --> pdb=" O THR F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 73 removed outlier: 3.808A pdb=" N LEU F 67 " --> pdb=" O ASP F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 129 removed outlier: 3.535A pdb=" N ARG F 115 " --> pdb=" O ASP F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 145 removed outlier: 3.652A pdb=" N ALA F 145 " --> pdb=" O ASN F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 153 removed outlier: 6.294A pdb=" N ARG F 150 " --> pdb=" O PHE F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 204 Processing helix chain 'F' and resid 256 through 265 Processing helix chain 'F' and resid 297 through 301 removed outlier: 3.775A pdb=" N LYS F 301 " --> pdb=" O PRO F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 314 removed outlier: 3.830A pdb=" N ARG F 314 " --> pdb=" O ASN F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 333 Processing helix chain 'G' and resid 34 through 39 removed outlier: 4.162A pdb=" N GLN G 37 " --> pdb=" O ASP G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 62 removed outlier: 3.610A pdb=" N ARG G 62 " --> pdb=" O THR G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 73 Processing helix chain 'G' and resid 111 through 129 Processing helix chain 'G' and resid 131 through 144 Processing helix chain 'G' and resid 145 through 152 removed outlier: 6.426A pdb=" N ARG G 150 " --> pdb=" O PHE G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 189 through 204 Processing helix chain 'G' and resid 256 through 265 Processing helix chain 'G' and resid 303 through 314 Processing helix chain 'G' and resid 319 through 333 Processing sheet with id=AA1, first strand: chain 'A' and resid 229 through 231 removed outlier: 5.260A pdb=" N ALA A 230 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ASN B 282 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ALA B 253 " --> pdb=" O TRP B 316 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG B 315 " --> pdb=" O GLN B 306 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN B 306 " --> pdb=" O ARG B 315 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER B 317 " --> pdb=" O TYR B 304 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR B 304 " --> pdb=" O SER B 317 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 278 through 280 Processing sheet with id=AA3, first strand: chain 'B' and resid 8 through 16 removed outlier: 3.815A pdb=" N LEU B 109 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG B 14 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL B 107 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N SER B 16 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU B 105 " --> pdb=" O SER B 16 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY B 112 " --> pdb=" O ASP B 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 8 through 16 removed outlier: 3.815A pdb=" N LEU B 109 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG B 14 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL B 107 " --> pdb=" O ARG B 14 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N SER B 16 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU B 105 " --> pdb=" O SER B 16 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N HIS B 104 " --> pdb=" O PHE B 66 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N PHE B 66 " --> pdb=" O HIS B 104 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLU B 106 " --> pdb=" O HIS B 64 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE B 62 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 70 through 71 removed outlier: 4.431A pdb=" N SER B 71 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL B 80 " --> pdb=" O SER B 71 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 185 through 188 removed outlier: 3.814A pdb=" N VAL B 187 " --> pdb=" O GLN B 288 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN B 288 " --> pdb=" O VAL B 187 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 12 through 13 removed outlier: 3.502A pdb=" N ALA C 13 " --> pdb=" O ALA C 108 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 19 through 20 removed outlier: 3.930A pdb=" N ASP C 19 " --> pdb=" O ARG C 98 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG C 98 " --> pdb=" O ASP C 19 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU C 211 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL C 214 " --> pdb=" O ARG C 161 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N VAL C 160 " --> pdb=" O PHE C 176 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N PHE C 176 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE C 162 " --> pdb=" O TRP C 174 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TRP C 174 " --> pdb=" O ILE C 162 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 19 through 20 removed outlier: 3.930A pdb=" N ASP C 19 " --> pdb=" O ARG C 98 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG C 98 " --> pdb=" O ASP C 19 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 45 through 50 removed outlier: 4.582A pdb=" N ALA C 82 " --> pdb=" O VAL C 225 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 18 through 20 removed outlier: 4.252A pdb=" N LEU D 211 " --> pdb=" O LEU D 97 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 169 through 170 removed outlier: 4.252A pdb=" N LEU D 211 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU D 24 " --> pdb=" O ARG D 94 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA D 23 " --> pdb=" O ILE D 255 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N ALA D 253 " --> pdb=" O LEU D 25 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 45 through 49 removed outlier: 4.299A pdb=" N ALA D 82 " --> pdb=" O VAL D 225 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 229 through 230 removed outlier: 4.427A pdb=" N THR D 245 " --> pdb=" O GLU D 230 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 18 through 20 removed outlier: 3.857A pdb=" N LEU E 91 " --> pdb=" O ALA E 217 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA E 217 " --> pdb=" O LEU E 91 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL E 93 " --> pdb=" O ALA E 215 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA E 215 " --> pdb=" O VAL E 93 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE E 95 " --> pdb=" O VAL E 213 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU E 97 " --> pdb=" O LEU E 211 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N LEU E 211 " --> pdb=" O LEU E 97 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL E 214 " --> pdb=" O ARG E 161 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG E 161 " --> pdb=" O VAL E 214 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG E 218 " --> pdb=" O ALA E 157 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA E 157 " --> pdb=" O ARG E 218 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 18 through 20 removed outlier: 3.737A pdb=" N THR E 90 " --> pdb=" O GLY E 28 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY E 28 " --> pdb=" O THR E 90 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG E 94 " --> pdb=" O LEU E 24 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU E 24 " --> pdb=" O ARG E 94 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA E 23 " --> pdb=" O ILE E 255 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 287 through 288 removed outlier: 3.786A pdb=" N VAL E 288 " --> pdb=" O LYS E 293 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS E 293 " --> pdb=" O VAL E 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'F' and resid 18 through 20 removed outlier: 3.901A pdb=" N LEU F 210 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG F 166 " --> pdb=" O GLU F 169 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 23 through 24 Processing sheet with id=AC2, first strand: chain 'F' and resid 47 through 51 removed outlier: 3.887A pdb=" N ASN F 75 " --> pdb=" O GLY F 51 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 229 through 230 removed outlier: 4.349A pdb=" N THR F 245 " --> pdb=" O GLU F 230 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 266 through 268 Processing sheet with id=AC5, first strand: chain 'G' and resid 12 through 13 removed outlier: 3.786A pdb=" N ALA G 108 " --> pdb=" O ALA G 13 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 18 through 20 removed outlier: 3.517A pdb=" N ARG G 98 " --> pdb=" O ASP G 19 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU G 211 " --> pdb=" O LEU G 97 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL G 99 " --> pdb=" O VAL G 209 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL G 209 " --> pdb=" O VAL G 99 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LEU G 210 " --> pdb=" O ILE G 165 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE G 165 " --> pdb=" O LEU G 210 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU G 212 " --> pdb=" O ASN G 163 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA G 157 " --> pdb=" O ARG G 218 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ARG G 172 " --> pdb=" O HIS G 164 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ARG G 166 " --> pdb=" O VAL G 170 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N VAL G 170 " --> pdb=" O ARG G 166 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 18 through 20 removed outlier: 3.517A pdb=" N ARG G 98 " --> pdb=" O ASP G 19 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG G 94 " --> pdb=" O LEU G 24 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA G 23 " --> pdb=" O ILE G 255 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 44 through 50 removed outlier: 3.962A pdb=" N VAL G 49 " --> pdb=" O GLN G 77 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLN G 77 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N SER G 243 " --> pdb=" O LEU G 76 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N THR G 78 " --> pdb=" O SER G 243 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N THR G 245 " --> pdb=" O THR G 78 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ASP G 80 " --> pdb=" O THR G 245 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N THR G 245 " --> pdb=" O GLU G 230 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 266 through 268 707 hydrogen bonds defined for protein. 1917 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 4 stacking parallelities Total time for adding SS restraints: 2.85 Time building geometry restraints manager: 2.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6241 1.34 - 1.46: 3313 1.46 - 1.58: 9864 1.58 - 1.70: 73 1.70 - 1.82: 26 Bond restraints: 19517 Sorted by residual: bond pdb=" CB ASN C 141 " pdb=" CG ASN C 141 " ideal model delta sigma weight residual 1.516 1.454 0.062 2.50e-02 1.60e+03 6.12e+00 bond pdb=" CA LEU D 183 " pdb=" C LEU D 183 " ideal model delta sigma weight residual 1.522 1.492 0.031 1.37e-02 5.33e+03 4.97e+00 bond pdb=" C ARG B 85 " pdb=" N ASN B 86 " ideal model delta sigma weight residual 1.331 1.357 -0.027 1.36e-02 5.41e+03 3.85e+00 bond pdb=" C ALA C 139 " pdb=" N HIS C 140 " ideal model delta sigma weight residual 1.334 1.309 0.025 1.27e-02 6.20e+03 3.83e+00 bond pdb=" C ALA C 139 " pdb=" O ALA C 139 " ideal model delta sigma weight residual 1.236 1.217 0.019 1.26e-02 6.30e+03 2.32e+00 ... (remaining 19512 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 26360 2.71 - 5.42: 259 5.42 - 8.13: 32 8.13 - 10.84: 9 10.84 - 13.54: 1 Bond angle restraints: 26661 Sorted by residual: angle pdb=" N ILE D 267 " pdb=" CA ILE D 267 " pdb=" C ILE D 267 " ideal model delta sigma weight residual 113.10 107.93 5.17 9.70e-01 1.06e+00 2.84e+01 angle pdb=" N ILE C 267 " pdb=" CA ILE C 267 " pdb=" C ILE C 267 " ideal model delta sigma weight residual 113.10 109.01 4.09 9.70e-01 1.06e+00 1.78e+01 angle pdb=" N ILE G 267 " pdb=" CA ILE G 267 " pdb=" C ILE G 267 " ideal model delta sigma weight residual 113.20 109.26 3.94 9.60e-01 1.09e+00 1.69e+01 angle pdb=" CA LEU B 181 " pdb=" CB LEU B 181 " pdb=" CG LEU B 181 " ideal model delta sigma weight residual 116.30 129.84 -13.54 3.50e+00 8.16e-02 1.50e+01 angle pdb=" CA ARG D 250 " pdb=" CB ARG D 250 " pdb=" CG ARG D 250 " ideal model delta sigma weight residual 114.10 121.74 -7.64 2.00e+00 2.50e-01 1.46e+01 ... (remaining 26656 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.76: 10415 20.76 - 41.53: 1144 41.53 - 62.29: 200 62.29 - 83.05: 45 83.05 - 103.81: 6 Dihedral angle restraints: 11810 sinusoidal: 5055 harmonic: 6755 Sorted by residual: dihedral pdb=" O4' A I 29 " pdb=" C1' A I 29 " pdb=" N9 A I 29 " pdb=" C4 A I 29 " ideal model delta sinusoidal sigma weight residual -106.00 -174.76 68.76 1 1.70e+01 3.46e-03 2.12e+01 dihedral pdb=" O4' U I 9 " pdb=" C1' U I 9 " pdb=" N1 U I 9 " pdb=" C2 U I 9 " ideal model delta sinusoidal sigma weight residual -128.00 -67.53 -60.47 1 1.70e+01 3.46e-03 1.68e+01 dihedral pdb=" CA GLY F 286 " pdb=" C GLY F 286 " pdb=" N SER F 287 " pdb=" CA SER F 287 " ideal model delta harmonic sigma weight residual -180.00 -159.76 -20.24 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 11807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2351 0.047 - 0.094: 499 0.094 - 0.141: 122 0.141 - 0.188: 4 0.188 - 0.235: 2 Chirality restraints: 2978 Sorted by residual: chirality pdb=" CB ILE F 53 " pdb=" CA ILE F 53 " pdb=" CG1 ILE F 53 " pdb=" CG2 ILE F 53 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CG LEU B 181 " pdb=" CB LEU B 181 " pdb=" CD1 LEU B 181 " pdb=" CD2 LEU B 181 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CB VAL E 126 " pdb=" CA VAL E 126 " pdb=" CG1 VAL E 126 " pdb=" CG2 VAL E 126 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.06e-01 ... (remaining 2975 not shown) Planarity restraints: 3390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 130 " 0.040 5.00e-02 4.00e+02 6.03e-02 5.82e+00 pdb=" N PRO A 131 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 131 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 131 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 170 " 0.209 9.50e-02 1.11e+02 9.38e-02 5.40e+00 pdb=" NE ARG B 170 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG B 170 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG B 170 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B 170 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 270 " -0.018 2.00e-02 2.50e+03 1.43e-02 5.11e+00 pdb=" CG TRP G 270 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP G 270 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP G 270 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP G 270 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP G 270 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP G 270 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 270 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 270 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP G 270 " -0.001 2.00e-02 2.50e+03 ... (remaining 3387 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 333 2.66 - 3.22: 17643 3.22 - 3.78: 28597 3.78 - 4.34: 36543 4.34 - 4.90: 59390 Nonbonded interactions: 142506 Sorted by model distance: nonbonded pdb=" O LYS G 47 " pdb=" OG1 THR G 78 " model vdw 2.104 3.040 nonbonded pdb=" O THR F 306 " pdb=" ND2 ASN F 310 " model vdw 2.111 3.120 nonbonded pdb=" NZ LYS F 299 " pdb=" O ARG G 62 " model vdw 2.124 3.120 nonbonded pdb=" O GLY A 446 " pdb=" OG SER A 450 " model vdw 2.126 3.040 nonbonded pdb=" NH2 ARG F 16 " pdb=" OP2 U I 24 " model vdw 2.163 3.120 ... (remaining 142501 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 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.590 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5404 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 : 0.003 0.062 19517 Z= 0.168 Angle : 0.728 13.544 26661 Z= 0.402 Chirality : 0.041 0.235 2978 Planarity : 0.005 0.094 3390 Dihedral : 17.051 103.813 7446 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.11 % Allowed : 28.87 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.17), residues: 2330 helix: 0.74 (0.19), residues: 718 sheet: -0.24 (0.32), residues: 264 loop : -0.97 (0.16), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 98 TYR 0.015 0.001 TYR F 247 PHE 0.021 0.002 PHE F 226 TRP 0.038 0.002 TRP G 270 HIS 0.016 0.002 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.17 (19517) covalent geometry : angle 0.72795 / 0.40 (26661) hydrogen bonds : bond 0.19951 / 13.67 ( 690) hydrogen bonds : angle 7.27898 / 5.27 ( 1917) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4660 Ramachandran restraints generated. 2330 Oldfield, 0 Emsley, 2330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4660 Ramachandran restraints generated. 2330 Oldfield, 0 Emsley, 2330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 179 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 MET cc_start: 0.6094 (ptp) cc_final: 0.5805 (pmm) REVERT: B 1 MET cc_start: 0.0214 (mmt) cc_final: -0.2030 (ptt) REVERT: B 194 GLN cc_start: 0.6639 (OUTLIER) cc_final: 0.6082 (mm-40) REVERT: C 15 GLU cc_start: 0.6755 (tt0) cc_final: 0.6409 (pm20) REVERT: C 256 HIS cc_start: 0.5915 (m-70) cc_final: 0.5365 (m90) REVERT: D 25 LEU cc_start: 0.6944 (OUTLIER) cc_final: 0.6213 (pp) REVERT: E 30 TRP cc_start: -0.0102 (OUTLIER) cc_final: -0.0820 (m-10) REVERT: E 60 LYS cc_start: 0.6437 (pttt) cc_final: 0.5834 (tppt) REVERT: E 151 ASN cc_start: 0.1727 (p0) cc_final: 0.0628 (t0) REVERT: E 274 GLU cc_start: 0.6615 (pm20) cc_final: 0.5628 (tm-30) REVERT: E 305 TYR cc_start: 0.2407 (m-80) cc_final: 0.2082 (m-10) REVERT: F 26 SER cc_start: 0.8354 (m) cc_final: 0.7855 (p) REVERT: F 55 ASN cc_start: 0.5952 (OUTLIER) cc_final: 0.4782 (t0) REVERT: G 251 ASP cc_start: 0.7758 (m-30) cc_final: 0.6585 (t0) outliers start: 21 outliers final: 15 residues processed: 195 average time/residue: 0.1403 time to fit residues: 41.0587 Evaluate side-chains 172 residues out of total 1891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 153 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain B residue 247 TRP Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain D residue 14 PHE Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 30 TRP Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain F residue 55 ASN Chi-restraints excluded: chain F residue 232 ILE Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain F residue 331 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.0770 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 235 optimal weight: 9.9990 overall best weight: 2.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 HIS C 140 HIS D 72 GLN ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 310 ASN ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4956 r_free = 0.4956 target = 0.206136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.179558 restraints weight = 46524.231| |-----------------------------------------------------------------------------| r_work (start): 0.4620 rms_B_bonded: 4.29 r_work (final): 0.4620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5752 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 19517 Z= 0.203 Angle : 0.688 10.878 26661 Z= 0.354 Chirality : 0.043 0.187 2978 Planarity : 0.006 0.070 3390 Dihedral : 11.905 110.953 3156 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.76 % Allowed : 23.11 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.17), residues: 2330 helix: 0.62 (0.19), residues: 728 sheet: -0.45 (0.31), residues: 271 loop : -1.10 (0.16), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG E 332 TYR 0.026 0.002 TYR F 247 PHE 0.026 0.003 PHE G 304 TRP 0.029 0.003 TRP D 270 HIS 0.011 0.002 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.20 (19517) covalent geometry : angle 0.68808 / 0.35 (26661) hydrogen bonds : bond 0.03852 / 2.69 ( 690) hydrogen bonds : angle 5.57233 / 4.07 ( 1917) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4660 Ramachandran restraints generated. 2330 Oldfield, 0 Emsley, 2330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4660 Ramachandran restraints generated. 2330 Oldfield, 0 Emsley, 2330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 159 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 GLN cc_start: 0.7280 (mm110) cc_final: 0.7076 (tm-30) REVERT: A 302 TRP cc_start: 0.6182 (m-10) cc_final: 0.5924 (m-90) REVERT: A 424 MET cc_start: 0.6601 (ptp) cc_final: 0.6133 (pmm) REVERT: A 445 MET cc_start: 0.5312 (tpp) cc_final: 0.5050 (tpp) REVERT: D 98 ARG cc_start: 0.6684 (mmp80) cc_final: 0.5836 (mmp80) REVERT: E 60 LYS cc_start: 0.6178 (pttt) cc_final: 0.5676 (mmmt) REVERT: E 314 ARG cc_start: 0.6840 (tpt90) cc_final: 0.6578 (tpt90) REVERT: F 26 SER cc_start: 0.8365 (m) cc_final: 0.8146 (p) REVERT: F 55 ASN cc_start: 0.5807 (p0) cc_final: 0.4838 (t0) REVERT: F 293 LYS cc_start: 0.3070 (tptt) cc_final: 0.2859 (tmtt) REVERT: G 264 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.6990 (mm) outliers start: 90 outliers final: 49 residues processed: 231 average time/residue: 0.1431 time to fit residues: 50.1571 Evaluate side-chains 190 residues out of total 1891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 140 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 ARG Chi-restraints excluded: chain A residue 369 CYS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 121 HIS Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 217 SER Chi-restraints excluded: chain B residue 247 TRP Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 327 ILE Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 107 SER Chi-restraints excluded: chain F residue 280 ILE Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 280 ILE Chi-restraints excluded: chain G residue 287 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 66 optimal weight: 0.7980 chunk 111 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 217 optimal weight: 0.8980 chunk 135 optimal weight: 20.0000 chunk 226 optimal weight: 0.0770 chunk 142 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 chunk 92 optimal weight: 0.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 GLN ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 256 HIS ** G 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4979 r_free = 0.4979 target = 0.208177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.181926 restraints weight = 46643.080| |-----------------------------------------------------------------------------| r_work (start): 0.4651 rms_B_bonded: 4.38 r_work (final): 0.4651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5669 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19517 Z= 0.109 Angle : 0.545 10.346 26661 Z= 0.278 Chirality : 0.040 0.240 2978 Planarity : 0.004 0.054 3390 Dihedral : 11.508 107.670 3136 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.33 % Allowed : 23.27 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.17), residues: 2330 helix: 0.97 (0.19), residues: 730 sheet: -0.53 (0.30), residues: 286 loop : -0.94 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 98 TYR 0.016 0.001 TYR E 125 PHE 0.013 0.001 PHE G 216 TRP 0.038 0.001 TRP D 270 HIS 0.012 0.001 HIS G 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (19517) covalent geometry : angle 0.54530 / 0.28 (26661) hydrogen bonds : bond 0.03529 / 2.47 ( 690) hydrogen bonds : angle 5.19146 / 3.79 ( 1917) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4660 Ramachandran restraints generated. 2330 Oldfield, 0 Emsley, 2330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4660 Ramachandran restraints generated. 2330 Oldfield, 0 Emsley, 2330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 162 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 TRP cc_start: 0.6147 (m-10) cc_final: 0.5857 (m-10) REVERT: A 424 MET cc_start: 0.6545 (ptp) cc_final: 0.6128 (pmm) REVERT: A 445 MET cc_start: 0.5166 (tpp) cc_final: 0.4669 (tpp) REVERT: B 1 MET cc_start: 0.0128 (mmp) cc_final: -0.2060 (ptt) REVERT: E 60 LYS cc_start: 0.6207 (pttt) cc_final: 0.5702 (mmmt) REVERT: E 231 LEU cc_start: 0.1823 (OUTLIER) cc_final: 0.1553 (tp) REVERT: E 274 GLU cc_start: 0.6855 (mp0) cc_final: 0.5700 (tm-30) REVERT: F 55 ASN cc_start: 0.5880 (p0) cc_final: 0.4951 (t0) REVERT: G 264 LEU cc_start: 0.7051 (OUTLIER) cc_final: 0.6810 (mm) outliers start: 63 outliers final: 39 residues processed: 208 average time/residue: 0.1485 time to fit residues: 47.0876 Evaluate side-chains 177 residues out of total 1891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 136 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 ARG Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 247 TRP Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain F residue 98 ARG Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 251 ASP Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 287 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 34 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 173 optimal weight: 9.9990 chunk 201 optimal weight: 8.9990 chunk 105 optimal weight: 9.9990 chunk 75 optimal weight: 0.0970 chunk 118 optimal weight: 0.9990 chunk 138 optimal weight: 7.9990 chunk 86 optimal weight: 0.0060 chunk 232 optimal weight: 0.2980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 82 ASN B 194 GLN D 229 GLN ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 241 GLN ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4985 r_free = 0.4985 target = 0.208839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.182620 restraints weight = 46496.488| |-----------------------------------------------------------------------------| r_work (start): 0.4660 rms_B_bonded: 4.33 r_work (final): 0.4660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5640 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19517 Z= 0.099 Angle : 0.521 11.296 26661 Z= 0.265 Chirality : 0.040 0.258 2978 Planarity : 0.004 0.056 3390 Dihedral : 11.424 106.443 3136 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.86 % Allowed : 23.64 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.17), residues: 2330 helix: 1.17 (0.19), residues: 730 sheet: -0.48 (0.29), residues: 286 loop : -0.83 (0.17), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 98 TYR 0.014 0.001 TYR E 125 PHE 0.014 0.001 PHE A 219 TRP 0.021 0.001 TRP D 270 HIS 0.007 0.001 HIS G 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00213 / 0.10 (19517) covalent geometry : angle 0.52115 / 0.27 (26661) hydrogen bonds : bond 0.03054 / 2.12 ( 690) hydrogen bonds : angle 4.95667 / 3.60 ( 1917) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4660 Ramachandran restraints generated. 2330 Oldfield, 0 Emsley, 2330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4660 Ramachandran restraints generated. 2330 Oldfield, 0 Emsley, 2330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 150 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 MET cc_start: 0.6501 (ptp) cc_final: 0.6194 (ptp) REVERT: A 445 MET cc_start: 0.5216 (tpp) cc_final: 0.4628 (tpp) REVERT: B 1 MET cc_start: 0.0068 (mmp) cc_final: -0.2112 (ptt) REVERT: B 247 TRP cc_start: 0.5268 (OUTLIER) cc_final: 0.4758 (t60) REVERT: C 316 GLU cc_start: 0.5354 (OUTLIER) cc_final: 0.4738 (pm20) REVERT: E 60 LYS cc_start: 0.6157 (pttt) cc_final: 0.5935 (mmmt) REVERT: E 231 LEU cc_start: 0.1925 (OUTLIER) cc_final: 0.1608 (tp) REVERT: F 55 ASN cc_start: 0.5984 (p0) cc_final: 0.5094 (t0) REVERT: F 229 GLN cc_start: 0.7470 (OUTLIER) cc_final: 0.6885 (pp30) REVERT: F 250 ARG cc_start: 0.6184 (mmp80) cc_final: 0.5244 (ptp-170) REVERT: G 251 ASP cc_start: 0.7590 (OUTLIER) cc_final: 0.6670 (t0) REVERT: G 264 LEU cc_start: 0.6951 (OUTLIER) cc_final: 0.6721 (mm) outliers start: 54 outliers final: 32 residues processed: 191 average time/residue: 0.1500 time to fit residues: 43.7480 Evaluate side-chains 170 residues out of total 1891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 132 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 247 TRP Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 332 ARG Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 98 ARG Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 107 SER Chi-restraints excluded: chain F residue 229 GLN Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 92 LYS Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 251 ASP Chi-restraints excluded: chain G residue 264 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 231 optimal weight: 4.9990 chunk 207 optimal weight: 10.0000 chunk 26 optimal weight: 20.0000 chunk 104 optimal weight: 0.9990 chunk 127 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 142 optimal weight: 6.9990 chunk 172 optimal weight: 5.9990 chunk 150 optimal weight: 0.8980 chunk 162 optimal weight: 7.9990 chunk 113 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 GLN ** C 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 HIS D 291 GLN ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 297 GLN ** F 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4907 r_free = 0.4907 target = 0.200892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.173494 restraints weight = 46801.015| |-----------------------------------------------------------------------------| r_work (start): 0.4554 rms_B_bonded: 4.33 r_work (final): 0.4554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5944 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 19517 Z= 0.218 Angle : 0.705 14.131 26661 Z= 0.361 Chirality : 0.045 0.290 2978 Planarity : 0.006 0.074 3390 Dihedral : 11.904 111.292 3136 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 5.29 % Allowed : 22.47 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.17), residues: 2330 helix: 0.59 (0.19), residues: 728 sheet: -0.71 (0.30), residues: 286 loop : -1.10 (0.17), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 136 TYR 0.028 0.002 TYR D 285 PHE 0.030 0.003 PHE C 216 TRP 0.073 0.003 TRP D 270 HIS 0.033 0.002 HIS D 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.22 (19517) covalent geometry : angle 0.70452 / 0.36 (26661) hydrogen bonds : bond 0.04123 / 2.92 ( 690) hydrogen bonds : angle 5.35875 / 3.87 ( 1917) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4660 Ramachandran restraints generated. 2330 Oldfield, 0 Emsley, 2330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4660 Ramachandran restraints generated. 2330 Oldfield, 0 Emsley, 2330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 146 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 GLN cc_start: 0.7560 (mm110) cc_final: 0.7056 (tm-30) REVERT: A 288 GLN cc_start: 0.7000 (OUTLIER) cc_final: 0.6417 (tp-100) REVERT: A 424 MET cc_start: 0.6573 (ptp) cc_final: 0.6300 (ptp) REVERT: A 445 MET cc_start: 0.5909 (tpp) cc_final: 0.5542 (tpp) REVERT: B 1 MET cc_start: -0.0024 (mmp) cc_final: -0.2099 (mtm) REVERT: B 102 ARG cc_start: 0.8015 (mmt90) cc_final: 0.7757 (mmm160) REVERT: B 137 MET cc_start: 0.8228 (mmm) cc_final: 0.7301 (mmt) REVERT: B 148 CYS cc_start: 0.7856 (p) cc_final: 0.7579 (p) REVERT: B 247 TRP cc_start: 0.5467 (OUTLIER) cc_final: 0.4810 (t60) REVERT: B 280 VAL cc_start: 0.6508 (OUTLIER) cc_final: 0.6199 (t) REVERT: C 270 TRP cc_start: 0.7310 (m-90) cc_final: 0.7080 (m-90) REVERT: D 77 GLN cc_start: 0.6324 (pm20) cc_final: 0.6099 (pm20) REVERT: D 219 ILE cc_start: 0.5836 (OUTLIER) cc_final: 0.5534 (mm) REVERT: E 60 LYS cc_start: 0.6012 (pttt) cc_final: 0.5802 (mmmt) REVERT: E 231 LEU cc_start: 0.1511 (OUTLIER) cc_final: 0.1127 (tp) REVERT: F 55 ASN cc_start: 0.6476 (p0) cc_final: 0.5432 (t0) REVERT: F 229 GLN cc_start: 0.7617 (OUTLIER) cc_final: 0.6797 (pp30) REVERT: G 208 HIS cc_start: 0.4421 (OUTLIER) cc_final: 0.2088 (t-90) REVERT: G 264 LEU cc_start: 0.7058 (OUTLIER) cc_final: 0.6799 (mm) outliers start: 100 outliers final: 61 residues processed: 234 average time/residue: 0.1280 time to fit residues: 46.9542 Evaluate side-chains 197 residues out of total 1891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 128 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 HIS Chi-restraints excluded: chain A residue 288 GLN Chi-restraints excluded: chain A residue 297 ARG Chi-restraints excluded: chain A residue 369 CYS Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 247 TRP Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 50 ARG Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 109 CYS Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 98 ARG Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 229 GLN Chi-restraints excluded: chain F residue 280 ILE Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 174 TRP Chi-restraints excluded: chain G residue 208 HIS Chi-restraints excluded: chain G residue 251 ASP Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 280 ILE Chi-restraints excluded: chain G residue 335 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 170 optimal weight: 0.0470 chunk 45 optimal weight: 6.9990 chunk 175 optimal weight: 9.9990 chunk 56 optimal weight: 7.9990 chunk 139 optimal weight: 0.6980 chunk 118 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 208 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 169 optimal weight: 7.9990 chunk 112 optimal weight: 0.3980 overall best weight: 2.4282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN ** C 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4909 r_free = 0.4909 target = 0.201056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.173886 restraints weight = 46444.087| |-----------------------------------------------------------------------------| r_work (start): 0.4560 rms_B_bonded: 4.32 r_work (final): 0.4560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5927 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19517 Z= 0.164 Angle : 0.602 11.417 26661 Z= 0.311 Chirality : 0.042 0.208 2978 Planarity : 0.005 0.059 3390 Dihedral : 11.865 110.107 3134 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.12 % Allowed : 23.90 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.17), residues: 2330 helix: 0.71 (0.19), residues: 724 sheet: -0.76 (0.30), residues: 280 loop : -1.07 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 174 TYR 0.020 0.002 TYR D 285 PHE 0.020 0.002 PHE G 304 TRP 0.027 0.002 TRP D 270 HIS 0.013 0.001 HIS D 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (19517) covalent geometry : angle 0.60152 / 0.31 (26661) hydrogen bonds : bond 0.03443 / 2.42 ( 690) hydrogen bonds : angle 5.22328 / 3.77 ( 1917) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4660 Ramachandran restraints generated. 2330 Oldfield, 0 Emsley, 2330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4660 Ramachandran restraints generated. 2330 Oldfield, 0 Emsley, 2330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 152 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 GLN cc_start: 0.7622 (mm110) cc_final: 0.7026 (tm-30) REVERT: A 424 MET cc_start: 0.6682 (ptp) cc_final: 0.6386 (ptp) REVERT: B 1 MET cc_start: 0.0143 (mmp) cc_final: -0.1886 (ptt) REVERT: B 137 MET cc_start: 0.8035 (mmm) cc_final: 0.6902 (mmt) REVERT: B 247 TRP cc_start: 0.5400 (OUTLIER) cc_final: 0.4534 (t60) REVERT: B 280 VAL cc_start: 0.6524 (OUTLIER) cc_final: 0.6270 (t) REVERT: C 184 ARG cc_start: -0.0346 (OUTLIER) cc_final: -0.1697 (tpp-160) REVERT: D 57 LEU cc_start: 0.7306 (mp) cc_final: 0.7043 (pp) REVERT: D 77 GLN cc_start: 0.6378 (pm20) cc_final: 0.6171 (pm20) REVERT: D 219 ILE cc_start: 0.5964 (OUTLIER) cc_final: 0.5684 (mm) REVERT: E 60 LYS cc_start: 0.6053 (pttt) cc_final: 0.5816 (mmmt) REVERT: E 325 TYR cc_start: 0.3217 (OUTLIER) cc_final: 0.2897 (t80) REVERT: F 55 ASN cc_start: 0.6387 (p0) cc_final: 0.5403 (t0) REVERT: F 229 GLN cc_start: 0.7503 (OUTLIER) cc_final: 0.6891 (pp30) REVERT: G 174 TRP cc_start: 0.4715 (OUTLIER) cc_final: 0.3933 (m-10) REVERT: G 264 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6880 (mm) outliers start: 78 outliers final: 57 residues processed: 219 average time/residue: 0.1323 time to fit residues: 45.0808 Evaluate side-chains 198 residues out of total 1891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 133 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 HIS Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 247 TRP Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 184 ARG Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 228 SER Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 109 CYS Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 325 TYR Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 98 ARG Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 229 GLN Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 174 TRP Chi-restraints excluded: chain G residue 251 ASP Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 280 ILE Chi-restraints excluded: chain G residue 287 SER Chi-restraints excluded: chain G residue 335 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 218 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 193 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 170 optimal weight: 3.9990 chunk 142 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 133 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 122 HIS A 360 HIS ** B 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 HIS D 229 GLN ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4912 r_free = 0.4912 target = 0.201171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4594 r_free = 0.4594 target = 0.174160 restraints weight = 46688.564| |-----------------------------------------------------------------------------| r_work (start): 0.4568 rms_B_bonded: 4.35 r_work (final): 0.4568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5906 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19517 Z= 0.134 Angle : 0.576 12.083 26661 Z= 0.295 Chirality : 0.041 0.218 2978 Planarity : 0.004 0.055 3390 Dihedral : 11.796 108.599 3134 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.65 % Allowed : 24.70 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.17), residues: 2330 helix: 0.78 (0.19), residues: 726 sheet: -0.68 (0.30), residues: 284 loop : -0.98 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 174 TYR 0.012 0.001 TYR E 125 PHE 0.017 0.002 PHE G 216 TRP 0.016 0.001 TRP D 270 HIS 0.006 0.001 HIS D 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (19517) covalent geometry : angle 0.57585 / 0.29 (26661) hydrogen bonds : bond 0.03165 / 2.24 ( 690) hydrogen bonds : angle 5.08873 / 3.67 ( 1917) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4660 Ramachandran restraints generated. 2330 Oldfield, 0 Emsley, 2330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4660 Ramachandran restraints generated. 2330 Oldfield, 0 Emsley, 2330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 148 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 GLN cc_start: 0.7566 (mm110) cc_final: 0.7001 (tm-30) REVERT: A 288 GLN cc_start: 0.7020 (OUTLIER) cc_final: 0.6408 (tp-100) REVERT: A 424 MET cc_start: 0.6730 (ptp) cc_final: 0.6322 (ptp) REVERT: A 438 LEU cc_start: -0.4314 (OUTLIER) cc_final: -0.4576 (tp) REVERT: A 445 MET cc_start: 0.5899 (tpp) cc_final: 0.5671 (tpp) REVERT: B 1 MET cc_start: 0.0241 (mmp) cc_final: -0.1861 (ptt) REVERT: B 137 MET cc_start: 0.8042 (mmm) cc_final: 0.6836 (mmt) REVERT: B 148 CYS cc_start: 0.7821 (p) cc_final: 0.7422 (p) REVERT: B 247 TRP cc_start: 0.5408 (OUTLIER) cc_final: 0.4526 (t60) REVERT: B 280 VAL cc_start: 0.6480 (OUTLIER) cc_final: 0.6225 (t) REVERT: D 57 LEU cc_start: 0.7336 (mp) cc_final: 0.7128 (pp) REVERT: D 77 GLN cc_start: 0.6472 (pm20) cc_final: 0.6258 (pm20) REVERT: D 219 ILE cc_start: 0.5754 (OUTLIER) cc_final: 0.5386 (mm) REVERT: E 60 LYS cc_start: 0.6026 (pttt) cc_final: 0.5787 (mmmt) REVERT: E 325 TYR cc_start: 0.3235 (OUTLIER) cc_final: 0.2910 (t80) REVERT: F 55 ASN cc_start: 0.6379 (p0) cc_final: 0.5580 (t0) REVERT: F 229 GLN cc_start: 0.7436 (OUTLIER) cc_final: 0.6835 (pp30) REVERT: G 174 TRP cc_start: 0.4677 (OUTLIER) cc_final: 0.3775 (m-10) REVERT: G 264 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.6803 (mm) outliers start: 69 outliers final: 51 residues processed: 207 average time/residue: 0.1350 time to fit residues: 44.0770 Evaluate side-chains 194 residues out of total 1891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 134 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 288 GLN Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 121 HIS Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 247 TRP Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 109 CYS Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 325 TYR Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 98 ARG Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 229 GLN Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 92 LYS Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 174 TRP Chi-restraints excluded: chain G residue 251 ASP Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 280 ILE Chi-restraints excluded: chain G residue 287 SER Chi-restraints excluded: chain G residue 335 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 5 optimal weight: 0.1980 chunk 63 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 183 optimal weight: 0.3980 chunk 40 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 185 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 178 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 55 ASN G 72 GLN ** G 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4900 r_free = 0.4900 target = 0.199744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.172675 restraints weight = 46625.545| |-----------------------------------------------------------------------------| r_work (start): 0.4551 rms_B_bonded: 4.30 r_work (final): 0.4551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5950 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19517 Z= 0.149 Angle : 0.596 12.044 26661 Z= 0.308 Chirality : 0.042 0.208 2978 Planarity : 0.005 0.051 3390 Dihedral : 11.804 107.551 3132 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.81 % Allowed : 24.91 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.17), residues: 2330 helix: 0.81 (0.19), residues: 719 sheet: -0.52 (0.32), residues: 263 loop : -0.99 (0.17), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 314 TYR 0.023 0.002 TYR D 285 PHE 0.018 0.002 PHE G 216 TRP 0.017 0.002 TRP A 422 HIS 0.005 0.001 HIS C 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (19517) covalent geometry : angle 0.59575 / 0.31 (26661) hydrogen bonds : bond 0.03327 / 2.42 ( 690) hydrogen bonds : angle 5.13924 / 3.69 ( 1917) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4660 Ramachandran restraints generated. 2330 Oldfield, 0 Emsley, 2330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4660 Ramachandran restraints generated. 2330 Oldfield, 0 Emsley, 2330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 140 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 263 GLN cc_start: 0.7641 (mm110) cc_final: 0.6983 (tm-30) REVERT: A 288 GLN cc_start: 0.7083 (OUTLIER) cc_final: 0.6456 (tp-100) REVERT: A 424 MET cc_start: 0.6813 (ptp) cc_final: 0.6504 (ptp) REVERT: A 438 LEU cc_start: -0.4306 (OUTLIER) cc_final: -0.4552 (tp) REVERT: B 1 MET cc_start: -0.0103 (mmp) cc_final: -0.1923 (ptt) REVERT: B 137 MET cc_start: 0.7995 (mmm) cc_final: 0.6769 (mmt) REVERT: B 148 CYS cc_start: 0.7726 (p) cc_final: 0.7265 (p) REVERT: B 247 TRP cc_start: 0.5374 (OUTLIER) cc_final: 0.4435 (t-100) REVERT: B 280 VAL cc_start: 0.6578 (OUTLIER) cc_final: 0.6297 (t) REVERT: C 16 ARG cc_start: 0.5845 (ptt90) cc_final: 0.4268 (tpp80) REVERT: C 184 ARG cc_start: -0.0389 (OUTLIER) cc_final: -0.1829 (tpp-160) REVERT: D 77 GLN cc_start: 0.6413 (pm20) cc_final: 0.6188 (pm20) REVERT: D 219 ILE cc_start: 0.5731 (OUTLIER) cc_final: 0.5383 (mm) REVERT: E 60 LYS cc_start: 0.6034 (pttt) cc_final: 0.5741 (mmmt) REVERT: E 325 TYR cc_start: 0.3315 (OUTLIER) cc_final: 0.3003 (t80) REVERT: F 55 ASN cc_start: 0.6438 (p0) cc_final: 0.5562 (t0) REVERT: F 229 GLN cc_start: 0.7420 (OUTLIER) cc_final: 0.6153 (mp10) REVERT: G 174 TRP cc_start: 0.4727 (OUTLIER) cc_final: 0.3875 (m-10) REVERT: G 264 LEU cc_start: 0.7025 (OUTLIER) cc_final: 0.6771 (mm) outliers start: 72 outliers final: 56 residues processed: 202 average time/residue: 0.1354 time to fit residues: 42.3883 Evaluate side-chains 196 residues out of total 1891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 130 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 GLN Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 121 HIS Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 247 TRP Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 184 ARG Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 109 CYS Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 325 TYR Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 98 ARG Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 229 GLN Chi-restraints excluded: chain F residue 280 ILE Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 92 LYS Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 174 TRP Chi-restraints excluded: chain G residue 251 ASP Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 280 ILE Chi-restraints excluded: chain G residue 287 SER Chi-restraints excluded: chain G residue 335 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 155 optimal weight: 0.0670 chunk 21 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 207 optimal weight: 5.9990 chunk 152 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 24 optimal weight: 0.2980 chunk 145 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 overall best weight: 1.4320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 280 GLN ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4906 r_free = 0.4906 target = 0.200156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.173167 restraints weight = 46427.079| |-----------------------------------------------------------------------------| r_work (start): 0.4562 rms_B_bonded: 4.31 r_work (final): 0.4562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5922 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19517 Z= 0.127 Angle : 0.579 12.971 26661 Z= 0.297 Chirality : 0.041 0.240 2978 Planarity : 0.004 0.054 3390 Dihedral : 11.762 106.858 3132 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.54 % Allowed : 25.28 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.17), residues: 2330 helix: 0.89 (0.19), residues: 718 sheet: -0.68 (0.30), residues: 278 loop : -0.93 (0.17), residues: 1334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 174 TYR 0.013 0.001 TYR C 271 PHE 0.017 0.002 PHE G 216 TRP 0.016 0.001 TRP A 422 HIS 0.008 0.001 HIS D 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (19517) covalent geometry : angle 0.57854 / 0.30 (26661) hydrogen bonds : bond 0.03145 / 2.22 ( 690) hydrogen bonds : angle 5.07430 / 3.64 ( 1917) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4660 Ramachandran restraints generated. 2330 Oldfield, 0 Emsley, 2330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4660 Ramachandran restraints generated. 2330 Oldfield, 0 Emsley, 2330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 140 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 263 GLN cc_start: 0.7699 (mm110) cc_final: 0.7030 (tm-30) REVERT: A 288 GLN cc_start: 0.7052 (OUTLIER) cc_final: 0.6430 (tp-100) REVERT: A 424 MET cc_start: 0.6820 (ptp) cc_final: 0.6500 (ptp) REVERT: A 438 LEU cc_start: -0.4191 (OUTLIER) cc_final: -0.4455 (tp) REVERT: B 1 MET cc_start: 0.0104 (mmp) cc_final: -0.1759 (ptt) REVERT: B 137 MET cc_start: 0.7954 (mmm) cc_final: 0.6682 (mmt) REVERT: B 148 CYS cc_start: 0.7553 (p) cc_final: 0.7097 (p) REVERT: B 247 TRP cc_start: 0.5357 (OUTLIER) cc_final: 0.4459 (t-100) REVERT: B 280 VAL cc_start: 0.6392 (OUTLIER) cc_final: 0.6117 (t) REVERT: C 16 ARG cc_start: 0.5794 (ptt90) cc_final: 0.4251 (tpp80) REVERT: C 184 ARG cc_start: -0.0323 (OUTLIER) cc_final: -0.1793 (tpp-160) REVERT: D 72 GLN cc_start: 0.6660 (mm110) cc_final: 0.6415 (mp10) REVERT: D 77 GLN cc_start: 0.6439 (pm20) cc_final: 0.6207 (pm20) REVERT: D 219 ILE cc_start: 0.5653 (OUTLIER) cc_final: 0.5328 (mm) REVERT: D 270 TRP cc_start: 0.5819 (m-90) cc_final: 0.5004 (m-90) REVERT: E 60 LYS cc_start: 0.6033 (pttt) cc_final: 0.5742 (mmmt) REVERT: F 55 ASN cc_start: 0.6380 (p0) cc_final: 0.5576 (t0) REVERT: F 229 GLN cc_start: 0.7348 (OUTLIER) cc_final: 0.6095 (mp10) REVERT: G 174 TRP cc_start: 0.4721 (OUTLIER) cc_final: 0.3511 (m-10) REVERT: G 264 LEU cc_start: 0.7007 (OUTLIER) cc_final: 0.6766 (mm) outliers start: 67 outliers final: 52 residues processed: 196 average time/residue: 0.1397 time to fit residues: 41.9179 Evaluate side-chains 193 residues out of total 1891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 132 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 GLN Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 121 HIS Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 247 TRP Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 184 ARG Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 280 ILE Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 109 CYS Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 98 ARG Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 229 GLN Chi-restraints excluded: chain F residue 280 ILE Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 331 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 92 LYS Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 174 TRP Chi-restraints excluded: chain G residue 251 ASP Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 335 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 170 optimal weight: 6.9990 chunk 122 optimal weight: 8.9990 chunk 220 optimal weight: 0.8980 chunk 80 optimal weight: 0.2980 chunk 37 optimal weight: 0.8980 chunk 227 optimal weight: 7.9990 chunk 192 optimal weight: 3.9990 chunk 159 optimal weight: 0.0040 chunk 179 optimal weight: 0.9980 chunk 187 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 HIS ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4921 r_free = 0.4921 target = 0.201430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.175412 restraints weight = 45044.362| |-----------------------------------------------------------------------------| r_work (start): 0.4589 rms_B_bonded: 4.22 r_work (final): 0.4589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5839 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19517 Z= 0.104 Angle : 0.571 13.569 26661 Z= 0.286 Chirality : 0.041 0.283 2978 Planarity : 0.004 0.053 3390 Dihedral : 11.617 105.512 3130 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.59 % Allowed : 26.34 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.17), residues: 2330 helix: 1.06 (0.19), residues: 720 sheet: -0.64 (0.30), residues: 280 loop : -0.82 (0.17), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 417 TYR 0.013 0.001 TYR E 125 PHE 0.014 0.001 PHE D 186 TRP 0.016 0.001 TRP A 422 HIS 0.008 0.001 HIS D 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (19517) covalent geometry : angle 0.57101 / 0.29 (26661) hydrogen bonds : bond 0.02892 / 2.08 ( 690) hydrogen bonds : angle 4.90583 / 3.52 ( 1917) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4660 Ramachandran restraints generated. 2330 Oldfield, 0 Emsley, 2330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4660 Ramachandran restraints generated. 2330 Oldfield, 0 Emsley, 2330 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 143 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 263 GLN cc_start: 0.7623 (mm110) cc_final: 0.6984 (tm-30) REVERT: A 288 GLN cc_start: 0.6973 (OUTLIER) cc_final: 0.6397 (tp-100) REVERT: A 424 MET cc_start: 0.6817 (ptp) cc_final: 0.6526 (ptp) REVERT: A 438 LEU cc_start: -0.4187 (OUTLIER) cc_final: -0.4431 (tp) REVERT: B 1 MET cc_start: 0.0196 (mmp) cc_final: -0.1679 (ptt) REVERT: B 72 GLN cc_start: 0.7157 (pt0) cc_final: 0.6930 (pp30) REVERT: B 137 MET cc_start: 0.7896 (mmm) cc_final: 0.6632 (mmt) REVERT: B 148 CYS cc_start: 0.7519 (p) cc_final: 0.7058 (p) REVERT: B 192 MET cc_start: 0.5523 (mmt) cc_final: 0.5122 (mpp) REVERT: B 247 TRP cc_start: 0.5228 (OUTLIER) cc_final: 0.4444 (t60) REVERT: B 280 VAL cc_start: 0.6176 (OUTLIER) cc_final: 0.5915 (t) REVERT: C 16 ARG cc_start: 0.5760 (ptt90) cc_final: 0.4288 (tpp80) REVERT: C 184 ARG cc_start: -0.0395 (OUTLIER) cc_final: -0.1772 (tpp-160) REVERT: D 77 GLN cc_start: 0.6447 (pm20) cc_final: 0.6224 (pm20) REVERT: D 219 ILE cc_start: 0.5572 (OUTLIER) cc_final: 0.5211 (mm) REVERT: D 270 TRP cc_start: 0.5691 (m-90) cc_final: 0.5461 (m-90) REVERT: E 60 LYS cc_start: 0.6071 (pttt) cc_final: 0.5761 (mmmt) REVERT: F 55 ASN cc_start: 0.6439 (p0) cc_final: 0.5635 (t0) REVERT: F 229 GLN cc_start: 0.7293 (OUTLIER) cc_final: 0.6068 (mp10) REVERT: F 250 ARG cc_start: 0.6160 (mmp80) cc_final: 0.5414 (ptp-170) REVERT: G 174 TRP cc_start: 0.4700 (OUTLIER) cc_final: 0.3462 (m-10) REVERT: G 264 LEU cc_start: 0.6937 (OUTLIER) cc_final: 0.6701 (mm) outliers start: 49 outliers final: 36 residues processed: 182 average time/residue: 0.1313 time to fit residues: 37.2060 Evaluate side-chains 177 residues out of total 1891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 132 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 GLN Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 121 HIS Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 247 TRP Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 184 ARG Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 98 ARG Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 229 GLN Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 174 TRP Chi-restraints excluded: chain G residue 251 ASP Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 335 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 205 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 92 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 170 optimal weight: 0.2980 chunk 174 optimal weight: 4.9990 chunk 221 optimal weight: 3.9990 chunk 160 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 141 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 = 0.4883 r_free = 0.4883 target = 0.197369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.170881 restraints weight = 45177.862| |-----------------------------------------------------------------------------| r_work (start): 0.4537 rms_B_bonded: 4.22 r_work (final): 0.4537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5977 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19517 Z= 0.169 Angle : 0.629 13.526 26661 Z= 0.323 Chirality : 0.043 0.245 2978 Planarity : 0.005 0.055 3390 Dihedral : 11.751 107.114 3128 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.07 % Allowed : 25.86 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.17), residues: 2330 helix: 0.90 (0.19), residues: 718 sheet: -0.62 (0.31), residues: 262 loop : -0.96 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 98 TYR 0.017 0.002 TYR F 305 PHE 0.019 0.002 PHE G 216 TRP 0.019 0.002 TRP A 422 HIS 0.008 0.001 HIS D 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (19517) covalent geometry : angle 0.62881 / 0.32 (26661) hydrogen bonds : bond 0.03384 / 2.40 ( 690) hydrogen bonds : angle 5.14199 / 3.68 ( 1917) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3214.57 seconds wall clock time: 56 minutes 19.20 seconds (3379.20 seconds total)