Starting phenix.real_space_refine on Mon May 4 07:59:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jpg_61699/05_2026/9jpg_61699.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jpg_61699/05_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_61699/05_2026/9jpg_61699.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jpg_61699/05_2026/9jpg_61699.map" model { file = "/net/cci-nas-00/data/ceres_data/9jpg_61699/05_2026/9jpg_61699.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jpg_61699/05_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-2.1rc2-6044/lib/python3.9/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: 4.95, per 1000 atoms: 0.26 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: 2.06 Conformation dependent library (CDL) restraints added in 981.4 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: 2.28 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: 3.32 Time building geometry restraints manager: 2.60 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: 4.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 21.230 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5295 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= 0.165 Angle : 0.728 13.544 26661 Z= 0.397 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 covalent geometry : bond 0.00333 (19517) covalent geometry : angle 0.72796 (26661) hydrogen bonds : bond 0.19951 ( 690) hydrogen bonds : angle 7.27898 ( 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 : 0.641 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: 0.1601 time to fit residues: 46.8901 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 : 0.751 ------------------------------------------------------------------------------- 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: 7.9990 overall best weight: 2.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN ** A 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS A 408 HIS ** B 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN D 164 HIS ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 GLN E 164 HIS ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 310 ASN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4908 r_free = 0.4908 target = 0.200748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.173455 restraints weight = 46552.018| |-----------------------------------------------------------------------------| r_work (start): 0.4559 rms_B_bonded: 4.30 r_work (final): 0.4559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5830 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 19517 Z= 0.211 Angle : 0.719 10.774 26661 Z= 0.371 Chirality : 0.044 0.176 2978 Planarity : 0.006 0.062 3390 Dihedral : 12.395 114.951 3156 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 5.39 % Allowed : 22.53 % Favored : 72.08 % 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: -0.82 (0.17), residues: 2330 helix: 0.41 (0.19), residues: 724 sheet: -0.62 (0.29), residues: 291 loop : -1.07 (0.16), residues: 1315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG E 332 TYR 0.030 0.002 TYR F 247 PHE 0.026 0.003 PHE G 216 TRP 0.044 0.003 TRP D 270 HIS 0.011 0.002 HIS G 140 Details of bonding type rmsd covalent geometry : bond 0.00466 (19517) covalent geometry : angle 0.71921 (26661) hydrogen bonds : bond 0.04256 ( 690) hydrogen bonds : angle 5.55593 ( 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 276 residues out of total 1891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 174 time to evaluate : 0.753 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: 0.7618 (mm110) cc_final: 0.6927 (tm-30) REVERT: A 288 GLN cc_start: 0.6906 (OUTLIER) cc_final: 0.6345 (tp-100) REVERT: A 424 MET cc_start: 0.6611 (ptp) cc_final: 0.6265 (ptp) REVERT: A 445 MET cc_start: 0.5350 (tpp) cc_final: 0.5065 (tpp) REVERT: B 148 CYS cc_start: 0.7745 (p) cc_final: 0.7424 (p) REVERT: B 247 TRP cc_start: 0.5441 (OUTLIER) cc_final: 0.4509 (t60) REVERT: C 144 ASN cc_start: 0.5367 (p0) cc_final: 0.4422 (t0) REVERT: E 14 PHE cc_start: 0.7646 (OUTLIER) cc_final: 0.7061 (m-80) REVERT: E 60 LYS cc_start: 0.6136 (pttt) cc_final: 0.5824 (mmmt) REVERT: E 244 LYS cc_start: 0.3811 (pttt) cc_final: 0.3466 (mmtt) REVERT: E 274 GLU cc_start: 0.6882 (pm20) cc_final: 0.5963 (tm-30) REVERT: E 308 LEU cc_start: 0.6259 (tp) cc_final: 0.5955 (tp) REVERT: F 55 ASN cc_start: 0.6146 (p0) cc_final: 0.5391 (t0) REVERT: G 174 TRP cc_start: 0.4656 (OUTLIER) cc_final: 0.3169 (m-10) REVERT: G 264 LEU cc_start: 0.7159 (OUTLIER) cc_final: 0.6918 (mm) outliers start: 102 outliers final: 53 residues processed: 256 average time/residue: 0.1512 time to fit residues: 58.7339 Evaluate side-chains 196 residues out of total 1891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 138 time to evaluate : 0.626 ------------------------------------------------------------------------------- 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 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 51 THR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 121 HIS Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 247 TRP 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 24 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 151 ASN 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 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 78 THR Chi-restraints excluded: chain D residue 134 LEU 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 14 PHE Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 98 ARG Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 174 TRP Chi-restraints excluded: chain G residue 203 LEU 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 66 optimal weight: 6.9990 chunk 111 optimal weight: 0.9980 chunk 25 optimal weight: 30.0000 chunk 217 optimal weight: 3.9990 chunk 135 optimal weight: 8.9990 chunk 226 optimal weight: 0.8980 chunk 142 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 83 optimal weight: 10.0000 chunk 92 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 HIS B 194 GLN ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 GLN ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 297 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4937 r_free = 0.4937 target = 0.203518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.176514 restraints weight = 46674.850| |-----------------------------------------------------------------------------| r_work (start): 0.4601 rms_B_bonded: 4.35 r_work (final): 0.4601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5726 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 19517 Z= 0.107 Angle : 0.540 9.437 26661 Z= 0.275 Chirality : 0.040 0.161 2978 Planarity : 0.004 0.047 3390 Dihedral : 11.730 106.356 3138 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.23 % Allowed : 23.90 % Favored : 72.87 % 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: -0.39 (0.17), residues: 2330 helix: 0.92 (0.19), residues: 720 sheet: -0.47 (0.30), residues: 268 loop : -0.86 (0.17), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 98 TYR 0.019 0.001 TYR E 125 PHE 0.013 0.002 PHE D 186 TRP 0.019 0.001 TRP D 270 HIS 0.011 0.001 HIS G 140 Details of bonding type rmsd covalent geometry : bond 0.00231 (19517) covalent geometry : angle 0.54030 (26661) hydrogen bonds : bond 0.03175 ( 690) hydrogen bonds : angle 4.98790 ( 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 241 residues out of total 1891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 180 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 GLN cc_start: 0.7626 (mm110) cc_final: 0.7022 (tm-30) REVERT: A 267 TRP cc_start: 0.5365 (t-100) cc_final: 0.4970 (t-100) REVERT: A 424 MET cc_start: 0.6608 (ptp) cc_final: 0.6150 (pmm) REVERT: A 445 MET cc_start: 0.5720 (tpp) cc_final: 0.5512 (tpp) REVERT: B 148 CYS cc_start: 0.7479 (p) cc_final: 0.7273 (t) REVERT: B 247 TRP cc_start: 0.5142 (OUTLIER) cc_final: 0.4442 (t60) REVERT: B 274 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6164 (tp30) REVERT: B 280 VAL cc_start: 0.6394 (OUTLIER) cc_final: 0.6165 (t) REVERT: D 219 ILE cc_start: 0.5492 (OUTLIER) cc_final: 0.5226 (mm) REVERT: E 60 LYS cc_start: 0.6118 (pttt) cc_final: 0.5553 (mmmt) REVERT: F 55 ASN cc_start: 0.6244 (p0) cc_final: 0.5426 (t0) REVERT: F 98 ARG cc_start: 0.7035 (OUTLIER) cc_final: 0.6161 (ttt180) REVERT: F 229 GLN cc_start: 0.7353 (OUTLIER) cc_final: 0.6744 (pp30) REVERT: G 50 ARG cc_start: 0.4386 (OUTLIER) cc_final: 0.4128 (ttm170) outliers start: 61 outliers final: 28 residues processed: 231 average time/residue: 0.1472 time to fit residues: 52.4133 Evaluate side-chains 179 residues out of total 1891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 144 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 121 HIS Chi-restraints excluded: chain B residue 247 TRP Chi-restraints excluded: chain B residue 274 GLU 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 59 THR Chi-restraints excluded: chain C residue 86 SER 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 228 SER Chi-restraints excluded: chain C residue 335 VAL 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 45 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 264 LEU 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 213 VAL Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 98 ARG Chi-restraints excluded: chain F residue 229 GLN Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain G residue 50 ARG Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 335 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 34 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 173 optimal weight: 2.9990 chunk 201 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 118 optimal weight: 8.9990 chunk 138 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 232 optimal weight: 0.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 HIS ** B 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 GLN ** E 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 323 GLN ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 GLN ** 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 = 0.4929 r_free = 0.4929 target = 0.202247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.175280 restraints weight = 46513.802| |-----------------------------------------------------------------------------| r_work (start): 0.4591 rms_B_bonded: 4.33 r_work (final): 0.4591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5749 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19517 Z= 0.109 Angle : 0.525 10.008 26661 Z= 0.267 Chirality : 0.040 0.201 2978 Planarity : 0.004 0.051 3390 Dihedral : 11.579 104.480 3132 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 3.28 % Allowed : 24.11 % Favored : 72.61 % 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: -0.21 (0.17), residues: 2330 helix: 1.09 (0.19), residues: 720 sheet: -0.34 (0.30), residues: 282 loop : -0.77 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 98 TYR 0.017 0.001 TYR E 125 PHE 0.014 0.002 PHE G 216 TRP 0.018 0.001 TRP C 270 HIS 0.011 0.001 HIS D 140 Details of bonding type rmsd covalent geometry : bond 0.00239 (19517) covalent geometry : angle 0.52488 (26661) hydrogen bonds : bond 0.02903 ( 690) hydrogen bonds : angle 4.74549 ( 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 226 residues out of total 1891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 164 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 263 GLN cc_start: 0.7708 (mm110) cc_final: 0.7128 (tm-30) REVERT: A 424 MET cc_start: 0.6802 (ptp) cc_final: 0.6411 (ptp) REVERT: B 247 TRP cc_start: 0.5163 (OUTLIER) cc_final: 0.4392 (t60) REVERT: B 280 VAL cc_start: 0.6302 (OUTLIER) cc_final: 0.6063 (t) REVERT: C 142 LEU cc_start: 0.7529 (mt) cc_final: 0.7320 (mt) REVERT: D 219 ILE cc_start: 0.5708 (OUTLIER) cc_final: 0.5400 (mm) REVERT: E 60 LYS cc_start: 0.6081 (pttt) cc_final: 0.5799 (mmmt) REVERT: F 55 ASN cc_start: 0.6220 (p0) cc_final: 0.5469 (t0) REVERT: F 98 ARG cc_start: 0.7149 (OUTLIER) cc_final: 0.6252 (ttt180) REVERT: F 250 ARG cc_start: 0.6184 (mmp80) cc_final: 0.5291 (ptp-170) REVERT: F 330 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8165 (mt) REVERT: G 174 TRP cc_start: 0.4697 (OUTLIER) cc_final: 0.3444 (m-10) outliers start: 62 outliers final: 37 residues processed: 215 average time/residue: 0.1450 time to fit residues: 48.0281 Evaluate side-chains 186 residues out of total 1891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 143 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE 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 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 59 THR Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 116 ASP Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 214 VAL 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 158 VAL Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 18 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 320 VAL Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 174 TRP Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 251 ASP Chi-restraints excluded: chain G residue 280 ILE Chi-restraints excluded: chain G residue 287 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 231 optimal weight: 7.9990 chunk 207 optimal weight: 0.2980 chunk 26 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 81 optimal weight: 0.0050 chunk 142 optimal weight: 6.9990 chunk 172 optimal weight: 0.9990 chunk 150 optimal weight: 9.9990 chunk 162 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 overall best weight: 1.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 HIS ** F 141 ASN ** 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 324 HIS ** 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 = 0.4882 r_free = 0.4882 target = 0.197070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.169704 restraints weight = 46025.553| |-----------------------------------------------------------------------------| r_work (start): 0.4530 rms_B_bonded: 4.28 r_work (final): 0.4530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5906 moved from start: 0.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19517 Z= 0.148 Angle : 0.589 9.322 26661 Z= 0.302 Chirality : 0.041 0.234 2978 Planarity : 0.005 0.061 3390 Dihedral : 11.794 107.539 3130 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.81 % Allowed : 23.37 % Favored : 71.81 % 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: -0.40 (0.17), residues: 2330 helix: 0.85 (0.19), residues: 719 sheet: -0.51 (0.29), residues: 293 loop : -0.83 (0.17), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 250 TYR 0.015 0.002 TYR F 305 PHE 0.020 0.002 PHE G 216 TRP 0.025 0.002 TRP G 270 HIS 0.010 0.001 HIS D 140 Details of bonding type rmsd covalent geometry : bond 0.00327 (19517) covalent geometry : angle 0.58898 (26661) hydrogen bonds : bond 0.03353 ( 690) hydrogen bonds : angle 5.04553 ( 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 254 residues out of total 1891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 163 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 GLN cc_start: 0.7841 (mm110) cc_final: 0.7339 (tm-30) REVERT: A 288 GLN cc_start: 0.7006 (OUTLIER) cc_final: 0.6420 (tp-100) REVERT: A 424 MET cc_start: 0.6771 (ptp) cc_final: 0.6412 (ptp) REVERT: A 445 MET cc_start: 0.5586 (tpt) cc_final: 0.5306 (tpp) REVERT: B 72 GLN cc_start: 0.7319 (pt0) cc_final: 0.7002 (pp30) REVERT: B 280 VAL cc_start: 0.6734 (OUTLIER) cc_final: 0.6516 (t) REVERT: C 184 ARG cc_start: -0.0343 (OUTLIER) cc_final: -0.1665 (tpp-160) REVERT: D 219 ILE cc_start: 0.5748 (OUTLIER) cc_final: 0.5443 (mm) REVERT: D 269 THR cc_start: 0.6859 (OUTLIER) cc_final: 0.6547 (m) REVERT: D 270 TRP cc_start: 0.5955 (m-90) cc_final: 0.5002 (m-90) REVERT: E 60 LYS cc_start: 0.6191 (pttt) cc_final: 0.5838 (mmmt) REVERT: E 274 GLU cc_start: 0.7830 (mp0) cc_final: 0.6800 (tm-30) REVERT: F 229 GLN cc_start: 0.7363 (OUTLIER) cc_final: 0.5905 (mp10) REVERT: F 330 LEU cc_start: 0.8654 (mp) cc_final: 0.8360 (mt) REVERT: G 174 TRP cc_start: 0.5086 (OUTLIER) cc_final: 0.3765 (m-10) REVERT: G 264 LEU cc_start: 0.7059 (OUTLIER) cc_final: 0.6795 (mm) outliers start: 91 outliers final: 66 residues processed: 241 average time/residue: 0.1464 time to fit residues: 53.7250 Evaluate side-chains 210 residues out of total 1891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 136 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 288 GLN Chi-restraints excluded: chain A residue 369 CYS Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 444 VAL 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 B residue 324 HIS Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 16 ARG 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 140 HIS Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 184 ARG Chi-restraints excluded: chain C residue 189 ASP 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 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 11 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 34 ASP 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 210 LEU Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 269 THR 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 213 VAL Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain F residue 58 LYS 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 183 LEU Chi-restraints excluded: chain F residue 229 GLN Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain G residue 15 GLU Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 174 TRP Chi-restraints excluded: chain G residue 203 LEU 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 289 THR 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: 0.0050 chunk 45 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 139 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 208 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 169 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 ASN ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 GLN ** 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** ** 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 = 0.4862 r_free = 0.4862 target = 0.195249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.168627 restraints weight = 44799.168| |-----------------------------------------------------------------------------| r_work (start): 0.4517 rms_B_bonded: 4.20 r_work (final): 0.4517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5934 moved from start: 0.5330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19517 Z= 0.152 Angle : 0.583 8.777 26661 Z= 0.300 Chirality : 0.041 0.194 2978 Planarity : 0.004 0.053 3390 Dihedral : 11.792 104.177 3130 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 5.13 % Allowed : 24.01 % Favored : 70.86 % 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: -0.44 (0.17), residues: 2330 helix: 0.81 (0.19), residues: 720 sheet: -0.51 (0.30), residues: 288 loop : -0.85 (0.17), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 265 TYR 0.023 0.002 TYR F 247 PHE 0.021 0.002 PHE G 216 TRP 0.017 0.002 TRP A 422 HIS 0.008 0.001 HIS D 140 Details of bonding type rmsd covalent geometry : bond 0.00336 (19517) covalent geometry : angle 0.58285 (26661) hydrogen bonds : bond 0.03236 ( 690) hydrogen bonds : angle 5.05116 ( 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 248 residues out of total 1891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 151 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 GLN cc_start: 0.7763 (mm110) cc_final: 0.7255 (tm-30) REVERT: A 288 GLN cc_start: 0.6999 (OUTLIER) cc_final: 0.6525 (pm20) REVERT: B 72 GLN cc_start: 0.7290 (pt0) cc_final: 0.6977 (pp30) REVERT: B 280 VAL cc_start: 0.7000 (OUTLIER) cc_final: 0.6796 (t) REVERT: C 184 ARG cc_start: -0.0037 (OUTLIER) cc_final: -0.2103 (tpp-160) REVERT: D 219 ILE cc_start: 0.5802 (OUTLIER) cc_final: 0.5456 (mm) REVERT: D 267 ILE cc_start: 0.4719 (mt) cc_final: 0.3880 (pt) REVERT: D 269 THR cc_start: 0.7033 (OUTLIER) cc_final: 0.6823 (m) REVERT: D 270 TRP cc_start: 0.5981 (m-90) cc_final: 0.5400 (m-90) REVERT: E 231 LEU cc_start: 0.1752 (OUTLIER) cc_final: 0.1145 (tp) REVERT: F 98 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.6353 (ttt180) REVERT: F 229 GLN cc_start: 0.7318 (OUTLIER) cc_final: 0.5933 (mp10) REVERT: F 305 TYR cc_start: 0.5601 (OUTLIER) cc_final: 0.3933 (m-80) REVERT: G 174 TRP cc_start: 0.5014 (OUTLIER) cc_final: 0.4054 (m-10) REVERT: G 264 LEU cc_start: 0.7024 (OUTLIER) cc_final: 0.6780 (mm) outliers start: 97 outliers final: 62 residues processed: 233 average time/residue: 0.1535 time to fit residues: 54.4442 Evaluate side-chains 201 residues out of total 1891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 128 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 288 GLN Chi-restraints excluded: chain A residue 369 CYS Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 67 GLU 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 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 81 VAL Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 184 ARG Chi-restraints excluded: chain C residue 189 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 C residue 316 GLU Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 11 VAL 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 158 VAL Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 280 ILE 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 96 THR 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 E residue 277 LEU 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 305 TYR Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain G residue 15 GLU Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 174 TRP Chi-restraints excluded: chain G residue 203 LEU 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 289 THR Chi-restraints excluded: chain G residue 305 TYR 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: 1.9990 chunk 59 optimal weight: 1.9990 chunk 193 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 170 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 133 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN D 229 GLN ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4872 r_free = 0.4872 target = 0.195880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.169005 restraints weight = 46344.623| |-----------------------------------------------------------------------------| r_work (start): 0.4532 rms_B_bonded: 4.28 r_work (final): 0.4532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5912 moved from start: 0.5569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19517 Z= 0.120 Angle : 0.553 9.379 26661 Z= 0.282 Chirality : 0.041 0.189 2978 Planarity : 0.004 0.057 3390 Dihedral : 11.686 103.831 3130 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.12 % Allowed : 24.75 % Favored : 71.13 % 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: -0.31 (0.17), residues: 2330 helix: 0.95 (0.19), residues: 721 sheet: -0.34 (0.30), residues: 274 loop : -0.81 (0.17), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 265 TYR 0.015 0.001 TYR E 125 PHE 0.017 0.002 PHE G 216 TRP 0.021 0.001 TRP A 422 HIS 0.006 0.001 HIS D 140 Details of bonding type rmsd covalent geometry : bond 0.00266 (19517) covalent geometry : angle 0.55277 (26661) hydrogen bonds : bond 0.03011 ( 690) hydrogen bonds : angle 4.89952 ( 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 226 residues out of total 1891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 148 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 GLN cc_start: 0.7852 (mm110) cc_final: 0.7358 (tm-30) REVERT: A 288 GLN cc_start: 0.7060 (OUTLIER) cc_final: 0.6527 (tp-100) REVERT: A 445 MET cc_start: 0.5755 (tpt) cc_final: 0.4820 (tpp) REVERT: B 72 GLN cc_start: 0.7230 (pt0) cc_final: 0.6938 (pp30) REVERT: B 99 GLU cc_start: 0.6063 (OUTLIER) cc_final: 0.5714 (pm20) REVERT: B 137 MET cc_start: 0.7744 (mmm) cc_final: 0.7199 (mmt) REVERT: B 280 VAL cc_start: 0.6848 (OUTLIER) cc_final: 0.6627 (t) REVERT: C 53 ILE cc_start: 0.8367 (mp) cc_final: 0.7944 (mt) REVERT: C 184 ARG cc_start: -0.0147 (OUTLIER) cc_final: -0.2000 (tpp-160) REVERT: D 219 ILE cc_start: 0.5691 (OUTLIER) cc_final: 0.5351 (mm) REVERT: D 229 GLN cc_start: 0.5997 (OUTLIER) cc_final: 0.4494 (tt0) REVERT: D 335 VAL cc_start: 0.3452 (OUTLIER) cc_final: 0.3190 (t) REVERT: E 197 GLU cc_start: 0.8188 (pp20) cc_final: 0.7977 (pp20) REVERT: E 231 LEU cc_start: 0.1603 (OUTLIER) cc_final: 0.1057 (tp) REVERT: F 98 ARG cc_start: 0.7286 (OUTLIER) cc_final: 0.6330 (ttt180) REVERT: F 229 GLN cc_start: 0.7266 (OUTLIER) cc_final: 0.5860 (mp10) REVERT: G 47 LYS cc_start: 0.6788 (tppt) cc_final: 0.6290 (ttpt) REVERT: G 174 TRP cc_start: 0.4481 (OUTLIER) cc_final: 0.3430 (m-10) REVERT: G 209 VAL cc_start: 0.3592 (OUTLIER) cc_final: 0.3388 (p) REVERT: G 264 LEU cc_start: 0.6883 (OUTLIER) cc_final: 0.6638 (mm) outliers start: 78 outliers final: 58 residues processed: 212 average time/residue: 0.1426 time to fit residues: 46.0924 Evaluate side-chains 202 residues out of total 1891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 131 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 288 GLN Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 99 GLU 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 8 THR Chi-restraints excluded: chain C residue 16 ARG 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 81 VAL Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain C residue 184 ARG Chi-restraints excluded: chain C residue 189 ASP 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 11 VAL 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 219 ILE Chi-restraints excluded: chain D residue 229 GLN 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 D residue 335 VAL 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 213 VAL Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain F residue 58 LYS 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 183 LEU Chi-restraints excluded: chain F residue 229 GLN Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain G residue 15 GLU Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 174 TRP Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 209 VAL Chi-restraints excluded: chain G residue 251 ASP Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 289 THR 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: 30.0000 chunk 63 optimal weight: 7.9990 chunk 139 optimal weight: 9.9990 chunk 183 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 215 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 185 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 chunk 178 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN A 262 GLN A 280 GLN ** B 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 GLN C 329 ASN ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 151 ASN ** F 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 GLN ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 164 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4714 r_free = 0.4714 target = 0.182840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.154438 restraints weight = 46959.557| |-----------------------------------------------------------------------------| r_work (start): 0.4326 rms_B_bonded: 4.41 r_work (final): 0.4326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6302 moved from start: 0.7492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 19517 Z= 0.377 Angle : 0.941 12.564 26661 Z= 0.490 Chirality : 0.053 0.331 2978 Planarity : 0.007 0.085 3390 Dihedral : 13.023 111.279 3130 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 23.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 5.50 % Allowed : 24.11 % Favored : 70.39 % 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: -1.74 (0.16), residues: 2330 helix: -0.64 (0.18), residues: 723 sheet: -1.17 (0.30), residues: 276 loop : -1.45 (0.16), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG D 98 TYR 0.033 0.003 TYR F 247 PHE 0.036 0.004 PHE G 216 TRP 0.043 0.004 TRP E 311 HIS 0.012 0.002 HIS F 140 Details of bonding type rmsd covalent geometry : bond 0.00837 (19517) covalent geometry : angle 0.94062 (26661) hydrogen bonds : bond 0.05466 ( 690) hydrogen bonds : angle 6.57287 ( 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 245 residues out of total 1891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 141 time to evaluate : 0.689 Fit side-chains revert: symmetry clash REVERT: A 227 HIS cc_start: 0.5706 (OUTLIER) cc_final: 0.5013 (m-70) REVERT: A 288 GLN cc_start: 0.6926 (OUTLIER) cc_final: 0.6379 (pm20) REVERT: A 393 ARG cc_start: 0.8128 (mtt180) cc_final: 0.7892 (mpp-170) REVERT: B 72 GLN cc_start: 0.7345 (pt0) cc_final: 0.6946 (pp30) REVERT: C 336 PHE cc_start: 0.5530 (m-80) cc_final: 0.4044 (m-80) REVERT: D 22 ASP cc_start: 0.4465 (OUTLIER) cc_final: 0.3778 (m-30) REVERT: D 25 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7688 (mt) REVERT: D 219 ILE cc_start: 0.6020 (OUTLIER) cc_final: 0.5609 (mm) REVERT: D 241 GLN cc_start: 0.4195 (OUTLIER) cc_final: 0.2468 (pm20) REVERT: E 274 GLU cc_start: 0.8085 (mp0) cc_final: 0.7001 (tm-30) REVERT: E 308 LEU cc_start: 0.7382 (tp) cc_final: 0.7000 (mm) REVERT: E 314 ARG cc_start: 0.7179 (ptp-170) cc_final: 0.6216 (ptp-170) REVERT: F 98 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.6245 (ttm170) REVERT: F 229 GLN cc_start: 0.7511 (OUTLIER) cc_final: 0.6243 (mp10) REVERT: G 47 LYS cc_start: 0.7179 (tppt) cc_final: 0.6655 (ttpt) REVERT: G 125 TYR cc_start: 0.6318 (t80) cc_final: 0.6006 (t80) REVERT: G 174 TRP cc_start: 0.4719 (OUTLIER) cc_final: 0.3287 (m-10) REVERT: G 264 LEU cc_start: 0.7176 (OUTLIER) cc_final: 0.6918 (mm) REVERT: G 296 ARG cc_start: 0.5800 (OUTLIER) cc_final: 0.4996 (mmt90) outliers start: 104 outliers final: 63 residues processed: 224 average time/residue: 0.1568 time to fit residues: 53.0622 Evaluate side-chains 195 residues out of total 1891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 121 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 122 HIS Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain A residue 288 GLN Chi-restraints excluded: chain A residue 373 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 67 GLU 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 267 VAL Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain C residue 7 ASN Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 297 GLN Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 22 ASP 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 219 ILE Chi-restraints excluded: chain D residue 226 PHE Chi-restraints excluded: chain D residue 241 GLN Chi-restraints excluded: chain D residue 243 SER 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 109 CYS Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain F residue 58 LYS Chi-restraints excluded: chain F residue 81 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 170 VAL Chi-restraints excluded: chain F residue 183 LEU 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 158 VAL Chi-restraints excluded: chain G residue 174 TRP Chi-restraints excluded: chain G residue 203 LEU 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 289 THR Chi-restraints excluded: chain G residue 296 ARG Chi-restraints excluded: chain G residue 305 TYR 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: 6.9990 chunk 21 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 207 optimal weight: 0.5980 chunk 152 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 24 optimal weight: 0.2980 chunk 145 optimal weight: 0.7980 chunk 17 optimal weight: 0.3980 chunk 102 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 HIS ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 GLN D 127 ASN ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 ASN ** 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 ** 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 = 0.4797 r_free = 0.4797 target = 0.190082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.162480 restraints weight = 45614.105| |-----------------------------------------------------------------------------| r_work (start): 0.4438 rms_B_bonded: 4.42 r_work (final): 0.4438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6061 moved from start: 0.7292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19517 Z= 0.136 Angle : 0.635 10.029 26661 Z= 0.327 Chirality : 0.043 0.229 2978 Planarity : 0.005 0.059 3390 Dihedral : 12.167 104.489 3128 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.49 % Allowed : 26.49 % 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: -1.09 (0.17), residues: 2330 helix: 0.12 (0.19), residues: 719 sheet: -1.20 (0.30), residues: 286 loop : -1.07 (0.17), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 98 TYR 0.019 0.002 TYR F 247 PHE 0.020 0.002 PHE F 226 TRP 0.054 0.002 TRP G 270 HIS 0.006 0.001 HIS G 140 Details of bonding type rmsd covalent geometry : bond 0.00302 (19517) covalent geometry : angle 0.63452 (26661) hydrogen bonds : bond 0.03330 ( 690) hydrogen bonds : angle 5.53425 ( 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 220 residues out of total 1891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 154 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 HIS cc_start: 0.5685 (OUTLIER) cc_final: 0.4541 (m-70) REVERT: A 288 GLN cc_start: 0.7135 (OUTLIER) cc_final: 0.6718 (pm20) REVERT: A 445 MET cc_start: 0.5705 (tpp) cc_final: 0.5396 (tpp) REVERT: B 1 MET cc_start: 0.0593 (mmt) cc_final: -0.1499 (mtm) REVERT: B 72 GLN cc_start: 0.7252 (pt0) cc_final: 0.6873 (pp30) REVERT: B 137 MET cc_start: 0.7577 (mmm) cc_final: 0.7371 (mmt) REVERT: D 219 ILE cc_start: 0.5814 (OUTLIER) cc_final: 0.5426 (mm) REVERT: E 313 LEU cc_start: 0.7303 (mt) cc_final: 0.6954 (tp) REVERT: E 314 ARG cc_start: 0.7201 (ptp-170) cc_final: 0.6177 (ptp-170) REVERT: F 229 GLN cc_start: 0.7226 (OUTLIER) cc_final: 0.6098 (mp10) REVERT: F 305 TYR cc_start: 0.5675 (OUTLIER) cc_final: 0.5090 (m-10) REVERT: G 33 ARG cc_start: 0.1523 (mmm-85) cc_final: -0.1383 (mmm160) REVERT: G 47 LYS cc_start: 0.6929 (tppt) cc_final: 0.6625 (ttpt) REVERT: G 55 ASN cc_start: 0.7026 (t0) cc_final: 0.6814 (t0) REVERT: G 125 TYR cc_start: 0.6427 (t80) cc_final: 0.5945 (t80) outliers start: 66 outliers final: 50 residues processed: 205 average time/residue: 0.1489 time to fit residues: 47.1752 Evaluate side-chains 186 residues out of total 1891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 131 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain A residue 288 GLN Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 59 VAL 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 8 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 107 SER Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 151 ASN Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 127 ASN 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 269 THR 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 213 VAL Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 229 GLN Chi-restraints excluded: chain F residue 305 TYR Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 174 TRP Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 251 ASP Chi-restraints excluded: chain G residue 289 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 170 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 220 optimal weight: 10.0000 chunk 80 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 227 optimal weight: 3.9990 chunk 192 optimal weight: 0.3980 chunk 159 optimal weight: 0.0770 chunk 179 optimal weight: 2.9990 chunk 187 optimal weight: 5.9990 chunk 208 optimal weight: 1.9990 overall best weight: 0.8742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 172 ASN ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 ASN ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 ASN ** 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 164 HIS ** G 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4816 r_free = 0.4816 target = 0.191700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.164546 restraints weight = 45918.227| |-----------------------------------------------------------------------------| r_work (start): 0.4462 rms_B_bonded: 4.41 r_work (final): 0.4462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6006 moved from start: 0.7257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19517 Z= 0.118 Angle : 0.612 10.466 26661 Z= 0.312 Chirality : 0.042 0.201 2978 Planarity : 0.005 0.056 3390 Dihedral : 11.905 104.386 3126 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.96 % Allowed : 27.55 % Favored : 69.49 % 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: -0.64 (0.17), residues: 2330 helix: 0.60 (0.19), residues: 713 sheet: -1.14 (0.29), residues: 299 loop : -0.79 (0.18), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 98 TYR 0.018 0.001 TYR D 125 PHE 0.016 0.002 PHE F 226 TRP 0.066 0.002 TRP G 270 HIS 0.005 0.001 HIS C 324 Details of bonding type rmsd covalent geometry : bond 0.00265 (19517) covalent geometry : angle 0.61189 (26661) hydrogen bonds : bond 0.03054 ( 690) hydrogen bonds : angle 5.16556 ( 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 200 residues out of total 1891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 144 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 HIS cc_start: 0.5730 (OUTLIER) cc_final: 0.4522 (m-70) REVERT: A 288 GLN cc_start: 0.7075 (OUTLIER) cc_final: 0.6637 (tp-100) REVERT: A 445 MET cc_start: 0.5898 (tpp) cc_final: 0.5616 (tpp) REVERT: B 1 MET cc_start: 0.0648 (mmt) cc_final: -0.1657 (mtm) REVERT: B 72 GLN cc_start: 0.7195 (pt0) cc_final: 0.6830 (pp30) REVERT: B 137 MET cc_start: 0.7637 (mmm) cc_final: 0.7305 (mmt) REVERT: B 192 MET cc_start: 0.6301 (mmm) cc_final: 0.6068 (mtp) REVERT: C 53 ILE cc_start: 0.8440 (mp) cc_final: 0.8002 (mt) REVERT: D 219 ILE cc_start: 0.5658 (OUTLIER) cc_final: 0.5311 (mm) REVERT: F 229 GLN cc_start: 0.7263 (OUTLIER) cc_final: 0.5857 (mp10) REVERT: F 305 TYR cc_start: 0.5359 (OUTLIER) cc_final: 0.4803 (m-10) REVERT: G 47 LYS cc_start: 0.7006 (tppt) cc_final: 0.6604 (ttpt) REVERT: G 55 ASN cc_start: 0.7040 (t0) cc_final: 0.6762 (t0) REVERT: G 125 TYR cc_start: 0.6273 (t80) cc_final: 0.5831 (t80) outliers start: 56 outliers final: 48 residues processed: 189 average time/residue: 0.1448 time to fit residues: 42.5743 Evaluate side-chains 186 residues out of total 1891 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 133 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 122 HIS Chi-restraints excluded: chain A residue 227 HIS Chi-restraints excluded: chain A residue 288 GLN Chi-restraints excluded: chain A residue 444 VAL 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 247 TRP Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 324 HIS Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 140 HIS Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 316 GLU Chi-restraints excluded: chain D residue 8 THR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 127 ASN 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 269 THR Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain E residue 5 THR 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 213 VAL Chi-restraints excluded: chain E residue 223 GLN Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain F residue 58 LYS Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 105 THR Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 170 VAL Chi-restraints excluded: chain F residue 229 GLN Chi-restraints excluded: chain F residue 305 TYR Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 174 TRP Chi-restraints excluded: chain G residue 203 LEU Chi-restraints excluded: chain G residue 251 ASP Chi-restraints excluded: chain G residue 280 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 205 optimal weight: 8.9990 chunk 112 optimal weight: 0.3980 chunk 70 optimal weight: 5.9990 chunk 132 optimal weight: 0.0770 chunk 92 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 170 optimal weight: 0.9980 chunk 174 optimal weight: 10.0000 chunk 221 optimal weight: 0.0970 chunk 160 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 HIS D 72 GLN D 127 ASN ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 ASN ** 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 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4833 r_free = 0.4833 target = 0.193219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.166002 restraints weight = 46094.137| |-----------------------------------------------------------------------------| r_work (start): 0.4483 rms_B_bonded: 4.48 r_work (final): 0.4483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5956 moved from start: 0.7258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 19517 Z= 0.110 Angle : 0.595 10.313 26661 Z= 0.300 Chirality : 0.041 0.187 2978 Planarity : 0.004 0.058 3390 Dihedral : 11.662 102.587 3126 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.96 % Allowed : 27.60 % Favored : 69.43 % 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: -0.40 (0.18), residues: 2330 helix: 0.86 (0.20), residues: 715 sheet: -0.91 (0.30), residues: 282 loop : -0.72 (0.17), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 98 TYR 0.014 0.001 TYR E 125 PHE 0.016 0.002 PHE F 226 TRP 0.063 0.002 TRP G 270 HIS 0.005 0.001 HIS C 324 Details of bonding type rmsd covalent geometry : bond 0.00248 (19517) covalent geometry : angle 0.59512 (26661) hydrogen bonds : bond 0.02885 ( 690) hydrogen bonds : angle 4.92318 ( 1917) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3699.22 seconds wall clock time: 64 minutes 34.82 seconds (3874.82 seconds total)