Starting phenix.real_space_refine on Fri Aug 7 13:34:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jph_61700/08_2026/9jph_61700.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jph_61700/08_2026/9jph_61700.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jph_61700/08_2026/9jph_61700.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jph_61700/08_2026/9jph_61700.map" model { file = "/net/cci-nas-00/data/ceres_data/9jph_61700/08_2026/9jph_61700.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jph_61700/08_2026/9jph_61700.cif" } resolution = 3.11 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= 0.041 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 32 5.49 5 S 20 5.16 5 C 13344 2.51 5 N 3927 2.21 5 O 4146 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 85 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21469 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 2553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2553 Classifications: {'peptide': 319} Modifications used: {'COO': 1} 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: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2606 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 12, 'TRANS': 324} Chain: "D" Number of atoms: 2615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2615 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 12, 'TRANS': 325} Chain: "E" Number of atoms: 2648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2648 Classifications: {'peptide': 342} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 329} Chain: "F" Number of atoms: 2615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2615 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 12, 'TRANS': 325} Chain: "G" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2597 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 12, 'TRANS': 323} Chain: "H" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2606 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 12, 'TRANS': 324} Chain: "J" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 686 Classifications: {'RNA': 32} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 8, 'rna3p_pur': 12, 'rna3p_pyr': 5} Link IDs: {'rna2p': 15, 'rna3p': 16} Time building chain proxies: 4.44, per 1000 atoms: 0.21 Number of scatterers: 21469 At special positions: 0 Unit cell: (118.911, 131.472, 155.756, 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 20 16.00 P 32 15.00 O 4146 8.00 N 3927 7.00 C 13344 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.94 Conformation dependent library (CDL) restraints added in 882.3 milliseconds 5312 Ramachandran restraints generated. 2656 Oldfield, 0 Emsley, 2656 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4972 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 47 sheets defined 38.1% alpha, 22.4% beta 0 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'A' and resid 135 through 140 removed outlier: 3.648A pdb=" N GLU A 138 " --> pdb=" O GLY A 135 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A 140 " --> pdb=" O HIS A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 251 Processing helix chain 'A' and resid 251 through 263 Processing helix chain 'A' and resid 286 through 290 Processing helix chain 'A' and resid 292 through 297 Processing helix chain 'A' and resid 324 through 329 Processing helix chain 'A' and resid 333 through 350 Processing helix chain 'A' and resid 354 through 379 Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 395 through 403 Processing helix chain 'A' and resid 404 through 409 removed outlier: 3.610A pdb=" N HIS A 408 " --> pdb=" O LEU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 420 Processing helix chain 'A' and resid 421 through 439 Processing helix chain 'A' and resid 446 through 473 removed outlier: 3.575A pdb=" N SER A 450 " --> pdb=" O GLY A 446 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU A 460 " --> pdb=" O ASP A 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 53 removed outlier: 3.585A pdb=" N PHE B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ALA B 50 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N THR B 51 " --> pdb=" O ARG B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 Processing helix chain 'B' and resid 122 through 136 removed outlier: 4.071A pdb=" N ALA B 136 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 180 Processing helix chain 'B' and resid 189 through 201 Processing helix chain 'B' and resid 208 through 217 Processing helix chain 'B' and resid 227 through 233 removed outlier: 3.938A pdb=" N ALA B 232 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER B 233 " --> pdb=" O GLU B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 302 Processing helix chain 'C' and resid 30 through 39 removed outlier: 3.917A pdb=" N ASP C 34 " --> pdb=" O ALA C 31 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER C 36 " --> pdb=" O ARG C 33 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N GLN C 37 " --> pdb=" O ASP C 34 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TRP C 39 " --> pdb=" O SER C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 62 Processing helix chain 'C' and resid 63 through 73 removed outlier: 3.706A pdb=" N SER C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) 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 153 Processing helix chain 'C' and resid 177 through 182 removed outlier: 3.790A pdb=" N GLY C 182 " --> pdb=" O ALA C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 204 Processing helix chain 'C' and resid 256 through 265 removed outlier: 3.525A pdb=" N ILE C 260 " --> pdb=" O HIS C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 314 removed outlier: 3.654A pdb=" N LEU C 307 " --> pdb=" O ASP C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 333 Processing helix chain 'D' and resid 29 through 39 removed outlier: 3.570A pdb=" N ARG D 33 " --> pdb=" O TRP D 30 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ASP D 34 " --> pdb=" O ALA D 31 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER D 36 " --> pdb=" O ARG D 33 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N GLN D 37 " --> pdb=" O ASP D 34 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TRP D 39 " --> pdb=" O SER D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 62 removed outlier: 3.780A pdb=" N ARG D 62 " --> pdb=" O THR D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 73 removed outlier: 3.597A pdb=" N LEU D 67 " --> pdb=" O ASP D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 130 Processing helix chain 'D' and resid 131 through 144 Processing helix chain 'D' and resid 145 through 152 removed outlier: 3.546A pdb=" N LEU D 148 " --> pdb=" O ALA D 145 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ARG D 150 " --> pdb=" O PHE D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 182 removed outlier: 4.049A pdb=" N GLY D 182 " --> pdb=" O ALA D 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 178 through 182' Processing helix chain 'D' and resid 189 through 205 Processing helix chain 'D' and resid 256 through 265 removed outlier: 3.565A pdb=" N ILE D 260 " --> pdb=" O HIS D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 313 Processing helix chain 'D' and resid 319 through 332 Processing helix chain 'E' and resid 29 through 39 removed outlier: 3.791A pdb=" N ARG E 33 " --> pdb=" O TRP E 30 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ASP E 34 " --> pdb=" O ALA E 31 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N GLN E 37 " --> pdb=" O ASP E 34 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN E 38 " --> pdb=" O ALA E 35 " (cutoff:3.500A) Processing helix 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 131 through 144 Processing helix chain 'E' and resid 145 through 152 removed outlier: 6.269A pdb=" N ARG E 150 " --> pdb=" O PHE E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 182 Processing helix chain 'E' and resid 189 through 204 Processing helix chain 'E' and resid 256 through 265 Processing helix chain 'E' and resid 303 through 314 Processing helix chain 'E' and resid 319 through 333 Processing helix chain 'F' and resid 29 through 33 removed outlier: 4.086A pdb=" N ARG F 33 " --> pdb=" O TRP F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 39 Processing helix chain 'F' and resid 63 through 73 removed outlier: 3.669A pdb=" N SER F 73 " --> pdb=" O ALA F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 129 Processing helix chain 'F' and resid 131 through 144 removed outlier: 3.515A pdb=" N ALA F 135 " --> pdb=" O PHE F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 147 No H-bonds generated for 'chain 'F' and resid 145 through 147' Processing helix chain 'F' and resid 148 through 153 removed outlier: 4.231A pdb=" N VAL F 153 " --> pdb=" O TRP F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 182 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 Processing helix chain 'F' and resid 303 through 314 Processing helix chain 'F' and resid 319 through 333 Processing helix chain 'G' and resid 29 through 39 removed outlier: 3.789A pdb=" N ARG G 33 " --> pdb=" O TRP G 30 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ASP G 34 " --> pdb=" O ALA G 31 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER G 36 " --> pdb=" O ARG G 33 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N GLN G 37 " --> pdb=" O ASP G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 62 Processing helix chain 'G' and resid 63 through 73 removed outlier: 3.565A pdb=" N SER G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 130 Processing helix chain 'G' and resid 131 through 144 Processing helix chain 'G' and resid 145 through 153 removed outlier: 6.204A pdb=" N ARG G 150 " --> pdb=" O PHE G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 182 removed outlier: 3.576A pdb=" N ILE G 181 " --> pdb=" O ASP G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 189 through 205 Processing helix chain 'G' and resid 256 through 265 removed outlier: 3.709A pdb=" N ARG G 265 " --> pdb=" O GLY G 261 " (cutoff:3.500A) Processing helix chain 'G' and resid 297 through 301 Processing helix chain 'G' and resid 303 through 313 Processing helix chain 'G' and resid 319 through 333 Processing helix chain 'H' and resid 29 through 33 removed outlier: 3.502A pdb=" N ARG H 33 " --> pdb=" O TRP H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 62 removed outlier: 3.609A pdb=" N ARG H 62 " --> pdb=" O THR H 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 59 through 62' Processing helix chain 'H' and resid 63 through 73 Processing helix chain 'H' and resid 111 through 129 removed outlier: 3.612A pdb=" N ARG H 115 " --> pdb=" O ASP H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 144 Processing helix chain 'H' and resid 145 through 152 removed outlier: 6.335A pdb=" N ARG H 150 " --> pdb=" O PHE H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 182 removed outlier: 3.707A pdb=" N GLY H 182 " --> pdb=" O ALA H 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 189 through 205 removed outlier: 3.637A pdb=" N ASP H 193 " --> pdb=" O ASP H 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 256 through 265 Processing helix chain 'H' and resid 303 through 313 Processing helix chain 'H' and resid 319 through 333 Processing sheet with id=AA1, first strand: chain 'A' and resid 104 through 105 Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 108 removed outlier: 3.534A pdb=" N THR A 108 " --> pdb=" O PHE A 233 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 217 through 220 removed outlier: 8.531A pdb=" N ARG B 278 " --> pdb=" O TYR A 226 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU A 228 " --> pdb=" O ARG B 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 271 through 273 Processing sheet with id=AA5, first strand: chain 'A' and resid 278 through 281 Processing sheet with id=AA6, first strand: chain 'B' and resid 66 through 68 removed outlier: 3.526A pdb=" N GLU B 67 " --> pdb=" O HIS B 104 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ALA B 103 " --> pdb=" O ASN B 19 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL B 107 " --> pdb=" O LEU B 15 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU B 109 " --> pdb=" O PRO B 13 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LEU B 111 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N LEU B 11 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL B 113 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N LEU B 9 " --> pdb=" O VAL B 113 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 143 through 145 removed outlier: 4.226A pdb=" N SER B 16 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N LEU B 9 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL B 113 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N LEU B 11 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LEU B 111 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU B 109 " --> pdb=" O PRO B 13 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL B 107 " --> pdb=" O LEU B 15 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ALA B 103 " --> pdb=" O ASN B 19 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N GLU B 106 " --> pdb=" O CYS B 63 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N CYS B 63 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N SER B 108 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ILE B 61 " --> pdb=" O SER B 108 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU B 110 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL B 59 " --> pdb=" O LEU B 110 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG B 114 " --> pdb=" O GLU B 55 " (cutoff:3.500A) removed outlier: 13.337A pdb=" N VAL B 59 " --> pdb=" O SER B 188 " (cutoff:3.500A) removed outlier: 8.900A pdb=" N SER B 188 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ILE B 61 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE B 184 " --> pdb=" O CYS B 63 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLU B 281 " --> pdb=" O TYR B 255 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N TYR B 255 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU B 283 " --> pdb=" O ALA B 253 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 70 through 71 Processing sheet with id=AA9, first strand: chain 'B' and resid 304 through 308 Processing sheet with id=AB1, first strand: chain 'C' and resid 108 through 109 removed outlier: 4.182A pdb=" N ALA C 108 " --> pdb=" O ALA C 13 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA C 13 " --> pdb=" O ALA C 108 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 18 through 19 removed outlier: 3.979A pdb=" N VAL C 209 " --> pdb=" O VAL C 99 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LEU C 210 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU C 159 " --> pdb=" O PHE C 216 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ARG C 166 " --> pdb=" O VAL C 170 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL C 170 " --> pdb=" O ARG C 166 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 18 through 19 Processing sheet with id=AB4, first strand: chain 'C' and resid 44 through 50 removed outlier: 4.279A pdb=" N ALA C 82 " --> pdb=" O VAL C 225 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 266 through 268 Processing sheet with id=AB6, first strand: chain 'C' and resid 287 through 288 removed outlier: 3.743A pdb=" N LYS C 293 " --> pdb=" O VAL C 288 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 108 through 109 removed outlier: 3.538A pdb=" N GLY D 334 " --> pdb=" O PHE D 14 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 18 through 20 removed outlier: 3.606A pdb=" N VAL D 99 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL D 209 " --> pdb=" O VAL D 99 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU D 210 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL D 158 " --> pdb=" O ASP D 177 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ASP D 177 " --> pdb=" O VAL D 158 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL D 160 " --> pdb=" O ARG D 175 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ARG D 175 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE D 162 " --> pdb=" O ALA D 173 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ALA D 173 " --> pdb=" O ILE D 162 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N HIS D 164 " --> pdb=" O ALA D 171 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 18 through 20 removed outlier: 3.952A pdb=" N LYS D 92 " --> pdb=" O SER D 26 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 45 through 50 removed outlier: 4.447A pdb=" N ALA D 82 " --> pdb=" O VAL D 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 45 through 50 removed outlier: 7.058A pdb=" N LYS D 242 " --> pdb=" O LEU D 76 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR D 78 " --> pdb=" O LYS D 242 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LYS D 244 " --> pdb=" O THR D 78 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 287 through 288 removed outlier: 3.777A pdb=" N VAL D 288 " --> pdb=" O LYS D 293 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS D 293 " --> pdb=" O VAL D 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'E' and resid 108 through 109 removed outlier: 4.445A pdb=" N ALA E 108 " --> pdb=" O ALA E 13 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA E 13 " --> pdb=" O ALA E 108 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 18 through 20 removed outlier: 3.562A pdb=" N PHE E 95 " --> pdb=" O VAL E 213 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL E 99 " --> pdb=" O VAL E 209 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N VAL E 209 " --> pdb=" O VAL E 99 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU E 210 " --> pdb=" O ILE E 165 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA E 157 " --> pdb=" O ARG E 218 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 169 through 173 removed outlier: 6.421A pdb=" N HIS E 164 " --> pdb=" O ALA E 171 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ALA E 173 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE E 162 " --> pdb=" O ALA E 173 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA E 157 " --> pdb=" O ARG E 218 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU E 210 " --> pdb=" O ILE E 165 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N VAL E 209 " --> pdb=" O VAL E 99 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL E 99 " --> pdb=" O VAL E 209 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE E 95 " --> pdb=" O VAL E 213 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ALA E 253 " --> pdb=" O LEU E 25 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 44 through 51 removed outlier: 3.777A pdb=" N GLY E 51 " --> pdb=" O ASN E 75 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASN E 75 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ALA E 82 " --> pdb=" O VAL E 225 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 44 through 51 removed outlier: 3.777A pdb=" N GLY E 51 " --> pdb=" O ASN E 75 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASN E 75 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LYS E 242 " --> pdb=" O LEU E 76 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N THR E 78 " --> pdb=" O LYS E 242 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LYS E 244 " --> pdb=" O THR E 78 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N LEU E 246 " --> pdb=" O ASP E 80 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N ALA E 82 " --> pdb=" O LEU E 246 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR E 245 " --> pdb=" O GLU E 230 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 287 through 288 Processing sheet with id=AD1, first strand: chain 'F' and resid 12 through 13 removed outlier: 3.780A pdb=" N ALA F 108 " --> pdb=" O ALA F 13 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 18 through 20 removed outlier: 3.521A pdb=" N LYS F 92 " --> pdb=" O SER F 26 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 18 through 20 removed outlier: 3.554A pdb=" N VAL F 99 " --> pdb=" O VAL F 209 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL F 209 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU F 210 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU F 159 " --> pdb=" O PHE F 216 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ARG F 166 " --> pdb=" O VAL F 170 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N VAL F 170 " --> pdb=" O ARG F 166 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 43 through 50 removed outlier: 4.493A pdb=" N SER F 43 " --> pdb=" O ASN F 83 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN F 83 " --> pdb=" O SER F 43 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ALA F 82 " --> pdb=" O VAL F 225 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 248 through 249 Processing sheet with id=AD6, first strand: chain 'F' and resid 266 through 268 Processing sheet with id=AD7, first strand: chain 'G' and resid 12 through 13 removed outlier: 3.597A pdb=" N ALA G 108 " --> pdb=" O ALA G 13 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 18 through 20 removed outlier: 3.567A pdb=" N VAL G 93 " --> pdb=" O ALA G 215 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU G 210 " --> pdb=" O ILE G 165 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL G 160 " --> pdb=" O ARG G 175 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG G 175 " --> pdb=" O VAL G 160 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE G 162 " --> pdb=" O ALA G 173 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ALA G 173 " --> pdb=" O ILE G 162 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N HIS G 164 " --> pdb=" O ALA G 171 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 18 through 20 removed outlier: 5.077A pdb=" N ALA G 253 " --> pdb=" O LEU G 25 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 45 through 50 removed outlier: 4.504A pdb=" N ALA G 82 " --> pdb=" O VAL G 225 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 45 through 50 removed outlier: 7.524A pdb=" N SER G 243 " --> pdb=" O LEU G 76 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N THR G 78 " --> pdb=" O SER G 243 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 266 through 268 Processing sheet with id=AE4, first strand: chain 'G' and resid 287 through 288 Processing sheet with id=AE5, first strand: chain 'H' and resid 108 through 109 Processing sheet with id=AE6, first strand: chain 'H' and resid 18 through 20 removed outlier: 3.850A pdb=" N VAL H 209 " --> pdb=" O VAL H 99 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU H 210 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ILE H 162 " --> pdb=" O ALA H 173 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ALA H 173 " --> pdb=" O ILE H 162 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N HIS H 164 " --> pdb=" O ALA H 171 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 23 through 24 Processing sheet with id=AE8, first strand: chain 'H' and resid 27 through 28 removed outlier: 3.505A pdb=" N LEU H 91 " --> pdb=" O ALA H 217 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA H 217 " --> pdb=" O LEU H 91 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 45 through 51 removed outlier: 3.864A pdb=" N ASN H 75 " --> pdb=" O GLY H 51 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 266 through 268 removed outlier: 3.524A pdb=" N ILE H 280 " --> pdb=" O ASP H 268 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 287 through 288 964 hydrogen bonds defined for protein. 2577 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 3.29 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3661 1.32 - 1.44: 5879 1.44 - 1.57: 12324 1.57 - 1.69: 68 1.69 - 1.82: 29 Bond restraints: 21961 Sorted by residual: bond pdb=" CG GLN G 37 " pdb=" CD GLN G 37 " ideal model delta sigma weight residual 1.516 1.613 -0.097 2.50e-02 1.60e+03 1.49e+01 bond pdb=" CD GLN G 37 " pdb=" NE2 GLN G 37 " ideal model delta sigma weight residual 1.328 1.403 -0.075 2.10e-02 2.27e+03 1.28e+01 bond pdb=" N9 A J 2 " pdb=" C4 A J 2 " ideal model delta sigma weight residual 1.374 1.354 0.020 6.00e-03 2.78e+04 1.12e+01 bond pdb=" N1 C J 6 " pdb=" C6 C J 6 " ideal model delta sigma weight residual 1.367 1.348 0.019 6.00e-03 2.78e+04 1.03e+01 bond pdb=" CB VAL B 187 " pdb=" CG1 VAL B 187 " ideal model delta sigma weight residual 1.521 1.422 0.099 3.30e-02 9.18e+02 9.07e+00 ... (remaining 21956 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.60: 29633 3.60 - 7.19: 290 7.19 - 10.79: 25 10.79 - 14.38: 9 14.38 - 17.98: 1 Bond angle restraints: 29958 Sorted by residual: angle pdb=" C SER A 306 " pdb=" N LEU A 307 " pdb=" CA LEU A 307 " ideal model delta sigma weight residual 123.56 105.58 17.98 1.98e+00 2.55e-01 8.24e+01 angle pdb=" N1 U J 1 " pdb=" C6 U J 1 " pdb=" C5 U J 1 " ideal model delta sigma weight residual 122.70 126.12 -3.42 5.00e-01 4.00e+00 4.69e+01 angle pdb=" C TRP C 149 " pdb=" CA TRP C 149 " pdb=" CB TRP C 149 " ideal model delta sigma weight residual 116.54 109.61 6.93 1.15e+00 7.56e-01 3.63e+01 angle pdb=" CB GLN G 38 " pdb=" CG GLN G 38 " pdb=" CD GLN G 38 " ideal model delta sigma weight residual 112.60 122.59 -9.99 1.70e+00 3.46e-01 3.45e+01 angle pdb=" C ALA A 140 " pdb=" CA ALA A 140 " pdb=" CB ALA A 140 " ideal model delta sigma weight residual 116.54 110.35 6.19 1.15e+00 7.56e-01 2.90e+01 ... (remaining 29953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 11917 17.93 - 35.86: 1040 35.86 - 53.79: 238 53.79 - 71.72: 60 71.72 - 89.65: 20 Dihedral angle restraints: 13275 sinusoidal: 5576 harmonic: 7699 Sorted by residual: dihedral pdb=" CA ALA H 41 " pdb=" C ALA H 41 " pdb=" N VAL H 42 " pdb=" CA VAL H 42 " ideal model delta harmonic sigma weight residual 180.00 152.70 27.30 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CA CYS F 109 " pdb=" C CYS F 109 " pdb=" N ASN F 110 " pdb=" CA ASN F 110 " ideal model delta harmonic sigma weight residual -180.00 -153.68 -26.32 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA ASN C 163 " pdb=" C ASN C 163 " pdb=" N HIS C 164 " pdb=" CA HIS C 164 " ideal model delta harmonic sigma weight residual 180.00 154.71 25.29 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 13272 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2250 0.049 - 0.098: 844 0.098 - 0.147: 227 0.147 - 0.196: 20 0.196 - 0.246: 4 Chirality restraints: 3345 Sorted by residual: chirality pdb=" CB ILE B 144 " pdb=" CA ILE B 144 " pdb=" CG1 ILE B 144 " pdb=" CG2 ILE B 144 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CB ILE B 326 " pdb=" CA ILE B 326 " pdb=" CG1 ILE B 326 " pdb=" CG2 ILE B 326 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CB ILE F 162 " pdb=" CA ILE F 162 " pdb=" CG1 ILE F 162 " pdb=" CG2 ILE F 162 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 3342 not shown) Planarity restraints: 3843 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP G 39 " -0.021 2.00e-02 2.50e+03 1.84e-02 8.44e+00 pdb=" CG TRP G 39 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP G 39 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP G 39 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP G 39 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP G 39 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP G 39 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 39 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 39 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP G 39 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG G 250 " -0.014 2.00e-02 2.50e+03 2.85e-02 8.13e+00 pdb=" C ARG G 250 " 0.049 2.00e-02 2.50e+03 pdb=" O ARG G 250 " -0.019 2.00e-02 2.50e+03 pdb=" N ASP G 251 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA H 215 " -0.013 2.00e-02 2.50e+03 2.65e-02 7.03e+00 pdb=" C ALA H 215 " 0.046 2.00e-02 2.50e+03 pdb=" O ALA H 215 " -0.017 2.00e-02 2.50e+03 pdb=" N PHE H 216 " -0.015 2.00e-02 2.50e+03 ... (remaining 3840 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 242 2.53 - 3.12: 17008 3.12 - 3.72: 33892 3.72 - 4.31: 48093 4.31 - 4.90: 78088 Nonbonded interactions: 177323 Sorted by model distance: nonbonded pdb=" OE1 GLN F 291 " pdb=" OH TYR F 295 " model vdw 1.940 3.040 nonbonded pdb=" OD1 ASN F 141 " pdb=" ND2 ASN F 144 " model vdw 2.029 3.120 nonbonded pdb=" OG SER G 228 " pdb=" OP2 A J 19 " model vdw 2.044 3.040 nonbonded pdb=" NH1 ARG F 166 " pdb=" OE2 GLU G 156 " model vdw 2.062 3.120 nonbonded pdb=" OH TYR H 271 " pdb=" O GLY H 278 " model vdw 2.069 3.040 ... (remaining 177318 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' and resid 4 through 339) selection = (chain 'D' and resid 4 through 339) selection = (chain 'E' and resid 4 through 339) selection = (chain 'F' and resid 4 through 339) selection = chain 'G' selection = (chain 'H' and resid 4 through 339) } 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: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.980 Find NCS groups from input model: 0.640 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:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5909 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.099 21961 Z= 0.355 Angle : 1.012 17.977 29958 Z= 0.573 Chirality : 0.053 0.246 3345 Planarity : 0.007 0.096 3843 Dihedral : 14.819 89.648 8303 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 24.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.00 % Allowed : 13.77 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.83 % 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: -0.87 (0.15), residues: 2656 helix: -0.25 (0.17), residues: 799 sheet: -0.05 (0.24), residues: 441 loop : -0.89 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 175 TYR 0.035 0.004 TYR E 325 PHE 0.031 0.004 PHE A 219 TRP 0.050 0.004 TRP G 39 HIS 0.012 0.002 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00748 / 0.35 (21961) covalent geometry : angle 1.01179 / 0.57 (29958) hydrogen bonds : bond 0.21811 / 15.14 ( 919) hydrogen bonds : angle 8.77200 / 6.22 ( 2577) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5312 Ramachandran restraints generated. 2656 Oldfield, 0 Emsley, 2656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5312 Ramachandran restraints generated. 2656 Oldfield, 0 Emsley, 2656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 205 time to evaluate : 0.736 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 215 LYS cc_start: 0.2523 (tttt) cc_final: 0.1910 (tttt) REVERT: B 283 LEU cc_start: 0.7668 (pp) cc_final: 0.7418 (mt) REVERT: C 50 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7255 (ttt90) REVERT: C 75 ASN cc_start: 0.7449 (p0) cc_final: 0.6712 (m-40) REVERT: C 179 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7604 (mp) REVERT: C 230 GLU cc_start: 0.7319 (mp0) cc_final: 0.6964 (mp0) REVERT: D 24 LEU cc_start: 0.7162 (mt) cc_final: 0.6788 (pp) REVERT: D 193 ASP cc_start: 0.6914 (m-30) cc_final: 0.6593 (m-30) REVERT: D 247 TYR cc_start: 0.7037 (t80) cc_final: 0.6135 (t80) REVERT: D 265 ARG cc_start: 0.7045 (OUTLIER) cc_final: 0.6711 (ptt-90) REVERT: F 313 LEU cc_start: 0.5037 (OUTLIER) cc_final: 0.4627 (tp) REVERT: G 37 GLN cc_start: 0.8374 (mt0) cc_final: 0.7933 (pm20) REVERT: G 83 ASN cc_start: 0.7882 (m-40) cc_final: 0.7670 (p0) REVERT: H 128 ASP cc_start: 0.5719 (t0) cc_final: 0.5384 (t0) REVERT: H 321 GLU cc_start: 0.8599 (mp0) cc_final: 0.8387 (mp0) outliers start: 43 outliers final: 30 residues processed: 237 average time/residue: 0.1538 time to fit residues: 55.8507 Evaluate side-chains 201 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 167 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain C residue 7 ASN Chi-restraints excluded: chain C residue 50 ARG Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 221 ASP Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 179 LEU Chi-restraints excluded: chain D residue 221 ASP Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 265 ARG Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 301 LYS Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain F residue 110 ASN Chi-restraints excluded: chain F residue 187 LYS Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 289 THR Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 335 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 30.0000 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 329 ASN D 72 GLN ** E 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 262 ASN ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4990 r_free = 0.4990 target = 0.238009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.187116 restraints weight = 36700.918| |-----------------------------------------------------------------------------| r_work (start): 0.4416 rms_B_bonded: 4.64 r_work: 0.4196 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21961 Z= 0.165 Angle : 0.678 10.615 29958 Z= 0.351 Chirality : 0.044 0.194 3345 Planarity : 0.005 0.073 3843 Dihedral : 11.202 90.829 3472 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.02 % Allowed : 12.56 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.83 % 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: -0.43 (0.16), residues: 2656 helix: 0.30 (0.17), residues: 835 sheet: 0.16 (0.25), residues: 407 loop : -0.73 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 152 TYR 0.024 0.002 TYR D 125 PHE 0.015 0.002 PHE F 14 TRP 0.024 0.002 TRP A 302 HIS 0.006 0.001 HIS B 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (21961) covalent geometry : angle 0.67776 / 0.35 (29958) hydrogen bonds : bond 0.04955 / 3.40 ( 919) hydrogen bonds : angle 6.27365 / 4.43 ( 2577) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5312 Ramachandran restraints generated. 2656 Oldfield, 0 Emsley, 2656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5312 Ramachandran restraints generated. 2656 Oldfield, 0 Emsley, 2656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 198 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 LYS cc_start: 0.3111 (tttt) cc_final: 0.1848 (tttt) REVERT: A 396 GLU cc_start: 0.6104 (mm-30) cc_final: 0.5879 (mm-30) REVERT: B 11 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.7013 (tp) REVERT: B 283 LEU cc_start: 0.8337 (pp) cc_final: 0.7451 (mt) REVERT: B 310 ASP cc_start: 0.7003 (m-30) cc_final: 0.6164 (p0) REVERT: C 75 ASN cc_start: 0.7394 (p0) cc_final: 0.6712 (m-40) REVERT: C 179 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7424 (mp) REVERT: D 247 TYR cc_start: 0.6852 (t80) cc_final: 0.6302 (t80) REVERT: D 265 ARG cc_start: 0.6991 (OUTLIER) cc_final: 0.6032 (ttp80) REVERT: F 199 ILE cc_start: 0.7359 (mt) cc_final: 0.7040 (mm) REVERT: G 37 GLN cc_start: 0.8592 (mt0) cc_final: 0.8138 (pm20) REVERT: G 76 LEU cc_start: 0.6038 (OUTLIER) cc_final: 0.4222 (tp) REVERT: G 283 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.7102 (mp0) REVERT: H 128 ASP cc_start: 0.5659 (t0) cc_final: 0.5366 (t0) outliers start: 65 outliers final: 33 residues processed: 251 average time/residue: 0.1413 time to fit residues: 54.6956 Evaluate side-chains 208 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 170 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain C residue 7 ASN Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain D residue 265 ARG Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain E residue 14 PHE Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain F residue 258 GLN Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 283 GLU Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 303 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 185 optimal weight: 20.0000 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 122 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 ASN E 75 ASN ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 GLN G 83 ASN ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4966 r_free = 0.4966 target = 0.231853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.183005 restraints weight = 36539.821| |-----------------------------------------------------------------------------| r_work (start): 0.4410 rms_B_bonded: 4.45 r_work: 0.4190 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.4190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6877 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 21961 Z= 0.203 Angle : 0.674 10.543 29958 Z= 0.346 Chirality : 0.045 0.187 3345 Planarity : 0.006 0.069 3843 Dihedral : 10.968 92.390 3431 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.12 % Allowed : 13.73 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.16), residues: 2656 helix: 0.31 (0.17), residues: 840 sheet: 0.08 (0.25), residues: 414 loop : -0.80 (0.16), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG F 115 TYR 0.027 0.002 TYR C 125 PHE 0.020 0.002 PHE G 14 TRP 0.017 0.002 TRP A 302 HIS 0.008 0.001 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.20 (21961) covalent geometry : angle 0.67405 / 0.35 (29958) hydrogen bonds : bond 0.04591 / 3.14 ( 919) hydrogen bonds : angle 5.99386 / 4.22 ( 2577) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5312 Ramachandran restraints generated. 2656 Oldfield, 0 Emsley, 2656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5312 Ramachandran restraints generated. 2656 Oldfield, 0 Emsley, 2656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 185 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 LYS cc_start: 0.2825 (tttt) cc_final: 0.2037 (tttt) REVERT: A 396 GLU cc_start: 0.6394 (mm-30) cc_final: 0.6129 (mm-30) REVERT: B 283 LEU cc_start: 0.8171 (pp) cc_final: 0.7331 (mt) REVERT: B 310 ASP cc_start: 0.6893 (m-30) cc_final: 0.6126 (p0) REVERT: C 75 ASN cc_start: 0.7283 (p0) cc_final: 0.6744 (m-40) REVERT: C 179 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7425 (mp) REVERT: C 230 GLU cc_start: 0.7524 (mp0) cc_final: 0.7251 (pm20) REVERT: D 119 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7711 (mt) REVERT: D 247 TYR cc_start: 0.6836 (t80) cc_final: 0.6230 (t80) REVERT: F 270 TRP cc_start: 0.5655 (m-10) cc_final: 0.5002 (m-10) REVERT: F 295 TYR cc_start: 0.5729 (m-80) cc_final: 0.5190 (m-80) REVERT: G 37 GLN cc_start: 0.8629 (mt0) cc_final: 0.8183 (pm20) REVERT: G 76 LEU cc_start: 0.5992 (OUTLIER) cc_final: 0.4122 (tp) REVERT: H 128 ASP cc_start: 0.5671 (t0) cc_final: 0.5455 (t0) outliers start: 67 outliers final: 46 residues processed: 234 average time/residue: 0.1430 time to fit residues: 52.2668 Evaluate side-chains 221 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 172 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 7 ASN Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 109 CYS Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 283 GLU Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 303 ASP Chi-restraints excluded: chain H residue 329 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 250 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 49 optimal weight: 7.9990 chunk 202 optimal weight: 0.9990 chunk 217 optimal weight: 7.9990 chunk 237 optimal weight: 8.9990 chunk 28 optimal weight: 20.0000 chunk 120 optimal weight: 6.9990 chunk 102 optimal weight: 9.9990 chunk 88 optimal weight: 7.9990 chunk 167 optimal weight: 20.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 HIS ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 HIS ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 ASN ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 ASN ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4952 r_free = 0.4952 target = 0.229654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.181537 restraints weight = 36759.993| |-----------------------------------------------------------------------------| r_work (start): 0.4405 rms_B_bonded: 4.25 r_work: 0.4186 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 21961 Z= 0.212 Angle : 0.661 10.257 29958 Z= 0.340 Chirality : 0.044 0.194 3345 Planarity : 0.005 0.060 3843 Dihedral : 10.921 93.944 3424 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.68 % Allowed : 14.66 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.16), residues: 2656 helix: 0.31 (0.17), residues: 838 sheet: -0.12 (0.25), residues: 423 loop : -0.86 (0.16), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 115 TYR 0.028 0.002 TYR C 125 PHE 0.021 0.002 PHE A 326 TRP 0.018 0.002 TRP C 30 HIS 0.010 0.001 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.21 (21961) covalent geometry : angle 0.66058 / 0.34 (29958) hydrogen bonds : bond 0.04231 / 2.87 ( 919) hydrogen bonds : angle 5.86983 / 4.14 ( 2577) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5312 Ramachandran restraints generated. 2656 Oldfield, 0 Emsley, 2656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5312 Ramachandran restraints generated. 2656 Oldfield, 0 Emsley, 2656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 180 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 LEU cc_start: 0.6361 (OUTLIER) cc_final: 0.5994 (pp) REVERT: A 215 LYS cc_start: 0.2846 (tttt) cc_final: 0.2013 (tttt) REVERT: A 396 GLU cc_start: 0.6397 (mm-30) cc_final: 0.6123 (mm-30) REVERT: B 283 LEU cc_start: 0.8089 (pp) cc_final: 0.7276 (mt) REVERT: B 310 ASP cc_start: 0.6868 (m-30) cc_final: 0.6085 (p0) REVERT: C 75 ASN cc_start: 0.7220 (p0) cc_final: 0.6732 (m-40) REVERT: C 179 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7415 (mp) REVERT: C 230 GLU cc_start: 0.7513 (mp0) cc_final: 0.7251 (pm20) REVERT: D 119 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7721 (mt) REVERT: D 247 TYR cc_start: 0.6897 (t80) cc_final: 0.6239 (t80) REVERT: F 187 LYS cc_start: 0.2073 (OUTLIER) cc_final: 0.0635 (pttt) REVERT: F 270 TRP cc_start: 0.5721 (m-10) cc_final: 0.5019 (m-10) REVERT: G 37 GLN cc_start: 0.8567 (mt0) cc_final: 0.8113 (pm20) REVERT: G 38 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.6902 (tm-30) REVERT: G 76 LEU cc_start: 0.6010 (OUTLIER) cc_final: 0.4080 (tp) REVERT: H 50 ARG cc_start: 0.7173 (OUTLIER) cc_final: 0.6029 (mtp180) REVERT: H 128 ASP cc_start: 0.5742 (t70) cc_final: 0.5514 (t0) REVERT: H 264 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.7150 (mt) REVERT: H 315 ASP cc_start: 0.6229 (t0) cc_final: 0.5903 (t0) outliers start: 79 outliers final: 53 residues processed: 235 average time/residue: 0.1386 time to fit residues: 50.9826 Evaluate side-chains 229 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 168 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 7 ASN Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 86 SER Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 109 CYS Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 187 LYS Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 283 GLU Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 303 ASP Chi-restraints excluded: chain H residue 329 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 97 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 chunk 143 optimal weight: 20.0000 chunk 249 optimal weight: 2.9990 chunk 77 optimal weight: 0.0980 chunk 92 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 244 optimal weight: 5.9990 chunk 250 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 ASN ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 ASN ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4988 r_free = 0.4988 target = 0.233373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.186673 restraints weight = 36510.669| |-----------------------------------------------------------------------------| r_work (start): 0.4484 rms_B_bonded: 4.51 r_work: 0.4256 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.4256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6746 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 21961 Z= 0.113 Angle : 0.564 9.559 29958 Z= 0.292 Chirality : 0.042 0.173 3345 Planarity : 0.005 0.070 3843 Dihedral : 10.635 94.237 3424 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.75 % Allowed : 15.82 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.83 % 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: -0.15 (0.16), residues: 2656 helix: 0.76 (0.18), residues: 830 sheet: 0.06 (0.25), residues: 416 loop : -0.63 (0.17), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 115 TYR 0.031 0.002 TYR C 125 PHE 0.018 0.001 PHE E 304 TRP 0.022 0.001 TRP A 422 HIS 0.004 0.001 HIS G 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (21961) covalent geometry : angle 0.56389 / 0.29 (29958) hydrogen bonds : bond 0.03578 / 2.42 ( 919) hydrogen bonds : angle 5.42374 / 3.82 ( 2577) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5312 Ramachandran restraints generated. 2656 Oldfield, 0 Emsley, 2656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5312 Ramachandran restraints generated. 2656 Oldfield, 0 Emsley, 2656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 192 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 LEU cc_start: 0.6125 (OUTLIER) cc_final: 0.5203 (pp) REVERT: A 215 LYS cc_start: 0.2792 (tttt) cc_final: 0.1571 (tttt) REVERT: A 396 GLU cc_start: 0.6333 (mm-30) cc_final: 0.6012 (mm-30) REVERT: B 11 LEU cc_start: 0.7112 (OUTLIER) cc_final: 0.6842 (tp) REVERT: B 167 GLU cc_start: 0.7441 (pm20) cc_final: 0.6775 (pp20) REVERT: B 310 ASP cc_start: 0.6728 (m-30) cc_final: 0.6137 (p0) REVERT: B 320 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.7553 (mtp85) REVERT: C 68 ASP cc_start: 0.6469 (m-30) cc_final: 0.6244 (m-30) REVERT: C 75 ASN cc_start: 0.7223 (p0) cc_final: 0.6731 (m-40) REVERT: C 179 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7277 (mp) REVERT: D 24 LEU cc_start: 0.6516 (mt) cc_final: 0.6252 (pp) REVERT: D 119 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7735 (mt) REVERT: D 247 TYR cc_start: 0.6776 (t80) cc_final: 0.6270 (t80) REVERT: F 187 LYS cc_start: 0.1790 (OUTLIER) cc_final: 0.0400 (pttt) REVERT: F 270 TRP cc_start: 0.5531 (m-10) cc_final: 0.5090 (m-10) REVERT: F 304 PHE cc_start: 0.4227 (t80) cc_final: 0.3977 (t80) REVERT: G 38 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7035 (tm-30) REVERT: G 76 LEU cc_start: 0.5814 (OUTLIER) cc_final: 0.3917 (tp) REVERT: H 50 ARG cc_start: 0.7000 (OUTLIER) cc_final: 0.6033 (mtp-110) REVERT: H 128 ASP cc_start: 0.5773 (t70) cc_final: 0.5568 (t0) REVERT: H 264 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.7045 (mt) REVERT: H 315 ASP cc_start: 0.6301 (t0) cc_final: 0.5858 (t0) outliers start: 59 outliers final: 31 residues processed: 233 average time/residue: 0.1439 time to fit residues: 53.1026 Evaluate side-chains 214 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 173 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 109 CYS Chi-restraints excluded: chain F residue 187 LYS Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 283 GLU Chi-restraints excluded: chain H residue 329 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 26 optimal weight: 9.9990 chunk 254 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 233 optimal weight: 2.9990 chunk 229 optimal weight: 6.9990 chunk 197 optimal weight: 2.9990 chunk 143 optimal weight: 20.0000 chunk 114 optimal weight: 0.0980 chunk 1 optimal weight: 40.0000 chunk 181 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 GLN ** D 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4942 r_free = 0.4942 target = 0.230379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.181218 restraints weight = 36615.668| |-----------------------------------------------------------------------------| r_work (start): 0.4426 rms_B_bonded: 3.93 r_work: 0.4224 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.4224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21961 Z= 0.162 Angle : 0.592 9.108 29958 Z= 0.306 Chirality : 0.042 0.179 3345 Planarity : 0.005 0.051 3843 Dihedral : 10.669 95.191 3421 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.65 % Allowed : 16.52 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.16), residues: 2656 helix: 0.71 (0.17), residues: 828 sheet: -0.04 (0.25), residues: 414 loop : -0.66 (0.17), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 189 TYR 0.026 0.002 TYR C 125 PHE 0.019 0.002 PHE A 326 TRP 0.018 0.001 TRP A 422 HIS 0.007 0.001 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (21961) covalent geometry : angle 0.59208 / 0.31 (29958) hydrogen bonds : bond 0.03726 / 2.53 ( 919) hydrogen bonds : angle 5.45105 / 3.85 ( 2577) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5312 Ramachandran restraints generated. 2656 Oldfield, 0 Emsley, 2656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5312 Ramachandran restraints generated. 2656 Oldfield, 0 Emsley, 2656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 172 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 LEU cc_start: 0.5246 (OUTLIER) cc_final: 0.4443 (mt) REVERT: A 215 LYS cc_start: 0.2713 (tttt) cc_final: 0.1432 (tttt) REVERT: A 396 GLU cc_start: 0.6366 (mm-30) cc_final: 0.5951 (mm-30) REVERT: B 310 ASP cc_start: 0.6729 (m-30) cc_final: 0.6116 (p0) REVERT: B 320 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7574 (mtp85) REVERT: C 75 ASN cc_start: 0.7266 (p0) cc_final: 0.6783 (m-40) REVERT: C 179 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7392 (mp) REVERT: D 24 LEU cc_start: 0.6428 (mt) cc_final: 0.6137 (pp) REVERT: D 98 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7868 (ttm170) REVERT: D 169 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7079 (pm20) REVERT: D 247 TYR cc_start: 0.6795 (t80) cc_final: 0.6242 (t80) REVERT: F 187 LYS cc_start: 0.1969 (OUTLIER) cc_final: 0.0514 (pttt) REVERT: F 270 TRP cc_start: 0.5762 (m-10) cc_final: 0.5154 (m-10) REVERT: F 304 PHE cc_start: 0.4282 (t80) cc_final: 0.4027 (t80) REVERT: G 38 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7087 (tm-30) REVERT: G 76 LEU cc_start: 0.5939 (OUTLIER) cc_final: 0.4002 (tp) REVERT: H 128 ASP cc_start: 0.5971 (t70) cc_final: 0.5770 (t0) REVERT: H 315 ASP cc_start: 0.6221 (t0) cc_final: 0.5784 (t0) outliers start: 57 outliers final: 40 residues processed: 204 average time/residue: 0.1446 time to fit residues: 47.2852 Evaluate side-chains 213 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 165 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 109 CYS Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 187 LYS Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 264 LEU Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 283 GLU Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 329 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 248 optimal weight: 0.9990 chunk 155 optimal weight: 30.0000 chunk 262 optimal weight: 10.0000 chunk 138 optimal weight: 8.9990 chunk 157 optimal weight: 30.0000 chunk 37 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 156 optimal weight: 7.9990 chunk 195 optimal weight: 4.9990 chunk 16 optimal weight: 0.0010 overall best weight: 1.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 ASN ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 127 ASN F 323 GLN G 83 ASN ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4946 r_free = 0.4946 target = 0.230845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.179978 restraints weight = 37079.292| |-----------------------------------------------------------------------------| r_work (start): 0.4419 rms_B_bonded: 3.99 r_work: 0.4249 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.4249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21961 Z= 0.132 Angle : 0.557 8.999 29958 Z= 0.289 Chirality : 0.041 0.179 3345 Planarity : 0.004 0.049 3843 Dihedral : 10.585 95.769 3421 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.75 % Allowed : 16.85 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.83 % 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: -0.10 (0.16), residues: 2656 helix: 0.83 (0.17), residues: 829 sheet: 0.04 (0.26), residues: 408 loop : -0.60 (0.17), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 115 TYR 0.027 0.002 TYR C 125 PHE 0.019 0.001 PHE A 326 TRP 0.024 0.001 TRP A 422 HIS 0.006 0.001 HIS A 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (21961) covalent geometry : angle 0.55705 / 0.29 (29958) hydrogen bonds : bond 0.03478 / 2.36 ( 919) hydrogen bonds : angle 5.29118 / 3.74 ( 2577) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5312 Ramachandran restraints generated. 2656 Oldfield, 0 Emsley, 2656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5312 Ramachandran restraints generated. 2656 Oldfield, 0 Emsley, 2656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 180 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 LEU cc_start: 0.5242 (OUTLIER) cc_final: 0.4496 (mt) REVERT: A 215 LYS cc_start: 0.2475 (tttt) cc_final: 0.2216 (tttt) REVERT: B 11 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.6823 (tp) REVERT: B 167 GLU cc_start: 0.7433 (pm20) cc_final: 0.6706 (pp20) REVERT: B 310 ASP cc_start: 0.6762 (m-30) cc_final: 0.6155 (p0) REVERT: B 320 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.7539 (mtp85) REVERT: C 68 ASP cc_start: 0.6542 (m-30) cc_final: 0.6332 (m-30) REVERT: C 75 ASN cc_start: 0.7266 (p0) cc_final: 0.6746 (m-40) REVERT: C 179 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7391 (mp) REVERT: D 24 LEU cc_start: 0.6327 (mt) cc_final: 0.6080 (pp) REVERT: D 98 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7800 (ttm170) REVERT: D 119 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7729 (mt) REVERT: D 247 TYR cc_start: 0.6765 (t80) cc_final: 0.6213 (t80) REVERT: F 187 LYS cc_start: 0.2185 (OUTLIER) cc_final: 0.0748 (pttt) REVERT: G 38 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7080 (tm-30) REVERT: G 76 LEU cc_start: 0.5950 (OUTLIER) cc_final: 0.4027 (tp) REVERT: H 128 ASP cc_start: 0.6016 (t70) cc_final: 0.5806 (t0) REVERT: H 315 ASP cc_start: 0.6287 (t0) cc_final: 0.5821 (t0) outliers start: 59 outliers final: 41 residues processed: 218 average time/residue: 0.1540 time to fit residues: 52.0837 Evaluate side-chains 211 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 161 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain B residue 320 ARG Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 187 LYS Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 308 LEU Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 283 GLU Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 329 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 25 optimal weight: 8.9990 chunk 214 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 257 optimal weight: 8.9990 chunk 143 optimal weight: 20.0000 chunk 161 optimal weight: 30.0000 chunk 47 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 246 optimal weight: 0.0970 chunk 233 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 overall best weight: 2.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 ASN ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4944 r_free = 0.4944 target = 0.228734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.179711 restraints weight = 36780.060| |-----------------------------------------------------------------------------| r_work (start): 0.4398 rms_B_bonded: 4.06 r_work: 0.4184 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.4184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 21961 Z= 0.184 Angle : 0.630 11.648 29958 Z= 0.323 Chirality : 0.043 0.178 3345 Planarity : 0.005 0.055 3843 Dihedral : 10.711 96.575 3421 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.26 % Allowed : 16.80 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.83 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.16), residues: 2656 helix: 0.62 (0.17), residues: 830 sheet: -0.08 (0.25), residues: 414 loop : -0.71 (0.17), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 189 TYR 0.020 0.002 TYR F 305 PHE 0.024 0.002 PHE A 326 TRP 0.020 0.002 TRP A 422 HIS 0.010 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (21961) covalent geometry : angle 0.63022 / 0.32 (29958) hydrogen bonds : bond 0.03815 / 2.59 ( 919) hydrogen bonds : angle 5.45928 / 3.86 ( 2577) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5312 Ramachandran restraints generated. 2656 Oldfield, 0 Emsley, 2656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5312 Ramachandran restraints generated. 2656 Oldfield, 0 Emsley, 2656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 165 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 LEU cc_start: 0.5184 (OUTLIER) cc_final: 0.4445 (mt) REVERT: A 215 LYS cc_start: 0.2829 (tttt) cc_final: 0.1541 (tttt) REVERT: A 267 TRP cc_start: 0.4311 (OUTLIER) cc_final: 0.4094 (t-100) REVERT: A 414 MET cc_start: 0.6104 (tpt) cc_final: 0.5185 (mtt) REVERT: B 310 ASP cc_start: 0.6941 (m-30) cc_final: 0.6202 (p0) REVERT: C 68 ASP cc_start: 0.6669 (m-30) cc_final: 0.6441 (m-30) REVERT: C 75 ASN cc_start: 0.7316 (p0) cc_final: 0.6708 (m-40) REVERT: C 179 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7412 (mp) REVERT: D 24 LEU cc_start: 0.6382 (mt) cc_final: 0.6080 (pp) REVERT: D 98 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7887 (ttm170) REVERT: D 119 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7749 (mt) REVERT: D 169 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7041 (pm20) REVERT: D 247 TYR cc_start: 0.6862 (t80) cc_final: 0.6268 (t80) REVERT: F 187 LYS cc_start: 0.2833 (OUTLIER) cc_final: 0.1351 (pttt) REVERT: G 6 LEU cc_start: 0.4351 (OUTLIER) cc_final: 0.4099 (tp) REVERT: G 38 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7073 (tm-30) REVERT: G 76 LEU cc_start: 0.6043 (OUTLIER) cc_final: 0.3889 (tp) REVERT: H 50 ARG cc_start: 0.7172 (OUTLIER) cc_final: 0.6020 (mtp180) REVERT: H 128 ASP cc_start: 0.6055 (t70) cc_final: 0.5853 (t0) REVERT: H 315 ASP cc_start: 0.6388 (t0) cc_final: 0.5996 (t0) outliers start: 70 outliers final: 51 residues processed: 207 average time/residue: 0.1423 time to fit residues: 46.5363 Evaluate side-chains 223 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 161 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 267 TRP Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 109 CYS Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 187 LYS Chi-restraints excluded: chain F residue 249 VAL Chi-restraints excluded: chain F residue 251 ASP Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 283 GLU Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 329 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 127 optimal weight: 1.9990 chunk 4 optimal weight: 20.0000 chunk 243 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 263 optimal weight: 20.0000 chunk 13 optimal weight: 7.9990 chunk 184 optimal weight: 20.0000 chunk 107 optimal weight: 3.9990 chunk 152 optimal weight: 0.6980 chunk 150 optimal weight: 40.0000 chunk 210 optimal weight: 0.0980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 HIS C 141 ASN ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 241 GLN ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 ASN ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4965 r_free = 0.4965 target = 0.231010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.182518 restraints weight = 36473.772| |-----------------------------------------------------------------------------| r_work (start): 0.4431 rms_B_bonded: 4.13 r_work: 0.4214 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.4214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6851 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21961 Z= 0.127 Angle : 0.566 9.188 29958 Z= 0.293 Chirality : 0.041 0.179 3345 Planarity : 0.004 0.052 3843 Dihedral : 10.563 96.597 3419 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.65 % Allowed : 17.22 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.83 % 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: -0.14 (0.16), residues: 2656 helix: 0.80 (0.18), residues: 832 sheet: 0.01 (0.26), residues: 410 loop : -0.62 (0.17), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 115 TYR 0.022 0.002 TYR C 125 PHE 0.023 0.001 PHE A 326 TRP 0.026 0.001 TRP A 422 HIS 0.019 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (21961) covalent geometry : angle 0.56612 / 0.29 (29958) hydrogen bonds : bond 0.03422 / 2.31 ( 919) hydrogen bonds : angle 5.27002 / 3.73 ( 2577) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5312 Ramachandran restraints generated. 2656 Oldfield, 0 Emsley, 2656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5312 Ramachandran restraints generated. 2656 Oldfield, 0 Emsley, 2656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 166 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 LEU cc_start: 0.5216 (OUTLIER) cc_final: 0.4525 (mt) REVERT: A 215 LYS cc_start: 0.2892 (tttt) cc_final: 0.1613 (tttt) REVERT: B 167 GLU cc_start: 0.7306 (pm20) cc_final: 0.6535 (pp20) REVERT: B 310 ASP cc_start: 0.6877 (m-30) cc_final: 0.6206 (p0) REVERT: C 68 ASP cc_start: 0.6548 (m-30) cc_final: 0.6321 (m-30) REVERT: C 75 ASN cc_start: 0.7230 (p0) cc_final: 0.6697 (m-40) REVERT: C 179 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7395 (mp) REVERT: D 98 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7782 (ttm170) REVERT: D 119 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7741 (mt) REVERT: D 169 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7016 (pm20) REVERT: D 247 TYR cc_start: 0.6774 (t80) cc_final: 0.6232 (t80) REVERT: F 187 LYS cc_start: 0.2614 (OUTLIER) cc_final: 0.1216 (pttt) REVERT: G 6 LEU cc_start: 0.4315 (OUTLIER) cc_final: 0.4046 (tp) REVERT: G 38 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7066 (tm-30) REVERT: G 83 ASN cc_start: 0.8152 (m-40) cc_final: 0.7763 (p0) REVERT: H 128 ASP cc_start: 0.5981 (t70) cc_final: 0.5770 (t0) REVERT: H 315 ASP cc_start: 0.6409 (t0) cc_final: 0.5953 (t0) outliers start: 57 outliers final: 41 residues processed: 206 average time/residue: 0.1458 time to fit residues: 48.3410 Evaluate side-chains 205 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 156 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 187 LYS Chi-restraints excluded: chain F residue 251 ASP Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 249 VAL Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 283 GLU Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 329 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 178 optimal weight: 8.9990 chunk 83 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 264 optimal weight: 40.0000 chunk 82 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 208 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 249 optimal weight: 3.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 151 ASN ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4966 r_free = 0.4966 target = 0.230950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.182935 restraints weight = 36743.117| |-----------------------------------------------------------------------------| r_work (start): 0.4445 rms_B_bonded: 3.89 r_work: 0.4232 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.4232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21961 Z= 0.125 Angle : 0.561 9.288 29958 Z= 0.290 Chirality : 0.042 0.310 3345 Planarity : 0.004 0.048 3843 Dihedral : 10.549 96.575 3419 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.42 % Allowed : 17.36 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.83 % 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: -0.05 (0.16), residues: 2656 helix: 0.92 (0.18), residues: 832 sheet: 0.04 (0.26), residues: 410 loop : -0.60 (0.17), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 115 TYR 0.025 0.002 TYR F 305 PHE 0.018 0.001 PHE A 326 TRP 0.102 0.002 TRP A 267 HIS 0.017 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (21961) covalent geometry : angle 0.56074 / 0.29 (29958) hydrogen bonds : bond 0.03343 / 2.26 ( 919) hydrogen bonds : angle 5.18722 / 3.67 ( 2577) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5312 Ramachandran restraints generated. 2656 Oldfield, 0 Emsley, 2656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5312 Ramachandran restraints generated. 2656 Oldfield, 0 Emsley, 2656 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 167 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 LEU cc_start: 0.5260 (OUTLIER) cc_final: 0.4623 (mt) REVERT: A 215 LYS cc_start: 0.2656 (tttt) cc_final: 0.1411 (tttt) REVERT: B 67 GLU cc_start: 0.6078 (tm-30) cc_final: 0.5742 (mp0) REVERT: B 167 GLU cc_start: 0.7377 (pm20) cc_final: 0.6639 (pp20) REVERT: B 310 ASP cc_start: 0.6768 (m-30) cc_final: 0.6199 (p0) REVERT: C 68 ASP cc_start: 0.6557 (m-30) cc_final: 0.6225 (p0) REVERT: C 75 ASN cc_start: 0.7269 (p0) cc_final: 0.6722 (m-40) REVERT: C 179 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7280 (mp) REVERT: D 119 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7658 (mt) REVERT: D 169 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.6991 (pm20) REVERT: D 247 TYR cc_start: 0.6753 (t80) cc_final: 0.6183 (t80) REVERT: F 187 LYS cc_start: 0.2642 (OUTLIER) cc_final: 0.1228 (pttt) REVERT: G 6 LEU cc_start: 0.4266 (OUTLIER) cc_final: 0.3992 (tp) REVERT: G 38 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7118 (tm-30) REVERT: H 315 ASP cc_start: 0.6388 (t0) cc_final: 0.5939 (t0) outliers start: 52 outliers final: 42 residues processed: 201 average time/residue: 0.1448 time to fit residues: 46.8125 Evaluate side-chains 207 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 158 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 87 ASP Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 169 GLU Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 288 VAL Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 187 LYS Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 50 ARG Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 264 LEU Chi-restraints excluded: chain H residue 274 GLU Chi-restraints excluded: chain H residue 283 GLU Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 329 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 151 optimal weight: 50.0000 chunk 48 optimal weight: 9.9990 chunk 237 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 163 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 chunk 160 optimal weight: 0.0170 chunk 171 optimal weight: 0.4980 chunk 12 optimal weight: 0.0980 chunk 202 optimal weight: 1.9990 chunk 179 optimal weight: 0.3980 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 HIS ** E 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 ASN G 151 ASN H 329 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4984 r_free = 0.4984 target = 0.235052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.186557 restraints weight = 37175.815| |-----------------------------------------------------------------------------| r_work (start): 0.4497 rms_B_bonded: 4.07 r_work: 0.4284 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.4284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21961 Z= 0.100 Angle : 0.541 9.742 29958 Z= 0.281 Chirality : 0.041 0.227 3345 Planarity : 0.004 0.049 3843 Dihedral : 10.444 96.189 3419 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.63 % Allowed : 18.33 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.83 % 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: 0.24 (0.16), residues: 2656 helix: 1.31 (0.18), residues: 829 sheet: 0.15 (0.25), residues: 405 loop : -0.49 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 250 TYR 0.044 0.001 TYR F 305 PHE 0.015 0.001 PHE E 304 TRP 0.091 0.002 TRP A 267 HIS 0.010 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (21961) covalent geometry : angle 0.54125 / 0.28 (29958) hydrogen bonds : bond 0.03077 / 2.08 ( 919) hydrogen bonds : angle 4.96071 / 3.52 ( 2577) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5825.22 seconds wall clock time: 100 minutes 11.82 seconds (6011.82 seconds total)