Starting phenix.real_space_refine on Sat Jul 4 16:05:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jph_61700/07_2026/9jph_61700.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jph_61700/07_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_61700/07_2026/9jph_61700.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jph_61700/07_2026/9jph_61700.map" model { file = "/net/cci-nas-00/data/ceres_data/9jph_61700/07_2026/9jph_61700.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jph_61700/07_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 4.39, per 1000 atoms: 0.20 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: 1.69 Conformation dependent library (CDL) restraints added in 909.8 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: 1.81 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: 3.74 Time building geometry restraints manager: 2.15 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: 29637 3.60 - 7.19: 286 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: 2285 0.049 - 0.098: 833 0.098 - 0.147: 210 0.147 - 0.196: 13 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: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.600 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.960 ------------------------------------------------------------------------------- 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= 0.352 Angle : 1.004 17.977 29958 Z= 0.560 Chirality : 0.052 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 1.00370 / 0.56 (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 : 0.645 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: 0.1465 time to fit residues: 53.4096 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 : 0.756 ------------------------------------------------------------------------------- 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 ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4984 r_free = 0.4984 target = 0.235937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.186225 restraints weight = 36945.252| |-----------------------------------------------------------------------------| r_work (start): 0.4435 rms_B_bonded: 4.53 r_work: 0.4213 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.4213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21961 Z= 0.166 Angle : 0.672 10.572 29958 Z= 0.351 Chirality : 0.044 0.195 3345 Planarity : 0.005 0.068 3843 Dihedral : 11.200 92.535 3472 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.93 % Allowed : 12.66 % 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: -0.42 (0.16), residues: 2656 helix: 0.31 (0.17), residues: 835 sheet: 0.17 (0.25), residues: 407 loop : -0.73 (0.16), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 297 TYR 0.024 0.002 TYR D 125 PHE 0.016 0.002 PHE F 14 TRP 0.026 0.002 TRP A 302 HIS 0.006 0.001 HIS B 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 (21961) covalent geometry : angle 0.67226 / 0.35 (29958) hydrogen bonds : bond 0.04844 / 3.32 ( 919) hydrogen bonds : angle 6.25214 / 4.41 ( 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 258 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 195 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 LYS cc_start: 0.3072 (tttt) cc_final: 0.1825 (tttt) REVERT: A 396 GLU cc_start: 0.6042 (mm-30) cc_final: 0.5829 (mm-30) REVERT: B 283 LEU cc_start: 0.8306 (pp) cc_final: 0.7450 (mt) REVERT: B 310 ASP cc_start: 0.6940 (m-30) cc_final: 0.6128 (p0) REVERT: C 75 ASN cc_start: 0.7353 (p0) cc_final: 0.6690 (m-40) REVERT: C 179 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7425 (mp) REVERT: D 247 TYR cc_start: 0.6834 (t80) cc_final: 0.6282 (t80) REVERT: D 265 ARG cc_start: 0.6988 (OUTLIER) cc_final: 0.5950 (ttp80) REVERT: F 199 ILE cc_start: 0.7436 (mt) cc_final: 0.7103 (mm) REVERT: G 37 GLN cc_start: 0.8577 (mt0) cc_final: 0.8155 (pm20) REVERT: G 76 LEU cc_start: 0.6089 (OUTLIER) cc_final: 0.4323 (tp) REVERT: G 185 ASP cc_start: 0.6043 (p0) cc_final: 0.5365 (p0) REVERT: G 283 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.7075 (mp0) REVERT: H 128 ASP cc_start: 0.5651 (t0) cc_final: 0.5376 (t0) outliers start: 63 outliers final: 33 residues processed: 246 average time/residue: 0.1485 time to fit residues: 56.4976 Evaluate side-chains 207 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 170 time to evaluate : 0.733 ------------------------------------------------------------------------------- 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 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 162 ILE Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 265 ARG 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 109 CYS 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: 0.9990 chunk 12 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 23 optimal weight: 40.0000 chunk 37 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 87 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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** G 83 ASN ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4962 r_free = 0.4962 target = 0.231070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.182585 restraints weight = 36499.124| |-----------------------------------------------------------------------------| r_work (start): 0.4402 rms_B_bonded: 4.61 r_work: 0.4186 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 21961 Z= 0.211 Angle : 0.673 10.548 29958 Z= 0.348 Chirality : 0.044 0.169 3345 Planarity : 0.005 0.060 3843 Dihedral : 10.982 93.900 3431 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.07 % Allowed : 13.91 % Favored : 83.02 % 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: 833 sheet: 0.08 (0.25), residues: 414 loop : -0.80 (0.16), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 115 TYR 0.026 0.002 TYR C 125 PHE 0.021 0.002 PHE G 14 TRP 0.018 0.002 TRP A 302 HIS 0.009 0.001 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.21 (21961) covalent geometry : angle 0.67267 / 0.35 (29958) hydrogen bonds : bond 0.04652 / 3.17 ( 919) hydrogen bonds : angle 6.03439 / 4.25 ( 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 245 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 179 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 LYS cc_start: 0.2802 (tttt) cc_final: 0.2010 (tttt) REVERT: A 396 GLU cc_start: 0.6391 (mm-30) cc_final: 0.6130 (mm-30) REVERT: B 283 LEU cc_start: 0.8188 (pp) cc_final: 0.7338 (mt) REVERT: B 310 ASP cc_start: 0.6911 (m-30) cc_final: 0.6114 (p0) REVERT: B 320 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7448 (mtp85) REVERT: C 75 ASN cc_start: 0.7225 (p0) cc_final: 0.6695 (m-40) REVERT: C 179 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7452 (mp) REVERT: C 192 LEU cc_start: 0.7139 (OUTLIER) cc_final: 0.6765 (tt) REVERT: C 230 GLU cc_start: 0.7553 (mp0) cc_final: 0.7296 (pm20) REVERT: D 119 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7713 (mt) REVERT: D 247 TYR cc_start: 0.6846 (t80) cc_final: 0.6220 (t80) REVERT: F 270 TRP cc_start: 0.5679 (m-10) cc_final: 0.5003 (m-10) REVERT: F 295 TYR cc_start: 0.5722 (m-80) cc_final: 0.5145 (m-80) REVERT: G 37 GLN cc_start: 0.8600 (mt0) cc_final: 0.8164 (pm20) REVERT: G 76 LEU cc_start: 0.6080 (OUTLIER) cc_final: 0.4239 (tp) REVERT: G 185 ASP cc_start: 0.6018 (p0) cc_final: 0.5617 (p0) REVERT: H 50 ARG cc_start: 0.7210 (OUTLIER) cc_final: 0.6953 (mtp-110) REVERT: H 128 ASP cc_start: 0.5657 (t0) cc_final: 0.5423 (t0) outliers start: 66 outliers final: 42 residues processed: 228 average time/residue: 0.1462 time to fit residues: 52.1836 Evaluate side-chains 218 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 170 time to evaluate : 0.685 ------------------------------------------------------------------------------- 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 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 297 VAL 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 86 SER Chi-restraints excluded: chain C residue 174 TRP Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 192 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 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 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 99 VAL Chi-restraints excluded: chain H residue 245 THR Chi-restraints excluded: chain H residue 264 LEU 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: 9.9990 chunk 49 optimal weight: 6.9990 chunk 202 optimal weight: 5.9990 chunk 217 optimal weight: 7.9990 chunk 237 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 120 optimal weight: 8.9990 chunk 102 optimal weight: 0.0040 chunk 88 optimal weight: 0.6980 chunk 167 optimal weight: 30.0000 overall best weight: 2.1398 ------------------------------------------------------------------------------- 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 110 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 = 0.4945 r_free = 0.4945 target = 0.230826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.180110 restraints weight = 37357.540| |-----------------------------------------------------------------------------| r_work (start): 0.4417 rms_B_bonded: 4.29 r_work: 0.4202 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21961 Z= 0.153 Angle : 0.591 9.653 29958 Z= 0.308 Chirality : 0.042 0.160 3345 Planarity : 0.005 0.052 3843 Dihedral : 10.779 94.708 3424 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.16 % Allowed : 14.38 % Favored : 82.46 % 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: -0.34 (0.16), residues: 2656 helix: 0.54 (0.17), residues: 835 sheet: 0.03 (0.25), residues: 416 loop : -0.73 (0.16), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 115 TYR 0.028 0.002 TYR C 125 PHE 0.020 0.002 PHE A 326 TRP 0.017 0.001 TRP C 30 HIS 0.009 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (21961) covalent geometry : angle 0.59138 / 0.31 (29958) hydrogen bonds : bond 0.03919 / 2.65 ( 919) hydrogen bonds : angle 5.66965 / 3.99 ( 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 251 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 183 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 LEU cc_start: 0.6143 (OUTLIER) cc_final: 0.5774 (pp) REVERT: A 215 LYS cc_start: 0.2784 (tttt) cc_final: 0.1532 (tttt) REVERT: A 396 GLU cc_start: 0.6444 (mm-30) cc_final: 0.6157 (mm-30) REVERT: B 283 LEU cc_start: 0.8110 (pp) cc_final: 0.7310 (mt) REVERT: B 310 ASP cc_start: 0.6826 (m-30) cc_final: 0.6126 (p0) REVERT: B 320 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7342 (mtp85) REVERT: C 75 ASN cc_start: 0.7196 (p0) cc_final: 0.6694 (m-40) REVERT: C 94 ARG cc_start: 0.7466 (tpp80) cc_final: 0.7242 (tpp80) REVERT: C 179 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7391 (mp) REVERT: C 230 GLU cc_start: 0.7484 (mp0) cc_final: 0.7269 (pm20) REVERT: D 24 LEU cc_start: 0.6541 (mt) cc_final: 0.6243 (pp) REVERT: D 119 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7714 (mt) REVERT: D 247 TYR cc_start: 0.6806 (t80) cc_final: 0.6239 (t80) REVERT: F 187 LYS cc_start: 0.1896 (OUTLIER) cc_final: 0.0450 (pttt) REVERT: F 270 TRP cc_start: 0.5646 (m-10) cc_final: 0.5028 (m-10) REVERT: G 76 LEU cc_start: 0.5935 (OUTLIER) cc_final: 0.4025 (tp) REVERT: G 185 ASP cc_start: 0.6122 (p0) cc_final: 0.5733 (p0) REVERT: H 128 ASP cc_start: 0.5820 (t70) cc_final: 0.5592 (t0) REVERT: H 264 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.7084 (mt) outliers start: 68 outliers final: 38 residues processed: 231 average time/residue: 0.1402 time to fit residues: 50.6542 Evaluate side-chains 212 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 167 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 143 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 467 ILE 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 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 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 D residue 66 LYS Chi-restraints excluded: chain D residue 119 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 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 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 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 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 329 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 97 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 143 optimal weight: 20.0000 chunk 249 optimal weight: 5.9990 chunk 77 optimal weight: 0.0670 chunk 92 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 244 optimal weight: 3.9990 chunk 250 optimal weight: 5.9990 chunk 53 optimal weight: 0.3980 chunk 8 optimal weight: 9.9990 overall best weight: 1.1720 ------------------------------------------------------------------------------- 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 141 ASN ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4962 r_free = 0.4962 target = 0.232570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.182622 restraints weight = 37189.810| |-----------------------------------------------------------------------------| r_work (start): 0.4467 rms_B_bonded: 4.13 r_work: 0.4249 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.4249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21961 Z= 0.118 Angle : 0.547 10.428 29958 Z= 0.285 Chirality : 0.041 0.160 3345 Planarity : 0.004 0.045 3843 Dihedral : 10.584 94.660 3422 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.42 % Allowed : 15.64 % Favored : 81.95 % 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: 0.84 (0.17), residues: 834 sheet: 0.14 (0.25), residues: 415 loop : -0.58 (0.17), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 115 TYR 0.031 0.002 TYR C 125 PHE 0.019 0.001 PHE E 304 TRP 0.022 0.001 TRP A 422 HIS 0.011 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (21961) covalent geometry : angle 0.54739 / 0.29 (29958) hydrogen bonds : bond 0.03560 / 2.40 ( 919) hydrogen bonds : angle 5.36107 / 3.78 ( 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 244 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 192 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 LEU cc_start: 0.6125 (OUTLIER) cc_final: 0.5206 (pp) REVERT: A 215 LYS cc_start: 0.2767 (tttt) cc_final: 0.2434 (tttt) REVERT: A 396 GLU cc_start: 0.6302 (mm-30) cc_final: 0.5962 (mm-30) REVERT: B 310 ASP cc_start: 0.6762 (m-30) cc_final: 0.6202 (p0) REVERT: C 75 ASN cc_start: 0.7237 (p0) cc_final: 0.6689 (m-40) REVERT: C 179 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7342 (mp) REVERT: D 24 LEU cc_start: 0.6404 (mt) cc_final: 0.6140 (pp) REVERT: D 119 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7701 (mt) REVERT: D 247 TYR cc_start: 0.6792 (t80) cc_final: 0.6264 (t80) REVERT: F 187 LYS cc_start: 0.1781 (OUTLIER) cc_final: 0.0250 (pttt) REVERT: F 224 GLU cc_start: 0.3427 (tp30) cc_final: 0.3222 (tp30) REVERT: F 270 TRP cc_start: 0.5593 (m-10) cc_final: 0.5155 (m-10) REVERT: G 38 GLN cc_start: 0.7835 (OUTLIER) cc_final: 0.6992 (tm-30) REVERT: G 76 LEU cc_start: 0.5997 (OUTLIER) cc_final: 0.4096 (tp) REVERT: G 185 ASP cc_start: 0.6053 (p0) cc_final: 0.5698 (p0) REVERT: H 128 ASP cc_start: 0.5830 (t70) cc_final: 0.5614 (t0) REVERT: H 315 ASP cc_start: 0.6296 (t0) cc_final: 0.5838 (t0) outliers start: 52 outliers final: 36 residues processed: 226 average time/residue: 0.1342 time to fit residues: 48.1532 Evaluate side-chains 211 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 169 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 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 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 8 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 119 LEU 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 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 49 VAL Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 99 VAL 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 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 329 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 26 optimal weight: 10.0000 chunk 254 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 233 optimal weight: 2.9990 chunk 229 optimal weight: 7.9990 chunk 197 optimal weight: 1.9990 chunk 143 optimal weight: 20.0000 chunk 114 optimal weight: 0.5980 chunk 1 optimal weight: 40.0000 chunk 181 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- 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 360 HIS ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4946 r_free = 0.4946 target = 0.229009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.180563 restraints weight = 36759.947| |-----------------------------------------------------------------------------| r_work (start): 0.4400 rms_B_bonded: 4.36 r_work: 0.4178 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 21961 Z= 0.204 Angle : 0.643 10.002 29958 Z= 0.330 Chirality : 0.043 0.152 3345 Planarity : 0.005 0.058 3843 Dihedral : 10.747 96.923 3421 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.35 % Allowed : 15.68 % Favored : 80.97 % 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: -0.37 (0.16), residues: 2656 helix: 0.55 (0.17), residues: 838 sheet: -0.10 (0.25), residues: 418 loop : -0.73 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 115 TYR 0.027 0.002 TYR C 125 PHE 0.018 0.002 PHE D 95 TRP 0.015 0.002 TRP C 30 HIS 0.009 0.002 HIS B 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.20 (21961) covalent geometry : angle 0.64309 / 0.33 (29958) hydrogen bonds : bond 0.03981 / 2.71 ( 919) hydrogen bonds : angle 5.55763 / 3.93 ( 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 241 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 169 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 LEU cc_start: 0.5236 (OUTLIER) cc_final: 0.4442 (mt) REVERT: A 215 LYS cc_start: 0.2909 (tttt) cc_final: 0.2067 (tttt) REVERT: A 396 GLU cc_start: 0.6436 (mm-30) cc_final: 0.6031 (mm-30) REVERT: B 167 GLU cc_start: 0.7516 (pm20) cc_final: 0.6842 (pp20) REVERT: B 310 ASP cc_start: 0.6886 (m-30) cc_final: 0.6161 (p0) REVERT: C 68 ASP cc_start: 0.6674 (m-30) cc_final: 0.6464 (m-30) REVERT: C 75 ASN cc_start: 0.7386 (p0) cc_final: 0.6834 (m-40) REVERT: C 91 LEU cc_start: 0.7082 (OUTLIER) cc_final: 0.6880 (tp) REVERT: C 179 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7408 (mp) REVERT: D 24 LEU cc_start: 0.6418 (mt) cc_final: 0.6128 (pp) REVERT: D 98 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.8001 (ttm170) REVERT: D 169 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7161 (pm20) REVERT: D 247 TYR cc_start: 0.6891 (t80) cc_final: 0.6290 (t80) REVERT: F 187 LYS cc_start: 0.2218 (OUTLIER) cc_final: 0.0746 (pttt) REVERT: G 38 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7053 (tm-30) REVERT: G 76 LEU cc_start: 0.5986 (OUTLIER) cc_final: 0.4119 (tp) REVERT: G 185 ASP cc_start: 0.6216 (p0) cc_final: 0.5839 (p0) REVERT: H 128 ASP cc_start: 0.5983 (t70) cc_final: 0.5765 (t0) REVERT: H 264 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7132 (mt) REVERT: H 315 ASP cc_start: 0.6243 (t0) cc_final: 0.5858 (t0) outliers start: 72 outliers final: 51 residues processed: 217 average time/residue: 0.1332 time to fit residues: 46.7866 Evaluate side-chains 222 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 162 time to evaluate : 0.574 ------------------------------------------------------------------------------- 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 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 297 VAL Chi-restraints excluded: chain B residue 318 THR 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 91 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 98 ARG Chi-restraints excluded: chain D residue 169 GLU 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 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 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 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 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=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: 7.9990 chunk 157 optimal weight: 30.0000 chunk 37 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 60 optimal weight: 0.1980 chunk 156 optimal weight: 10.0000 chunk 195 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- 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 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** 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 = 0.4963 r_free = 0.4963 target = 0.230800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.183277 restraints weight = 36374.895| |-----------------------------------------------------------------------------| r_work (start): 0.4444 rms_B_bonded: 4.44 r_work: 0.4220 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.4220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 21961 Z= 0.138 Angle : 0.569 12.056 29958 Z= 0.294 Chirality : 0.041 0.150 3345 Planarity : 0.004 0.073 3843 Dihedral : 10.610 97.209 3421 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.79 % Allowed : 16.94 % Favored : 80.27 % 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: -0.16 (0.16), residues: 2656 helix: 0.75 (0.17), residues: 836 sheet: 0.01 (0.25), residues: 406 loop : -0.62 (0.17), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 115 TYR 0.028 0.002 TYR C 125 PHE 0.018 0.001 PHE F 304 TRP 0.021 0.001 TRP A 422 HIS 0.006 0.001 HIS A 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (21961) covalent geometry : angle 0.56945 / 0.29 (29958) hydrogen bonds : bond 0.03545 / 2.41 ( 919) hydrogen bonds : angle 5.32949 / 3.76 ( 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 243 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 183 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 LEU cc_start: 0.5218 (OUTLIER) cc_final: 0.4454 (mt) REVERT: A 215 LYS cc_start: 0.2928 (tttt) cc_final: 0.1644 (tttt) REVERT: B 310 ASP cc_start: 0.6797 (m-30) cc_final: 0.6142 (p0) REVERT: C 68 ASP cc_start: 0.6574 (m-30) cc_final: 0.6350 (m-30) REVERT: C 75 ASN cc_start: 0.7234 (p0) cc_final: 0.6679 (m-40) REVERT: C 91 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6863 (tp) REVERT: C 179 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7386 (mp) REVERT: D 119 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7754 (mt) REVERT: D 247 TYR cc_start: 0.6776 (t80) cc_final: 0.6217 (t80) REVERT: F 187 LYS cc_start: 0.2229 (OUTLIER) cc_final: 0.0777 (pttt) REVERT: G 6 LEU cc_start: 0.4345 (OUTLIER) cc_final: 0.4089 (tp) REVERT: G 38 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7085 (tm-30) REVERT: G 76 LEU cc_start: 0.6028 (OUTLIER) cc_final: 0.4105 (tp) REVERT: G 83 ASN cc_start: 0.8098 (m-40) cc_final: 0.7604 (p0) REVERT: G 185 ASP cc_start: 0.6221 (p0) cc_final: 0.5883 (p0) REVERT: H 128 ASP cc_start: 0.6044 (t70) cc_final: 0.5802 (t0) REVERT: H 264 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.7094 (mt) REVERT: H 315 ASP cc_start: 0.6298 (t0) cc_final: 0.5863 (t0) outliers start: 60 outliers final: 39 residues processed: 225 average time/residue: 0.1427 time to fit residues: 50.4510 Evaluate side-chains 214 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 166 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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 143 SER Chi-restraints excluded: chain B residue 152 CYS Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 7 ASN Chi-restraints excluded: chain C residue 91 LEU 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 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 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 76 LEU Chi-restraints excluded: chain G residue 99 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 8 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 25 optimal weight: 0.8980 chunk 214 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 257 optimal weight: 10.0000 chunk 143 optimal weight: 20.0000 chunk 161 optimal weight: 30.0000 chunk 47 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 246 optimal weight: 0.4980 chunk 233 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 overall best weight: 4.0786 ------------------------------------------------------------------------------- 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** 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** F 127 ASN ** F 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4941 r_free = 0.4941 target = 0.232808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.183639 restraints weight = 36747.535| |-----------------------------------------------------------------------------| r_work (start): 0.4370 rms_B_bonded: 3.97 r_work: 0.4161 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.4161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 21961 Z= 0.238 Angle : 0.700 10.906 29958 Z= 0.360 Chirality : 0.045 0.178 3345 Planarity : 0.006 0.055 3843 Dihedral : 10.860 98.499 3421 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.49 % Allowed : 16.43 % Favored : 80.08 % 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: -0.61 (0.16), residues: 2656 helix: 0.32 (0.17), residues: 833 sheet: -0.22 (0.25), residues: 424 loop : -0.87 (0.16), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 320 TYR 0.022 0.002 TYR H 325 PHE 0.021 0.002 PHE D 95 TRP 0.017 0.002 TRP A 422 HIS 0.011 0.002 HIS B 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.24 (21961) covalent geometry : angle 0.69987 / 0.36 (29958) hydrogen bonds : bond 0.04231 / 2.88 ( 919) hydrogen bonds : angle 5.67930 / 4.02 ( 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 240 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 165 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 LEU cc_start: 0.5167 (OUTLIER) cc_final: 0.4419 (mt) REVERT: A 215 LYS cc_start: 0.2874 (tttt) cc_final: 0.2092 (tttt) REVERT: B 121 HIS cc_start: 0.4819 (OUTLIER) cc_final: 0.3547 (m90) REVERT: B 167 GLU cc_start: 0.7379 (pm20) cc_final: 0.6888 (pp20) REVERT: B 310 ASP cc_start: 0.7006 (m-30) cc_final: 0.6165 (p0) REVERT: C 68 ASP cc_start: 0.6663 (m-30) cc_final: 0.6440 (m-30) REVERT: C 75 ASN cc_start: 0.7303 (p0) cc_final: 0.6725 (m-40) REVERT: C 179 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7342 (mp) REVERT: D 98 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7952 (ttm170) REVERT: D 119 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7725 (mt) REVERT: D 169 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7144 (pm20) REVERT: D 247 TYR cc_start: 0.6960 (t80) cc_final: 0.6297 (t80) REVERT: F 187 LYS cc_start: 0.2822 (OUTLIER) cc_final: 0.1366 (pttt) REVERT: G 38 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7179 (tm-30) REVERT: G 76 LEU cc_start: 0.6148 (OUTLIER) cc_final: 0.4145 (tp) REVERT: G 185 ASP cc_start: 0.6116 (p0) cc_final: 0.5803 (p0) REVERT: H 128 ASP cc_start: 0.6054 (t70) cc_final: 0.5837 (t0) REVERT: H 264 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7225 (mt) REVERT: H 315 ASP cc_start: 0.6380 (t0) cc_final: 0.6086 (t0) outliers start: 75 outliers final: 53 residues processed: 213 average time/residue: 0.1439 time to fit residues: 48.7275 Evaluate side-chains 226 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 163 time to evaluate : 0.609 ------------------------------------------------------------------------------- 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 325 VAL 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 121 HIS 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 300 ASP Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 7 ASN 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 98 ARG Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 169 GLU 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 308 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 105 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 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 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 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: 0.2980 chunk 4 optimal weight: 0.0980 chunk 243 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 263 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 184 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 152 optimal weight: 0.6980 chunk 150 optimal weight: 30.0000 chunk 210 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 141 ASN ** C 164 HIS ** 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4981 r_free = 0.4981 target = 0.233230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.185635 restraints weight = 36303.390| |-----------------------------------------------------------------------------| r_work (start): 0.4462 rms_B_bonded: 4.01 r_work: 0.4242 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.4242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 21961 Z= 0.112 Angle : 0.567 10.013 29958 Z= 0.295 Chirality : 0.042 0.168 3345 Planarity : 0.004 0.073 3843 Dihedral : 10.552 98.049 3419 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.86 % Allowed : 18.10 % 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: -0.15 (0.16), residues: 2656 helix: 0.86 (0.18), residues: 828 sheet: -0.11 (0.25), residues: 420 loop : -0.64 (0.17), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B 320 TYR 0.024 0.001 TYR F 305 PHE 0.021 0.002 PHE F 304 TRP 0.028 0.001 TRP A 422 HIS 0.013 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (21961) covalent geometry : angle 0.56657 / 0.29 (29958) hydrogen bonds : bond 0.03367 / 2.28 ( 919) hydrogen bonds : angle 5.21783 / 3.68 ( 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 219 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 179 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 143 LEU cc_start: 0.5177 (OUTLIER) cc_final: 0.4481 (mt) REVERT: A 215 LYS cc_start: 0.2890 (tttt) cc_final: 0.2538 (tttt) REVERT: B 167 GLU cc_start: 0.7440 (pm20) cc_final: 0.6776 (pp20) REVERT: B 310 ASP cc_start: 0.6868 (m-30) cc_final: 0.6192 (p0) REVERT: C 68 ASP cc_start: 0.6494 (m-30) cc_final: 0.6221 (p0) REVERT: C 179 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7310 (mp) REVERT: C 233 LEU cc_start: 0.6991 (mt) cc_final: 0.6118 (tp) REVERT: D 119 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7747 (mt) REVERT: D 247 TYR cc_start: 0.6752 (t80) cc_final: 0.6207 (t80) REVERT: F 187 LYS cc_start: 0.2593 (OUTLIER) cc_final: 0.1207 (pttt) REVERT: G 38 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7105 (tm-30) REVERT: G 76 LEU cc_start: 0.5870 (OUTLIER) cc_final: 0.3858 (tp) REVERT: G 83 ASN cc_start: 0.8143 (m-40) cc_final: 0.7764 (p0) REVERT: G 185 ASP cc_start: 0.5978 (p0) cc_final: 0.5744 (p0) REVERT: H 264 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.7052 (mt) REVERT: H 315 ASP cc_start: 0.6371 (t0) cc_final: 0.5945 (t0) outliers start: 40 outliers final: 27 residues processed: 207 average time/residue: 0.1395 time to fit residues: 46.0478 Evaluate side-chains 200 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 166 time to evaluate : 0.687 ------------------------------------------------------------------------------- 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 1 MET Chi-restraints excluded: chain B residue 3 VAL 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 277 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 7 ASN 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 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 38 GLN Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 315 ASP 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 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: 3.9990 chunk 83 optimal weight: 0.8980 chunk 28 optimal weight: 9.9990 chunk 264 optimal weight: 30.0000 chunk 82 optimal weight: 0.9980 chunk 6 optimal weight: 0.4980 chunk 4 optimal weight: 9.9990 chunk 208 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 249 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 GLN A 301 ASN ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 399 GLN ** 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** H 329 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4976 r_free = 0.4976 target = 0.232321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.184486 restraints weight = 36452.349| |-----------------------------------------------------------------------------| r_work (start): 0.4455 rms_B_bonded: 4.19 r_work: 0.4240 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.4240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21961 Z= 0.117 Angle : 0.572 17.994 29958 Z= 0.295 Chirality : 0.041 0.245 3345 Planarity : 0.004 0.047 3843 Dihedral : 10.519 98.234 3419 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.91 % Allowed : 18.10 % Favored : 79.99 % 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: -0.02 (0.16), residues: 2656 helix: 0.99 (0.18), residues: 830 sheet: 0.00 (0.26), residues: 410 loop : -0.59 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 115 TYR 0.026 0.002 TYR F 305 PHE 0.016 0.001 PHE F 304 TRP 0.100 0.002 TRP A 267 HIS 0.023 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (21961) covalent geometry : angle 0.57211 / 0.29 (29958) hydrogen bonds : bond 0.03346 / 2.27 ( 919) hydrogen bonds : angle 5.17050 / 3.66 ( 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 213 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 172 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 LEU cc_start: 0.5237 (OUTLIER) cc_final: 0.4603 (mt) REVERT: A 215 LYS cc_start: 0.2664 (tttt) cc_final: 0.1438 (tttt) REVERT: A 414 MET cc_start: 0.6064 (tpt) cc_final: 0.5224 (mtt) REVERT: A 418 LEU cc_start: 0.6970 (mt) cc_final: 0.6758 (mp) REVERT: B 167 GLU cc_start: 0.7380 (pm20) cc_final: 0.6751 (pp20) REVERT: B 310 ASP cc_start: 0.6853 (m-30) cc_final: 0.6251 (p0) REVERT: B 320 ARG cc_start: 0.6331 (ptt180) cc_final: 0.5883 (ptp90) REVERT: C 68 ASP cc_start: 0.6571 (m-30) cc_final: 0.6299 (p0) REVERT: C 179 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7198 (mp) REVERT: C 233 LEU cc_start: 0.6973 (mt) cc_final: 0.6120 (tp) REVERT: D 119 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7608 (mt) REVERT: D 247 TYR cc_start: 0.6770 (t80) cc_final: 0.6224 (t80) REVERT: F 187 LYS cc_start: 0.2674 (OUTLIER) cc_final: 0.1265 (pttt) REVERT: G 38 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7048 (tm-30) REVERT: G 185 ASP cc_start: 0.5904 (p0) cc_final: 0.5664 (p0) REVERT: H 315 ASP cc_start: 0.6353 (t0) cc_final: 0.5912 (t0) outliers start: 41 outliers final: 29 residues processed: 201 average time/residue: 0.1323 time to fit residues: 42.0671 Evaluate side-chains 198 residues out of total 2149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 164 time to evaluate : 0.703 ------------------------------------------------------------------------------- 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 325 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 3 VAL 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 277 LEU Chi-restraints excluded: chain C residue 6 LEU Chi-restraints excluded: chain C residue 7 ASN 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 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 307 LEU Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 264 LEU Chi-restraints excluded: chain G residue 315 ASP 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 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: 7.9990 chunk 237 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 163 optimal weight: 9.9990 chunk 58 optimal weight: 8.9990 chunk 160 optimal weight: 9.9990 chunk 171 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 202 optimal weight: 7.9990 chunk 179 optimal weight: 2.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 324 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4908 r_free = 0.4908 target = 0.229743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.176231 restraints weight = 37384.709| |-----------------------------------------------------------------------------| r_work (start): 0.4283 rms_B_bonded: 3.40 r_work: 0.4145 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.106 21961 Z= 0.354 Angle : 0.817 16.508 29958 Z= 0.421 Chirality : 0.050 0.286 3345 Planarity : 0.007 0.068 3843 Dihedral : 11.047 100.140 3419 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.42 % Allowed : 17.68 % Favored : 79.90 % 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: -0.94 (0.16), residues: 2656 helix: 0.01 (0.17), residues: 836 sheet: -0.36 (0.25), residues: 425 loop : -1.07 (0.16), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG F 115 TYR 0.034 0.003 TYR F 305 PHE 0.030 0.003 PHE D 95 TRP 0.094 0.003 TRP A 267 HIS 0.021 0.003 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00825 / 0.35 (21961) covalent geometry : angle 0.81655 / 0.42 (29958) hydrogen bonds : bond 0.04731 / 3.25 ( 919) hydrogen bonds : angle 5.89083 / 4.18 ( 2577) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6034.18 seconds wall clock time: 103 minutes 48.10 seconds (6228.10 seconds total)