Starting phenix.real_space_refine on Sun Aug 24 12:16:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zwo_60534/08_2025/8zwo_60534.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zwo_60534/08_2025/8zwo_60534.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zwo_60534/08_2025/8zwo_60534.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zwo_60534/08_2025/8zwo_60534.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zwo_60534/08_2025/8zwo_60534.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zwo_60534/08_2025/8zwo_60534.map" } resolution = 2.99 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= 0.000 sd= 0.001 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 11 5.49 5 S 130 5.16 5 C 12466 2.51 5 N 3409 2.21 5 O 3755 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19771 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3660 Classifications: {'peptide': 461} Link IDs: {'PTRANS': 29, 'TRANS': 431} Chain breaks: 5 Chain: "B" Number of atoms: 2492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2492 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 12, 'TRANS': 303} Chain: "C" Number of atoms: 2533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2533 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 12, 'TRANS': 305} Chain breaks: 1 Chain: "D" Number of atoms: 2310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2310 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 11, 'TRANS': 285} Chain breaks: 4 Chain: "E" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2750 Classifications: {'peptide': 345} Link IDs: {'PTRANS': 14, 'TRANS': 330} Chain breaks: 1 Chain: "F" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1954 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 7, 'TRANS': 246} Chain breaks: 1 Chain: "G" Number of atoms: 1980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1980 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 7, 'TRANS': 249} Chain: "H" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1972 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 7, 'TRANS': 248} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.32, per 1000 atoms: 0.22 Number of scatterers: 19771 At special positions: 0 Unit cell: (132.06, 125.55, 125.55, 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 130 16.00 P 11 15.00 O 3755 8.00 N 3409 7.00 C 12466 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.48 Conformation dependent library (CDL) restraints added in 676.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4764 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 14 sheets defined 52.4% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 290 through 294 removed outlier: 3.610A pdb=" N LEU A 294 " --> pdb=" O TYR A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 392 removed outlier: 4.352A pdb=" N ALA A 384 " --> pdb=" O LYS A 380 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N HIS A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 418 removed outlier: 3.665A pdb=" N ARG A 410 " --> pdb=" O PRO A 406 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR A 411 " --> pdb=" O GLU A 407 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE A 413 " --> pdb=" O PHE A 409 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A 415 " --> pdb=" O THR A 411 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ALA A 416 " --> pdb=" O ARG A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 428 removed outlier: 3.559A pdb=" N LYS A 428 " --> pdb=" O ALA A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 479 Processing helix chain 'A' and resid 498 through 503 Processing helix chain 'A' and resid 517 through 530 Processing helix chain 'A' and resid 534 through 544 Processing helix chain 'A' and resid 548 through 556 removed outlier: 3.634A pdb=" N LEU A 556 " --> pdb=" O CYS A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 595 removed outlier: 3.835A pdb=" N VAL A 589 " --> pdb=" O GLY A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 641 Processing helix chain 'A' and resid 645 through 656 Processing helix chain 'A' and resid 665 through 689 removed outlier: 3.702A pdb=" N HIS A 687 " --> pdb=" O ALA A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 696 removed outlier: 3.845A pdb=" N ARG A 696 " --> pdb=" O GLN A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 698 No H-bonds generated for 'chain 'A' and resid 697 through 698' Processing helix chain 'A' and resid 699 through 709 removed outlier: 4.318A pdb=" N VAL A 703 " --> pdb=" O PRO A 699 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL A 707 " --> pdb=" O VAL A 703 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU A 708 " --> pdb=" O ALA A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 745 Processing helix chain 'A' and resid 753 through 760 Processing helix chain 'A' and resid 761 through 770 removed outlier: 4.349A pdb=" N ALA A 770 " --> pdb=" O LEU A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 799 Processing helix chain 'A' and resid 821 through 826 Processing helix chain 'A' and resid 837 through 856 Processing helix chain 'B' and resid 37 through 42 Processing helix chain 'B' and resid 46 through 50 removed outlier: 3.607A pdb=" N ILE B 50 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 67 Processing helix chain 'B' and resid 81 through 95 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 117 Processing helix chain 'B' and resid 118 through 126 Processing helix chain 'B' and resid 142 through 146 Processing helix chain 'B' and resid 147 through 161 removed outlier: 4.538A pdb=" N ARG B 156 " --> pdb=" O GLN B 152 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR B 161 " --> pdb=" O THR B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 177 Processing helix chain 'B' and resid 178 through 184 removed outlier: 3.527A pdb=" N GLN B 182 " --> pdb=" O ILE B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 210 Processing helix chain 'B' and resid 214 through 226 removed outlier: 3.584A pdb=" N GLN B 226 " --> pdb=" O ILE B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 244 Processing helix chain 'B' and resid 247 through 255 Processing helix chain 'B' and resid 259 through 272 Processing helix chain 'B' and resid 274 through 288 Processing helix chain 'B' and resid 291 through 305 removed outlier: 3.819A pdb=" N THR B 305 " --> pdb=" O ARG B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 330 Processing helix chain 'B' and resid 333 through 348 removed outlier: 3.750A pdb=" N THR B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 26 Processing helix chain 'C' and resid 30 through 34 removed outlier: 3.642A pdb=" N LEU C 34 " --> pdb=" O LEU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 50 Processing helix chain 'C' and resid 65 through 78 Processing helix chain 'C' and resid 79 through 86 removed outlier: 3.921A pdb=" N GLY C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N SER C 85 " --> pdb=" O LYS C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 103 Processing helix chain 'C' and resid 103 through 111 Processing helix chain 'C' and resid 126 through 130 Processing helix chain 'C' and resid 131 through 145 Processing helix chain 'C' and resid 157 through 161 Processing helix chain 'C' and resid 178 through 193 Proline residue: C 184 - end of helix Processing helix chain 'C' and resid 198 through 210 Processing helix chain 'C' and resid 212 through 227 Processing helix chain 'C' and resid 231 through 240 Processing helix chain 'C' and resid 243 through 257 Processing helix chain 'C' and resid 258 through 274 Processing helix chain 'C' and resid 276 through 291 removed outlier: 3.583A pdb=" N HIS C 289 " --> pdb=" O HIS C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 313 Processing helix chain 'C' and resid 317 through 338 removed outlier: 3.852A pdb=" N THR C 332 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASP C 334 " --> pdb=" O GLN C 330 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU C 335 " --> pdb=" O VAL C 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 44 removed outlier: 3.592A pdb=" N TYR D 44 " --> pdb=" O TRP D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 64 removed outlier: 4.047A pdb=" N VAL D 59 " --> pdb=" O GLN D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 96 Processing helix chain 'D' and resid 116 through 128 Processing helix chain 'D' and resid 151 through 155 Processing helix chain 'D' and resid 156 through 168 Processing helix chain 'D' and resid 181 through 185 removed outlier: 4.108A pdb=" N SER D 184 " --> pdb=" O ASN D 181 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG D 185 " --> pdb=" O TYR D 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 181 through 185' Processing helix chain 'D' and resid 186 through 191 Processing helix chain 'D' and resid 203 through 218 Processing helix chain 'D' and resid 223 through 234 Processing helix chain 'D' and resid 240 through 252 Processing helix chain 'D' and resid 258 through 267 removed outlier: 3.567A pdb=" N ILE D 262 " --> pdb=" O THR D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 284 removed outlier: 3.684A pdb=" N GLY D 284 " --> pdb=" O ALA D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 299 Processing helix chain 'D' and resid 302 through 315 Processing helix chain 'D' and resid 320 through 340 Processing helix chain 'D' and resid 343 through 360 Processing helix chain 'E' and resid 3 through 8 removed outlier: 3.702A pdb=" N TYR E 8 " --> pdb=" O TRP E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 16 removed outlier: 3.527A pdb=" N LEU E 16 " --> pdb=" O LEU E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 32 Processing helix chain 'E' and resid 47 through 60 Processing helix chain 'E' and resid 61 through 66 Processing helix chain 'E' and resid 96 through 102 removed outlier: 6.698A pdb=" N ASN E 102 " --> pdb=" O ASP E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 119 Processing helix chain 'E' and resid 137 through 140 Processing helix chain 'E' and resid 141 through 155 Processing helix chain 'E' and resid 172 through 179 Processing helix chain 'E' and resid 188 through 203 Processing helix chain 'E' and resid 208 through 219 Processing helix chain 'E' and resid 222 through 237 Processing helix chain 'E' and resid 249 through 265 removed outlier: 3.687A pdb=" N GLN E 265 " --> pdb=" O ALA E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 284 Processing helix chain 'E' and resid 287 through 302 removed outlier: 3.699A pdb=" N HIS E 301 " --> pdb=" O SER E 297 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN E 302 " --> pdb=" O GLU E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 325 removed outlier: 4.566A pdb=" N GLY E 309 " --> pdb=" O GLY E 305 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N GLU E 310 " --> pdb=" O GLN E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 349 removed outlier: 3.945A pdb=" N HIS E 331 " --> pdb=" O LYS E 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 21 removed outlier: 4.447A pdb=" N ASP F 21 " --> pdb=" O GLU F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 57 No H-bonds generated for 'chain 'F' and resid 55 through 57' Processing helix chain 'F' and resid 72 through 80 Processing helix chain 'F' and resid 141 through 153 Processing helix chain 'F' and resid 209 through 216 Processing helix chain 'F' and resid 217 through 222 Proline residue: F 220 - end of helix No H-bonds generated for 'chain 'F' and resid 217 through 222' Processing helix chain 'G' and resid 9 through 21 removed outlier: 3.592A pdb=" N LYS G 13 " --> pdb=" O GLY G 9 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASP G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 57 No H-bonds generated for 'chain 'G' and resid 55 through 57' Processing helix chain 'G' and resid 72 through 80 Processing helix chain 'G' and resid 141 through 155 removed outlier: 3.732A pdb=" N HIS G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE G 154 " --> pdb=" O ASP G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 194 removed outlier: 3.932A pdb=" N GLU G 193 " --> pdb=" O LYS G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 216 Processing helix chain 'G' and resid 217 through 219 No H-bonds generated for 'chain 'G' and resid 217 through 219' Processing helix chain 'H' and resid 9 through 21 removed outlier: 3.981A pdb=" N LYS H 13 " --> pdb=" O GLY H 9 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ASP H 21 " --> pdb=" O GLU H 17 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 80 Processing helix chain 'H' and resid 141 through 155 removed outlier: 3.602A pdb=" N HIS H 153 " --> pdb=" O ARG H 149 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE H 154 " --> pdb=" O ASP H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 217 Processing helix chain 'H' and resid 218 through 222 Processing sheet with id=AA1, first strand: chain 'A' and resid 177 through 180 Processing sheet with id=AA2, first strand: chain 'A' and resid 394 through 395 removed outlier: 6.198A pdb=" N SER A 394 " --> pdb=" O CYS A 431 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N VAL A 433 " --> pdb=" O SER A 394 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 803 through 807 removed outlier: 3.529A pdb=" N ARG A 816 " --> pdb=" O ARG A 804 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 72 through 75 removed outlier: 5.896A pdb=" N ILE B 73 " --> pdb=" O LEU B 188 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 102 through 105 removed outlier: 5.891A pdb=" N LYS B 136 " --> pdb=" O ARG B 166 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ALA B 168 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE B 138 " --> pdb=" O ALA B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 87 through 91 removed outlier: 6.345A pdb=" N LYS C 120 " --> pdb=" O ARG C 150 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N CYS C 152 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL C 122 " --> pdb=" O CYS C 152 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ILE C 154 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU C 124 " --> pdb=" O ILE C 154 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU C 56 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N CYS C 155 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LEU C 58 " --> pdb=" O CYS C 155 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU C 57 " --> pdb=" O PHE C 172 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 145 through 147 removed outlier: 6.687A pdb=" N LYS D 145 " --> pdb=" O ARG D 175 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N CYS D 177 " --> pdb=" O LYS D 145 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL D 147 " --> pdb=" O CYS D 177 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N ILE D 179 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LEU D 75 " --> pdb=" O PHE D 197 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 68 through 74 removed outlier: 3.617A pdb=" N ILE E 82 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU E 38 " --> pdb=" O LEU E 163 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N CYS E 165 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL E 40 " --> pdb=" O CYS E 165 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 59 through 61 removed outlier: 3.579A pdb=" N THR F 59 " --> pdb=" O ARG F 5 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N SER G 172 " --> pdb=" O ALA G 157 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ALA G 157 " --> pdb=" O SER G 172 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL G 203 " --> pdb=" O CYS G 162 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 66 through 71 removed outlier: 8.915A pdb=" N GLU F 25 " --> pdb=" O MET F 40 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N MET F 40 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N CYS F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLN F 38 " --> pdb=" O CYS F 27 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LYS F 240 " --> pdb=" O THR F 224 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N THR F 224 " --> pdb=" O LYS F 240 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 203 through 208 removed outlier: 4.095A pdb=" N VAL F 203 " --> pdb=" O CYS F 162 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N CYS F 162 " --> pdb=" O VAL F 203 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ALA F 157 " --> pdb=" O SER F 172 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N SER F 172 " --> pdb=" O ALA F 157 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU H 3 " --> pdb=" O ARG H 61 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR H 59 " --> pdb=" O ARG H 5 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 59 through 61 removed outlier: 3.619A pdb=" N THR G 59 " --> pdb=" O ARG G 5 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER H 172 " --> pdb=" O ALA H 157 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ALA H 157 " --> pdb=" O SER H 172 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 66 through 71 removed outlier: 3.648A pdb=" N MET G 68 " --> pdb=" O TRP G 28 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N GLU G 25 " --> pdb=" O MET G 40 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N MET G 40 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N CYS G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLN G 38 " --> pdb=" O CYS G 27 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LYS G 240 " --> pdb=" O THR G 224 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N THR G 224 " --> pdb=" O LYS G 240 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 69 through 71 removed outlier: 6.630A pdb=" N GLU H 25 " --> pdb=" O MET H 40 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N MET H 40 " --> pdb=" O GLU H 25 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N CYS H 27 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN H 38 " --> pdb=" O CYS H 27 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER H 39 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY H 245 " --> pdb=" O ILE H 241 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N SER H 230 " --> pdb=" O PRO H 234 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LYS H 240 " --> pdb=" O THR H 224 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N THR H 224 " --> pdb=" O LYS H 240 " (cutoff:3.500A) 1095 hydrogen bonds defined for protein. 3132 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.70 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6425 1.34 - 1.45: 2192 1.45 - 1.57: 11250 1.57 - 1.69: 18 1.69 - 1.81: 200 Bond restraints: 20085 Sorted by residual: bond pdb=" N VAL B 115 " pdb=" CA VAL B 115 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.28e-02 6.10e+03 6.25e+00 bond pdb=" N VAL B 116 " pdb=" CA VAL B 116 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.38e-02 5.25e+03 5.13e+00 bond pdb=" CB PRO A 835 " pdb=" CG PRO A 835 " ideal model delta sigma weight residual 1.492 1.563 -0.071 5.00e-02 4.00e+02 2.01e+00 bond pdb=" CG PRO A 835 " pdb=" CD PRO A 835 " ideal model delta sigma weight residual 1.503 1.547 -0.044 3.40e-02 8.65e+02 1.68e+00 bond pdb=" SD MET E 340 " pdb=" CE MET E 340 " ideal model delta sigma weight residual 1.791 1.759 0.032 2.50e-02 1.60e+03 1.65e+00 ... (remaining 20080 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 26602 1.84 - 3.69: 479 3.69 - 5.53: 60 5.53 - 7.37: 18 7.37 - 9.22: 5 Bond angle restraints: 27164 Sorted by residual: angle pdb=" N VAL B 115 " pdb=" CA VAL B 115 " pdb=" C VAL B 115 " ideal model delta sigma weight residual 111.56 107.07 4.49 8.60e-01 1.35e+00 2.73e+01 angle pdb=" C ARG B 155 " pdb=" N ARG B 156 " pdb=" CA ARG B 156 " ideal model delta sigma weight residual 122.38 114.17 8.21 1.81e+00 3.05e-01 2.06e+01 angle pdb=" C ASP B 114 " pdb=" N VAL B 115 " pdb=" CA VAL B 115 " ideal model delta sigma weight residual 123.08 118.95 4.13 1.01e+00 9.80e-01 1.67e+01 angle pdb=" CB ARG B 156 " pdb=" CG ARG B 156 " pdb=" CD ARG B 156 " ideal model delta sigma weight residual 111.30 120.52 -9.22 2.30e+00 1.89e-01 1.61e+01 angle pdb=" C THR A 417 " pdb=" N GLN A 418 " pdb=" CA GLN A 418 " ideal model delta sigma weight residual 122.83 117.18 5.65 1.54e+00 4.22e-01 1.34e+01 ... (remaining 27159 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 11265 17.60 - 35.20: 900 35.20 - 52.80: 197 52.80 - 70.40: 47 70.40 - 88.00: 28 Dihedral angle restraints: 12437 sinusoidal: 5123 harmonic: 7314 Sorted by residual: dihedral pdb=" CA PHE A 705 " pdb=" C PHE A 705 " pdb=" N HIS A 706 " pdb=" CA HIS A 706 " ideal model delta harmonic sigma weight residual 180.00 154.29 25.71 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA ILE A 744 " pdb=" C ILE A 744 " pdb=" N ALA A 745 " pdb=" CA ALA A 745 " ideal model delta harmonic sigma weight residual -180.00 -155.69 -24.31 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA TYR D 182 " pdb=" C TYR D 182 " pdb=" N VAL D 183 " pdb=" CA VAL D 183 " ideal model delta harmonic sigma weight residual 180.00 -157.97 -22.03 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 12434 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2233 0.039 - 0.078: 672 0.078 - 0.117: 219 0.117 - 0.156: 41 0.156 - 0.195: 5 Chirality restraints: 3170 Sorted by residual: chirality pdb=" CB ILE A 744 " pdb=" CA ILE A 744 " pdb=" CG1 ILE A 744 " pdb=" CG2 ILE A 744 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.52e-01 chirality pdb=" CA VAL B 115 " pdb=" N VAL B 115 " pdb=" C VAL B 115 " pdb=" CB VAL B 115 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.43e-01 chirality pdb=" CG LEU A 762 " pdb=" CB LEU A 762 " pdb=" CD1 LEU A 762 " pdb=" CD2 LEU A 762 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.20e-01 ... (remaining 3167 not shown) Planarity restraints: 3456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA H 252 " -0.046 5.00e-02 4.00e+02 6.97e-02 7.78e+00 pdb=" N PRO H 253 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO H 253 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO H 253 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 834 " -0.035 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO A 835 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 835 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 835 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 156 " -0.169 9.50e-02 1.11e+02 7.60e-02 4.28e+00 pdb=" NE ARG B 156 " 0.005 2.00e-02 2.50e+03 pdb=" CZ ARG B 156 " 0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG B 156 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 156 " -0.011 2.00e-02 2.50e+03 ... (remaining 3453 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 282 2.64 - 3.21: 18578 3.21 - 3.77: 31088 3.77 - 4.34: 43704 4.34 - 4.90: 71391 Nonbonded interactions: 165043 Sorted by model distance: nonbonded pdb=" OG1 THR A 417 " pdb=" OE1 GLN A 418 " model vdw 2.078 3.040 nonbonded pdb=" OE1 GLU G 192 " pdb=" OG SER G 223 " model vdw 2.137 3.040 nonbonded pdb=" OD2 ASP A 435 " pdb=" NH1 ARG B 156 " model vdw 2.151 3.120 nonbonded pdb=" O ALA A 551 " pdb=" OG1 THR A 555 " model vdw 2.156 3.040 nonbonded pdb=" OE2 GLU G 115 " pdb=" ND2 ASN H 177 " model vdw 2.173 3.120 ... (remaining 165038 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 'F' selection = (chain 'G' and (resid 1 through 189 or resid 191 through 255)) selection = (chain 'H' and (resid 1 through 189 or resid 191 through 255)) } 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: 7.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 16.240 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 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 : 0.004 0.071 20087 Z= 0.170 Angle : 0.627 9.217 27164 Z= 0.331 Chirality : 0.043 0.195 3170 Planarity : 0.005 0.076 3456 Dihedral : 14.335 88.004 7673 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.81 % Favored : 96.10 % Rotamer: Outliers : 0.09 % Allowed : 0.09 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.17), residues: 2464 helix: 1.02 (0.15), residues: 1167 sheet: 0.05 (0.23), residues: 518 loop : -0.75 (0.23), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 156 TYR 0.032 0.002 TYR D 182 PHE 0.013 0.001 PHE D 96 TRP 0.034 0.002 TRP C 22 HIS 0.006 0.001 HIS F 153 Details of bonding type rmsd covalent geometry : bond 0.00390 (20085) covalent geometry : angle 0.62670 (27164) hydrogen bonds : bond 0.15944 ( 1095) hydrogen bonds : angle 6.52852 ( 3132) Misc. bond : bond 0.00182 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 377 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 114 ILE cc_start: 0.7141 (mm) cc_final: 0.6866 (mm) REVERT: E 111 MET cc_start: 0.7263 (mmt) cc_final: 0.7031 (mmm) REVERT: E 113 LYS cc_start: 0.7584 (mmtp) cc_final: 0.7193 (mppt) REVERT: F 108 GLN cc_start: 0.7573 (tp-100) cc_final: 0.7314 (tm-30) REVERT: F 204 GLN cc_start: 0.7295 (tt0) cc_final: 0.6626 (tm-30) REVERT: F 213 ASN cc_start: 0.8173 (m-40) cc_final: 0.7968 (m-40) REVERT: G 64 ARG cc_start: 0.7339 (ptt-90) cc_final: 0.7131 (ptt-90) REVERT: H 1 MET cc_start: 0.4416 (tpt) cc_final: 0.3968 (tmm) REVERT: H 47 LEU cc_start: 0.7725 (mm) cc_final: 0.7373 (tp) REVERT: H 61 ARG cc_start: 0.5104 (ppt170) cc_final: 0.4546 (ptm160) REVERT: H 68 MET cc_start: 0.5974 (pmm) cc_final: 0.5753 (pmm) REVERT: H 119 MET cc_start: 0.6386 (ptm) cc_final: 0.5886 (pmt) outliers start: 2 outliers final: 2 residues processed: 378 average time/residue: 0.6951 time to fit residues: 291.0230 Evaluate side-chains 268 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 266 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain H residue 156 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 0.0170 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 235 optimal weight: 2.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 645 HIS C 29 GLN C 132 GLN C 221 GLN D 308 ASN ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 49 GLN G 204 GLN H 65 ASN H 177 ASN ** H 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.161742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.120061 restraints weight = 28618.160| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.21 r_work: 0.3314 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20087 Z= 0.180 Angle : 0.620 8.567 27164 Z= 0.322 Chirality : 0.044 0.163 3170 Planarity : 0.005 0.057 3456 Dihedral : 7.863 86.760 2808 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.86 % Favored : 96.10 % Rotamer: Outliers : 1.83 % Allowed : 9.87 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.17), residues: 2464 helix: 1.05 (0.15), residues: 1186 sheet: -0.03 (0.22), residues: 523 loop : -0.82 (0.23), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 156 TYR 0.015 0.002 TYR E 318 PHE 0.013 0.001 PHE H 103 TRP 0.016 0.002 TRP F 28 HIS 0.007 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00415 (20085) covalent geometry : angle 0.62030 (27164) hydrogen bonds : bond 0.04283 ( 1095) hydrogen bonds : angle 5.21037 ( 3132) Misc. bond : bond 0.00177 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 301 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 GLU cc_start: 0.7573 (mp0) cc_final: 0.7120 (mp0) REVERT: A 484 ARG cc_start: 0.5199 (mmm-85) cc_final: 0.4318 (mmt90) REVERT: A 823 GLU cc_start: 0.8574 (pp20) cc_final: 0.8361 (pp20) REVERT: B 117 ARG cc_start: 0.7741 (mtm180) cc_final: 0.6974 (mtm110) REVERT: B 132 LYS cc_start: 0.7902 (ptmm) cc_final: 0.7700 (pttp) REVERT: B 332 ASN cc_start: 0.8787 (p0) cc_final: 0.8585 (p0) REVERT: D 187 ILE cc_start: 0.8450 (tp) cc_final: 0.8242 (tp) REVERT: D 317 ASN cc_start: 0.8126 (m-40) cc_final: 0.7869 (m110) REVERT: D 329 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7559 (tp30) REVERT: E 58 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.6996 (mp0) REVERT: E 111 MET cc_start: 0.7362 (mmt) cc_final: 0.7141 (mmm) REVERT: F 108 GLN cc_start: 0.7889 (tp-100) cc_final: 0.7339 (tm-30) REVERT: F 204 GLN cc_start: 0.7290 (tt0) cc_final: 0.6659 (tm-30) REVERT: G 101 LEU cc_start: 0.8615 (mp) cc_final: 0.8410 (mt) REVERT: G 146 ARG cc_start: 0.7966 (ttt90) cc_final: 0.7543 (tpt-90) REVERT: H 28 TRP cc_start: 0.5999 (m100) cc_final: 0.5590 (m100) REVERT: H 47 LEU cc_start: 0.7896 (mm) cc_final: 0.7464 (tp) REVERT: H 93 GLU cc_start: 0.4881 (OUTLIER) cc_final: 0.4394 (pt0) REVERT: H 119 MET cc_start: 0.6332 (ptm) cc_final: 0.5891 (pmt) REVERT: H 199 MET cc_start: 0.4866 (tmm) cc_final: 0.4576 (tmm) outliers start: 40 outliers final: 21 residues processed: 323 average time/residue: 0.6237 time to fit residues: 224.7058 Evaluate side-chains 284 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 260 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain H residue 210 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 13 optimal weight: 3.9990 chunk 98 optimal weight: 0.5980 chunk 162 optimal weight: 0.0370 chunk 89 optimal weight: 0.4980 chunk 16 optimal weight: 0.4980 chunk 90 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 140 optimal weight: 0.5980 chunk 239 optimal weight: 4.9990 chunk 135 optimal weight: 0.7980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 49 GLN ** H 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.163114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.119927 restraints weight = 29028.708| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.22 r_work: 0.3327 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20087 Z= 0.144 Angle : 0.574 8.134 27164 Z= 0.296 Chirality : 0.042 0.156 3170 Planarity : 0.005 0.053 3456 Dihedral : 7.422 89.990 2803 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.01 % Allowed : 12.97 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.17), residues: 2464 helix: 1.19 (0.15), residues: 1187 sheet: -0.16 (0.22), residues: 529 loop : -0.78 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 185 TYR 0.013 0.002 TYR G 211 PHE 0.014 0.001 PHE H 103 TRP 0.016 0.001 TRP F 28 HIS 0.006 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00327 (20085) covalent geometry : angle 0.57411 (27164) hydrogen bonds : bond 0.03834 ( 1095) hydrogen bonds : angle 4.89518 ( 3132) Misc. bond : bond 0.00132 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 290 time to evaluate : 0.724 Fit side-chains revert: symmetry clash REVERT: A 175 GLU cc_start: 0.7572 (mp0) cc_final: 0.7145 (mp0) REVERT: A 484 ARG cc_start: 0.5142 (mmm-85) cc_final: 0.4472 (mmt90) REVERT: A 592 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7200 (tp30) REVERT: A 646 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8253 (tm-30) REVERT: A 823 GLU cc_start: 0.8447 (pp20) cc_final: 0.8231 (pp20) REVERT: B 117 ARG cc_start: 0.7718 (mtm180) cc_final: 0.6934 (mtm110) REVERT: B 132 LYS cc_start: 0.7848 (ptmm) cc_final: 0.7633 (pttp) REVERT: B 332 ASN cc_start: 0.8758 (p0) cc_final: 0.8537 (p0) REVERT: D 187 ILE cc_start: 0.8449 (tp) cc_final: 0.8208 (tp) REVERT: D 221 LYS cc_start: 0.8244 (mppt) cc_final: 0.7922 (mptt) REVERT: D 258 THR cc_start: 0.8593 (p) cc_final: 0.8019 (t) REVERT: E 111 MET cc_start: 0.7349 (mmt) cc_final: 0.7127 (mmm) REVERT: E 154 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7638 (tttt) REVERT: F 8 GLN cc_start: 0.7371 (tt0) cc_final: 0.7084 (tm-30) REVERT: F 108 GLN cc_start: 0.7834 (tp-100) cc_final: 0.7241 (tm-30) REVERT: F 204 GLN cc_start: 0.7367 (tt0) cc_final: 0.6625 (tm-30) REVERT: G 101 LEU cc_start: 0.8580 (mp) cc_final: 0.8373 (mt) REVERT: H 28 TRP cc_start: 0.5956 (m100) cc_final: 0.5543 (m100) REVERT: H 40 MET cc_start: 0.6732 (ptm) cc_final: 0.6387 (ptm) REVERT: H 47 LEU cc_start: 0.7867 (mm) cc_final: 0.7385 (tp) REVERT: H 93 GLU cc_start: 0.4946 (OUTLIER) cc_final: 0.4548 (mm-30) REVERT: H 119 MET cc_start: 0.6179 (ptm) cc_final: 0.5836 (pmt) REVERT: H 139 MET cc_start: 0.6861 (ptt) cc_final: 0.6437 (ptt) REVERT: H 199 MET cc_start: 0.4773 (tmm) cc_final: 0.4475 (tmm) outliers start: 44 outliers final: 20 residues processed: 315 average time/residue: 0.6419 time to fit residues: 226.1431 Evaluate side-chains 283 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 260 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 646 GLU Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 818 GLU Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain E residue 154 LYS Chi-restraints excluded: chain E residue 347 MET Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 210 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 81 optimal weight: 0.9980 chunk 163 optimal weight: 0.0040 chunk 77 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 214 optimal weight: 0.0470 chunk 156 optimal weight: 1.9990 chunk 204 optimal weight: 0.8980 chunk 30 optimal weight: 0.0980 chunk 86 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 135 optimal weight: 0.8980 overall best weight: 0.3690 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 49 GLN ** H 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.163813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.120318 restraints weight = 28922.012| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.30 r_work: 0.3328 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20087 Z= 0.133 Angle : 0.556 8.276 27164 Z= 0.287 Chirality : 0.041 0.176 3170 Planarity : 0.004 0.063 3456 Dihedral : 7.254 86.874 2803 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.56 % Allowed : 14.07 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.17), residues: 2464 helix: 1.29 (0.15), residues: 1175 sheet: -0.13 (0.22), residues: 527 loop : -0.75 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 105 TYR 0.014 0.001 TYR B 213 PHE 0.017 0.001 PHE H 103 TRP 0.015 0.001 TRP F 28 HIS 0.005 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00303 (20085) covalent geometry : angle 0.55642 (27164) hydrogen bonds : bond 0.03606 ( 1095) hydrogen bonds : angle 4.71680 ( 3132) Misc. bond : bond 0.00117 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 288 time to evaluate : 0.795 Fit side-chains revert: symmetry clash REVERT: A 175 GLU cc_start: 0.7584 (mp0) cc_final: 0.7090 (mp0) REVERT: A 484 ARG cc_start: 0.5117 (OUTLIER) cc_final: 0.4438 (mmt90) REVERT: A 592 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7199 (tp30) REVERT: A 646 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8286 (tm-30) REVERT: A 823 GLU cc_start: 0.8394 (pp20) cc_final: 0.8159 (pp20) REVERT: B 117 ARG cc_start: 0.7819 (mtm180) cc_final: 0.7035 (mtm110) REVERT: B 132 LYS cc_start: 0.7822 (ptmm) cc_final: 0.7610 (pttp) REVERT: B 332 ASN cc_start: 0.8723 (p0) cc_final: 0.8514 (p0) REVERT: D 187 ILE cc_start: 0.8514 (tp) cc_final: 0.8251 (tp) REVERT: D 216 LYS cc_start: 0.8140 (mmtp) cc_final: 0.7829 (mmtm) REVERT: D 221 LYS cc_start: 0.8258 (mppt) cc_final: 0.7952 (mptt) REVERT: D 258 THR cc_start: 0.8532 (p) cc_final: 0.8022 (t) REVERT: D 329 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7625 (tp30) REVERT: E 58 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7353 (mp0) REVERT: E 70 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7951 (mp0) REVERT: F 108 GLN cc_start: 0.7848 (tp-100) cc_final: 0.7221 (tm-30) REVERT: F 196 THR cc_start: 0.8253 (OUTLIER) cc_final: 0.7801 (p) REVERT: F 204 GLN cc_start: 0.7446 (tt0) cc_final: 0.6693 (tm-30) REVERT: H 40 MET cc_start: 0.6621 (ptm) cc_final: 0.6306 (ptm) REVERT: H 47 LEU cc_start: 0.7846 (mm) cc_final: 0.7345 (tp) REVERT: H 93 GLU cc_start: 0.4840 (OUTLIER) cc_final: 0.4533 (mm-30) REVERT: H 119 MET cc_start: 0.6165 (ptm) cc_final: 0.5862 (pmt) REVERT: H 136 VAL cc_start: 0.7171 (t) cc_final: 0.6961 (p) REVERT: H 199 MET cc_start: 0.4827 (tmm) cc_final: 0.4561 (tmm) outliers start: 56 outliers final: 29 residues processed: 321 average time/residue: 0.6410 time to fit residues: 230.6767 Evaluate side-chains 297 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 262 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 484 ARG Chi-restraints excluded: chain A residue 646 GLU Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 733 MET Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 317 ASN Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 347 MET Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 113 ASP Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 210 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 203 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 136 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 225 optimal weight: 2.9990 chunk 221 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 108 optimal weight: 0.0010 overall best weight: 1.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 GLN ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 GLN E 206 ASN E 331 HIS ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 HIS H 246 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.159896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.117567 restraints weight = 28953.605| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.19 r_work: 0.3275 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 20087 Z= 0.257 Angle : 0.652 9.999 27164 Z= 0.335 Chirality : 0.045 0.165 3170 Planarity : 0.005 0.068 3456 Dihedral : 7.524 84.109 2803 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.97 % Allowed : 15.94 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.17), residues: 2464 helix: 1.00 (0.15), residues: 1175 sheet: -0.14 (0.22), residues: 525 loop : -0.87 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 634 TYR 0.022 0.002 TYR H 114 PHE 0.015 0.002 PHE H 103 TRP 0.017 0.002 TRP F 28 HIS 0.009 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00608 (20085) covalent geometry : angle 0.65238 (27164) hydrogen bonds : bond 0.04331 ( 1095) hydrogen bonds : angle 4.83803 ( 3132) Misc. bond : bond 0.00248 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 281 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 GLU cc_start: 0.7591 (mp0) cc_final: 0.7033 (mp0) REVERT: A 484 ARG cc_start: 0.5196 (mmm-85) cc_final: 0.4574 (mmt90) REVERT: A 592 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7099 (tp30) REVERT: A 646 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8173 (tm-30) REVERT: A 823 GLU cc_start: 0.8545 (pp20) cc_final: 0.8255 (pp20) REVERT: B 117 ARG cc_start: 0.7854 (mtm180) cc_final: 0.7037 (mtm110) REVERT: B 332 ASN cc_start: 0.8742 (p0) cc_final: 0.8528 (p0) REVERT: D 187 ILE cc_start: 0.8453 (tp) cc_final: 0.8151 (tp) REVERT: D 216 LYS cc_start: 0.8132 (mmtp) cc_final: 0.7735 (mmtm) REVERT: D 221 LYS cc_start: 0.8273 (mppt) cc_final: 0.7905 (mptt) REVERT: D 329 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7561 (tp30) REVERT: E 58 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7359 (mp0) REVERT: E 70 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7991 (mp0) REVERT: E 111 MET cc_start: 0.7434 (mmm) cc_final: 0.7121 (mmm) REVERT: F 1 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.7615 (ttt) REVERT: F 108 GLN cc_start: 0.7924 (tp-100) cc_final: 0.7221 (tm-30) REVERT: F 204 GLN cc_start: 0.7313 (tt0) cc_final: 0.6603 (tm-30) REVERT: F 229 MET cc_start: 0.7862 (ptm) cc_final: 0.7604 (ptm) REVERT: H 87 ILE cc_start: 0.7002 (mp) cc_final: 0.6708 (pt) REVERT: H 93 GLU cc_start: 0.5011 (OUTLIER) cc_final: 0.4407 (pt0) REVERT: H 119 MET cc_start: 0.6164 (ptm) cc_final: 0.5826 (pmt) REVERT: H 136 VAL cc_start: 0.7223 (t) cc_final: 0.7011 (p) REVERT: H 199 MET cc_start: 0.4850 (tmm) cc_final: 0.4575 (tmm) outliers start: 65 outliers final: 32 residues processed: 321 average time/residue: 0.5732 time to fit residues: 206.0437 Evaluate side-chains 290 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 252 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 GLN Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 646 GLU Chi-restraints excluded: chain A residue 647 LYS Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 317 ASN Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain D residue 333 GLU Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain E residue 70 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 137 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 141 optimal weight: 0.7980 chunk 156 optimal weight: 0.7980 chunk 124 optimal weight: 0.4980 chunk 215 optimal weight: 0.8980 chunk 60 optimal weight: 0.2980 chunk 110 optimal weight: 0.5980 chunk 160 optimal weight: 1.9990 chunk 30 optimal weight: 0.1980 chunk 57 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 188 optimal weight: 6.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 GLN E 206 ASN ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 204 GLN H 246 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.162781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.129059 restraints weight = 28755.811| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 3.40 r_work: 0.3252 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20087 Z= 0.144 Angle : 0.577 8.667 27164 Z= 0.297 Chirality : 0.041 0.200 3170 Planarity : 0.005 0.064 3456 Dihedral : 7.217 81.832 2803 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.11 % Allowed : 16.81 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.17), residues: 2464 helix: 1.21 (0.15), residues: 1175 sheet: -0.10 (0.22), residues: 510 loop : -0.81 (0.23), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 107 TYR 0.019 0.002 TYR E 155 PHE 0.016 0.001 PHE B 243 TRP 0.017 0.001 TRP F 28 HIS 0.004 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00335 (20085) covalent geometry : angle 0.57713 (27164) hydrogen bonds : bond 0.03626 ( 1095) hydrogen bonds : angle 4.64083 ( 3132) Misc. bond : bond 0.00129 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 285 time to evaluate : 0.795 Fit side-chains revert: symmetry clash REVERT: A 175 GLU cc_start: 0.7467 (mp0) cc_final: 0.7229 (mp0) REVERT: A 398 MET cc_start: 0.5860 (OUTLIER) cc_final: 0.5519 (tpp) REVERT: A 592 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7152 (tp30) REVERT: A 646 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8002 (tm-30) REVERT: A 823 GLU cc_start: 0.8373 (pp20) cc_final: 0.8090 (pp20) REVERT: B 117 ARG cc_start: 0.7798 (mtm180) cc_final: 0.6977 (mtm110) REVERT: B 132 LYS cc_start: 0.7702 (ptmm) cc_final: 0.7460 (pttp) REVERT: B 332 ASN cc_start: 0.8601 (p0) cc_final: 0.8390 (p0) REVERT: D 216 LYS cc_start: 0.8141 (mmtp) cc_final: 0.7834 (mmtm) REVERT: D 221 LYS cc_start: 0.8221 (mppt) cc_final: 0.7866 (mptt) REVERT: E 111 MET cc_start: 0.7326 (mmm) cc_final: 0.6920 (mmt) REVERT: E 154 LYS cc_start: 0.7864 (ttmt) cc_final: 0.7353 (mmtm) REVERT: F 1 MET cc_start: 0.7794 (OUTLIER) cc_final: 0.7551 (ttt) REVERT: F 108 GLN cc_start: 0.7832 (tp-100) cc_final: 0.7233 (tm-30) REVERT: F 204 GLN cc_start: 0.7250 (tt0) cc_final: 0.6526 (tm-30) REVERT: F 229 MET cc_start: 0.7773 (ptm) cc_final: 0.7527 (ptm) REVERT: G 49 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8237 (tt0) REVERT: H 93 GLU cc_start: 0.4825 (OUTLIER) cc_final: 0.4521 (mm-30) REVERT: H 114 TYR cc_start: 0.7044 (m-80) cc_final: 0.6690 (m-80) REVERT: H 119 MET cc_start: 0.6036 (ptm) cc_final: 0.5700 (pmt) REVERT: H 199 MET cc_start: 0.4775 (tmm) cc_final: 0.4538 (tmm) outliers start: 68 outliers final: 33 residues processed: 328 average time/residue: 0.5786 time to fit residues: 213.9831 Evaluate side-chains 294 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 256 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 418 GLN Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 646 GLU Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 347 MET Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain G residue 49 GLN Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 244 MET Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 137 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 229 optimal weight: 5.9990 chunk 211 optimal weight: 0.7980 chunk 185 optimal weight: 3.9990 chunk 163 optimal weight: 0.1980 chunk 102 optimal weight: 1.9990 chunk 89 optimal weight: 0.3980 chunk 92 optimal weight: 0.5980 chunk 218 optimal weight: 0.5980 chunk 118 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 240 optimal weight: 7.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 246 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.162586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.128689 restraints weight = 28863.415| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 3.41 r_work: 0.3252 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20087 Z= 0.152 Angle : 0.586 8.718 27164 Z= 0.300 Chirality : 0.041 0.188 3170 Planarity : 0.005 0.064 3456 Dihedral : 7.163 79.418 2803 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.02 % Allowed : 17.91 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.17), residues: 2464 helix: 1.28 (0.15), residues: 1171 sheet: -0.10 (0.22), residues: 513 loop : -0.73 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 146 TYR 0.039 0.002 TYR E 155 PHE 0.017 0.001 PHE H 103 TRP 0.016 0.001 TRP F 28 HIS 0.004 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00355 (20085) covalent geometry : angle 0.58553 (27164) hydrogen bonds : bond 0.03641 ( 1095) hydrogen bonds : angle 4.57451 ( 3132) Misc. bond : bond 0.00135 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 273 time to evaluate : 0.582 Fit side-chains revert: symmetry clash REVERT: A 175 GLU cc_start: 0.7463 (mp0) cc_final: 0.7021 (mp0) REVERT: A 398 MET cc_start: 0.5797 (tpp) cc_final: 0.5531 (tpp) REVERT: A 592 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7088 (tp30) REVERT: A 646 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8015 (tm-30) REVERT: A 823 GLU cc_start: 0.8350 (pp20) cc_final: 0.8070 (pp20) REVERT: B 117 ARG cc_start: 0.7821 (mtm180) cc_final: 0.7012 (mtm110) REVERT: B 132 LYS cc_start: 0.7726 (ptmm) cc_final: 0.7483 (pttp) REVERT: B 332 ASN cc_start: 0.8629 (p0) cc_final: 0.8420 (p0) REVERT: C 89 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8190 (mt-10) REVERT: D 216 LYS cc_start: 0.8144 (mmtp) cc_final: 0.7856 (mmtm) REVERT: D 221 LYS cc_start: 0.8222 (mppt) cc_final: 0.7947 (mptt) REVERT: D 329 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7412 (tp30) REVERT: E 111 MET cc_start: 0.7320 (mmm) cc_final: 0.7054 (mmt) REVERT: E 154 LYS cc_start: 0.7801 (ttmt) cc_final: 0.7266 (mmtm) REVERT: F 1 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7571 (ttt) REVERT: F 108 GLN cc_start: 0.7803 (tp-100) cc_final: 0.7250 (tm-30) REVERT: F 199 MET cc_start: 0.7410 (tmm) cc_final: 0.7102 (tmm) REVERT: F 204 GLN cc_start: 0.7251 (tt0) cc_final: 0.6552 (tm-30) REVERT: F 229 MET cc_start: 0.7798 (ptm) cc_final: 0.7554 (ptm) REVERT: G 49 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8233 (tt0) REVERT: H 47 LEU cc_start: 0.8329 (tp) cc_final: 0.7767 (mm) REVERT: H 93 GLU cc_start: 0.4919 (OUTLIER) cc_final: 0.4451 (pt0) REVERT: H 199 MET cc_start: 0.4816 (tmm) cc_final: 0.4559 (tmm) outliers start: 66 outliers final: 39 residues processed: 320 average time/residue: 0.5485 time to fit residues: 198.3502 Evaluate side-chains 300 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 256 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 GLN Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 646 GLU Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 347 MET Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain G residue 49 GLN Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 203 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 65 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 153 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 161 optimal weight: 0.9990 chunk 172 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.161055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.117391 restraints weight = 28741.617| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.25 r_work: 0.3278 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 20087 Z= 0.209 Angle : 0.626 9.338 27164 Z= 0.321 Chirality : 0.043 0.182 3170 Planarity : 0.005 0.062 3456 Dihedral : 7.289 78.284 2803 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.92 % Allowed : 18.64 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.17), residues: 2464 helix: 1.15 (0.15), residues: 1171 sheet: -0.16 (0.22), residues: 519 loop : -0.75 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 107 TYR 0.024 0.002 TYR H 114 PHE 0.016 0.002 PHE H 103 TRP 0.019 0.002 TRP F 28 HIS 0.005 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00492 (20085) covalent geometry : angle 0.62555 (27164) hydrogen bonds : bond 0.03940 ( 1095) hydrogen bonds : angle 4.63590 ( 3132) Misc. bond : bond 0.00190 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 259 time to evaluate : 0.820 Fit side-chains revert: symmetry clash REVERT: A 175 GLU cc_start: 0.7551 (mp0) cc_final: 0.7058 (mp0) REVERT: A 592 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7197 (tp30) REVERT: A 646 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8213 (tm-30) REVERT: A 823 GLU cc_start: 0.8554 (pp20) cc_final: 0.8208 (pp20) REVERT: B 117 ARG cc_start: 0.7875 (mtm180) cc_final: 0.7044 (mtm110) REVERT: B 332 ASN cc_start: 0.8813 (p0) cc_final: 0.8600 (p0) REVERT: C 94 ASP cc_start: 0.8662 (m-30) cc_final: 0.8425 (m-30) REVERT: D 107 ARG cc_start: 0.8300 (mtp-110) cc_final: 0.8093 (mtm110) REVERT: D 216 LYS cc_start: 0.8192 (mmtp) cc_final: 0.7851 (mmtm) REVERT: D 221 LYS cc_start: 0.8286 (mppt) cc_final: 0.8000 (mptt) REVERT: D 329 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7680 (tp30) REVERT: E 111 MET cc_start: 0.7446 (mmm) cc_final: 0.7057 (mmt) REVERT: E 154 LYS cc_start: 0.7782 (ttmt) cc_final: 0.7169 (mmtm) REVERT: F 1 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.7628 (ttt) REVERT: F 86 ASP cc_start: 0.8312 (m-30) cc_final: 0.8103 (m-30) REVERT: F 108 GLN cc_start: 0.7815 (tp-100) cc_final: 0.7175 (tm-30) REVERT: F 204 GLN cc_start: 0.7323 (tt0) cc_final: 0.6537 (tm-30) REVERT: F 229 MET cc_start: 0.7899 (ptm) cc_final: 0.7657 (ptm) REVERT: G 49 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.7984 (tm130) REVERT: H 47 LEU cc_start: 0.8297 (tp) cc_final: 0.7788 (mm) REVERT: H 93 GLU cc_start: 0.4902 (OUTLIER) cc_final: 0.4423 (pt0) outliers start: 64 outliers final: 45 residues processed: 303 average time/residue: 0.6240 time to fit residues: 212.4348 Evaluate side-chains 301 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 251 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 GLN Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 646 GLU Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 209 SER Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain G residue 49 GLN Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 203 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 167 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 163 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 50 optimal weight: 0.0770 chunk 166 optimal weight: 0.5980 chunk 176 optimal weight: 0.9980 chunk 191 optimal weight: 0.8980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.162214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.128181 restraints weight = 28705.426| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 3.36 r_work: 0.3261 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20087 Z= 0.158 Angle : 0.608 12.253 27164 Z= 0.310 Chirality : 0.042 0.196 3170 Planarity : 0.005 0.063 3456 Dihedral : 7.172 78.539 2803 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.51 % Allowed : 19.19 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.17), residues: 2464 helix: 1.25 (0.15), residues: 1170 sheet: -0.10 (0.22), residues: 501 loop : -0.70 (0.23), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 91 TYR 0.041 0.002 TYR E 155 PHE 0.014 0.001 PHE H 103 TRP 0.018 0.001 TRP F 28 HIS 0.004 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00371 (20085) covalent geometry : angle 0.60836 (27164) hydrogen bonds : bond 0.03659 ( 1095) hydrogen bonds : angle 4.56721 ( 3132) Misc. bond : bond 0.00136 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 272 time to evaluate : 0.672 Fit side-chains revert: symmetry clash REVERT: A 175 GLU cc_start: 0.7447 (mp0) cc_final: 0.7129 (mp0) REVERT: A 592 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7154 (tp30) REVERT: A 646 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7964 (tm-30) REVERT: A 823 GLU cc_start: 0.8344 (pp20) cc_final: 0.8052 (pp20) REVERT: B 117 ARG cc_start: 0.7864 (mtm180) cc_final: 0.7043 (mtm110) REVERT: B 132 LYS cc_start: 0.7695 (ptmm) cc_final: 0.7454 (pttp) REVERT: B 332 ASN cc_start: 0.8612 (p0) cc_final: 0.8401 (p0) REVERT: C 89 GLU cc_start: 0.8406 (mt-10) cc_final: 0.8164 (mt-10) REVERT: C 94 ASP cc_start: 0.8464 (m-30) cc_final: 0.8261 (m-30) REVERT: D 107 ARG cc_start: 0.8243 (mtp-110) cc_final: 0.8026 (mtm110) REVERT: D 216 LYS cc_start: 0.8160 (mmtp) cc_final: 0.7845 (mmtm) REVERT: D 221 LYS cc_start: 0.8199 (mppt) cc_final: 0.7966 (mptt) REVERT: D 329 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7411 (tp30) REVERT: E 111 MET cc_start: 0.7343 (mmm) cc_final: 0.7082 (mmt) REVERT: E 154 LYS cc_start: 0.7735 (ttmt) cc_final: 0.7241 (mmtm) REVERT: F 1 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.7504 (ttt) REVERT: F 108 GLN cc_start: 0.7774 (tp-100) cc_final: 0.7195 (tm-30) REVERT: F 204 GLN cc_start: 0.7198 (tt0) cc_final: 0.6488 (tm-30) REVERT: F 229 MET cc_start: 0.7799 (ptm) cc_final: 0.7563 (ptm) REVERT: G 49 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.7852 (tm130) REVERT: G 146 ARG cc_start: 0.7751 (ttt90) cc_final: 0.7463 (tpt-90) REVERT: H 47 LEU cc_start: 0.8299 (tp) cc_final: 0.7823 (mm) REVERT: H 93 GLU cc_start: 0.4840 (OUTLIER) cc_final: 0.4362 (pt0) REVERT: H 119 MET cc_start: 0.6033 (ptm) cc_final: 0.5497 (pmt) outliers start: 55 outliers final: 43 residues processed: 313 average time/residue: 0.5752 time to fit residues: 202.3646 Evaluate side-chains 309 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 261 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 GLN Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 646 GLU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain D residue 333 GLU Chi-restraints excluded: chain E residue 58 GLU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain G residue 49 GLN Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 210 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 12 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 218 optimal weight: 2.9990 chunk 213 optimal weight: 0.8980 chunk 227 optimal weight: 2.9990 chunk 215 optimal weight: 0.8980 chunk 180 optimal weight: 0.4980 chunk 209 optimal weight: 0.8980 chunk 169 optimal weight: 0.7980 chunk 148 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.161527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.118339 restraints weight = 28971.018| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.38 r_work: 0.3272 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20087 Z= 0.184 Angle : 0.622 9.411 27164 Z= 0.319 Chirality : 0.043 0.186 3170 Planarity : 0.005 0.063 3456 Dihedral : 7.226 78.304 2803 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.42 % Allowed : 19.64 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.17), residues: 2464 helix: 1.19 (0.15), residues: 1171 sheet: -0.11 (0.22), residues: 509 loop : -0.74 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 107 TYR 0.023 0.002 TYR B 213 PHE 0.019 0.001 PHE H 103 TRP 0.020 0.001 TRP F 28 HIS 0.005 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00434 (20085) covalent geometry : angle 0.62189 (27164) hydrogen bonds : bond 0.03817 ( 1095) hydrogen bonds : angle 4.60340 ( 3132) Misc. bond : bond 0.00157 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 269 time to evaluate : 0.853 Fit side-chains revert: symmetry clash REVERT: A 175 GLU cc_start: 0.7409 (mp0) cc_final: 0.7084 (mp0) REVERT: A 592 GLU cc_start: 0.7474 (mm-30) cc_final: 0.7018 (tp30) REVERT: A 646 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7858 (tm-30) REVERT: A 823 GLU cc_start: 0.8370 (pp20) cc_final: 0.8030 (pp20) REVERT: B 117 ARG cc_start: 0.7815 (mtm180) cc_final: 0.6927 (mtm110) REVERT: B 332 ASN cc_start: 0.8662 (p0) cc_final: 0.8448 (p0) REVERT: C 89 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8111 (mt-10) REVERT: D 107 ARG cc_start: 0.8257 (mtp-110) cc_final: 0.8033 (mtm110) REVERT: D 187 ILE cc_start: 0.8421 (tp) cc_final: 0.8045 (tp) REVERT: D 216 LYS cc_start: 0.8145 (mmtp) cc_final: 0.7843 (mmtm) REVERT: D 221 LYS cc_start: 0.8191 (mppt) cc_final: 0.7932 (mptt) REVERT: D 329 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7363 (tp30) REVERT: E 111 MET cc_start: 0.7361 (mmm) cc_final: 0.7034 (mmt) REVERT: E 154 LYS cc_start: 0.7637 (ttmt) cc_final: 0.7156 (mmtm) REVERT: E 155 TYR cc_start: 0.7512 (m-10) cc_final: 0.7302 (m-10) REVERT: F 108 GLN cc_start: 0.7772 (tp-100) cc_final: 0.7181 (tm-30) REVERT: F 204 GLN cc_start: 0.7191 (tt0) cc_final: 0.6450 (tm-30) REVERT: F 229 MET cc_start: 0.7793 (ptm) cc_final: 0.7552 (ptm) REVERT: G 49 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.7852 (tm130) REVERT: G 146 ARG cc_start: 0.7880 (ttt90) cc_final: 0.7427 (tpt-90) REVERT: H 47 LEU cc_start: 0.8315 (tp) cc_final: 0.7827 (mm) REVERT: H 93 GLU cc_start: 0.4943 (OUTLIER) cc_final: 0.4391 (pt0) REVERT: H 119 MET cc_start: 0.6004 (ptm) cc_final: 0.5499 (pmt) outliers start: 53 outliers final: 45 residues processed: 308 average time/residue: 0.6137 time to fit residues: 212.7291 Evaluate side-chains 313 residues out of total 2189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 264 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 GLN Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 646 GLU Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 125 ASP Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 211 LEU Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain D residue 333 GLU Chi-restraints excluded: chain E residue 67 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 131 VAL Chi-restraints excluded: chain E residue 347 MET Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain G residue 49 GLN Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 185 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 137 VAL Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 210 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 14 optimal weight: 1.9990 chunk 201 optimal weight: 0.5980 chunk 37 optimal weight: 0.0060 chunk 26 optimal weight: 0.7980 chunk 147 optimal weight: 0.0970 chunk 42 optimal weight: 0.8980 chunk 15 optimal weight: 0.0980 chunk 222 optimal weight: 0.9990 chunk 233 optimal weight: 0.7980 chunk 27 optimal weight: 0.4980 chunk 38 optimal weight: 0.7980 overall best weight: 0.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 ASN E 331 HIS ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 246 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.163781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.129987 restraints weight = 28894.463| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 3.36 r_work: 0.3282 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20087 Z= 0.126 Angle : 0.591 9.413 27164 Z= 0.302 Chirality : 0.041 0.192 3170 Planarity : 0.004 0.062 3456 Dihedral : 7.016 79.989 2803 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.15 % Allowed : 20.05 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.17), residues: 2464 helix: 1.38 (0.15), residues: 1172 sheet: -0.10 (0.22), residues: 509 loop : -0.68 (0.23), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 107 TYR 0.023 0.001 TYR B 213 PHE 0.017 0.001 PHE H 103 TRP 0.017 0.001 TRP F 28 HIS 0.004 0.001 HIS A 637 Details of bonding type rmsd covalent geometry : bond 0.00286 (20085) covalent geometry : angle 0.59059 (27164) hydrogen bonds : bond 0.03408 ( 1095) hydrogen bonds : angle 4.48569 ( 3132) Misc. bond : bond 0.00095 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7045.46 seconds wall clock time: 120 minutes 52.39 seconds (7252.39 seconds total)