Starting phenix.real_space_refine on Fri Aug 7 22:20:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kd2_37122/08_2026/8kd2_37122.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kd2_37122/08_2026/8kd2_37122.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kd2_37122/08_2026/8kd2_37122.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kd2_37122/08_2026/8kd2_37122.map" model { file = "/net/cci-nas-00/data/ceres_data/8kd2_37122/08_2026/8kd2_37122.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kd2_37122/08_2026/8kd2_37122.cif" } resolution = 3.02 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= 0.002 sd= 0.009 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 348 5.49 5 S 77 5.16 5 C 14551 2.51 5 N 4411 2.21 5 O 5307 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24694 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3097 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 15, 'TRANS': 375} Chain breaks: 1 Chain: "B" Number of atoms: 4361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 4361 Classifications: {'peptide': 519} Link IDs: {'PTRANS': 12, 'TRANS': 506} Chain breaks: 4 Chain: "D" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1474 Classifications: {'peptide': 182} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "E" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2399 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 17, 'TRANS': 272} Chain breaks: 5 Chain: "F" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 146 Classifications: {'peptide': 19} Link IDs: {'TRANS': 18} Chain breaks: 1 Chain: "G" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 160 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain breaks: 1 Chain: "O" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "P" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "Q" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "R" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 715 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "S" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "T" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 618 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "U" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "V" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 721 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "X" Number of atoms: 3590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 3590 Classifications: {'DNA': 174} Link IDs: {'rna3p': 173} Chain: "Y" Number of atoms: 3544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 3544 Classifications: {'DNA': 174} Link IDs: {'rna3p': 173} Time building chain proxies: 4.59, per 1000 atoms: 0.19 Number of scatterers: 24694 At special positions: 0 Unit cell: (134.9, 126.38, 189.57, 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 77 16.00 P 348 15.00 O 5307 8.00 N 4411 7.00 C 14551 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS E 303 " - pdb=" SG CYS E 306 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.97 Conformation dependent library (CDL) restraints added in 900.3 milliseconds 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4102 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 16 sheets defined 58.2% alpha, 3.7% beta 137 base pairs and 269 stacking pairs defined. Time for finding SS restraints: 3.69 Creating SS restraints... Processing helix chain 'A' and resid 26 through 30 Processing helix chain 'A' and resid 42 through 55 removed outlier: 4.186A pdb=" N ARG A 46 " --> pdb=" O PRO A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 61 removed outlier: 3.536A pdb=" N LYS A 60 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 75 Processing helix chain 'A' and resid 79 through 89 Processing helix chain 'A' and resid 97 through 104 removed outlier: 3.612A pdb=" N PHE A 104 " --> pdb=" O GLU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 137 Processing helix chain 'A' and resid 164 through 173 removed outlier: 3.636A pdb=" N ILE A 171 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 197 removed outlier: 3.550A pdb=" N PHE A 197 " --> pdb=" O VAL A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 243 through 262 Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 272 through 276 removed outlier: 4.038A pdb=" N SER A 275 " --> pdb=" O GLY A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 300 removed outlier: 4.060A pdb=" N CYS A 294 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL A 295 " --> pdb=" O HIS A 291 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A 298 " --> pdb=" O CYS A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 330 removed outlier: 3.863A pdb=" N ASN A 330 " --> pdb=" O THR A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 381 Processing helix chain 'B' and resid 667 through 676 Processing helix chain 'B' and resid 678 through 694 removed outlier: 3.599A pdb=" N THR B 683 " --> pdb=" O LYS B 679 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLU B 684 " --> pdb=" O HIS B 680 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TYR B 692 " --> pdb=" O ILE B 688 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER B 693 " --> pdb=" O LEU B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 710 Processing helix chain 'B' and resid 714 through 723 removed outlier: 4.009A pdb=" N PHE B 723 " --> pdb=" O TRP B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 790 Processing helix chain 'B' and resid 801 through 840 Processing helix chain 'B' and resid 843 through 848 removed outlier: 4.090A pdb=" N ASN B 848 " --> pdb=" O ASN B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 871 Processing helix chain 'B' and resid 872 through 886 removed outlier: 4.072A pdb=" N PHE B 877 " --> pdb=" O LYS B 873 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU B 878 " --> pdb=" O GLU B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 929 removed outlier: 4.314A pdb=" N GLU B 911 " --> pdb=" O ARG B 907 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LYS B 914 " --> pdb=" O ARG B 910 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N PHE B 925 " --> pdb=" O GLN B 921 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LYS B 926 " --> pdb=" O LYS B 922 " (cutoff:3.500A) Processing helix chain 'B' and resid 934 through 943 Processing helix chain 'B' and resid 944 through 957 Processing helix chain 'B' and resid 958 through 960 No H-bonds generated for 'chain 'B' and resid 958 through 960' Processing helix chain 'B' and resid 982 through 998 removed outlier: 4.267A pdb=" N TYR B 986 " --> pdb=" O LYS B 982 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP B 987 " --> pdb=" O ASN B 983 " (cutoff:3.500A) Processing helix chain 'B' and resid 1003 through 1022 Processing helix chain 'B' and resid 1142 through 1164 removed outlier: 3.523A pdb=" N ILE B1161 " --> pdb=" O ARG B1157 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N MET B1164 " --> pdb=" O GLU B1160 " (cutoff:3.500A) Processing helix chain 'B' and resid 1164 through 1174 removed outlier: 3.717A pdb=" N VAL B1168 " --> pdb=" O MET B1164 " (cutoff:3.500A) Processing helix chain 'B' and resid 1179 through 1183 Processing helix chain 'B' and resid 1202 through 1217 Processing helix chain 'B' and resid 1220 through 1233 removed outlier: 3.588A pdb=" N TYR B1232 " --> pdb=" O LEU B1228 " (cutoff:3.500A) Processing helix chain 'B' and resid 1236 through 1240 removed outlier: 3.561A pdb=" N TYR B1240 " --> pdb=" O PHE B1237 " (cutoff:3.500A) Processing helix chain 'B' and resid 1241 through 1259 removed outlier: 3.753A pdb=" N THR B1255 " --> pdb=" O LYS B1251 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU B1256 " --> pdb=" O HIS B1252 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N MET B1257 " --> pdb=" O ALA B1253 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP B1259 " --> pdb=" O THR B1255 " (cutoff:3.500A) Processing helix chain 'B' and resid 1260 through 1274 removed outlier: 3.901A pdb=" N ASN B1274 " --> pdb=" O VAL B1270 " (cutoff:3.500A) Processing helix chain 'B' and resid 1284 through 1292 removed outlier: 4.430A pdb=" N LEU B1288 " --> pdb=" O ILE B1284 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 240 Processing helix chain 'D' and resid 253 through 265 Processing helix chain 'D' and resid 273 through 292 removed outlier: 4.292A pdb=" N GLN D 277 " --> pdb=" O GLY D 273 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASP D 290 " --> pdb=" O LYS D 286 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS D 291 " --> pdb=" O LEU D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 297 removed outlier: 3.506A pdb=" N MET D 296 " --> pdb=" O CYS D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 316 removed outlier: 3.867A pdb=" N ASP D 316 " --> pdb=" O LYS D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 337 removed outlier: 3.595A pdb=" N LEU D 331 " --> pdb=" O GLY D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 343 removed outlier: 3.989A pdb=" N LEU D 341 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER D 343 " --> pdb=" O PRO D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 348 through 369 removed outlier: 3.893A pdb=" N LEU D 354 " --> pdb=" O GLN D 350 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET D 368 " --> pdb=" O VAL D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'D' and resid 391 through 399 removed outlier: 3.550A pdb=" N LEU D 399 " --> pdb=" O GLU D 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 311 removed outlier: 4.134A pdb=" N ILE E 310 " --> pdb=" O CYS E 306 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE E 311 " --> pdb=" O LYS E 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 306 through 311' Processing helix chain 'E' and resid 321 through 330 removed outlier: 4.212A pdb=" N ASN E 325 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS E 328 " --> pdb=" O SER E 324 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ASN E 330 " --> pdb=" O PHE E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 335 No H-bonds generated for 'chain 'E' and resid 333 through 335' Processing helix chain 'E' and resid 336 through 342 removed outlier: 3.558A pdb=" N ASN E 342 " --> pdb=" O LYS E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 357 through 361 Processing helix chain 'E' and resid 400 through 407 removed outlier: 3.529A pdb=" N ASP E 404 " --> pdb=" O SER E 400 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 434 removed outlier: 4.001A pdb=" N ASN E 433 " --> pdb=" O HIS E 430 " (cutoff:3.500A) Processing helix chain 'E' and resid 544 through 561 Processing helix chain 'F' and resid 348 through 351 removed outlier: 3.758A pdb=" N SER F 351 " --> pdb=" O ASP F 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 348 through 351' Processing helix chain 'F' and resid 352 through 360 removed outlier: 3.778A pdb=" N ILE F 356 " --> pdb=" O CYS F 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 322 through 330 removed outlier: 3.539A pdb=" N ASN G 330 " --> pdb=" O PHE G 326 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 57 removed outlier: 3.543A pdb=" N LEU O 48 " --> pdb=" O GLY O 44 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 76 Processing helix chain 'O' and resid 85 through 114 Processing helix chain 'O' and resid 120 through 131 Processing helix chain 'P' and resid 24 through 29 removed outlier: 4.065A pdb=" N GLN P 27 " --> pdb=" O ASP P 24 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE P 29 " --> pdb=" O ILE P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 30 through 41 Processing helix chain 'P' and resid 49 through 76 removed outlier: 4.114A pdb=" N GLU P 53 " --> pdb=" O LEU P 49 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA P 76 " --> pdb=" O TYR P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 93 removed outlier: 3.528A pdb=" N VAL P 86 " --> pdb=" O THR P 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 37 Processing helix chain 'Q' and resid 45 through 73 removed outlier: 4.139A pdb=" N VAL Q 49 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 90 removed outlier: 3.542A pdb=" N ASP Q 90 " --> pdb=" O ALA Q 86 " (cutoff:3.500A) Processing helix chain 'Q' and resid 90 through 97 Processing helix chain 'R' and resid 34 through 46 Processing helix chain 'R' and resid 52 through 81 removed outlier: 3.802A pdb=" N ASN R 81 " --> pdb=" O LEU R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 99 Processing helix chain 'R' and resid 100 through 119 removed outlier: 3.626A pdb=" N ALA R 104 " --> pdb=" O PRO R 100 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 57 removed outlier: 3.822A pdb=" N SER S 57 " --> pdb=" O ARG S 53 " (cutoff:3.500A) Processing helix chain 'S' and resid 63 through 79 removed outlier: 3.581A pdb=" N PHE S 67 " --> pdb=" O ARG S 63 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP S 77 " --> pdb=" O GLU S 73 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N PHE S 78 " --> pdb=" O ILE S 74 " (cutoff:3.500A) Processing helix chain 'S' and resid 85 through 114 Processing helix chain 'S' and resid 120 through 132 Processing helix chain 'T' and resid 30 through 41 Processing helix chain 'T' and resid 49 through 76 removed outlier: 4.149A pdb=" N GLU T 53 " --> pdb=" O LEU T 49 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA T 76 " --> pdb=" O TYR T 72 " (cutoff:3.500A) Processing helix chain 'T' and resid 82 through 92 removed outlier: 3.800A pdb=" N VAL T 86 " --> pdb=" O THR T 82 " (cutoff:3.500A) Processing helix chain 'U' and resid 16 through 22 Processing helix chain 'U' and resid 26 through 37 Processing helix chain 'U' and resid 45 through 74 removed outlier: 4.251A pdb=" N VAL U 49 " --> pdb=" O ALA U 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 79 through 90 removed outlier: 3.572A pdb=" N ASP U 90 " --> pdb=" O ALA U 86 " (cutoff:3.500A) Processing helix chain 'U' and resid 90 through 97 Processing helix chain 'V' and resid 34 through 46 Processing helix chain 'V' and resid 52 through 81 Processing helix chain 'V' and resid 87 through 98 Processing helix chain 'V' and resid 101 through 120 removed outlier: 3.947A pdb=" N LYS V 105 " --> pdb=" O GLY V 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 64 removed outlier: 8.838A pdb=" N TYR A 64 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N TYR A 23 " --> pdb=" O TYR A 64 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA A 22 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ALA A 142 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL A 267 " --> pdb=" O MET A 306 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N VAL A 308 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N LEU A 269 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU A 181 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N GLN A 270 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE A 183 " --> pdb=" O GLN A 270 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL A 180 " --> pdb=" O MET A 204 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N CYS A 206 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N TYR A 182 " --> pdb=" O CYS A 206 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N PHE A 208 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ASP A 184 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N LYS A 210 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N VAL A 236 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N SER A 207 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LEU A 238 " --> pdb=" O SER A 207 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N HIS A 209 " --> pdb=" O LEU A 238 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 756 through 757 removed outlier: 3.567A pdb=" N LYS B 756 " --> pdb=" O VAL B 783 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL B 783 " --> pdb=" O LYS B 756 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 1136 through 1141 removed outlier: 3.715A pdb=" N PHE B1136 " --> pdb=" O PHE B1305 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 244 through 246 Processing sheet with id=AA5, first strand: chain 'E' and resid 437 through 439 Processing sheet with id=AA6, first strand: chain 'E' and resid 475 through 476 removed outlier: 3.821A pdb=" N LYS E 476 " --> pdb=" O LYS E 490 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS E 490 " --> pdb=" O LYS E 476 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 521 through 523 removed outlier: 3.696A pdb=" N ILE E 542 " --> pdb=" O GLN E 521 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'O' and resid 83 through 84 removed outlier: 6.976A pdb=" N ARG O 83 " --> pdb=" O VAL P 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'O' and resid 118 through 119 Processing sheet with id=AB1, first strand: chain 'P' and resid 96 through 98 removed outlier: 6.175A pdb=" N THR P 96 " --> pdb=" O THR U 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'Q' and resid 42 through 43 removed outlier: 7.091A pdb=" N ARG Q 42 " --> pdb=" O ILE R 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'Q' and resid 77 through 78 Processing sheet with id=AB4, first strand: chain 'Q' and resid 100 through 102 Processing sheet with id=AB5, first strand: chain 'S' and resid 83 through 84 removed outlier: 6.957A pdb=" N ARG S 83 " --> pdb=" O VAL T 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'U' and resid 42 through 43 removed outlier: 7.355A pdb=" N ARG U 42 " --> pdb=" O ILE V 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'U' and resid 77 through 78 841 hydrogen bonds defined for protein. 2481 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 357 hydrogen bonds 714 hydrogen bond angles 0 basepair planarities 137 basepair parallelities 269 stacking parallelities Total time for adding SS restraints: 7.73 Time building geometry restraints manager: 2.73 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: 6292 1.34 - 1.46: 7273 1.46 - 1.58: 11520 1.58 - 1.70: 694 1.70 - 1.82: 119 Bond restraints: 25898 Sorted by residual: bond pdb=" C3' DC Y 33 " pdb=" C2' DC Y 33 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.23e+01 bond pdb=" C3' DG X -22 " pdb=" C2' DG X -22 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.85e+00 bond pdb=" C3' DG X -6 " pdb=" C2' DG X -6 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.42e+00 bond pdb=" C1' DT X 15 " pdb=" N1 DT X 15 " ideal model delta sigma weight residual 1.468 1.509 -0.041 1.40e-02 5.10e+03 8.71e+00 bond pdb=" C5' DG Y -24 " pdb=" C4' DG Y -24 " ideal model delta sigma weight residual 1.512 1.532 -0.020 7.00e-03 2.04e+04 8.29e+00 ... (remaining 25893 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 35693 2.38 - 4.75: 648 4.75 - 7.13: 76 7.13 - 9.50: 21 9.50 - 11.88: 5 Bond angle restraints: 36443 Sorted by residual: angle pdb=" N3 DT X -79 " pdb=" C4 DT X -79 " pdb=" O4 DT X -79 " ideal model delta sigma weight residual 119.90 122.76 -2.86 6.00e-01 2.78e+00 2.28e+01 angle pdb=" O4' DG Y 2 " pdb=" C4' DG Y 2 " pdb=" C3' DG Y 2 " ideal model delta sigma weight residual 106.00 103.24 2.76 6.00e-01 2.78e+00 2.12e+01 angle pdb=" N3 DT X -23 " pdb=" C4 DT X -23 " pdb=" O4 DT X -23 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.02e+01 angle pdb=" N3 DT X 31 " pdb=" C4 DT X 31 " pdb=" O4 DT X 31 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.02e+01 angle pdb=" N3 DT X 66 " pdb=" C4 DT X 66 " pdb=" O4 DT X 66 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.98e+01 ... (remaining 36438 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.36: 11714 27.36 - 54.71: 2548 54.71 - 82.07: 390 82.07 - 109.42: 12 109.42 - 136.78: 2 Dihedral angle restraints: 14666 sinusoidal: 8322 harmonic: 6344 Sorted by residual: dihedral pdb=" C4' DC X 11 " pdb=" C3' DC X 11 " pdb=" O3' DC X 11 " pdb=" P DG X 12 " ideal model delta sinusoidal sigma weight residual 220.00 83.22 136.78 1 3.50e+01 8.16e-04 1.35e+01 dihedral pdb=" C4' DC Y -73 " pdb=" C3' DC Y -73 " pdb=" O3' DC Y -73 " pdb=" P DT Y -72 " ideal model delta sinusoidal sigma weight residual 220.00 85.00 135.00 1 3.50e+01 8.16e-04 1.34e+01 dihedral pdb=" CA MET A 360 " pdb=" C MET A 360 " pdb=" N PHE A 361 " pdb=" CA PHE A 361 " ideal model delta harmonic sigma weight residual -180.00 -162.00 -18.00 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 14663 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3345 0.060 - 0.120: 656 0.120 - 0.181: 36 0.181 - 0.241: 3 0.241 - 0.301: 1 Chirality restraints: 4041 Sorted by residual: chirality pdb=" CG LEU D 363 " pdb=" CB LEU D 363 " pdb=" CD1 LEU D 363 " pdb=" CD2 LEU D 363 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CB THR B 833 " pdb=" CA THR B 833 " pdb=" OG1 THR B 833 " pdb=" CG2 THR B 833 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA ASN E 517 " pdb=" N ASN E 517 " pdb=" C ASN E 517 " pdb=" CB ASN E 517 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.63e-01 ... (remaining 4038 not shown) Planarity restraints: 3424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 916 " 0.030 2.00e-02 2.50e+03 2.41e-02 1.45e+01 pdb=" CG TRP B 916 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP B 916 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP B 916 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 916 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 916 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 916 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 916 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 916 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 916 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 105 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.45e+00 pdb=" C ASN A 105 " -0.044 2.00e-02 2.50e+03 pdb=" O ASN A 105 " 0.017 2.00e-02 2.50e+03 pdb=" N VAL A 106 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 301 " 0.013 2.00e-02 2.50e+03 1.47e-02 5.43e+00 pdb=" CG TRP E 301 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP E 301 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP E 301 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP E 301 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 301 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 301 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 301 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 301 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP E 301 " 0.000 2.00e-02 2.50e+03 ... (remaining 3421 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.15: 1 2.15 - 2.83: 7181 2.83 - 3.52: 35443 3.52 - 4.21: 64119 4.21 - 4.90: 100474 Nonbonded interactions: 207218 Sorted by model distance: nonbonded pdb=" CB GLU B 813 " pdb=" CD2 LEU E 48 " model vdw 1.457 3.860 nonbonded pdb=" N2 DG X 20 " pdb=" O6 DG Y -19 " model vdw 2.168 3.120 nonbonded pdb=" OH TYR A 343 " pdb=" OE2 GLU B 822 " model vdw 2.210 3.040 nonbonded pdb=" CA GLU B 813 " pdb=" CD2 LEU E 48 " model vdw 2.212 3.890 nonbonded pdb=" O SER A 275 " pdb=" OG SER A 275 " model vdw 2.238 3.040 ... (remaining 207213 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 'O' selection = chain 'S' } ncs_group { reference = (chain 'P' and resid 24 through 100) selection = chain 'T' } ncs_group { reference = chain 'Q' selection = chain 'U' } ncs_group { reference = chain 'R' selection = (chain 'V' and resid 29 through 119) } 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=0.00 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: 12.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 27.250 Find NCS groups from input model: 0.200 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: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 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 : 0.005 0.045 25899 Z= 0.408 Angle : 0.803 11.877 36445 Z= 0.589 Chirality : 0.046 0.301 4041 Planarity : 0.005 0.083 3424 Dihedral : 25.700 136.778 10561 Min Nonbonded Distance : 1.457 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.68 % Allowed : 37.92 % Favored : 61.40 % 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 are not related in a simple way. whole: -0.56 (0.17), residues: 2112 helix: 0.58 (0.15), residues: 1142 sheet: 0.55 (0.64), residues: 75 loop : -1.73 (0.18), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG O 129 TYR 0.029 0.002 TYR P 88 PHE 0.033 0.002 PHE A 160 TRP 0.064 0.003 TRP B 916 HIS 0.016 0.001 HIS R 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.41 (25898) covalent geometry : angle 0.80282 / 0.59 (36443) SS BOND : bond 0.00084 / 0.04 ( 1) SS BOND : angle 0.15635 / 0.09 ( 2) hydrogen bonds : bond 0.11807 / 7.58 ( 1198) hydrogen bonds : angle 4.90347 / 3.43 ( 3195) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 253 time to evaluate : 0.569 Fit side-chains REVERT: B 717 PHE cc_start: 0.2539 (OUTLIER) cc_final: 0.2129 (t80) outliers start: 13 outliers final: 4 residues processed: 258 average time/residue: 0.1351 time to fit residues: 58.0032 Evaluate side-chains 236 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 231 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 717 PHE Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain O residue 120 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 40.0000 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.0060 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.9980 chunk 235 optimal weight: 6.9990 overall best weight: 1.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 54 ASN ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS A 341 ASN A 364 ASN ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 ASN B 815 HIS B 829 GLN B 959 GLN B 974 GLN B1254 HIS D 295 ASN E 304 ASN E 346 HIS E 510 GLN ** O 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 25 ASN ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN T 25 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.139626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.110410 restraints weight = 60295.100| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 1.89 r_work: 0.3666 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 25899 Z= 0.248 Angle : 0.729 15.200 36445 Z= 0.389 Chirality : 0.047 0.321 4041 Planarity : 0.005 0.052 3424 Dihedral : 27.898 139.408 6166 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 6.42 % Allowed : 28.53 % Favored : 65.05 % 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 are not related in a simple way. whole: -0.21 (0.18), residues: 2112 helix: 0.82 (0.15), residues: 1156 sheet: 0.53 (0.60), residues: 81 loop : -1.53 (0.19), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG O 129 TYR 0.029 0.002 TYR B 755 PHE 0.018 0.002 PHE A 160 TRP 0.040 0.003 TRP B 916 HIS 0.013 0.002 HIS D 369 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.25 (25898) covalent geometry : angle 0.72934 / 0.39 (36443) SS BOND : bond 0.00027 / 0.01 ( 1) SS BOND : angle 1.19117 / 0.69 ( 2) hydrogen bonds : bond 0.05389 / 3.65 ( 1198) hydrogen bonds : angle 3.79451 / 2.67 ( 3195) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 263 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 ASN cc_start: 0.8161 (t0) cc_final: 0.7910 (t0) REVERT: A 204 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7091 (ttp) REVERT: A 289 GLU cc_start: 0.6659 (tm-30) cc_final: 0.6419 (tm-30) REVERT: B 708 PHE cc_start: 0.5097 (t80) cc_final: 0.4830 (t80) REVERT: B 709 TYR cc_start: 0.6225 (OUTLIER) cc_final: 0.4019 (t80) REVERT: B 860 MET cc_start: 0.5737 (mmp) cc_final: 0.5269 (mpp) REVERT: B 962 LYS cc_start: 0.5103 (OUTLIER) cc_final: 0.4334 (ptpp) REVERT: B 1164 MET cc_start: 0.6790 (OUTLIER) cc_final: 0.5503 (pp-130) REVERT: B 1167 ARG cc_start: 0.7396 (OUTLIER) cc_final: 0.6577 (pmt-80) REVERT: B 1220 GLU cc_start: 0.6100 (OUTLIER) cc_final: 0.5853 (mt-10) REVERT: B 1284 ILE cc_start: 0.7009 (OUTLIER) cc_final: 0.6762 (pp) REVERT: D 220 ILE cc_start: 0.5536 (mt) cc_final: 0.5187 (mm) REVERT: D 269 LEU cc_start: 0.3906 (OUTLIER) cc_final: 0.3706 (pp) REVERT: D 275 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.7272 (mp10) REVERT: D 354 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.6927 (pp) REVERT: E 305 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.6528 (pt0) REVERT: E 369 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7622 (ptt180) REVERT: E 432 GLU cc_start: 0.8039 (pm20) cc_final: 0.7796 (pm20) REVERT: E 472 THR cc_start: 0.6315 (OUTLIER) cc_final: 0.6035 (p) REVERT: E 511 LYS cc_start: 0.2522 (mmtt) cc_final: 0.1677 (pttt) REVERT: P 85 ASP cc_start: 0.8357 (p0) cc_final: 0.8103 (p0) REVERT: P 91 LYS cc_start: 0.8600 (ttmt) cc_final: 0.8346 (ttpt) REVERT: Q 36 LYS cc_start: 0.7411 (OUTLIER) cc_final: 0.7147 (pptt) REVERT: Q 56 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8185 (tt0) REVERT: Q 91 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8004 (tt0) REVERT: R 90 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7796 (mp0) REVERT: S 59 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6891 (pm20) REVERT: S 109 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.9022 (mp) REVERT: T 50 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8390 (tt) REVERT: U 56 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.7996 (tm-30) outliers start: 123 outliers final: 50 residues processed: 356 average time/residue: 0.1730 time to fit residues: 97.7029 Evaluate side-chains 310 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 239 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain B residue 668 PHE Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 756 LYS Chi-restraints excluded: chain B residue 810 ILE Chi-restraints excluded: chain B residue 815 HIS Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 962 LYS Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1024 ILE Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1146 ILE Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1167 ARG Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1196 LEU Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain B residue 1220 GLU Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain B residue 1312 VAL Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 275 GLN Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 305 GLN Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain E residue 35 ARG Chi-restraints excluded: chain E residue 305 GLU Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 346 HIS Chi-restraints excluded: chain E residue 369 ARG Chi-restraints excluded: chain E residue 423 THR Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 36 LYS Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 91 GLU Chi-restraints excluded: chain R residue 43 LYS Chi-restraints excluded: chain R residue 53 SER Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain S residue 109 LEU Chi-restraints excluded: chain S residue 133 GLU Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain T residue 44 LYS Chi-restraints excluded: chain T residue 50 ILE Chi-restraints excluded: chain T residue 80 THR Chi-restraints excluded: chain T residue 87 VAL Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 56 GLU Chi-restraints excluded: chain V residue 49 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 133 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 14 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 177 optimal weight: 0.6980 chunk 182 optimal weight: 1.9990 chunk 193 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 chunk 223 optimal weight: 20.0000 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 HIS A 296 ASN A 341 ASN ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 959 GLN B 974 GLN ** B 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1254 HIS ** E 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 75 HIS Q 104 GLN ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.136670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.106559 restraints weight = 59747.081| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 1.94 r_work: 0.3588 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 25899 Z= 0.186 Angle : 0.614 10.843 36445 Z= 0.336 Chirality : 0.043 0.259 4041 Planarity : 0.005 0.083 3424 Dihedral : 27.953 138.343 6159 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 5.63 % Allowed : 27.44 % Favored : 66.93 % 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 are not related in a simple way. whole: -0.09 (0.18), residues: 2112 helix: 0.95 (0.15), residues: 1157 sheet: 0.27 (0.59), residues: 82 loop : -1.49 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG E 50 TYR 0.027 0.002 TYR B 755 PHE 0.037 0.002 PHE B 977 TRP 0.023 0.002 TRP E 301 HIS 0.028 0.002 HIS E 346 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.19 (25898) covalent geometry : angle 0.61363 / 0.34 (36443) SS BOND : bond 0.00059 / 0.03 ( 1) SS BOND : angle 0.73046 / 0.40 ( 2) hydrogen bonds : bond 0.04516 / 3.01 ( 1198) hydrogen bonds : angle 3.68105 / 2.60 ( 3195) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 265 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 ASN cc_start: 0.8331 (t0) cc_final: 0.8127 (t0) REVERT: A 289 GLU cc_start: 0.6790 (tm-30) cc_final: 0.6562 (tm-30) REVERT: B 709 TYR cc_start: 0.6363 (OUTLIER) cc_final: 0.3924 (t80) REVERT: B 805 GLU cc_start: 0.7127 (pp20) cc_final: 0.6801 (pp20) REVERT: B 860 MET cc_start: 0.5877 (mmp) cc_final: 0.5381 (mpp) REVERT: B 986 TYR cc_start: 0.6012 (OUTLIER) cc_final: 0.4707 (t80) REVERT: B 1136 PHE cc_start: 0.3631 (OUTLIER) cc_final: 0.2980 (m-10) REVERT: B 1164 MET cc_start: 0.7140 (OUTLIER) cc_final: 0.5800 (pp-130) REVERT: B 1167 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.6597 (pmt-80) REVERT: B 1248 SER cc_start: 0.7891 (t) cc_final: 0.7407 (m) REVERT: B 1284 ILE cc_start: 0.7022 (OUTLIER) cc_final: 0.6793 (pp) REVERT: D 220 ILE cc_start: 0.5701 (mt) cc_final: 0.5254 (mm) REVERT: D 354 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.6982 (pp) REVERT: E 50 ARG cc_start: 0.6801 (OUTLIER) cc_final: 0.6490 (mtp180) REVERT: E 472 THR cc_start: 0.6431 (OUTLIER) cc_final: 0.6145 (p) REVERT: P 85 ASP cc_start: 0.8335 (p0) cc_final: 0.8080 (p0) REVERT: P 91 LYS cc_start: 0.8567 (ttmt) cc_final: 0.8313 (ttpt) REVERT: Q 56 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8208 (tt0) REVERT: Q 74 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8308 (mptp) REVERT: Q 75 LYS cc_start: 0.8679 (ptpt) cc_final: 0.8418 (ptpt) REVERT: R 68 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7236 (mp0) REVERT: R 90 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7886 (mp0) REVERT: S 109 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8717 (mp) REVERT: T 50 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.8335 (tt) REVERT: T 79 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8471 (tppt) REVERT: U 56 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8078 (tm-30) REVERT: V 90 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8144 (mp0) REVERT: V 102 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7640 (mm-30) REVERT: V 105 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8096 (pttp) outliers start: 108 outliers final: 45 residues processed: 350 average time/residue: 0.1549 time to fit residues: 85.1135 Evaluate side-chains 314 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 250 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 150 HIS Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain B residue 668 PHE Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain B residue 779 ASN Chi-restraints excluded: chain B residue 815 HIS Chi-restraints excluded: chain B residue 817 TYR Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 927 SER Chi-restraints excluded: chain B residue 986 TYR Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1024 ILE Chi-restraints excluded: chain B residue 1136 PHE Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1146 ILE Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1167 ARG Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1196 LEU Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 305 GLN Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain E residue 35 ARG Chi-restraints excluded: chain E residue 50 ARG Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 423 THR Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 74 LYS Chi-restraints excluded: chain R residue 68 GLU Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain S residue 109 LEU Chi-restraints excluded: chain T residue 44 LYS Chi-restraints excluded: chain T residue 50 ILE Chi-restraints excluded: chain T residue 79 LYS Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 56 GLU Chi-restraints excluded: chain V residue 49 THR Chi-restraints excluded: chain V residue 90 GLU Chi-restraints excluded: chain V residue 105 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 115 optimal weight: 0.8980 chunk 203 optimal weight: 0.7980 chunk 38 optimal weight: 10.0000 chunk 199 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 139 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 214 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 105 ASN ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 ASN B 690 ASN B 829 GLN B 959 GLN B1173 ASN B1254 HIS ** E 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 104 GLN ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN T 25 ASN U 73 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.135371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.105208 restraints weight = 59359.524| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 1.80 r_work: 0.3581 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25899 Z= 0.152 Angle : 0.580 9.265 36445 Z= 0.317 Chirality : 0.041 0.268 4041 Planarity : 0.004 0.049 3424 Dihedral : 27.931 138.992 6159 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 5.27 % Allowed : 27.54 % Favored : 67.19 % 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 are not related in a simple way. whole: 0.06 (0.18), residues: 2112 helix: 1.12 (0.15), residues: 1156 sheet: 0.00 (0.58), residues: 83 loop : -1.46 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 247 TYR 0.029 0.002 TYR B 755 PHE 0.019 0.001 PHE A 160 TRP 0.018 0.001 TRP E 301 HIS 0.024 0.001 HIS A 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (25898) covalent geometry : angle 0.58026 / 0.32 (36443) SS BOND : bond 0.00140 / 0.07 ( 1) SS BOND : angle 1.00092 / 0.56 ( 2) hydrogen bonds : bond 0.04017 / 2.70 ( 1198) hydrogen bonds : angle 3.53157 / 2.50 ( 3195) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 264 time to evaluate : 0.763 Fit side-chains revert: symmetry clash REVERT: A 74 MET cc_start: 0.6770 (OUTLIER) cc_final: 0.6237 (ttp) REVERT: A 105 ASN cc_start: 0.8372 (t0) cc_final: 0.8050 (t0) REVERT: A 289 GLU cc_start: 0.6783 (tm-30) cc_final: 0.6555 (tm-30) REVERT: B 709 TYR cc_start: 0.6530 (OUTLIER) cc_final: 0.4052 (t80) REVERT: B 791 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7972 (mp0) REVERT: B 805 GLU cc_start: 0.7177 (pp20) cc_final: 0.6840 (pp20) REVERT: B 817 TYR cc_start: 0.8717 (OUTLIER) cc_final: 0.8380 (t80) REVERT: B 818 ASP cc_start: 0.7507 (m-30) cc_final: 0.7204 (m-30) REVERT: B 860 MET cc_start: 0.5894 (mmp) cc_final: 0.5426 (mpp) REVERT: B 868 ARG cc_start: 0.7221 (tmt-80) cc_final: 0.6717 (mtp85) REVERT: B 912 TRP cc_start: 0.7481 (OUTLIER) cc_final: 0.6610 (t-100) REVERT: B 986 TYR cc_start: 0.6007 (OUTLIER) cc_final: 0.4687 (t80) REVERT: B 1136 PHE cc_start: 0.3811 (OUTLIER) cc_final: 0.3126 (m-10) REVERT: B 1164 MET cc_start: 0.7232 (OUTLIER) cc_final: 0.5921 (pp-130) REVERT: B 1167 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.6692 (pmt-80) REVERT: B 1194 MET cc_start: 0.5087 (mmt) cc_final: 0.4883 (mmm) REVERT: B 1248 SER cc_start: 0.7880 (t) cc_final: 0.7398 (m) REVERT: B 1284 ILE cc_start: 0.7063 (OUTLIER) cc_final: 0.6835 (pp) REVERT: D 220 ILE cc_start: 0.5783 (mt) cc_final: 0.5347 (mm) REVERT: D 354 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.6995 (pp) REVERT: D 386 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.6866 (pt) REVERT: E 465 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8411 (ttmt) REVERT: E 472 THR cc_start: 0.6447 (OUTLIER) cc_final: 0.6143 (p) REVERT: E 511 LYS cc_start: 0.5291 (pptt) cc_final: 0.4671 (pttt) REVERT: P 85 ASP cc_start: 0.8282 (p0) cc_final: 0.8034 (p0) REVERT: Q 56 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8169 (tt0) REVERT: Q 74 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8247 (mptp) REVERT: Q 91 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8042 (tt0) REVERT: R 68 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7239 (mp0) REVERT: R 90 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7839 (mp0) REVERT: R 113 LYS cc_start: 0.8049 (ptmm) cc_final: 0.7690 (ttpp) REVERT: T 88 TYR cc_start: 0.8049 (m-10) cc_final: 0.7748 (m-80) REVERT: U 56 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8068 (tm-30) REVERT: V 90 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8046 (mp0) REVERT: V 105 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.7979 (pttp) outliers start: 101 outliers final: 41 residues processed: 342 average time/residue: 0.1730 time to fit residues: 93.2822 Evaluate side-chains 315 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 253 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain B residue 668 PHE Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain B residue 779 ASN Chi-restraints excluded: chain B residue 817 TYR Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 912 TRP Chi-restraints excluded: chain B residue 917 ARG Chi-restraints excluded: chain B residue 986 TYR Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1024 ILE Chi-restraints excluded: chain B residue 1136 PHE Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1167 ARG Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1196 LEU Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain E residue 35 ARG Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 423 THR Chi-restraints excluded: chain E residue 465 LYS Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 74 LYS Chi-restraints excluded: chain Q residue 91 GLU Chi-restraints excluded: chain Q residue 104 GLN Chi-restraints excluded: chain R residue 60 ASN Chi-restraints excluded: chain R residue 68 GLU Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 87 THR Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 133 GLU Chi-restraints excluded: chain T residue 44 LYS Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 56 GLU Chi-restraints excluded: chain V residue 90 GLU Chi-restraints excluded: chain V residue 105 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 195 optimal weight: 0.5980 chunk 221 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 199 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 232 optimal weight: 9.9990 chunk 239 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 210 optimal weight: 40.0000 chunk 179 optimal weight: 0.7980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 31 ASN A 76 GLN ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 ASN ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 ASN B 815 HIS ** B 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1254 HIS ** E 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 448 HIS ** E 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 GLN P 25 ASN ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 92 GLN T 25 ASN U 73 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.125359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.095049 restraints weight = 57301.815| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.71 r_work: 0.3369 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 25899 Z= 0.325 Angle : 0.788 11.489 36445 Z= 0.422 Chirality : 0.051 0.329 4041 Planarity : 0.006 0.059 3424 Dihedral : 28.175 137.697 6159 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 6.52 % Allowed : 25.25 % Favored : 68.23 % 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 are not related in a simple way. whole: -0.54 (0.17), residues: 2112 helix: 0.51 (0.15), residues: 1153 sheet: -0.43 (0.57), residues: 85 loop : -1.51 (0.20), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG U 42 TYR 0.041 0.003 TYR B 755 PHE 0.035 0.002 PHE A 160 TRP 0.020 0.002 TRP B1151 HIS 0.010 0.002 HIS R 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00712 / 0.32 (25898) covalent geometry : angle 0.78817 / 0.42 (36443) SS BOND : bond 0.00040 / 0.02 ( 1) SS BOND : angle 1.03492 / 0.58 ( 2) hydrogen bonds : bond 0.06024 / 4.08 ( 1198) hydrogen bonds : angle 4.00740 / 2.83 ( 3195) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 291 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.7478 (tpp) cc_final: 0.6540 (tpp) REVERT: A 72 GLN cc_start: 0.7032 (OUTLIER) cc_final: 0.6701 (pt0) REVERT: A 74 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7641 (ttp) REVERT: A 105 ASN cc_start: 0.8693 (t0) cc_final: 0.8353 (t0) REVERT: A 288 MET cc_start: 0.7447 (mmp) cc_final: 0.7188 (mmt) REVERT: A 289 GLU cc_start: 0.7141 (tm-30) cc_final: 0.6910 (tm-30) REVERT: A 347 TYR cc_start: 0.8022 (m-80) cc_final: 0.7765 (m-80) REVERT: B 709 TYR cc_start: 0.7184 (OUTLIER) cc_final: 0.4599 (t80) REVERT: B 817 TYR cc_start: 0.8842 (OUTLIER) cc_final: 0.8552 (t80) REVERT: B 818 ASP cc_start: 0.7949 (m-30) cc_final: 0.7400 (m-30) REVERT: B 860 MET cc_start: 0.6295 (mmp) cc_final: 0.5752 (mpp) REVERT: B 868 ARG cc_start: 0.7495 (tmt-80) cc_final: 0.6944 (mtp85) REVERT: B 912 TRP cc_start: 0.7963 (OUTLIER) cc_final: 0.7396 (t-100) REVERT: B 917 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.7439 (ttm170) REVERT: B 962 LYS cc_start: 0.5272 (OUTLIER) cc_final: 0.4478 (ptpp) REVERT: B 986 TYR cc_start: 0.6375 (OUTLIER) cc_final: 0.5082 (t80) REVERT: B 989 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7520 (mm) REVERT: B 1164 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.6626 (pp-130) REVERT: B 1167 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.6991 (pmt-80) REVERT: B 1220 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.6971 (mt-10) REVERT: B 1248 SER cc_start: 0.8238 (t) cc_final: 0.7913 (m) REVERT: B 1284 ILE cc_start: 0.7126 (OUTLIER) cc_final: 0.6912 (pp) REVERT: D 220 ILE cc_start: 0.5988 (mt) cc_final: 0.5537 (mm) REVERT: D 347 MET cc_start: 0.5797 (tmt) cc_final: 0.4788 (tpt) REVERT: E 49 LYS cc_start: 0.8642 (tptp) cc_final: 0.8331 (tptp) REVERT: E 472 THR cc_start: 0.7242 (OUTLIER) cc_final: 0.6890 (p) REVERT: E 511 LYS cc_start: 0.5478 (pptt) cc_final: 0.4873 (pttt) REVERT: O 59 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.7895 (pp20) REVERT: P 25 ASN cc_start: 0.8780 (m-40) cc_final: 0.8525 (m110) REVERT: Q 15 LYS cc_start: 0.7124 (tptt) cc_final: 0.6851 (tptt) REVERT: Q 74 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8412 (mptp) REVERT: Q 91 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8393 (tt0) REVERT: R 68 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7704 (mp0) REVERT: R 90 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8053 (mp0) REVERT: T 50 ILE cc_start: 0.9008 (OUTLIER) cc_final: 0.8696 (tt) REVERT: U 56 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8415 (tm-30) REVERT: V 105 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8601 (pttp) outliers start: 125 outliers final: 61 residues processed: 386 average time/residue: 0.1785 time to fit residues: 108.3473 Evaluate side-chains 348 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 265 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain B residue 815 HIS Chi-restraints excluded: chain B residue 817 TYR Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 907 ARG Chi-restraints excluded: chain B residue 912 TRP Chi-restraints excluded: chain B residue 917 ARG Chi-restraints excluded: chain B residue 962 LYS Chi-restraints excluded: chain B residue 986 TYR Chi-restraints excluded: chain B residue 989 LEU Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1024 ILE Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1167 ARG Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1196 LEU Chi-restraints excluded: chain B residue 1220 GLU Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1250 VAL Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain B residue 1290 VAL Chi-restraints excluded: chain B residue 1312 VAL Chi-restraints excluded: chain B residue 1322 LEU Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 389 ASN Chi-restraints excluded: chain E residue 35 ARG Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 423 THR Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 493 LYS Chi-restraints excluded: chain E residue 498 ILE Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain O residue 92 LEU Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 74 LYS Chi-restraints excluded: chain Q residue 91 GLU Chi-restraints excluded: chain R residue 48 ASP Chi-restraints excluded: chain R residue 61 SER Chi-restraints excluded: chain R residue 68 GLU Chi-restraints excluded: chain R residue 84 SER Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain T residue 25 ASN Chi-restraints excluded: chain T residue 44 LYS Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 50 ILE Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 56 GLU Chi-restraints excluded: chain V residue 49 THR Chi-restraints excluded: chain V residue 88 SER Chi-restraints excluded: chain V residue 105 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 188 optimal weight: 0.8980 chunk 118 optimal weight: 0.0980 chunk 67 optimal weight: 2.9990 chunk 197 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 59 optimal weight: 0.2980 chunk 107 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN A 341 ASN ** B 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1173 ASN B1254 HIS ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 469 HIS O 68 GLN O 125 GLN Q 104 GLN ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 81 ASN R 92 GLN T 25 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.127591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.097725 restraints weight = 57364.751| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 1.92 r_work: 0.3393 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25899 Z= 0.147 Angle : 0.629 10.017 36445 Z= 0.338 Chirality : 0.043 0.251 4041 Planarity : 0.004 0.048 3424 Dihedral : 28.143 139.653 6159 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.23 % Allowed : 27.18 % Favored : 68.60 % 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 are not related in a simple way. whole: -0.22 (0.18), residues: 2112 helix: 0.84 (0.15), residues: 1162 sheet: -0.73 (0.55), residues: 84 loop : -1.45 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 92 TYR 0.029 0.002 TYR B 755 PHE 0.045 0.001 PHE A 160 TRP 0.024 0.001 TRP E 301 HIS 0.008 0.001 HIS A 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.15 (25898) covalent geometry : angle 0.62883 / 0.34 (36443) SS BOND : bond 0.00200 / 0.11 ( 1) SS BOND : angle 0.99902 / 0.55 ( 2) hydrogen bonds : bond 0.04134 / 2.76 ( 1198) hydrogen bonds : angle 3.70162 / 2.62 ( 3195) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 299 time to evaluate : 0.787 Fit side-chains revert: symmetry clash REVERT: A 72 GLN cc_start: 0.6701 (OUTLIER) cc_final: 0.6401 (pt0) REVERT: A 74 MET cc_start: 0.7737 (OUTLIER) cc_final: 0.7231 (ttp) REVERT: A 105 ASN cc_start: 0.8524 (t0) cc_final: 0.8217 (t0) REVERT: A 288 MET cc_start: 0.7268 (mmp) cc_final: 0.7020 (mmt) REVERT: A 289 GLU cc_start: 0.6911 (tm-30) cc_final: 0.6703 (tm-30) REVERT: A 313 TYR cc_start: 0.6930 (m-80) cc_final: 0.6678 (m-80) REVERT: A 347 TYR cc_start: 0.7876 (m-80) cc_final: 0.7466 (m-80) REVERT: B 709 TYR cc_start: 0.6993 (OUTLIER) cc_final: 0.4388 (t80) REVERT: B 756 LYS cc_start: 0.7720 (OUTLIER) cc_final: 0.6565 (pttm) REVERT: B 802 GLN cc_start: 0.7210 (tm-30) cc_final: 0.6986 (tm-30) REVERT: B 817 TYR cc_start: 0.8733 (OUTLIER) cc_final: 0.8383 (t80) REVERT: B 818 ASP cc_start: 0.7679 (m-30) cc_final: 0.7413 (m-30) REVERT: B 860 MET cc_start: 0.6122 (mmp) cc_final: 0.5637 (mpp) REVERT: B 868 ARG cc_start: 0.7341 (tmt-80) cc_final: 0.6825 (mtp85) REVERT: B 912 TRP cc_start: 0.7758 (OUTLIER) cc_final: 0.7124 (t-100) REVERT: B 917 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7438 (ttm170) REVERT: B 986 TYR cc_start: 0.6213 (OUTLIER) cc_final: 0.4950 (t80) REVERT: B 1164 MET cc_start: 0.7625 (OUTLIER) cc_final: 0.6440 (pp-130) REVERT: B 1167 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.7006 (pmt-80) REVERT: B 1220 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6876 (mt-10) REVERT: B 1248 SER cc_start: 0.8054 (t) cc_final: 0.7730 (m) REVERT: B 1284 ILE cc_start: 0.7185 (OUTLIER) cc_final: 0.6950 (pp) REVERT: D 220 ILE cc_start: 0.6010 (mt) cc_final: 0.5521 (mm) REVERT: D 347 MET cc_start: 0.5660 (tmt) cc_final: 0.4696 (tpp) REVERT: E 49 LYS cc_start: 0.8558 (tptp) cc_final: 0.8228 (tptp) REVERT: E 472 THR cc_start: 0.7098 (OUTLIER) cc_final: 0.6713 (p) REVERT: E 506 TYR cc_start: 0.7278 (m-80) cc_final: 0.6679 (m-80) REVERT: E 511 LYS cc_start: 0.5511 (pptt) cc_final: 0.5005 (pttt) REVERT: E 544 GLU cc_start: 0.7884 (pp20) cc_final: 0.7287 (tt0) REVERT: P 25 ASN cc_start: 0.8667 (m-40) cc_final: 0.8455 (m110) REVERT: P 88 TYR cc_start: 0.8673 (m-10) cc_final: 0.8452 (m-80) REVERT: Q 15 LYS cc_start: 0.7206 (tptt) cc_final: 0.7001 (tptt) REVERT: Q 56 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8204 (tt0) REVERT: Q 74 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8191 (mptp) REVERT: R 90 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8301 (mp0) REVERT: S 57 SER cc_start: 0.8364 (t) cc_final: 0.8105 (p) REVERT: U 56 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8157 (tm-30) REVERT: V 90 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8176 (mp0) REVERT: V 102 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7694 (mm-30) REVERT: V 105 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8189 (pttp) outliers start: 81 outliers final: 40 residues processed: 358 average time/residue: 0.1719 time to fit residues: 96.6491 Evaluate side-chains 334 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 275 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 756 LYS Chi-restraints excluded: chain B residue 817 TYR Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 907 ARG Chi-restraints excluded: chain B residue 912 TRP Chi-restraints excluded: chain B residue 917 ARG Chi-restraints excluded: chain B residue 927 SER Chi-restraints excluded: chain B residue 986 TYR Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1024 ILE Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1167 ARG Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1196 LEU Chi-restraints excluded: chain B residue 1220 GLU Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain B residue 1286 TYR Chi-restraints excluded: chain B residue 1312 VAL Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain D residue 392 SER Chi-restraints excluded: chain E residue 35 ARG Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain P residue 92 ARG Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 74 LYS Chi-restraints excluded: chain R residue 81 ASN Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain T residue 44 LYS Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 56 GLU Chi-restraints excluded: chain V residue 76 ARG Chi-restraints excluded: chain V residue 90 GLU Chi-restraints excluded: chain V residue 105 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 13 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 223 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 115 optimal weight: 0.4980 chunk 204 optimal weight: 0.8980 chunk 187 optimal weight: 0.9980 chunk 233 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 HIS ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 ASN ** B 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1254 HIS ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 68 GLN O 108 ASN ** Q 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 104 GLN ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN S 108 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.127222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.097070 restraints weight = 57607.439| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.71 r_work: 0.3418 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25899 Z= 0.158 Angle : 0.619 9.858 36445 Z= 0.331 Chirality : 0.042 0.245 4041 Planarity : 0.004 0.048 3424 Dihedral : 28.068 140.206 6159 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.49 % Allowed : 26.81 % Favored : 68.70 % 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 are not related in a simple way. whole: -0.09 (0.18), residues: 2112 helix: 0.97 (0.15), residues: 1162 sheet: -0.83 (0.55), residues: 84 loop : -1.40 (0.20), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 92 TYR 0.024 0.002 TYR B 755 PHE 0.035 0.001 PHE A 160 TRP 0.028 0.001 TRP E 301 HIS 0.005 0.001 HIS B1293 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 (25898) covalent geometry : angle 0.61907 / 0.33 (36443) SS BOND : bond 0.00155 / 0.08 ( 1) SS BOND : angle 0.93580 / 0.52 ( 2) hydrogen bonds : bond 0.04084 / 2.73 ( 1198) hydrogen bonds : angle 3.63190 / 2.57 ( 3195) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 280 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.7547 (tpp) cc_final: 0.6929 (tpp) REVERT: A 72 GLN cc_start: 0.6913 (OUTLIER) cc_final: 0.6605 (pt0) REVERT: A 74 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.7317 (ttp) REVERT: A 105 ASN cc_start: 0.8635 (t0) cc_final: 0.8336 (t0) REVERT: A 289 GLU cc_start: 0.7193 (tm-30) cc_final: 0.6992 (tm-30) REVERT: A 313 TYR cc_start: 0.7102 (m-80) cc_final: 0.6821 (m-80) REVERT: A 347 TYR cc_start: 0.7938 (m-80) cc_final: 0.7554 (m-80) REVERT: B 709 TYR cc_start: 0.7093 (OUTLIER) cc_final: 0.4451 (t80) REVERT: B 756 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.6768 (pttm) REVERT: B 802 GLN cc_start: 0.7161 (tm-30) cc_final: 0.6903 (tm-30) REVERT: B 818 ASP cc_start: 0.7730 (m-30) cc_final: 0.7329 (m-30) REVERT: B 860 MET cc_start: 0.6144 (mmp) cc_final: 0.5648 (mpp) REVERT: B 868 ARG cc_start: 0.7391 (tmt-80) cc_final: 0.6919 (mtp85) REVERT: B 912 TRP cc_start: 0.7889 (OUTLIER) cc_final: 0.7250 (t-100) REVERT: B 917 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.7532 (ttm170) REVERT: B 986 TYR cc_start: 0.6269 (OUTLIER) cc_final: 0.4947 (t80) REVERT: B 1164 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.6508 (pp-130) REVERT: B 1167 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.7023 (pmt-80) REVERT: B 1220 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.7059 (mt-10) REVERT: B 1225 GLU cc_start: 0.7337 (mm-30) cc_final: 0.6668 (mt-10) REVERT: B 1248 SER cc_start: 0.8197 (t) cc_final: 0.7891 (m) REVERT: B 1284 ILE cc_start: 0.7123 (OUTLIER) cc_final: 0.6885 (pp) REVERT: D 220 ILE cc_start: 0.5988 (mt) cc_final: 0.5470 (mm) REVERT: D 347 MET cc_start: 0.5798 (tmt) cc_final: 0.4905 (tpt) REVERT: E 49 LYS cc_start: 0.8623 (tptp) cc_final: 0.8275 (tptp) REVERT: E 472 THR cc_start: 0.7159 (OUTLIER) cc_final: 0.6785 (p) REVERT: E 511 LYS cc_start: 0.5518 (pptt) cc_final: 0.5050 (pttt) REVERT: E 544 GLU cc_start: 0.7944 (pp20) cc_final: 0.7469 (tt0) REVERT: O 59 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.7878 (pp20) REVERT: P 25 ASN cc_start: 0.8806 (m-40) cc_final: 0.8499 (m-40) REVERT: Q 15 LYS cc_start: 0.7244 (tptt) cc_final: 0.7038 (tptt) REVERT: Q 56 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8351 (tt0) REVERT: Q 74 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8229 (mptp) REVERT: Q 91 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8426 (tt0) REVERT: R 90 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8371 (mp0) REVERT: S 57 SER cc_start: 0.8486 (t) cc_final: 0.8001 (p) REVERT: T 50 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8374 (tt) REVERT: U 56 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.8403 (tm-30) REVERT: V 90 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8313 (mp0) REVERT: V 102 GLU cc_start: 0.8385 (mm-30) cc_final: 0.7911 (mm-30) REVERT: V 105 LYS cc_start: 0.8918 (OUTLIER) cc_final: 0.8368 (pttp) outliers start: 86 outliers final: 50 residues processed: 339 average time/residue: 0.1447 time to fit residues: 78.1149 Evaluate side-chains 344 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 273 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain B residue 756 LYS Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 907 ARG Chi-restraints excluded: chain B residue 912 TRP Chi-restraints excluded: chain B residue 917 ARG Chi-restraints excluded: chain B residue 927 SER Chi-restraints excluded: chain B residue 986 TYR Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1024 ILE Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1167 ARG Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1219 LEU Chi-restraints excluded: chain B residue 1220 GLU Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain B residue 1286 TYR Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain D residue 392 SER Chi-restraints excluded: chain E residue 35 ARG Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 498 ILE Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain P residue 92 ARG Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 74 LYS Chi-restraints excluded: chain Q residue 91 GLU Chi-restraints excluded: chain Q residue 104 GLN Chi-restraints excluded: chain R residue 48 ASP Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain S residue 92 LEU Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain T residue 29 ILE Chi-restraints excluded: chain T residue 44 LYS Chi-restraints excluded: chain T residue 50 ILE Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 56 GLU Chi-restraints excluded: chain V residue 76 ARG Chi-restraints excluded: chain V residue 88 SER Chi-restraints excluded: chain V residue 90 GLU Chi-restraints excluded: chain V residue 105 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 44 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 120 optimal weight: 0.0980 chunk 71 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 143 optimal weight: 0.0970 chunk 23 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 ASN ** B 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1254 HIS ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 422 GLN O 125 GLN ** Q 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.127772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.097572 restraints weight = 57749.345| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 1.86 r_work: 0.3412 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25899 Z= 0.138 Angle : 0.605 9.613 36445 Z= 0.325 Chirality : 0.041 0.240 4041 Planarity : 0.004 0.049 3424 Dihedral : 28.009 140.505 6159 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.43 % Allowed : 26.50 % Favored : 69.07 % 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 are not related in a simple way. whole: 0.06 (0.18), residues: 2112 helix: 1.11 (0.15), residues: 1170 sheet: -0.88 (0.55), residues: 84 loop : -1.38 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 92 TYR 0.054 0.002 TYR P 88 PHE 0.027 0.001 PHE A 160 TRP 0.033 0.001 TRP E 301 HIS 0.004 0.001 HIS B1293 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 (25898) covalent geometry : angle 0.60546 / 0.32 (36443) SS BOND : bond 0.00193 / 0.10 ( 1) SS BOND : angle 0.95146 / 0.53 ( 2) hydrogen bonds : bond 0.03878 / 2.59 ( 1198) hydrogen bonds : angle 3.56321 / 2.52 ( 3195) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 279 time to evaluate : 0.801 Fit side-chains revert: symmetry clash REVERT: A 40 MET cc_start: 0.7470 (tpp) cc_final: 0.5761 (tpp) REVERT: A 72 GLN cc_start: 0.6781 (OUTLIER) cc_final: 0.6484 (pt0) REVERT: A 74 MET cc_start: 0.7747 (OUTLIER) cc_final: 0.7296 (ttp) REVERT: A 105 ASN cc_start: 0.8541 (t0) cc_final: 0.8230 (t0) REVERT: A 120 CYS cc_start: 0.8533 (m) cc_final: 0.8236 (m) REVERT: A 313 TYR cc_start: 0.6997 (m-80) cc_final: 0.6715 (m-80) REVERT: B 671 LYS cc_start: 0.8334 (mmtm) cc_final: 0.7913 (mtmt) REVERT: B 709 TYR cc_start: 0.6941 (OUTLIER) cc_final: 0.4337 (t80) REVERT: B 756 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.6468 (pttm) REVERT: B 802 GLN cc_start: 0.7172 (tm-30) cc_final: 0.6850 (tm-30) REVERT: B 805 GLU cc_start: 0.7398 (pp20) cc_final: 0.6993 (pp20) REVERT: B 818 ASP cc_start: 0.7567 (m-30) cc_final: 0.7253 (m-30) REVERT: B 860 MET cc_start: 0.6116 (mmp) cc_final: 0.5636 (mpp) REVERT: B 868 ARG cc_start: 0.7344 (tmt-80) cc_final: 0.6877 (mtp85) REVERT: B 912 TRP cc_start: 0.7791 (OUTLIER) cc_final: 0.6744 (t-100) REVERT: B 916 TRP cc_start: 0.8171 (m-10) cc_final: 0.7707 (m-10) REVERT: B 917 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7484 (ttm170) REVERT: B 986 TYR cc_start: 0.6207 (OUTLIER) cc_final: 0.5131 (t80) REVERT: B 1164 MET cc_start: 0.7621 (OUTLIER) cc_final: 0.6477 (pp-130) REVERT: B 1167 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.7026 (pmt-80) REVERT: B 1248 SER cc_start: 0.8076 (t) cc_final: 0.7753 (m) REVERT: B 1284 ILE cc_start: 0.7146 (OUTLIER) cc_final: 0.6916 (pp) REVERT: D 220 ILE cc_start: 0.5977 (mt) cc_final: 0.5488 (mm) REVERT: D 235 ASP cc_start: 0.8409 (OUTLIER) cc_final: 0.8208 (t0) REVERT: D 347 MET cc_start: 0.5810 (tmt) cc_final: 0.4930 (tpt) REVERT: E 472 THR cc_start: 0.7117 (OUTLIER) cc_final: 0.6732 (p) REVERT: E 511 LYS cc_start: 0.5510 (pptt) cc_final: 0.5095 (pttt) REVERT: E 544 GLU cc_start: 0.7867 (pp20) cc_final: 0.7403 (tt0) REVERT: O 59 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7659 (pp20) REVERT: P 25 ASN cc_start: 0.8701 (m-40) cc_final: 0.8449 (m-40) REVERT: Q 15 LYS cc_start: 0.7237 (tptt) cc_final: 0.7013 (tptt) REVERT: Q 56 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8180 (tt0) REVERT: Q 74 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8146 (mptp) REVERT: Q 91 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8223 (tt0) REVERT: R 90 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8213 (mp0) REVERT: T 50 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8317 (tt) REVERT: U 56 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8177 (tt0) REVERT: V 90 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8087 (mp0) REVERT: V 102 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7744 (mm-30) REVERT: V 105 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8230 (pttp) outliers start: 85 outliers final: 51 residues processed: 337 average time/residue: 0.1622 time to fit residues: 86.2006 Evaluate side-chains 345 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 273 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 MET Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain B residue 756 LYS Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 907 ARG Chi-restraints excluded: chain B residue 912 TRP Chi-restraints excluded: chain B residue 917 ARG Chi-restraints excluded: chain B residue 927 SER Chi-restraints excluded: chain B residue 986 TYR Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1024 ILE Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1167 ARG Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1219 LEU Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain B residue 1286 TYR Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 235 ASP Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 321 VAL Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 337 VAL Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain D residue 392 SER Chi-restraints excluded: chain E residue 35 ARG Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain E residue 556 TYR Chi-restraints excluded: chain O residue 59 GLU Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain P residue 92 ARG Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 74 LYS Chi-restraints excluded: chain Q residue 91 GLU Chi-restraints excluded: chain R residue 48 ASP Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain S residue 92 LEU Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain T residue 29 ILE Chi-restraints excluded: chain T residue 44 LYS Chi-restraints excluded: chain T residue 50 ILE Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 56 GLU Chi-restraints excluded: chain U residue 114 VAL Chi-restraints excluded: chain V residue 76 ARG Chi-restraints excluded: chain V residue 90 GLU Chi-restraints excluded: chain V residue 105 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 19 optimal weight: 0.3980 chunk 125 optimal weight: 4.9990 chunk 175 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 210 optimal weight: 40.0000 chunk 47 optimal weight: 0.0870 chunk 65 optimal weight: 0.9980 chunk 169 optimal weight: 0.5980 chunk 27 optimal weight: 0.0870 chunk 75 optimal weight: 2.9990 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 ASN B 815 HIS ** B 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1293 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 ASN ** E 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 125 GLN ** Q 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 104 GLN ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN R 81 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.128486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.097793 restraints weight = 58125.258| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 1.85 r_work: 0.3440 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 25899 Z= 0.130 Angle : 0.593 9.332 36445 Z= 0.319 Chirality : 0.040 0.233 4041 Planarity : 0.004 0.049 3424 Dihedral : 27.906 140.557 6159 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.33 % Allowed : 26.55 % Favored : 69.12 % 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 are not related in a simple way. whole: 0.10 (0.18), residues: 2112 helix: 1.21 (0.15), residues: 1166 sheet: -1.03 (0.53), residues: 95 loop : -1.45 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 46 TYR 0.026 0.002 TYR R 80 PHE 0.020 0.001 PHE A 160 TRP 0.034 0.001 TRP E 301 HIS 0.009 0.001 HIS B 815 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 (25898) covalent geometry : angle 0.59345 / 0.32 (36443) SS BOND : bond 0.00217 / 0.11 ( 1) SS BOND : angle 1.02021 / 0.57 ( 2) hydrogen bonds : bond 0.03698 / 2.45 ( 1198) hydrogen bonds : angle 3.50631 / 2.48 ( 3195) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 284 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 GLN cc_start: 0.6802 (OUTLIER) cc_final: 0.6468 (pt0) REVERT: A 74 MET cc_start: 0.7670 (OUTLIER) cc_final: 0.7228 (ttp) REVERT: A 105 ASN cc_start: 0.8534 (t0) cc_final: 0.8213 (t0) REVERT: A 120 CYS cc_start: 0.8418 (m) cc_final: 0.8144 (m) REVERT: A 145 TYR cc_start: 0.8519 (m-10) cc_final: 0.8304 (m-80) REVERT: A 305 MET cc_start: 0.7971 (ttt) cc_final: 0.7621 (ttt) REVERT: B 671 LYS cc_start: 0.8436 (mmtm) cc_final: 0.8029 (mtmt) REVERT: B 709 TYR cc_start: 0.6869 (OUTLIER) cc_final: 0.4228 (t80) REVERT: B 756 LYS cc_start: 0.7592 (OUTLIER) cc_final: 0.6417 (pttm) REVERT: B 802 GLN cc_start: 0.7087 (tm-30) cc_final: 0.6781 (tm-30) REVERT: B 805 GLU cc_start: 0.7411 (pp20) cc_final: 0.7034 (pp20) REVERT: B 818 ASP cc_start: 0.7487 (m-30) cc_final: 0.7174 (m-30) REVERT: B 860 MET cc_start: 0.6079 (mmp) cc_final: 0.5591 (mpp) REVERT: B 868 ARG cc_start: 0.7327 (tmt-80) cc_final: 0.6859 (mtp85) REVERT: B 912 TRP cc_start: 0.7838 (OUTLIER) cc_final: 0.6782 (t-100) REVERT: B 916 TRP cc_start: 0.8129 (m-10) cc_final: 0.7644 (m-10) REVERT: B 986 TYR cc_start: 0.6213 (OUTLIER) cc_final: 0.5162 (t80) REVERT: B 1164 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.6316 (pp-130) REVERT: B 1167 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.6969 (pmt-80) REVERT: B 1248 SER cc_start: 0.8051 (t) cc_final: 0.7734 (m) REVERT: B 1284 ILE cc_start: 0.7172 (OUTLIER) cc_final: 0.6930 (pp) REVERT: D 220 ILE cc_start: 0.6012 (mt) cc_final: 0.5514 (mm) REVERT: D 347 MET cc_start: 0.5870 (tmt) cc_final: 0.4908 (tpp) REVERT: E 472 THR cc_start: 0.7055 (OUTLIER) cc_final: 0.6660 (p) REVERT: E 511 LYS cc_start: 0.5592 (pptt) cc_final: 0.5188 (pttt) REVERT: E 544 GLU cc_start: 0.7889 (pp20) cc_final: 0.7447 (tt0) REVERT: P 25 ASN cc_start: 0.8669 (m-40) cc_final: 0.8436 (m-40) REVERT: P 91 LYS cc_start: 0.8556 (ttmt) cc_final: 0.8338 (ttpt) REVERT: Q 56 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8208 (tt0) REVERT: Q 74 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8070 (mptp) REVERT: Q 91 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8216 (tt0) REVERT: R 90 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.7898 (mp0) REVERT: T 50 ILE cc_start: 0.8583 (OUTLIER) cc_final: 0.8278 (tt) REVERT: U 56 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8163 (tt0) REVERT: V 90 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8068 (mp0) REVERT: V 105 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8176 (pttp) outliers start: 83 outliers final: 45 residues processed: 343 average time/residue: 0.1752 time to fit residues: 94.8447 Evaluate side-chains 337 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 274 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain B residue 756 LYS Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 907 ARG Chi-restraints excluded: chain B residue 912 TRP Chi-restraints excluded: chain B residue 927 SER Chi-restraints excluded: chain B residue 986 TYR Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1024 ILE Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1167 ARG Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1219 LEU Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain B residue 1286 TYR Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain D residue 392 SER Chi-restraints excluded: chain E residue 35 ARG Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain E residue 556 TYR Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 74 LYS Chi-restraints excluded: chain Q residue 91 GLU Chi-restraints excluded: chain R residue 48 ASP Chi-restraints excluded: chain R residue 81 ASN Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain T residue 50 ILE Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 56 GLU Chi-restraints excluded: chain U residue 114 VAL Chi-restraints excluded: chain V residue 76 ARG Chi-restraints excluded: chain V residue 90 GLU Chi-restraints excluded: chain V residue 105 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 231 optimal weight: 9.9990 chunk 143 optimal weight: 0.0670 chunk 150 optimal weight: 4.9990 chunk 137 optimal weight: 10.0000 chunk 148 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 169 optimal weight: 0.5980 chunk 236 optimal weight: 4.9990 chunk 122 optimal weight: 0.6980 chunk 164 optimal weight: 0.7980 chunk 200 optimal weight: 2.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 HIS A 341 ASN ** B 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1254 HIS E 304 ASN ** E 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 125 GLN ** Q 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 104 GLN ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN R 81 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.128005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.097261 restraints weight = 58190.642| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.89 r_work: 0.3420 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.4695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25899 Z= 0.137 Angle : 0.605 9.489 36445 Z= 0.322 Chirality : 0.041 0.248 4041 Planarity : 0.004 0.056 3424 Dihedral : 27.883 140.227 6159 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.86 % Allowed : 27.44 % Favored : 68.70 % 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 are not related in a simple way. whole: 0.11 (0.18), residues: 2112 helix: 1.22 (0.15), residues: 1168 sheet: -1.05 (0.53), residues: 95 loop : -1.44 (0.20), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 906 TYR 0.039 0.002 TYR P 88 PHE 0.047 0.001 PHE A 160 TRP 0.034 0.001 TRP E 301 HIS 0.008 0.001 HIS B 815 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 (25898) covalent geometry : angle 0.60511 / 0.32 (36443) SS BOND : bond 0.00176 / 0.09 ( 1) SS BOND : angle 0.98478 / 0.56 ( 2) hydrogen bonds : bond 0.03745 / 2.49 ( 1198) hydrogen bonds : angle 3.50523 / 2.48 ( 3195) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 278 time to evaluate : 0.799 Fit side-chains revert: symmetry clash REVERT: A 72 GLN cc_start: 0.6838 (OUTLIER) cc_final: 0.6510 (pt0) REVERT: A 74 MET cc_start: 0.7691 (OUTLIER) cc_final: 0.7285 (ttp) REVERT: A 105 ASN cc_start: 0.8567 (t0) cc_final: 0.8251 (t0) REVERT: A 120 CYS cc_start: 0.8508 (m) cc_final: 0.8224 (m) REVERT: A 145 TYR cc_start: 0.8529 (m-10) cc_final: 0.8283 (m-80) REVERT: A 305 MET cc_start: 0.8030 (ttt) cc_final: 0.7672 (ttt) REVERT: B 671 LYS cc_start: 0.8418 (mmtm) cc_final: 0.8068 (mtmt) REVERT: B 709 TYR cc_start: 0.6883 (OUTLIER) cc_final: 0.4254 (t80) REVERT: B 756 LYS cc_start: 0.7625 (OUTLIER) cc_final: 0.6448 (pttm) REVERT: B 802 GLN cc_start: 0.7123 (tm-30) cc_final: 0.6794 (tm-30) REVERT: B 805 GLU cc_start: 0.7430 (pp20) cc_final: 0.7072 (pp20) REVERT: B 818 ASP cc_start: 0.7540 (m-30) cc_final: 0.7234 (m-30) REVERT: B 821 ILE cc_start: 0.8750 (mm) cc_final: 0.8450 (mm) REVERT: B 860 MET cc_start: 0.6034 (mmp) cc_final: 0.5588 (mpp) REVERT: B 868 ARG cc_start: 0.7311 (tmt-80) cc_final: 0.6906 (mtp85) REVERT: B 912 TRP cc_start: 0.7868 (OUTLIER) cc_final: 0.6804 (t-100) REVERT: B 916 TRP cc_start: 0.8144 (m-10) cc_final: 0.7648 (m-10) REVERT: B 917 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7670 (ttm170) REVERT: B 986 TYR cc_start: 0.6209 (OUTLIER) cc_final: 0.5101 (t80) REVERT: B 1164 MET cc_start: 0.7596 (OUTLIER) cc_final: 0.6329 (pp-130) REVERT: B 1167 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.6993 (pmt-80) REVERT: B 1248 SER cc_start: 0.8093 (t) cc_final: 0.7778 (m) REVERT: B 1284 ILE cc_start: 0.7125 (OUTLIER) cc_final: 0.6882 (pp) REVERT: D 220 ILE cc_start: 0.6063 (mt) cc_final: 0.5569 (mm) REVERT: D 347 MET cc_start: 0.5819 (tmt) cc_final: 0.4861 (tpp) REVERT: E 472 THR cc_start: 0.7115 (OUTLIER) cc_final: 0.6708 (p) REVERT: E 506 TYR cc_start: 0.7319 (m-80) cc_final: 0.6676 (m-80) REVERT: E 511 LYS cc_start: 0.5566 (pptt) cc_final: 0.5212 (pttt) REVERT: E 544 GLU cc_start: 0.7808 (pp20) cc_final: 0.7388 (tt0) REVERT: P 25 ASN cc_start: 0.8703 (m-40) cc_final: 0.8431 (m-40) REVERT: P 91 LYS cc_start: 0.8605 (ttmt) cc_final: 0.8335 (ttpt) REVERT: Q 56 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8219 (tt0) REVERT: Q 74 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8032 (mptp) REVERT: Q 91 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8254 (tt0) REVERT: R 90 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7894 (mp0) REVERT: T 50 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8320 (tt) REVERT: U 17 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.6627 (ttp80) REVERT: U 56 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8165 (tt0) REVERT: V 90 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8097 (mp0) REVERT: V 105 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8425 (pttp) outliers start: 74 outliers final: 48 residues processed: 330 average time/residue: 0.1752 time to fit residues: 91.2798 Evaluate side-chains 342 residues out of total 1917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 274 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLN Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 232 TYR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 709 TYR Chi-restraints excluded: chain B residue 718 THR Chi-restraints excluded: chain B residue 756 LYS Chi-restraints excluded: chain B residue 883 LEU Chi-restraints excluded: chain B residue 907 ARG Chi-restraints excluded: chain B residue 912 TRP Chi-restraints excluded: chain B residue 917 ARG Chi-restraints excluded: chain B residue 927 SER Chi-restraints excluded: chain B residue 986 TYR Chi-restraints excluded: chain B residue 996 ILE Chi-restraints excluded: chain B residue 1010 LEU Chi-restraints excluded: chain B residue 1020 LEU Chi-restraints excluded: chain B residue 1024 ILE Chi-restraints excluded: chain B residue 1144 ILE Chi-restraints excluded: chain B residue 1164 MET Chi-restraints excluded: chain B residue 1167 ARG Chi-restraints excluded: chain B residue 1179 THR Chi-restraints excluded: chain B residue 1219 LEU Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1284 ILE Chi-restraints excluded: chain B residue 1286 TYR Chi-restraints excluded: chain D residue 222 LEU Chi-restraints excluded: chain D residue 230 SER Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 344 SER Chi-restraints excluded: chain D residue 360 GLU Chi-restraints excluded: chain D residue 392 SER Chi-restraints excluded: chain E residue 35 ARG Chi-restraints excluded: chain E residue 415 LEU Chi-restraints excluded: chain E residue 436 LEU Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 540 THR Chi-restraints excluded: chain E residue 556 TYR Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 56 GLU Chi-restraints excluded: chain Q residue 62 ILE Chi-restraints excluded: chain Q residue 74 LYS Chi-restraints excluded: chain Q residue 91 GLU Chi-restraints excluded: chain R residue 48 ASP Chi-restraints excluded: chain R residue 81 ASN Chi-restraints excluded: chain R residue 90 GLU Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain S residue 103 LEU Chi-restraints excluded: chain T residue 29 ILE Chi-restraints excluded: chain T residue 50 ILE Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain U residue 17 ARG Chi-restraints excluded: chain U residue 56 GLU Chi-restraints excluded: chain U residue 114 VAL Chi-restraints excluded: chain V residue 76 ARG Chi-restraints excluded: chain V residue 90 GLU Chi-restraints excluded: chain V residue 105 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 176 optimal weight: 0.3980 chunk 177 optimal weight: 0.5980 chunk 241 optimal weight: 20.0000 chunk 226 optimal weight: 50.0000 chunk 58 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 chunk 221 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 220 optimal weight: 9.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 341 ASN ** B 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1254 HIS E 304 ASN ** E 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 125 GLN ** Q 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN R 81 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.127896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.097123 restraints weight = 58031.976| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 1.88 r_work: 0.3421 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.176 25899 Z= 0.177 Angle : 0.721 59.156 36445 Z= 0.406 Chirality : 0.043 0.851 4041 Planarity : 0.004 0.062 3424 Dihedral : 27.881 140.203 6159 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.86 % Allowed : 27.49 % Favored : 68.65 % Cbeta Deviations : 0.05 % 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 are not related in a simple way. whole: 0.10 (0.18), residues: 2112 helix: 1.20 (0.15), residues: 1168 sheet: -1.04 (0.53), residues: 95 loop : -1.44 (0.20), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG P 92 TYR 0.036 0.002 TYR P 88 PHE 0.043 0.001 PHE A 160 TRP 0.031 0.001 TRP E 301 HIS 0.007 0.001 HIS B 815 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.18 (25898) covalent geometry : angle 0.72079 / 0.41 (36443) SS BOND : bond 0.00161 / 0.08 ( 1) SS BOND : angle 0.97982 / 0.56 ( 2) hydrogen bonds : bond 0.03740 / 2.48 ( 1198) hydrogen bonds : angle 3.50386 / 2.48 ( 3195) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7044.53 seconds wall clock time: 121 minutes 19.70 seconds (7279.70 seconds total)